CLUSTAL Alignment (several examples)


Sample code :


/**
  * Here is some samples of how to use the functions
  * @param SequenceAlignmentInterface $sequenceAlignmentManager
  * @return Response
  * @throws \Exception
  */
public function clustalseqalignment(SequenceAlignmentInterface $sequenceAlignmentManager)
{
    set_time_limit(0); // we never know ...
    $sequenceAlignmentManager->setFilename("data/clustal.txt");
    $sequenceAlignmentManager->setFormat("CLUSTAL");
    $sequenceAlignmentManager->parseFile();
 
    // You wanna sort your array ? :)
    $sequenceAlignmentManager->sortAlpha("ASC");
    $sequenceAlSort = $sequenceAlignmentManager->getSeqSet();
    // You wanna fetch something ?
    $oOffset13 = $sequenceAlignmentManager->getSeqSet()->offsetGet(13);
    // You wanna know the longest sequence ?
    $iMaxLength = $sequenceAlignmentManager->getMaxiLength();
    // You wanna know the number of gaps ?
    $iNumberGaps = $sequenceAlignmentManager->getGapCount();
    // Have the same length ?
    $bIsFlush = $sequenceAlignmentManager->getIsFlush();
    // Char at res 10 (10th sequence)
    $sCharAtRes = $sequenceAlignmentManager->charAtRes(10, 10);
    // Substring between two residues in a sequence
    $sSubstrBwRes = $sequenceAlignmentManager->substrBwRes(10,10);
    // Converts a column number to a residue number in a sequence
    $iColToRes = $sequenceAlignmentManager->colToRes(10, 50);
    // Converts a residue number to a column number in a sequence
    $iResToCol = $sequenceAlignmentManager->resToCol(10, 47);
    // Creates a new alignment set from index 5 to 10
    $sequenceAlignmentManager->subalign(5, 10);
    $oSubALign = $sequenceAlignmentManager;
    // Creates a new alignment with selected indexes
    $sequenceAlignmentManager->select(1,2,3);
    $oSelectAlign = $sequenceAlignmentManager;
 
    // Determines the index position of both variant and invariant residues according
    // to a given "percentage threshold" similar to that in the consensus() method.
    $aResVar = $sequenceAlignmentManager->resVar();
 
    // Returns the consensus string for an alignment set
    $aConsensus = $sequenceAlignmentManager->consensus();
 
    // Adding a new sequence object
    $sequenceAlignmentManager->addSequence($oOffset13);
    $sequenceAlignmentManagerAdd = $sequenceAlignmentManager;
    // Dropping a sequence
    $sequenceAlignmentManager->deleteSequence("sp|P04637|P53_HUMAN");
    $sequenceAlignmentManagerDel = $sequenceAlignmentManager;
 
 
    return $this->render('default/clustalseqalignment.html.twig',
        [
            'sequenceAlSort'              => $sequenceAlSort,
            'offset13'                    => $oOffset13,
            'maxLength'                   => $iMaxLength,
            'numberGaps'                  => $iNumberGaps,
            'isFlush'                     => $bIsFlush,
            'sCharAtRes'                  => $sCharAtRes,
            'sSubstrBwRes'                => $sSubstrBwRes,
            'colToRes'                    => $iColToRes,
            'resToCol'                    => $iResToCol,
            'subALign'                    => $oSubALign,
            'selectAlign'                 => $oSelectAlign,
            'resVar'                      => $aResVar,
            'consensus'                   => $aConsensus,
            'sequenceAlignmentManagerAdd' => $sequenceAlignmentManagerAdd,
            'sequenceAlignmentManagerDel' => $sequenceAlignmentManagerDel
        ]
    );
}

Result :

Sort sequences :

ArrayIterator {#680
  flag::STD_PROP_LIST: false
  flag::ARRAY_AS_PROPS: false
  storage: array:34 [
    0 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#653
      -primAcc: "sp|O09185|P53_CRIGR"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDLSIEL-PLSQETFSDLWKLLPPNNVLSTLPS-SDSIEE-LFLSENVTGWLEDSGGALQGVAAAA---ASTAEDPVTET-------PAPVASAPATPWPLSSSVPSYKTYQGDYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVNSTPPPGTRVRAMAIYKKLQYMTEVVRRCPHHERSSE-GDSLAPPQHLIRVEGNLHAEYLDDKQTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDPSGNLLGRNSFEVRICACPGRDRRTEEKNFQKKGEPCPELP---PKSAKRALPT--NTS--SSPP-PK-----KKTLDGEYFTLKIRGHERFKMFQELNEALELKDAQASKGSEDNGAHSSYL-----KSKKGQSASRLKKLMIKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    1 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#669
      -primAcc: "sp|O12946|P53_PLAFE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MMDEQGLDGMQILPGSQDSFSELWASVQTPSIATI---------AEEF-------------DD---H---LGNLLQNGFDMNLFE-------LPPEMVAKDSVTPPSSTVPVVTDYPGEYGFQLRFQKSGTAKSVTSTFSELLKKLYCQLAKTSPVEVLLSKEPPQGAVLRATAVYKKTEHVADVVRRCPHHQT----EDTAEHRSHLIRLEGSQRALYFEDPHTKRQSVTVPYEPPQLGSETTAILLSFMCNSSCMGGMNRRQILTILTLETPDGLVLGRRCFEVRVCACPGRDRKTDEESSTKTPNGPKQTK-------KRKQAPSNSAPHTT-TVMKSKSSSSAEEEDKEVFTVLVKGRERYEIIKKINEAFEGAAEKEKAKN------------KVAVKQELPVPSSGKRLVQRGERSDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    2 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#664
      -primAcc: "sp|O36006|P53_MARMO"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEAQSDLSIEP-PLSQETFSDLWNLLPENNVLSPVLS-PPM-DDLLLSSEDVENWFDK--GPDEAL---QMSAAPAPKAPTPAA-------STLAAPSPATSWPLSSSVPSQNTYPGVYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSECTTIHYNYMCNSSCMGGMNRRPILTIITLEGSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKRGEPCPEPP---PRSTKRALPN--GTS--SSPQ-PK-----KKPLDGEYFTLKIRGRARFEMFQELNEALELKDAQAEKEPGESRPHPSYL-----KSKKGQSTSRHKKIIFKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    3 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#679
      -primAcc: "sp|O57538|P53_XIPHE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "-ME----EADLTLPLSQDTFHDLWNNVFLSTEN--------------------ESLAPPE--G---L---LSQ------NMDFWE--------DPETMQETKNVPTAPTVPAISNYAGEHGFNLEFNDSGTAKSVTSTYSVKLGKLFCQLAKTTPIGVLVKEEPPQGAVIRATSVYKKTEHVGEVVKRCPHHQS----EDLSDNKSHLIRVEGSQLAQYFEDPNTRRHSVTVPYERPQLGSEMTTILLSFMCNSSCMGGMNRRPILTILTLETTEGEVLGRRCFEVRVCACPGRDRKTEEGNLEK--SGTKQTK-------KRKSAP---APDTS-TAKKSKSASSGEDEDKEIYTLSIRGRNRYLWFKSLNDGLELMDKTG-----------------PKIKQEIPAPSSGKRLLKGGSDSD---"
      -description: null
      -organism: null
      -fragment: null
    }
    4 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#660
      -primAcc: "sp|O93379|P53_ICTPU"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEGNGERDTMMVEPPDSQEFAELWLRN--------------------LIVRDNSLWGKEEEIPDDLQ---E---VPCD-----VL-------LSDMLQPQSSSSPPTSTVPVTSDYPGLLNFTLHFQESSGTKSVTCTYSPDLNKLFCQLAKTCPVLMAVSSSPPPGSVLRATAVYKRSEHVAEVVRRCPHHERSNDSSDGPAPPGHLLRVEGNSRAVYQEDGNTQAHSVVVPYEPPQVGSQSTTVLYNYMCNSSCMGGMNRRPILTIITLETQDGHLLGRRTFEVRVCACPGRDRKTEESNFKKQQEPKTSGK---T-LTKRSMKD--PPSHPEASKKSK-----NSSSDDEIYTLQVRGKERYEFLKKINDGLELSDVVPPADQEKYRQKLLSKTCRKERDGAAGEPKRGKKRLVKEEKCDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    5 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#666
      -primAcc: "sp|P02340|P53_MOUSE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQSDISLEL-PLSQETFSGLWKLLPPEDILPS-----PHCMDDLLLPQDVEEFFEG---PSEAL---RVSGAPAAQDPVTET-------PGPVAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCSD-GDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELP---PGSAKRALPT--CTS--ASPP-QK-----KKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSRAHSSYL-----KTKKGQSTSRHKKTMVKKVGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    6 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#659
      -primAcc: "sp|P04637|P53_HUMAN"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHL-----KSKKGQSTSRHKKLMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    7 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#677
      -primAcc: "sp|P07193|P53_XENLA"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "-MEPSSETGMDP-PLSQETFEDLWSLLPDPLQTVTCR------------LDNLSEFPDY------PL-AADMT-----------V-------LQEGLMGNAVPTVTSCAVPSTDDYAGKYGLQLDFQQNGTAKSVTCTYSPELNKLFCQLAKTCPLLVRVESPPPRGSILRATAVYKKSEHVAEVVKRCPHHERSVEPGEDAAPPSHLMRVEGNLQAYYMEDVNSGRHSVCVPYEGPQVGTECTTVLYNYMCNSSCMGGMNRRPILTIITLETPQGLLLGRRCFEVRVCACPGRDRRTEEDNYTKKRGLKPSG--------KRELAH--PPS--SEPPLPK-KRLVVVDDDEEIFTLRIKGRSRYEMIKKLNDALELQESLDQQK--------VTIKCR--KCRDEIKPKKGKKLLVKDEQPDSE-"
      -description: null
      -organism: null
      -fragment: null
    }
    8 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#650
      -primAcc: "sp|P10360|P53_CHICK"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MAE-----EMEPLLEPTEVFMDLWSMLPY-------------SMQQLPLPEDHSNWQELSPLEPSDP---PPPPPPPPLPLAAAA-------PPPLNPPTPPRAAPSPVVPSTEDYGGDFDFRVGFVEAGTAKSVTCTYSPVLNKVYCRLAKPCPVQVRVGVAPPPGSSLRAVAVYKKSEHVAEVVRRCPHHERCGGGTDGLAPAQHLIRVEGNPQARYHDDETTKRHSVVVPYEPPEVGSDCTTVLYNFMCNSSCMGGMNRRPILTILTLEGPGGQLLGRRCFEVRVCACPGRDRKIEEENFRKRGGAG--------GVAKRAMSP--PTEA-PEPPKKR-----VLNPDNEIFYLQVRGRRRYEMLKEINEALQLAEGGSAPRPSKGRR----------VKVEGPQPSCGKKLLQKGSD-----"
      -description: null
      -organism: null
      -fragment: null
    }
    9 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#672
      -primAcc: "sp|P10361|P53_RAT"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEDSQSDMSIEL-PLSQETFSCLWKLLPPDDILPTTATGSPNSMEDLFLPQDVAELLEG---PEEAL---QVS-APAAQEPGTEA-------PAPVAPASATPWPLSSSVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSISLNKLFCQLAKTCPVQLWVTSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-GDGLAPPQHLIRVEGNPYAEYLDDRQTFRHSVVVPYEPPEVGSDYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEEHCPELP---PGSAKRALPT--STS--SSPQ-QK-----KKPLDGEYFTLKIRGRERFEMFRELNEALELKDARAAEESGDSRAHSSYP-----KTKKGQSTSRHKKPMIKKVGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    10 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#652
      -primAcc: "sp|P13481|P53_CHLAE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPHMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    11 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#667
      -primAcc: "sp|P25035|P53_ONCMY"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MADLAEN---VSLPLSQESFEDLWKMNLNLVAV---------------QPPETESWVGYDNFMMEAP-------LQVEFDPSLFEVSATEPAPQPSISTLDTGSPPTSTVPTTSDYPGALGFQLRFLQSSTAKSVTCTYSPDLNKLFCQLAKTCPVQIVVDHPPPPGAVVRALAIYKKLSDVADVVRRCPHHQSTSENNEGPAPRGHLVRVEGNQRSEYMEDGNTLRHSVLVPYEPPQVGSECTTVLYNFMCNSSCMGGMNRRPILTIITLETQEGQLLGRRSFEVRVCACPGRDRKTEEINLKKQQETTLETKTKPAQGIKRAMKE-ASLPA-PQPGASKKTKSSPAVSDDEIYTLQIRGKEKYEMLKKFNDSLELSELVPVADADKYRQKCLTKRVA--KRDFGVGPKKRKKLLVKEEKSDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    12 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#657
      -primAcc: "sp|P41685|P53_FELCA"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MQEPPLELTIEP-PLSQETFSELWNLLPENNVLSSELS-SAM--NELPLSEDVANWLDE--APDDAS---GMSAVPAPAAPAP------------ATPAPAISWPLSSFVPSQKTYPGAYGFHLGFLQSGTAKSVTCTYSPPLNKLFCQLAKTCPVQLWVRSPPPPGTCVRAMAIYKKSEFMTEVVRRCPHHERCPDSSDGLAPPQHLIRVEGNLHAKYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPIITIITLEDSNGKLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCPEPP---PGSTKRALPP--STS--STPP-QK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQSGKEPGGSRAHSSHL-----KAKKGQSTSRHKKPMLKREGLDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    13 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#673
      -primAcc: "sp|P51664|P53_SHEEP"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQAELGVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYSEDVVTWLDE--CPNEAP---QMPEPPAQA-----------------ALAPATSWPLSSFVPSQKTYPGNYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRSPHHERSSDYSDGLAPPQHLIRVEGNLRAEYFDDRNTFRHSVVVPYESPEIESECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSRGNLLGRSSFEVRVCACPGRDRRTEEENFRKKGQSCPEPP---PGSTKRALPS--STS--SSPQ-QK-----KKPLDGEYFTLQIRGRKRFEMFRELNEALELMDAQAGREPGESRAHSSHL-----KSKKGPSPSCHKKPMLKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    14 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#661
      -primAcc: "sp|P56423|P53_MACFA"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPPMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHQLP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    15 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#663
      -primAcc: "sp|P56424|P53_MACMU"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPPMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHQLP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    16 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#662
      -primAcc: "sp|P61260|P53_MACFU"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPPMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHQLP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    17 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#648
      -primAcc: "sp|P67938|P53_BOSIN"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQAELNVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYT-DVATWLDE--CPNEAP---QMPEPSAPAAPPP------------ATPAPATSWPLSSFVPSQKTYPGNYGFRLGFLQSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRCPHHERSSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYESPEIDSECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSCGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGQSCPEPP---PRSTKRALPT--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGFKRYEMFRELNDALELKDALDGREPGESRAHSSHL-----KSKKRPSPSCHKKPMLKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    18 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#649
      -primAcc: "sp|P67939|P53_BOVIN"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQAELNVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYT-DVATWLDE--CPNEAP---QMPEPSAPAAPPP------------ATPAPATSWPLSSFVPSQKTYPGNYGFRLGFLQSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRCPHHERSSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYESPEIDSECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSCGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGQSCPEPP---PRSTKRALPT--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGFKRYEMFRELNDALELKDALDGREPGESRAHSSHL-----KSKKRPSPSCHKKPMLKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    19 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#654
      -primAcc: "sp|P79734|P53_DANRE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "-----------MAQNDSQEFAELWEKNL----IIQPP-------------GGGSCWDIIN---DEEY-------LPGSFDPNFFE-------NVLEEQPQPSTLPPTSTVPETSDYPGDHGFRLRFPQSGTAKSVTCTYSPDLNKLFCQLAKTCPVQMVVDVAPPQGSVVRATAIYKKSEHVAEVVRRCPHHERTPD-GDNLAPAGHLIRVEGNQRANYREDNITLRHSVFVPYEAPQLGAEWTTVLLNYMCNSSCMGGMNRRPILTIITLETQEGQLLGRRSFEVRVCACPGRDRKTEESNFKKDQETKTMAKT--TTGTKRSLVK-ESSSATLRPEGSK-KAKG-SSSDEEIFTLQVRGRERYEILKKLNDSLELSDVVPASDAEKYRQKFMTK--NKKENRESSEPKQGKKLMVKDEGRSDSD"
      -description: null
      -organism: null
      -fragment: null
    }
    20 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#668
      -primAcc: "sp|P79820|P53_ORYLA"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "------MDPVPDLPESQGSFQELWETVSYPPLETL---------SLPTVNEPTGSWVATGDMF---L---LDQDLSGTFDDKIFD-------IPIEPVPTNEVNPPPTTVPVTTDYPGSYELELRFQKSGTAKSVTSTYSETLNKLYCQLAKTSPIEVRVSKEPPKGAILRATAVYKKTEHVADVVRRCPHHQN----EDSVEHRSHLIRVEGSQLAQYFEDPYTKRQSVTVPYEPPQPGSEMTTILLSYMCNSSCMGGMNRRPILTILTLET-EGLVLGRRCFEVRICACPGRDRKTEEESRQKTQP-----K-------KRKVTPNTS----S-SKRKKSHSSGEEEDNREVFHFEVYGRERYEFLKKINDGLELLEKESKSKN----------------KDSGMVPSSGKKLKSN--------"
      -description: null
      -organism: null
      -fragment: null
    }
    21 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#658
      -primAcc: "sp|P79892|P53_HORSE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "---------------------------------------PAV-NN-LLLSPDVVNWLDE--GPDEAP---RMPAAPA-----P------------LAPAPATSWPLSSFVPSQKTYPGCYGFRLGFLNSGTAKSVTCTYSPTLNKLFCQLAKTCPVQLLVSSPPPPGTRVRAMAIYKKSEFMTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKEEPCPEPP---PRSTKRVLSS--NTS--SSPP-QK-----KKPLDGEYFT----------------------------------------------------------------------"
      -description: null
      -organism: null
      -fragment: null
    }
    22 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#665
      -primAcc: "sp|Q00366|P53_MESAU"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDLSIEL-PLSQETFSDLWKLLPPNNVLSTLPS-SDSIEE-LFLSENVAGWLEDPGEALQGSAAAAAPAAPAAEDPVAET-------PAPVASAPATPWPLSSSVPSYKTYQGDYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVSSTPPPGTRVRAMAIYKKLQYMTEVVRRCPHHERSSE-GDGLAPPQHLIRVEGNMHAEYLDDKQTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDPSGNLLGRNSFEVRICACPGRDRRTEEKNFQKKGEPCPELP---PKSAKRALPT--NTS--SSPQ-PK-----RKTLDGEYFTLKIRGQERFKMFQELNEALELKDAQALKASEDSGAHSSYL-----KSKKGQSASRLKKLMIKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    23 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#656
      -primAcc: "sp|Q29480|P53_EQUAS"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "------------------------------------------------------------------------------------------------------------------------------------------YSPALNKMFCQLAKTCPVYLRISSPPPPGTRVRAMAIYKKSEFMTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAEYLDDRNTLRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKEEPCPEPP---PRSTKRVLSS--NTS--SSPP-QK-----EDPLDGEYFTLH--------------------------------------------------------------------"
      -description: null
      -organism: null
      -fragment: null
    }
    24 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#647
      -primAcc: "sp|Q29537|P53_CANFA"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQSELNIDP-PLSQETFSELWNLLPENNVLSSELC-PAV-DE-LLLPESVVNWLDE--DSDDAP---RMPATSA-----P------------TAPGPAPSWPLSSSVPSPKTYPGTYGFRLGFLHSGTAKSVTWTYSPLLNKLFCQLAKTCPVQLWVSSPPPPNTCVRAMAIYKKSEFVTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAKYLDDRNTFRHSVVVPYEPPEVGSDYTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNVLGRNSFEVRVCACPGRDRRTEEENFHKKGEPCPEPP---PGSTKRALPP--STS--SSPP-QK-----KKPLDGEYFTLQIRGRERYEMFRNLNEALELKDAQSGKEPGGSRAHSSHL-----KAKKGQSTSRHKKLMFKREGLDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    25 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#675
      -primAcc: "sp|Q64662|P53_SPEBE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "---------------------DLWNLLPENNVLSPVLS-PPM-DDLLLSSEDVENWFDK--GPDEAL---QMSAAPAPKAPTPAA-------STLAAPTPAISWPLSSSVPSQNTYPGVYGFRLGFIHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSESTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKRGEPCPEPP---PGSTKRALPT--GTN--SSPQ-PK-----KKPLDGEYFTLKIRGRA---------------------------------------------------------------"
      -description: null
      -organism: null
      -fragment: null
    }
    26 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#655
      -primAcc: "sp|Q8SPZ3|P53_DELLE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQAELGVEP-PLSQETFSDLWKLLPENNLLSSELS-PA-VDDLLLSPEDVANWLDE--RPDEAP---QMPEPPAPAAPTP------------AAPAPATSWPLSSFVPSQKTYPGSYGFHLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVSSPPPPGTRVRAMAIYKKSEYMTEVVRRCPHHERCSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDSNGNLLGRNSFEVRVCACPGRDRRTEEENFHKKGQSCPELP---TGSAKRALPT--GTS--SSPP-QK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGESRAHSSHL-----KSKKGQSPSRHKKLMFKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    27 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#678
      -primAcc: "sp|Q92143|P53_XIPMA"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "-ME----EADLTLPLSQDTFHDLWNNVFLSTEN--------------------ESLPPPE--G---L---LSQ------NMDFWE--------DPETMQETKNVPTAPTVPAISNYAGEHGFNLEFNDSGTAKSVTSTYSVKLGKLFCQLAKTTPIGVLVKEEPPQGAVIRATAVYKKTEHVGEVVKRCPHHQS----EDLSDNKSHLIRVEGSQLAQYFEDPNTRRHSVTVPYERPQLGSEMTTILLSFMCNSSCMGGMNRRPILTILTLETTEGEVLGRRCFEVRVCACPGRDRKTEEGNLEK--SGTKQTK-------KRKSAP---APDTS-TAKKSKSASSGEDEDKEIYTLSIRGRNRYLWFKSLNDGLELMDKTG-----------------PKIKQEIPAPSSGKRLLKGGSDSD---"
      -description: null
      -organism: null
      -fragment: null
    }
    28 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#671
      -primAcc: "sp|Q95330|P53_RABIT"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQSDLSLEP-PLSQETFSDLWKLLPENNLLTTSLN-PPV--DDLLSAEDVANWLNE--DPEEGL---RVPAAPAPEAPAPAA-------PALAAPAPATSWPLSSSVPSQKTYHGNYGFRLGFLHSGTAKSVTCTYSPCLNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCPELP---PGSSKRALPT--TTTD-SSPQ-TK-----KKPLDGEYFILKIRGRERFEMFRELNEALELKDAQAEKEPGGSRAHSSYL-----KAKKGQSTSRHKKPMFKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    29 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#676
      -primAcc: "sp|Q9TTA1|P53_TUPBE"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPDLNKLFCQLAKTCPVQLWVDSAPPPGTRVRAMAIYKQSQYVTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLHAEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGKLLGRNSFEVRICACPGRDRRTEEENFRKKGESCPKLP---TGSIKRALPT--GSS--SSPQ-PK-----KKPLDEEYFTLQIRGRERFEMLREINEALELKDAMAGKESAGSRAHSSHL-----KSKKGQSTSRHRKLMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    30 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#670
      -primAcc: "sp|Q9TUB2|P53_PIG"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEESQSELGVEP-PLSQETFSDLWKLLPENNLLSSELS-LAAVNDLLLSP--VTNWLDE--NPDDAS---RVPAPPAATAPAP------------AAPAPATSWPLSSFVPSQKTYPGSYDFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVSSPPPPGTRVRAMAIYKKSEYMTEVVRRCPHHERSSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDASGNLLGRNSFEVRVCACPGRDRRTEEENFLKKGQSCPEPP---PGSTKRALPT--STS--SSPV-QK-----KKPLDGEYFTLQIRGRERFEMFRELNDALELKDAQTARESGENRAHSSHL-----KSKKGQSPSRHKKPMFKREGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    31 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#646
      -primAcc: "sp|Q9W678|P53_BARBU"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "-------------MAESQEFAELWERNL----IST-Q-------------EAGTCWELIN---D-EY-------LPSSFDPNIFD-------NVLTEQPQPSTSPPTASVPVATDYPGEHGFKLGFPQSGTAKSVTCTYSSDLNKLFCQLAKTCPVQMVVNVAPPQGSVIRATAIYKKSEHVAEVVRRCPHHERTPD-GDGLAPAAHLIRVEGNSRALYREDDVNSRHSVVVPYEVPQLGSEFTTVLYNFMCNSSCMGGMNRRPILTIISLETHDGQLLGRRSFEVRVCACPGRDRKTEESNFRKDQETKTLDKI--PSANKRSLTK-DSTSSVPRPEGSK-KAKLSGSSDEEIYTLQVRGKERYEMLKKINDSLELSDVVPPSEMDRYRQKLLTK--GKKKDGQTPEPKRGKKLMVKDEKSDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    32 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#674
      -primAcc: "sp|Q9W679|P53_TETMU"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "-ME----EENISLPLSQDTFQDLWDNVSAPPISTI---------QTAAL--ENEAWPAERQMN---M---MCNFMDSTFNEALFN-------LLPEPPSRDGANSSSPTVPVTTDYPGEYGFKLRFQKSGTAKSVTSTYSEILNKLYCQLAKTSLVEVLLGKDPPMGAVLRATAIYKKTEHVAEVVRRCPHHQN----EDSAEHRSHLIRMEGSERAQYFEHPHTKRQSVTVPYEPPQLGSEFTTILLSFMCNSSCMGGMNRRPILTILTLETQEGIVLGRRCFEVRVCACPGRDRKTEETNSTKMQNDAKDAK-------KRKSVP---TPDST-TIKKSKTASSAEEDNNEVYTLQIRGRKRYEMLKKINDGLDLLENKP--KS------------KATHRPDGPIPPSGKRLLHRGEKSDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    33 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#651
      -primAcc: "sp|Q9WUR6|P53_CAVPO"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPHSDLSIEP-PLSQETFSDLWKLLPENNVLSDSLS-PPM-DHLLLSPEEVASWLGENP--DGDG---HVSAAPVSEAPTSAG-------PALVAPAPATSWPLSSSVPSHKPYRGSYGFEVHFLKSGTAKSVTCTYSPGLNKLFCQLAKTCPVQVWVESPPPPGTRVRALAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLHAEYVDDRTTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGKLLGRDSFEVRVCACPGRDRRTEEENFRKKGGLCPEPT---PGNIKRALPT--STS--SSPQ-PK-----KKPLDAEYFTLKIRGRKNFEILREINEALEFKDAQTEKEPGESRPHSSYP-----KSKKGQSTSCHKKLMFKREGLDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
  ]
}

13th sequence

Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#673
  -primAcc: "sp|P51664|P53_SHEEP"
  -entryName: null
  -seqLength: 426
  -start: 0
  -end: 425
  -molType: null
  -date: null
  -source: null
  -sequence: "MEESQAELGVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYSEDVVTWLDE--CPNEAP---QMPEPPAQA-----------------ALAPATSWPLSSFVPSQKTYPGNYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRSPHHERSSDYSDGLAPPQHLIRVEGNLRAEYFDDRNTFRHSVVVPYESPEIESECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSRGNLLGRSSFEVRVCACPGRDRRTEEENFRKKGQSCPEPP---PGSTKRALPS--STS--SSPQ-QK-----KKPLDGEYFTLQIRGRKRFEMFRELNEALELMDAQAGREPGESRAHSSHL-----KSKKGPSPSCHKKPMLKREGPDSD-"
  -description: null
  -organism: null
  -fragment: null
}

Length of the longuest sequence

426

Number of gaps

1878

Do the sequences have the same length ?

true

Char at res 10 (10th sequence)

"E"

Substring between two residues in a sequence

"EP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPHMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-"

Converts a column number to a residue number in a sequence

47

Converts a residue number to a column number in a sequence

50

Creates a new alignment set from index 5 to 10

Amelaye\BioPHP\Domain\Sequence\Service\SequenceAlignmentManager {#419
  -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Builder\SequenceBuilder {#420
    -sequence: Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#659
      -primAcc: "sp|P04637|P53_HUMAN"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHL-----KSKKGQSTSRHKKLMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager {#421
      -elements: null
      -aminoApi: Amelaye\BioPHP\Api\AminoApi {#422
        #bioapiClient: GuzzleHttp\Client {#432
          -config: array:9 [
            "base_uri" => GuzzleHttp\Psr7\Uri {#433
              -scheme: "http"
              -userInfo: ""
              -host: "api.amelayes-biophp.net"
              -port: null
              -path: ""
              -query: ""
              -fragment: ""
            }
            "handler" => GuzzleHttp\HandlerStack {#423
              -handler: GuzzleHttp\Handler\StreamHandler {#424
                -lastHeaders: []
              }
              -stack: array:6 [
                0 => array:2 [
                  0 => Closure(callable $handler) {#425
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "http_errors"
                ]
                1 => array:2 [
                  0 => Closure(callable $handler) {#426
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "allow_redirects"
                ]
                2 => array:2 [
                  0 => Closure(callable $handler) {#427
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "cookies"
                ]
                3 => array:2 [
                  0 => Closure(callable $handler) {#428
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "prepare_body"
                ]
                4 => array:2 [
                  0 => Csa\GuzzleHttp\Middleware\Stopwatch\StopwatchMiddleware {#429
                    -stopwatch: Symfony\Component\Stopwatch\Stopwatch {#137
                      -morePrecision: true
                      -sections: array:1 [
                        "__root__" => Symfony\Component\Stopwatch\Section {#136
                          -events: array:1 [
                            "__section__.child" => Symfony\Component\Stopwatch\StopwatchEvent {#153
                              -periods: []
                              -origin: 1607215713141.4
                              -category: "section"
                              -morePrecision: true
                              -started: array:1 [
                                0 => 0.0
                              ]
                            }
                          ]
                          -origin: null
                          -morePrecision: true
                          -id: null
                          -children: array:1 [
                            0 => Symfony\Component\Stopwatch\Section {#154
                              -events: array:36 [
                                "__section__" => Symfony\Component\Stopwatch\StopwatchEvent {#155
                                  -periods: []
                                  -origin: 1607215713141.4
                                  -category: "default"
                                  -morePrecision: true
                                  -started: array:1 [
                                    0 => 0.0
                                  ]
                                }
                                "kernel.request" => Symfony\Component\Stopwatch\StopwatchEvent {#156
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#197
                                      -start: 0.0
                                      -end: 5.6
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "section"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\DebugHandlersListener" => Symfony\Component\Stopwatch\StopwatchEvent {#157
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#159
                                      -start: 0.1
                                      -end: 0.3
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\ValidateRequestListener" => Symfony\Component\Stopwatch\StopwatchEvent {#160
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#161
                                      -start: 0.3
                                      -end: 0.4
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\TestSessionListener" => Symfony\Component\Stopwatch\StopwatchEvent {#162
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#170
                                      -start: 0.4
                                      -end: 0.9
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\SessionListener" => Symfony\Component\Stopwatch\StopwatchEvent {#171
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#173
                                      -start: 0.9
                                      -end: 1.0
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\LocaleListener" => Symfony\Component\Stopwatch\StopwatchEvent {#174
                                  -periods: array:2 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#175
                                      -start: 1.0
                                      -end: 1.0
                                      -memory: 2097152
                                    }
                                    1 => Symfony\Component\Stopwatch\StopwatchPeriod {#187
                                      -start: 3.5
                                      -end: 3.5
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\RouterListener" => Symfony\Component\Stopwatch\StopwatchEvent {#176
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#190
                                      -start: 1.0
                                      -end: 3.4
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Bundle\FrameworkBundle\EventListener\ResolveControllerNameSubscriber" => Symfony\Component\Stopwatch\StopwatchEvent {#189
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#188
                                      -start: 3.5
                                      -end: 3.5
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\LocaleAwareListener" => Symfony\Component\Stopwatch\StopwatchEvent {#186
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#184
                                      -start: 3.6
                                      -end: 3.8
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Bundle\SecurityBundle\Debug\TraceableFirewallListener" => Symfony\Component\Stopwatch\StopwatchEvent {#185
                                  -periods: array:2 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#196
                                      -start: 3.8
                                      -end: 4.4
                                      -memory: 2097152
                                    }
                                    1 => Symfony\Component\Stopwatch\StopwatchPeriod {#205
                                      -start: 4.4
                                      -end: 5.6
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
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                        0 => "jms_serializer.stopwatch_subscriber"
                        1 => "onPostSerialize"
                      ]
                      1 => null
                      2 => null
                      3 => null
                    ]
                  ]
                ]
                -classListeners: []
              }
              -expressionEvaluator: JMS\Serializer\Expression\ExpressionEvaluator {#443}
            }
            1 => JMS\Serializer\GraphNavigator\Factory\SerializationGraphNavigatorFactory {#450
              -metadataFactory: Metadata\MetadataFactory {#435}
              -handlerRegistry: JMS\Serializer\Handler\LazyHandlerRegistry {#439}
              -accessor: JMS\Serializer\Accessor\DefaultAccessorStrategy {#442}
              -dispatcher: JMS\Serializer\EventDispatcher\LazyEventDispatcher {#456}
              -expressionEvaluator: JMS\Serializer\Expression\ExpressionEvaluator {#443}
            }
          ]
        }
        #apiKey: null
      }
      -nucleotidApi: Amelaye\BioPHP\Api\NucleotidApi {#502
        #bioapiClient: GuzzleHttp\Client {#432}
        #serializer: JMS\Serializer\Serializer {#434}
        #apiKey: null
      }
      -nucleotids: array:8 [
        0 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#532
          -id: null
          -letter: "A"
          -complement: "T"
          -nature: "DNA"
          -weight: 313.245
        }
        1 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#525
          -id: null
          -letter: "T"
          -complement: "A"
          -nature: "DNA"
          -weight: 304.225
        }
        2 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#581
          -id: null
          -letter: "G"
          -complement: "C"
          -nature: "DNA"
          -weight: 329.245
        }
        3 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#582
          -id: null
          -letter: "C"
          -complement: "G"
          -nature: "DNA"
          -weight: 289.215
        }
        4 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#583
          -id: null
          -letter: "A"
          -complement: "U"
          -nature: "RNA"
          -weight: 329.245
        }
        5 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#584
          -id: null
          -letter: "U"
          -complement: "A"
          -nature: "RNA"
          -weight: 306.195
        }
        6 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#585
          -id: null
          -letter: "G"
          -complement: "C"
          -nature: "RNA"
          -weight: 345.245
        }
        7 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#586
          -id: null
          -letter: "C"
          -complement: "G"
          -nature: "RNA"
          -weight: 305.215
        }
      ]
      -water: Amelaye\BioPHP\Api\DTO\ElementDTO {#609
        -id: 6
        -name: "water"
        -weight: 18.015
      }
      -aminos: array:26 [
        0 => Amelaye\BioPHP\Api\DTO\AminoDTO {#530
          -id: "*"
          -name: "STOP"
          -name1Letter: "*"
          -name3Letters: "STP"
          -weight1: 0.0
          -weight2: 0.0
          -residueMolWeight: 0.0
        }
        1 => Amelaye\BioPHP\Api\DTO\AminoDTO {#539
          -id: "A"
          -name: "Alanine"
          -name1Letter: "A"
          -name3Letters: "Ala"
          -weight1: 89.09
          -weight2: 89.09
          -residueMolWeight: 71.07
        }
        2 => Amelaye\BioPHP\Api\DTO\AminoDTO {#540
          -id: "B"
          -name: "Aspartate or asparagine"
          -name1Letter: "B"
          -name3Letters: "N/A"
          -weight1: 132.12
          -weight2: 132.1
          -residueMolWeight: 0.0
        }
        3 => Amelaye\BioPHP\Api\DTO\AminoDTO {#541
          -id: "C"
          -name: "Cysteine"
          -name1Letter: "C"
          -name3Letters: "Cys"
          -weight1: 121.15
          -weight2: 121.15
          -residueMolWeight: 103.1
        }
        4 => Amelaye\BioPHP\Api\DTO\AminoDTO {#542
          -id: "D"
          -name: "Aspartic acid"
          -name1Letter: "D"
          -name3Letters: "Asp"
          -weight1: 133.1
          -weight2: 133.1
          -residueMolWeight: 115.08
        }
        5 => Amelaye\BioPHP\Api\DTO\AminoDTO {#543
          -id: "E"
          -name: "Glutamic acid"
          -name1Letter: "E"
          -name3Letters: "Glu"
          -weight1: 147.13
          -weight2: 147.13
          -residueMolWeight: 129.11
        }
        6 => Amelaye\BioPHP\Api\DTO\AminoDTO {#544
          -id: "F"
          -name: "Phenylalanine"
          -name1Letter: "F"
          -name3Letters: "Phe"
          -weight1: 165.19
          -weight2: 165.19
          -residueMolWeight: 147.17
        }
        7 => Amelaye\BioPHP\Api\DTO\AminoDTO {#545
          -id: "G"
          -name: "Glycine"
          -name1Letter: "G"
          -name3Letters: "Gly"
          -weight1: 75.07
          -weight2: 75.07
          -residueMolWeight: 57.05
        }
        8 => Amelaye\BioPHP\Api\DTO\AminoDTO {#546
          -id: "H"
          -name: "Histidine"
          -name1Letter: "H"
          -name3Letters: "His"
          -weight1: 155.16
          -weight2: 155.16
          -residueMolWeight: 137.14
        }
        9 => Amelaye\BioPHP\Api\DTO\AminoDTO {#547
          -id: "I"
          -name: "Isoleucine"
          -name1Letter: "I"
          -name3Letters: "Ile"
          -weight1: 131.18
          -weight2: 131.18
          -residueMolWeight: 113.15
        }
        10 => Amelaye\BioPHP\Api\DTO\AminoDTO {#548
          -id: "K"
          -name: "Lysine"
          -name1Letter: "K"
          -name3Letters: "Lys"
          -weight1: 146.19
          -weight2: 146.19
          -residueMolWeight: 128.17
        }
        11 => Amelaye\BioPHP\Api\DTO\AminoDTO {#549
          -id: "L"
          -name: "Leucine"
          -name1Letter: "L"
          -name3Letters: "Leu"
          -weight1: 131.18
          -weight2: 131.18
          -residueMolWeight: 113.15
        }
        12 => Amelaye\BioPHP\Api\DTO\AminoDTO {#550
          -id: "M"
          -name: "Methionine"
          -name1Letter: "M"
          -name3Letters: "Met"
          -weight1: 149.22
          -weight2: 149.22
          -residueMolWeight: 131.19
        }
        13 => Amelaye\BioPHP\Api\DTO\AminoDTO {#551
          -id: "N"
          -name: "Asparagine"
          -name1Letter: "N"
          -name3Letters: "Asn"
          -weight1: 132.12
          -weight2: 132.12
          -residueMolWeight: 114.08
        }
        14 => Amelaye\BioPHP\Api\DTO\AminoDTO {#552
          -id: "O"
          -name: "Pyrrolysine"
          -name1Letter: "O"
          -name3Letters: "Pyr"
          -weight1: 255.31
          -weight2: 255.31
          -residueMolWeight: 0.0
        }
        15 => Amelaye\BioPHP\Api\DTO\AminoDTO {#553
          -id: "P"
          -name: "Proline"
          -name1Letter: "P"
          -name3Letters: "Pro"
          -weight1: 115.13
          -weight2: 115.13
          -residueMolWeight: 97.11
        }
        16 => Amelaye\BioPHP\Api\DTO\AminoDTO {#554
          -id: "Q"
          -name: "Glutamine"
          -name1Letter: "Q"
          -name3Letters: "Gin"
          -weight1: 146.15
          -weight2: 146.15
          -residueMolWeight: 128.13
        }
        17 => Amelaye\BioPHP\Api\DTO\AminoDTO {#555
          -id: "R"
          -name: "Arginine"
          -name1Letter: "R"
          -name3Letters: "Arg"
          -weight1: 174.21
          -weight2: 174.21
          -residueMolWeight: 156.18
        }
        18 => Amelaye\BioPHP\Api\DTO\AminoDTO {#556
          -id: "S"
          -name: "Serine"
          -name1Letter: "S"
          -name3Letters: "Ser"
          -weight1: 105.09
          -weight2: 105.09
          -residueMolWeight: 87.07
        }
        19 => Amelaye\BioPHP\Api\DTO\AminoDTO {#557
          -id: "T"
          -name: "Threonine"
          -name1Letter: "T"
          -name3Letters: "Thr"
          -weight1: 119.12
          -weight2: 119.12
          -residueMolWeight: 101.1
        }
        20 => Amelaye\BioPHP\Api\DTO\AminoDTO {#558
          -id: "U"
          -name: "Selenocysteine"
          -name1Letter: "U"
          -name3Letters: "Sec"
          -weight1: 168.05
          -weight2: 168.05
          -residueMolWeight: 0.0
        }
        21 => Amelaye\BioPHP\Api\DTO\AminoDTO {#559
          -id: "V"
          -name: "Valine"
          -name1Letter: "V"
          -name3Letters: "Val"
          -weight1: 117.15
          -weight2: 117.15
          -residueMolWeight: 99.13
        }
        22 => Amelaye\BioPHP\Api\DTO\AminoDTO {#560
          -id: "W"
          -name: "Tryptophan"
          -name1Letter: "W"
          -name3Letters: "Trp"
          -weight1: 204.22
          -weight2: 204.22
          -residueMolWeight: 186.2
        }
        23 => Amelaye\BioPHP\Api\DTO\AminoDTO {#561
          -id: "X"
          -name: "Any"
          -name1Letter: "X"
          -name3Letters: "XXX"
          -weight1: 75.07
          -weight2: 204.22
          -residueMolWeight: 114.82
        }
        24 => Amelaye\BioPHP\Api\DTO\AminoDTO {#562
          -id: "Y"
          -name: "Tyrosine"
          -name1Letter: "Y"
          -name3Letters: "Tyr"
          -weight1: 181.19
          -weight2: 181.19
          -residueMolWeight: 163.17
        }
        25 => Amelaye\BioPHP\Api\DTO\AminoDTO {#563
          -id: "Z"
          -name: "Glutamate or glutamine"
          -name1Letter: "Z"
          -name3Letters: "N/A"
          -weight1: 146.15
          -weight2: 147.13
          -residueMolWeight: 0.0
        }
      ]
    }
  }
  -aAlphabet: array:26 [
    0 => "A"
    1 => "B"
    2 => "C"
    3 => "D"
    4 => "E"
    5 => "F"
    6 => "G"
    7 => "H"
    8 => "I"
    9 => "J"
    10 => "K"
    11 => "L"
    12 => "M"
    13 => "N"
    14 => "O"
    15 => "P"
    16 => "Q"
    17 => "R"
    18 => "S"
    19 => "T"
    20 => "U"
    21 => "V"
    22 => "W"
    23 => "X"
    24 => "Y"
    25 => "Z"
  ]
  -iLength: 426
  -iGapCount: 166
  -aSeqSet: ArrayIterator {#681
    flag::STD_PROP_LIST: false
    flag::ARRAY_AS_PROPS: false
    storage: array:3 [
      0 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#677
        -primAcc: "sp|P07193|P53_XENLA"
        -entryName: null
        -seqLength: 426
        -start: 0
        -end: 425
        -molType: null
        -date: null
        -source: null
        -sequence: "-MEPSSETGMDP-PLSQETFEDLWSLLPDPLQTVTCR------------LDNLSEFPDY------PL-AADMT-----------V-------LQEGLMGNAVPTVTSCAVPSTDDYAGKYGLQLDFQQNGTAKSVTCTYSPELNKLFCQLAKTCPLLVRVESPPPRGSILRATAVYKKSEHVAEVVKRCPHHERSVEPGEDAAPPSHLMRVEGNLQAYYMEDVNSGRHSVCVPYEGPQVGTECTTVLYNYMCNSSCMGGMNRRPILTIITLETPQGLLLGRRCFEVRVCACPGRDRRTEEDNYTKKRGLKPSG--------KRELAH--PPS--SEPPLPK-KRLVVVDDDEEIFTLRIKGRSRYEMIKKLNDALELQESLDQQK--------VTIKCR--KCRDEIKPKKGKKLLVKDEQPDSE-"
        -description: null
        -organism: null
        -fragment: null
      }
      1 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#650
        -primAcc: "sp|P10360|P53_CHICK"
        -entryName: null
        -seqLength: 426
        -start: 0
        -end: 425
        -molType: null
        -date: null
        -source: null
        -sequence: "MAE-----EMEPLLEPTEVFMDLWSMLPY-------------SMQQLPLPEDHSNWQELSPLEPSDP---PPPPPPPPLPLAAAA-------PPPLNPPTPPRAAPSPVVPSTEDYGGDFDFRVGFVEAGTAKSVTCTYSPVLNKVYCRLAKPCPVQVRVGVAPPPGSSLRAVAVYKKSEHVAEVVRRCPHHERCGGGTDGLAPAQHLIRVEGNPQARYHDDETTKRHSVVVPYEPPEVGSDCTTVLYNFMCNSSCMGGMNRRPILTILTLEGPGGQLLGRRCFEVRVCACPGRDRKIEEENFRKRGGAG--------GVAKRAMSP--PTEA-PEPPKKR-----VLNPDNEIFYLQVRGRRRYEMLKEINEALQLAEGGSAPRPSKGRR----------VKVEGPQPSCGKKLLQKGSD-----"
        -description: null
        -organism: null
        -fragment: null
      }
      2 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#673
        -primAcc: "sp|P51664|P53_SHEEP"
        -entryName: null
        -seqLength: 426
        -start: 0
        -end: 425
        -molType: null
        -date: null
        -source: null
        -sequence: "MEESQAELGVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYSEDVVTWLDE--CPNEAP---QMPEPPAQA-----------------ALAPATSWPLSSFVPSQKTYPGNYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRSPHHERSSDYSDGLAPPQHLIRVEGNLRAEYFDDRNTFRHSVVVPYESPEIESECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSRGNLLGRSSFEVRVCACPGRDRRTEEENFRKKGQSCPEPP---PGSTKRALPS--STS--SSPQ-QK-----KKPLDGEYFTLQIRGRKRFEMFRELNEALELMDAQAGREPGESRAHSSHL-----KSKKGPSPSCHKKPMLKREGPDSD-"
        -description: null
        -organism: null
        -fragment: null
      }
    ]
  }
  -bFlush: true
  -sFilename: "data/clustal.txt"
  -sFormat: "CLUSTAL"
}

Creates a new alignment with selected indexes

Amelaye\BioPHP\Domain\Sequence\Service\SequenceAlignmentManager {#419
  -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Builder\SequenceBuilder {#420
    -sequence: Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#659
      -primAcc: "sp|P04637|P53_HUMAN"
      -entryName: null
      -seqLength: 426
      -start: 0
      -end: 425
      -molType: null
      -date: null
      -source: null
      -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHL-----KSKKGQSTSRHKKLMFKTEGPDSD-"
      -description: null
      -organism: null
      -fragment: null
    }
    -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager {#421
      -elements: null
      -aminoApi: Amelaye\BioPHP\Api\AminoApi {#422
        #bioapiClient: GuzzleHttp\Client {#432
          -config: array:9 [
            "base_uri" => GuzzleHttp\Psr7\Uri {#433
              -scheme: "http"
              -userInfo: ""
              -host: "api.amelayes-biophp.net"
              -port: null
              -path: ""
              -query: ""
              -fragment: ""
            }
            "handler" => GuzzleHttp\HandlerStack {#423
              -handler: GuzzleHttp\Handler\StreamHandler {#424
                -lastHeaders: []
              }
              -stack: array:6 [
                0 => array:2 [
                  0 => Closure(callable $handler) {#425
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "http_errors"
                ]
                1 => array:2 [
                  0 => Closure(callable $handler) {#426
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "allow_redirects"
                ]
                2 => array:2 [
                  0 => Closure(callable $handler) {#427
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "cookies"
                ]
                3 => array:2 [
                  0 => Closure(callable $handler) {#428
                    class: "GuzzleHttp\Middleware"
                  }
                  1 => "prepare_body"
                ]
                4 => array:2 [
                  0 => Csa\GuzzleHttp\Middleware\Stopwatch\StopwatchMiddleware {#429
                    -stopwatch: Symfony\Component\Stopwatch\Stopwatch {#137
                      -morePrecision: true
                      -sections: array:1 [
                        "__root__" => Symfony\Component\Stopwatch\Section {#136
                          -events: array:1 [
                            "__section__.child" => Symfony\Component\Stopwatch\StopwatchEvent {#153
                              -periods: []
                              -origin: 1607215713141.4
                              -category: "section"
                              -morePrecision: true
                              -started: array:1 [
                                0 => 0.0
                              ]
                            }
                          ]
                          -origin: null
                          -morePrecision: true
                          -id: null
                          -children: array:1 [
                            0 => Symfony\Component\Stopwatch\Section {#154
                              -events: array:36 [
                                "__section__" => Symfony\Component\Stopwatch\StopwatchEvent {#155
                                  -periods: []
                                  -origin: 1607215713141.4
                                  -category: "default"
                                  -morePrecision: true
                                  -started: array:1 [
                                    0 => 0.0
                                  ]
                                }
                                "kernel.request" => Symfony\Component\Stopwatch\StopwatchEvent {#156
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#197
                                      -start: 0.0
                                      -end: 5.6
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "section"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\DebugHandlersListener" => Symfony\Component\Stopwatch\StopwatchEvent {#157
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#159
                                      -start: 0.1
                                      -end: 0.3
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\ValidateRequestListener" => Symfony\Component\Stopwatch\StopwatchEvent {#160
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#161
                                      -start: 0.3
                                      -end: 0.4
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\TestSessionListener" => Symfony\Component\Stopwatch\StopwatchEvent {#162
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#170
                                      -start: 0.4
                                      -end: 0.9
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\SessionListener" => Symfony\Component\Stopwatch\StopwatchEvent {#171
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#173
                                      -start: 0.9
                                      -end: 1.0
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\LocaleListener" => Symfony\Component\Stopwatch\StopwatchEvent {#174
                                  -periods: array:2 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#175
                                      -start: 1.0
                                      -end: 1.0
                                      -memory: 2097152
                                    }
                                    1 => Symfony\Component\Stopwatch\StopwatchPeriod {#187
                                      -start: 3.5
                                      -end: 3.5
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\RouterListener" => Symfony\Component\Stopwatch\StopwatchEvent {#176
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#190
                                      -start: 1.0
                                      -end: 3.4
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Bundle\FrameworkBundle\EventListener\ResolveControllerNameSubscriber" => Symfony\Component\Stopwatch\StopwatchEvent {#189
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#188
                                      -start: 3.5
                                      -end: 3.5
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Component\HttpKernel\EventListener\LocaleAwareListener" => Symfony\Component\Stopwatch\StopwatchEvent {#186
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#184
                                      -start: 3.6
                                      -end: 3.8
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "Symfony\Bundle\SecurityBundle\Debug\TraceableFirewallListener" => Symfony\Component\Stopwatch\StopwatchEvent {#185
                                  -periods: array:2 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#196
                                      -start: 3.8
                                      -end: 4.4
                                      -memory: 2097152
                                    }
                                    1 => Symfony\Component\Stopwatch\StopwatchPeriod {#205
                                      -start: 4.4
                                      -end: 5.6
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "event_listener"
                                  -morePrecision: true
                                  -started: []
                                }
                                "controller.get_callable" => Symfony\Component\Stopwatch\StopwatchEvent {#206
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#198
                                      -start: 6.4
                                      -end: 6.7
                                      -memory: 2097152
                                    }
                                  ]
                                  -origin: 1607215713141.4
                                  -category: "default"
                                  -morePrecision: true
                                  -started: []
                                }
                                "kernel.controller" => Symfony\Component\Stopwatch\StopwatchEvent {#320
                                  -periods: array:1 [
                                    0 => Symfony\Component\Stopwatch\StopwatchPeriod {#388
                                      -start: 8.8
                                      -end: 13.5
                                      -memory: 2097152
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                1 => Hoa\Compiler\Llk\Rule\Entry {#534
                  #_rule: "simple_type"
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                2 => Hoa\Compiler\Llk\Rule\Entry {#533
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                }
                3 => Hoa\Compiler\Llk\Rule\Token {#576
                  #_tokenName: "name"
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                4 => Hoa\Compiler\Llk\Rule\Ekzit {#535
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                5 => Hoa\Compiler\Llk\Rule\Ekzit {#524}
                6 => Hoa\Compiler\Llk\Rule\Ekzit {#529}
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                    #_id: "token"
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            -visitor: JMS\Serializer\Type\TypeVisitor {#501}
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            "xml" => JMS\Serializer\Visitor\Factory\XmlSerializationVisitorFactory {#460
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            "xml" => JMS\Serializer\Visitor\Factory\XmlDeserializationVisitorFactory {#462
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          -deserializationContextFactory: JMS\SerializerBundle\ContextFactory\ConfiguredContextFactory {#464
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                  -factory: Symfony\Component\DependencyInjection\Container::getService($registry, string $id, ?string $method, $load) {#33
                    this: Container4EQfUsr\srcApp_KernelTestDebugContainer {#32 …20}
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                      1 => "jms_serializer.constraint_violation_handler"
                      2 => "getJmsSerializer_ConstraintViolationHandlerService"
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