Codon-Aware aligner (cawlign)

A standalone C++ port of bealign, a part of the BioExt (https://github.com/veg/BioExt) package. The purpose of this program is to align/map sequences in a FASTA file to a reference sequence and output the alignment as another FASTA file. The underlying code was originally designed to map HIV-1 reads generated by a 454 instrument to references while accounting for homopolymer errors (e.g. PMID 21632754). It has since become a part of the HIV-TRACE

Key features.

1. Lightweight and self-contained.
2. Allows codon-aware alignment while handling out-of-frame events.
3. Flexible specification of scoring matrices.
4. OpenMP support.

Installation.

Requires CMake.

$git clone https://github.com/veg/cawlign
$cd cawlign
$cmake ./
$make 
$make install

Usage

usage: cawlign [-h] [-v] [-o OUTPUT] [-r REFERENCE] [-s SCORE] [-t DATATYPE] [-l LOCAL_ALIGNMENT] [-f FORMAT] [-S SPACE] [-a] [-q] [-I] [FASTA]

perform a pairwise alignment between a reference sequence and a set of other sequences

optional arguments:
  -h, --help               show this help message and exit
  -v, --version            show "cawlign" version 
  -o OUTPUT                direct the output to a file named OUTPUT (default=stdout)
  -r REFERENCE             read the reference sequence from this file (default="HXB2_pol")
                           first checks to see if the filepath exists, if not looks inside the res/references directory
                           relative to the install path (/usr/local/share/cawlign by default)
  -s SCORE                 read the scoring matrices and options from this file (default="Nucleotide-BLAST")
                           first checks to see if the filepath exists, if not looks inside the res/scoring directory
                           relative to the install path (/usr/local/share/cawlign by default)
                           see INSERT URL later for how to read and create alignment scoring files
  -t DATATYPE              datatype (default=nucleotide)
                           nucleotide : align sequences in the nucleotide space;
                           protein    : align sequences in the protein space;
                           codon: align sequences in the codon space (reference must be in frame; stop codons are defined in the scoring file);
  -l LOCAL_ALIGNMENT       global/local alignment (default=trim)
                           global : full string alignment; all gaps in the alignments are scored the same
                           local  : partial string local (smith-waterman type) alignment which maximizes the alignment score
  -f FORMAT                controls the format of the output (default=refmap)
                           refmap   : aligns query sequences to the reference and does NOT retain instertions relative to the reference;
                           pairwise : aligns query sequences to the reference and DOES retain instertions relative to the reference;
                                      no MSA is generated, but rather pair-wise alignments are all reported (2x the number of sequences);
  -S SPACE                 which version of the algorithm to use (an integer >0, default=quadratic):
                           quadratic : build the entire dynamic programming matrix (NxM);
                           linear    : use the divide and conquer recursion to keep only 6 columns in memory (~ max (N,M));
                                       NOT IMPLEMENTED FOR CODON DATA
  -a                       do NOT use affine gap scoring (use by default)
  -I                       write out the reference sequence for refmap and refalign output options (default = no) 
  FASTA                    read sequences to compare from this file (default=stdin)

Example use

Align a specified sequence to the default reference (HIV-1 HXB2 pol), in nucleotide space, using the default nucleotide scoring matrix.

$cawlign test/cases/MZ766877.fa 

>MZ766877.1
CCTCAGATCACTCTTTGGCAGCGGCCCCTTGTCTCAATAAAAGTAGGGGGCCAAATAAGAGAGGCTCTTTTAGATACAGG
AGCAGATGATACAGTATTAGAAGACATGA-
TTTGCCAAGAAAATAGAAACCAAAAATGATAGAAGGAATTAGAAGTTTTATCAAAGTAAAACAGTATGAACAAATACCTA
TAGAAATTTGTA-
AGAAAAAGCTATAAGTACAGTATTAGTAAGACCTACACCTGTCAACATAATTAGAAAGAATATGTTGACTCAGCTCGGAT
GTACACTAAATTTTCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTAAAACCAGGAATAGATAGTCCAAAAATTAAA
CAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGCAATTTGTGAAGAAATGGAGAAAGAAAGAAAAATTACAAA
AGTAGGGCCTGAAAACCCATACAACACTCCAGTGTTTGCCATAAAAAAGAAGGACAGCACTAAGTGGAGAAAATTAGTAG
ATTTCAAAGAACTCAATAAAAGAACTCAAGACTTTTAAGAAGTTCAATTAAGAATACCACACCCAGCAAAGTTAAAGAAG
AGAAAATCAGTGACAGTGCTAGATGTAGGAGATGCATATTTTTCAGTCCCTTTAGATGAAAGCTTCAGGAAGTATACTGC
ATTCACCATACCTAGTATAAATAATGAAACACCAGGAATTAGATACCAATATAATGTGCTTCCACAAGGATAGAAAAGAT
CACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAAAGCCCTTTAGGACAAAAAATCCAGACATAGTTATCTATCAA
TATATAGATGACTTGTATGTAGGCTCTGACTTAGAAATAAGGCAACATAGGGCAAAGGTAGAGAAGCTAAGAGAACATTT
GTTGAGATGAGGACTTACCACACCAGACAAAAAGCATCAGAAAGAGCCCCCATTTCTTTAGATAAAGTATGAACTCCATC
CTGACAAATGGACAGTACAACCTATAACGCTGCCAGAAAAGAACAGCTGGACTGTCAATGATATACAGAAGTTAGTAAGA
AAATTAAACTAGGCCAGCCAGATCTATGCAAAGATTA--
GTAAAACAACTGTGCAAACTCCTTAGGGGGACTAAAGCACTAACAGACATAGTACCACTGACTAAAGAAGCAGAATTAGA
ATTAGCAGAGAACAGAGAAATTCTAAAAGAACCAGTACATAAGGTATATTATGACCCATCAAAAGACTTAATAGCTAAAA
TACAGAAACAGGGGCATGGCCAATGGACATACCAAATTTACCAAGAGCCGTTCAAAAATCTGAAAACAGGGAAGTATGCA
AAAATGAAGCATGCCCACACTAATGATGTGAAACAGTTAACAAAGGCAGTGCAAAAAATAACTCTAGAAAGCATAGTAAT
ATGAAGAAAAACTCCTAAATTTAGATTACCCATCCAAAAAGAAACGTAGGAGACATAGTGGACAGACTATTAGCAAGCCA
CCTAGATTCCTAAGTAGGAGTTTGTTAATACCCCTCCCCTAGTAAAATTATAGTATCAGCTAGAAAAAGAACCCATAGTA
AGAGCAGAAACTTTTTATGTAGATAGAGCAGCTAATAAAGAAACTAAAGCAGGAAAAGCAAAGTATGTTACTGACAGAGG
AAGGCAAAAAGTTGTTTCCCTAACTGAAACAACAAACCAGAAAACTGAATTACAAGCAATTCAGCTAGCTTTACAAGATT
CAGGATCAGAAGTAAACATAGTAACAGACTCACAGTATGCATTAAGAATCATTCAAGGACAACCAGATAAGAGTGAATCA
GAGATAGTCAACCAAATAATAGAACAATTAATAAACAAGGAGAGGGTATACCTGTCATAGGTACCAGCACATAAAGGAAT
TAGAGGAAATGAACAAGTAAATAAATTAGTAAGTAATAGAATCAGGAAAGTGCTATTTCTAGATAAAATAAATAAGGCTC
AAGAAGAGCATGAAAAATATCACAGCAATTGAAGAGCAATGGCTAGTAAGTTTAACCTGCCACCAGTTGTAGCAAAAGAA
ATAGTAGCTAGCTGTGATAAGTGTCAGCTAAAAAGGGAAGCCATACATAGACAAGTAGACTGTAGTCCAAAGATATGGCA
ATTAGATTGTACACATCTAGAAAGGAAAGTCATCCTAGTAGCAGTCCATGTAGCCAGTGGCTATATAGAAGCAGAAGTTA
TCCCAGCAGAAACAGGACAAGAAACAGCATACTATATACTAAAATTAGCAGGAAGATGGCCAGTCAAAACCATACATACA
GACAATGGCACTAATTTCACCAGTGCTGCAGTTAAAGCAGCCTGCTGGTGGGCAAGTATCCAACAAGAATTTAGAATTCC
CTACAATCCCCAAAGTCAAGAAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGAGCAAG
CTGAGCACCTTAAGACAGCAGTACAAATAGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTAGGGGGTATAGT
GCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAGACTAAAGAATTACAAAAACAAATTACAAAAATCCAAAA
TTTTCGGGTTTATTACAGAGACAGCAGAGATCCTATTTGGAAAGGACCAGCCAAACTACTGTGGAAAGGTGAAGGGGCAG
TAGTAATACAAGATAATAGTGACATAAAAGTAGTACCAAGGAGGAAAGTAAAAATCATTAAGGACTATGGAAAACAGATG
GCAGGTGCTGATTGTGTGGCAGGTAGACAGGATGAGGAT

Align a specified sequence to the default reference (HIV-1 HXB2 pol), in nucleotide space, using the default nucleotide scoring matrix, and a linear space algorithm

cawlign -S linear test/cases/MZ766877.fa
>MZ766877.1
CCTCAGATCACTCTTTGGCAGCGGCCCCTTGTCTCAATAAAAGTAGGGGGCCAAATAAGAGAGGCTCTTTTAGATACAGG
AGCAGATGATACAGTATTAGAAGACAT-
AGTTTGCCAAGAAAATAGAAACCAAAAATGATAGAAGGAATTAGAAGTTTTATCAAAGTAAAACAGTATGAACAAATACC
TATAGAAATTTGT-
AAGAAAAAGCTATAAGTACAGTATTAGTAAGACCTACACCTGTCAACATAATTAGAAAGAATATGTTGACTCAGCTCGGA
TGTACACTAAATTTTCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTAAAACCAGGAATAGATAGTCCAAAAATTAA
ACAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGCAATTTGTGAAGAAATGGAGAAAGAAAGAAAAATTACAA
AAGTAGGGCCTGAAAACCCATACAACACTCCAGTGTTTGCCATAAAAAAGAAGGACAGCACTAAGTGGAGAAAATTAGTA
GATTTCAAAGAACTCAATAAAAGAACTCAAGACTTTTAAGAAGTTCAATTAAGAATACCACACCCAGCAAAGTTAAAGAA
GAGAAAATCAGTGACAGTGCTAGATGTAGGAGATGCATATTTTTCAGTCCCTTTAGATGAAAGCTTCAGGAAGTATACTG
CATTCACCATACCTAGTATAAATAATGAAACACCAGGAATTAGATACCAATATAATGTGCTTCCACAAGGATAGAAAAGA
TCACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAAAGCCCTTTAGGACAAAAAATCCAGACATAGTTATCTATCA
ATATATAGATGACTTGTATGTAGGCTCTGACTTAGAAATAAGGCAACATAGGGCAAAGGTAGAGAAGCTAAGAGAACATT
TGTTGAGATGAGGACTTACCACACCAGACAAAAAGCATCAGAAAGAGCCCCCATTTCTTTAGATAAAGTATGAACTCCAT
CCTGACAAATGGACAGTACAACCTATAACGCTGCCAGAAAAGAACAGCTGGACTGTCAATGATATACAGAAGTTAGTAAG
AAAATTAAACTAGGCCAGCCAGATCTATGCAAAGATT--
AGTAAAACAACTGTGCAAACTCCTTAGGGGGACTAAAGCACTAACAGACATAGTACCACTGACTAAAGAAGCAGAATTAG
AATTAGCAGAGAACAGAGAAATTCTAAAAGAACCAGTACATAAGGTATATTATGACCCATCAAAAGACTTAATAGCTAAA
ATACAGAAACAGGGGCATGGCCAATGGACATACCAAATTTACCAAGAGCCGTTCAAAAATCTGAAAACAGGGAAGTATGC
AAAAATGAAGCATGCCCACACTAATGATGTGAAACAGTTAACAAAGGCAGTGCAAAAAATAACTCTAGAAAGCATAGTAA
TATGAAGAAAAACTCCTAAATTTAGATTACCCATCCAAAAAGAAACGTAGGAGACATAGTGGACAGACTATTAGCAAGCC
ACCTAGATTCCTAAGTAGGAGTTTGTTAATACCCCTCCCCTAGTAAAATTATAGTATCAGCTAGAAAAAGAACCCATAGT
AAGAGCAGAAACTTTTTATGTAGATAGAGCAGCTAATAAAGAAACTAAAGCAGGAAAAGCAAAGTATGTTACTGACAGAG
GAAGGCAAAAAGTTGTTTCCCTAACTGAAACAACAAACCAGAAAACTGAATTACAAGCAATTCAGCTAGCTTTACAAGAT
TCAGGATCAGAAGTAAACATAGTAACAGACTCACAGTATGCATTAAGAATCATTCAAGGACAACCAGATAAGAGTGAATC
AGAGATAGTCAACCAAATAATAGAACAATTAATAAACAAGGAGAGGGTATACCTGTCATAGGTACCAGCACATAAAGGAA
TTAGAGGAAATGAACAAGTAAATAAATTAGTAAGTAATAGAATCAGGAAAGTGCTATTTCTAGATAAAATAAATAAGGCT
CAAGAAGAGCATGAAAAATATCACAGCAATTGAAGAGCAATGGCTAGTAAGTTTAACCTGCCACCAGTTGTAGCAAAAGA
AATAGTAGCTAGCTGTGATAAGTGTCAGCTAAAAAGGGAAGCCATACATAGACAAGTAGACTGTAGTCCAAAGATATGGC
AATTAGATTGTACACATCTAGAAAGGAAAGTCATCCTAGTAGCAGTCCATGTAGCCAGTGGCTATATAGAAGCAGAAGTT
ATCCCAGCAGAAACAGGACAAGAAACAGCATACTATATACTAAAATTAGCAGGAAGATGGCCAGTCAAAACCATACATAC
AGACAATGGCACTAATTTCACCAGTGCTGCAGTTAAAGCAGCCTGCTGGTGGGCAAGTATCCAACAAGAATTTAGAATTC
CCTACAATCCCCAAAGTCAAGAAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGAGCAA
GCTGAGCACCTTAAGACAGCAGTACAAATAGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTAGGGGGTATAG
TGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAGACTAAAGAATTACAAAAACAAATTACAAAAATCCAAA
ATTTTCGGGTTTATTACAGAGACAGCAGAGATCCTATTTGGAAAGGACCAGCCAAACTACTGTGGAAAGGTGAAGGGGCA
GTAGTAATACAAGATAATAGTGACATAAAAGTAGTACCAAGGAGGAAAGTAAAAATCATTAAGGACTATGGAAAACAGAT
GGCAGGTGCTGATTGTGTGGCAGGTAGACAGGATGAGGAT

Align a specified sequence to the default reference (HIV-1 HXB2 pol), in codon space, using the BLOSUM62 scoring matrix

$cawlign -t codon -s BLOSUM62 test/cases/MZ766877.fa
>MZ766877.1
CCTCAGATCACTCTTTGGCAGCGGCCCCTTGTCTCAATAAAAGTAGGGGGCCAAATAAGAGAGGCTCTTTTAGATACAGG
AGCAGATGATACAGTATTAGAAGACATAGATTTGCCA---
AGAAAAAAACCAAAAATGATAGAAGGAATTAGAAGTTTTATCAAAGTAAAACAGTATGAACAAATACCTATAGAAATTTG
TAAGAAAAAGGCTATAAGTACAGTATTAGTAAGACCTACACCTGTCAACATAATTAGAAAGAATATGTTGACTCAGCTCG
GATGTACACTAAATTTTCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTAAAACCAGGAATAGATAGTCCAAAAATT
AAACAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGCAATTTGTGAAGAAATGGAGAAAGAAAGAAAAATTAC
AAAAGTAGGGCCTGAAAACCCATACAACACTCCAGTGTTTGCCATAAAAAAGAAGGACAGCACTAAGTGGAGAAAATTAG
TAGATTTCAAAGAACTCAATAAAAGAACTCAAGACTTT---
GAAGTTCAATTAAGAATACCACACCCAGCAAAGTTAAAGAAGAGAAAATCAGTGACAGTGCTAGATGTAGGAGATGCATA
TTTTTCAGTCCCTTTAGATGAAAGCTTCAGGAAGTATACTGCATTCACCATACCTAGTATAAATAATGAAACACCAGGAA
TTAGATACCAATATAATGTGCTTCCACAAGGA---
AAAAGATCACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAAAGCCCTTTAGGACAAAAAATCCAGACATAGTTAT
CTATCAATATATAGATGACTTGTATGTAGGCTCTGACTTAGAAATAAGGCAACATAGGGCAAAGGTAGAGAAGCTAAGAG
AACATTTGTTGAGA---GGACTTACCACACCAGACAAAAAGCATCAGAAAGAGCCCCCATTTCTT---
ATAAAGTATGAACTCCATCCTGACAAATGGACAGTACAACCTATAACGCTGCCAGAAAAGAACAGCTGGACTGTCAATGA
TATACAGAAGTTAGTAAGAAAATTAAAC---
GCCAGCCAGATCTATGCAAAGATTAGTACAAAACAACTGTGCAAACTCCTTAGGGGGACTAAAGCACTAACAGACATAGT
ACCACTGACTAAAGAAGCAGAATTAGAATTAGCAGAGAACAGAGAAATTCTAAAAGAACCAGTACATAAGGTATATTATG
ACCCATCAAAAGACTTAATAGCTAAAATACAGAAACAGGGGCATGGCCAATGGACATACCAAATTTACCAAGAGCCGTTC
AAAAATCTGAAAACAGGGAAGTATGCAAAAATGAAGCATGCCCACACTAATGATGTGAAACAGTTAACAAAGGCAGTGCA
AAAAATAACTCTAGAAAGCATAGTAATA------AAAACTCCTAAATTTAGATTACCCATCCAAAAAGAAACG-------
--------------------------------------------GAGTTTGTTAATACCCCTCCCCTAGTAAAATTA---
TATCAGCTAGAAAAAGAACCCATAGTAAGAGCAGAAACTTTTTATGTAGATAGAGCAGCTAATAAAGAAACTAAAGCAGG
AAAAGCAAAGTATGTTACTGACAGAGGAAGGCAAAAAGTTGTTTCCCTAACTGAAACAACAAACCAGAAAACTGAATTAC
AAGCAATTCAGCTAGCTTTACAAGATTCAGGATCAGAAGTAAACATAGTAACAGACTCACAGTATGCATTAAGAATCATT
CAAGGACAACCAGATAAGAGTGAATCAGAGATAGTCAACCAAATAATAGAACAATTAATAAACAAGGAGAGGGTATACCT
GTCA---
GTACCAGCACATAAAGGAATTAGAGGAAATGAACAAGTAAATAAATTAGTAAGTAATAGAATCAGGAAAGTGCTATTTCT
AGATAAAATAAATAAGGCTCAAGAAGAGCATGAAAAATATCACAGCAAT---
AGAGCAATGGCTAGTAAGTTTAACCTGCCACCAGTTGTAGCAAAAGAAATAGTAGCTAGCTGTGATAAGTGTCAGCTAAA
AAGGGAAGCCATACATAGACAAGTAGACTGTAGTCCAAAGATATGGCAATTAGATTGTACACATCTAGAAAGGAAAGTCA
TCCTAGTAGCAGTCCATGTAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAAGAAACAGCATAC
TATATACTAAAATTAGCAGGAAGATGGCCAGTCAAAACCATACATACAGACAATGGCACTAATTTCACCAGTGCTGCAGT
TAAAGCAGCCTGCTGGTGGGCAAGTATCCAACAAGAATTTAGAATTCCCTACAATCCCCAAAGTCAAGAAGTAGTAGAAT
CCATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGAGCAAGCTGAGCACCTTAAGACAGCAGTACAAATAGCA
GTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTAGGGGGTATAGTGCAGGGGAAAGAATAATAGACATAATAGCAAC
AGACATACAGACTAAAGAATTACAAAAACAAATTACAAAAATCCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGATC
CTATTTGGAAAGGACCAGCCAAACTACTGTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTA
GTACCAAGGAGGAAAGTAAAAATCATTAAGGACTATGGAAAACAGATGGCAGGTGCTGATTGTGTGGCAGGTAGACAGGA
TGAGGAT

Align a specified sequence to a specific reference (HIV-1 HXB2 rt), in codon space, using the BLOSUM62 scoring matrix and include the reference sequence (NOT including insertions in the reference)

>HXB2_rt
CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC
>MZ766877.1
CCAATTAGTCCCATTGAAACTGTACCAGTAAAACTAAAACCAGGAATAGATAGTCCAAAAATTAAACAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGCAATTTGTGAAGAAATGGAGAAAGAAAGAAAAATTACAAAAGTAGGGCCTGAAAACCCATACAACACTCCAGTGTTTGCCATAAAAAAGAAGGACAGCACTAAGTGGAGAAAATTAGTAGATTTCAAAGAACTCAATAAAAGAACTCAAGACTTT---GAAGTTCAATTAAGAATACCACACCCAGCAAAGTTAAAGAAGAGAAAATCAGTGACAGTGCTAGATGTAGGAGATGCATATTTTTCAGTCCCTTTAGATGAAAGCTTCAGGAAGTATACTGCATTCACCATACCTAGTATAAATAATGAAACACCAGGAATTAGATACCAATATAATGTGCTTCCACAAGGA---AAAAGATCACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAAAGCCCTTTAGGACAAAAAATCCAGACATAGTTATCTATCAATATATAGATGACTTGTATGTAGGCTCTGACTTAGAAATAAGGCAACATAGGGCAAAGGTAGAGAAGCTAAGAGAACATTTGTTGAGA---GGACTTACCACACCAGACAAAAAGCATCAGAAAGAGCCCCCATTTCTT---ATAAAGTATGAACTCCATCCTGACAAATGGACAGTACAACCTATAACGCTGCCAGAAAAGAACAGCTGGACTGTCAATGATATACAGAAGTTAGTAAGAAAATTAAAC---GCCAGCCAGATCTATGCAAAGATTAGTACAAAACAACTGTGCAAACTCCTTAGGGGGACTAAAGCACTAACAGACATAGTACCACTGACTAAAGAAGCAGAATTAGAATTAGCAGAGAACAGAGAAATTCTAAAAGAACCAGTACATAAGGTATATTATGACCCATCAAAAGACTTAATAGCTAAAATACAGAAACAGGGGCATGGCCAATGGACATACCAAATTTACCAAGAGCCGTTCAAAAATCTGAAAACAGGGAAGTATGCAAAAATGAAGCATGCCCACACTAATGATGTGAAACAGTTAACAAAGGCAGTGCAAAAAATAACTCTAGAAAGCATAGTAATA------AAAACTCCTAAATTTAGATTACCCATCCAAAAAGAAACG---------------------------------------------------GAGTTTGTTAATACCCCTCCCCTAGTAAAATTA---TATCAGCTAGAAAAAGAACCCATAGTAAGAGCAGAAACTTTT

Align a specified sequence to a specific reference (HIV-1 HXB2 rt), in codon space, using the BLOSUM62 scoring matrix report pairwise alignment (including insertions in the reference)

cawlign -t codon -r HXB2_rt -f pairwise -s BLOSUM62 test/cases/MZ766877.fa 
>HXB2_rt
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTC---TGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGA---TGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGG---TGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTT---TGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAAT---TGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATA------TGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACA---------------------------------------------------TGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTA---TGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>MZ766877.1
GCGCCCGAACAGGGACTTGAAAGCGAAAGTGAGACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGCTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGGCTGGTGAGTACGCCAAATTTTATTTGACTAGCGGAGGCTAGAAGGAGAGAGATAGGTGCGAGAGCGTCAATATTAAGAGGAGGAAAATTAGATTCATAGGAGAGAATTAAGTTAAGGCCAGGGGGAAAGAAATGTTATCGGCTAAAACACTTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTTTTAGAAACGTCAGATGGCTGTAAACAAATACTAAGACAGCTTCAGCCAGCTCTTCAGACAGGAACAGAGGAAATTAAATCATTATTCAACACAGTAGCAACTCTTTATTGTGTACATCAAGGGATAAAGGTACAAGACACCAAAGAAGCCTTAGACAAGATAGAGGAAGAACAAAAACAAAGTCAGAAAAAGGCACAACAAGCAGAAGCGGCTGACAAAGGAAAGGTCAGTCAAAATTATCCTATAGTGCAGAATCTCCAAGGGCAAATGGTACACCAGGCCCTGTCACCTAGAACTTTGAATGCATAGGTAAAAGTAGTAGAGGAGAAAAGTTTTAACCCTGAGGTAATACCCATGTTTTCAGCATTATCAGAGGGAGCCACCCCATCAGATTTAAACACCATGTTAAATACAATAGGGGGACATCAAGCAGCCATGCAAATGTTAAAGGATACTATCAATGAGGAGGCTGCAGAATAGGACAGATTACATCCAGTACAGGCAGGGCCTGTTGCACCAGGCCAAATGAGGGACCCAAAGGGAAGTGACATAGCAAGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAGCAACCCACCTATGCCAGTGGGAGACATCTATAAAAGATAGATAATTCTGAGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAACCTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTAGATGACAGACACCTTGTTAGTCCAAAATGCGAACCCAGACTGTAAGACCATTTTAAGAGCATTAAGACCAGAGGCTACATTAGAAGAAATGATGACAGCATGTCAAGGAGTGGGAGGACCTGGCCACAAAGCAAAAGTCTTGGCTGAAGCAATGAGCCAGGTAGGCAATACAAACATAATGATGCAGAGAAGCAATTTTAGAAGCAATAAAAGAATTGTTAAGTGTTTCAACTGTGGCAAGGAGGGGCACATAGCCAAAAATTGCAGGGCCCCTAAGAAAAAAGGCTGTTAGAAATGTGGAAAAGAAGGACACCAAATGAAGGATTGCTCTGAAAGGCAGGCTAATTTTTTAAGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGAAATTTCCTTCAGAGCAGACCAAGGCCAACAGCCCCACCAGTAAAGCCAACAGCTCCACCAGTAGAGAGCTTCAGGTTCGAGGAGACAACCCCCTCGATGAAACCAGAGTCGAAGGACGAGGACGCTTTAACTTCCCTCAGATCACTCTTTGGCAGCGGCCCCTTGTCTCAATAAAAGTAGGGGGCCAAATAAGAGAGGCTCTTTTAGATACAGGAGCAGATGATACAGTATTAGAAGACATAGATTTGCCAAGAAAATAGAAACCAAAAATGATAGAAGGAATTAGAAGTTTTATCAAAGTAAAACAGTATGAACAAATACCTATAGAAATTTGTAAGAAAAAGGCTATAAGTACAGTATTAGTAAGACCTACACCTGTCAACATAATTAGAAAGAATATGTTGACTCAGCTCGGATGTACACTAAATTTTCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTAAAACCAGGAATAGATAGTCCAAAAATTAAACAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGCAATTTGTGAAGAAATGGAGAAAGAAAGAAAAATTACAAAAGTAGGGCCTGAAAACCCATACAACACTCCAGTGTTTGCCATAAAAAAGAAGGACAGCACTAAGTGGAGAAAATTAGTAGATTTCAAAGAACTCAATAAAAGAACTCAAGACTTTTAA---GAAGTTCAATTAAGAATACCACACCCAGCAAAGTTAAAGAAGAGAAAATCAGTGACAGTGCTAGATGTAGGAGATGCATATTTTTCAGTCCCTTTAGATGAAAGCTTCAGGAAGTATACTGCATTCACCATACCTAGTATAAATAATGAAACACCAGGAATTAGATACCAATATAATGTGCTTCCACAAGGATAG---AAAAGATCACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAAAGCCCTTTAGGACAAAAAATCCAGACATAGTTATCTATCAATATATAGATGACTTGTATGTAGGCTCTGACTTAGAAATAAGGCAACATAGGGCAAAGGTAGAGAAGCTAAGAGAACATTTGTTGAGATGA---GGACTTACCACACCAGACAAAAAGCATCAGAAAGAGCCCCCATTTCTTTAG---ATAAAGTATGAACTCCATCCTGACAAATGGACAGTACAACCTATAACGCTGCCAGAAAAGAACAGCTGGACTGTCAATGATATACAGAAGTTAGTAAGAAAATTAAACTAG---GCCAGCCAGATCTATGCAAAGATTAGTACAAAACAACTGTGCAAACTCCTTAGGGGGACTAAAGCACTAACAGACATAGTACCACTGACTAAAGAAGCAGAATTAGAATTAGCAGAGAACAGAGAAATTCTAAAAGAACCAGTACATAAGGTATATTATGACCCATCAAAAGACTTAATAGCTAAAATACAGAAACAGGGGCATGGCCAATGGACATACCAAATTTACCAAGAGCCGTTCAAAAATCTGAAAACAGGGAAGTATGCAAAAATGAAGCATGCCCACACTAATGATGTGAAACAGTTAACAAAGGCAGTGCAAAAAATAACTCTAGAAAGCATAGTAATATGAAGA------AAAACTCCTAAATTTAGATTACCCATCCAAAAAGAAACGTAGGAGACATAGTGGACAGACTATTAGCAAGCCACCTAGATTCCTAAGTAG---------------------------------------------------GAGTTTGTTAATACCCCTCCCCTAGTAAAATTATAG---TATCAGCTAGAAAAAGAACCCATAGTAAGAGCAGAAACTTTTTATGTAGATAGAGCAGCTAATAAAGAAACTAAAGCAGGAAAAGCAAAGTATGTTACTGACAGAGGAAGGCAAAAAGTTGTTTCCCTAACTGAAACAACAAACCAGAAAACTGAATTACAAGCAATTCAGCTAGCTTTACAAGATTCAGGATCAGAAGTAAACATAGTAACAGACTCACAGTATGCATTAAGAATCATTCAAGGACAACCAGATAAGAGTGAATCAGAGATAGTCAACCAAATAATAGAACAATTAATAAACAAGGAGAGGGTATACCTGTCATAGGTACCAGCACATAAAGGAATTAGAGGAAATGAACAAGTAAATAAATTAGTAAGTAATAGAATCAGGAAAGTGCTATTTCTAGATAAAATAAATAAGGCTCAAGAAGAGCATGAAAAATATCACAGCAATTGAAGAGCAATGGCTAGTAAGTTTAACCTGCCACCAGTTGTAGCAAAAGAAATAGTAGCTAGCTGTGATAAGTGTCAGCTAAAAAGGGAAGCCATACATAGACAAGTAGACTGTAGTCCAAAGATATGGCAATTAGATTGTACACATCTAGAAAGGAAAGTCATCCTAGTAGCAGTCCATGTAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAAGAAACAGCATACTATATACTAAAATTAGCAGGAAGATGGCCAGTCAAAACCATACATACAGACAATGGCACTAATTTCACCAGTGCTGCAGTTAAAGCAGCCTGCTGGTGGGCAAGTATCCAACAAGAATTTAGAATTCCCTACAATCCCCAAAGTCAAGAAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGAGCAAGCTGAGCACCTTAAGACAGCAGTACAAATAGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTAGGGGGTATAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAGACTAAAGAATTACAAAAACAAATTACAAAAATCCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGATCCTATTTGGAAAGGACCAGCCAAACTACTGTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTACCAAGGAGGAAAGTAAAAATCATTAAGGACTATGGAAAACAGATGGCAGGTGCTGATTGTGTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTCTAGTGAAGCACCATATGTATATGTCAAAGAGAGCCAGTGGCTGGTTTTACAGACACCATTATGAAAGTAGGCATCCAAAAGTAAGTTCAGAAACACACATCCCATTAGGGGAGGCTAAATTAGTCATAACAACATATTAGGGTTTGCAAACAGGAGAAAGAGAATGGCATTTAGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAGACCAGCTAATCCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGACAAGCCATATTAGGACACATAGTTATTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTGACAGCATTAGTAAAACCAAAAAAGAGAAAGCCACCCCTGCCTAGTGTTAGGAAGTTAGTAGAAGATAGATAGAACAAGCCCCAGAGAACCAAGGGCCGCAGAAGGAACCATACAATGAATGGGCACTAGAGCTTTTAGAGGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGAGTATGGCTCCATAGCTTAGGACAGTATATCTATGAAACATATGGAGACACTTAGACAGAAGTTGAAGCTTTGATAAGAATACTGCAACAACTATTGTTTATTCATTTCAGAATTAGGTGCCAGCATAGCAGAATAGGCATTATACCACATAGAAGAGCAAGAAATGGAGCTAATAGATCCTAACCTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTACAACCCCTTGTACTCCATGCTATTGTAAAAGATGCAGCTATCATTGTTTAGTTTGCTTTCAGAAAAAAGGCTTAGGCATTTACTATGGCAGAAAGAAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAATAAGGATCATCAAAATCCTATACCAGAGCAGTAAGTACCATATAGTAGATGTAATGTTAGATCTAGATTATAGAATAGGAGTAGCAGCACTTGTAGTAGCACTAATCATAGCAATAATTGTGTGGATAATAGTATATCTAGAATATAGAAAACTAGTAAAACAAAAGAGAATAGATTAGTTAATTAAGAGAATTAAAGAAAAAGAAGAAGACAGTGGCAATGAGAGTGAGGGAGATACTGAGGAATTGGCAACAATAGTAGATATAGGGCATCTTAAGCTTTTGGCTGCTAATGAGTTGTAATGTGAGAGGAAATTTGTAGGTCACAGTCTATTATGGAGTACCTGTGTGGAAAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGACAGAAGCGCATAATGTCTAGGCTACACATGCCTGTGTACCCACAGACCCTAACCCACAGGAAATAGTTTTAGAAAATGTAACAGAAAATTTTAATATGTAAGAAAATAGTATGGTAGATCAGATGCATAAAGATGTAATCAGTTTATAAGATCAAAGCCTAAAGCCATGTGTAAAGATGACCCCACTCTGTGTCACTCTACATTGTACAAATGTAACAGGTAATGATAGCCGTACTGTTGACAATGACACCATAAGAGAAATAAAAAATTGCTCTTTCAATGCAACTACAGAAATAAAAGATAAGATAAAGAAGGAGTATGCACTTTTCTATAGACTTGATGTAGTACCACTTAAGGACACCAACTCTAGTGAATATATATTAATAAATTGTAATTCTTCAACCATATCACAGGCCTGTCCAAAGATCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCGGCTAGTTATGCGATTCTAAAATGTAATAATAAAACATTTAATAGGTCAGGACCATGTCAGAATGTCAGTACAGTACAATGTACACATAGAATTAAGCCAGTGGTATCAACTCAATTACTGTTAAATAGTAGCCTAGCAGAAGAAGAGATAATAATCAGATCTAAGAATCTGAGCGAGATTAGACACACAATAATAGTACATCTTAATAAATCTGTAAAGATTATATGTACAAGACCCAACAATAATACAAGAAAAAGTGTAAAGATAGGACCAAGACAGACATTCTATGCAACAGAAGATATAATAAGAGACATAAGACAAGCACACTGTAACATTAATAAAAAGAACTAGACTGAAACCTTAGAAAGGGTAGGGGAAAAATTAAAGGAACACTTCCCTAATAAAACAATAACATTTAAACCATCCGCAGGAAAGGACCCAGAAGTCACAACACATATGTTTAATTGTAGAGGAGAATTTTTCTATTGCAACACATCAGGCCTGTTTAATAGTACATTTAATGGTACACACCTGAATAATACATTCAGGCCTAATAGTACAGACATCATCACACTCCAATGCAGAATAAAACAAATTGTAAACATGTGGCAGGAAGTAAGACGAGCAATGTATGCCCCTCCCATTGCAGGAAATATAACATGTAGATCAAATATCACAGGACTACTATTGACACGTGATGGCGGAAAGAATGAAACTAATGATACCACAGAGATATTCAGACCTATAAAAAGAGATATGAAAGATAATTAGAGAAGTGAACTATATAAATATAAAGTAGTAGAAATTAAGCCATTAAGAATAGCACCCACCGAGGCAAAAAGGAGAGTGGTGGAGAGAGAAAAAAGAGCAGTAGGACTAAGAGCTGTGTTCCTTAGGTTCTTAGGAGCAGCAGGAAGCACTATAGGCGCAGCGTCAATAACGCTGACAGTACAAGCCAGACAATTGCTGTCTAGAATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAGCAGCATATGTTGCAACTCACGGTCTAGGGCATTAAGCAACTCCAGGCAAGAGTCCTTGCTATAGAAAGATACCTAAAAGATCAACAGCTCCTAGGGATTTAGGGCTGCTCTAGAAAACTCATCTGCACCACTGCAGTGTCTTAGAACAGTAGTTAGAGTAATAAAACTCTAAGAGATATTTAGAATAACATGACCTAGATGCAGTAGGATAAAGAAATTAGTAATTATACAGAAATAATATATGATCTACTTGAAAAATCGCAGATCCAGCAAGAAAACAATAAAAAAGATTTACTAGCATTGGACAGTTAGAATAATCTGTAGAATTAGTTTAACATATCAAATTAGTTGTGGTATATAAAAATATTTATAATGATAGTAGGAGGCTTGATAAGTTTGAGAATAACTTTTGCTGTGCTTTCTATAGTGAATAGAGTTAGGCAAGGATACTCACCTCTGTCATTGCAGACCCTTACCCAGAACCCAGAAAGACTCGACAGGCTCAGAAGAATCGAAGAAGAAAGTAGAGAGCAAGACAAAGACAAATCCATTCGATTAGTGAGCAGATTCTTAGCACTTGCCTAGGACGACCTGCGGAGCCTATGCCTTTTCAGCTACCACCGATTGAGAGACTTTATATTGATTGCAGCGAGAGCAGTAGAACTTCTAAGACACAGCAGTCTCAGAGGACTACAGAAAGGTTAGGAAATCCTTAAGTATCTAGGAAGTCTTGTGCAATATTGAGGTCTAGAGCTAAAAAAGAGTGCTATTAATTTGTTTGATACCATAGCAATAGCAGTAGCTGAAGGAACAGATAAGATTCTAATATACTTACAAAGAATTTATAAAGCCATCTGCAACATACAAGAATAAGACAAAGATTTGCAGCAGCTTTGCAATAAAATAGGGGGCAAGTGGTCAAAAAGCAGTGTAGTAAGGTGGCCTGCTATAAAAGAAAGAATACAACGCACTGCTCCAGCAGCAGAAGGAGTAAGAGCAGCATCTCAAGACCTAGATAGACACAGGGCACTTACAACCAGCAATACAGCCACCAATAATGCTGCTTGTGCCTGGCTAGAAGCGCAAGAGGAGAGAGACGATGTAAGCTTTCCAGTCAGACCTCAGGTACCTTTAAGGCCAATGACATATAAGGCAGCATTTGATCTCGGCTTCTTTTTAAAAGAAAAGGGGGGACTGGAAGGGTTAATTTACTCTAGGAAAAGGCAAGAGATTCTTGATTTGTAGGTCTATCACACACAAGGCTTCTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGATACCCACTGACCTTTGGATGGCCATTCAAGCTAGTGCCAGTCGACCCAAGGGAAATAGAAGAGAACAGCAACAGGGAGAACAACTGCTTGCTACACCCTGAGAACCAGCATAGAATGGAGGATGACCACAGAGAAGTGTTAAGATGGAAGTTTGACAGTCAACTAGCACGCAGACATATGGCCCGTGAGCTACATCCGGAGTAGTACAAAGACTAAGACTGCTGACACAGAAAGGACTTTCCGCTAGGACTTTCCACTGAGGCGTTCCAGGAGGTGTGGTCTAGGCGGAACAAGGAGTAGTCAACCCTCAGACGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTAGGTCTCTCTAAGTAGACCAGATCCGAGCCTAGGAGCTCTCTAGCTATCTAAGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGC