biosmallscripts
July 15, 2025 ยท View on GitHub
Small scripts to alleviate daily hassles in the dry lab. See here (in Japanese) for the details and motivation behind each piece.
2023-12-21: plot_linear_genome.py and plot_circular_genome.py will be merged into a single package, which will be made public soon.
2024-01-22: our new genome drawer gbdraw will be released soon!
May 2025: gbdraw is available from bioconda!
Streamlit apps
Some of the scripts have been made available as streamlit web apps!
ORFIND: A lightweight open reading frame (ORF) finder
SkewPlot: Visualize dinucleotide skew (e.g. GC skew) in microbial genomes
blast2bed.py
convert BLASTN/BLASTX/TBLASTX output into BED format
Requirements
- Python3
usage: blast2bed.py [-h] -i INPUT [-o OUTPUT] [-s SCORE] [-e EVALUE]
convert BLASTN/BLASTX/TBLASTX output into BED format
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
tab-separated blast output (required) with "-outfmt "[6|7]"
-o OUTPUT, --output OUTPUT
output BED format file (default: stdout)
-s SCORE, --score SCORE
score (default: 0)
-e EVALUE, --evalue EVALUE
E-value threshold (default: 1e-30)
gb2faa.py
Extract protein sequences from a genbank file downloaded from NCBI
Requirements
Usage
$ ./gb2faa.py
usage: gb2faa.py [-h] -i INPUT [-o OUTPUT]
Extract protein sequences from a genbank file
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
GenBank flat file format of the genomic sequence(s) (required)
-o OUTPUT, --output OUTPUT
output fasta file (default: out.faa)
annotate_gff3.py
Add functional annotation to the 9th column of a gff3 file
Requirements
Usage
$ ./annotate_gff3.py -h
usage: annotate_gff3.py [-h] -g GFF -b BLAST -f FUNC [-o OUT] [-p PREFIX]
add functional annotation to the 9th column of a gff3 file
optional arguments:
-h, --help show this help message and exit
-g GFF, --gff GFF Annotation in gff3 format (required)
-b BLAST, --blast BLAST
tab-separated blast output (required) with "-outfmt "[6|7] qaccver saccver pident length
mismatch gapopen qstart qend sstart send evalue bitscore qlen slen qcovs""
-f FUNC, --func FUNC tab-separated function table (required)
-o OUT, --out OUT Annotation in gff3 format (default: stdout)
-p PREFIX, --prefix PREFIX
locus ID prefix (default: gene)
blast2dotplot.py
Draw a dot plot based on a pairwise BLASTN/TBLASTX result
Requirements
Usage
$ ./blast2dotplot.py
usage: blast2dotplot.py [-h] --input FILE
Draw a dot plot based on a pairwise BLASTN/TBLASTX result
optional arguments:
-h, --help show this help message and exit
--input FILE, --in FILE, -i FILE
input BLASTN/TBLASTX result file in XML format (-outfmt 5)
scaffold2contigs.py
Requirements
Usage
$ ./scaffold2contigs.py
usage: scaffold2contigs.py [-h] --input INPUT [--output OUTPUT] [-d DIGIT]
Split scaffolds into contigs
optional arguments:
-h, --help show this help message and exit
--input INPUT, -i INPUT, --in INPUT
Input FASTA file
--output OUTPUT, -o OUTPUT, --out OUTPUT
output FASTA file (default: stdout)
-d DIGIT, --digit DIGIT
number of digits for zero-padding (default:3)
$ less in.fa
>scaffold1
ACTGTGCATNNNNNNACGCTGCANnnNNCTGCAnnnCTGCAnnNNNNCTGCA
>scaffold2
ACGACGACGCGATAGAGnnnnnnAGACGAGAGNNNnnACGACGACG
$ ./scaffold2contigs.py -i in.fa
>scaffold1_001
ACTGTGCAT
>scaffold1_002
ACGCTGCA
>scaffold1_003
CTGCA
>scaffold1_004
CTGCA
>scaffold1_005
CTGCA
>scaffold2_001
ACGACGACGCGATAGAG
>scaffold2_002
AGACGAGAG
>scaffold2_003
ACGACGACG
depth_alignment_breakpoint.py
ddbj_to_gff3.py
Requirements
Usage
$ ./ddbj_to_gff3.py -h
usage: ddbj_to_gff3.py [-h] -i INPUT [-o OUTPUT]
Convert DDBJ/GenBank flatfile into gff3
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
input GenBank/DDBJ flatfile (required)
-o OUTPUT, --output OUTPUT
output gff3 file (default:out.gff3)
gb2nrfaa.py
Extract the longest isoforms of protein-coding genes from a NCBI RefSeq euaryotic genome assembly
Requirements
Usage
$ ./gb2nrfaa.py -h
usage: gb2nrfaa.py [-h] -i INPUT [-o OUTPUT]
Extract the longest isoforms of protein-coding genes from a NCBI RefSeq euaryotic genome assembly
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
GenBank flat file format of the genomic sequence(s) (required)
-o OUTPUT, --output OUTPUT
output fasta-formatted file (required)
##get_flanking_reads.py Extract flanking reads from a BAM file
Requirements
$ ./get_flanking_reads.py
usage: get_flanking_reads.py [-h] --input FILE [--output FILE] -r REF [-w WINDOW] [-m MIN] [-f FLANK] [-p PRIME] [-q]
Extract flanking reads from a BAM file
optional arguments:
-h, --help show this help message and exit
--input FILE, -i FILE, --in FILE
Input BAM file
--output FILE, -o FILE, --out FILE, --output FILE
output txt file
-r REF, --ref REF reference entry name
-w WINDOW, --window WINDOW
window (defalt:100)
-m MIN, --min MIN minimum outut read lenth threshold (defalt:200)
-f FLANK, --flank FLANK
flanking bases (defalt:100)
-p PRIME, --prime PRIME
5'/3'-end
-q, --fastq output fastq
orfind.py
ORF prediction allowing CDS overlaps and GFF3 output
Requirements
Usage
$ ./orfind.py -h
usage: orfind.py [-h] -i INPUT [-o OUT_GFF] [-a OUT_FAA] [-f OUT_FNA] [-g TRANS_TABLE] [-m MIN_AA_LEN]
Predict ORFs
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
sequence file in FASTA format (required)
-o OUT_GFF, --out_gff OUT_GFF
output annotation in gff3 format (default: stdout)
-a OUT_FAA, --out_faa OUT_FAA
output protein sequences in FASTA format (optional)
-f OUT_FNA, --out_fna OUT_FNA
output CDS sequences in FASTA format (optional)
-g TRANS_TABLE, --trans_table TRANS_TABLE
translation table (default: 1)
-m MIN_AA_LEN, --min_aa_len MIN_AA_LEN
minimum protein length (default: 50)
plot_linear_genome.py
Generate plot in SVG
Requirements
Usage
$ ./plot_linear_genome.py
usage: plot_linear_genome.py [-h] -i [INPUT ...] [-b [BLAST ...]] [-t TABLE] [-o OUTPUT] [-n NT] [-w WINDOW] [-s STEP]
[--separate_strands] [--show_gc] [--align_center] [--evalue EVALUE] [--bitscore BITSCORE]
[--identity IDENTITY]
Generate plot in SVG
optional arguments:
-h, --help show this help message and exit
-i [INPUT ...], --input [INPUT ...]
genbank (required)
-b [BLAST ...], --blast [BLAST ...]
input BLAST result file in tab-separated format (-outfmt 6 or 7) (optional)
-t TABLE, --table TABLE
color table (optional)
-o OUTPUT, --output OUTPUT
output prefix (default: diagram)
-n NT, --nt NT dinucleotide (default: GC).
-w WINDOW, --window WINDOW
window size (default: 1000)
-s STEP, --step STEP step size (default: 100)
--separate_strands separate forward and reverse strands (default: False). Features of undefined strands are shown
on the forward strand.
--show_gc plot GC content below genome (default: False).
--align_center Align genomes to the center (default: False).
--evalue EVALUE evalue threshold (default=1e-2)
--bitscore BITSCORE bitscore threshold (default=50)
--identity IDENTITY identity threshold (default=0)
Example:lymphocystis disease virus
- Lymphocystis disease virus 1, complete genome (NC_001824.1)
- Lymphocystis disease virus Sa isolate SA9, complete genome (NC_033423.1)
- Lymphocystis disease virus 2 LCDV-JP_Oita_2018 DNA, complete genome (LC534415.1)
$ tblastx -query NC_001824.fasta -subject NC_033423.fasta -outfmt 7 -out NC_001824_NC_033423.tblastx.out
$ tblastx -query NC_033423.fasta -subject LC534415.fasta -outfmt 7 -out NC_033423_LC534415.tblastx.out
./plot_linear_genome.py -i NC_001824.gb NC_033423.gb LC534415.gb -b NC_001824_NC_033423.tblastx.out NC_033423_LC534415.tblastx.out --separate_strands --align_center --evalue 1e-10 --bitscore 100 # output: out.svg
plot_circular_genome.py
Generate genome diagram in SVG
Requirements
Usage
$ ./plot_circular_genome.py -h
usage: plot_circular_genome.py [-h] -i INPUT [-t TABLE] [-n NT] [-w WINDOW] [-s STEP]
Generate genome diagram in SVG.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Genbank/DDBJ flatfile (required)
-t TABLE, --table TABLE
color table (optional)
-n NT, --nt NT dinucleotide (default: GC).
-w WINDOW, --window WINDOW
window size (default: 1000)
-s STEP, --step STEP step size (default: 100)
plot_skew.py
Generate dinucleotide skew plot(s) of FASTA format DNA sequences in SVG format. Plots are saved separately for each entry in a multifasta file
Requirements
Usage
$ ./plot_skew.py
usage: plot_skew.py [-h] -i INPUT [-n NT] [-w WINDOW] [-s STEP]
Generate dinucleotide skew plot(s) of FASTA format DNA sequences in SVG format. Plots are saved separately for each entry in a multifasta file
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Fasta (required)
-n NT, --nt NT dinucleotide (default: GC).
-w WINDOW, --window WINDOW
window size (default: 1000)
-s STEP, --step STEP step size (default: 100)
Example: Escherichia coli str. K-12 substr. MG1655, complete genome NC_000913.3
$ ./plot_skew.py NC_000913.3.fasta # (output: NC_000913.3.svg)
vcf_to_sv_density_plot.py
msa_to_txt.py
Requirements
Usage
$ ./msa_to_txt.py
usage: aln_to_txt_wrap.py [-h] --input FILE [--output FILE] [-r REF] [-s START] [-e END] [-g GAP] [-w WRAP] [--gap_inclusive]
Convert FASTA-format multiple sequence alignment into a txt file. Assumes Courier New
optional arguments:
-h, --help show this help message and exit
--input FILE, -i FILE, --in FILE
Input FASTA file
--output FILE, -o FILE, --out FILE, --output FILE
output txt file
-r REF, --ref REF reference entry name
-s START, --start START
start position
-e END, --end END end position
-g GAP, --gap GAP gap character (default: "-")
-w WRAP, --wrap WRAP line width (default: 100)
--gap_inclusive Gap inclusive (default: False).
$ less 16S.aligned.fasta
>NR_024570.1 Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence
---------AGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGG-AAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAG-CAC-AAAGAGGGGGACCTTAGGGC--------CTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCAACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCNGCGTGTATGAAGAAGGCCTTC-GGGTTGTAAAGTACTTTCAGCGGGGAGGAAG-GGAGTAAAGTTAATACCTTTGCTCATTGACGTTACC-CGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCA-GGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTT-GAGGCGTGGCTTCCGGANNTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAA-TGAATTGACGGGGGCC-GCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTT-CAGAGATGAGAATGTGCCT-----TCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGC-GGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAG-AATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACTTCGG-GAGGGCG----------------------------------------------------------------------------------
>NR_044682.2 Haemophilus influenzae strain 680 16S ribosomal RNA, partial sequence
A-ATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAACGGTAGCAGGAGAAAGCTTGCTTTCTTGCTGACGAGTGGCGGACGGGTGAGTAATGCTTGGG-AATCTGGCTTATGGAGGGGGATAACGACGGGAAACTGTCGCTAATACCGCGTATTATCGGAAG-ATG-AAAGTGCGGGACTGAGAGGC--------CGCATGCCATAGGATGAGCCCAAGTGGGATTAGGTAGTTGGTGGGGTAAATGCCTACCAAGCCTGCGATCTCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCNATGGGGGGAACCCTGACGCAGCCATGCCGCGTGAATGAAGAAGGCCTTC-GGGTTGTAAAGTTCTTTCGGTATTGAGGAAG-GTTGATGTGTTAATAGCACATCAAATTGACGTTAAA-TACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGNGTGCGAGCGTTAATCGGAATAACTGGGCGTAAAGGGCACGCAGGCGGTTATTTAAGTGAGGTGTGAAAGCCCCGGGCTTAACCTGGGNATTGCATTTCAGACTGGGTAACTAGAGTACTTTAGGGAGGGGTAGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAATACCGAAGGCGAAGGCAGCCCCTTGGGAATGTACTGACGCTCA-TGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGCTGTCGATTTGGGGGTTGGGGTTT---AACTCTGGCACCCGTAGCTAACGTGATAAATCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAA-TGAATTGACGGGGGCCNGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCTAAGAAGAGCT-CAGAGATGAGCTTGTGCCT-----TCGGGAACTTAGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGC-GACTTGGTCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTNGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGCGTATACAGAGGGAAGCGAAGCTGCGAGGTGGAGCGAATCTCATAAAGTACGTCTAAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGCGAATCAG-AATGTCGCGGTGAATACGTTCCCGGGCNTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGTACCAGAAGTAGATAGCTTAACCTTTT-GGAGGGCGTTTACCACGGTATGATTCATGACTGGGG-----------------------------------------------------
>NR_112116.2 Bacillus subtilis strain IAM 12118 16S ribosomal RNA, complete sequence
TTATCGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGG--ACAGATGGGAGCTTGCTCCCTGAT--GTTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCTAATACCGGATGGTTGTTTGAA-CCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTC-GGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACC-TAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGA-GGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAA-GGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCC-TAGAGATAGGACGTCCCCT-----TCGGGGGCAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTGGATCTTAGTTGCCAGC--ATTCAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCAGCGAAACCGCGAGGTTAAGCCAATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAG-CATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGAGGTAACCTTTTAGGAGCCAGCCGCCGAAGGTGGGACAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTT
>NR_044761.1 Helicobacter pylori strain ATCC 43504 16S ribosomal RNA, partial sequence
TTTATGGAGAGTTTGATCCTGGCTCAGAGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGAT-GAAGCTTCTAGCTTGCTAGAGTGCTGATTAGTGGCGCACGGGTGAGTAACGCATAGGTCATGTGCCTCTTAGTTTGGGATAGCCATTGGAAACGATGATTAATACCAGATACTCCCTACGG-GGG---------------AAAGAT--------TTATCGCTAAGAGATCAGCCTATGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCTATGACGGGTATCCGGCCTGAGAGGGTGAACGGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATATTGCTCAATGGGGGAAACCCTGAAGCAGCAACGCCGCGTGGAGGATGAAGGTTTTA-GGATTGTAAACTCCTTTTGTTAGAGAAGATA--------------------------ATGACGGTATC-TAACGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGCGGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGGATGCTAGTTGTTGGAGGGCTTAGTCTCTCCAGTAATGCAGCTAACGCATTAAGCATCCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAA-GGAATAGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGATACACGAAGAACCTTACCTAGGCTTGACATTGAGAGAATCCGC-TAGAAATAGTGGAGTGTCTAGCTTGCTAGACCTTGAAAACAGGTGCTGCACGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCTTTCTTAGTTGCTAACAGGTTATGCTGAGAACTCTAAGGATACTGCCTCCG-TAAGGAGGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTACGCCTAGGGCTACACACGTGCTACAATGGGGTGCACAAAGAGAAGCAATACTGTGAAGTGGAGCCAATCTT-CAAAACACCTCTCAGTTCGGATTGTAGGCTGCAACTCGCCTGCATGAAGCTGGAATCGCTAGTAATCGCAAATCAGCCATGTTGCGGTGAATACGTTCCCGGGTCTTGTACTCACCGCCCGTCACACCATGGGAGTTGTGTTTGCCTTAAGTCAGGATGCTAAATT-------GGCTACTGCCCACGGCACACACAGCGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGTGAACCTGCGGCTGGATCACCTCCTT-
>NR_025900.1 Thermus aquaticus strain YT-1 16S ribosomal RNA, partial sequence
---------------------GCTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGG-CCGTGGGGTATCTCAC---------GGTCAGCGGCGGACGGGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGACAACATGGGGAAACCCAGGCTAATCCCCCATGTGGACACATC-CTGTGGGGTGTGTTTAAAGGGTTT--------TGCCCGCTTCCGGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAAGAGCCCACCAAGGCGACGACGGGTAGCCGGTCTGAGAGGACGGCCGGCCACAGGGGCACTGAGACACGGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGACGGAGCGACGCCGCTTGGAGGAGGAAGCCCTTC-GGGGTGTAAACTCCTGAACCCGGGACGAAAC--------CCCCGATGAGG----GGACTGACGGTACC--GGGGTAATAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGCGCGAGCGTTACCCGGATTTACTGGGCGTAAAGGGCGTGTAGGCGGCTTGGGGCGTCCCATGTGAAAGGCCACGGCTCAACCGTGGAGGAGCGTGGGATACGCTCAGGCTAGACGGTGGGAGAGGGTGGTGGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGATGGCGAAGGCAGCCACCTGGTCCACTCGTGACGCTGA-GGCGCGAAAGCGTGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTCTCTGGG-------TTATCTGGGGGCCGAAGCTAACGCGTTAAGCGCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAA-GGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGCCTTGACATGCTAGGGAACCTGGGTGAAAGCCTGGGGTGCCCCGCG-AGGGGAGCCCTAGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCGTTAGTTGCCAGCGGGTGAAGCCGGGCACTCTAACGGGACTGCCTGCG-AAAGCAGGAGGAAGGCGGGGACGACGTCTGGTCATCATGGCCCTTACGGCCTGGGCGACACACGTGCTACAATGCCCACTACAGAGCGAGGCGACCTGGCAACAGGGAGCGAATCGCAAAAAGGTGGGCGTAGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGCCATGGGAGCGGGTTCTACCCGAAGTCGCCGGG--AGCCT----TAGGGCAGGCGCCGAGGGTAGGGCCCGTGACTGGGGCGAAGTCGTAACAAGGTAGCTGTACCG--------------------------
>NR_041751.1 Mycoplasma pneumoniae FH strain ATCC 15531 16S ribosomal RNA, partial sequence
-----------------------------TTAACGCTGGCGGCATGCCTAATACATGCAAGTCGATCGAA-AGTAGTAATACT---------------TTAGAGGCGAACGGGTGAGTAACACGTATCCAATCTACCTTATAATGGGGGATAACTAGTTGAAAGACTAGCTAATACCGCATAAGAACTTTGGTTCGCATGAATCAAAGTTGAAAGGACCTGCAAGGGTTCGTTATTTGATGAGGGTGCGCCATATCAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCAATGACGTGTAGCTATGCTGAGAAGTAGAATAGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATTTTTCACAATGAGCGAAAGCTTGATGGAGCAATGCCGCGTGAACGATGAAGGTCTTTAAGATTGTAAAGTTCTTTTATTTGGGAAGAAT-GACTTTAGCAGGTAATGGCTAGAGTTTGACTGTACCATTTTGAATAAGTGACGACTAACTATGTGCCAGCAGTCGCGGTAATACATAGGTCGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCAAGCGCAGGCGGATTGAAAAGTCTGGTGTTAAAGGCAGCTGCTTAACAGTTGTA-TGCATTGGAAACTATTAATCTAGAGTGTGGTAGGGAGTTTTGGAATTTCATGTGGAGCGGTGAAATGCGTAGATATATGAAGGAACACCAGTGGCGAAGGCGAAAACTTAGGCCATTACTGACGCTTA-GGCTTGAAAGTGTGGGGAGCAAATAGGATTAGATACCCTAGTAGTCCACACCGTAAACGATAGATACTAGCTGTCGGGGCG----ATCCCCTCGGTAGTGAAGTTAACACATTAAGTATCTCGCCTGGGTAGTACATTCGCAAGAATGAAACTCAAACGGAATTGACGGGGACCCGCACAAGTGGTGGAGCATGTTGCTTAATTCGACGGTACACGAAAAACCTTACCTAGACTTGACATCCTTGGCAAAGTTATGGAAACATAATGGAGGTT----------AACCGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTAC----------------ATTGTCTAGCGAGACTGCTAATG-CAAATTGGAGGAAGGAAGGGATGACGTCAAATCATCATGCCCCTTATGTCTAGGGCTGCAAACGTGCTACAATGGCCAATACAAACAGTCGCCAGCTTGTAAAAGTGAGCAAATCTG-TAAAGTTGGTCTCAGTTCGGATTGAGGGCTGCAATTCGTCCTCATGAAGTCGGAATCACTAGTAATCGCGAATCAGCTATGTCGCGGTGAATACGTTCTCGGGTCTTGTACACACCGCCCGTCAAACTATGAAAGCTGGTAATATTTAAAAACGTGTTGCTAACCATTA-GGAAGCGCATGTCAAGGATAGCACCGGTGATTGGAGTTAAGTCGTAACAAGGTACCCCTACGAGAACGTGGGGGTGGATCACCTCCTTT
$ msa_to_txt.py -i 16S.aligned.fasta -o 16S.aligned.txt
$ less 16S.aligned.txt
...... ..************ **.*** ************. ** * .. .
NR_024570.1 1 ---------AGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTTGCTGACG 91
NR_044682.2 1 A-ATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAACGGTAGCAGGAGAAAGCTTGCTTTCTTGCTGACG 99
NR_112116.2 1 TTATCGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGG--ACAGATGGGAGCTTGCTCCCTGAT--GTT 96
NR_044761.1 1 TTTATGGAGAGTTTGATCCTGGCTCAGAGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGAT-GAAGCTTCTAGCTTGCTAGAGTGCTGATT 99
NR_025900.1 1 ---------------------GCTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGG-CCGTGGGGTATCTCAC---------GGTC 69
NR_041751.1 1 -----------------------------TTAACGCTGGCGGCATGCCTAATACATGCAAGTCGATCGAA-AGTAGTAATACT---------------TT 55
** **** ************ . * .. * .* .*. . ****.*.* .****. ..****.** .* . .
NR_024570.1 92 AGTGGCGGACGGGTGAGTAATGTCTGGG-AAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAG-CAC-AAA 188
NR_044682.2 100 AGTGGCGGACGGGTGAGTAATGCTTGGG-AATCTGGCTTATGGAGGGGGATAACGACGGGAAACTGTCGCTAATACCGCGTATTATCGGAAG-ATG-AAA 196
NR_112116.2 97 AGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCTAATACCGGATGGTTGTTTGAA-CCGCATG 195
NR_044761.1 100 AGTGGCGCACGGGTGAGTAACGCATAGGTCATGTGCCTCTTAGTTTGGGATAGCCATTGGAAACGATGATTAATACCAGATACTCCCTACGG-GGG---- 194
NR_025900.1 70 AGCGGCGGACGGGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGACAACATGGGGAAACCCAGGCTAATCCCCCATGTGGACACATC-CTGTGGG 168
NR_041751.1 56 AGAGGCGAACGGGTGAGTAACACGTATCCAATCTACCTTATAATGGGGGATAACTAGTTGAAAGACTAGCTAATACCGCATAAGAACTTTGGTTCGCATG 155
. .. ***. ... . ** **.*.**.***. ***** ** ***.**.* . ** **.
NR_024570.1 189 GAGGGGGACCTTAGGGC--------CTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAG 280
NR_044682.2 197 GTGCGGGACTGAGAGGC--------CGCATGCCATAGGATGAGCCCAAGTGGGATTAGGTAGTTGGTGGGGTAAATGCCTACCAAGCCTGCGATCTCTAG 288
NR_112116.2 196 GTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAG 295
NR_044761.1 195 -----------AAAGAT--------TTATCGCTAAGAGATCAGCCTATGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCTATGACGGGTAT 275
NR_025900.1 169 GTGTGTTTAAAGGGTTT--------TGCCCGCTTCCGGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAAGAGCCCACCAAGGCGACGACGGGTAG 260
NR_041751.1 156 AATCAAAGTTGAAAGGACCTGCAAGGGTTCGTTATTTGATGAGGGTGCGCCATATCAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCAATGACGTGTAG 255
* . ******.* *. . *..*** .** ************ **. ********************* .***** ** * *.***.. * ** ..***
NR_024570.1 281 CTGGTCTGAGAGGATGACCAGCAACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGA 380
NR_044682.2 289 CTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCNATGGGGGGAACCCTGA 388
NR_112116.2 296 CCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGA 395
NR_044761.1 276 CCGGCCTGAGAGGGTGAACGGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATATTGCTCAATGGGGGAAACCCTGA 375
NR_025900.1 261 CCGGTCTGAGAGGACGGCCGGCCACAGGGGCACTGAGACACGGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGA 360
NR_041751.1 256 CTATGCTGAGAAGTAGAATAGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATTTTTCACAATGAGCGAAAGCTTGA 355
* *** * **.**.** . ** ****. ** .* ..***** . ** . . .. .*. ****. **
NR_024570.1 381 TGCAGCCATGCNGCGTGTATGAAGAAGGCCTTC-GGGTTGTAAAGTACTTTCAGCGGGGAGGAAG-GGAGTAAAGTTAATACCTTTGCTCATTGACGTTA 478
NR_044682.2 389 CGCAGCCATGCCGCGTGAATGAAGAAGGCCTTC-GGGTTGTAAAGTTCTTTCGGTATTGAGGAAG-GTTGATGTGTTAATAGCACATCAAATTGACGTTA 486
NR_112116.2 396 CGGAGCAACGCCGCGTGAGTGATGAAGGTTTTC-GGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTA 494
NR_044761.1 376 AGCAGCAACGCCGCGTGGAGGATGAAGGTTTTA-GGATTGTAAACTCCTTTTGTTAGAGAAGATA--------------------------ATGACGGTA 448
NR_025900.1 361 CGGAGCGACGCCGCTTGGAGGAGGAAGCCCTTC-GGGGTGTAAACTCCTGAACCCGGGACGAAAC--------CCCCGATGAGG----GGACTGACGGTA 447
NR_041751.1 356 TGGAGCAATGCCGCGTGAACGATGAAGGTCTTTAAGATTGTAAAGTTCTTTTATTTGGGAAGAAT-GACTTTAGCAGGTAATGGCTAGAGTTTGACTGTA 454
. ... .**. **.*.**** .**********.***********. **. ** ******. **** * * *********** .. .* ****
NR_024570.1 479 CC-CGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGC 577
NR_044682.2 487 AA-TACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGNGTGCGAGCGTTAATCGGAATAACTGGGCGTAAAGGGCACGCAGGC 585
NR_112116.2 495 CC-TAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGC 593
NR_044761.1 449 TC-TAACGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGC 547
NR_025900.1 448 CC--GGGGTAATAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGCGCGAGCGTTACCCGGATTTACTGGGCGTAAAGGGCGTGTAGGC 545
NR_041751.1 455 CCATTTTGAATAAGTGACGACTAACTATGTGCCAGCAGTCGCGGTAATACATAGGTCGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCAAGCGCAGGC 554
** .. .**. . ***.*** * .*** ***. * .*.* .* **. ** **.. . ** * .* *****.. *.*.
NR_024570.1 578 GGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGT 677
NR_044682.2 586 GGTTATTTAAGTGAGGTGTGAAAGCCCCGGGCTTAACCTGGGNATTGCATTTCAGACTGGGTAACTAGAGTACTTTAGGGAGGGGTAGAATTCCACGTGT 685
NR_112116.2 594 GGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGT 693
NR_044761.1 548 GGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGT 647
NR_025900.1 546 GGCTTGGGGCGTCCCATGTGAAAGGCCACGGCTCAACCGTGGAGGAGCGTGGGATACGCTCAGGCTAGACGGTGGGAGAGGGTGGTGGAATTCCCGGAGT 645
NR_041751.1 555 GGATTGAAAAGTCTGGTGTTAAAGGCAGCTGCTTAACAGTTGTA-TGCATTGGAAACTATTAATCTAGAGTGTGGTAGGGAGTTTTGGAATTTCATGTGG 653
**.***.****.**.*** *. ..***** .*. ..******** . *.* ..******* * * ..*****.*********.**..*
NR_024570.1 678 AGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCA-GGTGCGAAAGCGTGGGGAGCAAACAG 776
NR_044682.2 686 AGCGGTGAAATGCGTAGAGATGTGGAGGAATACCGAAGGCGAAGGCAGCCCCTTGGGAATGTACTGACGCTCA-TGTGCGAAAGCGTGGGGAGCAAACAG 784
NR_112116.2 694 AGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGA-GGAGCGAAAGCGTGGGGAGCGAACAG 792
NR_044761.1 648 AGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAG 747
NR_025900.1 646 AGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGATGGCGAAGGCAGCCACCTGGTCCACTCGTGACGCTGA-GGCGCGAAAGCGTGGGGAGCAAACCG 744
NR_041751.1 654 AGCGGTGAAATGCGTAGATATATGAAGGAACACCAGTGGCGAAGGCGAAAACTTAGGCCATTACTGACGCTTA-GGCTTGAAAGTGTGGGGAGCAAATAG 752
************..*********.*. ******.*. .* . . * * . * *. ****.. .***. .*****
NR_024570.1 777 GATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTT-GAGGCGTGGCTTCCGGANNTAACGCGTTAAGTCGACCGCCT 875
NR_044682.2 785 GATTAGATACCCTGGTAGTCCACGCTGTAAACGCTGTCGATTTGGGGGTTGGGGTTT---AACTCTGGCACCCGTAGCTAACGTGATAAATCGACCGCCT 881
NR_112116.2 793 GATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCT 892
NR_044761.1 748 GATTAGATACCCTGGTAGTCCACGCCCTAAACGATGGATGCTAGTTGTTGGAGGGCTTAGTCTCTCCAGTAATGCAGCTAACGCATTAAGCATCCCGCCT 847
NR_025900.1 745 GATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTCTCTGGG-------TTATCTGGGGGCCGAAGCTAACGCGTTAAGCGCGCCGCCT 837
NR_041751.1 753 GATTAGATACCCTAGTAGTCCACACCGTAAACGATAGATACTAGCTGTCGGGGCG----ATCCCCTCGGTAGTGAAGTTAACACATTAAGTATCTCGCCT 848
***.*****.. ****** * ********* ****.******* ** *******.************.*.********* * ** ****.*******
NR_024570.1 876 GGGGAGTACGGCCGCAAGGTTAAAACTCAAA-TGAATTGACGGGGGCC-GCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTA 973
NR_044682.2 882 GGGGAGTACGGCCGCAAGGTTAAAACTCAAA-TGAATTGACGGGGGCCNGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTA 980
NR_112116.2 893 GGGGAGTACGGTCGCAAGACTGAAACTCAAA-GGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTA 991
NR_044761.1 848 GGGGAGTACGGTCGCAAGATTAAAACTCAAA-GGAATAGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGATACACGAAGAACCTTA 946
NR_025900.1 838 GGGGAGTACGGCCGCAAGGCTGAAACTCAAA-GGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTA 936
NR_041751.1 849 GGGTAGTACATTCGCAAGAATGAAACTCAAACGGAATTGACGGGGACCCGCACAAGTGGTGGAGCATGTTGCTTAATTCGACGGTACACGAAAAACCTTA 948
** . ******** . * . ** * . . .. .. * ******* ****.** .*************** *
NR_024570.1 974 CCTGGTCTTGACATCCACGGAAGTTTT-CAGAGATGAGAATGTGCCT-----TCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTG 1067
NR_044682.2 981 CCTACTCTTGACATCCTAAGAAGAGCT-CAGAGATGAGCTTGTGCCT-----TCGGGAACTTAGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTG 1074
NR_112116.2 992 CCAGGTCTTGACATCCTCTGACAATCC-TAGAGATAGGACGTCCCCT-----TCGGGGGCAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCG 1085
NR_044761.1 947 CCTAGGCTTGACATTGAGAGAATCCGC-TAGAAATAGTGGAGTGTCTAGCTTGCTAGACCTTGAAAACAGGTGCTGCACGGCTGTCGTCAGCTCGTGTCG 1045
NR_025900.1 937 CCAGGCCTTGACATGCTAGGGAACCTGGGTGAAAGCCTGGGGTGCCCCGCG-AGGGGAGCCCTAGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGTCG 1035
NR_041751.1 949 CCTAGACTTGACATCCTTGGCAAAGTTATGGAAACATAATGGAGGTT----------AACCGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCG 1038
*** ********************************* ** ***.* . . . . . ..** *. * .*****. * ** ***
NR_024570.1 1068 TGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGC-GGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGA 1166
NR_044682.2 1075 TGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGC-GACTTGGTCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGA 1173
NR_112116.2 1086 TGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTGGATCTTAGTTGCCAGC--ATTCAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGA 1183
NR_044761.1 1046 TGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCTTTCTTAGTTGCTAACAGGTTATGCTGAGAACTCTAAGGATACTGCCTCCG-TAAGGAGGA 1144
NR_025900.1 1036 TGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCGTTAGTTGCCAGCGGGTGAAGCCGGGCACTCTAACGGGACTGCCTGCG-AAAGCAGGA 1134
NR_041751.1 1039 TGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTAC----------------ATTGTCTAGCGAGACTGCTAATG-CAAATTGGA 1121
****** **** ******.. ******** ****** * . ****..**.*************. *** *. * ** * * * **
NR_024570.1 1167 GGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAG 1266
NR_044682.2 1174 GGAAGGTNGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGCGTATACAGAGGGAAGCGAAGCTGCGAGGTGGAG 1273
NR_112116.2 1184 GGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCAGCGAAACCGCGAGGTTAAG 1283
NR_044761.1 1145 GGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTACGCCTAGGGCTACACACGTGCTACAATGGGGTGCACAAAGAGAAGCAATACTGTGAAGTGGAG 1244
NR_025900.1 1135 GGAAGGCGGGGACGACGTCTGGTCATCATGGCCCTTACGGCCTGGGCGACACACGTGCTACAATGCCCACTACAGAGCGAGGCGACCTGGCAACAGGGAG 1234
NR_041751.1 1122 GGAAGGAAGGGATGACGTCAAATCATCATGCCCCTTATGTCTAGGGCTGCAAACGTGCTACAATGGCCAATACAAACAGTCGCCAGCTTGTAAAAGTGAG 1221
* .*.* *** .* *** *****.* * ******..** * *.***** ******.**********.. ***** *** ..*******
NR_024570.1 1267 CGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAG-AATGCCACGGTGAA 1365
NR_044682.2 1274 CGAATCTCATAAAGTACGTCTAAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGCGAATCAG-AATGTCGCGGTGAA 1372
NR_112116.2 1284 CCAATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAG-CATGCCGCGGTGAA 1382
NR_044761.1 1245 CCAATCTT-CAAAACACCTCTCAGTTCGGATTGTAGGCTGCAACTCGCCTGCATGAAGCTGGAATCGCTAGTAATCGCAAATCAGCCATGTTGCGGTGAA 1343
NR_025900.1 1235 CGAATCGCAAAAAGGTGGGCGTAGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAA 1334
NR_041751.1 1222 CAAATCTG-TAAAGTTGGTCTCAGTTCGGATTGAGGGCTGCAATTCGTCCTCATGAAGTCGGAATCACTAGTAATCGCGAATCAGCTATGTCGCGGTGAA 1320
*******.**** .******.************..*.*.* .** ... . **.. . .*.. . ... . . .
NR_024570.1 1366 TACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACTTCGG-GAGGGCG-------------- 1450
NR_044682.2 1373 TACGTTCCCGGGCNTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGTACCAGAAGTAGATAGCTTAACCTTTT-GGAGGGCGTTTACCACGGTAT 1471
NR_112116.2 1383 TACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGAGGTAACCTTTTAGGAGCCAGCCGCCGAAGGTGG 1482
NR_044761.1 1344 TACGTTCCCGGGTCTTGTACTCACCGCCCGTCACACCATGGGAGTTGTGTTTGCCTTAAGTCAGGATGCTAAATT-------GGCTACTGCCCACGGCAC 1436
NR_025900.1 1335 TACGTTCCCGGGCCTTGTACACACCGCCCGTCACGCCATGGGAGCGGGTTCTACCCGAAGTCGCCGGG--AGCCT----TAGGGCAGGCGCCGAGGGTAG 1428
NR_041751.1 1321 TACGTTCTCGGGTCTTGTACACACCGCCCGTCAAACTATGAAAGCTGGTAATATTTAAAAACGTGTTGCTAACCATTA-GGAAGCGCATGTCAAGGATAG 1419
.. ... .
NR_024570.1 1451 -------------------------------------------------------------------- 1451
NR_044682.2 1472 GATTCATGACTGGGG----------------------------------------------------- 1486
NR_112116.2 1483 GACAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTT 1550
NR_044761.1 1437 ACACAGCGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGTGAACCTGCGGCTGGATCACCTCCTT- 1503
NR_025900.1 1429 GGCCCGTGACTGGGGCGAAGTCGTAACAAGGTAGCTGTACCG-------------------------- 1470
NR_041751.1 1420 CACCGGTGATTGGAGTTAAGTCGTAACAAGGTACCCCTACGAGAACGTGGGGGTGGATCACCTCCTTT 1487