1
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>003197.2:c1179912-1178219_reverse_complement
AGGCTTTTAAAAGCCTCCTGGGTTTTTAGTGAAGCTGAGTGATAGAAGCTCTGTATTTGCATAGCGTTTT
GTCGGGCGCTTTAGCCGGCGCTTTGCCCTGGCCTGAGAGAATCTGCATTCCGTTGTATAAGGTTTTTTGT
CCTTCTGATGCTGTAGATAATTCCCCCATGTCGCGCCGGGTTCTCGCAGGACAATAATTTCCGGGCGAGC
AGAACGGTTGCCGCGACGGTAAGAAGATCGCGCTGTAAGTTATAGAGGTTATGCAGCGAGTGGTTAGACG
CCGGTCCGCTTTAACTTTGGCTAACTCCATTTGGTTTGCCATTGACGTTAGAACCGGGTCTTGTTTACCC
GTGCTGCAATAAGTTCGATAAGATTTTTCTTCAATGCTTTTGCCGCGGCTTCTTCTTGTTTTGTTGCTGG
GCATCTCTAAACGCTACTGCCGCAAAGCGATGAGCTTCTTTTGCAGGTAAGCCATCCTGCTGCTGAGTGC
GTGATGCCCGTTATGCGTGAGTGTATTTTTTATGGTTTGCCAGGGCTGGTTATTAAGCTGCTTGACCTGA
CATAAGCACTGGGAAAGATATCTTTTGCGCCGATTTTCATCTCTGCTGCAGGGAGCTGCGTGTTGGTATA
ACCGTGGACATCCACAAATTATTGGCGTGATGAATATTCTTGGTATCCCAACTGCATACGCCCTTTCCCT
ATAGGGGGAAAGCACGCCATGACGTATCCCGCAAAAAAGCGTTTTATCTTTACCGTCCTCATGCACACTC
GTGCCGCAGTTAATACTTCTTTGGCTTTGTTTTCAGCGCCGACGTGACGCAGAAGCGGATCTTTTTCATG
ACGGATACCAGTTTCAGGCTTACCGCCTCGCCCGCTAAGGCTTTGTTAAGCAACTCAGGTTTACTAAAAA
CCATGCGCGCATTTGGTCCTCGACCATCGTTCCCTCTTTGCCGAAAATATTCGACGCGGTGAGTAACCCG
CCGTCTGTAGATCGCCATCTTTATTGCGGATTTTTAAATGAATCATTTTTCCCGGCTGGGTCAACGATTG
CCAAAGCCGAGCTTGAGCGCCAGCTCATTAACACCCACATTAAATGCGGCGACGTCCGGTTTTATTTTTA
TTCAGGGCGTAAATCATTGCCTAATAACTGATGTAGCGCCTCGGCATTATAGCTATCCGATGCCTTAAGG
ATGTATTGACGACCTCATAATTATCCGGGTATTGCGCCAGCCATTCGCCAACCCAGCCACCTGGTCTGGC
AGTTTATAGGGTTCGCCGCCATCTTTATGATGTTGGTTATTTTTCCATATATCCTTAATCTGGCGCGCTA
TTTGCCGCTTTTACAATTCCAGGCGGGTACCGCGTCAATTTCATGGGCTAACATGGCAAGGCGTTGTGCG
TTAACATATGGGTCTGATGTAAGGAAATGATCTCTCGCTTGATTTCTGAATCCATCATCCCTGTACGATC
TTACCGCTATTCAGTAATACTTTTTGGAAAATTTTCTGTCCACCGCTATCCGGAAGACTACCAGGCGCAC
CACCTCTGGCGATAAATTTTTCATTACTTTGTTTCCCGCCCCGCCCGTATTTTGTTTCTGAATCTCCAGG
ATGAAGAAATGCCTTTTACTGACTGCCAAATATTTTCATCCCCAACTCGTTTTTGATAGGAAAGATTGAG
TCAAGATGTGATTA
>003197.2:c3026750-3024686_reverse_complement
TTTGATCTCGGTCTGCATACCTGGCATTATGACGGGGGGCTGAGTCCTTACACTTGTAACCATTATTAAT
CCCCTGACAGCGTCGCTGTGGCACTTTCTCTGACTGCGGAAAGATTCGCCGCAAGATTCGTGGCCTGCGT
TTAAACAATGCATCCAGACTCGCCTGTTTGATCAGCGCGGGAAAATCTTCCAGTTGCGGGCCTTTAATTT
CGCTTTCTTACCGGCGACATTATTTGAATTGGTAAAAACTTCTTTTAACGCCTCAGCGTCTTTCCCGCAT
GCGTCTTCGCCTCAGGAGAATCACTGGTGGCGTTGAGCGCTGAACGAAAGAGCCCGGCAAACTCCATTAT
AAAGCTGACTTTTCTTTCAGGCCATCTTTTATGATTTGCGCGGTATACTCTGCCCCCACCTTCATCAGTA
ATCTAACAGCTGCTTTTCCAGGTTTTCCAGCTTCGCTTCCGCTTTCTTTGTTTCTGGCAGCCATGGCCCA
GCATCACCTCCTGCATAACAAGATTCGTCGATAATTTACTTAATTCACCGCCAGTGTTATTTTTGATAAT
GTAAGATTGCTGCGGGTTAACGGATCTAACGTACAGCCAAAGTTATGTTCAATGCAGCTGGCAATATAGG
TTGCGTTAATTTTTGGTGGCACATATCAAGCGCCTCAACAGCCTTCGCCGCCGCTTTGTCAACAAGGTGC
GTAGCAGCAGGGGTATCAACGTTTGCATTTCAAGGTGCCGGGCTTCCCGTCCTACGCTGGTACCCTGCTC
GGTCCAGCCGCAGGCTCCGGAATTTTAGGGTCAGGCAGTTTATCTGCAGGAATTTGTGCAAAAACATTAC
GTTACTGCTATCAATATTAATATTGATATTAATACCCGTAGGTTCTGCTTTTTTCCCACCATCAGGTACT
CGATATGGCGCTGGCTATTATCGACATGGCTTCGGCTATTGTTAATATGCTTACTGTTATCCACGCTATG
CGTTGGCTGTTATCAATAAATGTTCGGCTATTATCAATCGTCTTCCGGCTATTATCATGGTTGCTATTAT
AGTCGAATCCACACGCGAATGACTATGACTTACGTTGCTGCTGTTAGTCGAATGGTGTGACTCGCCATTG
CAATTTTACCCGCGATGCCATGGTCAATTGCCCCTGTGCTGGCGCTGTGTGCCGTCTCCGTTTGATGCGT
ACCACCTTTCCATCTTTACTTTCGGATGAAGCGTTGGTCACAGCCTCTGCCGTCGCATGAGCCGTGACGT
GCTCTTGCTGGTTACGCCATCGACTTCATCAAAAGAGGTTGTTTCACCCGTAGTGCCCTTTTCTGACGTG
CTGCCGTCTGGCTTTGCTGTTTATTATCATCAACGCCGTGCACCGTGGCCTGTACCGGCTTGCCGATAAT
TGTAAGGTATCGGTTTTAACATTCTCGACGCCAGCCAGTTGACTGGCAAGCGGCTTCACATTCACAATCT
CTTATCTGTCTGACTATTATCATTATCGGTCGTACCGGCTTTATTACCTGTAATTACCGTCGTGTCTGAT
TATTCGTAACGCTCGGTACTGTTGAGAGGAAACTATTTTGCTTAAACTTCAAACCAGAAAATGGGCCAGT
GTATCTGGCTCCAGGGCTTTACGTATCACACCCAAAAACGTCTCACGGGCGTCGAAATGCATTGAATGCA
TATCGTGTCATTGGGTAATATTTCCGCACGCAAGCCGTCAAACGCTCTGCGTACAGGGAACGGTGTGGAG
TCTCCATTTTCGCTTTCAATTCTGGGTGCTTGTCAATATCGCTACATTGCGCTTTCAACGCTGCACTCTT
CTGGCAAACTGCAGTGCAATCTCAGCCAGTTTTTCTTTTTGTGGATGATGAGTAATGACCTCTTTGAGAG
GATAAGGCCGTCCAGCACATTACTTAACACATAGTCAGTTTCCCCTTTTAGCCTGGTCAGCCCCGCCTCT
TAACCCGATCCACGCCAGGTTTATTCAGGTATGACTCGTAAGCCGGGCCAGCTCGCCAGCTACCGTCTCC
TTAACGCTGCATGTGCAAGCCATCAACGGTAGTAA
>003197.2:c3010816-3009905_reverse_complement
TATTACGAGTCGTAGGACTTAGCATACTTTTCCCTCCACATGATAGCTCCTGCACCGAAAATATCATCTT
ACAATACAGGTCAATGCTTCGGTGTTTAGCTCCCCGCTGACGTCAGGCTGAGGCGATAAACTCGCCCCCA
TTCGAGATCGGTTTCCTCGTAACTGATATGAATCCAGCTGCCATCTATAATTTCACTTTCCAGACGCTCA
CTGACATAACAAATTTAAGATTTAACTCTGGATACTTCTTATTGGCCTGTGCAACAAGAAAAGGCATCAT
TTTACGAGAAATCGGGCAGATTCAACGCCTTCCATTCTGGTCTCCTTTATAGAGGAAACAAGCTCATGGA
AATCACCGATGTCTTTCCGTCCATAACTCTAAAATCGACGACTGAAATATGGATACCTGAACTTCCCATA
CAAGAGCTGCTTTGGTCCTCAACGCCAGTAAAGCAGGTCCAAAAGCGCTACACGCTGCTGGTTCGAACAA
CATTCAGAAGAGCTTCGTTGAATGTCCAGCTCGACCATAGCAAAATAACAATCAGGCAGTTGTTCACGTT
TTCATGAATTTTTACTAAGTTCATAAATTCAAGCTGAAGTTTTTTGGCGAGCGCCAGGCTAAAAATACCG
GCAGATAGCGGTCTGCTTTATCGGACGGGAGAAAAGGTTCTTCACCACACAGACGTTCACAAATATTATC
GCCGCCGGATTGGCCTCCACATATTCATTTAATCGTTGTGCGCCTTGAGTATGTTTGTAAAAACTCACCG
TAGCATAACGGCATTGTTATCGAATCGCTCATAAAGCGTTTCATTCTTTTTGTTTACTATACTGCTTCCC
ACGGTTTAAGTAAAGACTTATATTCAGCTATCCTTTTTTTATGAGCGGATATAGAGAGTTTTTTATCGTT
TT
>003277.2:c27903-27178_reverse_complement
CCCCATCATAAGCAGCTACAATATTCAAAGGAGGGATGTTTAGATTTAGATTAGGCCTATTTATGGGCAT
ATCTTCCGCATTTGGTTGTGCAAGGAGTTGAAATTATTTTTCAGGTGCTTATTTGTAGATGGTATTTCCG
AAAGAAACCACTCTGGCGCATCCCTGAATAGTCAGGCACATCCAGCGCCTCTTTAAAGTGGGATACCGGC
GTGATTCTCGACGAGCATGGATGAAAACATCGTAACCATGGTTATTCAGCTGAAAACCTTGGCTCATAGC
GCTTGTGGCACCATATCCCTGAGCACACTGATGTGGAACTTGTCACCGGCAAATTTGCCCTGAGACTGAG
CATATCGGTCACTTTCCACTTATCTACCGGACTGTCCTCTGAAAACAGCAATCCGGACAGCGCTTGAAAT
CCTGGTCTGGTTTTATATACAACGTGAACTGAGCGCCCAGGCTAACACGGGCTTGTTGAACGACCTTCTC
AGTCTGGATTCCAGACACTCTATAAATTGCCGTGTCTTGTGGAGAAACGACGCACTGTACTGCGAATTTT
GAGATATTTCCAATTTTCAGGATGAACGTCTGACTCAGGACACTGTCCTGAAATAACCCCATTTTCGGAT
GTTCCTCACGTAAAGCCTGTCTCTGCATTTCGCCACCATCACGCCCACTTCGTAGTTCATTACGATAACT
TTACTCTGTCATCAAACGATAAAACG
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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Jun 10 at 16:20
  • $\begingroup$ Welcome to the site @tonu. Please make your question clear within the question. Finally, what coding are you happy with, bash(shell), R, Python, Perl, awk etc ...? $\endgroup$
    – M__ ♦
    Jun 10 at 16:24
  • $\begingroup$ @Tonu this has been correctly answered could you please consider upvoting/accepting? $\endgroup$
    – M__ ♦
    Sep 15 at 16:04

1 Answer 1

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Since you tag python, I suggest a simple Biopython solution:

from Bio import SeqIO

print(sum(s.seq.count("TAA") for s in SeqIO.parse("file.fa", "fasta")))
# 97 on your input file

If you wanted an overlapping sequence count, Biopython has a method for this too:

print(sum(s.seq.count_overlap("TAA") for s in SeqIO.parse("file.fa", "fasta")))

Here they are the same, but for a string like "TAT" they could be different:

>>> from Bio.Seq import Seq
>>> Seq("TATAT").count("TAT")
1
>>> Seq("TATAT").count_overlap("TAT")
2
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