Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ240734
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 108648
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Found at i:10663 original size:24 final size:24
Alignment explanation
Indices: 10631--10677 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
10621 AAGCAGCGCG
* *
10631 TCGTGCTATAATCGGACACTTCCA
1 TCGTGCTATAAGCGGACAATTCCA
*
10655 TCGTGCTATGAGCGGACAATTCC
1 TCGTGCTATAAGCGGACAATTCC
10678 GAAGAAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (24 bp):
TCGTGCTATAAGCGGACAATTCCA
Left flanking sequence: Indices 10131 -- 10630
TAATTGAATCAGTCAAGATCAAATCTGTTTATCAAAGTGCTTCTCCGATTGCTCAAGACATCTCT
TTTCAACCGAGGAACAAAACAAGATCATTTCGTTCCATTTTTAGTAAAATAGTGAAGGATATTCC
ATTAGTAATGAAAAAGGGGGTGGAGGGGATCCGTATATGTTGTTCAGGTCGATTAAAAGGTGCAG
AAATAGCTAGAACTGAATGCGGAAAGTATGGAAAAACATCTCGTAATGTATTTAACCAGAAAATA
GATTATGCTCCTGCGGAAGTATCTACTCGTTACGGAATCTCAGGTGTCAAAGTGTGGATTTCATA
TAGTAAAAAAAAAAAGGGACGTGCTATATCCGAAACGTACGAAATATAGTAAATATCGTAAAGGC
AGATGTAGTAGGGGTTGCAAACCGGACGGTACACAACTTGGTTTTGGAAGATATGGCACTAAAAG
TTGTAGAGCTGGTCGTCTTTCATATCGAGCCATTGAAGCAGCGCG
Right flanking sequence: Indices 10678 -- 11177
GAAGAAATGGTAAGATATGGGTAAGAGTTTTCGCAGATATCCCTATTACCGGGAAACCTACAGAA
GTAAGAATGGGAAGAGGAAAAGGAAATCCTACGGGTTGGATTGCTCGTGTGTCCACGGGGCAAAT
CCTATTTGAAATGGATGGTGTGAGTTTGTCAAATGCTCGACAAGCCGCTAGATTAGCGGCGCATA
AACTATGTTCGTCAACCAAGTTTGTTCAGTGGTCGTAAGCTAATTAGTTAGTGGGGAAATTCAAA
AGAATTAGGCGAAGTGTTTGTTCCTGAACGAGGGAAGTGGAAAGACACTAAGGGAGAGGGATATA
CTCCTTTTTAGAATCGCCGAAATTGTACGACTGTTCCAGGCGTACGACCCGGATACGTTAAGGTT
TCTTTCTTCCGGACCGGTTTATAAAGTTCTAGTAGTAAGAATAAATAAGAAAGAGAAGAGCTAAG
ATTCAGGAAAGGAAGTTGTTTCAGTCAAACTAAAAGTAAGTGGGC
Found at i:12366 original size:30 final size:30
Alignment explanation
Indices: 12300--12369 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
12290 GGCACGTTCA
* *
12300 ATAT-ATCGTTGTGATCATTGTGGTAGAAG
1 ATATAATCATTGTGATCATTGTGGTACAAG
*
12329 GTATAATCATTGTGATCATTGTGGTACAACG
1 ATATAATCATTGTGATCATTGTGGTACAA-G
12360 AT-TAATCATT
1 ATATAATCATT
12370 TTCCTCGTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.09
30 30 0.86
31 2 0.06
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (30 bp):
ATATAATCATTGTGATCATTGTGGTACAAG
Left flanking sequence: Indices 11800 -- 12299
TACTTCTACTTCTTGGAAGAAATTTTCTTGATATTTTGCATCTCGAATTGTATTCCCGCGAAAGG
CATGTTAAAGTTGAAAAAGGAATCCTTCGAATCTTTGTTGCGAAGTCGATAAATTATACGCCCTC
TGGTTGAATCATAACGACTTACTTAAATTTTTACTTTATATAGTTCGCTTGAATTTCGATTTTCA
TATTCGATCGAATTTCGACTTTATATAGTTAGAATAACCCAGTTGAAGCGTAATGATCATACGTC
ATTATATACTCTTTCATATAGATAGCGCAACCCTATTTTGATTTTTACCCTTTTTTTTTGAAATG
GAAATACCTACGTAACCTATGTAATGCATTGTATGTCCCATAATACGGACCATTCTTCTACTCTT
TGCCGAAAGGCGATGGTAATACAATTATATTAAGTAGTAGAGGAAATCGAATTTTTTTCTTAAAA
AAAATGATATATTTAGTATATTAGGAGGAAACTATGGCACGTTCA
Right flanking sequence: Indices 12370 -- 12869
TTCCTCGTGGTACAAGCCATAATCATTTTCCTCGTGGTAAAGGTCGTAATGCCAGAGGAAGAAAA
ATCGATTGGATTGAAGGGCGAACGACGGGAATTGAACCCGCGCATAGTGGATTCACAATCCACCG
CCTTAATCCACTTGGCCACATCCGCCCCCAGCGGTGGATGTTCTTTTTTTATTGTTATTTATTTT
GTTATTTTCTTTTTATAATTCTAGTCTTTCACTTCTTTTTAAATTTACTTAAACGAATTTAAAAA
TTTTACCATCCATATAAAAAGGAAAAACCCGAAATATTCAAGTCGAAAAATGAATCAAAATAAAT
ATAAGGAGCAATCCCCCCATCTTGTATATAACAAGAAAGCGGTTATTGCTCCTTTCATTTTATTT
TCAAAAACTCCTGCTATACACTAAGACCAAGTCCTTATCCATTTGTAGATGGAGCTTCGATAGCA
GCTAGGTCTAGAGGGAAGTTGTGAGCGTTACGTTCATGCATAACT
Found at i:12419 original size:27 final size:27
Alignment explanation
Indices: 12349--12408 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
12339 TGTGATCATT
*
12349 GTGGTACAA-CGATTAATCATTTTCCTC
1 GTGGTACAAGCCA-TAATCATTTTCCTC
12376 GTGGTACAAGCCATAATCATTTTCCTC
1 GTGGTACAAGCCATAATCATTTTCCTC
12403 GTGGTA
1 GTGGTA
12409 AAGGTCGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GTGGTACAAGCCATAATCATTTTCCTC
Left flanking sequence: Indices 11849 -- 12348
GTATTCCCGCGAAAGGCATGTTAAAGTTGAAAAAGGAATCCTTCGAATCTTTGTTGCGAAGTCGA
TAAATTATACGCCCTCTGGTTGAATCATAACGACTTACTTAAATTTTTACTTTATATAGTTCGCT
TGAATTTCGATTTTCATATTCGATCGAATTTCGACTTTATATAGTTAGAATAACCCAGTTGAAGC
GTAATGATCATACGTCATTATATACTCTTTCATATAGATAGCGCAACCCTATTTTGATTTTTACC
CTTTTTTTTTGAAATGGAAATACCTACGTAACCTATGTAATGCATTGTATGTCCCATAATACGGA
CCATTCTTCTACTCTTTGCCGAAAGGCGATGGTAATACAATTATATTAAGTAGTAGAGGAAATCG
AATTTTTTTCTTAAAAAAAATGATATATTTAGTATATTAGGAGGAAACTATGGCACGTTCAATAT
ATCGTTGTGATCATTGTGGTAGAAGGTATAATCATTGTGATCATT
Right flanking sequence: Indices 12409 -- 12908
AAGGTCGTAATGCCAGAGGAAGAAAAATCGATTGGATTGAAGGGCGAACGACGGGAATTGAACCC
GCGCATAGTGGATTCACAATCCACCGCCTTAATCCACTTGGCCACATCCGCCCCCAGCGGTGGAT
GTTCTTTTTTTATTGTTATTTATTTTGTTATTTTCTTTTTATAATTCTAGTCTTTCACTTCTTTT
TAAATTTACTTAAACGAATTTAAAAATTTTACCATCCATATAAAAAGGAAAAACCCGAAATATTC
AAGTCGAAAAATGAATCAAAATAAATATAAGGAGCAATCCCCCCATCTTGTATATAACAAGAAAG
CGGTTATTGCTCCTTTCATTTTATTTTCAAAAACTCCTGCTATACACTAAGACCAAGTCCTTATC
CATTTGTAGATGGAGCTTCGATAGCAGCTAGGTCTAGAGGGAAGTTGTGAGCGTTACGTTCATGC
ATAACTTCCATACCAAGGTTAGCACGGTTAATGATATCAGCCCAA
Found at i:17759 original size:13 final size:13
Alignment explanation
Indices: 17741--17767 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17731 AATACAAGAT
17741 TTTTAAATTTTTA
1 TTTTAAATTTTTA
17754 TTTTAAATTTTTA
1 TTTTAAATTTTTA
17767 T
1 T
17768 ATTTGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTTA
Left flanking sequence: Indices 17241 -- 17740
GAGAAAAAAAATCTCAATGATTTAAAATTCCAATATGTAAGGTCTATGATAAAGGGCAGTGTAAT
AAAGCATGACTACTGATTTATATCCATACCCTAATTAATTTAATTTAATTAAATAAATCAATTAA
TAGAAGAAAAAAAGCAAGAGCTTCGAGCCAATAAAGACTGAGAAGAGTGGCTCACGACCTCATTT
TATTAGTATTATGAGCTCCATTGTGAAATTCGGACCTAACCATTAAGTAAGAAGCGATGGGAACG
ACGGAACCTGTGAATGCAAAAGATCATATTGAAAAAATCTGAATAATTCACTGGTCGGGATGGCG
GAATGAGCCGGAGATCAATTCATCTATTCTGAGATCTGGGACGTGCTAGTCCTACAACTGAAATA
GAAATTGAAAGAGTCAATATTCGCCCGCGAAAACTTTCTTTTTTTATTGCAAAAGCAAAAAGCAA
TAGGATAAAAGACAGAATTAAGGATTAGTTAGAATAATACAAGAT
Right flanking sequence: Indices 17768 -- 18267
ATTTGTTTGAATTTGAATTAAGTTAATTAAGATAGAGAAAATTAAATTAAGTTAAGATATATATG
TATTTACTGAGGAATACGAAGAATCGTTGGACTCTTTGAGATTTCATCAAATCTAAAAAATCCCC
CACACATATCTGCCACCCTTTAGAGGGAATAAAGACACTCCCCCGGAAAGAAGATCCCAAAAGCC
GGTCTCTGTGTTCCAATATTAGCGGTAGAGTTGTTACTCCCGCAGAGGATTCTTGCAGAGGGGAT
AACATCCCATGGGTAAGGCAACGGGGAGTGATACTGTGATCACGGGCATAAATCAATAATATGTA
GGCTGCTACAGAACAGAAAATCCACTATACATTCATAGAACCTTTTAGAGGGAAATATGAATCCA
TTGAGTGCTAAGTGTCATAAGAGAACTGAGCCCCAGGCCCTTTATTCCAGAGTAAGGAATAGAGT
ACAGGGCCGACTAAGAGTTTTGGGCCGTCTATAATATTAGCTTTC
Done.