Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold657
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34262
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:16056 original size:39 final size:40
Alignment explanation
Indices: 15979--16125 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
15969 TAGCTCCTCG
* * *
15979 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
16019 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
16058 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
16098 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
16126 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:16136 original size:80 final size:80
Alignment explanation
Indices: 16025--16205 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
16015 CTCATTCAAT
* * *
16025 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
16088 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
16104 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
16168 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
16185 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
16206 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:16165 original size:40 final size:40
Alignment explanation
Indices: 16022--16205 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
16012 TAACTCATTC
* *
16022 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
16062 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
16102 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
16142 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
16183 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16206 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:23954 original size:80 final size:80
Alignment explanation
Indices: 23858--24038 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
23848 CTCATTCAAT
* * *
23858 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
*
23920 TTAGT-A-TCTCGCACAAA
64 -TAGTCACT-TAGCACAAA
**
23937 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
24002 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
24018 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
24039 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:23998 original size:40 final size:40
Alignment explanation
Indices: 23855--24038 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
23845 TAACTCATTC
* *
23855 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
23895 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
23935 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
23975 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
24016 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
24039 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:25796 original size:15 final size:15
Alignment explanation
Indices: 25776--25804 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25766 AGTTGATTTG
25776 CTATTACACCTCTAT
1 CTATTACACCTCTAT
25791 CTATTACACCTCTA
1 CTATTACACCTCTA
25805 ATCCAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (15 bp):
CTATTACACCTCTAT
Found at i:25818 original size:15 final size:16
Alignment explanation
Indices: 25780--25829 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
25770 GATTTGCTAT
* *
25780 TACACCTCT-ATCTAT
1 TACACCTCTAATCCAA
25795 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
25811 TACA-CTCTAATCCAA
1 TACACCTCTAATCCAA
25826 TACA
1 TACA
25830 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 24 0.75
16 8 0.25
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.30
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28095 original size:39 final size:40
Alignment explanation
Indices: 28043--28172 Score: 174
Period size: 40 Copynumber: 3.3 Consensus size: 40
28033 GGACTAAGAT
*
28043 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTT-AGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
28082 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
28122 CCGAAGGCATTCGTACGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
28162 CCGAAGGCATT
1 CCGAAGGCATT
28173 GAATGAGTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 32 0.41
40 47 0.59
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Done.