Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3625
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: 43594
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:10905 original size:42 final size:41
Alignment explanation
Indices: 10740--10904 Score: 161
Period size: 42 Copynumber: 3.9 Consensus size: 41
10730 AATCATACCA
* * * *
10740 ATGCCTTATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACA-CGAAACTCATATCG
* * * * **
10782 ATACCAATAGCCTAGCTATGGTCTTACACGATTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAACTCATATCG
* * *
10824 ATGCCATGTCCCAGACATGATCTTACACGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACACGAAA-CTCAT-ATCG
10866 ATGCCATATCCCAGATATGGTCTTACACGTAAACTCATA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAACTCATA
10905 ACCCTAATGT
Statistics
Matches: 99, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
41 20 0.20
42 56 0.57
43 23 0.23
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAACTCATATCG
Found at i:12419 original size:32 final size:32
Alignment explanation
Indices: 12378--12440 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12368 AATCCTTTCC
12378 AGCTAAAATGGCAAAGCCAATCGATATGCTAT
1 AGCTAAAATGGCAAAGCCAATCGATATGCTAT
*
12410 AGCTCAAATGGCAAAGCCAATCGATATGCTA
1 AGCTAAAATGGCAAAGCCAATCGATATGCTA
12441 CTAACCCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
AGCTAAAATGGCAAAGCCAATCGATATGCTAT
Found at i:27433 original size:31 final size:31
Alignment explanation
Indices: 27363--27434 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
27353 TTGGAGGATT
*
27363 ACACGCCCATGTGGGTGGGCCGTGTAGTTCC
1 ACACGCCCGTGTGGGTGGGCCGTGTAGTTCC
*
27394 ACACGCCCGTGTGGGTGGGCCGTGTGGTTCC
1 ACACGCCCGTGTGGGTGGGCCGTGTAGTTCC
*
27425 ACATGCCCGT
1 ACACGCCCGT
27435 ATCCTCAGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (31 bp):
ACACGCCCGTGTGGGTGGGCCGTGTAGTTCC
Found at i:28582 original size:42 final size:42
Alignment explanation
Indices: 28536--28688 Score: 166
Period size: 42 Copynumber: 3.6 Consensus size: 42
28526 AATCATACCA
* *
28536 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACATGAGATCTCATATCG
* * * * *
28578 ATGCCAATAACCCAGCA-ATGGTCTTACACGA-TTTTCATATAG
1 ATGCC-ATATCCCAG-ATATGGTCTTACATGAGATCTCATATCG
* * * *
28620 ATGCCATGTCCCAGACATGGTCTTACATGAAATCTCATAACG
1 ATGCCATATCCCAGATATGGTCTTACATGAGATCTCATATCG
*
28662 ATGTCATATCCCAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
28689 CTTAAACTCA
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 20 0.22
42 49 0.54
43 19 0.21
44 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGAGATCTCATATCG
Found at i:28700 original size:84 final size:84
Alignment explanation
Indices: 28536--28700 Score: 190
Period size: 84 Copynumber: 2.0 Consensus size: 84
28526 AATCATACCA
* * ** *
28536 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCGATGCCAATAACCCAGCAATGGTC
1 ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACGATGCCAATAACCCAGCAATGGTC
***
28601 TTACACGATTTTCATATAG
66 TTACACGAAACTCATATAG
* * *
28620 ATGCCATGTCCCAGACATGGTCTTACATGAAATCTCATAACGATGTC-ATATCCCAG-ATATGGT
1 ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACGATGCCAATAACCCAGCA-ATGGT
*
28683 CTTACACTTAAACTCATA
65 CTTACAC-GAAACTCATA
28701 ACCCTAATGT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 1 0.01
83 20 0.30
84 46 0.69
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (84 bp):
ATGCCATATCCCAGACATGGTCTTACATGAAATCTCATAACGATGCCAATAACCCAGCAATGGTC
TTACACGAAACTCATATAG
Found at i:32246 original size:2 final size:2
Alignment explanation
Indices: 32239--32274 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32229 TTTATGGTTT
32239 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
32275 AAGAAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37930 original size:39 final size:40
Alignment explanation
Indices: 37845--37930 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 40
37835 AAAATAACTC
**
37845 TTAATTTAAAGAAAATAAATGTAATTATCTAAAAAAGATT
1 TTAATTTAAAGAAAATAAACATAATTATCTAAAAAAGATT
*
37885 TCAATTTAAA-AAAATAAACATAATTATCTAAAAAA-AGTT
1 TTAATTTAAAGAAAATAAACATAATTATCTAAAAAAGA-TT
37924 TTAATTT
1 TTAATTT
37931 TTTAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 1 0.02
39 31 0.76
40 9 0.22
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (40 bp):
TTAATTTAAAGAAAATAAACATAATTATCTAAAAAAGATT
Found at i:38066 original size:14 final size:15
Alignment explanation
Indices: 38049--38085 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
38039 ATAATGAATT
38049 ATATTTCACTTA-AA
1 ATATTTCACTTATAA
*
38063 ATATTTTACTTATAA
1 ATATTTCACTTATAA
38078 A-ATTTCAC
1 ATATTTCAC
38086 ATCAACTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATTTCACTTATAA
Found at i:41178 original size:40 final size:40
Alignment explanation
Indices: 41141--41322 Score: 203
Period size: 40 Copynumber: 4.5 Consensus size: 40
41131 GCTACTCGTT
*
41141 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
41181 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
41221 CAAATGCCTTCGGG-CTTAGCCCGGAATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTTAGTAACTCGCA
* * * * *
41261 C-AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41301 CAAA-GCCTTCGGGAACTTAGCC
1 CAAATGCCTTCGGG-ACTTAGCC
41323 GGACATCATT
Statistics
Matches: 121, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.02
39 24 0.20
40 82 0.68
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41309 original size:79 final size:80
Alignment explanation
Indices: 41141--41322 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 80
41131 GCTACTCGTT
*
41141 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
* *
41206 ATTTAGTAACTCGCA
66 ATATAGTAACTAGCA
* **
41221 CAAATGCCTTCGGG-CTTAGCCCGGAATT-TAGTATCTCGCACAA-TGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGG--TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACC
* *
41282 CGGATATGGTCACTTAGCA
63 CGGATATAGTAAC-TAGCA
41301 CAAA-GCCTTCGGGAACTTAGCC
1 CAAATGCCTTCGGG-ACTTAGCC
41323 GGACATCATT
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
78 3 0.03
79 40 0.45
80 36 0.41
81 9 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCA
Done.