Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2686
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: 41464
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:213 original size:57 final size:57
Alignment explanation
Indices: 125--240 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
115 ACAAGCTTGA
125 TGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCTATTAAGCTGCCCAT
1 TGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCTATTAAGCTGCCCAT
182 TGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCTATTAAGCTGCCCAT
1 TGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCTATTAAGCTGCCCAT
239 TG
1 TG
241 GTCCGATAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (57 bp):
TGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCTATTAAGCTGCCCAT
Found at i:3073 original size:23 final size:22
Alignment explanation
Indices: 3022--3073 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
3012 CCTCGTCTTT
*
3022 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
3044 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
3067 TTCTTTT
1 TTCTTTT
3074 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:9103 original size:22 final size:20
Alignment explanation
Indices: 9071--9119 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
9061 GCCGAATTTA
9071 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
9094 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
9114 TGAACA
1 TGAACA
9120 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:10175 original size:28 final size:26
Alignment explanation
Indices: 10144--10207 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
10134 AATTACTTGA
* **
10144 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTA-G-ATGCAAAATTACCATT
*
10172 ATACCCCTAGGTGCAAAATTACCATT
1 ATACCCCTAGATGCAAAATTACCATT
10198 ATACCCCTAG
1 ATACCCCTAG
10208 GGTTACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 9 0.28
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCATT
Found at i:10354 original size:27 final size:26
Alignment explanation
Indices: 10324--10399 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
10314 GGTGGCTATG
*
10324 CCACAATTGTCTGATCTGGTGGCTCCA
1 CCAC-ATTATCTGATCTGGTGGCTCCA
* * **
10351 CCACATATATCTGTTCTAGTGGCTCTG
1 CCACAT-TATCTGATCTGGTGGCTCCA
10378 CCACGATTATCTGTATCTGGTG
1 CCAC-ATTATCTG-ATCTGGTG
10400 ACTCTGTCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.05
27 29 0.74
28 8 0.21
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (26 bp):
CCACATTATCTGATCTGGTGGCTCCA
Found at i:14768 original size:14 final size:14
Alignment explanation
Indices: 14749--14793 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
14739 AACTCATCTT
*
14749 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
14763 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
14776 AATTTAATTTAATG
1 AGTTTAATTTAATG
14790 AGTT
1 AGTT
14794 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:15806 original size:29 final size:29
Alignment explanation
Indices: 15773--15829 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
15763 ATAACCAAAC
*
15773 CTACAAAAACTTTACATCCATAAACCCAA
1 CTACAAAAACTTCACATCCATAAACCCAA
* * *
15802 CTACATAAACTTCATATCCATAACCCCA
1 CTACAAAAACTTCACATCCATAAACCCA
15830 TCTTTGAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (29 bp):
CTACAAAAACTTCACATCCATAAACCCAA
Found at i:17163 original size:18 final size:18
Alignment explanation
Indices: 17140--17189 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
17130 GAAAGACAAA
*
17140 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
17158 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
17176 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
17190 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:17166 original size:24 final size:24
Alignment explanation
Indices: 17137--17214 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
17127 AATGAAAGAC
* *
17137 AAAGAAAAAGAGATTGAGAGTGAA
1 AAAGAAAAAGAGATTGAGAGAGAG
* * *
17161 AAAGAAAATGAGATTGAAAAAGAG
1 AAAGAAAAAGAGATTGAGAGAGAG
* *
17185 AATGAAAAAGAGTTTGAGAGAGAG
1 AAAGAAAAAGAGATTGAGAGAGAG
17209 AAAGAA
1 AAAGAA
17215 TGTGAACAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (24 bp):
AAAGAAAAAGAGATTGAGAGAGAG
Found at i:19686 original size:14 final size:14
Alignment explanation
Indices: 19667--19711 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
19657 AACTCATCTT
*
19667 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
19681 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
19694 AATTTAATTTAATG
1 AGTTTAATTTAATG
19708 AGTT
1 AGTT
19712 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:21985 original size:18 final size:18
Alignment explanation
Indices: 21962--21996 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21952 AAAAAAAATC
*
21962 AATCAAAAAAGTCAAAAA
1 AATCAAAAAAGACAAAAA
21980 AATCAAAAAAGACAAAA
1 AATCAAAAAAGACAAAA
21997 TTCAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.11, G:0.06, T:0.09
Consensus pattern (18 bp):
AATCAAAAAAGACAAAAA
Found at i:35016 original size:14 final size:14
Alignment explanation
Indices: 34997--35041 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
34987 ACTCATTCTT
*
34997 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
35011 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
35024 AATTTAATTTAATG
1 AGTTTAATTTAATG
35038 AGTT
1 AGTT
35042 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:41379 original size:14 final size:14
Alignment explanation
Indices: 41360--41387 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41350 AGGGTTCTTA
41360 TTCCAGATTTAATT
1 TTCCAGATTTAATT
41374 TTCCAGATTTAATT
1 TTCCAGATTTAATT
41388 CGTTCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TTCCAGATTTAATT
Done.