Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold9642.1
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: 4308
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Found at i:321 original size:21 final size:21
Alignment explanation
Indices: 293--343 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
283 AGGGTTTCTT
**
293 GGTTTTTTTTTT-TTGGGTTA
1 GGTTTTTTTTTTGGGGGGTTA
313 GGTTTTTTTTTTGGGGGGTTA
1 GGTTTTTTTTTTGGGGGGTTA
334 GGTTTTTTTT
1 GGTTTTTTTT
344 GGGAGGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.04, C:0.00, G:0.29, T:0.67
Consensus pattern (21 bp):
GGTTTTTTTTTTGGGGGGTTA
Found at i:351 original size:22 final size:21
Alignment explanation
Indices: 307--354 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
297 TTTTTTTTTT
**
307 GGGTTAGGTTTTTTTTTTGGG
1 GGGTTAGGTTTTTTTTGGGGG
328 GGGTTAGGTTTTTTTTGGGAGG
1 GGGTTAGGTTTTTTTTGGG-GG
350 GGGTT
1 GGGTT
355 TAATGGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (21 bp):
GGGTTAGGTTTTTTTTGGGGG
Found at i:1206 original size:30 final size:30
Alignment explanation
Indices: 1170--1231 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1160 TTTTGAAAAA
1170 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
1200 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
1230 CA
1 CA
1232 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:1285 original size:87 final size:84
Alignment explanation
Indices: 1131--1288 Score: 244
Period size: 87 Copynumber: 1.8 Consensus size: 84
1121 GACTGGAGGT
*
1131 TCAATTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
1 TCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
1196 CTCGCAGAAATTAAAAAGC
66 CTCGCAGAAATTAAAAAGC
* * *
1215 TCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAACAGAAATTAAAAGGCTTAACTCA
1 TCAACTCACATCTCGCAATATGAGTTG-A--TTTTTGAAAAACAGAAATTAAAAGACTCAACTCA
*
1280 CCTCTCGCA
63 ACTCTCGCA
1289 ACATGAGTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 25 0.38
85 1 0.02
87 40 0.61
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (84 bp):
TCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
CTCGCAGAAATTAAAAAGC
Found at i:1288 original size:57 final size:55
Alignment explanation
Indices: 1200--1321 Score: 174
Period size: 57 Copynumber: 2.2 Consensus size: 55
1190 TCAACTCTCG
*
1200 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAA-AA
1 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTG-A--TTTTTGAAACAA
* *
1257 CAGAAATTAAAAGGCTTAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA
1 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA
*
1312 CAAAAATTAA
1 CAGAAATTAA
1322 GAATACCTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
54 9 0.15
55 11 0.18
56 1 0.02
57 39 0.65
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (55 bp):
CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA
Found at i:1520 original size:49 final size:49
Alignment explanation
Indices: 1454--1549 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
1444 GAATTTTGAA
*
1454 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
1503 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1550 CTTGCAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:1721 original size:54 final size:55
Alignment explanation
Indices: 1621--1726 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
1611 GAACCGAGGC
* *
1621 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
1675 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
1727 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:1733 original size:13 final size:13
Alignment explanation
Indices: 1706--1739 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1696 GAGTTGATTC
*
1706 TTGAACAACATAAA
1 TTGAA-AACAGAAA
1720 TTGAAAACAGAAA
1 TTGAAAACAGAAA
1733 TTGAAAA
1 TTGAAAA
1740 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:1772 original size:140 final size:140
Alignment explanation
Indices: 1577--2204 Score: 1125
Period size: 140 Copynumber: 4.5 Consensus size: 140
1567 AATTTTTTTT
1577 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
1641 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
1706 TTGAACAACATAAA
127 TTGAACAACATAAA
1720 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
1785 CTGATTTTGAAAAGGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
*
1850 ACAACGTAAA
131 ACAACATAAA
*
1860 TTGAAAACAGAAATTGAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
1925 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
*
1990 ACAACGTAAA
131 ACAACATAAA
*
2000 TTGAAAACAGAAATTGAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
2065 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTTATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
2130 ACAACGA-AAA
131 ACAAC-ATAAA
2140 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
2205 TTGAAATTAA
Statistics
Matches: 474, Mismatches: 9, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
139 3 0.01
140 442 0.93
142 23 0.05
143 6 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACATAAA
Found at i:1861 original size:54 final size:54
Alignment explanation
Indices: 1761--1866 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
1751 GACCTGAGGC
* *
1761 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAGGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAACGTA-AAATTGAAAAGGT
* *
1815 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AACGTAAAATTGAAAA
1867 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAACGTAAAATTGAAAAGGT
Found at i:2001 original size:54 final size:54
Alignment explanation
Indices: 1901--2006 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
1891 GACCTGAGGC
*
1901 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
1955 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
2007 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:2271 original size:72 final size:71
Alignment explanation
Indices: 2137--2302 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
2127 TGAACAACGA
* * * *
2137 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
2202 GAGTTG
66 GAGTTG
*
2208 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
2273 TGAGTTG
65 TGAGTTG
**
2280 ATTTTAAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
2303 GGCTTAATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:3483 original size:39 final size:40
Alignment explanation
Indices: 3440--3518 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
3430 ACTCGGTAAC
*
3440 TCTTT-CCATCCATCTCGGTGAGGATCAAAGCTCCGCCCG
1 TCTTTCCCATCCATCTCGATGAGGATCAAAGCTCCGCCCG
3479 TCTTTCCCATCCATCTCGATGAGGATCAAAGCTCCGCCCG
1 TCTTTCCCATCCATCTCGATGAGGATCAAAGCTCCGCCCG
3519 AGAATGTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.19, C:0.37, G:0.19, T:0.25
Consensus pattern (40 bp):
TCTTTCCCATCCATCTCGATGAGGATCAAAGCTCCGCCCG
Done.