Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1325
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: 59029
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1251 original size:1 final size:1
Alignment explanation
Indices: 1245--1346 Score: 186
Period size: 1 Copynumber: 102.0 Consensus size: 1
1235 CGAAGGTTTG
**
1245 TTTTTTTTTTTTTTTTTTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1347 AACTGAAAAA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 99 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:2140 original size:11 final size:10
Alignment explanation
Indices: 2124--2157 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
2114 AGTTCTAAAG
2124 TTTTATTTTAT
1 TTTTA-TTTAT
2135 TTTTATTTAT
1 TTTTATTTAT
2145 TTATTATTTAT
1 TT-TTATTTAT
2156 TT
1 TT
2158 ACTTAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:2145 original size:15 final size:15
Alignment explanation
Indices: 2125--2158 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2115 GTTCTAAAGT
2125 TTTATTTTATT-TTTA
1 TTTA-TTTATTATTTA
2140 TTTATTTATTATTTA
1 TTTATTTATTATTTA
2155 TTTA
1 TTTA
2159 CTTAGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:2158 original size:11 final size:11
Alignment explanation
Indices: 2130--2158 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2120 AAAGTTTTAT
2130 TTTATTT-TTA
1 TTTATTTATTA
2140 TTTATTTATTA
1 TTTATTTATTA
2151 TTTATTTA
1 TTTATTTA
2159 CTTAGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:9025 original size:1 final size:1
Alignment explanation
Indices: 9019--9092 Score: 130
Period size: 1 Copynumber: 74.0 Consensus size: 1
9009 TGGTGTAGGC
**
9019 GGGGGGGGGGTTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
9084 GGGGGGGGG
1 GGGGGGGGG
9093 CAGTTTCATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:9463 original size:14 final size:13
Alignment explanation
Indices: 9428--9453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9418 CAGCTTCGCA
9428 AAAAAAAAAGTTT
1 AAAAAAAAAGTTT
9441 AAAAAAAAAGTTT
1 AAAAAAAAAGTTT
9454 TCGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAAAAAAAGTTT
Found at i:9463 original size:19 final size:19
Alignment explanation
Indices: 9441--9494 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
9431 AAAAAAGTTT
* * *
9441 AAAAAAAAAGTTTTCGAAA
1 AAAAAAAAAATTTGCCAAA
9460 AAAAAAAAAATTTGCCAAAA
1 AAAAAAAAAATTTGCC-AAA
9480 AAAAAAAAAATTTGC
1 AAAAAAAAAATTTGC
9495 AACGGTCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAAAAAAAATTTGCCAAA
Found at i:9489 original size:20 final size:20
Alignment explanation
Indices: 9457--9494 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9447 AAAGTTTTCG
9457 AAAAAAAAAAAAATTTGCCA
1 AAAAAAAAAAAAATTTGCCA
9477 AAAAAAAAAAAAATTTGC
1 AAAAAAAAAAAAATTTGC
9495 AACGGTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAAAAAAAAAAATTTGCCA
Found at i:22058 original size:29 final size:28
Alignment explanation
Indices: 22025--22089 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
22015 TCAAAAATTC
**
22025 AAAAAAAAAGTGAAAAAAA-TCGAGCAAGA
1 AAAAAAAAAGAAAAAAAAAGT-GAGCAA-A
*
22054 AAAAAGAAAGAAAAAAAAAGTGAGCAAA
1 AAAAAAAAAGAAAAAAAAAGTGAGCAAA
22082 AAAAAAAA
1 AAAAAAAA
22090 TCAAGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 22 0.71
30 1 0.03
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAAAAAGTGAGCAAA
Found at i:22082 original size:15 final size:15
Alignment explanation
Indices: 22037--22087 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
22027 AAAAAAAGTG
22037 AAAAAAA-TCGAGCAA
1 AAAAAAAGT-GAGCAA
* **
22052 GAAAAAAGAAAG-AA
1 AAAAAAAGTGAGCAA
22066 AAAAAAAGTGAGCAA
1 AAAAAAAGTGAGCAA
22081 AAAAAAA
1 AAAAAAA
22088 AATCAAGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAAAAGTGAGCAA
Found at i:30492 original size:24 final size:25
Alignment explanation
Indices: 30439--30492 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
30429 AACAAATTCT
* *
30439 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
30464 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
30487 TTTTTT
1 TTTTTT
30493 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:32760 original size:15 final size:15
Alignment explanation
Indices: 32742--32786 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
32732 CTAGACCGTA
32742 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
32757 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
*
32772 TCGAAATTTTTTTTT
1 T-GCAATTTTTTTTT
32787 AACTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:32768 original size:16 final size:16
Alignment explanation
Indices: 32742--32786 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
32732 CTAGACCGTA
32742 TGCAA-TTTTTTTTTT
1 TGCAATTTTTTTTTTT
32757 TGCAATTTTTTTTTTT
1 TGCAATTTTTTTTTTT
* *
32773 CGAAATTTTTTTTT
1 TGCAATTTTTTTTT
32787 AACTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (16 bp):
TGCAATTTTTTTTTTT
Found at i:32793 original size:12 final size:13
Alignment explanation
Indices: 32749--32799 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
32739 GTATGCAATT
*
32749 TTTTTTTTTGCAATT
1 TTTTTTTTT-CAA-A
32764 TTTTTTTTTCGAAA
1 TTTTTTTTTC-AAA
*
32778 TTTTTTTTT-AAC
1 TTTTTTTTTCAAA
32790 TTTTTTTTTC
1 TTTTTTTTTC
32800 GAAGCTACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 11 0.34
14 10 0.31
15 11 0.34
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:41342 original size:23 final size:22
Alignment explanation
Indices: 41290--41342 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41280 TCCACGTCTT
*
41290 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41312 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
41335 TTTCTTTT
1 TTTCTTTT
41343 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55275 original size:30 final size:31
Alignment explanation
Indices: 55241--55322 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
55231 TTTGAAAAGA
*
55241 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
55271 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
55301 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
55323 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:55295 original size:24 final size:24
Alignment explanation
Indices: 55246--55315 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
55236 AAAGAAAAAA
*
55246 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
55270 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
55294 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
55316 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:57458 original size:30 final size:29
Alignment explanation
Indices: 57424--57516 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
57414 AGCTCACTCC
57424 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ATTCAGCTCACGAGCTAAACCT
* * * * *
57454 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAA-TTCAGCTCACGAGCTAAACCT
* *
57484 CAGCTCAA--C-GCTCACGAGCTAAAGCT
1 TAGCTCAATTCAGCTCACGAGCTAAACCT
57510 TAGCTCA
1 TAGCTCA
57517 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
26 17 0.35
27 1 0.02
29 1 0.02
30 30 0.61
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (29 bp):
TAGCTCAATTCAGCTCACGAGCTAAACCT
Done.