Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1877
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: 57276
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3779 original size:18 final size:15
Alignment explanation
Indices: 3744--3782 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 15
3734 TGCAAGCGAG
3744 AGAAATTGAAAAAAA
1 AGAAATTGAAAAAAA
3759 AGAAGATTGAAAAAGAAA
1 AGAA-ATTG-AAAA-AAA
3777 AGAAAT
1 AGAAAT
3783 CCAAAAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
17 6 0.29
18 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (15 bp):
AGAAATTGAAAAAAA
Found at i:5551 original size:20 final size:20
Alignment explanation
Indices: 5505--5551 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5495 AGCTCGTTTC
*
5505 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
5525 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
5545 CAGCTCA
1 CAGCTCA
5552 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:10543 original size:49 final size:49
Alignment explanation
Indices: 10486--10583 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
10476 AAGGTTTGTT
10486 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
10535 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
10584 AAATCAAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.14
Consensus pattern (49 bp):
TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
Found at i:12141 original size:11 final size:11
Alignment explanation
Indices: 12125--12176 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
12115 TAGTAGTTTC
12125 TTCAAAAAAAA
1 TTCAAAAAAAA
12136 TTC-AAAAAAA
1 TTCAAAAAAAA
12146 -T-AAAAAAAA
1 TTCAAAAAAAA
12155 TTCAAAAAAAA
1 TTCAAAAAAAA
12166 TTCAAAAAAAA
1 TTCAAAAAAAA
12177 AAATTTGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.21
10 8 0.21
11 22 0.58
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:12144 original size:10 final size:10
Alignment explanation
Indices: 12129--12175 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
12119 AGTTTCTTCA
12129 AAAAAAATTC
1 AAAAAAATTC
*
12139 AAAAAAA-TA
1 AAAAAAATTC
12148 AAAAAAATTC
1 AAAAAAATTC
12158 AAAAAAAATTC
1 -AAAAAAATTC
12169 AAAAAAA
1 AAAAAAA
12176 AAAATTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 8 0.24
10 15 0.45
11 10 0.30
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:12173 original size:19 final size:19
Alignment explanation
Indices: 12128--12164 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12118 TAGTTTCTTC
12128 AAAAAAAATTCAAAAAAAT
1 AAAAAAAATTCAAAAAAAT
12147 AAAAAAAATTCAAAAAAA
1 AAAAAAAATTCAAAAAAA
12165 ATTCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAAAATTCAAAAAAAT
Found at i:12238 original size:14 final size:14
Alignment explanation
Indices: 12219--12272 Score: 90
Period size: 14 Copynumber: 3.7 Consensus size: 14
12209 GATATCAAGT
12219 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
12233 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
12247 TGAAAAAAAAAATTCG
1 TG--AAAAAAAATTCG
12263 TGAAAAAAAA
1 TGAAAAAAAA
12273 GAAGAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 24 0.63
16 14 0.37
ACGTcount: A:0.63, C:0.06, G:0.13, T:0.19
Consensus pattern (14 bp):
TGAAAAAAAATTCG
Found at i:12242 original size:16 final size:16
Alignment explanation
Indices: 12221--12272 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
12211 TATCAAGTTG
12221 AAAAAAAATTCGTG--
1 AAAAAAAATTCGTGAA
12235 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
12251 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
12267 AAAAAA
1 AAAAAA
12273 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.39
16 22 0.61
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:19953 original size:23 final size:22
Alignment explanation
Indices: 19901--19953 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
19891 TCCACGTCTT
*
19901 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
19923 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
19946 TTTCTTTT
1 TTTCTTTT
19954 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:25507 original size:49 final size:49
Alignment explanation
Indices: 25450--25547 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
25440 AAGGTTTGTT
25450 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
25499 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
25548 AAATCAAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.14
Consensus pattern (49 bp):
TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
Found at i:27317 original size:17 final size:17
Alignment explanation
Indices: 27295--27328 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27285 TACAACCTGT
27295 TCTGTTATGCGTTATAC
1 TCTGTTATGCGTTATAC
27312 TCTGTTATGCGTTATAC
1 TCTGTTATGCGTTATAC
27329 ATGTGGCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (17 bp):
TCTGTTATGCGTTATAC
Found at i:30892 original size:22 final size:22
Alignment explanation
Indices: 30841--30906 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
30831 GGTATTTGGG
* *
30841 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
30862 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
30884 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
30907 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:38517 original size:23 final size:22
Alignment explanation
Indices: 38465--38517 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38455 TCCACGTCTT
*
38465 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38487 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38510 TTTCTTTT
1 TTTCTTTT
38518 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:44683 original size:45 final size:45
Alignment explanation
Indices: 44634--44866 Score: 387
Period size: 45 Copynumber: 5.2 Consensus size: 45
44624 TCGGCCATGG
* * * *
44634 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
**
44679 TGCTTCCTTTAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
44724 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
44769 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
44814 TGCTTCCTCAAATTC-TCCAATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCC-ATGAATTATGCATGATGTTGGTCAAA
*
44859 TGTTTCCT
1 TGCTTCCT
44867 TAATTTCATG
Statistics
Matches: 178, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 3 0.02
45 175 0.98
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:50575 original size:20 final size:20
Alignment explanation
Indices: 50552--50605 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
50542 AGTTTTTCCC
*
50552 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
50572 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
50592 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
50606 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:50587 original size:30 final size:30
Alignment explanation
Indices: 50552--50625 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
50542 AGTTTTTCCC
50552 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
50582 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
50612 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
50626 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:50615 original size:20 final size:20
Alignment explanation
Indices: 50552--50616 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
50542 AGTTTTTCCC
* * * *
50552 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
50572 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
50591 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
50612 AGCTC
1 AGCTC
50617 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:53397 original size:90 final size:88
Alignment explanation
Indices: 53245--53473 Score: 297
Period size: 91 Copynumber: 2.6 Consensus size: 88
53235 TTGGCCATGG
* * * * *
53245 TGCTTCC-CAATTTGTTCCATAAATTATGCAGATGTT-G-CAAATGCTTCCTTAAATCTTCCATG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCTGATGTTGGTCAAATGC-TCCTCAAATCTTCCATG
53307 AATTATGCATGATG-TTGGTCAAA
65 AATTATGCATGATGTTTGGTCAAA
*
53330 TTGCTTCCTCAAATTCTTCCTATGAATTATGCTGATGTTGGTCAAATGCTCCTCAAATGTCTCCA
1 -TGCTTCCTCAAATTCTTCC-ATGAATTATGCTGATGTTGGTCAAATGCTCCTCAAATCT-TCCA
53395 TGAATTATGCATGATGTTTGGTCAAA
63 TGAATTATGCATGATGTTTGGTCAAA
*
53421 TGCTTCCTCTCAAATTC-TCCAATGAATTATGCTGATGTTGGTCAAATGTTCCT
1 TGCTT-C-CTCAAATTCTTCC-ATGAATTATGCTGATGTTGGTCAAATGCTCCT
53474 TAATTCATGC
Statistics
Matches: 127, Mismatches: 8, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
86 7 0.06
87 9 0.07
88 16 0.13
89 10 0.08
90 32 0.25
91 44 0.35
92 9 0.07
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (88 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCTGATGTTGGTCAAATGCTCCTCAAATCTTCCATGA
ATTATGCATGATGTTTGGTCAAA
Done.