Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2100
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: 31356
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:2444 original size:28 final size:27
Alignment explanation
Indices: 2325--2504 Score: 152
Period size: 27 Copynumber: 6.6 Consensus size: 27
2315 TAAATTGTAC
2325 AGCACTAAGGTGTGCGATTTGACTATGT
1 AGCACTAA-GTGTGCGATTTGACTATGT
* * * *
2353 TGCACTAAGTGTGCGAACGATGGAATATG-
1 AGCACTAAGTGTGCG-A--TTTGACTATGT
* *
2382 ATGCACT-AGTGTGCGAATTGACCA-G-
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2407 CGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2435 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2462 AGCACTAAGTGTGCGAGTTGATTATTAT
1 AGCACTAAGTGTGCGATTTGACTA-TGT
*
2490 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2505 GACTCAATAT
Statistics
Matches: 125, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
24 5 0.04
25 10 0.08
26 11 0.09
27 40 0.32
28 39 0.31
29 8 0.06
30 12 0.10
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:7747 original size:28 final size:28
Alignment explanation
Indices: 7707--7763 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
7697 ATTTGGGTGT
7707 TGTTGATAGGCTGACTAAGTCGGCTCAC
1 TGTTGATAGGCTGACTAAGTCGGCTCAC
7735 TGTTGATAGGCTGACTAAGTCGGCTCAC
1 TGTTGATAGGCTGACTAAGTCGGCTCAC
7763 T
1 T
7764 TTATCCCCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (28 bp):
TGTTGATAGGCTGACTAAGTCGGCTCAC
Found at i:10564 original size:27 final size:27
Alignment explanation
Indices: 10533--10710 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10523 TAAATTGTAC
10533 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
10560 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10586 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
10614 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
10642 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10669 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10696 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10711 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:10647 original size:82 final size:81
Alignment explanation
Indices: 10534--10689 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10524 AAATTGTACA
* *
10534 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
10598 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10615 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
10680 TGCGAGTTGA
65 TGCGAATTGA
10690 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10701 original size:82 final size:81
Alignment explanation
Indices: 10530--10710 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
10520 GATTAAATTG
* *
10530 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
10595 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
10611 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
10675 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
10693 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10711 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:18718 original size:19 final size:18
Alignment explanation
Indices: 18682--18721 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18672 TTTCCACTCG
*
18682 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
18700 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
18719 TTT
1 TTT
18722 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:19797 original size:12 final size:12
Alignment explanation
Indices: 19795--19828 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
19785 TTCACAATTT
19795 TTTTTTTTCACAA
1 TTTTTTTTCA-AA
19808 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
19821 TTTTTTTT
1 TTTTTTTT
19829 TCACAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 2 0.10
14 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:19798 original size:14 final size:14
Alignment explanation
Indices: 19779--19834 Score: 87
Period size: 13 Copynumber: 3.9 Consensus size: 14
19769 ACTAGCTCTC
19779 TTTTTTTTCACAATTT
1 TTTTTTTTCACAA--T
19795 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
19809 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
19822 TTTTTTTTCACAA
1 TTTTTTTTCACAA
19835 CTTGATATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.33
14 13 0.33
16 13 0.33
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:19800 original size:16 final size:16
Alignment explanation
Indices: 19779--19829 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
19769 ACTAGCTCTC
19779 TTTTTTTTCACAATTT
1 TTTTTTTTCACAATTT
19795 TTTTTTTTCACAA--T
1 TTTTTTTTCACAATTT
19809 TTTTTTTTCA-AATTT
1 TTTTTTTTCACAATTT
19824 TTTTTT
1 TTTTTT
19830 CACAACTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.06
14 11 0.33
15 7 0.21
16 13 0.39
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTTCACAATTT
Found at i:19893 original size:14 final size:13
Alignment explanation
Indices: 19875--19900 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19865 AAACCAAAAT
19875 TTTTTTTTTCGAG
1 TTTTTTTTTCGAG
19888 TTTTTTTTTCGAG
1 TTTTTTTTTCGAG
19901 AAACTACTAT
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:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCGAG
Found at i:25612 original size:23 final size:22
Alignment explanation
Indices: 25561--25612 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
25551 CCTCGTTTTT
*
25561 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
25583 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
25606 TTCTTTT
1 TTCTTTT
25613 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
Done.