Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1721
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: 14716
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Found at i:1230 original size:18 final size:18
Alignment explanation
Indices: 1188--1223 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1178 AATGAAAATG
1188 ATGCAATTTTTAAAACAT
1 ATGCAATTTTTAAAACAT
1206 ATGCAATTTTTAAAACAT
1 ATGCAATTTTTAAAACAT
1224 TCTCAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
ATGCAATTTTTAAAACAT
Found at i:1620 original size:2 final size:2
Alignment explanation
Indices: 1613--1641 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1603 GTTTTGGATT
1613 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1642 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4389 original size:12 final size:12
Alignment explanation
Indices: 4372--4418 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
4362 ACTTGTATAA
4372 TTTTTATATTAT
1 TTTTTATATTAT
*
4384 TTTTTATCTTAT
1 TTTTTATATTAT
*
4396 ATTTTA-ATTAT
1 TTTTTATATTAT
* *
4407 TCTTTATGTTAT
1 TTTTTATATTAT
4419 GTTTCATGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTTTATATTAT
Found at i:4406 original size:23 final size:24
Alignment explanation
Indices: 4373--4418 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4363 CTTGTATAAT
*
4373 TTTTATATTATTTTTTATCTTATA
1 TTTTATATTATTCTTTATCTTATA
*
4397 TTTTA-ATTATTCTTTATGTTAT
1 TTTTATATTATTCTTTATCTTAT
4419 GTTTCATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATATTATTCTTTATCTTATA
Found at i:4630 original size:55 final size:59
Alignment explanation
Indices: 4512--4631 Score: 151
Period size: 56 Copynumber: 2.1 Consensus size: 59
4502 GTTCGTATCG
* * *
4512 TATCTCAATTCATGACATATTTTACATAATTTATAATAATAATTTAATTTAAAATATCA
1 TATCTTAATTCATGACATATTTTACATAATTTATAACAATAATTTAATTTAAAAAATCA
* *
4571 TATCTTAATTCAT-A-ATATTTT-CATAATTTCT-ACAGTAATTTAATTTTAAAAAATC-
1 TATCTTAATTCATGACATATTTTACATAATTTATAACAATAATTTAA-TTTAAAAAATCA
4626 TATCTT
1 TATCTT
4632 TTTACATGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
55 16 0.29
56 19 0.35
57 7 0.13
58 1 0.02
59 12 0.22
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (59 bp):
TATCTTAATTCATGACATATTTTACATAATTTATAACAATAATTTAATTTAAAAAATCA
Found at i:4814 original size:16 final size:16
Alignment explanation
Indices: 4733--4828 Score: 90
Period size: 16 Copynumber: 6.1 Consensus size: 16
4723 ATCACTATCA
4733 TATTTATATTAT-TTT
1 TATTTATATTATATTT
*
4748 TATGTCATATTATA-TT
1 TAT-TTATATTATATTT
* * *
4764 TAATTATTTTATATTA
1 TATTTATATTATATTT
*
4780 TATTTATATTATATCT
1 TATTTATATTATATTT
*
4796 TATTTATTTTATATTT
1 TATTTATATTATATTT
* *
4812 TATATA-ATTAAATTT
1 TATTTATATTATATTT
4827 TA
1 TA
4829 ATTTCAAATT
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
15 20 0.31
16 44 0.69
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (16 bp):
TATTTATATTATATTT
Found at i:4877 original size:14 final size:14
Alignment explanation
Indices: 4808--4891 Score: 70
Period size: 14 Copynumber: 6.1 Consensus size: 14
4798 TTTATTTTAT
4808 ATTTTATATAATTAA
1 ATTTTAT-TAATTAA
*
4823 ATTTTAATT--TCAA
1 ATTTT-ATTAATTAA
4836 A-TTTATCT-ATTAA
1 ATTTTAT-TAATTAA
*
4849 ATATTTTTTAA-TAA
1 AT-TTTATTAATTAA
4863 ATTTTATTAATTAA
1 ATTTTATTAATTAA
*
4877 ATTTTATTACTTAA
1 ATTTTATTAATTAA
4891 A
1 A
4892 AATTTTATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
11 2 0.04
12 4 0.07
13 15 0.26
14 23 0.40
15 11 0.19
16 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTATTAATTAA
Found at i:4891 original size:28 final size:28
Alignment explanation
Indices: 4798--4914 Score: 82
Period size: 27 Copynumber: 4.1 Consensus size: 28
4788 TTATATCTTA
*
4798 TTTATT-TTATATTTTATATAATTAAAT
1 TTTATTATTAAATTTTATATAATTAAAT
* *
4825 TTTAATT-TCAAA-TTTATCT-ATTAAAT
1 TTT-ATTATTAAATTTTATATAATTAAAT
* *
4851 ATTTTTTAATAAATTTTAT-TAATTAAAT
1 -TTTATTATTAAATTTTATATAATTAAAT
*
4879 TTTATTACTTAAAAATTTTATAAATATTAAAAT
1 TTTATTA-TT--AAATTTTATATA-ATT-AAAT
4912 TTT
1 TTT
4915 CTAACGAAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
26 9 0.13
27 22 0.31
28 19 0.27
30 9 0.13
31 1 0.01
32 3 0.04
33 7 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATTAAATTTTATATAATTAAAT
Found at i:5343 original size:17 final size:18
Alignment explanation
Indices: 5286--5343 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
5276 TTTTTATCTT
*
5286 ATAAACTTTAATTATTATTA
1 ATAAA-TTTAATTA-TAATA
5306 ATAAAATTTAATTATAA-A
1 AT-AAATTTAATTATAATA
*
5324 ATAAATTTTATTA-AATA
1 ATAAATTTAATTATAATA
5341 ATA
1 ATA
5344 TTTATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 2 0.06
17 14 0.41
18 3 0.09
19 2 0.06
20 10 0.29
21 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAATTTAATTATAATA
Found at i:5369 original size:53 final size:55
Alignment explanation
Indices: 5319--5434 Score: 136
Period size: 54 Copynumber: 2.2 Consensus size: 55
5309 AAATTTAATT
* *
5319 ATAAAATAAATTTTATTA-AAT-AATATTTATATATTTAAAT-T-TTATATTTAAA
1 ATAAAATAAATTTAATTATAATAAAAATTTAT-TATTTAAATATATTATATTTAAA
*
5371 ATTAAA-AAATTTAATTATAATACAAAATTTATTATTTAAATATATTAT-TTTAAAA
1 ATAAAATAAATTTAATTATAATA-AAAATTTATTATTTAAATATATTATATTT-AAA
5426 ATAAAATAA
1 ATAAAATAA
5435 TTAATAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
51 10 0.19
52 8 0.15
53 9 0.17
54 12 0.23
55 12 0.23
56 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (55 bp):
ATAAAATAAATTTAATTATAATAAAAATTTATTATTTAAATATATTATATTTAAA
Found at i:5680 original size:11 final size:11
Alignment explanation
Indices: 5666--5711 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
5656 ATATATGAAA
5666 AATAAAAAAAT
1 AATAAAAAAAT
*
5677 AATATAAAAAT
1 AATAAAAAAAT
* *
5688 AATTAAAACAT
1 AATAAAAAAAT
*
5699 AATATAAAAAT
1 AATAAAAAAAT
5710 AA
1 AA
5712 ATAGACATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:5724 original size:22 final size:22
Alignment explanation
Indices: 5658--5714 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
5648 ACTATTAAAT
5658 ATATGAAAAAT-AA-AAAA-ATA
1 ATAT-AAAAATAAATAAAACATA
*
5678 ATATAAAAATAATTAAAACATA
1 ATATAAAAATAAATAAAACATA
5700 ATATAAAAATAAATA
1 ATATAAAAATAAATA
5715 GACATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 4 0.12
22 17 0.53
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
ATATAAAAATAAATAAAACATA
Found at i:8713 original size:13 final size:13
Alignment explanation
Indices: 8695--8719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8685 CATTATGCTT
8695 TGTATCGATACAA
1 TGTATCGATACAA
8708 TGTATCGATACA
1 TGTATCGATACA
8720 TTTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8716 original size:33 final size:32
Alignment explanation
Indices: 8674--8735 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
8664 ACACACCCAG
*
8674 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATT-TGCATTGTATCGATACA
*
8707 ATGTATCGATACATTTTCATTGTATCGAT
1 ATGTATCGATACATTTGCATTGTATCGAT
8736 TCATGGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (32 bp):
ATGTATCGATACATTTGCATTGTATCGATACA
Found at i:8732 original size:19 final size:20
Alignment explanation
Indices: 8704--8760 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
8694 TTGTATCGAT
**
8704 ACAA-TGTATCGATACATTT
1 ACAATTGTATCGATACATGG
* *
8723 TC-ATTGTATCGATTCATGG
1 ACAATTGTATCGATACATGG
8742 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
8761 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 15 0.50
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:8825 original size:13 final size:13
Alignment explanation
Indices: 8807--8831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8797 ATACATGGCA
8807 CATTGTATCGATG
1 CATTGTATCGATG
8820 CATTGTATCGAT
1 CATTGTATCGAT
8832 ACATAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATG
Found at i:9956 original size:3 final size:3
Alignment explanation
Indices: 9942--9972 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
9932 CATCGAAGAC
*
9942 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
9973 TTGACTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Done.