Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold623
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: 47185
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.15
Warning! 23849 characters in sequence are not A, C, G, or T
Found at i:1972 original size:27 final size:28
Alignment explanation
Indices: 1937--1990 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
1927 GCTGGACTTG
*
1937 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGCAATAAAATT
* * *
1965 GACA-CATTTATAACATGCATTAAAAT
1 GACATCATTAAAAACATGCAATAAAAT
1991 AAAACACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (28 bp):
GACATCATTAAAAACATGCAATAAAATT
Found at i:5274 original size:45 final size:45
Alignment explanation
Indices: 5225--5330 Score: 167
Period size: 45 Copynumber: 2.4 Consensus size: 45
5215 TCGGCCATGG
* *
5225 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
* * *
5270 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
5315 TGCTTCCTCAAATTCT
1 TGCTTCCTCAAATTCT
5331 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
Found at i:13556 original size:30 final size:29
Alignment explanation
Indices: 13508--13564 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
13498 GAGAAAATGA
*
13508 AAAAGAAAAAGAAGATGAG-TGTGAGATAG
1 AAAAGAAAAAGAAAATGAGAT-TGAGATAG
*
13537 AAAAGAAAATTGAAAATGAGATTGAGAT
1 AAAAGAAAA-AGAAAATGAGATTGAGAT
13565 TGAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 14 0.58
31 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (29 bp):
AAAAGAAAAAGAAAATGAGATTGAGATAG
Found at i:13582 original size:54 final size:54
Alignment explanation
Indices: 13524--13647 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
13514 AAAAGAAGAT
* * * * * *
13524 GAGTGTGAGATAGAAAAGAAAATTGAAAATGAGATTGAGATTG-AGAATAAAAAC
1 GAGTGTGAAAAAGAAAAGAAAACTAAAAAAGAGAGTGAGATTGAAGAA-AAAAAC
* *
13578 GAGTGTGAAAAAGAAAATAAAACTAAAAAAGAGAGTGAGATTGAAGAAAGAAAC
1 GAGTGTGAAAAAGAAAAGAAAACTAAAAAAGAGAGTGAGATTGAAGAAAAAAAC
* *
13632 GAGAGTGCAAAAGAAA
1 GAGTGTGAAAAAGAAA
13648 TGAGTGATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 55 0.93
55 4 0.07
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (54 bp):
GAGTGTGAAAAAGAAAAGAAAACTAAAAAAGAGAGTGAGATTGAAGAAAAAAAC
Found at i:32728 original size:14 final size:15
Alignment explanation
Indices: 32701--32729 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
32691 ATGCATCTTC
32701 ACATTCATTGAATCT
1 ACATTCATTGAATCT
32716 ACATTCA-TGAATCT
1 ACATTCATTGAATCT
32730 GCCCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (15 bp):
ACATTCATTGAATCT
Found at i:34524 original size:20 final size:20
Alignment explanation
Indices: 34501--34538 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34491 TTGAGTTGAA
34501 TTGAACTCGAATGAGCTGAC
1 TTGAACTCGAATGAGCTGAC
* *
34521 TTGAGCTCGAGTGAGCTG
1 TTGAACTCGAATGAGCTG
34539 GAAACGAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (20 bp):
TTGAACTCGAATGAGCTGAC
Found at i:39633 original size:21 final size:22
Alignment explanation
Indices: 39607--39665 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
39597 TCAATTTCAA
39607 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTCTTTTTGTTTT
*
39628 CTCACTCTTTT-TTTCT-TTTT
1 CTCACTCTTTTCTTTTTGTTTT
39648 C-CA-TCTTTTCTTTTTGTT
1 CTCACTCTTTTCTTTTTGTT
39666 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 6 0.18
19 6 0.18
20 7 0.21
21 10 0.30
22 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (22 bp):
CTCACTCTTTTCTTTTTGTTTT
Found at i:39661 original size:20 final size:20
Alignment explanation
Indices: 39607--39665 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
39597 TCAATTTCAA
39607 CTCACTTTTTCTTTTTGTTTT
1 CTCAC-TTTTCTTTTTGTTTT
39628 CTCACTCTTT-TTTTCT-TTTT
1 CTCACT-TTTCTTTT-TGTTTT
39648 C-CATCTTTTCTTTTTGTT
1 CTCA-CTTTTCTTTTTGTT
39666 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 6 0.18
20 18 0.55
21 9 0.27
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (20 bp):
CTCACTTTTCTTTTTGTTTT
Found at i:39667 original size:18 final size:19
Alignment explanation
Indices: 39609--39667 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
39599 AATTTCAACT
39609 CACT-TTTTCTTTTTGTTTTC
1 CACTCTTTTCTTTTTG--TTC
*
39629 TCACTCTTTT-TTTCTTTTTC
1 -CACTCTTTTCTTT-TTGTTC
39649 CA-TCTTTTCTTTTTGTTC
1 CACTCTTTTCTTTTTGTTC
39667 C
1 C
39668 TTTGCCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 3 0.09
21 7 0.21
22 6 0.18
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (19 bp):
CACTCTTTTCTTTTTGTTC
Found at i:41733 original size:20 final size:19
Alignment explanation
Indices: 41708--41745 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
41698 AACATTTTCG
41708 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
41728 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
41746 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:43528 original size:11 final size:11
Alignment explanation
Indices: 43512--43550 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
43502 TCGAGATTGT
43512 AAAAAAA-TCA
1 AAAAAAATTCA
*
43522 AAAAAAATTTGA
1 AAAAAAA-TTCA
43534 AAAAAAATTCA
1 AAAAAAATTCA
43545 AAAAAA
1 AAAAAA
43551 GTTTGTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.28
11 9 0.36
12 9 0.36
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:43545 original size:23 final size:22
Alignment explanation
Indices: 43512--43555 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
43502 TCGAGATTGT
43512 AAAAAAATCAAAAAAAATTTGA
1 AAAAAAATCAAAAAAAATTTGA
*
43534 AAAAAAATTCAAAAAAAGTTTG
1 AAAAAAA-TCAAAAAAAATTTG
43556 TACTCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAAAATCAAAAAAAATTTGA
Found at i:44335 original size:41 final size:41
Alignment explanation
Indices: 44278--44360 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
44268 TGATCGTGAC
44278 TTGCATGATGAATCTGCCATTTCTTTCCAACGAGAAGCTTG
1 TTGCATGATGAATCTGCCATTTCTTTCCAACGAGAAGCTTG
44319 TTGCATGATGAATCTGCCATTTCTTTCCAACGAGAAGCTTG
1 TTGCATGATGAATCTGCCATTTCTTTCCAACGAGAAGCTTG
44360 T
1 T
44361 CGTTATGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
TTGCATGATGAATCTGCCATTTCTTTCCAACGAGAAGCTTG
Found at i:44505 original size:20 final size:21
Alignment explanation
Indices: 44475--44521 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
44465 AATCTTGAAT
*
44475 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
44496 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
44517 GAAAT
1 GAAAT
44522 AAATGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:44529 original size:21 final size:21
Alignment explanation
Indices: 44491--44536 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
44481 GAGAGAAGAA
*
44491 AAAAAGAAATGAGAGAAAAAG
1 AAAAAGAAATGAAAGAAAAAG
*
44512 AAAAAGAAAT-AAATGAAAATG
1 AAAAAGAAATGAAA-GAAAAAG
44533 AAAA
1 AAAA
44537 TGAGAGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (21 bp):
AAAAAGAAATGAAAGAAAAAG
Done.