Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold854
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: 47868
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:181 original size:29 final size:28
Alignment explanation
Indices: 112--182 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
102 ATTAAAAATA
* *
112 TAATAAAATTAACATAAATTATTTAATT
1 TAATAAAATTAAAATAAATAATTTAATT
* *
140 TATTAATAA-TAAAATTTAATAATTTAATT
1 TAATAA-AATTAAAA-TAAATAATTTAATT
169 TAATAAAATTAAAA
1 TAATAAAATTAAAA
183 ATCTGTAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TAATAAAATTAAAATAAATAATTTAATT
Found at i:674 original size:26 final size:25
Alignment explanation
Indices: 619--674 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
609 TTTTTTTTAG
*
619 GAAAAACTATCCCCTTTTTCATTTT
1 GAAAAACTATCCCCTTTTTCACTTT
* *
644 AAAAAACTA-CCCATCTTTTTTACTTT
1 GAAAAACTATCCC--CTTTTTCACTTT
670 GAAAA
1 GAAAA
675 GAAAACTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 3 0.12
25 8 0.32
26 14 0.56
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (25 bp):
GAAAAACTATCCCCTTTTTCACTTT
Found at i:2108 original size:30 final size:30
Alignment explanation
Indices: 2055--2113 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2045 CATATATAAT
* *
2055 TGATCTAATTTATTAATAATAAAATTTTAA
1 TGATCTAATTTATGAATAATAAAAGTTTAA
*
2085 TGATCTAATTTGATGAA-ATTAAAAGTTTA
1 TGATCTAATTT-ATGAATAATAAAAGTTTA
2114 TGACTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (30 bp):
TGATCTAATTTATGAATAATAAAAGTTTAA
Found at i:2390 original size:22 final size:20
Alignment explanation
Indices: 2359--2408 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 20
2349 AAGTTTTGAA
2359 TAAATTAAAAATTATTAATTATT
1 TAAA-TAAAAATT-TTAATTA-T
2382 TAAATAAAAAATTTTAATTAT
1 TAAAT-AAAAATTTTAATTAT
2403 TAAATA
1 TAAATA
2409 TATATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.04
21 6 0.23
22 8 0.31
23 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATAAAAATTTTAATTAT
Found at i:3390 original size:37 final size:37
Alignment explanation
Indices: 3348--3418 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
3338 GGTTAAAAAG
*
3348 TTTATATTATTATTTA-AAATAATATTAAAATAAATTT
1 TTTATATTAATATTTATAAATAA-ATTAAAATAAATTT
* *
3385 TTTATATTAATATTTATAATTAAATTTAAATAAA
1 TTTATATTAATATTTATAAATAAATTAAAATAAA
3419 AATAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 25 0.83
38 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTATATTAATATTTATAAATAAATTAAAATAAATTT
Found at i:3892 original size:18 final size:20
Alignment explanation
Indices: 3860--3897 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3850 TGAAATCAGT
3860 AAAATCAATATATTAAATAA
1 AAAATCAATATATTAAATAA
3880 AAAAT-AATA-ATTAAATAA
1 AAAATCAATATATTAAATAA
3898 TTTGTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATCAATATATTAAATAA
Found at i:5046 original size:2 final size:2
Alignment explanation
Indices: 5039--5065 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5029 ATCTATATCC
5039 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5066 AGCATGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5906 original size:2 final size:2
Alignment explanation
Indices: 5894--5927 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5884 GATATAGCAA
5894 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5928 TAAAAGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8647 original size:32 final size:32
Alignment explanation
Indices: 8606--8670 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
8596 AAGTAAAAAA
8606 AAAAAAAAAGAAATCATTTAGCCTGATACAAG
1 AAAAAAAAAGAAATCATTTAGCCTGATACAAG
8638 AAAAAAAAAGAAATCATTTAGCCTGATACAAG
1 AAAAAAAAAGAAATCATTTAGCCTGATACAAG
8670 A
1 A
8671 TAAACTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (32 bp):
AAAAAAAAAGAAATCATTTAGCCTGATACAAG
Found at i:8757 original size:23 final size:22
Alignment explanation
Indices: 8731--8774 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
8721 TTGACTTGAA
8731 TTTTTATTTATTTAATAAATAAT
1 TTTTTATTTATTT-ATAAATAAT
*
8754 TTTTTATTTATTTTTAAATAA
1 TTTTTATTTATTTATAAATAA
8775 AATATATAAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTATTTATTTATAAATAAT
Found at i:10601 original size:11 final size:11
Alignment explanation
Indices: 10587--10635 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
10577 ATTTTGACCA
*
10587 TCTTTTTCTTT
1 TCTTTTTCTCT
10598 TC-TTTTC-CT
1 TCTTTTTCTCT
*
10607 TTTTTTTC-CT
1 TCTTTTTCTCT
10617 TCTTTTTCTCT
1 TCTTTTTCTCT
*
10628 GCTTTTTC
1 TCTTTTTC
10636 ACTGTCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 19 0.59
11 11 0.34
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (11 bp):
TCTTTTTCTCT
Found at i:10968 original size:2 final size:2
Alignment explanation
Indices: 10957--10994 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
10947 ATATGTAAAA
*
10957 AT AT -T AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10995 CAGTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12301 original size:10 final size:10
Alignment explanation
Indices: 12286--12310 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12276 TATTTTATTA
12286 TTTTATAATT
1 TTTTATAATT
12296 TTTTATAATT
1 TTTTATAATT
12306 TTTTA
1 TTTTA
12311 ATTGACTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATAATT
Found at i:12301 original size:18 final size:18
Alignment explanation
Indices: 12278--12313 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12268 GACTAATATA
*
12278 TTTTATTATTTTATAATT
1 TTTTATAATTTTATAATT
*
12296 TTTTATAATTTTTTAATT
1 TTTTATAATTTTATAATT
12314 GACTTGTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATAATTTTATAATT
Found at i:19622 original size:36 final size:36
Alignment explanation
Indices: 19578--19723 Score: 161
Period size: 36 Copynumber: 4.1 Consensus size: 36
19568 GCTCCTACTT
19578 ATGCTTCTCCGAGAAGATCTTACAGGACTTCTGCTA
1 ATGCTTCTCCGAGAAGATCTTACAGGACTTCTGCTA
* ** *
19614 ATGCTTCTCCGACAATCTCTTACAGGACTTCGGCTA
1 ATGCTTCTCCGAGAAGATCTTACAGGACTTCTGCTA
** * *
19650 ATGCTTCTCCGAGAAGATCTTGGAGGACTTCTACTT
1 ATGCTTCTCCGAGAAGATCTTACAGGACTTCTGCTA
* * *
19686 ATGCTTCTTTTCGA-AAG-TCTAACAGGGCTTCTGCTA
1 ATGCTTC--TCCGAGAAGATCTTACAGGACTTCTGCTA
19722 AT
1 AT
19724 TGATTTTCTT
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
36 82 0.92
37 3 0.03
38 4 0.04
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (36 bp):
ATGCTTCTCCGAGAAGATCTTACAGGACTTCTGCTA
Found at i:21624 original size:88 final size:84
Alignment explanation
Indices: 21462--21635 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 84
21452 TTTGTTTCTC
*
21462 AACAACCAACCATTAGTACTCGAATAACCAAAAAAAAAAAAAGGATAGAATAAGAAAACATTCTC
1 AACAACCAACCATTAGTACTCAAATAACCAAAAAAAAAAAAAGGATAGAATAAGAAAACATTCTC
*
21527 CTGTAATGAACAGGAAGCA
66 ATGTAATGAACAGGAAGCA
* * *
21546 AACAACCAACCATTAGTACTCAAATAACAAAAAGAAAAAGAAAAAAAAGGATAG-A-AAGATATC
1 AACAACCAACCATTAGTACTCAAATAAC-----CAAAAA-AAAAAAAAGGATAGAATAAGAAAAC
**
21609 ATTCTCATGTAATGAATGGGAAGCA
60 ATTCTCATGTAATGAACAGGAAGCA
21634 AA
1 AA
21636 GGAAACAGTA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
84 27 0.35
88 30 0.39
89 6 0.08
90 14 0.18
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (84 bp):
AACAACCAACCATTAGTACTCAAATAACCAAAAAAAAAAAAAGGATAGAATAAGAAAACATTCTC
ATGTAATGAACAGGAAGCA
Found at i:26719 original size:25 final size:23
Alignment explanation
Indices: 26662--26724 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
26652 ATTATCTAAT
*
26662 TTTTCTTTTTATTTAAAAAATTAC
1 TTTTC-TTTTATTTAAAAAATAAC
*
26686 TAATT-TTTTATTTGAAGAAAATAAC
1 T-TTTCTTTTATTT-AA-AAAATAAC
26711 TTTTCTTTTATTTA
1 TTTTCTTTTATTTA
26725 CCGATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 8 0.25
24 6 0.19
25 18 0.56
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (23 bp):
TTTTCTTTTATTTAAAAAATAAC
Found at i:27404 original size:16 final size:18
Alignment explanation
Indices: 27374--27406 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
27364 CTTTCCTTTC
27374 TTTTCATTTTCTTTATTT
1 TTTTCATTTTCTTTATTT
27392 TTTTC-TTTT-TTTATT
1 TTTTCATTTTCTTTATT
27407 ATTATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCATTTTCTTTATTT
Found at i:28992 original size:15 final size:14
Alignment explanation
Indices: 28972--29006 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28962 AATGATATGC
28972 AATTTTATTTTATTT
1 AATTTTATTTT-TTT
28987 AATTTTATTTTTTT
1 AATTTTATTTTTTT
*
29001 CATTTT
1 AATTTT
29007 GAAAATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
AATTTTATTTTTTT
Found at i:29646 original size:27 final size:26
Alignment explanation
Indices: 29599--29653 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
29589 AATAAAAATT
*
29599 ATTTTATATTAATTATATATTTTTAA
1 ATTTTATATTAATTATATATTATTAA
*
29625 ATTTATATATATAATT-TTTATTATTAA
1 ATTT-TATAT-TAATTATATATTATTAA
29652 AT
1 AT
29654 AATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 16 0.64
28 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTATATTAATTATATATTATTAA
Found at i:39501 original size:27 final size:24
Alignment explanation
Indices: 39448--39515 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
39438 TGTATTAATA
39448 ATTTATTATTAAAATATAAAAATT
1 ATTTATTATTAAAATATAAAAATT
39472 ATTTATGT-TTAATAATATTAAAGAATT
1 ATTTAT-TATTAA-AATA-TAAA-AATT
* **
39499 ATTAAAAATTAAAATAT
1 ATTTATTATTAAAATAT
39516 TAAAGACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
24 10 0.28
25 6 0.17
26 8 0.22
27 12 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (24 bp):
ATTTATTATTAAAATATAAAAATT
Found at i:39514 original size:26 final size:26
Alignment explanation
Indices: 39455--39521 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
39445 ATAATTTATT
* **
39455 ATTAAAATA-TAAA-AATTATTTATG
1 ATTAAAATATTAAAGAATTATTAAAA
*
39479 TTTAATAATATTAAAGAATTATTAAAA
1 ATTAA-AATATTAAAGAATTATTAAAA
39506 ATTAAAATATTAAAGA
1 ATTAAAATATTAAAGA
39522 CTTTTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.11
25 4 0.11
26 15 0.43
27 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
ATTAAAATATTAAAGAATTATTAAAA
Found at i:40120 original size:16 final size:18
Alignment explanation
Indices: 40099--40138 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
40089 AATATTGATA
40099 TTAATAAAATTA-TA-TT
1 TTAATAAAATTATTATTT
*
40115 TTAATAATATTATTATTT
1 TTAATAAAATTATTATTT
40133 TTAATA
1 TTAATA
40139 TTAATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATAAAATTATTATTT
Found at i:41307 original size:22 final size:23
Alignment explanation
Indices: 41259--41308 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
41249 ATATTTTTAA
41259 TTAAA-TTTAATTATAAAAATAT
1 TTAAATTTTAATTATAAAAATAT
* * *
41281 ATAAATTTTAA-TATAAAATTTT
1 TTAAATTTTAATTATAAAAATAT
41303 TTAAAT
1 TTAAAT
41309 GTTATTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAATTTTAATTATAAAAATAT
Found at i:43001 original size:20 final size:18
Alignment explanation
Indices: 42967--43004 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
42957 TATAAAAGTG
42967 TTTTAATTAAATTAAATA
1 TTTTAATTAAATTAAATA
42985 TTTTAATTATAAGTTAAATA
1 TTTTAATTA-AA-TTAAATA
43005 AATATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTAATTAAATTAAATA
Found at i:43015 original size:25 final size:25
Alignment explanation
Indices: 42973--43021 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42963 AGTGTTTTAA
* *
42973 TTAAATTAAATATTTTAATTATAAG
1 TTAAATTAAATATATTAATAATAAG
42998 TTAAA-TAAATATAATTAATAATAA
1 TTAAATTAAATAT-ATTAATAATAA
43022 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAAATTAAATATATTAATAATAAG
Found at i:43835 original size:30 final size:30
Alignment explanation
Indices: 43799--43855 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
43789 CCATATGCCT
43799 ATGCTCAAGCACAATGATGAATAATAACTG
1 ATGCTCAAGCACAATGATGAATAATAACTG
43829 ATGCTCAAGCACAATGATGAATAATAA
1 ATGCTCAAGCACAATGATGAATAATAA
43856 TAATGGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (30 bp):
ATGCTCAAGCACAATGATGAATAATAACTG
Found at i:43920 original size:33 final size:34
Alignment explanation
Indices: 43857--43926 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
43847 GAATAATAAT
43857 AATGGCAAACCACCAAATCACCCATTTAATCAAC
1 AATGGCAAACCACCAAATCACCCATTTAATCAAC
*
43891 AATGGTAAACCACCAAATCA-CCATTTAATCAAC
1 AATGGCAAACCACCAAATCACCCATTTAATCAAC
43924 AAT
1 AAT
43927 TCTCTCACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 16 0.46
34 19 0.54
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.20
Consensus pattern (34 bp):
AATGGCAAACCACCAAATCACCCATTTAATCAAC
Done.