Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold583
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: 49921
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1385 original size:17 final size:17
Alignment explanation
Indices: 1365--1403 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1355 AATTTTTCTT
1365 AAAAAAAATTAAATTTG
1 AAAAAAAATTAAATTTG
* *
1382 AAAAAATATTAATTTTG
1 AAAAAAAATTAAATTTG
*
1399 CAAAA
1 AAAAA
1404 TTTTATATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (17 bp):
AAAAAAAATTAAATTTG
Found at i:1874 original size:13 final size:14
Alignment explanation
Indices: 1846--1872 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1836 ATATTTTATT
1846 TTAATACTTAAAAA
1 TTAATACTTAAAAA
1860 TTAATACTTAAAA
1 TTAATACTTAAAA
1873 TTTATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAATACTTAAAAA
Found at i:2435 original size:2 final size:2
Alignment explanation
Indices: 2430--2469 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2420 TACAAGTAAC
2430 AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2469 A
1 A
2470 CTTACATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2447 original size:12 final size:12
Alignment explanation
Indices: 2430--2469 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
2420 TACAAGTAAC
2430 ATATATATATAT
1 ATATATATATAT
2442 ATATATATA-AT
1 ATATATATATAT
2453 ATA-ATATATA-
1 ATATATATATAT
2463 ATATATA
1 ATATATA
2470 CTTACATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.31
11 9 0.35
12 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATATATAT
Found at i:12027 original size:2 final size:2
Alignment explanation
Indices: 12014--12048 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12004 CTTCATTTAC
* *
12014 GT GT GT GC GT GT GT GT GT GT GT GT GT GT GT CT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
12049 ATGCTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.49, T:0.46
Consensus pattern (2 bp):
GT
Found at i:13143 original size:22 final size:21
Alignment explanation
Indices: 13115--13158 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
13105 TAGGCTTCGA
13115 ATTATGTTAGT-ATGAGGTTAGC
1 ATTATGTTA-TAATGA-GTTAGC
13137 ATTATGTTATAATGAGTTAGC
1 ATTATGTTATAATGAGTTAGC
13158 A
1 A
13159 CTTTTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (21 bp):
ATTATGTTATAATGAGTTAGC
Found at i:22339 original size:2 final size:2
Alignment explanation
Indices: 22332--22359 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22322 TAACTTGCCT
22332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22360 AAAGAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22494 original size:12 final size:13
Alignment explanation
Indices: 22469--22497 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22459 AAAGAATAAT
22469 TTTATTTTTATTA
1 TTTATTTTTATTA
22482 TTTATTTTT-TTA
1 TTTATTTTTATTA
22494 TTTA
1 TTTA
22498 AATTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTATTA
Found at i:22662 original size:18 final size:19
Alignment explanation
Indices: 22629--22665 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
22619 TATTTTATTT
22629 TATTATTTAATATATTAAA
1 TATTATTTAATATATTAAA
*
22648 TATTATTT-TTATATTAAA
1 TATTATTTAATATATTAAA
22666 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATTTAATATATTAAA
Found at i:22807 original size:15 final size:16
Alignment explanation
Indices: 22787--22823 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
22777 ATGTTATTTT
22787 TTAAATTTAA-TTAAA
1 TTAAATTTAAGTTAAA
*
22802 TTAAATTTAAGTTAAT
1 TTAAATTTAAGTTAAA
22818 TTAAAT
1 TTAAAT
22824 ATTTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TTAAATTTAAGTTAAA
Found at i:22829 original size:18 final size:19
Alignment explanation
Indices: 22806--22844 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
22796 ATTAAATTAA
22806 ATTTAAGTTA-ATTTAAAT
1 ATTTAAGTTATATTTAAAT
*
22824 ATTTAATTTATTATTTAAAT
1 ATTTAAGTTA-TATTTAAAT
22844 A
1 A
22845 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTAAGTTATATTTAAAT
Found at i:23948 original size:15 final size:17
Alignment explanation
Indices: 23930--23966 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
23920 TTTAAAATTA
23930 TAAATA-TTT-AATATC
1 TAAATATTTTAAATATC
23945 TAAATATTTTAAATATC
1 TAAATATTTTAAATATC
23962 -AAATA
1 TAAATA
23967 AATAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
17 6 0.30
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATTTTAAATATC
Found at i:24040 original size:14 final size:15
Alignment explanation
Indices: 24023--24056 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
24013 TTAAATAGTC
24023 TAATTTAATT-AATA
1 TAATTTAATTAAATA
*
24037 TAATTTATTTAAATA
1 TAATTTAATTAAATA
24052 TAATT
1 TAATT
24057 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTTAATTAAATA
Found at i:25513 original size:16 final size:16
Alignment explanation
Indices: 25494--25525 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25484 TTTAACTCAC
*
25494 ATGAATTTAATTATTT
1 ATGAATTTAAATATTT
25510 ATGAATTTAAATATTT
1 ATGAATTTAAATATTT
25526 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATGAATTTAAATATTT
Found at i:27402 original size:17 final size:15
Alignment explanation
Indices: 27365--27396 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27355 GGTAAAATTT
27365 TTTA-TAATATATTA
1 TTTATTAATATATTA
27379 TTTATTAATATATT-
1 TTTATTAATATATTA
27393 TTTA
1 TTTA
27397 ATATTAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTAATATATTA
Found at i:28124 original size:16 final size:16
Alignment explanation
Indices: 28105--28154 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
28095 TCAAGTTTAG
28105 ATCATTTCGAATTCAA
1 ATCATTTCGAATTCAA
*
28121 ATCATTAT-GAATTCGA
1 ATCATT-TCGAATTCAA
*
28137 ATCATTTCGGATTCAA
1 ATCATTTCGAATTCAA
28153 AT
1 AT
28155 TCGAGTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (16 bp):
ATCATTTCGAATTCAA
Found at i:28416 original size:21 final size:20
Alignment explanation
Indices: 28383--28421 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28373 AATAAATATA
28383 ATTTTTAGAAAATAATATTTG
1 ATTTTTAGAAAAT-ATATTTG
**
28404 ATTTTTATTAAATATATT
1 ATTTTTAGAAAATATATT
28422 ATGTAGGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTTAGAAAATATATTTG
Found at i:28532 original size:20 final size:19
Alignment explanation
Indices: 28492--28538 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
28482 ATTATATTAA
28492 TAAAAAATTAATTTTAGAT
1 TAAAAAATTAATTTTAGAT
**
28511 TAAGAAAATTAATTTTCTAT
1 TAA-AAAATTAATTTTAGAT
28531 TAAAAAAT
1 TAAAAAAT
28539 AGGTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
TAAAAAATTAATTTTAGAT
Found at i:31985 original size:18 final size:18
Alignment explanation
Indices: 31964--32014 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
31954 GGTTAAGAGA
31964 TTATAAATAATTTTATTT
1 TTATAAATAATTTTATTT
31982 TTATTAAAT-A--TTATTT
1 TTA-TAAATAATTTTATTT
* *
31998 TTAAAAATAATTATATT
1 TTATAAATAATTTTATT
32015 ATATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
18 8 0.30
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATAAATAATTTTATTT
Found at i:44440 original size:2 final size:2
Alignment explanation
Indices: 44433--44461 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44423 ATAAAATTTT
44433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44462 GCAATGTAGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44965 original size:18 final size:17
Alignment explanation
Indices: 44921--44970 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
44911 TATGATACGA
44921 TTTAATTAAAATAAATTT
1 TTTAATT-AAATAAATTT
* *
44939 TTATCATTAAATATATTAT
1 TT-TAATTAAATAAATT-T
44958 TTTAATTAAATAA
1 TTTAATTAAATAA
44971 TATAACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATTAAATAAATTT
Found at i:46651 original size:25 final size:23
Alignment explanation
Indices: 46622--46667 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
46612 AATATTATCT
46622 ATATAATATAATATAAAAAAATTAC
1 ATATAAT-TAAT-TAAAAAAATTAC
*
46647 ATATAATTAATTAATAAAATT
1 ATATAATTAATTAAAAAAATT
46668 TACAACTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAATTAATTAAAAAAATTAC
Found at i:47517 original size:44 final size:45
Alignment explanation
Indices: 47454--47548 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 45
47444 ATATAAACAA
* **
47454 AAACA-AATAACAAAATGCAAAAAGTAATTAAAAGAATTACCTTC
1 AAACATAATAACAAAATGCAAAAAATAATTAAAAGAATTACCCCC
*
47498 AAACATAA-AACAAAATGCAAAAAATAATTAAAAGTATTACCCCC
1 AAACATAATAACAAAATGCAAAAAATAATTAAAAGAATTACCCCC
47542 AAACATA
1 AAACATA
47549 GTTTTTAGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (45 bp):
AAACATAATAACAAAATGCAAAAAATAATTAAAAGAATTACCCCC
Found at i:47761 original size:58 final size:59
Alignment explanation
Indices: 47657--47834 Score: 215
Period size: 58 Copynumber: 3.1 Consensus size: 59
47647 CCATATTAAA
* * ** *
47657 TATTTT-AAA-TT-AATCAAATCAAATCTAATTTAATTAAATATATGATTCATGATAAT
1 TATTTTAAAATTTAAATTAAATCAAATATAAAATAATTAAATATATGATTTATGATAAT
*
47713 TATTTTAAAATTTAAATTAAAT-TAAT-TCAAAATAATTAAA-AGTATGATTTATGATAAT
1 TATTTTAAAATTTAAATTAAATCAAATAT-AAAATAATTAAATA-TATGATTTATGATAAT
* * *
47771 TATTTTAAAATTTAGATTAAATCAAATATAAAATAATTAAATACATCATTTATGATAAT
1 TATTTTAAAATTTAAATTAAATCAAATATAAAATAATTAAATATATGATTTATGATAAT
47830 TATTT
1 TATTT
47835 AAAGCAATTT
Statistics
Matches: 105, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
56 6 0.06
57 5 0.05
58 51 0.49
59 41 0.39
60 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (59 bp):
TATTTTAAAATTTAAATTAAATCAAATATAAAATAATTAAATATATGATTTATGATAAT
Found at i:47855 original size:59 final size:57
Alignment explanation
Indices: 47705--47848 Score: 132
Period size: 59 Copynumber: 2.4 Consensus size: 57
47695 TATATGATTC
* * * * *
47705 ATGATAATTATTTTAAAATTTAAATTA--AATTAATTCAAAATAATTAAAAGTATGATTT
1 ATGATAATTATTTAAAAATTTACATTATCAAAT-A-T-AAAATAATTAAAAGCATCATTT
* *
47763 ATGATAATTATTTTAAAATTTAGATTAAATCAAATATAAAATAATTAAATA-CATCATTT
1 ATGATAATTATTTAAAAATTTACATT--ATCAAATATAAAATAATTAAA-AGCATCATTT
47822 ATGATAATTATTTAAAGCAATTTACAT
1 ATGATAATTATTTAAA--AATTTACAT
47849 GTTCAAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
58 25 0.34
59 33 0.45
60 3 0.04
61 9 0.12
62 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (57 bp):
ATGATAATTATTTAAAAATTTACATTATCAAATATAAAATAATTAAAAGCATCATTT
Found at i:48913 original size:14 final size:14
Alignment explanation
Indices: 48865--48924 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
48855 GTATATTTGA
* *
48865 ATTAATATTTAATA
1 ATTAAAATTTAATT
*
48879 ATTAAAATTT-TTT
1 ATTAAAATTTAATT
*
48892 ATTTAAATTTAATT
1 ATTAAAATTTAATT
* *
48906 ATTAAAATATAAAT
1 ATTAAAATTTAATT
48920 ATTAA
1 ATTAA
48925 TATAATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAAAATTTAATT
Done.