Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold660
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: 24966
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:306 original size:17 final size:16
Alignment explanation
Indices: 284--319 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
274 GTACTATAAT
284 TATATTTAAAATATTTA
1 TATATTTAAAA-ATTTA
*
301 TATATTTAATAATTTA
1 TATATTTAAAAATTTA
317 TAT
1 TAT
320 TATATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTTAAAAATTTA
Found at i:590 original size:11 final size:10
Alignment explanation
Indices: 574--625 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
564 ATTGATTTAT
574 ATATTTAATTA
1 ATATTTAA-TA
585 ATATTTAATA
1 ATATTTAATA
595 ATATTTAA-A
1 ATATTTAATA
604 AT-TTTAATA
1 ATATTTAATA
613 TTATATTT-ATA
1 --ATATTTAATA
624 AT
1 AT
626 TTTTTTAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 5 0.14
9 6 0.16
10 10 0.27
11 13 0.35
12 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATTTAATA
Found at i:620 original size:20 final size:19
Alignment explanation
Indices: 571--628 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
561 TAAATTGATT
571 TATATATTTAATTAATATTTAA
1 TATATATTTAA--AAT-TTTAA
593 TA-ATATTTAAAATTTTAA
1 TATATATTTAAAATTTTAA
*
611 TATTATATTTATAATTTT
1 TA-TATATTTAAAATTTT
629 TTTAATCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.21
19 3 0.09
20 13 0.39
21 8 0.24
22 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATTTAAAATTTTAA
Found at i:1287 original size:2 final size:2
Alignment explanation
Indices: 1280--1316 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1270 AAGTTTTGGA
1280 AT AT AT AT AT 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 AT AT AT AT AT A
1317 AACTTTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4493 original size:23 final size:25
Alignment explanation
Indices: 4467--4528 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
4457 ATTTTTATAC
*
4467 GAATAAA-TTATAAATTTTT-TTCA
1 GAATAAACTTATAAATTTTTGTTAA
4490 GAATATAACTTAT-AATTTTTGTTAA
1 GAATA-AACTTATAAATTTTTGTTAA
*
4515 G-ATAAATTTATAAA
1 GAATAAACTTATAAA
4529 CTCTCTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 11 0.33
24 14 0.42
25 8 0.24
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (25 bp):
GAATAAACTTATAAATTTTTGTTAA
Found at i:4616 original size:46 final size:46
Alignment explanation
Indices: 4502--4662 Score: 157
Period size: 46 Copynumber: 3.5 Consensus size: 46
4492 ATATAACTTA
* * *
4502 TAATTTTTGT-TAAGATAAATTTATAAACTCTCTTCATAAAATAATTTA
1 TAATTTTTGTATAA-ATAAAATTATAAACTTTC-TCAT-AAATAATTTG
** *
4550 TAATTTTTGCGTGAAA-AAAATTATAAACTTTCTCATAAATTATTTG
1 TAATTTTTGTAT-AAATAAAATTATAAACTTTCTCATAAATAATTTG
* * * *
4596 TAATTTTTATATAAATAAAATTATAAA-TATTCTAACAAATAATTAG
1 TAATTTTTGTATAAATAAAATTATAAACT-TTCTCATAAATAATTTG
*
4642 TAACTTTTGTATAAATAAAAT
1 TAATTTTTGTATAAATAAAAT
4663 CATCTCATAA
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
45 4 0.04
46 60 0.63
47 4 0.04
48 23 0.24
49 2 0.02
50 2 0.02
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (46 bp):
TAATTTTTGTATAAATAAAATTATAAACTTTCTCATAAATAATTTG
Found at i:4936 original size:13 final size:13
Alignment explanation
Indices: 4920--4944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4910 ATCTTTTTAA
4920 AATATTTATATTT
1 AATATTTATATTT
4933 AATATTTATATT
1 AATATTTATATT
4945 AATTACTTAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:6418 original size:33 final size:33
Alignment explanation
Indices: 6377--6439 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
6367 TTATTGCTCT
*
6377 TCTTAACCCCTGTGATTGCCAAATAAGATGTCC
1 TCTTAACCCCTGTAATTGCCAAATAAGATGTCC
6410 TCTTAACCCCTGTAATTGCCAAATAAGATG
1 TCTTAACCCCTGTAATTGCCAAATAAGATG
6440 GTCTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (33 bp):
TCTTAACCCCTGTAATTGCCAAATAAGATGTCC
Found at i:9052 original size:29 final size:29
Alignment explanation
Indices: 9016--9073 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
9006 GCGTGTTAAC
9016 GTGATTAG-AGAGATAGCTGTCAATAACAA
1 GTGATTAGAAG-GATAGCTGTCAATAACAA
9045 GTGATTAGAAGGATAGCTGTCAATAACAA
1 GTGATTAGAAGGATAGCTGTCAATAACAA
9074 AATTATAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (29 bp):
GTGATTAGAAGGATAGCTGTCAATAACAA
Found at i:13682 original size:29 final size:29
Alignment explanation
Indices: 13646--13703 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
13636 GAGTGTTAAC
*
13646 GTGATTAGAGAGATAGTTGTCAATAACAA
1 GTGATTAGAGAGATAGCTGTCAATAACAA
*
13675 GTGATTAGAGGGATAGCTGTCAATAACAA
1 GTGATTAGAGAGATAGCTGTCAATAACAA
13704 AATTATAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (29 bp):
GTGATTAGAGAGATAGCTGTCAATAACAA
Found at i:13718 original size:29 final size:29
Alignment explanation
Indices: 13649--13718 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
13639 TGTTAACGTG
* *
13649 ATTAGA-GAGATAGTTGTCAATAACAAGTG
1 ATTAGAGGAGATAGCTGTCAATAACAAG-A
13678 ATTAGAGG-GATAGCTGTCAATAACAA-A
1 ATTAGAGGAGATAGCTGTCAATAACAAGA
*
13705 ATTATAGGAAGATA
1 ATTAGAGG-AGATA
13719 AATTTAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 7 0.20
29 27 0.77
30 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (29 bp):
ATTAGAGGAGATAGCTGTCAATAACAAGA
Found at i:14534 original size:20 final size:20
Alignment explanation
Indices: 14504--14562 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
14494 TACTAAATTT
14504 TTTTAAATATTAAATAAATAA
1 TTTT-AATATTAAATAAATAA
14525 TTTTAATATTAAATAAAT-A
1 TTTTAATATTAAATAAATAA
14544 -TTTAATA-T-AATAAATAA
1 TTTTAATATTAAATAAATAA
14561 TT
1 TT
14563 AATAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 8 0.22
19 1 0.03
20 14 0.39
21 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAATATTAAATAAATAA
Found at i:14539 original size:16 final size:17
Alignment explanation
Indices: 14517--14562 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
14507 TAAATATTAA
14517 ATAAATAATTTTAATAT
1 ATAAATAATTTTAATAT
14534 -TAAATAAATATTTAATAT
1 ATAAAT-AAT-TTTAATAT
14552 AATAAATAATT
1 -ATAAATAATT
14563 AATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.20
17 3 0.12
18 9 0.36
19 3 0.12
20 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATAATTTTAATAT
Found at i:15282 original size:22 final size:23
Alignment explanation
Indices: 15257--15299 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
15247 TAAATTAATT
15257 TAAAT-TTAATTATAAA-AATAAA
1 TAAATATT-ATTATAAATAATAAA
15279 TAAATATTATTATAAATAATA
1 TAAATATTATTATAAATAATA
15300 TAATTAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATTATTATAAATAATAAA
Found at i:15729 original size:19 final size:18
Alignment explanation
Indices: 15701--15761 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
15691 TACATAAAAA
15701 AATA-TTTAATAAATTCAT
1 AATATTTTAAT-AATTCAT
* *
15719 AATTTTTTAATAATTTAT
1 AATATTTTAATAATTCAT
* * *
15737 AATATTTTAATGATTAAA
1 AATATTTTAATAATTCAT
15755 AATATTT
1 AATATTT
15762 AATTTATATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 30 0.83
19 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATTTTAATAATTCAT
Found at i:15738 original size:18 final size:19
Alignment explanation
Indices: 15701--15747 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
15691 TACATAAAAA
15701 AATA-TTTAATAAATTCAT
1 AATATTTTAATAAATTCAT
* *
15719 AATTTTTTAAT-AATTTAT
1 AATATTTTAATAAATTCAT
15737 AATATTTTAAT
1 AATATTTTAAT
15748 GATTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTTTAATAAATTCAT
Found at i:19264 original size:2 final size:2
Alignment explanation
Indices: 19252--19286 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19242 AAAATTGGCT
*
19252 AC AC TC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19287 GAGAGCTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:21679 original size:17 final size:17
Alignment explanation
Indices: 21659--21751 Score: 56
Period size: 17 Copynumber: 5.5 Consensus size: 17
21649 TTAATCAATG
21659 TAAAATATGATGATATT
1 TAAAATATGATGATATT
21676 TAAAATAT-AT-AT-TT
1 TAAAATATGATGATATT
21690 AATAAAA-ATGAT-ATAATAT
1 --TAAAATATGATGAT-AT-T
* *
21709 TATAAATTTTAATCGATA--
1 TA-AAA-TATGAT-GATATT
21727 TAAAATATGATGATATT
1 TAAAATATGATGATATT
21744 TAAAATAT
1 TAAAATAT
21752 ATATTTAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 26
0.66 0.04 0.29
Matches are distributed among these distances:
14 2 0.03
15 8 0.14
16 15 0.25
17 21 0.36
18 6 0.10
19 1 0.02
20 3 0.05
21 1 0.02
22 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (17 bp):
TAAAATATGATGATATT
Found at i:21698 original size:34 final size:34
Alignment explanation
Indices: 21660--21767 Score: 123
Period size: 34 Copynumber: 3.2 Consensus size: 34
21650 TAATCAATGT
21660 AAAATATGATGATATTTAAAATATATATTTAATA
1 AAAATATGATGATATTTAAAATATATATTTAATA
* * * **
21694 AAAATGAT-ATAATA-TTATAAAT-TTTAATCGATA
1 AAAAT-ATGATGATATTTA-AAATATATATTTAATA
21727 TAAAATATGATGATATTTAAAATATATATTTAATA
1 -AAAATATGATGATATTTAAAATATATATTTAATA
21762 AAAATA
1 AAAATA
21768 ATATATTATA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
33 12 0.21
34 34 0.59
35 12 0.21
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.40
Consensus pattern (34 bp):
AAAATATGATGATATTTAAAATATATATTTAATA
Found at i:21710 original size:68 final size:68
Alignment explanation
Indices: 21623--21786 Score: 258
Period size: 68 Copynumber: 2.4 Consensus size: 68
21613 TTTTATCTTT
* * *
21623 ATAAAAATAATACAGTATTATAAATTTTAATCAATGTAAAATATGATGATATTTAAAATATATAT
1 ATAAAAATAATATAATATTATAAATTTTAATCAATATAAAATATGATGATATTTAAAATATATAT
21688 TTA
66 TTA
* *
21691 ATAAAAATGATATAATATTATAAATTTTAATCGATATAAAATATGATGATATTTAAAATATATAT
1 ATAAAAATAATATAATATTATAAATTTTAATCAATATAAAATATGATGATATTTAAAATATATAT
21756 TTA
66 TTA
*
21759 ATAAAAATAATATATTA-TATATAATTTT
1 ATAAAAATAATATAATATTATA-AATTTT
21787 GTATAATATT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
67 4 0.05
68 84 0.95
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (68 bp):
ATAAAAATAATATAATATTATAAATTTTAATCAATATAAAATATGATGATATTTAAAATATATAT
TTA
Found at i:23222 original size:17 final size:19
Alignment explanation
Indices: 23197--23234 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
23187 TCGAGATAAG
23197 TATTAAATAT-AA-ATATT
1 TATTAAATATGAATATATT
*
23214 TATTTAATATGAATATATT
1 TATTAAATATGAATATATT
23233 TA
1 TA
23235 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATTAAATATGAATATATT
Found at i:23619 original size:20 final size:21
Alignment explanation
Indices: 23596--23638 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
23586 TATAAAGTCC
23596 AACAATTTAACT-TAAAAAAA
1 AACAATTTAACTGTAAAAAAA
* *
23616 AACACTTTAATTGTAAAAAAA
1 AACAATTTAACTGTAAAAAAA
23637 AA
1 AA
23639 AAATGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AACAATTTAACTGTAAAAAAA
Done.