Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2246
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: 156925
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
File 2 of 2
Found at i:131569 original size:17 final size:17
Alignment explanation
Indices: 131535--131617 Score: 68
Period size: 17 Copynumber: 5.1 Consensus size: 17
131525 TTTCGTGAAT
* *
131535 AATTA-TATCAAATTTA
1 AATTATTATTAAATATA
131551 AATTATTATTAAATATA
1 AATTATTATTAAATATA
*
131568 AAATATTA--AAATATA
1 AATTATTATTAAATATA
*
131583 AA-TATCT-TTAAATTTA
1 AATTAT-TATTAAATATA
* *
131599 ATTTATTACTAAATATA
1 AATTATTATTAAATATA
131616 AA
1 AA
131618 ACAGTAAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.06
15 10 0.19
16 13 0.25
17 27 0.51
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTATTATTAAATATA
Found at i:131576 original size:14 final size:15
Alignment explanation
Indices: 131557--131656 Score: 51
Period size: 15 Copynumber: 6.5 Consensus size: 15
131547 TTTAAATTAT
131557 TATT-AAATATAAAA
1 TATTAAAATATAAAA
131571 TATTAAAATATAAATA
1 TATTAAAATATAAA-A
* * * **
131587 TCTTTAAATTTAATT
1 TATTAAAATATAAAA
131602 TATTACTAAATATAAAA
1 TATTA--AAATATAAAA
* * *
131619 CAGTAAAACAT-AAA
1 TATTAAAATATAAAA
*
131633 TATTATTAAATGTAAAA
1 TATTA--AAATATAAAA
*
131650 TAATAAA
1 TATTAAA
131657 TACAAATATT
Statistics
Matches: 61, Mismatches: 18, Indels: 13
0.66 0.20 0.14
Matches are distributed among these distances:
14 10 0.16
15 19 0.31
16 15 0.25
17 17 0.28
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (15 bp):
TATTAAAATATAAAA
Found at i:131612 original size:48 final size:48
Alignment explanation
Indices: 131544--131648 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
131534 TAATTATATC
* * * *
131544 AAATTTAAATTATTATTAAATATAAAATATTAAAATATAAATATCT-TT
1 AAATTTAAATTATTACTAAATATAAAACAGTAAAACATAAATAT-TATT
*
131592 AAATTTAATTTATTACTAAATATAAAACAGTAAAACATAAATATTATT
1 AAATTTAAATTATTACTAAATATAAAACAGTAAAACATAAATATTATT
*
131640 AAATGTAAA
1 AAATTTAAA
131649 ATAATAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (48 bp):
AAATTTAAATTATTACTAAATATAAAACAGTAAAACATAAATATTATT
Found at i:133782 original size:19 final size:19
Alignment explanation
Indices: 133746--133783 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
133736 TTAATTTTTT
*
133746 ATTATAACTTTTTAAAAAA
1 ATTATAACTTCTTAAAAAA
133765 ATTATTAACTTCTTAAAAA
1 ATTA-TAACTTCTTAAAAA
133784 CCTATCTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAACTTCTTAAAAAA
Found at i:133886 original size:24 final size:24
Alignment explanation
Indices: 133833--133884 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
133823 TAAAACTAAC
*
133833 TATTTAATAAAAAATTCACTTTTT
1 TATTTAATAAAAAATTCAATTTTT
133857 TATTTAA-AAAAAATATCAA-TTTT
1 TATTTAATAAAAAAT-TCAATTTTT
133880 TATTT
1 TATTT
133885 TATTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTAATAAAAAATTCAATTTTT
Found at i:134028 original size:15 final size:16
Alignment explanation
Indices: 134002--134032 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
133992 ATATTAAATA
134002 TTAAATATTTATATTT
1 TTAAATATTTATATTT
134018 TTAAA-ATTTATATTT
1 TTAAATATTTATATTT
134033 ACATATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAAATATTTATATTT
Found at i:134091 original size:2 final size:2
Alignment explanation
Indices: 134084--134111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
134074 GTATATTTGC
134084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134112 TACTAAAGAA
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):
AT
Found at i:142485 original size:58 final size:59
Alignment explanation
Indices: 142340--142491 Score: 132
Period size: 58 Copynumber: 2.6 Consensus size: 59
142330 CCATAGATAC
* * *
142340 ACAAATTATCTTAAATAGT-TTTAAAATGCATGAAAAATGCTAAATGATCCCTAGATTATG
1 ACAAATTA-CTAAAATA-TCTTTAAAATGCATGAAAAATGCTAAATGATCCCTAAAATATG
** * ** * * *
142400 GTAAATTACTAAAAGGA-CCATAGAATGCAT-AAAATTGCATAAATGAT-CTTAAAATATG
1 ACAAATTACTAAAA-TATCTTTAAAATGCATGAAAAATGC-TAAATGATCCCTAAAATATG
*
142458 ACAAATTACTAAAATATCTTTAAAATGCAGGAAA
1 ACAAATTACTAAAATATCTTTAAAATGCATGAAA
142492 TAACAAAATG
Statistics
Matches: 69, Mismatches: 18, Indels: 11
0.70 0.18 0.11
Matches are distributed among these distances:
57 1 0.01
58 36 0.52
59 25 0.36
60 7 0.10
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (59 bp):
ACAAATTACTAAAATATCTTTAAAATGCATGAAAAATGCTAAATGATCCCTAAAATATG
Found at i:143600 original size:30 final size:31
Alignment explanation
Indices: 143549--143631 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 31
143539 TTAATTTAAA
*
143549 TTAATATTTAATAATTAAAAAT-TTTTTTAT
1 TTAATATTTAATAAATAAAAATATTTTTTAT
143579 TTAA-ATTTAATTAAATAAAAATAATTTTTTAT
1 TTAATATTTAA-TAAATAAAAAT-ATTTTTTAT
*
143611 TT-TTA-TTAAT-AATAAAAATAT
1 TTAATATTTAATAAATAAAAATAT
143632 AAATAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 2 0.04
29 15 0.32
30 15 0.32
31 4 0.09
32 11 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTAATATTTAATAAATAAAAATATTTTTTAT
Found at i:143918 original size:15 final size:16
Alignment explanation
Indices: 143880--143931 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
143870 AATTAAAATT
143880 ATTTTAATTAATTTAA
1 ATTTTAATTAATTTAA
*
143896 A-TTGAATTAA-TTAA
1 ATTTTAATTAATTTAA
* *
143910 ATTTTAATT-TTTTAT
1 ATTTTAATTAATTTAA
143925 ATTTTAA
1 ATTTTAA
143932 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 5 0.17
15 24 0.80
16 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTTAATTAATTTAA
Found at i:143936 original size:16 final size:15
Alignment explanation
Indices: 143910--143948 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
143900 AATTAATTAA
143910 ATTTT-AATTTTTTAT
1 ATTTTAAATTTTTT-T
143925 ATTTTAAATTTTTTT
1 ATTTTAAATTTTTTT
143940 ATTTTAAAT
1 ATTTTAAAT
143949 AAGTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTAAATTTTTTT
Found at i:144491 original size:13 final size:13
Alignment explanation
Indices: 144473--144506 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
144463 ACACTTCGAG
144473 ATTTTTTATTTCT
1 ATTTTTTATTTCT
*
144486 ATTTTTTTTTTCT
1 ATTTTTTATTTCT
*
144499 GTTTTTTA
1 ATTTTTTA
144507 CCTTTTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (13 bp):
ATTTTTTATTTCT
Found at i:144728 original size:22 final size:22
Alignment explanation
Indices: 144703--144744 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
144693 AAAAATTATT
144703 TTTATA-TTAATATTAATATATA
1 TTTATAGTTAA-ATTAATATATA
*
144725 TTTATAGTTAAATTTATATA
1 TTTATAGTTAAATTAATATA
144745 AAAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTATAGTTAAATTAATATATA
Found at i:145496 original size:20 final size:20
Alignment explanation
Indices: 145453--145501 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
145443 ATTTTATTTT
* *
145453 TTTGTTTTAGAATTTTTTATA
1 TTTG-TTTAGAATTTTTAAAA
145474 TTTGTTTAGAATTTTTAAAA
1 TTTGTTTAGAATTTTTAAAA
*
145494 TTTATTTA
1 TTTGTTTA
145502 ATATTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTGTTTAGAATTTTTAAAA
Found at i:145740 original size:2 final size:2
Alignment explanation
Indices: 145733--145765 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
145723 TAAGGTCCTC
145733 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 A
145766 AACTTATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:146878 original size:23 final size:23
Alignment explanation
Indices: 146852--146895 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
146842 TTTTTTAATA
146852 AAATATATCTT-ATGTATATATGT
1 AAATATATCTTAAT-TATATATGT
*
146875 AAATATATTTTAATTATATAT
1 AAATATATCTTAATTATATAT
146896 ATAAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (23 bp):
AAATATATCTTAATTATATATGT
Found at i:147144 original size:16 final size:17
Alignment explanation
Indices: 147107--147146 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
147097 GTAAATATAA
147107 ATTTAAAAATTATAAAT
1 ATTTAAAAATTATAAAT
*
147124 ATTTAAAATTTA-AAAT
1 ATTTAAAAATTATAAAT
*
147140 TTTTAAA
1 ATTTAAA
147147 CATCAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAAAAATTATAAAT
Found at i:149593 original size:34 final size:34
Alignment explanation
Indices: 149541--149643 Score: 136
Period size: 34 Copynumber: 3.0 Consensus size: 34
149531 ATTTTAAATA
* *
149541 GAGATTTGGGTAGCTTACCATTATTGATTAAATGG
1 GAGATTT-GGTAGGTTACCATTGTTGATTAAATGG
* *
149576 GTGATTTGGT-GGTTTACCATTGTTGACTAAATGG
1 GAGATTTGGTAGG-TTACCATTGTTGATTAAATGG
*
149610 GAGATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 GAGATTTGGTAGGTTACCATTGTTGATTAAATGG
149644 TGGTTTTTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
33 1 0.02
34 50 0.85
35 8 0.14
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (34 bp):
GAGATTTGGTAGGTTACCATTGTTGATTAAATGG
Found at i:150335 original size:32 final size:32
Alignment explanation
Indices: 150227--150324 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 32
150217 AAATTTTTAA
* *
150227 ATATGATATAAT---TATATAATATAAGTATG
1 ATATGATATAATAAATAAATAATATAACTATG
* * *
150256 ATAT-AAAAAATTAAA-ATATAATATAACTATG
1 ATATGATATAA-TAAATAAATAATATAACTATG
150287 ATATGATATAATAAATAAATAATATGAA-TATG
1 ATATGATATAATAAATAAATAATAT-AACTATG
150319 ATATGA
1 ATATGA
150325 ATTTATAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 4 0.07
29 5 0.09
31 23 0.41
32 22 0.39
33 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (32 bp):
ATATGATATAATAAATAAATAATATAACTATG
Found at i:151444 original size:2 final size:2
Alignment explanation
Indices: 151431--151466 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
151421 GAGTAATAAC
*
151431 TA TA TA TG 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 TA TA TA TA
151467 CACTATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151679 original size:2 final size:2
Alignment explanation
Indices: 151672--151697 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
151662 ACCTAATTCT
151672 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
151698 ATAGGTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152165 original size:29 final size:30
Alignment explanation
Indices: 152102--152179 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
152092 ATGTTATCTC
** *
152102 ATTAATAAATAAATATAAAATTTTTAATTT
1 ATTAATAAATAAATATAAAAAATTTAACTT
*
152132 TTTAA-AAATAAATATAAATAAATTT-ACTT
1 ATTAATAAATAAATATAAA-AAATTTAACTT
152161 ATTAATAAA-AAATATAAAA
1 ATTAATAAATAAATATAAAA
152180 TGATTCACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.02
29 29 0.71
30 11 0.27
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
ATTAATAAATAAATATAAAAAATTTAACTT
Found at i:154968 original size:30 final size:30
Alignment explanation
Indices: 154932--155000 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
154922 TGATAAAAAT
* *
154932 TTTTTAAAAGATCATAAATGAT-TAATATAA
1 TTTTTAAAAG-TCATAAATAATAAAATATAA
* *
154962 TTTTTAAAAGTTATATATAATAAAATATAA
1 TTTTTAAAAGTCATAAATAATAAAATATAA
154992 TTTTTAAAA
1 TTTTTAAAA
155001 TTATAGATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 8 0.24
30 26 0.76
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (30 bp):
TTTTTAAAAGTCATAAATAATAAAATATAA
Found at i:155062 original size:29 final size:29
Alignment explanation
Indices: 154932--155060 Score: 93
Period size: 29 Copynumber: 4.4 Consensus size: 29
154922 TGATAAAAAT
* * * * *
154932 TTTTTAAAAGATCATAAATGATTAATATAA
1 TTTTTAAAA-ATTATAGATAATAAATGTAA
* * *
154962 TTTTTAAAAGTTATATATAATAAAATATAA
1 TTTTTAAAAATTATAGATAAT-AAATGTAA
154992 TTTTT-AAAATTATAGATAA-AAATG-AA
1 TTTTTAAAAATTATAGATAATAAATGTAA
* * * *
155018 ATATTAGTAAAATTGTGGATAATAAATGTAA
1 TTTTTA--AAAATTATAGATAATAAATGTAA
155049 TTTTTAAAAATT
1 TTTTTAAAAATT
155061 GTAAAAAATA
Statistics
Matches: 79, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
26 5 0.06
27 4 0.05
29 38 0.48
30 26 0.33
31 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTTTAAAAATTATAGATAATAAATGTAA
Found at i:155928 original size:2 final size:2
Alignment explanation
Indices: 155853--155919 Score: 68
Period size: 2 Copynumber: 34.0 Consensus size: 2
155843 AGTATGCACA
* * *
155853 AT AT AT AT AGT AT -T A- AT AT AT AT TT AT AT ACT -T TT GT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
155894 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
155920 GACTATATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
1 3 0.05
2 50 0.89
3 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:156460 original size:20 final size:20
Alignment explanation
Indices: 156412--156460 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
156402 TTTTTAATTA
156412 TAAT-TTTTAAAATCTATAT
1 TAATATTTTAAAATCTATAT
* *
156431 TTATCA-TTTAAAATCTCTAT
1 TAAT-ATTTTAAAATCTATAT
156451 TAATATTTTA
1 TAATATTTTA
156461 GTTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATATTTTAAAATCTATAT
Done.