Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold495
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: 586005
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 5
Found at i:567273 original size:61 final size:60
Alignment explanation
Indices: 567185--567359 Score: 183
Period size: 61 Copynumber: 2.9 Consensus size: 60
567175 AAATTAAATT
* * * * **
567185 AAATTAATAGTTTGTTTAAGTATAAATTAAAAATTAAAAATTTATTTAGGTAAAAAATTAA
1 AAATTAAAAATTTATTTAAGTAAAAATTAAAAATTAAAAATTTATTTAAATAAAAAA-TAA
** * *
567246 AGCTTAAAAATTTATTTAGGTAAAAATTAAAAATTAAAAATTTATTTAAATATAAAATAA
1 AAATTAAAAATTTATTTAAGTAAAAATTAAAAATTAAAAATTTATTTAAATAAAAAATAA
* * * * *
567306 AAATTAAAAATTTATTTGAGT-ATAA-TAAACATATATAGATTTATTTAAATAAAA
1 AAATTAAAAATTTATTTAAGTAAAAATTAAAAAT-TAAAAATTTATTTAAATAAAA
567360 TTATAAAATT
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
58 6 0.06
59 21 0.22
60 20 0.21
61 47 0.50
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (60 bp):
AAATTAAAAATTTATTTAAGTAAAAATTAAAAATTAAAAATTTATTTAAATAAAAAATAA
Found at i:568009 original size:13 final size:15
Alignment explanation
Indices: 567989--568029 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
567979 ACAAATTAAC
567989 ATAAATTAATATAA-
1 ATAAATTAATATAAT
*
568003 A-AAATTAAAATAAT
1 ATAAATTAATATAAT
568017 ATAATATTAATAT
1 ATAA-ATTAATAT
568030 CATTTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 2 0.09
16 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATTAATATAAT
Found at i:569298 original size:19 final size:18
Alignment explanation
Indices: 569256--569299 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
569246 ATCTAACTTG
*
569256 ATTTAAAATTATATTTTT
1 ATTTAAAATAATATTTTT
*
569274 AATTAAAATAATATATTTT
1 ATTTAAAATAATAT-TTTT
569293 ATTTAAA
1 ATTTAAA
569300 TTTAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAAATAATATTTTT
Found at i:569300 original size:18 final size:20
Alignment explanation
Indices: 569256--569300 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
569246 ATCTAACTTG
*
569256 ATTTAAA-ATTATATTTTTA
1 ATTTAAATAATATATTTTTA
*
569275 ATTAAAATAATATA-TTTT-
1 ATTTAAATAATATATTTTTA
569293 ATTTAAAT
1 ATTTAAAT
569301 TTAATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATAATATATTTTTA
Found at i:569320 original size:21 final size:21
Alignment explanation
Indices: 569296--569335 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
569286 ATATTTTATT
569296 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
569317 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
569336 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:572443 original size:2 final size:2
Alignment explanation
Indices: 572438--572462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
572428 AAAAAAATTG
572438 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 T
572463 CCATCTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:572998 original size:11 final size:11
Alignment explanation
Indices: 572984--573032 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
572974 TTATTTTCAA
572984 TTTTTTTTTAC
1 TTTTTTTTTAC
*
572995 TTTTTTTTTCAA
1 TTTTTTTTT-AC
573007 TTTTTTTTTAC
1 TTTTTTTTTAC
*
573018 TTTTTTTTTTC
1 TTTTTTTTTAC
573029 TTTT
1 TTTT
573033 CTATTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTAC
Found at i:573006 original size:23 final size:23
Alignment explanation
Indices: 572977--573026 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
572967 GGGATCATTA
572977 TTTTCAATTTTTTTTTACTTTTT
1 TTTTCAATTTTTTTTTACTTTTT
573000 TTTTCAATTTTTTTTTACTTTTT
1 TTTTCAATTTTTTTTTACTTTTT
573023 TTTT
1 TTTT
573027 TCTTTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCAATTTTTTTTTACTTTTT
Found at i:576509 original size:20 final size:18
Alignment explanation
Indices: 576462--576553 Score: 77
Period size: 18 Copynumber: 5.1 Consensus size: 18
576452 AATTTATATA
576462 ATAAAA-ATTAT-TAATAT
1 ATAAAATATTATATAA-AT
576479 ATCAAAAT-TTATATAAAT
1 AT-AAAATATTATATAAAT
576497 ATAAAATATT-T-TAAAT
1 ATAAAATATTATATAAAT
* *
576513 ATAATTATAATATAATAAAAT
1 ATAA-AATATTAT-AT-AAAT
576534 ATATAAATATTATATAAAT
1 ATA-AAATATTATATAAAT
576553 A
1 A
576554 CATAAACCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
16 9 0.15
17 12 0.20
18 15 0.25
19 8 0.13
20 3 0.05
21 13 0.21
22 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATATTATATAAAT
Found at i:577737 original size:17 final size:16
Alignment explanation
Indices: 577706--577747 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
577696 CGTTATTTTC
*
577706 TAAAAAATTAGAAAAA
1 TAAAAAATTACAAAAA
577722 TAAAAAATTTACAAAAA
1 TAAAAAA-TTACAAAAA
*
577739 -AAAATATTA
1 TAAAAAATTA
577748 TTTTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 8 0.35
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
TAAAAAATTACAAAAA
Found at i:579618 original size:34 final size:34
Alignment explanation
Indices: 579573--579639 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
579563 TTCAAATATC
*
579573 TTAAATTTTATTTATGATTATTTGTGAACCAAAG
1 TTAAATTTTATTTATGATTATTAGTGAACCAAAG
* *
579607 TTAATTTTTATTTATGATTGTTAGTGAACCAAA
1 TTAAATTTTATTTATGATTATTAGTGAACCAAA
579640 TTTTACTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (34 bp):
TTAAATTTTATTTATGATTATTAGTGAACCAAAG
Found at i:580915 original size:77 final size:76
Alignment explanation
Indices: 580800--580945 Score: 211
Period size: 77 Copynumber: 1.9 Consensus size: 76
580790 TTAGTGTAAT
* * * * * *
580800 TAATTAGCTACTTAGAAGTATAATGACAAAATTTAATGAACTTGACATAAAATGATAAAATTTAA
1 TAATTAACTACTTAAAAATATAATGACAAAACTCAATGAACTTGACATAAAATGACAAAATTTAA
580865 TATTAATACTG
66 TATTAATACTG
* *
580876 TAATTAACTAGCTTAAAAATATAATGACAAAACTCAATGAACTTGACGTAAAATGACAACATTTA
1 TAATTAACTA-CTTAAAAATATAATGACAAAACTCAATGAACTTGACATAAAATGACAAAATTTA
580941 ATATT
65 ATATT
580946 GATCCATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
76 9 0.15
77 52 0.85
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (76 bp):
TAATTAACTACTTAAAAATATAATGACAAAACTCAATGAACTTGACATAAAATGACAAAATTTAA
TATTAATACTG
Found at i:582497 original size:2 final size:2
Alignment explanation
Indices: 582490--582524 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
582480 ATTAAGTCGT
582490 TA TA TA 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 TA TA TA T
582525 TTAACAGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:582970 original size:34 final size:34
Alignment explanation
Indices: 582927--583148 Score: 242
Period size: 34 Copynumber: 6.6 Consensus size: 34
582917 TTGATAAAAA
* *
582927 CTACCATTTAATCAACAATGGCAACCTACTAAAT
1 CTACCATTTAATCAACAATGGTAACCTACCAAAT
*
582961 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 CTACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
582995 C-ACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
* *
583029 -TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CTAC-CATTTAATCAACAATGGTAACCTACCAAAT
* *
583063 CTCCCATTTAGTCAACAAT-GTCAAACC-ACCAAAT
1 CTACCATTTAATCAACAATGGT--AACCTACCAAAT
*
583097 C-ACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
*
583131 C-ACTATTTAATCAACAAT
1 CTACCATTTAATCAACAAT
583149 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 15, Indels: 23
0.81 0.08 0.12
Matches are distributed among these distances:
33 23 0.14
34 130 0.80
35 9 0.06
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.27
Consensus pattern (34 bp):
CTACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:583107 original size:102 final size:102
Alignment explanation
Indices: 582931--583148 Score: 332
Period size: 102 Copynumber: 2.1 Consensus size: 102
582921 TAAAAACTAC
* *
582931 CATTTAATCAACAATGGCAACCTACTAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAAATC
* * **
582996 ACCCATTTAATCAATAATGGTAAGCTACCAAATTTCT
66 ACCCATTTAATCAACAATGGTAAACTACCAAATCACT
* * *
583033 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAAT-GTCAAACCACCAAAT
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGT-AAACCACCAAAT
583097 CACCCATTTAATCAACAATGGTAAACTACCAAATCACT
65 CACCCATTTAATCAACAATGGTAAACTACCAAATCACT
583135 -ATTTAATCAACAAT
1 CATTTAATCAACAAT
583149 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (102 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAAATC
ACCCATTTAATCAACAATGGTAAACTACCAAATCACT
Done.