Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold423
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: 617052
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 6 of 6
Found at i:598851 original size:24 final size:24
Alignment explanation
Indices: 598823--598897 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
598813 TTCACTTAAT
598823 TTATCTCCAATCCAAATTTGTTTA
1 TTATCTCCAATCCAAATTTGTTTA
* *** *
598847 TTATCT--ATTAGGATTTTAG-TT-
1 TTATCTCCAATCCAAATTT-GTTTA
598868 TTATCTCCAATCCAAATTTGTTTA
1 TTATCTCCAATCCAAATTTGTTTA
598892 TTATCT
1 TTATCT
598898 ATTAGGATTT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 6 0.17
22 9 0.25
23 9 0.25
24 12 0.33
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATCTCCAATCCAAATTTGTTTA
Found at i:598886 original size:45 final size:45
Alignment explanation
Indices: 598822--598914 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
598812 ATTCACTTAA
598822 TTTATCTCCAATCCAAATTTGTTTATTATCTATTAGGATTTTAGT
1 TTTATCTCCAATCCAAATTTGTTTATTATCTATTAGGATTTTAGT
598867 TTTATCTCCAATCCAAATTTGTTTATTATCTATTAGGATTTTAGT
1 TTTATCTCCAATCCAAATTTGTTTATTATCTATTAGGATTTTAGT
598912 TTT
1 TTT
598915 GATATAACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (45 bp):
TTTATCTCCAATCCAAATTTGTTTATTATCTATTAGGATTTTAGT
Found at i:602123 original size:23 final size:23
Alignment explanation
Indices: 602093--602139 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
602083 TCGGCTCCTA
602093 CCCACATGTACATGCTTTCATAT
1 CCCACATGTACATGCTTTCATAT
602116 CCCACATGTACATGCTTTCATAT
1 CCCACATGTACATGCTTTCATAT
602139 C
1 C
602140 TTCAAACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (23 bp):
CCCACATGTACATGCTTTCATAT
Found at i:602483 original size:11 final size:11
Alignment explanation
Indices: 602443--602500 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
602433 GTCTAAAAAA
602443 TTTAT-TTAGTT
1 TTTATATTA-TT
602454 TATTATATTATT
1 T-TTATATTATT
**
602466 TAAATATTATT
1 TTTATATTATT
602477 TTTATATTAATT
1 TTTATATT-ATT
602489 TTTATA-TATT
1 TTTATATTATT
602499 TT
1 TT
602501 AATAATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 5 0.12
11 16 0.40
12 16 0.40
13 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTATATTATT
Found at i:602484 original size:22 final size:23
Alignment explanation
Indices: 602456--602541 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 23
602446 ATTTAGTTTA
602456 TTATATT-ATTTAAATATTATTT
1 TTATATTAATTTAAATATTATTT
**
602478 TTATATTAATTTTTATA-TATTT
1 TTATATTAATTTAAATATTATTT
* *
602500 TAATAATTAAATTTAAAAAAATTATTT
1 TTAT-ATT-AATTT--AAATATTATTT
602527 TTAT-TT--TTTAAATAT
1 TTATATTAATTTAAATAT
602542 GAATGCAGAC
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
20 5 0.10
22 18 0.36
23 10 0.20
24 5 0.10
25 2 0.04
26 2 0.04
27 8 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATATTAATTTAAATATTATTT
Found at i:603040 original size:2 final size:2
Alignment explanation
Indices: 603033--603076 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
603023 ATCATGGAGA
603033 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
603075 AT
1 AT
603077 TAAACCAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:603100 original size:26 final size:26
Alignment explanation
Indices: 603071--603124 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
603061 ATATATATAT
603071 ATATATTAAACCAACTGGTTTCTTTG
1 ATATATTAAACCAACTGGTTTCTTTG
*
603097 ATATATTAAAGCAACTGGTTTCTTTG
1 ATATATTAAACCAACTGGTTTCTTTG
603123 AT
1 AT
603125 TTGGGAGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (26 bp):
ATATATTAAACCAACTGGTTTCTTTG
Found at i:603445 original size:34 final size:35
Alignment explanation
Indices: 603401--603466 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
603391 ATTTTGAATT
* *
603401 ATTATTATTATTTGACATAAGTATAAATTTAAGAA
1 ATTATTATTATTTAACATAAATATAAATTTAAGAA
* *
603436 ATTA-TATTATTTAATATAAATATAATTTTAA
1 ATTATTATTATTTAACATAAATATAAATTTAA
603467 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (35 bp):
ATTATTATTATTTAACATAAATATAAATTTAAGAA
Found at i:603809 original size:21 final size:21
Alignment explanation
Indices: 603783--603826 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
603773 ATGAATTTTC
603783 ATCTTTAAGT-TTTTAAAAATA
1 ATCTTTAA-TCTTTTAAAAATA
* *
603804 ATCTTTTATCTTTTGAAAATA
1 ATCTTTAATCTTTTAAAAATA
603825 AT
1 AT
603827 TATTGATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
ATCTTTAATCTTTTAAAAATA
Found at i:603839 original size:22 final size:21
Alignment explanation
Indices: 603793--603839 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
603783 ATCTTTAAGT
*
603793 TTTTAAAAATAATCTTTTATC
1 TTTTAAAAATAATCTTTGATC
*
603814 TTTTGAAAATAAT-TATTGATC
1 TTTTAAAAATAATCT-TTGATC
603835 ATTTT
1 -TTTT
603840 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTAAAAATAATCTTTGATC
Found at i:603963 original size:22 final size:21
Alignment explanation
Indices: 603920--603963 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
603910 ATTTTAATAT
* *
603920 TTATAATTTTTTATCCATAAA
1 TTATAATTTTTTATCAAAAAA
*
603941 TTATAATATTTTTATTAAAAAA
1 TTATAAT-TTTTTATCAAAAAA
603963 T
1 T
603964 AATATCGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAATTTTTTATCAAAAAA
Found at i:605052 original size:27 final size:27
Alignment explanation
Indices: 605018--605081 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
605008 TAAAATTTAT
*
605018 ATAATAT-AAATTATTAATATATCAAAAA
1 ATAATATAAAAATA-TAATATAT-AAAAA
605046 A-AATATAAAAATATAATATATAAAAA
1 ATAATATAAAAATATAATATATAAAAA
605072 ATAATTATAA
1 ATAA-TATAA
605082 TATGAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.19
27 15 0.47
28 11 0.34
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAATATAAAAATATAATATATAAAAA
Found at i:605749 original size:18 final size:20
Alignment explanation
Indices: 605707--605750 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
605697 ATATTTTTAA
*
605707 ATTTTTATTATTTTAAATAT
1 ATTTTTAATATTTTAAATAT
605727 ATTTTTAATA-TTT-AATAT
1 ATTTTTAATATTTTAAATAT
605745 -TTTTTA
1 ATTTTTA
605751 TATAAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 3 0.13
20 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTAATATTTTAAATAT
Found at i:605753 original size:27 final size:27
Alignment explanation
Indices: 605697--605773 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
605687 TATTATCATA
* *
605697 ATATTTTTAAATTTTTATTATTTTAAAT
1 ATATTTTT-AATATTTAATATTTTAAAT
**
605725 ATATTTTTAATATTTAATATTTTTTAT
1 ATATTTTTAATATTTAATATTTTAAAT
* *
605752 ATAAATTTGAATATTTAA-ATTT
1 AT-ATTTTTAATATTTAATATTT
605774 AATTTCTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.50
28 21 0.50
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (27 bp):
ATATTTTTAATATTTAATATTTTAAAT
Found at i:615601 original size:12 final size:11
Alignment explanation
Indices: 615566--615646 Score: 80
Period size: 10 Copynumber: 7.5 Consensus size: 11
615556 ACAAATCGAT
*
615566 TTATATTTTTA
1 TTATATTTATA
615577 -TATATTTATA
1 TTATATTTATA
615587 TTATATTTCATA
1 TTATATTT-ATA
615599 TTAT-TTTATA
1 TTATATTTATA
*
615609 TTATTTTTTATA
1 TTA-TATTTATA
615621 TTATATTTA-A
1 TTATATTTATA
*
615631 TT-TTTTTATA
1 TTATATTTATA
615641 TCTATA
1 T-TATA
615647 ATGATTATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
9 5 0.08
10 20 0.34
11 17 0.29
12 17 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTATA
Found at i:615634 original size:17 final size:17
Alignment explanation
Indices: 615581--615634 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
615571 TTTTTATATA
*
615581 TTTATATTATATTTCAT
1 TTTATATTATATTTAAT
* * *
615598 ATTATTTTATA-TTATTT
1 TTTATATTATATTTA-AT
615615 TTTATATTATATTTAAT
1 TTTATATTATATTTAAT
615632 TTT
1 TTT
615635 TTTATATCTA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 2 0.07
17 23 0.82
18 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATATTATATTTAAT
Found at i:615637 original size:22 final size:23
Alignment explanation
Indices: 615577--615646 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 23
615567 TATATTTTTA
*
615577 TATATTTATATTATATTTCATAT
1 TATATTTATATTATTTTTCATAT
*
615600 TAT-TTTATATTATTTTTTATAT
1 TATATTTATATTATTTTTCATAT
615622 TATATTTA-ATT-TTTTT-ATAT
1 TATATTTATATTATTTTTCATAT
615642 CTATA
1 -TATA
615647 ATGATTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.09
21 9 0.21
22 23 0.53
23 7 0.16
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (23 bp):
TATATTTATATTATTTTTCATAT
Found at i:616997 original size:17 final size:18
Alignment explanation
Indices: 616977--617016 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
616967 TATCTGTCAT
616977 ATATCTA-AATCTATTAA
1 ATATCTATAATCTATTAA
*
616994 ATATC-ATAATTTATTAA
1 ATATCTATAATCTATTAA
617011 ATATCT
1 ATATCT
617017 TTTAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATCTATAATCTATTAA
Done.