Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015843.1 Corchorus olitorius cultivar O-4 contig15876, whole genome shotgun sequence
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: 72258
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:9205 original size:9 final size:9
Alignment explanation
Indices: 9191--9223 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
9181 AAAATTGACG
9191 TAATAATAT
1 TAATAATAT
9200 TAATAATAT
1 TAATAATAT
9209 TAATAATAT
1 TAATAATAT
9218 TAATAA
1 TAATAA
9224 ATCAAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATAT
Found at i:12703 original size:30 final size:30
Alignment explanation
Indices: 12649--12708 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
12639 CCAATTCAAT
* *
12649 TTAAATTGTCTAAAAATCATAGTTTGAGGA
1 TTAAATTGTCTAAAAATCAAAGTTTAAGGA
*
12679 TTAAATTGTCTAAAAATTAAAGTTTAAGGA
1 TTAAATTGTCTAAAAATCAAAGTTTAAGGA
12709 CCAAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (30 bp):
TTAAATTGTCTAAAAATCAAAGTTTAAGGA
Found at i:12715 original size:30 final size:30
Alignment explanation
Indices: 12651--12715 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
12641 AATTCAATTT
* * **
12651 AAATTGTCTAAAAATCATAGTTTGAGGATT
1 AAATTGTCTAAAAATCAAAGTTTAAGGACC
*
12681 AAATTGTCTAAAAATTAAAGTTTAAGGACC
1 AAATTGTCTAAAAATCAAAGTTTAAGGACC
12711 AAATT
1 AAATT
12716 AATAATTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (30 bp):
AAATTGTCTAAAAATCAAAGTTTAAGGACC
Found at i:19986 original size:3 final size:3
Alignment explanation
Indices: 19978--20031 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
19968 GCGGAGCTAC
* *
19978 TGG TGG TGG TGG TGG TGG TGG TGG TTG TGG TGG TTG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
20026 TGG TGG
1 TGG TGG
20032 CAGAGTTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.63, T:0.37
Consensus pattern (3 bp):
TGG
Found at i:34562 original size:2 final size:2
Alignment explanation
Indices: 34555--34588 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34545 AAAAGAAACC
34555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34589 CAATATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:35952 original size:2 final size:2
Alignment explanation
Indices: 35940--35986 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
35930 CGACCCCGAA
35940 AT AT AT A- AT AT AT -T CAT A- 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
35980 AT AT AT A
1 AT AT AT A
35987 CACTTTATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.07
2 37 0.90
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36949 original size:14 final size:14
Alignment explanation
Indices: 36930--36959 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36920 TCATAGAAGC
36930 TGTTTTTTTGTTTT
1 TGTTTTTTTGTTTT
*
36944 TGTTTTTTTTTTTT
1 TGTTTTTTTGTTTT
36958 TG
1 TG
36960 ATATCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TGTTTTTTTGTTTT
Found at i:39320 original size:5 final size:5
Alignment explanation
Indices: 39310--39341 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
39300 GTAAAACTAA
39310 AATTT AATTT AATTT AATTT AATTT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AATTT AA
39342 GAATTACGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:39970 original size:6 final size:6
Alignment explanation
Indices: 39959--40020 Score: 106
Period size: 6 Copynumber: 10.0 Consensus size: 6
39949 TTAAAGAAAC
39959 CTATAT CTATAT CTATAT ACTATAT CTATAT CTATAT CTATAT CTATAT
1 CTATAT CTATAT CTATAT -CTATAT CTATAT CTATAT CTATAT CTATAT
40008 CTATAT ACTATAT
1 CTATAT -CTATAT
40021 AAGTCTAAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
6 42 0.78
7 12 0.22
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
CTATAT
Found at i:40293 original size:39 final size:40
Alignment explanation
Indices: 40237--40317 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
40227 TTTAATTCCT
40237 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
40277 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
40316 AT
1 AT
40318 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:40344 original size:25 final size:24
Alignment explanation
Indices: 40308--40354 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
40298 AATACTTACA
40308 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
40332 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
40355 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:40615 original size:105 final size:103
Alignment explanation
Indices: 40506--40714 Score: 366
Period size: 105 Copynumber: 2.0 Consensus size: 103
40496 GAATTACCTT
* *
40506 GCACACTAAGCTCTTAACAGGTTTTGAAAGCAAATTGAGTAAAAAAATATTCAAATTAA-CCTGA
1 GCACACTAAGCTCCTAACAGATTTTGAAAGCAAATTGAGT-AAAAAATATTCAAATTAACCCT-A
40570 AAGCATGACAAGAGAGAAGAAAAAACAAGATCTGATCAATC
64 AAGCATGA-AAGAGAGAAGAAAAAACAAGATCTGATCAATC
40611 GCACACTAAGCTCCTAACAGATTTTGAAAGCAAATTGAGTAAAAAATATTCAAATTAACCCTAAA
1 GCACACTAAGCTCCTAACAGATTTTGAAAGCAAATTGAGTAAAAAATATTCAAATTAACCCTAAA
40676 GCATGAAAGAGAGAAGAAAAAACAAGATCTGATCAATC
66 GCATGAAAGAGAGAAGAAAAAACAAGATCTGATCAATC
40714 G
1 G
40715 TGAAAAATGT
Statistics
Matches: 101, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
103 33 0.33
104 27 0.27
105 41 0.41
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (103 bp):
GCACACTAAGCTCCTAACAGATTTTGAAAGCAAATTGAGTAAAAAATATTCAAATTAACCCTAAA
GCATGAAAGAGAGAAGAAAAAACAAGATCTGATCAATC
Found at i:60896 original size:45 final size:44
Alignment explanation
Indices: 60845--60930 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 44
60835 GTGAAAGTTT
60845 CAAATTAAAA-TATCAAGG-GAAAAAATATCCATATTGTAAAAGCTA
1 CAAATTAAAAGT-TCAAGGAG-AAAAAT-TCCATATTGTAAAAGCTA
* *
60890 CAAATTAAAAGTTCAAGGAGAAAAATTTCATATTGTGAAAG
1 CAAATTAAAAGTTCAAGGAGAAAAATTCCATATTGTAAAAG
60931 TTTAGGGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
44 13 0.35
45 22 0.59
46 2 0.05
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (44 bp):
CAAATTAAAAGTTCAAGGAGAAAAATTCCATATTGTAAAAGCTA
Found at i:63712 original size:32 final size:32
Alignment explanation
Indices: 63666--63747 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
63656 CCCCGACAGA
*
63666 GGGGGCAAATTGTCCTGAACTTGGGAAGTTTT
1 GGGGACAAATTGTCCTGAACTTGGGAAGTTTT
63698 GGGGACAAATTGTCCTGAACTTGGGAAGTTTT
1 GGGGACAAATTGTCCTGAACTTGGGAAGTTTT
63730 GGGGACAAATTGTCCTGA
1 GGGGACAAATTGTCCTGA
63748 TTTTAGTTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.29
Consensus pattern (32 bp):
GGGGACAAATTGTCCTGAACTTGGGAAGTTTT
Found at i:65385 original size:22 final size:23
Alignment explanation
Indices: 65342--65385 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
65332 ATTTGTAATC
*
65342 TTACTTATGATCAATTGAAATTA
1 TTACTTATGATCAACTGAAATTA
* *
65365 TTACTT-TGATTAACTGCAATT
1 TTACTTATGATCAACTGAAATT
65386 GATGTGATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (23 bp):
TTACTTATGATCAACTGAAATTA
Found at i:66015 original size:93 final size:93
Alignment explanation
Indices: 65829--66000 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
65819 ATATTATAAA
*
65829 AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTTT
1 AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTAT
* * *
65894 AAAAGTAAAATAGTAAAATGGTAAAAAT
66 AAAAATAAAACAATAAAATGGTAAAAAT
* * *
65922 AAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTAAAACTAT
1 AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTAT
*
65987 AAAAATTAAACAAT
66 AAAAATAAAACAAT
66001 GACATTTAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (93 bp):
AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTAT
AAAAATAAAACAATAAAATGGTAAAAAT
Found at i:67489 original size:35 final size:35
Alignment explanation
Indices: 67449--67519 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
67439 CTAACAAAAA
67449 TCTGTAAATTTTAAACAATGTCATTAAAAAAATAT
1 TCTGTAAATTTTAAACAATGTCATTAAAAAAATAT
67484 TCTGTAAATTTTAAACAATGTCATTAAAAAAATAT
1 TCTGTAAATTTTAAACAATGTCATTAAAAAAATAT
67519 T
1 T
67520 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (35 bp):
TCTGTAAATTTTAAACAATGTCATTAAAAAAATAT
Found at i:67800 original size:31 final size:31
Alignment explanation
Indices: 67765--67826 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
67755 TATTCGAAAA
* *
67765 AATAAGGATATGATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCAATTCAAAAGTTT
*
67796 AATAAGGGTATAATAGGCAATTCAAAAGTTT
1 AATAAGGATATAATAGGCAATTCAAAAGTTT
67827 TACAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGGATATAATAGGCAATTCAAAAGTTT
Found at i:69075 original size:28 final size:29
Alignment explanation
Indices: 69022--69085 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 29
69012 ATTTATTCTG
69022 AATCAATGCCAAGGAAGAAATGAAACAAA
1 AATCAATGCCAAGGAAGAAATGAAACAAA
69051 AATCAATGCCAA-GAAGAAATGAAACAAA
1 AATCAATGCCAAGGAAGAAATGAAACAAA
*
69079 ATTCAAT
1 AATCAAT
69086 AATGGAAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 22 0.65
29 12 0.35
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (29 bp):
AATCAATGCCAAGGAAGAAATGAAACAAA
Found at i:69093 original size:27 final size:27
Alignment explanation
Indices: 69022--69093 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
69012 ATTTATTCTG
69022 AATCAATGCCAAGGAAGAAATGAAACAAA
1 AATCAAT--CAAGGAAGAAATGAAACAAA
69051 AATCAATGCCAA-GAAGAAATGAAACAAA
1 AATCAAT--CAAGGAAGAAATGAAACAAA
*
69079 ATTCAAT-AATGGAAG
1 AATCAATCAA-GGAAG
69094 CATATGAGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 2 0.05
27 4 0.10
28 22 0.55
29 12 0.30
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (27 bp):
AATCAATCAAGGAAGAAATGAAACAAA
Found at i:71357 original size:32 final size:32
Alignment explanation
Indices: 71316--71376 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
71306 AAATATGTTT
* *
71316 GAAAAATAAGGGTATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
71348 GAAAAATAAGGATATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
71377 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:72140 original size:123 final size:123
Alignment explanation
Indices: 71899--72258 Score: 639
Period size: 123 Copynumber: 2.9 Consensus size: 123
71889 ATTTAAGAAA
71899 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT----
71964 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
62 TA--TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
72029 G
123 G
72030 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
*
72095 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
66 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
72153 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
72218 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTT
66 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTT
Statistics
Matches: 228, Mismatches: 1, Indels: 8
0.96 0.00 0.03
Matches are distributed among these distances:
123 161 0.71
124 2 0.01
125 2 0.01
127 2 0.01
131 61 0.27
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (123 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Done.