Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014468.1 Corchorus capsularis cultivar CVL-1 contig14489, 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: 129004
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12595 original size:22 final size:23
Alignment explanation
Indices: 12560--12606 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
12550 GTAGTTAATC
*
12560 ATAAATTAACTAATTAAA-ACTA
1 ATAAAATAACTAATTAAATACTA
*
12582 ATAAAATAAGTAATTAAATACTA
1 ATAAAATAACTAATTAAATACTA
12605 AT
1 AT
12607 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAAATAACTAATTAAATACTA
Found at i:12618 original size:22 final size:22
Alignment explanation
Indices: 12571--12620 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12561 TAAATTAACT
*
12571 AATTAAAACTAATAAAATAAGT
1 AATTAAAACTAATAAAATAAGA
* *
12593 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAAATAAGA
12615 AATTAA
1 AATTAA
12621 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAAATAAGA
Found at i:12673 original size:32 final size:33
Alignment explanation
Indices: 12637--12727 Score: 114
Period size: 32 Copynumber: 2.8 Consensus size: 33
12627 TAAAGCAAAT
*
12637 TGGCCTTGCCACCCATTTTGGGCGGCATG-CCA
1 TGGCCTTGCCACCCAGTTTGGGCGGCATGCCCA
*
12669 TGGCCTTGCCACCCAGTTTGGGCGGCTTGCCCA
1 TGGCCTTGCCACCCAGTTTGGGCGGCATGCCCA
* * **
12702 TGG-CATGCCGCCCAGGCTGGGCGGCA
1 TGGCCTTGCCACCCAGTTTGGGCGGCA
12728 CAGCCCTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 45 0.88
33 6 0.12
ACGTcount: A:0.11, C:0.35, G:0.33, T:0.21
Consensus pattern (33 bp):
TGGCCTTGCCACCCAGTTTGGGCGGCATGCCCA
Found at i:21061 original size:17 final size:17
Alignment explanation
Indices: 21041--21076 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
21031 AACATCTTAC
*
21041 AATAGCTAACACTATCT
1 AATAACTAACACTATCT
21058 AATAACTAACACTATCT
1 AATAACTAACACTATCT
21075 AA
1 AA
21077 CAATAGCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (17 bp):
AATAACTAACACTATCT
Found at i:39392 original size:2 final size:2
Alignment explanation
Indices: 39331--39379 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
39321 ATAATATGCC
*
39331 AT AT AT AT A- AT ACT AGT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
39374 AT AT AT
1 AT AT AT
39380 TTTACACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
1 1 0.02
2 37 0.88
3 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:40810 original size:3 final size:3
Alignment explanation
Indices: 40802--40831 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40792 TTTACCTCTC
40802 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
40832 AAAACTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:42656 original size:21 final size:21
Alignment explanation
Indices: 42617--42657 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42607 AGCTTCTTTT
*
42617 TTAGTCAGTTTGTAGTAATTC
1 TTAGTCAGCTTGTAGTAATTC
42638 TTAGT-AGCTTGTAGTTAATT
1 TTAGTCAGCTTGTAG-TAATT
42658 TATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (21 bp):
TTAGTCAGCTTGTAGTAATTC
Found at i:69238 original size:168 final size:168
Alignment explanation
Indices: 68955--69294 Score: 590
Period size: 168 Copynumber: 2.0 Consensus size: 168
68945 CACTTGTTAG
68955 AATTCATTTAATTCCATTGATGAATTTAGAACTATTAGCTAAACATCCACAGAGAAAAGCAAAAC
1 AATTCATTTAATTCCATTGATGAATTTAGAACTATTAGCTAAACATCCACAGAGAAAAGCAAAAC
*
69020 TGAAATAAAGAGTCTAAATCATTCACGAAAACCGCGTGACTGTTACAGATAATATCTGTGAAAAG
66 TGAAATAAAGAGTCTAAATCATTCACGAAAACCGCGTGACTGTCACAGATAATATCTGTGAAAAG
*
69085 TCAATGGTTTGAAGGAGAAATGCACCAACTATTCCATA
131 TCAATAGTTTGAAGGAGAAATGCACCAACTATTCCATA
* *
69123 AATTCATTTAATTCCATTGATGAATTTAGAACTATTAGCTAAGCATTCACAGAGAAAAGCAAAAC
1 AATTCATTTAATTCCATTGATGAATTTAGAACTATTAGCTAAACATCCACAGAGAAAAGCAAAAC
* * * *
69188 TGGAATAAAGAGTCTGAATCGTTCACGAACACCGCGTGACTGTCACAGATAATATCTGTGAAAAG
66 TGAAATAAAGAGTCTAAATCATTCACGAAAACCGCGTGACTGTCACAGATAATATCTGTGAAAAG
* *
69253 TGAATAGTTTGAAGGAGAAATGCACCAACTATTCCATT
131 TCAATAGTTTGAAGGAGAAATGCACCAACTATTCCATA
69291 AATT
1 AATT
69295 TCAATTGCTT
Statistics
Matches: 162, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
168 162 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (168 bp):
AATTCATTTAATTCCATTGATGAATTTAGAACTATTAGCTAAACATCCACAGAGAAAAGCAAAAC
TGAAATAAAGAGTCTAAATCATTCACGAAAACCGCGTGACTGTCACAGATAATATCTGTGAAAAG
TCAATAGTTTGAAGGAGAAATGCACCAACTATTCCATA
Found at i:72811 original size:20 final size:20
Alignment explanation
Indices: 72786--72837 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
72776 CAACATTGCA
72786 ACAGCCCTTCGGATGAACTT
1 ACAGCCCTTCGGATGAACTT
72806 ACAGCCCTTCGGATGAACTT
1 ACAGCCCTTCGGATGAACTT
*
72826 ACAGCCCATCGG
1 ACAGCCCTTCGG
72838 CTACCTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (20 bp):
ACAGCCCTTCGGATGAACTT
Found at i:73518 original size:95 final size:92
Alignment explanation
Indices: 73355--73542 Score: 349
Period size: 95 Copynumber: 2.0 Consensus size: 92
73345 TTGAGTTAAT
73355 ACCACATAGGTTAATCAATAACCTCAAGGTTTCCAAACCCCAATTGCCAATGGGCAACAGATTAT
1 ACCACATAGGTTAATCAATAACCTCAAGGTTTCCAAACCCCAATTGCCAATGGGCAACAGATTAT
73420 ATATACACTTGGAAGTTGAAAAAGTAGTGA
66 ATATACACTTGG-A--TGAAAAAGTAGTGA
73450 ACCACATAGGTTAATCAATAACCTCAAGGTTTCCAAACCCCAATTGCCAATGGGCAACAGATTAT
1 ACCACATAGGTTAATCAATAACCTCAAGGTTTCCAAACCCCAATTGCCAATGGGCAACAGATTAT
73515 ATATACACTTGGATGAAAAAGTAGTGA
66 ATATACACTTGGATGAAAAAGTAGTGA
73542 A
1 A
73543 GATAAAGTTG
Statistics
Matches: 93, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
92 15 0.16
94 1 0.01
95 77 0.83
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (92 bp):
ACCACATAGGTTAATCAATAACCTCAAGGTTTCCAAACCCCAATTGCCAATGGGCAACAGATTAT
ATATACACTTGGATGAAAAAGTAGTGA
Found at i:93120 original size:14 final size:14
Alignment explanation
Indices: 93101--93131 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
93091 ATTAGTAGTT
93101 CTTCAGCGTTTGGA
1 CTTCAGCGTTTGGA
93115 CTTCAGCGTTTGGA
1 CTTCAGCGTTTGGA
93129 CTT
1 CTT
93132 GCGAATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.39
Consensus pattern (14 bp):
CTTCAGCGTTTGGA
Found at i:105148 original size:13 final size:13
Alignment explanation
Indices: 105114--105141 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
105104 AAAGTGGCTT
105114 TGATATTCAAAGG
1 TGATATTCAAAGG
105127 TGATATTCAAAGG
1 TGATATTCAAAGG
105140 TG
1 TG
105142 TAATTCAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (13 bp):
TGATATTCAAAGG
Found at i:109526 original size:20 final size:21
Alignment explanation
Indices: 109484--109528 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
109474 GCATTAAGTT
*
109484 AACTTTTTGTATGAATTCAAA
1 AACTTTTTGTATGAATGCAAA
*
109505 AACTTTTTGTAT-AATGCCAA
1 AACTTTTTGTATGAATGCAAA
109525 AACT
1 AACT
109529 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
AACTTTTTGTATGAATGCAAA
Found at i:110035 original size:30 final size:30
Alignment explanation
Indices: 109976--110037 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
109966 TCTTAGAGTC
* ** **
109976 AATATAGTGTAGCTCATGTTTGAGCAAAAA
1 AATATAGTGTAGCTCATGATAAAAAAAAAA
110006 AATATAGTGTAGCTCATGATAAAAAAAAAA
1 AATATAGTGTAGCTCATGATAAAAAAAAAA
110036 AA
1 AA
110038 AGTAGTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (30 bp):
AATATAGTGTAGCTCATGATAAAAAAAAAA
Found at i:112041 original size:237 final size:242
Alignment explanation
Indices: 111620--112103 Score: 793
Period size: 237 Copynumber: 2.0 Consensus size: 242
111610 TTTTTAAAGT
* *
111620 ATTGGTTAAGTGTTTCTTAGAAGATTTTGAATAGTAATTTATACTATATATATATTTGATTACTC
1 ATTGGTTAAGTGTTTCTTAGAAGATTTTGAATAGTAATTTATAC-ATATATATATTCGATGACTC
* *
111685 TTATATGATTTAATAATATATATACGATTTAAGCAATCTCTAACGCTAGATTTTTTTTTGAGGTA
65 TTATATGATTGAATAATATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTGAGGTA
*
111750 ATCTATAGCTAGATTTATCAATTAATATGGGTAATTGTCTTACCATAATATTAAAAAGGATTC-A
130 ATCTATAGCTAGATTTATCAATTAATATGGGTAATTGTCTTACCATAATATTAAAAAGAATTCAA
111814 CTGTTATTAATGTTTACAATTTGACTTGCAAATAGTGATTTGTCTTATA
195 CTGTTA-TAATGTTTACAATTTGACTTGCAAATAGTGATTTGTCTTATA
111863 ATTGGTTAAGTGTTTCTTAGAAGA-TTTGAAATAGTAATTTATAC-TATATATATTCGATGACTC
1 ATTGGTTAAGTGTTTCTTAGAAGATTTTG-AATAGTAATTTATACATATATATATTCGATGACTC
* *
111926 TTATAT-A-TGATTTA-ATATATACGATTTAAGCAATCTCTAAAGCTAGA-TTTTTTTTGAGGTA
65 TTATATGATTGAATAATATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTGAGGTA
*
111987 ATCTATAGCTAGATTTATCAATTAATATGGGTAATTGTCTTGCCATAATATTAAAAAGAATTCAG
130 ATCTATAGCTAGATTTATCAATTAATATGGGTAATTGTCTTACCATAATATTAAAAAGAATTCA-
*
112052 TACTGTTATAATTTTTACAATTTGACTTGCAAATAGTGATTTGTCTTATA
194 -ACTGTTATAATGTTTACAATTTGACTTGCAAATAGTGATTTGTCTTATA
112102 AT
1 AT
112104 GTTCACATAT
Statistics
Matches: 228, Mismatches: 9, Indels: 12
0.92 0.04 0.05
Matches are distributed among these distances:
237 75 0.33
238 32 0.14
239 47 0.21
240 8 0.04
241 23 0.10
242 4 0.02
243 39 0.17
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (242 bp):
ATTGGTTAAGTGTTTCTTAGAAGATTTTGAATAGTAATTTATACATATATATATTCGATGACTCT
TATATGATTGAATAATATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTGAGGTAA
TCTATAGCTAGATTTATCAATTAATATGGGTAATTGTCTTACCATAATATTAAAAAGAATTCAAC
TGTTATAATGTTTACAATTTGACTTGCAAATAGTGATTTGTCTTATA
Found at i:118936 original size:45 final size:45
Alignment explanation
Indices: 118872--118959 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
118862 CAATAGAGTA
118872 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTAG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTAG
* *
118917 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCT
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCT
118960 GGAGAAGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTAG
Found at i:119316 original size:167 final size:167
Alignment explanation
Indices: 119015--119346 Score: 443
Period size: 167 Copynumber: 2.0 Consensus size: 167
119005 AATGTCCTAA
* * * * * ** * *
119015 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGATAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
* ** *
119080 TTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGCCCTAAGTTTTGATTTTTGAGGG
66 TAACATTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGCCCTAAGTTTTGATTCTTGAGGG
* *
119145 GATTAAATAAGTAATCTTTTTGGTCATTTCTCAATGG
131 GATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
* *
119182 ACTTGAATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGATTGATGAT-GAGCTAGAGAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
* * * *
119246 TAACATTTTTCGT-TTTTACTTACTTGGCAGATTACTTAAATGTCCTAAATTTTTTATTCTTGAG
66 TAACATTTTTCGTCTTTT-CCTACTTGGCAGATTACTTAAATGCCCT-AAGTTTTGATTCTTGAG
119310 GGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
129 GGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
119347 AGACAAAGGA
Statistics
Matches: 142, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
165 4 0.03
166 46 0.32
167 92 0.65
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
TAACATTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGCCCTAAGTTTTGATTCTTGAGGG
GATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
Found at i:123356 original size:69 final size:69
Alignment explanation
Indices: 123245--123383 Score: 206
Period size: 69 Copynumber: 2.0 Consensus size: 69
123235 CATTTGTATC
* * * *
123245 TGACGTAGAATCTGGTTTCGGTTCCCCCGGTAAATATTCTCCTTCTTCACATTCTTTCATACATG
1 TGACGTAGAATCTGATTTCCGTTCCCACGATAAATATTCTCCTTCTTCACATTCTTTCATACATG
123310 TTGA
66 TTGA
* * * *
123314 TGACGTAGAATTTGATTTCCGTTCCCATGATAAATATTCTCCTTCTTTACATTCTTTGATACATG
1 TGACGTAGAATCTGATTTCCGTTCCCACGATAAATATTCTCCTTCTTCACATTCTTTCATACATG
123379 TTGA
66 TTGA
123383 T
1 T
123384 ATGAACAAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (69 bp):
TGACGTAGAATCTGATTTCCGTTCCCACGATAAATATTCTCCTTCTTCACATTCTTTCATACATG
TTGA
Done.