Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008821.1 Corchorus capsularis cultivar CVL-1 contig08842, 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: 83455
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:902 original size:40 final size:40
Alignment explanation
Indices: 844--920 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
834 GTCCCTCCTA
*
844 ATAATTAAGGAAACAAATTAAATCCAGGTTTAGCCCCCTG
1 ATAATTAAGGAAACAAATTAAATCCAGATTTAGCCCCCTG
* * *
884 ATAATTAAGGTAAGAAATTAAATTCAGATTTAGCCCC
1 ATAATTAAGGAAACAAATTAAATCCAGATTTAGCCCC
921 TAGTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (40 bp):
ATAATTAAGGAAACAAATTAAATCCAGATTTAGCCCCCTG
Found at i:6915 original size:109 final size:109
Alignment explanation
Indices: 6724--6942 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
6714 TAATAAGTTC
6724 AATGAACATGATTTTATTTGTAAGTAATAGGAAATGCAAAGAGGTAATAAAATATGTTGTTAATT
1 AATGAACATGATTTTATTTGTAAGTAATAGGAAATGCAAAGAGGTAATAAAATATGTTGTTAATT
6789 GGATAATAATACTCACATTGAACGAAGGGTGGTTTTTATTCAGA
66 GGATAATAATACTCACATTGAACGAAGGGTGGTTTTTATTCAGA
6833 AATGAACATGATTTTATTTGTAAGTAATAGGAAATGCAAAGAGGTAATAAAATATGTTGTTAATT
1 AATGAACATGATTTTATTTGTAAGTAATAGGAAATGCAAAGAGGTAATAAAATATGTTGTTAATT
6898 GGATAATAATACTCACATTGAACGAAGGGTGGTTTTTATTCAGA
66 GGATAATAATACTCACATTGAACGAAGGGTGGTTTTTATTCAGA
6942 A
1 A
6943 GGGGAAAAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (109 bp):
AATGAACATGATTTTATTTGTAAGTAATAGGAAATGCAAAGAGGTAATAAAATATGTTGTTAATT
GGATAATAATACTCACATTGAACGAAGGGTGGTTTTTATTCAGA
Found at i:19916 original size:155 final size:156
Alignment explanation
Indices: 19576--19936 Score: 396
Period size: 155 Copynumber: 2.3 Consensus size: 156
19566 CTGGACTTCA
* * **
19576 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGATCGAGACGA
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCCAATCGAGACGA
* * * *
19641 AACTTTGCCAAGGGACTTAGATTCTCACCACAAGACTATGGAAAAAATTCTATGTAAAACCGAGC
66 AACTTTGCCAAGGGACTTAGATTATCACCACAAGACTATGGAAAAAATTATAAGTAAAACCGAAC
* *
19706 TCTCCTTCATGGTGAACTAGGTTTCT
131 TCTCCTTCATAGAGAACTAGGTTTCT
* * *
19732 CTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCCAAT-GA-A-GC
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCCAATCGAGACG-
* * * *
19794 TAA-TTTTCCACAGTAGG-CTTAGATTATCTCCATAA-ATCTATGGGAAAAAA-TATAAGTAAAA
65 AAACTTTGCCA-AG--GGACTTAGATTATCACCACAAGA-CTAT-GGAAAAAATTATAAGTAAAA
* * *
19855 CCGAACTCT-CTTACATAGAGAAGTTGGTTTGT
125 CCGAACTCTCCTT-CATAGAGAACTAGGTTTCT
* * *
19887 CACCCCAAACTGTCATTAACTGAAAAACTAGCATAAGTTTTTCATCCTAA
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAA
19937 GTCTGTTTGA
Statistics
Matches: 172, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
153 7 0.04
154 9 0.05
155 96 0.56
156 60 0.35
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (156 bp):
CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCCAATCGAGACGA
AACTTTGCCAAGGGACTTAGATTATCACCACAAGACTATGGAAAAAATTATAAGTAAAACCGAAC
TCTCCTTCATAGAGAACTAGGTTTCT
Found at i:22437 original size:8 final size:8
Alignment explanation
Indices: 22424--22461 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
22414 GGGTCACCCG
22424 CTCAAGGA
1 CTCAAGGA
22432 CTCAAGGA
1 CTCAAGGA
22440 CTCAAGGA
1 CTCAAGGA
22448 CTCAAGGA
1 CTCAAGGA
22456 CTCAAG
1 CTCAAG
22462 CTCAAGACCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (8 bp):
CTCAAGGA
Found at i:28628 original size:2 final size:2
Alignment explanation
Indices: 28621--28647 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28611 GGGTAAATAA
28621 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 A
28648 AGCACCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31742 original size:28 final size:28
Alignment explanation
Indices: 31686--31742 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
31676 ATTGTTCCAA
***
31686 ATACAACCCAATATACTTCATTTTTTTG
1 ATACAACCCAATATACTTCATTAAGTTG
31714 ATACATACCCAATATACTTCA-TAAGTTG
1 ATACA-ACCCAATATACTTCATTAAGTTG
31742 A
1 A
31743 ATAGTTGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (28 bp):
ATACAACCCAATATACTTCATTAAGTTG
Found at i:44788 original size:2 final size:2
Alignment explanation
Indices: 44781--44807 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44771 AGATTATTAC
44781 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 T
44808 CTTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53633 original size:294 final size:300
Alignment explanation
Indices: 53104--53988 Score: 1194
Period size: 294 Copynumber: 2.9 Consensus size: 300
53094 ATCTCCTCAA
*
53104 AATATTATGCTA-TCAAAAAACAATGTAAATATTCAAATAAGGACTAAAAGTTGGGG-AGTACTC
1 AATATTATTCTACT-AAAAAACAATGTAAATATTCAAATAAGGACTAAAAGTTGGGGAAGTACTC
53167 AATTTAAAGTCTAATTCTTTATATTGAATCTAATTAGGTCTGAAAGTTTGGGTCATACCAACAAA
65 AA-TTAAAGTCTAATTCTTTATATTGAATCTAATTAGGTCTGAAAGTTTGGGTCATACCAACAAA
* * * ** *
53232 TAGTTGGTTCAAGTTGTTTGACACTTGTTTCCCTTAATCAAAATCTCGAGTTTGAGTCTTGTAAA
129 TAGTTGGTTCAAGTGGTTTGACACTTGTTCCCCTTAAACAAGGTCTCGGGTTTGAGTCTTGTAAA
*
53297 TGGAGAAAATCATTGTTATGAGAGTTTTATCCCCATATTGGGTCAACCCGGCTCGAACTATGTTA
194 TGGAGAAAATCATTGTTAGGAGAGTTTTATCCCCATATTGGGTCAACCCGGCTCGAACTATGTTA
* * *
53362 ACATGTAAATAAAGGGTAAC-A-T-AGT-GGG-AGAGAT-T-T
259 ACATGTAAATAAAGGGTAACAATTAAATAGGGTA-ACATATGG
* *
53398 AATATTATTCTACTAAAAAACAATGTAAATATTCAAATAAAGACTAAAAGTTGGGGAAGTACTTA
1 AATATTATTCTACTAAAAAACAATGTAAATATTCAAATAAGGACTAAAAGTTGGGGAAGTACTCA
*
53463 ATTCAAGTCTAATTCTTTATATTGAATCTAATTAGGTCTGAAAGTTTGGGTCATACCAACAAATA
66 ATTAAAGTCTAATTCTTTATATTGAATCTAATTAGGTCTGAAAGTTTGGGTCATACCAACAAATA
* *
53528 GTTGGTTCAAGTGGTTTGGCACTTGTTCCCCTTAAACAAGGTCTCGGGTTTGAGTCTTGTGAATG
131 GTTGGTTCAAGTGGTTTGACACTTGTTCCCCTTAAACAAGGTCTCGGGTTTGAGTCTTGTAAATG
* *
53593 GAGAAAATCATTGTTAGGAGAGTTTTGTCCCCATATTGGGTCAACCCGGCTCAAACTATGTTAAC
196 GAGAAAATCATTGTTAGGAGAGTTTTATCCCCATATTGGGTCAACCCGGCTCGAACTATGTTAAC
53658 ATGTAAATAAAGGGTAACATTGTAAATATTAAATAAAGGGTAACATAGTGGGAGAG
261 ATGTAAATAAAGGGTAAC-------A-ATTAAAT--AGGGTAACATA-T----G-G
53714 ATTTAATATTATTCTACTAAAAAACAATGTAAATATTCAAATAAGGACTAAAAGTTGGGGAAGTA
1 ----AATATTATTCTACTAAAAAACAATGTAAATATTCAAATAAGGACTAAAAGTTGGGGAAGTA
* * *
53779 CTCAATTTAAGTCTAATTCTTTATATTGAATCTATTTATGTCTGAAAGTTTGGGTCATACCAACA
62 CTCAATTAAAGTCTAATTCTTTATATTGAATCTAATTAGGTCTGAAAGTTTGGGTCATACCAACA
* *
53844 AATAATTGGTTCAAGTGGTTTGACACTTGTTCCCCTTAAACAAGGTCTTGGGTTTGAGTCTTGTA
127 AATAGTTGGTTCAAGTGGTTTGACACTTGTTCCCCTTAAACAAGGTCTCGGGTTTGAGTCTTGTA
* * * * * * * * *
53909 AATGGAGAAAACCATTGTTGGGAGAGCTTTATCCTCATAGTAGGTTAACCCGACTCGAACAATGT
192 AATGGAGAAAATCATTGTTAGGAGAGTTTTATCCCCATATTGGGTCAACCCGGCTCGAACTATGT
* *
53974 TAACTTGCAAATAAA
257 TAACATGTAAATAAA
53989 CCAAAAAAAA
Statistics
Matches: 522, Mismatches: 40, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
294 252 0.48
295 9 0.02
303 1 0.00
304 1 0.00
305 2 0.00
308 6 0.01
309 1 0.00
310 1 0.00
320 249 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (300 bp):
AATATTATTCTACTAAAAAACAATGTAAATATTCAAATAAGGACTAAAAGTTGGGGAAGTACTCA
ATTAAAGTCTAATTCTTTATATTGAATCTAATTAGGTCTGAAAGTTTGGGTCATACCAACAAATA
GTTGGTTCAAGTGGTTTGACACTTGTTCCCCTTAAACAAGGTCTCGGGTTTGAGTCTTGTAAATG
GAGAAAATCATTGTTAGGAGAGTTTTATCCCCATATTGGGTCAACCCGGCTCGAACTATGTTAAC
ATGTAAATAAAGGGTAACAATTAAATAGGGTAACATATGG
Found at i:53976 original size:320 final size:320
Alignment explanation
Indices: 53367--53988 Score: 1046
Period size: 320 Copynumber: 1.9 Consensus size: 320
53357 TGTTAACATG
53367 TAAATAAAGGGTAACATAGTGGGAGAGATTTAATATTATTCTACTAAAAAACAATGTAAATATTC
1 TAAATAAAGGGTAACATAGTGGGAGAGATTTAATATTATTCTACTAAAAAACAATGTAAATATTC
*
53432 AAATAAAGACTAAAAGTTGGGGAAGTACTTAATTCAAGTCTAATTCTTTATATTGAATCTAATTA
66 AAATAAAGACTAAAAGTTGGGGAAGTACTCAATTCAAGTCTAATTCTTTATATTGAATCTAATTA
* *
53497 GGTCTGAAAGTTTGGGTCATACCAACAAATAGTTGGTTCAAGTGGTTTGGCACTTGTTCCCCTTA
131 GGTCTGAAAGTTTGGGTCATACCAACAAATAATTGGTTCAAGTGGTTTGACACTTGTTCCCCTTA
* * * *
53562 AACAAGGTCTCGGGTTTGAGTCTTGTGAATGGAGAAAATCATTGTTAGGAGAGTTTTGTCCCCAT
196 AACAAGGTCTCGGGTTTGAGTCTTGTAAATGGAGAAAACCATTGTTAGGAGAGCTTTATCCCCAT
* * * * *
53627 ATTGGGTCAACCCGGCTCAAACTATGTTAACATGTAAATAAAGGGTAACATTGTAAATAT
261 AGTAGGTCAACCCGACTCAAACAATGTTAACATGCAAATAAAGGGTAACATTGTAAATAT
53687 TAAATAAAGGGTAACATAGTGGGAGAGATTTAATATTATTCTACTAAAAAACAATGTAAATATTC
1 TAAATAAAGGGTAACATAGTGGGAGAGATTTAATATTATTCTACTAAAAAACAATGTAAATATTC
* * *
53752 AAATAAGGACTAAAAGTTGGGGAAGTACTCAATTTAAGTCTAATTCTTTATATTGAATCTATTTA
66 AAATAAAGACTAAAAGTTGGGGAAGTACTCAATTCAAGTCTAATTCTTTATATTGAATCTAATTA
*
53817 TGTCTGAAAGTTTGGGTCATACCAACAAATAATTGGTTCAAGTGGTTTGACACTTGTTCCCCTTA
131 GGTCTGAAAGTTTGGGTCATACCAACAAATAATTGGTTCAAGTGGTTTGACACTTGTTCCCCTTA
* * *
53882 AACAAGGTCTTGGGTTTGAGTCTTGTAAATGGAGAAAACCATTGTTGGGAGAGCTTTATCCTCAT
196 AACAAGGTCTCGGGTTTGAGTCTTGTAAATGGAGAAAACCATTGTTAGGAGAGCTTTATCCCCAT
* * *
53947 AGTAGGTTAACCCGACTCGAACAATGTTAACTTGCAAATAAA
261 AGTAGGTCAACCCGACTCAAACAATGTTAACATGCAAATAAA
53989 CCAAAAAAAA
Statistics
Matches: 280, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
320 280 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (320 bp):
TAAATAAAGGGTAACATAGTGGGAGAGATTTAATATTATTCTACTAAAAAACAATGTAAATATTC
AAATAAAGACTAAAAGTTGGGGAAGTACTCAATTCAAGTCTAATTCTTTATATTGAATCTAATTA
GGTCTGAAAGTTTGGGTCATACCAACAAATAATTGGTTCAAGTGGTTTGACACTTGTTCCCCTTA
AACAAGGTCTCGGGTTTGAGTCTTGTAAATGGAGAAAACCATTGTTAGGAGAGCTTTATCCCCAT
AGTAGGTCAACCCGACTCAAACAATGTTAACATGCAAATAAAGGGTAACATTGTAAATAT
Found at i:54514 original size:21 final size:22
Alignment explanation
Indices: 54490--54532 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
54480 AAAAAGGGGA
54490 TTACTAAATACCGCCC-CCTTT
1 TTACTAAATACCGCCCTCCTTT
**
54511 TTACTAGGTACCGCCCTCCTTT
1 TTACTAAATACCGCCCTCCTTT
54533 GGACAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (22 bp):
TTACTAAATACCGCCCTCCTTT
Found at i:55002 original size:21 final size:21
Alignment explanation
Indices: 54973--55013 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54963 CGCGACCCGC
54973 TGTTCTTCTTCTTTTTTTTTT
1 TGTTCTTCTTCTTTTTTTTTT
*
54994 TGTTTTTCTTCTTTTTTTTT
1 TGTTCTTCTTCTTTTTTTTT
55014 CTTCTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (21 bp):
TGTTCTTCTTCTTTTTTTTTT
Found at i:62915 original size:3 final size:3
Alignment explanation
Indices: 62909--62939 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
62899 AGAAGAAGAA
62909 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
62940 GAGAAGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:77779 original size:20 final size:20
Alignment explanation
Indices: 77754--77792 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
77744 TTTTTCTAGA
77754 TTACTAAACACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
**
77774 TTACTAGTCACCGCCCCCT
1 TTACTAAACACCGCCCCCT
77793 CTTTGGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.46, G:0.08, T:0.26
Consensus pattern (20 bp):
TTACTAAACACCGCCCCCTT
Found at i:77988 original size:2 final size:2
Alignment explanation
Indices: 77981--78016 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
77971 CTAATAATTT
77981 TA TA TA TA 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
78017 GAAGAAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79057 original size:22 final size:21
Alignment explanation
Indices: 79008--79061 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
78998 TGTTGGTAAA
79008 TGTA-ATT-TTTTTTCATAAC
1 TGTATATTGTTTTTTCATAAC
*
79027 TGCACATATTGTTTTTTCTATAAC
1 TG--TATATTGTTTTTTC-ATAAC
79051 TGTATATTGTT
1 TGTATATTGTT
79062 ATAAGATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.07
21 1 0.04
22 11 0.39
23 7 0.25
24 7 0.25
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (21 bp):
TGTATATTGTTTTTTCATAAC
Done.