Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006077.1 Corchorus capsularis cultivar CVL-1 contig06095, 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: 56630
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:328 original size:3 final size:3
Alignment explanation
Indices: 320--373 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
310 TGACGGTAAG
*
320 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
368 GAA GAA
1 GAA GAA
374 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:7787 original size:27 final size:27
Alignment explanation
Indices: 7754--7821 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
7744 ATCCTAGGGA
*
7754 ACTAACTTTGAATGGGAAACTGTCTTC
1 ACTAACTTGGAATGGGAAACTGTCTTC
* *
7781 ACTAACTTGGAATGGGGAACTGTCTTG
1 ACTAACTTGGAATGGGAAACTGTCTTC
7808 ACTAACTTGGAATG
1 ACTAACTTGGAATG
7822 AGAGTCAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (27 bp):
ACTAACTTGGAATGGGAAACTGTCTTC
Found at i:12734 original size:27 final size:27
Alignment explanation
Indices: 12704--12771 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
12694 GTTAGACTCT
*
12704 CATTCCAAGTTAGTCA-AGACAGTTCCC
1 CATTCAAAGTTAGTCAGA-ACAGTTCCC
* *
12731 CATTCAAAGCTAGTCAGAACAGTTTCC
1 CATTCAAAGTTAGTCAGAACAGTTCCC
12758 CATTCAAAGTTAGT
1 CATTCAAAGTTAGT
12772 TCCCTAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (27 bp):
CATTCAAAGTTAGTCAGAACAGTTCCC
Found at i:13975 original size:92 final size:92
Alignment explanation
Indices: 13818--14003 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
13808 AATGCTTGAC
13818 GAAACACATGCTTGGGACTAGGATAACAGGCAAGAAAAACTAAACAGACAAGGAGGTGATGATAT
1 GAAACACATGCTTGGGACTAGGATAACAGGCAAGAAAAACTAAACAGACAAGGAGGTGATGATAT
13883 AAAAAAGGAAAATGGAGAATTGTAGGT
66 AAAAAAGGAAAATGGAGAATTGTAGGT
13910 GAAACACATGCTTGGGACTAGGATAACAGGCAAGAAAAACTAAACAGACAAGGAGGTGATGATAT
1 GAAACACATGCTTGGGACTAGGATAACAGGCAAGAAAAACTAAACAGACAAGGAGGTGATGATAT
*
13975 AAAATAGGAAAATGGAGAATTGTAGGT
66 AAAAAAGGAAAATGGAGAATTGTAGGT
14002 GA
1 GA
14004 GGTCAGAGAG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (92 bp):
GAAACACATGCTTGGGACTAGGATAACAGGCAAGAAAAACTAAACAGACAAGGAGGTGATGATAT
AAAAAAGGAAAATGGAGAATTGTAGGT
Found at i:15151 original size:25 final size:25
Alignment explanation
Indices: 15113--15163 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
15103 ATACAATCTC
15113 TCATAGAAAGACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATGTT
* *
15138 TCATGGAAATACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATGTT
15163 T
1 T
15164 TTGTAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (25 bp):
TCATAGAAAGACACCTTTTCATGTT
Found at i:20701 original size:22 final size:22
Alignment explanation
Indices: 20670--20714 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
20660 ATTTCAATAC
*
20670 ATTATGATT-ATATACATTTTTT
1 ATTATAATTAATATA-ATTTTTT
20692 ATTATAATTAATATAATTTTTT
1 ATTATAATTAATATAATTTTTT
20714 A
1 A
20715 CTATTATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTATAATTAATATAATTTTTT
Found at i:20885 original size:6 final size:6
Alignment explanation
Indices: 20876--20900 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20866 AAAAGGGTAA
20876 GGTTCC GGTTCC GGTTCC GGTTCC G
1 GGTTCC GGTTCC GGTTCC GGTTCC G
20901 AACCGAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (6 bp):
GGTTCC
Found at i:27600 original size:141 final size:139
Alignment explanation
Indices: 27347--27601 Score: 339
Period size: 139 Copynumber: 1.8 Consensus size: 139
27337 CCTATTCAAT
* *
27347 AATACCCTAAAATAAAGAGATTTATCCTACAAACCCAACTTACTTGTAACTAGGGACTAAACCTG
1 AATACCCTAAAATAAAGAGATTTACCCTACAAACCCAACTTACTTGTAACCAGGGACTAAACCTG
* *
27412 AAATTAATTTGTTATCTTAATTATTAGACATGATAACTGTCGATAAAATCAGACGGGACAACATA
66 AAATTAATTTGTTATCTTAATTATTAGACAGGATAAATGTCGATAAAATCAGACGGGACAACATA
27477 TTTTCCGTG
131 TTTTCCGTG
* * * ** * * * * *
27486 AATACCCTAAAATCAAGGGATTTACCCTGCAAACCCTCCTTATTTGTGACCGGGGGCTAAACTTG
1 AATACCCTAAAATAAAGAGATTTACCCTACAAACCCAACTTACTTGTAACCAGGGACTAAAC--C
* * *
27551 TGTAATTAATTTGTTATCTTAATTATTAGACAGGATAAATGTTGGTAAAAT
64 TGAAATTAATTTGTTATCTTAATTATTAGACAGGATAAATGTCGATAAAAT
27602 TCAGGGCAAC
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
139 51 0.53
141 46 0.47
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (139 bp):
AATACCCTAAAATAAAGAGATTTACCCTACAAACCCAACTTACTTGTAACCAGGGACTAAACCTG
AAATTAATTTGTTATCTTAATTATTAGACAGGATAAATGTCGATAAAATCAGACGGGACAACATA
TTTTCCGTG
Found at i:28162 original size:16 final size:16
Alignment explanation
Indices: 28141--28173 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28131 TTGCCCAAAC
28141 CCTCACGTTTTTCAGG
1 CCTCACGTTTTTCAGG
28157 CCTCACGTTTTTCAGG
1 CCTCACGTTTTTCAGG
28173 C
1 C
28174 GGACCTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.36
Consensus pattern (16 bp):
CCTCACGTTTTTCAGG
Found at i:32513 original size:67 final size:67
Alignment explanation
Indices: 32438--32571 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 67
32428 CAATATTCAA
* **
32438 AATTGAAACTTTTCCTCGTACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
1 AATTGAAACTTGTCCTAATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
32503 AG
66 AG
*
32505 AATTGAAACTTGTCCTAATTCATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
1 AATTGAAACTTGTCCTAATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
32570 AG
66 AG
32572 CCCAATCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (67 bp):
AATTGAAACTTGTCCTAATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
AG
Found at i:35397 original size:2 final size:2
Alignment explanation
Indices: 35384--35417 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35374 AGAATTAGTT
*
35384 TA TA TA TG 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
35418 AATGAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38053 original size:60 final size:60
Alignment explanation
Indices: 37960--38077 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 60
37950 AGATCATATG
* * * *
37960 AATATAGAGGTCCATGATAGCGTTGGTCGAGATGATGTTGGGATGAATGAATCTGCCCAA
1 AATATAGAGGTCCATAATAGCGTTGGTCAAGATGATGTTGGAATGAATGAATCGGCCCAA
* * *
38020 AATATAGAGGTCCCTAATAGCGTTTGTCAAGATGATGTTGGAATGATTGAATCGGCCC
1 AATATAGAGGTCCATAATAGCGTTGGTCAAGATGATGTTGGAATGAATGAATCGGCCC
38078 GAATTGTTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (60 bp):
AATATAGAGGTCCATAATAGCGTTGGTCAAGATGATGTTGGAATGAATGAATCGGCCCAA
Found at i:42589 original size:165 final size:161
Alignment explanation
Indices: 42215--42642 Score: 518
Period size: 165 Copynumber: 2.6 Consensus size: 161
42205 TCATTTGTCA
* *
42215 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCTCTTAAGAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGACATTTAA
* * ** * * **
42280 GTAATCTGTCAAGTA-GATAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCGATTCTTGATA
65 GTAATCTGTCAAGTAGGA-AAAGACGAAAAA-A--AGTTCTCAAACTCAAAAGCAAGCCTTGATA
* * * * * *
42344 GGGATCTTTTATTAATTCCATTATTCTATTCAAGTCC
126 GGGATATTTTAGTAATTCCACTACTATATTAAAGT-C
* * *
42381 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATTAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGACATTTAA
* *
42446 GTAATCTG-CAAAGTAGGAAAAGATGAAAAAAAGTTCTCCAAACTCCAAAAGCAAGCCTTGGTAG
65 GTAATCTGTC-AAGTAGGAAAAGACGAAAAAAAGTTCT-CAAACT-CAAAAGCAAGCCTTGATAG
42510 GGATATTTTAGTAATTCCACTACTATATTAAAGTC
127 GGATATTTTAGTAATTCCACTACTATATTAAAGTC
* *
42545 ATTTGAGAAACGACAAAAAAGTCTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGACATTTA
1 A-TTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGACATTTA
*
42610 AGTAATCTGTCAAGTGGGAAAAGACGAAAAAAA
64 AGTAATCTGTCAAGTAGGAAAAGACGAAAAAAA
42643 TTAGTTCTCT
Statistics
Matches: 227, Mismatches: 28, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
163 6 0.03
164 7 0.03
165 127 0.56
166 85 0.37
167 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (161 bp):
ATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGACATTTAAG
TAATCTGTCAAGTAGGAAAAGACGAAAAAAAGTTCTCAAACTCAAAAGCAAGCCTTGATAGGGAT
ATTTTAGTAATTCCACTACTATATTAAAGTC
Found at i:47614 original size:22 final size:23
Alignment explanation
Indices: 47589--47632 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47579 GCATAATCAA
*
47589 GACTCC-TTGTGAGAGCATTTGG
1 GACTCCTTTATGAGAGCATTTGG
*
47611 GACTCCTTTATGAGAGCGTTTG
1 GACTCCTTTATGAGAGCATTTG
47633 TCTTGCTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (23 bp):
GACTCCTTTATGAGAGCATTTGG
Found at i:48622 original size:29 final size:29
Alignment explanation
Indices: 48589--48646 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
48579 GTATGTATAC
* *
48589 AAGGAGATATCTAATTGTAATGAGATCTG
1 AAGGAGATATCTAACTGTAATGAAATCTG
48618 AAGGAGATATCTAACTGTAATGAAATCTG
1 AAGGAGATATCTAACTGTAATGAAATCTG
48647 CTATCTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (29 bp):
AAGGAGATATCTAACTGTAATGAAATCTG
Found at i:49038 original size:14 final size:14
Alignment explanation
Indices: 49021--49098 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
49011 CTATTCCTAC
49021 TATTATATTATTAT
1 TATTATATTATTAT
*
49035 TATTA-GTTATTAGT
1 TATTATATTATTA-T
49049 TA-TATATTATTAT
1 TATTATATTATTAT
49062 TA--ATATTAATTAAT
1 TATTATATT-ATT-AT
* * * *
49076 CAATAAATAATTAT
1 TATTATATTATTAT
49090 TATTATATT
1 TATTATATT
49099 TAAAATATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
12 5 0.10
13 14 0.29
14 24 0.49
15 3 0.06
16 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:49093 original size:3 final size:3
Alignment explanation
Indices: 49021--49069 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
49011 CTATTCCTAC
*
49021 TAT TA- TAT TAT TAT TAT TAGT TAT TAGT TAT ATAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT -TAT TAT TAT TAT TAT
49068 TA
1 TA
49070 ATTAATCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 29 0.73
4 9 0.22
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:49164 original size:2 final size:2
Alignment explanation
Indices: 49157--49193 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
49147 TATACTATCC
*
49157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49194 AAAAAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56136 original size:23 final size:23
Alignment explanation
Indices: 56106--56151 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
56096 GAACGCTTTC
56106 TCTCTCACAATT-AACTACTTCTA
1 TCTCTCACAATTGAA-TACTTCTA
56129 TCTCTCACAATTGAATACTTCTA
1 TCTCTCACAATTGAATACTTCTA
56152 GTCTTTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.39
Consensus pattern (23 bp):
TCTCTCACAATTGAATACTTCTA
Done.