Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009751.1 Corchorus capsularis cultivar CVL-1 contig09772, 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: 10979
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Found at i:6144 original size:35 final size:35
Alignment explanation
Indices: 6105--6594 Score: 829
Period size: 35 Copynumber: 14.0 Consensus size: 35
6095 CGGTCATCTT
* * * *
6105 AAGAAGTTTTCAGATGTTAGAGTTGATCTTATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
6140 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
6175 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
*
6210 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
*
6245 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
6280 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-TTC
*
6316 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
*
6351 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
6386 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
6421 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
**
6456 AAGAAGTTTTCAGAGGTCAGAGTTGATCTTGTTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
*
6491 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
*
6526 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
* *
6561 AAGAAGTTTCCA-ACGATCAGAGTTGATCTCATTT
1 AAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATTT
6595 TTAGTATTTT
Statistics
Matches: 436, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
34 1 0.00
35 401 0.92
36 34 0.08
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (35 bp):
AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
Found at i:6611 original size:35 final size:35
Alignment explanation
Indices: 6542--6798 Score: 311
Period size: 35 Copynumber: 7.3 Consensus size: 35
6532 TTTTCAGAGG
* * *
6542 TCAGAGTTGATCTC-CTTTCAAGAAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
* * * *
6577 TCAGAGTTGATCTCATTTTTAGTATTTTCGAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
6612 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
6647 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
6682 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACTA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
6717 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * * * * *
6752 TCAAAGGTGATCTCA-TTTCAAGAAATTTCCGATGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
6787 TCAGAGTTGATC
1 TCAGAGTTGATC
6799 CAGGGGAGTT
Statistics
Matches: 194, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
34 4 0.02
35 187 0.96
36 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:6639 original size:70 final size:71
Alignment explanation
Indices: 6191--6798 Score: 338
Period size: 70 Copynumber: 8.7 Consensus size: 71
6181 TTTTCAGAGG
* * * * * *
6191 TCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA-TTCCAAGAAGTT
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGTA-TT
*
6253 TT-CAGA-GG
63 TTCCA-ACGA
* * * * * * *
6261 TCAGAGTTGATCTCA-TATCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATATTCAAGAAGTT
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGTA-TT
*
6324 TT-CAGA-GG
63 TTCCA-ACGA
* * * * * * *
6332 TCAGAGTTGATCTCA-TATCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA-TATCAAGAAGTT
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGTA-TT
*
6394 TT-CAGA-GG
63 TTCCA-ACGA
* * * * *
6402 TCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA-TTTCAAGAAGTT
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGTA-TT
*
6464 TT-CAGA-GG
63 TTCCA-ACGA
* * * * * *
6472 TCAGAGTTGAT--CTTGTTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTC-GTTTCAAGAAGT
1 TCAGAGTTGATCGCAT-TTTCAAGAAGTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGTA-T
*
6533 TTT-CAGA-GG
62 TTTCCA-ACGA
* * * *
6542 TCAGAGTTGATCTC-CTTTCAAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTTAGTATTTTC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTATTTTC
*
6606 GAACGA
66 CAACGA
* * *
6612 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAATGATCAGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTATTTTC
6676 CAACGA
66 CAACGA
* * *
6682 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACTATCAGAGTTGATCACATTTTCAGTAGTTTC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTATTTTC
*
6746 CAACAA
66 CAACGA
* * * * * *
6752 TCAAAGGTGATCTCA-TTTCAAGAAATTTCCGATGATCAGAGTTGATC
1 TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATC
6799 CAGGGGAGTT
Statistics
Matches: 490, Mismatches: 36, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
68 1 0.00
69 10 0.02
70 403 0.82
71 75 0.15
72 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (71 bp):
TCAGAGTTGATCGCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTATTTTC
CAACGA
Found at i:6639 original size:105 final size:106
Alignment explanation
Indices: 6105--6664 Score: 812
Period size: 105 Copynumber: 5.3 Consensus size: 106
6095 CGGTCATCTT
* * * *
6105 AAGAAGTTTTCAGATGTTAGAGTTGATCTTATATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
6170 ATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA-TTTC
66 ATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTTC
*
6210 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
* *
6275 ATATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATTC
66 ATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTTC
*
6316 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
*
6381 ATATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA-TTTC
66 ATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTTC
*
6421 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTT
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
* *
6486 GTTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC-GTTTC
66 ATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTTC
* * *
6526 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCCTTTCAAGAAGTTTCCA-ACGATCAGAGTTGATCT
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCT
** * * *
6590 CATTTTTAGTA-TTTTC-GAACGATCAGAGTTGATCGCATTTTC
65 CATTTCAAGAAGTTTTCAG-A-GGTCAGAGTTGATCTCATTTTC
* * * *
6632 -AGTAGTTTCCA-ATGATCAGAGTTGATCGCATTT
1 AAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATTT
6665 TCAGTATTTT
Statistics
Matches: 418, Mismatches: 30, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
103 1 0.00
104 8 0.02
105 303 0.72
106 106 0.25
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (106 bp):
AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
ATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTTC
Found at i:7557 original size:74 final size:74
Alignment explanation
Indices: 7436--7584 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
7426 GTAATCACGC
7436 ACCCATGTCAATTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTTTTTTCCTCTTCTATTTT
1 ACCCATGTCAATTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTTTTTTCCTCTTCTATTTT
7501 CTTATCATT
66 CTTATCATT
7510 ACCCATGTCAATTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTTTTTTCCTCTTCTATTTT
1 ACCCATGTCAATTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTTTTTTCCTCTTCTATTTT
7575 CTTATCATT
66 CTTATCATT
7584 A
1 A
7585 TCATATGTAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (74 bp):
ACCCATGTCAATTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTTTTTTCCTCTTCTATTTT
CTTATCATT
Found at i:7562 original size:37 final size:37
Alignment explanation
Indices: 7447--7564 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 37
7437 CCCATGTCAA
7447 TTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTT
1 TTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTT
* * * ** **
7484 TTTTCCTCTTCTATTT-T-CTTATCATTAC-CCATGT-C-AA
1 TTTTCCT-TTGT-TTTATGTTTA-CAAT-CTGGAT-TCCTTT
7521 TTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTT
1 TTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTT
7558 TTTTCCT
1 TTTTCCT
7565 CTTCTATTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 20
0.63 0.15 0.22
Matches are distributed among these distances:
35 5 0.09
36 10 0.18
37 27 0.47
38 10 0.18
39 5 0.09
ACGTcount: A:0.14, C:0.20, G:0.08, T:0.58
Consensus pattern (37 bp):
TTTTCCTTTGTTTTATGTTTACAATCTGGATTCCTTT
Found at i:8067 original size:86 final size:87
Alignment explanation
Indices: 7969--8286 Score: 595
Period size: 87 Copynumber: 3.7 Consensus size: 87
7959 AAATTCTTAA
7969 AATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
*
8033 AACAAATAAATAATAAAAGTTG
66 AACAAATAAATAATAAAAATTG
8055 AATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
8119 AACAAATAAATAATAAAAATTG
66 AACAAATAAATAATAAAAATTG
8141 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
8206 AACAAATAAATAATAAAAATTG
66 AACAAATAAATAATAAAAATTG
* *
8228 AATAATAATGAGAATATTTTTCTAAATCTTGCCAGATTGTGGGAGAATTAGGAGATATT
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATT
8287 AAATAATAGT
Statistics
Matches: 228, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
86 101 0.44
87 127 0.56
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (87 bp):
AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
AACAAATAAATAATAAAAATTG
Found at i:8177 original size:173 final size:173
Alignment explanation
Indices: 7969--8286 Score: 593
Period size: 173 Copynumber: 1.8 Consensus size: 173
7959 AAATTCTTAA
7969 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
*
8034 ACAAATAAATAATAAAAGTTGAATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGA
66 ACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGA
*
8098 GATTTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTG
131 GAATTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTG
8141 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
*
8206 AACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAGATTGTGGG
65 AACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGG
8271 AGAATTAGGAGATATT
130 AGAATTAGGAGATATT
8287 AAATAATAGT
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
172 16 0.11
173 85 0.60
174 40 0.28
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (173 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
ACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGA
GAATTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTG
Found at i:9146 original size:29 final size:29
Alignment explanation
Indices: 9104--9165 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
9094 TAATCATTAA
* * *
9104 AATTCCGTCTACCAATATACGTGCTACGT
1 AATTCCATCTACCAATAAACGTGCTACAT
*
9133 AATTCCATCTACCAATAAACGTGTTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
9162 AATT
1 AATT
9166 ATTTAGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (29 bp):
AATTCCATCTACCAATAAACGTGCTACAT
Found at i:10260 original size:6 final size:6
Alignment explanation
Indices: 10250--10291 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
10240 AAAGTTAGTA
* *
10250 AAAAAA AAAAAC AATAAC AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
10292 TTTAGAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Done.