Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006718.1 Corchorus capsularis cultivar CVL-1 contig06739, 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: 22165
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:7045 original size:27 final size:26
Alignment explanation
Indices: 7015--7072 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
7005 TTATGAAGAA
*
7015 AAATTACTAGTTTACCCTTGGGGTGAG
1 AAATTACTAGTTTACCCTTGAGGTG-G
* * **
7042 AAATGACTATTTTGTCCTTGAGGTGG
1 AAATTACTAGTTTACCCTTGAGGTGG
7068 AAATT
1 AAATT
7073 TCTAAATTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (26 bp):
AAATTACTAGTTTACCCTTGAGGTGG
Found at i:7667 original size:29 final size:29
Alignment explanation
Indices: 7446--7659 Score: 205
Period size: 29 Copynumber: 7.2 Consensus size: 29
7436 TGATAGAAAA
* *
7446 AGTGTGCGGGAGATGCACATGAGTATGAT
1 AGTGTGCGGGAGATGCACATGAATATTAT
* * * *
7475 AGTGTACGGGAGATGTACACAAGTATCAGTAT
1 AGTGTGCGGGAGATG--CACATGAAT-ATTAT
* * *
7507 AGTGTGCAGGAGACGCACATGAATATTCT
1 AGTGTGCGGGAGATGCACATGAATATTAT
* *
7536 AGTGTGCGGGAGGTGCACATGAATATGAT
1 AGTGTGCGGGAGATGCACATGAATATTAT
* * * *
7565 AGTGTACGGGAGATGTACACAAGTATCAGTAT
1 AGTGTGCGGGAGATG--CACATGAAT-ATTAT
* *
7597 AGTGTGCAGGAGACGCACATGAATATTCA-
1 AGTGTGCGGGAGATGCACATGAATATT-AT
7626 AGTGTGCGGGAGATGCACATGAATATTAT
1 AGTGTGCGGGAGATGCACATGAATATTAT
7655 AGTGT
1 AGTGT
7660 ATGGGAGAAG
Statistics
Matches: 145, Mismatches: 32, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
28 1 0.01
29 86 0.59
30 15 0.10
31 13 0.09
32 30 0.21
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (29 bp):
AGTGTGCGGGAGATGCACATGAATATTAT
Found at i:7691 original size:61 final size:58
Alignment explanation
Indices: 7446--7698 Score: 181
Period size: 61 Copynumber: 4.2 Consensus size: 58
7436 TGATAGAAAA
* * *
7446 AGTGTGCGGGAGATGCACATGAGTATGATAGTGTACGGGAGATGTACACAAGTATCAGTAT
1 AGTGTGCGGGAGATGCACATGAATATTATAGTGTACGGGAGA-GTACACAA-TATTA-TAT
* * * * * *
7507 AGTGTGCAGGAGACGCACATGAATATTCTAGTGTGCGGGAG-GTGCAC-ATGAATATGAT
1 AGTGTGCGGGAGATGCACATGAATATTATAGTGTACGGGAGAGTACACAAT-ATTAT-AT
* * * * * * * * *
7565 AGTGTACGGGAGATGTACACAAGTATCAGTATAGTGTGCAGGAGACGCACATGAATATT-CA-
1 AGTGTGCGGGAGATG--CACATGAAT-ATTATAGTGTACGGGAGA-GTACA-CAATATTATAT
* *
7626 AGTGTGCGGGAGATGCACATGAATATTATAGTGTATGGGAGAAGTACACGAACATTAATAT
1 AGTGTGCGGGAGATGCACATGAATATTATAGTGTACGGGAG-AGTACAC-AATATT-ATAT
7687 AGTGTGCGGGAG
1 AGTGTGCGGGAG
7699 GTTCACACAA
Statistics
Matches: 145, Mismatches: 33, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
57 2 0.01
58 39 0.27
59 13 0.09
60 8 0.06
61 75 0.52
62 1 0.01
63 3 0.02
64 2 0.01
65 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (58 bp):
AGTGTGCGGGAGATGCACATGAATATTATAGTGTACGGGAGAGTACACAATATTATAT
Found at i:7713 original size:90 final size:90
Alignment explanation
Indices: 7445--7674 Score: 406
Period size: 90 Copynumber: 2.6 Consensus size: 90
7435 GTGATAGAAA
*
7445 AAGTGTGCGGGAGATGCACATGAGTATGATAGTGTACGGGAGATGTACACAAGTATCAGTATAGT
1 AAGTGTGCGGGAGATGCACATGAATATGATAGTGTACGGGAGATGTACACAAGTATCAGTATAGT
7510 GTGCAGGAGACGCACATGAATATTC
66 GTGCAGGAGACGCACATGAATATTC
* *
7535 TAGTGTGCGGGAGGTGCACATGAATATGATAGTGTACGGGAGATGTACACAAGTATCAGTATAGT
1 AAGTGTGCGGGAGATGCACATGAATATGATAGTGTACGGGAGATGTACACAAGTATCAGTATAGT
7600 GTGCAGGAGACGCACATGAATATTC
66 GTGCAGGAGACGCACATGAATATTC
* * *
7625 AAGTGTGCGGGAGATGCACATGAATATTATAGTGTATGGGAGAAGTACAC
1 AAGTGTGCGGGAGATGCACATGAATATGATAGTGTACGGGAGATGTACAC
7675 GAACATTAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 132 1.00
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (90 bp):
AAGTGTGCGGGAGATGCACATGAATATGATAGTGTACGGGAGATGTACACAAGTATCAGTATAGT
GTGCAGGAGACGCACATGAATATTC
Found at i:13442 original size:203 final size:203
Alignment explanation
Indices: 13088--13659 Score: 984
Period size: 203 Copynumber: 2.9 Consensus size: 203
13078 TTATTTAGTA
*
13088 GAGTTTAGAAAACTACACAAGCGGGTCCTAAAGTGTGACATGTGTCCCTTAGGGACTAGATTGAA
1 GAGTTTAGAAAACTACACAAGCGGGTCCTAAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAA
**
13153 ATATTTAAAGTTTAATTAATTCAAAAAATGGACATGTGTCAACTCCACAAACCGCTTGTGGAGTC
66 ATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTCAACTCCACAAACCGCTTGTGGAGTC
*
13218 CAAAATTTACACCGTCTGTGTATCATATAATCACCCTTTACATTAAGGCAAATTATACAATACAC
131 CAAAATTTACACCGCCTGTGTATCATATAATCACCCTTTACATTAAGGCAAATTATACAATACAC
*
13283 TGGCGGTG
196 CGGCGGTG
*
13291 GAGTTTAGAAAACTACACAAACGGGTCCTAAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAA
1 GAGTTTAGAAAACTACACAAGCGGGTCCTAAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAA
*
13356 ATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTCAACTCCACAAACCGCTTGTGGAATC
66 ATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTCAACTCCACAAACCGCTTGTGGAGTC
13421 CAAAATTTACACCGCCTGTGTATCATATAATCACCCTTTACATTAAGGCAAATTATACAATACAC
131 CAAAATTTACACCGCCTGTGTATCATATAATCACCCTTTACATTAAGGCAAATTATACAATACAC
13486 CGGCGGTG
196 CGGCGGTG
*
13494 GAG--T-------T-CACAAGCGGGTCCTAAAGGGTGACATGTGTCCCTTAGGTACTAGATTGAA
1 GAGTTTAGAAAACTACACAAGCGGGTCCTAAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAA
*
13549 ATATTTAAAACTTAATTAATTCAAAAAATAGACATGTGTCAACTCCACAAACCGCTTGTGGAGTC
66 ATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTCAACTCCACAAACCGCTTGTGGAGTC
*
13614 CAAAATTTACACCACCTGTGTATCATATAATCACCCTTTACATTAA
131 CAAAATTTACACCGCCTGTGTATCATATAATCACCCTTTACATTAA
13660 ATATTTGTAG
Statistics
Matches: 357, Mismatches: 12, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
193 156 0.44
194 1 0.00
201 1 0.00
203 199 0.56
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (203 bp):
GAGTTTAGAAAACTACACAAGCGGGTCCTAAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAA
ATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTCAACTCCACAAACCGCTTGTGGAGTC
CAAAATTTACACCGCCTGTGTATCATATAATCACCCTTTACATTAAGGCAAATTATACAATACAC
CGGCGGTG
Found at i:14633 original size:33 final size:33
Alignment explanation
Indices: 14565--14633 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
14555 TTAACATCTC
* *
14565 TAACTTTATAAGTCAAAGGAAATTATAGTATTT
1 TAACTTTATAAGTCAAAGGAAATAATAGTACTT
*
14598 TAACTTTATAAGTCAAAGGAAATAATTGTACTT
1 TAACTTTATAAGTCAAAGGAAATAATAGTACTT
14631 TAA
1 TAA
14634 ATTCTTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (33 bp):
TAACTTTATAAGTCAAAGGAAATAATAGTACTT
Found at i:14886 original size:23 final size:23
Alignment explanation
Indices: 14846--14889 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
14836 TAAAATAGTT
*
14846 ATAAAAATATTGAATTCAATTAA
1 ATAAAAATAGTGAATTCAATTAA
**
14869 ATAAAAATAGTGTTTTCAATT
1 ATAAAAATAGTGAATTCAATT
14890 GCAAAAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (23 bp):
ATAAAAATAGTGAATTCAATTAA
Found at i:15077 original size:86 final size:84
Alignment explanation
Indices: 14980--15230 Score: 307
Period size: 78 Copynumber: 3.0 Consensus size: 84
14970 GTTTTTTAAT
* * *
14980 TAAAATAGTAAAATATTAAAATATAATAGTTATAAGGTTAATAGATTTAATTATATAAAAATAGA
1 TAAAATGGT-AAA-ATTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
15045 GTTTTTAGTTGAGTACAATAG
64 GTTTTTAGTTGAGTAAAATAG
15066 TAAAATGG------TAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
1 TAAAATGGTAAAATTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
*
15125 TTTTAGTTTAGTAAAATAG
66 TTTTAGTTGAGTAAAATAG
* * *
15144 TAAAATGGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAATAAAAA
1 TAAAATGGTAAAAT--TAAAATATAATAGTTATAAGGATATTAGATTTAATT--AT--ATAAAAA
*
15209 TAAAGTTTTTAGTTGAGTAAAA
60 TAGAGTTTTTAGTTGAGTAAAA
15231 CTATAGAAAC
Statistics
Matches: 143, Mismatches: 10, Indels: 20
0.83 0.06 0.12
Matches are distributed among these distances:
78 74 0.52
86 40 0.28
88 2 0.01
90 27 0.19
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (84 bp):
TAAAATGGTAAAATTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
TTTTAGTTGAGTAAAATAG
Found at i:15146 original size:8 final size:8
Alignment explanation
Indices: 15133--15166 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
15123 GTTTTTAGTT
15133 TAGTAAAA
1 TAGTAAAA
15141 TAGTAAAA
1 TAGTAAAA
*
15149 TGGTAAAA
1 TAGTAAAA
*
15157 TGGTAAAA
1 TAGTAAAA
15165 TA
1 TA
15167 AAATAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (8 bp):
TAGTAAAA
Found at i:16479 original size:164 final size:165
Alignment explanation
Indices: 16098--16529 Score: 515
Period size: 161 Copynumber: 2.6 Consensus size: 165
16088 ATGAGGAGCG
* *
16098 AGAGAACTAATTTTTTTCGTCTTTTCCCACTTGATCA-ATTACTTAAATGCCCTAACTTTTGATT
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGA-CAGATTACTTAAATGTCCTAACTTTTGATT
* * * * *
16162 CTTGAGGTGATTAAATAACT-A-TTATTGGTCATTTCTCAATTAACTTTAATAGAGTAGTGGAAT
65 CTTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAATGAACTTGAATAGAGTAGTGAAAT
* * * **
16225 TACTAAAAGATCCCTACCAAGACTTGCTTTTGGAGTT
130 TAATAAAAAATCCCTA-CAAGACTTGATGATGGAGTT
* * * * *
16262 AGA-AA-T-TTTTTTTTCGTCTTTTCTTATTTGGCAGATTACTTAAATGTCCTAACTTTTGATTA
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTC
* * *
16324 TTGAGGGGATTAAAAATAAGTAATCTTTTTGGTCATTTCTTAATGGACTTGAATAGAGTAGTGAA
66 TTGAGGGGATT--AAATAACTAA-CTTTTTGGTCATTTCTCAATGAACTTGAATAGAGTAGTGAA
*
16389 ATTAATAAAAAATCCC-A-AGGA-TTGATGAT-GAGTT
128 ATTAATAAAAAATCCCTACAAGACTTGATGATGGAGTT
* * *
16423 AGAGAACTAATCTTTTTCGTCTTTACCTACTTGACAGATCACTTAAATGTCCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTC
*
16488 TTGATGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
66 TTGAGGGGATTAAATAACT-AACTTTTTGGTCATTTCTCAAT
16530 TGACAAATGA
Statistics
Matches: 226, Mismatches: 32, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
160 2 0.01
161 64 0.28
162 34 0.15
163 15 0.07
164 62 0.27
165 1 0.00
166 48 0.21
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (165 bp):
AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTC
TTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAATGAACTTGAATAGAGTAGTGAAATT
AATAAAAAATCCCTACAAGACTTGATGATGGAGTT
Done.