Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013115.1 Corchorus capsularis cultivar CVL-1 contig13136, 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: 21235
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Found at i:471 original size:181 final size:173
Alignment explanation
Indices: 135--484 Score: 522
Period size: 181 Copynumber: 2.0 Consensus size: 173
125 ATTTATACAA
* *
135 TACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGTGGTTTAACTTTAAGAGTTGACATGTGTA
1 TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGAGTTGACATGTGTA
* *
200 CCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAACTTCTTA
66 CCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATGTGTCAACTTCTTA
* *
265 ACCCTCTTATGGAGTCCAAAATTTACACTGACAGTGTATATAT
131 ACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATATAT
* *
308 TACACCGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGGTTTGACTTTAAGAGTTGACATGTGTA
1 TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGAGTTGACATGTGTA
*
373 -CCTTAGGGAGTATGTATTAATATTAAATTTTATATTTAATTAATTATGAAATAGGGTATGTGTC
66 CCCTTAGGGAATATGTATTAATATT-AA----ATA--T--TTAATTATGAAATAGGGTATGTGTC
*
437 AACTTCTTATCCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTAT
122 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTAT
485 TGTATAATAA
Statistics
Matches: 158, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
172 23 0.15
173 63 0.40
177 3 0.02
179 1 0.01
181 68 0.43
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (173 bp):
TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGAGTTGACATGTGTA
CCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATGTGTCAACTTCTTA
ACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATATAT
Found at i:664 original size:205 final size:206
Alignment explanation
Indices: 308--703 Score: 591
Period size: 205 Copynumber: 1.9 Consensus size: 206
298 GTGTATATAT
* * * * *
308 TACACCGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGGTTTGACTTTAAGAGTTGACATGTGTA
1 TACACCGTCAATGGAGTTTAGCAGACTACACGTGCGGAGTTTAACTTTAAGAGTTGACATGTGTA
* *
373 CCTTAGGGAGTATGTATTAATATTAAATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCA
66 CCTTAGGGAATATGTACTAATATTAAA---TATATTTAATTAATTATGAAATAGGGTATGTGTCA
*
438 ACTTCTTATCCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATAATCCTATAA
128 ACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATAATCCTATAA
503 GAAAATTTATACAA
193 GAAAATTTATACAA
*
517 TACACCGTCAATGGAGTTTAGC-GTACTACACGTGCGGAGTTTAACTTTAAGGGTTGACATGTGT
1 TACACCGTCAATGGAGTTTAGCAG-ACTACACGTGCGGAGTTTAACTTTAAGAGTTGACATGTGT
* *
581 ACTCTTAGGGAATATGTACTAATATT-AA-ATATTTAATTACTTATGAAATGGGGTATGTGTCAA
65 AC-CTTAGGGAATATGTACTAATATTAAATATATTTAATTAATTATGAAATAGGGTATGTGTCAA
* * * *
644 CTTTTTAACCCGCTTATGGAGTCCAAAATTTACATTGACATTGTATTGTATAATAATCCT
129 CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATAATCCT
704 TATTATAAAG
Statistics
Matches: 170, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
205 88 0.52
208 1 0.01
209 60 0.35
210 21 0.12
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (206 bp):
TACACCGTCAATGGAGTTTAGCAGACTACACGTGCGGAGTTTAACTTTAAGAGTTGACATGTGTA
CCTTAGGGAATATGTACTAATATTAAATATATTTAATTAATTATGAAATAGGGTATGTGTCAACT
TCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATAATCCTATAAGAA
AATTTATACAA
Found at i:1754 original size:3 final size:3
Alignment explanation
Indices: 1746--1789 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1736 TACAATAATT
1746 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1790 TACAAGGGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:7638 original size:166 final size:165
Alignment explanation
Indices: 7171--7652 Score: 547
Period size: 166 Copynumber: 2.9 Consensus size: 165
7161 GAGTCATTTG
* * * *
7171 TCAATTGAGAAATAACCAAAAAGTTTAGTTATTTAATCTCCTTCAAGAATCAAAAGTTAGGTCAT
1 TCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCACCTT-AAGAATCAAAAGTTAGGACAT
* * * *
7236 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATCAATCCTTG
* * * * * * *
7301 ATGGGGATATTTTATTAATTCCACTACTTTATTCAAG
129 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAA
* * ** * * *
7338 TCCATTGAGAAATGACCAAAAAGATTACTTAACTAATCCCCTCAAGAATCAAAAATTAGGACATT
1 TCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCACCTTAAGAATCAAAAGTTAGGACATT
* ** * * ** * *
7403 TAAGTAATCTGCCAATTAGGAAAAGAC-AAAAAAAAAAGTTATCTAC-TTCCAAAAGCAAGCCTT
65 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT-CGCTCC-TCATCAATCCTT
7466 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAA
128 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAA
*
7504 TCAATTGAGAAATGACCAAAAAGTCTAATTATTTAATCACCTTAAGAATCAAAAGTTAGGGCATT
1 TCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCACCTTAAGAATCAAAAGTTAGGACATT
* * **
7569 TAAGTAATCGGCCAAGT-GAGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCGGG
65 TAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATCAATCCTTG
*
7633 GTAGGGATCTTTAAGTAATT
129 GTAGGGATCTTTTAGTAATT
7653 TCCATATGTT
Statistics
Matches: 257, Mismatches: 52, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
165 17 0.07
166 188 0.73
167 52 0.20
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (165 bp):
TCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCACCTTAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATCAATCCTTGGT
AGGGATCTTTTAGTAATTCCACTACTCTATTAAAA
Found at i:8652 original size:21 final size:22
Alignment explanation
Indices: 8621--8665 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
8611 GTAAAAGTGT
*
8621 AAAAAGTGGGACGGTGTTTAAC
1 AAAAAGTGGGACGCTGTTTAAC
8643 AAAAAG-GGGACGCTGTTTAAC
1 AAAAAGTGGGACGCTGTTTAAC
8664 AA
1 AA
8666 TTCAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.40, C:0.11, G:0.29, T:0.20
Consensus pattern (22 bp):
AAAAAGTGGGACGCTGTTTAAC
Found at i:8713 original size:2 final size:2
Alignment explanation
Indices: 8706--8742 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
8696 AGCAATCCAG
*
8706 AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8743 AACATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16717 original size:22 final size:22
Alignment explanation
Indices: 16691--16737 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
16681 ATTTATTCAT
16691 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
16713 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
16735 TAT
1 TAT
16738 GTAGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:16733 original size:11 final size:11
Alignment explanation
Indices: 16691--16733 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
16681 ATTTATTCAT
*
16691 TATTAATTAAC
1 TATTAATTAGC
*
16702 TATTAATTAGA
1 TATTAATTAGC
16713 TATTAATTAGC
1 TATTAATTAGC
16724 TATTAATTAG
1 TATTAATTAG
16734 ATATGTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:17004 original size:27 final size:27
Alignment explanation
Indices: 16974--17031 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
16964 AGTTTGCTGT
* * * *
16974 AGTTTGGTATTGTTAAGGAGTATGAAC
1 AGTTTGGTAATGTAAAGGAGTAGGAAA
17001 AGTTTGGTAATGTAAAGGAGTAGGAAA
1 AGTTTGGTAATGTAAAGGAGTAGGAAA
17028 AGTT
1 AGTT
17032 GAGTAGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (27 bp):
AGTTTGGTAATGTAAAGGAGTAGGAAA
Found at i:17418 original size:59 final size:59
Alignment explanation
Indices: 17346--17459 Score: 219
Period size: 59 Copynumber: 1.9 Consensus size: 59
17336 ATGAGATGTC
17346 TTAAAAACCCACTTATAACATATTAAAAACCTACTTAACATATCAATAATTAAAGAGAA
1 TTAAAAACCCACTTATAACATATTAAAAACCTACTTAACATATCAATAATTAAAGAGAA
*
17405 TTAAAAACCCACTTATAACATATTAAGAACCTACTTAACATATCAATAATTAAAG
1 TTAAAAACCCACTTATAACATATTAAAAACCTACTTAACATATCAATAATTAAAG
17460 GGAACCTCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.28
Consensus pattern (59 bp):
TTAAAAACCCACTTATAACATATTAAAAACCTACTTAACATATCAATAATTAAAGAGAA
Found at i:17639 original size:2 final size:2
Alignment explanation
Indices: 17632--17660 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17622 GACAAAAATA
17632 AT 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 AT A
17661 CAGACAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18952 original size:17 final size:17
Alignment explanation
Indices: 18926--18958 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18916 AATAACTCAC
18926 TCAAAACCAAAATCAAA
1 TCAAAACCAAAATCAAA
*
18943 TCAAACCCAAAATCAA
1 TCAAAACCAAAATCAA
18959 TACCCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.27, G:0.00, T:0.12
Consensus pattern (17 bp):
TCAAAACCAAAATCAAA
Found at i:21187 original size:2 final size:2
Alignment explanation
Indices: 21180--21229 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
21170 TAATATGCAG
21180 TA TA TA 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 TA TA TA
21222 TA TA TA TA
1 TA TA TA TA
21230 GTAGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.