Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008925.1 Corchorus capsularis cultivar CVL-1 contig08946, 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: 12356
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1089 original size:38 final size:38
Alignment explanation
Indices: 1033--1108 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
1023 CCAGAGCCTT
*
1033 AATACTAGCTCTTTTGGAG-CTTTCAATCAAATTTGCAC
1 AATACTAGCTCTTCTGGAGTC-TTCAATCAAATTTGCAC
1071 AATACTAGCTCTTCTGGAGTCTTCAATCAAATTTGCAC
1 AATACTAGCTCTTCTGGAGTCTTCAATCAAATTTGCAC
1109 TATCCGATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (38 bp):
AATACTAGCTCTTCTGGAGTCTTCAATCAAATTTGCAC
Found at i:2460 original size:54 final size:54
Alignment explanation
Indices: 2385--2487 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
2375 ATATAATTTA
* * *
2385 AAGTTGATAGTATGACAACTTCGGGTGTCAAAGTTAGGCAACAATTAAATTTTT
1 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTAGGCAACAATTAAATTTTT
*
2439 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAA
1 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTAGGCAACAATTAAA
2488 CAAATATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (54 bp):
AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTAGGCAACAATTAAATTTTT
Found at i:2524 original size:58 final size:54
Alignment explanation
Indices: 2395--2528 Score: 144
Period size: 54 Copynumber: 2.4 Consensus size: 54
2385 AAGTTGATAG
* * ** *
2395 TATGACAACTTCGGGTGTCAAAGTTAGGCAACAATTAAATTTTTAAGTGGATAG
1 TATGACAACTTCGGGTGTCAAACTTAGGCAACAATTAAATATTTAAGTCCATAA
* * *
2449 TATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAACAAATATTTACA-TCCTTAA
1 TATGACAACTTCGGGTGTCAAACTTAGGCAACAATT----AAATATTTA-AGTCCATAA
2507 TATGACAACTTCGGGTGTCAAA
1 TATGACAACTTCGGGTGTCAAA
2529 ATGATACAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
54 33 0.50
58 32 0.48
59 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (54 bp):
TATGACAACTTCGGGTGTCAAACTTAGGCAACAATTAAATATTTAAGTCCATAA
Found at i:2564 original size:29 final size:29
Alignment explanation
Indices: 2508--2564 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2498 CATCCTTAAT
*
2508 ATGACAACTTCGGGTGTCAAAATGATACA
1 ATGACAACTTCGGGTGTCAAAATAATACA
*
2537 ATGACAACTTCGGGTGTCAAAGTAATAC
1 ATGACAACTTCGGGTGTCAAAATAATAC
2565 TATATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (29 bp):
ATGACAACTTCGGGTGTCAAAATAATACA
Found at i:2614 original size:33 final size:33
Alignment explanation
Indices: 2572--2668 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
2562 TACTATATTT
* *
2572 TTGATGTGACAACTTCAGGTGCCACTAATATGC
1 TTGATGTGACAACTTTAGGTGCCACTAATATAC
* *
2605 TTGATGTGACAACTTTAGGTGCCACTGATATAT
1 TTGATGTGACAACTTTAGGTGCCACTAATATAC
2638 TTGATGTGACAACTTTAGGTGCCACTAATAT
1 TTGATGTGACAACTTTAGGTGCCACTAATAT
2669 TCAAGATAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (33 bp):
TTGATGTGACAACTTTAGGTGCCACTAATATAC
Found at i:2768 original size:32 final size:33
Alignment explanation
Indices: 2708--2775 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
2698 TTTAATTATA
* *
2708 AAAGAAAGGTAGAAGGAGGAGATTATGCATGAT
1 AAAGAAAGGTAGAAGGAAGAGATCATGCATGAT
* *
2741 AAAGAAATGTAGAA-GAAGAGATCATGCATGTT
1 AAAGAAAGGTAGAAGGAAGAGATCATGCATGAT
2773 AAA
1 AAA
2776 TAAACTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.49, C:0.04, G:0.28, T:0.19
Consensus pattern (33 bp):
AAAGAAAGGTAGAAGGAAGAGATCATGCATGAT
Found at i:5353 original size:22 final size:23
Alignment explanation
Indices: 5328--5388 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
5318 AACGGAAAAG
5328 AAAAACTTTTTTTTTTCGACGCA
1 AAAAACTTTTTTTTTTCGACGCA
*
5351 AAAAACAATTTTTTTTATCGACGC-
1 AAAAAC--TTTTTTTTTTCGACGCA
5375 --AAACTTTTTTTTTT
1 AAAAACTTTTTTTTTT
5389 TAAGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 9 0.26
22 4 0.12
23 6 0.18
25 15 0.44
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.48
Consensus pattern (23 bp):
AAAAACTTTTTTTTTTCGACGCA
Found at i:5708 original size:6 final size:6
Alignment explanation
Indices: 5694--5723 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5684 AAAGCAAAGC
*
5694 AAATCT AAATAT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT
5724 GAAGCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATCT
Found at i:6678 original size:10 final size:10
Alignment explanation
Indices: 6663--6688 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6653 GAGGACTCTA
6663 GAATTTTCTG
1 GAATTTTCTG
6673 GAATTTTCTG
1 GAATTTTCTG
6683 GAATTT
1 GAATTT
6689 AGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Done.