Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010272.1 Corchorus capsularis cultivar CVL-1 contig10293, 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: 5925
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Found at i:2655 original size:22 final size:23
Alignment explanation
Indices: 2627--2686 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
2617 AGAAAGATGC
*
2627 AATCAGTAAAAG-GTAAAATGGT
1 AATCAGTAAAAGAGTAAAATGAT
*
2649 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAATGAT
2671 AATCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
2687 TAGAAGTCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAATGAT
Found at i:2752 original size:55 final size:55
Alignment explanation
Indices: 2679--2876 Score: 265
Period size: 55 Copynumber: 3.5 Consensus size: 55
2669 ATAATCAGTA
*
2679 AAGAGTAATAG-AAGTCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTT
1 AAGA-TAATAGTAA-TCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
* * * *
2735 AAGATAATAGTGATCAGTAAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTC
1 AAGATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
*
2790 AA-AGTAGACAGTAATCAGTAAATCAGTTAATTAAGTAAAAAGAGATTAATCAGAGTT
1 AAGA-TA-ATAGTAATCAGTAAATCAG-TAATTAAGTAAAAAGAGATTAATCAGAGTT
*
2847 AAGGTAATTAGTAATCAGTAAATCAGTAAT
1 AAGATAA-TAGTAATCAGTAAATCAGTAAT
2877 CAGGTAAAGG
Statistics
Matches: 124, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.01
55 48 0.39
56 27 0.22
57 48 0.39
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (55 bp):
AAGATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
Found at i:2782 original size:26 final size:26
Alignment explanation
Indices: 2695--2785 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 26
2685 AATAGAAGTC
2695 AGTAAATCAGTAATTAAGTAAAAAGA
1 AGTAAATCAGTAATTAAGTAAAAAGA
* * * **
2721 AATTAATCAG-AGTTAAGATAATAGTGA
1 AGTAAATCAGTAATTAAG-TAA-AAAGA
2748 TCAGTAAATCAGTAATTAAGTAAAAAGA
1 --AGTAAATCAGTAATTAAGTAAAAAGA
*
2776 GGTAAATCAG
1 AGTAAATCAG
2786 AGTCAAAGTA
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
25 6 0.12
26 20 0.41
27 3 0.06
28 3 0.06
29 11 0.22
30 6 0.12
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (26 bp):
AGTAAATCAGTAATTAAGTAAAAAGA
Found at i:2830 original size:57 final size:54
Alignment explanation
Indices: 2682--2876 Score: 257
Period size: 57 Copynumber: 3.5 Consensus size: 54
2672 ATCAGTAAAG
* *
2682 AGTAATAG-AAGTCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTA
1 AGTAATAGTAA-TCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTAA
* * *
2736 AGATAATAGTGATCAGTAAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAA
1 AG-TAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGT-AA
*
2792 AGTAGACAGTAATCAGTAAATCAGTTAATTAAGTAAAAAGAGATTAATCAGAGTTAA
1 AGTA-ATAGTAATCAGTAAATCAG-TAATTAAGTAAAAAGAGATTAATCAGAG-TAA
*
2849 GGTAATTAGTAATCAGTAAATCAGTAAT
1 AGTAA-TAGTAATCAGTAAATCAGTAAT
2877 CAGGTAAAGG
Statistics
Matches: 123, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
54 2 0.02
55 46 0.37
56 26 0.21
57 48 0.39
58 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (54 bp):
AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTAA
Found at i:3239 original size:21 final size:22
Alignment explanation
Indices: 3218--3534 Score: 215
Period size: 21 Copynumber: 14.1 Consensus size: 22
3208 TTGTAAGAGT
*
3218 AAAAGGTAATCATTAAAAAGTA
1 AAAAGGTAATCAGTAAAAAGTA
* *
3240 AGAAGGTAATCA--ACAAGAGTGA
1 AAAAGGTAATCAGTA-AAAAGT-A
*
3262 AATAA--TAGTCAGTAAAAAAGTA
1 AA-AAGGTAATCAGT-AAAAAGTA
* *
3284 AAATAAGTAATCAGT-AAGAGTGA
1 AAA-AGGTAATCAGTAAAAAGT-A
*
3307 AAAA-GTAA-CAAGTAAGAAGT-
1 AAAAGGTAATC-AGTAAAAAGTA
* * *
3327 AAAAGGAAATCAGT-AAGAGTG
1 AAAAGGTAATCAGTAAAAAGTA
* *
3348 AAAAGGTGATCAGTAAAAGGTAA
1 AAAAGGTAATCAGTAAAAAGT-A
* *
3371 AAAAGCTAATCAGTAGAAA-TA
1 AAAAGGTAATCAGTAAAAAGTA
*
3392 AAAAGGTAATCAGTAAAAAG-C
1 AAAAGGTAATCAGTAAAAAGTA
*
3413 AAAAGGCAATCAGTAAAAAGTA
1 AAAAGGTAATCAGTAAAAAGTA
*
3435 AAAAGAGTAATCAGTAAAAAAAGGAGCA
1 AAAAG-GTAATCAGT---AAAA--AGTA
*
3463 GAAAATGATAATCAGTAAAAGAGTA
1 -AAAA-GGTAATCAGTAAAA-AGTA
*
3488 AAATGGTAATCAGTAAAAAGTA
1 AAAAGGTAATCAGTAAAAAGTA
* *
3510 AGAAGGTAATCAGTAAAGAGTA
1 AAAAGGTAATCAGTAAAAAGTA
3532 AAA
1 AAA
3535 TCCGTAAAGA
Statistics
Matches: 232, Mismatches: 36, Indels: 54
0.72 0.11 0.17
Matches are distributed among these distances:
20 10 0.04
21 73 0.31
22 63 0.27
23 47 0.20
24 11 0.05
25 4 0.02
26 8 0.03
28 3 0.01
29 12 0.05
30 1 0.00
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (22 bp):
AAAAGGTAATCAGTAAAAAGTA
Found at i:3405 original size:65 final size:65
Alignment explanation
Indices: 3327--3450 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 65
3317 AGTAAGAAGT
* * ** *
3327 AAAAGGAAATCAGT-AAGAGTGAAAAGGTGATCAGTAAAAGGTAAAAA-AGCTAATCAGTAGAAA
1 AAAAGGAAATCAGTAAAAAG-CAAAAGGCAATCAGTAAAAAGTAAAAAGAG-TAATCAGTAGAAA
3390 TA
64 TA
*
3392 AAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAAGAGTAATCAGTA
1 AAAAGGAAATCAGTAAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAAGAGTAATCAGTA
3451 AAAAAAGGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
65 45 0.88
66 6 0.12
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.16
Consensus pattern (65 bp):
AAAAGGAAATCAGTAAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAAGAGTAATCAGTAGAAATA
Found at i:3535 original size:44 final size:43
Alignment explanation
Indices: 3212--3534 Score: 225
Period size: 44 Copynumber: 7.2 Consensus size: 43
3202 GGTAGTTTGT
*
3212 AAGAGTAAAAGGTAATCATTAAAAAGTAAGAAGGTAATCA--A
1 AAGAGTAAAAGGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
* * * *
3253 CAAGAGTGAAATA-ATAGTCAGTAAAAAAGTAAAATAAGTAATCAGT-
1 -AAGAGT-AAA-AGGTAATCAGT-AAAAAGTAAGA-AGGTAATCAGTA
* * *
3299 AAGAGTGAAAAAGTAA-CAAGTAAGAAGTAA-AAGGAAATCAGT-
1 AAGAGT-AAAAGGTAATC-AGTAAAAAGTAAGAAGGTAATCAGTA
* * * *
3341 AAGAGTGAAAAGGTGATCAGTAAAAGGTAAAAAAGCTAATCAGTA
1 AAGAGT-AAAAGGTAATCAGTAAAAAGT-AAGAAGGTAATCAGTA
* *
3386 GAA-A-TAAAAAGGTAATCAGTAAAAAGCAA-AAGGCAATCAGTA
1 -AAGAGT-AAAAGGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
* * *
3428 AAAAGTAAAAAGAGTAATCAGTAAAAAAAGGAGCAGAAAATGATAATCAGTAA
1 AAGAGT-AAAAG-GTAATCAGT--AAAAAGTA--AG--AA-GGTAATCAGT-A
3481 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
1 AAGAGTAAAA-GGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
3525 AAGAGTAAAA
1 AAGAGTAAAA
3535 TCCGTAAAGA
Statistics
Matches: 227, Mismatches: 28, Indels: 50
0.74 0.09 0.16
Matches are distributed among these distances:
41 2 0.01
42 49 0.22
43 22 0.10
44 70 0.31
45 33 0.15
46 11 0.05
48 3 0.01
50 7 0.03
51 2 0.01
52 21 0.09
53 7 0.03
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (43 bp):
AAGAGTAAAAGGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
Found at i:3536 original size:16 final size:16
Alignment explanation
Indices: 3517--3556 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3507 GTAAGAAGGT
3517 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
*
3533 AATCCGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
3549 AAT-AGTAA
1 AATCAGTAA
3557 TCAGTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:3592 original size:21 final size:21
Alignment explanation
Indices: 3559--3648 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
3549 AATAGTAATC
*
3559 AGTAAAAGA-TAACCAGTAAG
1 AGTAAAATAGTAACCAGTAAG
3579 AGTAAAATAGTAACCAGTAAG
1 AGTAAAATAGTAACCAGTAAG
* * **
3600 AGCAAACT-GATAATTAGTAAG
1 AGTAAAATAG-TAACCAGTAAG
* *
3621 AGTCAAATAGTAATCAGTAAAG
1 AGTAAAATAGTAACCAGT-AAG
3643 AGTAAA
1 AGTAAA
3649 GGGTGATCAG
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.16
21 38 0.68
22 9 0.16
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.20
Consensus pattern (21 bp):
AGTAAAATAGTAACCAGTAAG
Found at i:3738 original size:29 final size:28
Alignment explanation
Indices: 3713--3775 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
3703 GTAAAAAGTG
3713 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
3741 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
3768 GTAA-AAAT
1 GTAATAAAT
3776 GATAAAAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 1 0.03
27 18 0.62
28 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:3781 original size:29 final size:28
Alignment explanation
Indices: 3720--3783 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
3710 GTGGTAATAA
*
3720 ATAAAAGAGAGTAAGAAAAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAGAGTAAATG
*
3748 GTAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGT--AAATG
3777 ATAAAAG
1 ATAAAAG
3784 TAGCAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 16 0.53
28 5 0.17
29 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (28 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAATG
Done.