Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011609.1 Corchorus capsularis cultivar CVL-1 contig11630, 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: 27993
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2233 original size:31 final size:31
Alignment explanation
Indices: 2196--2258 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
2186 ATATTTTTCG
2196 ATTGTACCCTTATTTTTAAAATATATTTCTA
1 ATTGTACCCTTATTTTTAAAATATATTTCTA
* *
2227 ATTGTACTCTTTTTTTTAAAATATATTTCTA
1 ATTGTACCCTTATTTTTAAAATATATTTCTA
2258 A
1 A
2259 ATTACCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAATATATTTCTA
Found at i:2596 original size:19 final size:20
Alignment explanation
Indices: 2569--2606 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2559 TACAATTATT
2569 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2589 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2607 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:2826 original size:19 final size:21
Alignment explanation
Indices: 2772--2900 Score: 91
Period size: 22 Copynumber: 6.0 Consensus size: 21
2762 TCTCTCTATG
2772 TGGTTATCAAAATTTCATGAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
2794 TGGTTATTATAATTTCAT-GA
1 TGGTTATCAAAATTTCATAGA
* *
2814 -GGTTATCAAAATTCCATAGTG
1 TGGTTATCAAAATTTCATAG-A
*
2835 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATA-GA
** * * *
2857 TCAGGTTATTGAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATA-GA
*
2881 TGGTTATTAAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
2901 GGTGGTTAAC
Statistics
Matches: 83, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
19 14 0.17
20 3 0.04
21 1 0.01
22 48 0.58
23 1 0.01
24 16 0.19
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:2849 original size:41 final size:41
Alignment explanation
Indices: 2773--2852 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
2763 CTCTCTATGT
* ** *
2773 GGTTATCAAAATTTCATGAGATGGTTATTATAATTTCATGA
1 GGTTATCAAAATTCCATGAGATGGTTACCAAAATTTCATGA
*
2814 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCAT
1 GGTTATCAAAATTCCATGAG-ATGGTTACCAAAATTTCAT
2853 AGGATCAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (41 bp):
GGTTATCAAAATTCCATGAGATGGTTACCAAAATTTCATGA
Found at i:3067 original size:22 final size:22
Alignment explanation
Indices: 3019--3328 Score: 83
Period size: 22 Copynumber: 13.8 Consensus size: 22
3009 TTTCATGGAG
3019 AGGTTATCAAAAATTT-ATAGTG-
1 AGGTTATC-AAAATTTCATA-TGA
*
3041 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
* *
3063 AGGTTATAAAAGTCTCAATTTCATAAGA
1 AGGTTAT-CAA-----AATTTCATATGA
* *
3091 A-G-TACCAAAATTTGATA-GA
1 AGGTTATCAAAATTTCATATGA
*
3110 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* * *
3129 AGTAATTATCGAAATTTTATA-GA
1 AG--GTTATCAAAATTTCATATGA
*
3152 GATCGGATTATCAAAATTT-ATATAA
1 -A--GG-TTATCAAAATTTCATATGA
*
3177 AGATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
3199 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
3221 AGGTTATCAAAATTACATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* * *
3243 TGATTTATCAGAATTTCATATAGA
1 AG-GTTATCAAAATTTCATAT-GA
* * * * *
3267 TGGGTCAACAAAATTTTATA-AA
1 -AGGTTATCAAAATTTCATATGA
*
3289 GAGGTTATCAAAATTTCATA-AA
1 -AGGTTATCAAAATTTCATATGA
*
3311 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
3329 AAATGTGATT
Statistics
Matches: 216, Mismatches: 43, Indels: 58
0.68 0.14 0.18
Matches are distributed among these distances:
19 5 0.02
20 19 0.09
21 30 0.14
22 95 0.44
23 17 0.08
24 19 0.09
25 15 0.07
26 3 0.01
27 1 0.00
28 12 0.06
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:3471 original size:19 final size:19
Alignment explanation
Indices: 3434--3481 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
3424 TTATGAAGTA
3434 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
3454 ATCAAAATTC-AGGAAGGAT
1 ATCAAAATTCAAGG-AGGAT
3473 ATCAAAATT
1 ATCAAAATT
3482 TCATATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.11
19 17 0.63
20 7 0.26
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:3491 original size:22 final size:22
Alignment explanation
Indices: 3425--3636 Score: 86
Period size: 22 Copynumber: 9.9 Consensus size: 22
3415 AAACTTTTAT
*
3425 TATGAAGTA-ATCAAAATTTCA
1 TATGAAGGATATCAAAATTTCA
*
3446 -A-GGAGGATATCAAAA-TTC-
1 TATGAAGGATATCAAAATTTCA
*
3464 -AGGAAGGATATCAAAATTTCA
1 TATGAAGGATATCAAAATTTCA
3485 TATGAA-GATTATCAAAATTTCA
1 TATGAAGGA-TATCAAAATTTCA
** * *
3507 TAGTTTA-GTTTTCAAAATTTCA
1 TA-TGAAGGATATCAAAATTTCA
* * * *
3529 CAAGAGGGTTATCAAAATTTCA
1 TATGAAGGATATCAAAATTTCA
* * *
3551 TA-GTATGTAGATCAAAATTTCA
1 TATG-AAGGATATCAAAATTTCA
* * *
3573 TAGGGA-GATTAACAAAATTTCA
1 TATGAAGGA-TATCAAAATTTCA
* * **
3595 TAATG-ATGTTATCAAAAAATCA
1 T-ATGAAGGATATCAAAATTTCA
* * *
3617 TAGGGAGGTTATCAAAATTT
1 TATGAAGGATATCAAAATTT
3637 GTAGTTATCA
Statistics
Matches: 144, Mismatches: 33, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.01
19 20 0.14
20 11 0.08
21 6 0.04
22 99 0.69
23 7 0.05
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
TATGAAGGATATCAAAATTTCA
Found at i:3527 original size:44 final size:44
Alignment explanation
Indices: 3473--3726 Score: 152
Period size: 44 Copynumber: 5.9 Consensus size: 44
3463 CAGGAAGGAT
*
3473 ATCAAAATTTCATATGAAGATTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATAAGAAGATTATCAAAATTTCATAGTATGTAG
* * * *
3515 TTTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAAGAAGATTATCAAAATTTCATAGTATGTAG
* * * * *
3561 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGATGT-T
1 ATCAAAATTTCATAAGAAGATTATCAAAATTTCATAGT-ATGTAG
** * * * *
3605 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GTA-GT-T
1 ATCAAAATTTCATAAGAAGATTATCAAAATTTCATAGTATGTAG
* * * **
3643 ATCAAGATTTCATAAGAA-AGTTATCAAAATATT-ATAGGGAGGTTT
1 ATCAAAATTTCATAAGAAGA-TTATCAAAAT-TTCATA-GTATGTAG
* * *
3688 ATCAAAATTTTATAGGAAGACTTATCACAATTTCATAGT
1 ATCAAAATTTCATAAGAAGA-TTATCAAAATTTCATAGT
3727 GTGATTATCA
Statistics
Matches: 165, Mismatches: 32, Indels: 25
0.74 0.14 0.11
Matches are distributed among these distances:
38 25 0.15
39 1 0.01
40 3 0.02
41 2 0.01
43 4 0.02
44 90 0.55
45 24 0.15
46 16 0.10
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAAGAAGATTATCAAAATTTCATAGTATGTAG
Found at i:3714 original size:23 final size:22
Alignment explanation
Indices: 3402--3509 Score: 50
Period size: 22 Copynumber: 5.1 Consensus size: 22
3392 ATTACCAAAT
* * *
3402 TAGGAAGGTTATTAAACTTTTA
1 TAGGAAGATTATCAAAATTTTA
* * *
3424 TTATGAAG-TAATCAAAATTTCA
1 -TAGGAAGATTATCAAAATTTTA
*
3446 -AGGAGGA-TATCAAAA--TT-
1 TAGGAAGATTATCAAAATTTTA
* *
3463 CAGGAAGGA-TATCAAAATTTCA
1 TAGGAA-GATTATCAAAATTTTA
* *
3485 TATGAAGATTATCAAAATTTCA
1 TAGGAAGATTATCAAAATTTTA
3507 TAG
1 TAG
3510 TTTAGTTTTC
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
18 5 0.08
19 10 0.16
20 11 0.17
21 3 0.05
22 29 0.45
23 6 0.09
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (22 bp):
TAGGAAGATTATCAAAATTTTA
Found at i:3719 original size:23 final size:23
Alignment explanation
Indices: 3641--3744 Score: 79
Period size: 23 Copynumber: 4.6 Consensus size: 23
3631 AAATTTGTAG
* * * *
3641 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAC
* * **
3663 TTATCAAAATATTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAC
3686 TTATCAAAATTTTATAGGAAGAC
1 TTATCAAAATTTTATAGGAAGAC
* * *
3709 TTATCACAATTTCATAGTG-TGA-
1 TTATCAAAATTTTATAG-GAAGAC
3731 TTATCAAAATTTTA
1 TTATCAAAATTTTA
3745 GAGTGTGATT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
22 27 0.42
23 36 0.56
24 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAC
Found at i:3741 original size:22 final size:22
Alignment explanation
Indices: 3472--3896 Score: 113
Period size: 22 Copynumber: 19.5 Consensus size: 22
3462 TCAGGAAGGA
*
3472 TATCAAAATTTCATA-TGAAGAT
1 TATCAAAATTTCATAGTG-TGAT
*
3494 TATCAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
3516 TTTCAAAATTTCACAAGAG-GGT
1 TATCAAAATTTCA-TAGTGTGAT
*
3538 TATCAAAATTTCATAGTATG-T
1 TATCAAAATTTCATAGTGTGAT
* * *
3559 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGTGAT
* *
3582 TAACAAAATTTCATAATGATG-T
1 TATCAAAATTTCATAGTG-TGAT
** * * *
3604 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
3626 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGTGAT
* * **
3642 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
* * *
3664 TATCAAAATATT-ATAGGGAGGTT
1 TATCAAAAT-TTCATAGTG-TGAT
* *
3687 TATCAAAATTTTATAG-GAAGACT
1 TATCAAAATTTCATAGTG-TGA-T
*
3710 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
* *
3732 TATCAAAATTTTAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
3754 TA-CTAACAA-TTCATA-TG-GAGGT
1 TATC-AA-AATTTCATAGTGTGA--T
* * * ** *
3776 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGTGTGAT
* *
3798 TATCAATATATCATA-TAGATG-T
1 TATCAAAATTTCATAGT-G-TGAT
* * *
3820 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-TGAT
*
3843 TATCAAAATTTCAT--TGGGAAGT
1 TATCAAAATTTCATAGTGTG-A-T
* *
3865 TATCAAAATTTCATATTGAGAT
1 TATCAAAATTTCATAGTGTGAT
3887 CT-TCAAAATT
1 -TATCAAAATT
3897 CTTTAAGGAG
Statistics
Matches: 299, Mismatches: 65, Indels: 78
0.68 0.15 0.18
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
18 1 0.00
19 2 0.01
20 4 0.01
21 12 0.04
22 203 0.68
23 60 0.20
24 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:5413 original size:33 final size:34
Alignment explanation
Indices: 5376--5445 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 34
5366 ATCCTCATTA
*
5376 TATTAAAAAAAT-TGAAAAGAG-GTTGTGAAAGTT
1 TATTAAAAAAATGTGAAAAGAGAG-TGAGAAAGTT
5409 TATT--AAAAATGTGAAAAGAGAGTGAGAAAGTT
1 TATTAAAAAAATGTGAAAAGAGAGTGAGAAAGTT
5441 T-TTAA
1 TATTAA
5446 GAGATATTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
31 8 0.25
32 19 0.59
33 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (34 bp):
TATTAAAAAAATGTGAAAAGAGAGTGAGAAAGTT
Done.