Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011484.1 Corchorus capsularis cultivar CVL-1 contig11505, 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: 50778
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2641 original size:27 final size:28
Alignment explanation
Indices: 2610--2663 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
2600 GCATTTAAAC
2610 AAAGAATC-ATAGTGCTAATTA-AATTTT
1 AAAGAA-CAATAGTGCTAATTACAATTTT
2637 AAAGAACAATAGTGCTAATTACAATTT
1 AAAGAACAATAGTGCTAATTACAATTT
2664 CCATGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 1 0.04
27 19 0.76
28 5 0.20
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.33
Consensus pattern (28 bp):
AAAGAACAATAGTGCTAATTACAATTTT
Found at i:28580 original size:51 final size:50
Alignment explanation
Indices: 28504--28600 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 50
28494 CTCTAATCTC
* *
28504 GAAATTCAGAGAGCATGCATCAATCAGTTGAGTGAAAATGCTCGGTGTAAT
1 GAAATTCAGAGAACATGCATCAATCAGTTGAAT-AAAATGCTCGGTGTAAT
* * *
28555 GAAATTTAGAGAACATGTATCAATCAGTTGAATCAAATGCTCGGTG
1 GAAATTCAGAGAACATGCATCAATCAGTTGAATAAAATGCTCGGTG
28601 CAACGGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 12 0.29
51 29 0.71
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (50 bp):
GAAATTCAGAGAACATGCATCAATCAGTTGAATAAAATGCTCGGTGTAAT
Found at i:36358 original size:22 final size:22
Alignment explanation
Indices: 36330--36601 Score: 140
Period size: 22 Copynumber: 12.5 Consensus size: 22
36320 GTAATCACAT
*
36330 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAATCTCATTA
* *
36352 TGAAATTGTT-ATAACCTCACTA
1 TGAAATT-TTGATAATCTCATTA
*
36374 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AATC-TCATTA
* * **
36397 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATCTCATTA
* *
36420 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAA-TCTCATTA
*
36442 TGAAATCTTGATAA---C--TA
1 TGAAATTTTGATAATCTCATTA
* * **
36459 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAATCTCATTA
**
36480 TGATTTTTTGATAATCTCATTA
1 TGAAATTTTGATAATCTCATTA
* **
36502 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCTCATTA
36524 TGAAATTTTG---ATCTACATACTA
1 TGAAATTTTGATAATCT-CAT--TA
**
36546 TGAAATTTTGATAGCCCTC-TTA
1 TGAAATTTTGATA-ATCTCATTA
* *
36568 TGAAATTTTGA-AAACTAAATTA
1 TGAAATTTTGATAATCT-CATTA
36590 TGAAATTTTGAT
1 TGAAATTTTGAT
36602 TACTCCATAA
Statistics
Matches: 197, Mismatches: 31, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 1 0.01
19 5 0.03
20 3 0.02
21 5 0.03
22 124 0.63
23 40 0.20
24 3 0.02
25 1 0.01
26 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCATTA
Found at i:36402 original size:23 final size:23
Alignment explanation
Indices: 36371--36455 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
36361 TATAACCTCA
*
36371 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
36394 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
36417 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
36439 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
36456 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:36429 original size:46 final size:45
Alignment explanation
Indices: 36364--36455 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
36354 AAATTGTTAT
* *
36364 AACCTCACTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATA
1 AACCTCACTATAAAATTTTGATAAAT-TTCCTATAAAATCTTGATA
* * * *
36410 AACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATA
1 AACCTCACTATAAAATTTTGATAAATTTCCTATAAAATCTTGATA
36455 A
1 A
36456 CTACAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 17 0.43
46 23 0.57
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (45 bp):
AACCTCACTATAAAATTTTGATAAATTTCCTATAAAATCTTGATA
Found at i:36758 original size:22 final size:22
Alignment explanation
Indices: 36708--36759 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
36698 TCACATTTTG
36708 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
36729 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
36751 AAAATTTTG
1 AAAATTTTG
36760 TTGACCCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:36810 original size:22 final size:22
Alignment explanation
Indices: 36785--36885 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
36775 CACATTATAT
* *
36785 AATTTTGATAACCTCGCTTTGA
1 AATTTTGATAACATCGCTATGA
* *
36807 AATTTTGATAACAACGCTATGT
1 AATTTTGATAACATCGCTATGA
*
36829 AATTTTGATAATCTTC-CTAT-A
1 AATTTTGATAA-CATCGCTATGA
*
36850 AATTTTGATAATCCGATCTCTATGA
1 AATTTTGATAA--C-ATCGCTATGA
*
36875 AATTTCGATAA
1 AATTTTGATAA
36886 TCACTCTATG
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 11 0.17
22 34 0.53
23 4 0.06
24 4 0.06
25 11 0.17
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
AATTTTGATAACATCGCTATGA
Found at i:36833 original size:76 final size:76
Alignment explanation
Indices: 36695--36835 Score: 169
Period size: 76 Copynumber: 1.9 Consensus size: 76
36685 GAAATTTTTG
* * ** **
36695 TAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTG
1 TAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACGCTATAAAATTTTG
36760 TTGACCCCTTA
66 TTGACCCCTTA
* **
36771 TAATCACATTAT-ATAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACGCTATGTAATTT
1 TAATCACATTATGA-AAATTTGATAACCTC-CTTATGAAATTTTGATAACAACGCTATAAAATTT
36834 TG
64 TG
36836 ATAATCTTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 1 0.02
76 51 0.94
77 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (76 bp):
TAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACGCTATAAAATTTTG
TTGACCCCTTA
Found at i:36895 original size:22 final size:23
Alignment explanation
Indices: 36804--36896 Score: 86
Period size: 22 Copynumber: 4.1 Consensus size: 23
36794 AACCTCGCTT
*
36804 TGAAATTTTGATAA-CAACGCTA
1 TGAAATTTTGATAATCAACTCTA
* **
36826 TGTAATTTTGATAATCTTC-CTA
1 TGAAATTTTGATAATCAACTCTA
*
36848 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAAT-C-AACTCTA
*
36872 TGAAATTTCGATAATC-ACTCTA
1 TGAAATTTTGATAATCAACTCTA
36894 TGA
1 TGA
36897 GATTGGATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 12 0.20
22 26 0.44
23 4 0.07
24 5 0.08
25 12 0.20
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAATCAACTCTA
Found at i:36997 original size:26 final size:26
Alignment explanation
Indices: 36964--37029 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
36954 CCTTCATAAG
*
36964 AAATTTTGATAACTACACTATATATA
1 AAATTTTGATAACCACACTATATATA
36990 AAATTTTGATAACCACACTATATATA
1 AAATTTTGATAACCACACTATATATA
37016 AAATTTTGATAACC
1 AAATTTTGATAACC
37030 TCCCCATGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (26 bp):
AAATTTTGATAACCACACTATATATA
Found at i:37066 original size:44 final size:44
Alignment explanation
Indices: 37016--37116 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
37006 ACTATATATA
* *
37016 AAATTTTGATAACCTCCCCATGAAA-TATTAGTAACCTC-CTAATG
1 AAATTTTGATAACCACACCATGAAATTATTA-TAACCTCGCT-ATG
* * *
37060 AAATTTTGTTAACCACACTATGAAATTCTTATAACCTCGCTATG
1 AAATTTTGATAACCACACCATGAAATTATTATAACCTCGCTATG
*
37104 ACATTTTGATAAC
1 AAATTTTGATAAC
37117 ATCTTTGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 42 0.88
45 6 0.12
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACCACACCATGAAATTATTATAACCTCGCTATG
Found at i:37072 original size:22 final size:22
Alignment explanation
Indices: 37016--37116 Score: 91
Period size: 22 Copynumber: 4.6 Consensus size: 22
37006 ACTATATATA
* *
37016 AAATTTTGATAACCTCCCCATG
1 AAATTTTGATAACCTCACTATG
*
37038 AAATATT-AGTAACCTC-CTAATG
1 AAATTTTGA-TAACCTCACT-ATG
* *
37060 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAACCTCACTATG
*
37082 AAATTCTT-ATAACCTCGCTATG
1 AAATT-TTGATAACCTCACTATG
*
37104 ACATTTTGATAAC
1 AAATTTTGATAAC
37117 ATCTTTGATA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.06
22 56 0.88
23 4 0.06
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:37281 original size:22 final size:21
Alignment explanation
Indices: 37252--37328 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 21
37242 AACTTCCATA
*
37252 TTTG-TAACCACACTATGGAAT
1 TTTGATAACCAC-CTATGAAAT
*
37273 TTTGATAACCTCCTCATGAAAT
1 TTTGATAACCACCT-ATGAAAT
* * *
37295 TATAATAACCATCTTATGAAAT
1 TTTGATAACCA-CCTATGAAAT
37317 TTTGATAACCAC
1 TTTGATAACCAC
37329 ATAGAGACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 7 0.16
22 36 0.80
23 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
TTTGATAACCACCTATGAAAT
Found at i:37445 original size:19 final size:19
Alignment explanation
Indices: 37393--37448 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
37383 AAAATAATTT
37393 AATAA-GGAATAATTAAAAA
1 AATAATGGAATAATT-AAAA
** *
37412 AATAAT-TTATGATTAAAA
1 AATAATGGAATAATTAAAA
37430 AATAATGGAATAATTAAAA
1 AATAATGGAATAATTAAAA
37449 TATTATTTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (19 bp):
AATAATGGAATAATTAAAA
Found at i:37595 original size:2 final size:2
Alignment explanation
Indices: 37588--37612 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37578 AGATAAGAAT
37588 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
37613 GATTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40199 original size:15 final size:16
Alignment explanation
Indices: 40177--40214 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40167 CGCTCAAATG
40177 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
* *
40192 TTGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
40208 TCGGGTC
1 TCGGGTC
40215 TTTCTCGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.13, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:40743 original size:82 final size:82
Alignment explanation
Indices: 40632--40794 Score: 240
Period size: 82 Copynumber: 2.0 Consensus size: 82
40622 CCATATTAAA
** * *
40632 TATGGGTAATTATTTGATGAATTGACGGTGTAAATTTTATACTCCGCAAGCGGGTTGTGGAGTTG
1 TATGGGTAATTATTTGATGAACAGACGGTGTAAATTTTAGACTCCACAAGCGGGTTGTGGAGTTG
40697 ACACATATCTATTTTTT
66 ACACATATCTATTTTTT
*
40714 TATGGGTAATTATTTGAT-ACACCAG-CGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGT
1 TATGGGTAATTATTTGATGA-A-CAGACGGTGTAAATTTTAGACTCCACAAGCGGGTTGTGGAGT
*
40777 TGACACATGTCTATTTTT
64 TGACACATATCTATTTTT
40795 GAATTAATTA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 1 0.01
82 71 0.97
83 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (82 bp):
TATGGGTAATTATTTGATGAACAGACGGTGTAAATTTTAGACTCCACAAGCGGGTTGTGGAGTTG
ACACATATCTATTTTTT
Found at i:41030 original size:163 final size:162
Alignment explanation
Indices: 40748--41077 Score: 466
Period size: 163 Copynumber: 2.0 Consensus size: 162
40738 GCGGTGTAAA
* * * *
40748 TTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCTATTTTTGAATTAATTAAGTTTTAA
1 TTTTAGACTCCACAAGCGGGTTATAGAGTTGACACATGTCCATTTTTGAATTAATTAAGTTTTAA
*
40813 ATATTTCAATCTAGTCCCTAAAGGACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTCCTAA
66 ATATTTCAATATAGTCCCTAAAGGACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTCCTAA
* * *
40878 ATTCCACTGA-TAGTGTATTGTATAATTGCCTT
131 ACTCCAAT-ACCAGTGTATTGTATAATTGCCTT
* * *
40910 TTTTAGACTCCACAAGCGGGTTATAGAGTTGGCATATGTCCATTTTTTTAATTAATTAAGTTTTA
1 TTTTAGACTCCACAAGCGGGTTATAGAGTTGACACATGTCCA-TTTTTGAATTAATTAAGTTTTA
* * * *
40975 AATGTTTCAATATAGTCCCTAGAGGACACATGTCACCCTTCAGGA-TCGCCTTGTGTAGTCTGCT
65 AATATTTCAATATAGTCCCTAAAGGACACATGTCACCCTTCAGGACCCG-CTTGTGTAGTCTCCT
* *
41039 AAACTCTAATACCGGTGTATTGTATAATTGCCTT
129 AAACTCCAATACCAGTGTATTGTATAATTGCCTT
41073 TTTTA
1 TTTTA
41078 TTTAATTAAT
Statistics
Matches: 148, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
162 39 0.26
163 109 0.74
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (162 bp):
TTTTAGACTCCACAAGCGGGTTATAGAGTTGACACATGTCCATTTTTGAATTAATTAAGTTTTAA
ATATTTCAATATAGTCCCTAAAGGACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTCCTAA
ACTCCAATACCAGTGTATTGTATAATTGCCTT
Done.