Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014690.1 Corchorus capsularis cultivar CVL-1 contig14711, 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: 33400
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2931 original size:59 final size:61
Alignment explanation
Indices: 2837--2951 Score: 171
Period size: 59 Copynumber: 1.9 Consensus size: 61
2827 TACTCTGATA
**
2837 TTTTTGGAACTTGTTGGTTCTGATACAAGTTAGACCATAATCGAAATCAATTGTCATTGTC
1 TTTTTGGAACTTGTTGGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCATTGTC
* * *
2898 TTTTTGGAAC-T-TTGTTTCTGATATATGTTAGACCATAAAAGAAATCAATTGTCA
1 TTTTTGGAACTTGTTGGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCA
2952 CCACTTTTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 38 0.78
60 1 0.02
61 10 0.20
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (61 bp):
TTTTTGGAACTTGTTGGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCATTGTC
Found at i:3499 original size:23 final size:26
Alignment explanation
Indices: 3455--3508 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
3445 CAAAACAATG
3455 AATTTCAAGGCTTTTTTATCAA-A-AAA
1 AATTTCAAGGC--TTTTATCAAGATAAA
3481 AATTTCAAGGC-TTTATCAAGATAAA
1 AATTTCAAGGCTTTTATCAAGATAAA
3506 AAT
1 AAT
3509 CACTTAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 8 0.31
24 1 0.04
25 6 0.23
26 11 0.42
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (26 bp):
AATTTCAAGGCTTTTATCAAGATAAA
Found at i:11052 original size:24 final size:23
Alignment explanation
Indices: 11005--11050 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
10995 TAATTAAAGC
11005 AACAAAAATAGTGCACTTTGTTT
1 AACAAAAATAGTGCACTTTGTTT
11028 AACAAAAATAGTGCACTTTGTTT
1 AACAAAAATAGTGCACTTTGTTT
11051 TAGGGTTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
AACAAAAATAGTGCACTTTGTTT
Found at i:13317 original size:20 final size:18
Alignment explanation
Indices: 13271--13318 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
13261 AAAAATGCAT
13271 TATATA-ATTTATATATG
1 TATATACATTTATATATG
13288 TATAATTACATTTATGTATATG
1 TAT-A-TACATTTA--TATATG
13310 TATATACAT
1 TATATACAT
13319 AATGATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 2 0.08
20 10 0.38
21 1 0.04
22 9 0.35
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (18 bp):
TATATACATTTATATATG
Found at i:16819 original size:26 final size:25
Alignment explanation
Indices: 16770--16819 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
16760 ACTTGGTTAG
* *
16770 TAATTAATTTGTTCTTAATTAATCT
1 TAATTAATTTATTATTAATTAATCT
16795 TAATTAATTTAATTATTAATTAATC
1 TAATTAATTT-ATTATTAATTAATC
16820 ACTAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (25 bp):
TAATTAATTTATTATTAATTAATCT
Found at i:21441 original size:81 final size:81
Alignment explanation
Indices: 21339--21506 Score: 291
Period size: 81 Copynumber: 2.1 Consensus size: 81
21329 TCCTTCTAAG
*
21339 AGGTTGATTGGAATCAGTTTGAACAGTTTGATCTTGTAAAACTGGTAAGACAAGATCAGATGTGT
1 AGGTTGATTGGAATCAATTTGAACAGTTTGATCTTGTAAAACTGGTAAGACAAGATCAGATGTGT
21404 GATGAATAGTAGTGAA
66 GATGAATAGTAGTGAA
* * *
21420 AGGTTGATTGGAATCAATTTGAACAGTTTGGTCTTTTAAAACTGGTAAGACAAGATCAGATGTTT
1 AGGTTGATTGGAATCAATTTGAACAGTTTGATCTTGTAAAACTGGTAAGACAAGATCAGATGTGT
*
21485 GATGAATAGTAGTGAT
66 GATGAATAGTAGTGAA
21501 AGGTTG
1 AGGTTG
21507 TGATTCTGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (81 bp):
AGGTTGATTGGAATCAATTTGAACAGTTTGATCTTGTAAAACTGGTAAGACAAGATCAGATGTGT
GATGAATAGTAGTGAA
Found at i:22918 original size:18 final size:18
Alignment explanation
Indices: 22895--22932 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
22885 GAGTAACAGC
22895 TACCTTGGCTTTATTAGG
1 TACCTTGGCTTTATTAGG
22913 TACCTTGGCTTTATTAGG
1 TACCTTGGCTTTATTAGG
22931 TA
1 TA
22933 GATGAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (18 bp):
TACCTTGGCTTTATTAGG
Found at i:25111 original size:313 final size:313
Alignment explanation
Indices: 24543--25169 Score: 1245
Period size: 313 Copynumber: 2.0 Consensus size: 313
24533 GCTCTCCTAA
24543 CTAACTAATAACTAACACCTAACTTGCTATTAATGCTTAATTAAAACTCATCGTTTTGTTAATAT
1 CTAACTAATAACTAACACCTAACTTGCTATTAATGCTTAATTAAAACTCATCGTTTTGTTAATAT
*
24608 CTAATAGGATGGGCGGGGTGGGATTATGGAAAAGAAGATGGCTATCTCCTATTGTGTAGCCCATT
66 CTAATAGGATGGGCAGGGTGGGATTATGGAAAAGAAGATGGCTATCTCCTATTGTGTAGCCCATT
24673 TCCATATCCATATTGAATGTGTTCTCAATCAGGTACTTGGCAAAACACCAAATCAATTTACTTGT
131 TCCATATCCATATTGAATGTGTTCTCAATCAGGTACTTGGCAAAACACCAAATCAATTTACTTGT
24738 GTGAAATATATGTACATGTGTACTTTATAATTGACAAGGGGTTATAGTACTATTGATTCTAGCAT
196 GTGAAATATATGTACATGTGTACTTTATAATTGACAAGGGGTTATAGTACTATTGATTCTAGCAT
24803 TAAGGTCAGTTAGTTTTGATTTTGATTGCAATTGGATACTTAAAATATTGATC
261 TAAGGTCAGTTAGTTTTGATTTTGATTGCAATTGGATACTTAAAATATTGATC
24856 CTAACTAATAACTAACACCTAACTTGCTATTAATGCTTAATTAAAACTCATCGTTTTGTTAATAT
1 CTAACTAATAACTAACACCTAACTTGCTATTAATGCTTAATTAAAACTCATCGTTTTGTTAATAT
24921 CTAATAGGATGGGCAGGGTGGGATTATGGAAAAGAAGATGGCTATCTCCTATTGTGTAGCCCATT
66 CTAATAGGATGGGCAGGGTGGGATTATGGAAAAGAAGATGGCTATCTCCTATTGTGTAGCCCATT
24986 TCCATATCCATATTGAATGTGTTCTCAATCAGGTACTTGGCAAAACACCAAATCAATTTACTTGT
131 TCCATATCCATATTGAATGTGTTCTCAATCAGGTACTTGGCAAAACACCAAATCAATTTACTTGT
25051 GTGAAATATATGTACATGTGTACTTTATAATTGACAAGGGGTTATAGTACTATTGATTCTAGCAT
196 GTGAAATATATGTACATGTGTACTTTATAATTGACAAGGGGTTATAGTACTATTGATTCTAGCAT
25116 TAAGGTCAGTTAGTTTTGATTTTGATTGCAATTGGATACTTAAAATATTGATC
261 TAAGGTCAGTTAGTTTTGATTTTGATTGCAATTGGATACTTAAAATATTGATC
25169 C
1 C
25170 CATTTTAAAA
Statistics
Matches: 313, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
313 313 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (313 bp):
CTAACTAATAACTAACACCTAACTTGCTATTAATGCTTAATTAAAACTCATCGTTTTGTTAATAT
CTAATAGGATGGGCAGGGTGGGATTATGGAAAAGAAGATGGCTATCTCCTATTGTGTAGCCCATT
TCCATATCCATATTGAATGTGTTCTCAATCAGGTACTTGGCAAAACACCAAATCAATTTACTTGT
GTGAAATATATGTACATGTGTACTTTATAATTGACAAGGGGTTATAGTACTATTGATTCTAGCAT
TAAGGTCAGTTAGTTTTGATTTTGATTGCAATTGGATACTTAAAATATTGATC
Found at i:31315 original size:35 final size:36
Alignment explanation
Indices: 31257--31412 Score: 115
Period size: 35 Copynumber: 4.2 Consensus size: 36
31247 TGACCACCTT
31257 TTACTCTT-TACTGATTACTATTTTACTC-TTACTAA
1 TTAC-CTTCTACTGATTACTATTTTACTCTTTACTAA
*
31292 TTACCTTCTACTGATTA-TCATTTTACTCTTTACTGA
1 TTACCTTCTACTGATTACT-ATTTTACTCTTTACTAA
* ** *
31328 TTACCTTCTTACTTTTTACTGATTACCATTTTGTTC-TTACTGA
1 TTA-C--CTT-C----TACTGATTACTATTTTACTCTTTACTAA
* * *
31371 TTA-CTTTTACTAATTACTATTTTACTCTTTACTGA
1 TTACCTTCTACTGATTACTATTTTACTCTTTACTAA
31406 TTACCTT
1 TTACCTT
31413 TTTACTTTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
34 20 0.20
35 32 0.33
36 12 0.12
37 1 0.01
39 6 0.06
40 1 0.01
43 10 0.10
44 16 0.16
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (36 bp):
TTACCTTCTACTGATTACTATTTTACTCTTTACTAA
Found at i:31317 original size:22 final size:20
Alignment explanation
Indices: 31292--31380 Score: 65
Period size: 22 Copynumber: 4.2 Consensus size: 20
31282 CTCTTACTAA
31292 TTACCTTCTACTGATTATCATT
1 TTACCTT-TACTGATTA-CATT
*
31314 TTACTCTTTACTGATTACCTT
1 TTAC-CTTTACTGATTACATT
*
31335 CTTACTTTTTACTGATTACCATT
1 -TTAC-CTTTACTGATTA-CATT
**
31358 TT-GTTCTTACTGATTAC-TT
1 TTACCT-TTACTGATTACATT
31377 TTAC
1 TTAC
31381 TAATTACTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.07
20 3 0.05
21 13 0.23
22 31 0.54
23 6 0.11
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (20 bp):
TTACCTTTACTGATTACATT
Found at i:31411 original size:78 final size:78
Alignment explanation
Indices: 31252--31435 Score: 255
Period size: 78 Copynumber: 2.3 Consensus size: 78
31242 ATCACTGACC
* * *
31252 ACCTTTTACTCTTTACTGATTACTATTTTACTCTTACTAATTACCTTCTACTGATTATCATTTTA
1 ACCTTTTACTTTTTACTGATTACCATTTTACTCTTACTAATTACCTTCTACTAATTATCATTTTA
31317 CTCTTTACTGATT
66 CTCTTTACTGATT
** * *
31330 ACCTTCTTACTTTTTACTGATTACCATTTTGTTCTTACTGATTA-CTTTTACTAATTA-CTATTT
1 ACCTT-TTACTTTTTACTGATTACCATTTTACTCTTACTAATTACCTTCTACTAATTATC-ATTT
31393 TACTCTTTACTGATT
64 TACTCTTTACTGATT
*
31408 ACCTTTTTACTTTTTTCTGATTACCATT
1 ACC-TTTTACTTTTTACTGATTACCATT
31436 ACTTTTTACC
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
77 1 0.01
78 59 0.62
79 35 0.37
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (78 bp):
ACCTTTTACTTTTTACTGATTACCATTTTACTCTTACTAATTACCTTCTACTAATTATCATTTTA
CTCTTTACTGATT
Found at i:31427 original size:22 final size:22
Alignment explanation
Indices: 31371--31432 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
31361 TTCTTACTGA
*
31371 TTACT-TTTACTAATTA-CTATT
1 TTACTCTTTACTGATTACCT-TT
31392 TTACTCTTTACTGATTACCTTT
1 TTACTCTTTACTGATTACCTTT
* *
31414 TTACTTTTTTCTGATTACC
1 TTACTCTTTACTGATTACC
31433 ATTACTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.14
22 29 0.81
23 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.03, T:0.56
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCTTT
Found at i:31502 original size:30 final size:32
Alignment explanation
Indices: 31466--31552 Score: 88
Period size: 37 Copynumber: 2.6 Consensus size: 32
31456 TTGAATTTAA
31466 TTACCATTTTATTGATTACT-TCTTTA-TTTT
1 TTACCATTTTATTGATTACTCTCTTTATTTTT
* *
31496 TTACCATTTTACTCTTTACTGATCTCTCTTTATTTTT
1 TTACCATTTTA---TTGA-TTA-CTCTCTTTATTTTT
*
31533 TTACCATTTTACTGATTACT
1 TTACCATTTTATTGATTACT
31553 ATTTTACTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
30 11 0.24
32 2 0.04
33 5 0.11
34 4 0.09
35 2 0.04
36 6 0.13
37 15 0.33
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.59
Consensus pattern (32 bp):
TTACCATTTTATTGATTACTCTCTTTATTTTT
Found at i:31599 original size:26 final size:26
Alignment explanation
Indices: 31547--31600 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31537 CATTTTACTG
**
31547 ATTACTATTTTACTCTCTTGAGTTTA
1 ATTACTATTTTACTCTCTTGAACTTA
31573 ATTACTATTTTCACTCT-TTGAACTTA
1 ATTACTATTTT-ACTCTCTTGAACTTA
31599 AT
1 AT
31601 CACCATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (26 bp):
ATTACTATTTTACTCTCTTGAACTTA
Found at i:31608 original size:26 final size:26
Alignment explanation
Indices: 31553--31608 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
31543 ACTGATTACT
** * *
31553 ATTTTACTCTCTTGAGTTTAATTACT
1 ATTTTACTCTCTTGAACTTAATCACC
31579 ATTTTCACTCT-TTGAACTTAATCACC
1 ATTTT-ACTCTCTTGAACTTAATCACC
31605 ATTT
1 ATTT
31609 GCCATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (26 bp):
ATTTTACTCTCTTGAACTTAATCACC
Found at i:31623 original size:32 final size:33
Alignment explanation
Indices: 31587--31650 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
31577 CTATTTTCAC
*
31587 TCTTTGAACTTAATCACCA-TTTGCCATTTTAT
1 TCTTTGAACTTAATCACCATTTTACCATTTTAT
* *
31619 TCTTTGAATTTAATTACCATTTTACCATTTTA
1 TCTTTGAACTTAATCACCATTTTACCATTTTA
31651 CCCTTTACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50
Consensus pattern (33 bp):
TCTTTGAACTTAATCACCATTTTACCATTTTAT
Found at i:31736 original size:40 final size:41
Alignment explanation
Indices: 31692--31795 Score: 140
Period size: 40 Copynumber: 2.5 Consensus size: 41
31682 TTTTTATTCT
* *
31692 TTACCGATTTACTGATCACTTCTTTTACTTTTACTC-TTAA
1 TTACCGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
*
31732 TTACC-ATTTTACCGATTACTTCTTTTACTTTGACTCTTTAA
1 TTACCGA-TTTACTGATTACTTCTTTTACTTTGACTCTTTAA
*
31773 TTACTGATTTCACTGATTACTTC
1 TTACCGATTT-ACTGATTACTTC
31796 GTTAATCCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
39 1 0.02
40 31 0.56
41 11 0.20
42 12 0.22
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (41 bp):
TTACCGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
Done.