Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012516.1 Corchorus capsularis cultivar CVL-1 contig12537, 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: 84734
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:907 original size:56 final size:56
Alignment explanation
Indices: 821--934 Score: 194
Period size: 56 Copynumber: 2.0 Consensus size: 56
811 TTTGGTGATT
*
821 AAAAATTGATTAATTATTCTGTCTTTTTTACCTAA-ATAAAGTGATTAATTTTGAAG
1 AAAAATTGATTAATTATTATGTCTTTTTTACC-AATATAAAGTGATTAATTTTGAAG
*
877 AAAAATTGATTAATTATTATGTTTTTTTTACCAATATAAAGTGATTAATTTTGAAG
1 AAAAATTGATTAATTATTATGTCTTTTTTACCAATATAAAGTGATTAATTTTGAAG
933 AA
1 AA
935 TGAAAATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 2 0.04
56 53 0.96
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (56 bp):
AAAAATTGATTAATTATTATGTCTTTTTTACCAATATAAAGTGATTAATTTTGAAG
Found at i:1244 original size:23 final size:23
Alignment explanation
Indices: 1210--1258 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1200 AGACTCAACA
* *
1210 AATCGTGTTTTTAGTAAATTTTC
1 AATCGTGGTTTTAGTAAATTTCC
*
1233 AATCGTGGTTTTAGTATATTTCC
1 AATCGTGGTTTTAGTAAATTTCC
1256 AAT
1 AAT
1259 TCAGTTGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (23 bp):
AATCGTGGTTTTAGTAAATTTCC
Found at i:3382 original size:23 final size:22
Alignment explanation
Indices: 3328--3383 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3318 GAATGAAATG
*
3328 TTACTTATTTCTTTATAGCATTA
1 TTACTT-TTTCTTTATACCATTA
*
3351 TTA-TGTTTTCTTTATAACCTTTA
1 TTACT-TTTTCTTTAT-ACCATTA
3374 TTACTTTTTC
1 TTACTTTTTC
3384 AGTAACCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 10 0.36
23 17 0.61
24 1 0.04
ACGTcount: A:0.21, C:0.14, G:0.04, T:0.61
Consensus pattern (22 bp):
TTACTTTTTCTTTATACCATTA
Found at i:22254 original size:1 final size:1
Alignment explanation
Indices: 22248--22277 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
22238 CTATTGCTCC
22248 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22278 GTCTATTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23547 original size:8 final size:8
Alignment explanation
Indices: 23525--23580 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
23515 TTAAGATTAA
23525 TTATT-GT
1 TTATTAGT
*
23532 TAATTAGT
1 TTATTAGT
23540 TTATTAGTT
1 TTATTAG-T
23549 TTAATTAGT
1 TT-ATTAGT
23558 TTATTAGT
1 TTATTAGT
*
23566 GTTAATTAAT
1 -TT-ATTAGT
23576 TTATT
1 TTATT
23581 TACGATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
7 4 0.10
8 17 0.41
9 10 0.24
10 10 0.24
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (8 bp):
TTATTAGT
Found at i:23552 original size:18 final size:18
Alignment explanation
Indices: 23524--23580 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
23514 ATTAAGATTA
*
23524 ATTATTGTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
*
23542 ATTAGTTTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
*
23560 ATTAGTGTTAATTAATTT
1 ATTAGTGTTAATTAGTTT
23578 ATT
1 ATT
23581 TACGATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
ATTAGTGTTAATTAGTTT
Found at i:23572 original size:36 final size:38
Alignment explanation
Indices: 23510--23580 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
23500 AATTGTGAAA
* *
23510 TTTAATTAAGATTAATTATTGTTAATTAGTTTATTAGT
1 TTTAATTAAGATTAATTAGTGTTAATTAATTTATTAGT
*
23548 TTTAATT-AG-TTTATTAGTGTTAATTAATTTATT
1 TTTAATTAAGATTAATTAGTGTTAATTAATTTATT
23581 TACGATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 21 0.70
37 2 0.07
38 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (38 bp):
TTTAATTAAGATTAATTAGTGTTAATTAATTTATTAGT
Found at i:23744 original size:24 final size:24
Alignment explanation
Indices: 23694--23777 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
23684 CTCCGCCCGT
** * * *
23694 AGGGAGAGAGAGGCACAGTTTCAG
1 AGGGAGAGAGACACTCAGATTCTG
* *
23718 AGGGGGAGAGACACTCATATTCTG
1 AGGGAGAGAGACACTCAGATTCTG
** *
23742 AGGGAGAGAGAGGCTCAGATTCTA
1 AGGGAGAGAGACACTCAGATTCTG
23766 AGGGAGAGAGAC
1 AGGGAGAGAGAC
23778 GCTGTGAGGG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.39, T:0.14
Consensus pattern (24 bp):
AGGGAGAGAGACACTCAGATTCTG
Found at i:24221 original size:21 final size:21
Alignment explanation
Indices: 24195--24244 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
24185 CGTCCTGAAG
24195 TGCCAGAACAGTGCAACTGTT
1 TGCCAGAACAGTGCAACTGTT
24216 TGCCAGAACAGTGCAACTGTT
1 TGCCAGAACAGTGCAACTGTT
24237 TGCCAGAA
1 TGCCAGAA
24245 GTTAAGAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
TGCCAGAACAGTGCAACTGTT
Found at i:27656 original size:15 final size:15
Alignment explanation
Indices: 27645--27674 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27635 CCCCCTCCTT
*
27645 ACCCCACTCCTCCCC
1 ACCCCACCCCTCCCC
27660 ACCCCACCCCTCCCC
1 ACCCCACCCCTCCCC
27675 CATTTGAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.77, G:0.00, T:0.10
Consensus pattern (15 bp):
ACCCCACCCCTCCCC
Found at i:27701 original size:46 final size:47
Alignment explanation
Indices: 27646--27737 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 47
27636 CCCCTCCTTA
*
27646 CCCCACTCC-TCCCCACCCCACCCCTCCCCCATTTGAACCAAACAAGT
1 CCCCACTCCTTACCCACCCCACCCCT-CCCCATTTGAACCAAACAAGT
27693 CCCC-CTCCTTACCCACCCCACCCCTCCCCATTTGAACCAAACAAG
1 CCCCACTCCTTACCCACCCCACCCCTCCCCATTTGAACCAAACAAG
27738 GGCTAAGTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
46 24 0.56
47 19 0.44
ACGTcount: A:0.24, C:0.57, G:0.04, T:0.15
Consensus pattern (47 bp):
CCCCACTCCTTACCCACCCCACCCCTCCCCATTTGAACCAAACAAGT
Found at i:30354 original size:10 final size:10
Alignment explanation
Indices: 30339--30363 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30329 TTAGTTTAAA
30339 GATTTCAGAG
1 GATTTCAGAG
30349 GATTTCAGAG
1 GATTTCAGAG
30359 GATTT
1 GATTT
30364 GAAAGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (10 bp):
GATTTCAGAG
Found at i:31322 original size:37 final size:37
Alignment explanation
Indices: 31280--31374 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 37
31270 AATTTTTCTT
**
31280 TTTGTTTCCAACGTCCTATTTAATTTTGGATTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTACATTTTGTC
** *
31317 TTTGTTTCCAACGTTGTATTTAATTTTACCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTACATTTTGTC
* **
31354 TTAGTCACCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
31375 GGGTGCTTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.18, C:0.19, G:0.12, T:0.52
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTACATTTTGTC
Found at i:33425 original size:17 final size:16
Alignment explanation
Indices: 33403--33436 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
33393 TTCTGCTCTC
33403 TTTTTTCATCTTGTTTT
1 TTTTTTCAT-TTGTTTT
33420 TTTTTTCATTTGTTTT
1 TTTTTTCATTTGTTTT
33436 T
1 T
33437 GCATCTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTTTCATTTGTTTT
Found at i:35577 original size:30 final size:30
Alignment explanation
Indices: 35541--35602 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
35531 AGCCTCTGGT
35541 ATGTCTCACAGTGGATTTACTTTAGTAGTA
1 ATGTCTCACAGTGGATTTACTTTAGTAGTA
35571 ATGTCTCACAGTGGATTTACTTTAGTAGTA
1 ATGTCTCACAGTGGATTTACTTTAGTAGTA
35601 AT
1 AT
35603 AATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (30 bp):
ATGTCTCACAGTGGATTTACTTTAGTAGTA
Found at i:45259 original size:2 final size:2
Alignment explanation
Indices: 45252--45280 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45242 TTCTCGTTAT
45252 TA TA 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 TA TA T
45281 TTTCACACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57134 original size:3 final size:3
Alignment explanation
Indices: 57128--57152 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57118 ACTACTATTA
57128 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
57153 TACTTGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:59238 original size:12 final size:12
Alignment explanation
Indices: 59218--59257 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
59208 ATTTTTCCCC
* *
59218 TTTGCCTTTGGA
1 TTTGGCTTTGGT
59230 TTTGGCTTTGGT
1 TTTGGCTTTGGT
59242 TTTGG-TTTGGT
1 TTTGGCTTTGGT
59253 TTTGG
1 TTTGG
59258 TTGGAGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.03, C:0.07, G:0.33, T:0.57
Consensus pattern (12 bp):
TTTGGCTTTGGT
Found at i:59252 original size:11 final size:11
Alignment explanation
Indices: 59224--59259 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
59214 CCCCTTTGCC
*
59224 TTTGGATTTGG
1 TTTGGTTTTGG
59235 CTTTGGTTTTGG
1 -TTTGGTTTTGG
59247 TTTGGTTTTGG
1 TTTGGTTTTGG
59258 TT
1 TT
59260 GGAGAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.03, C:0.03, G:0.33, T:0.61
Consensus pattern (11 bp):
TTTGGTTTTGG
Found at i:59256 original size:17 final size:18
Alignment explanation
Indices: 59224--59259 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
59214 CCCCTTTGCC
59224 TTTGGATTTGGCTTTGGT
1 TTTGGATTTGGCTTTGGT
*
59242 TTTGG-TTTGGTTTTGGT
1 TTTGGATTTGGCTTTGGT
59259 T
1 T
59260 GGAGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.03, C:0.03, G:0.33, T:0.61
Consensus pattern (18 bp):
TTTGGATTTGGCTTTGGT
Found at i:61249 original size:2 final size:2
Alignment explanation
Indices: 61242--61275 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61232 GGAGTTTGGG
61242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61276 CTCTTTACCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71500 original size:180 final size:179
Alignment explanation
Indices: 71252--71714 Score: 465
Period size: 180 Copynumber: 2.6 Consensus size: 179
71242 CCGATCAAGA
* * ** * * * * * *
71252 TGATTCAAGTGTCT-ATTTAAAGGTTGTTCAATGATCTACAATTTTCATGAAAGG-TTCGAAAAC
1 TGATTCAAGTGTCTCA-TAAAAGGTTATTTTATGATCTTCAACTTTCATG-CAGGACTCCAAAGC
* * *
71315 TAAATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAATAATT-AGTTGTTTCGGTTAACGGGAAT
64 TAAATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAAAAATTAACTTGTTTCGGTTAACGAGAAT
* * **
71379 GGACT-ATCCACTTAATA-TAGCATTACTTTTGCTCCAGATGTCTTATTGAGC
129 -GAATGATCCACTTAATAGTA-CATAACTTTTGCTCCAGATGTCCGATTGAGC
71430 TGATTCAAGTGTCTCATAAAAGGTTATTTTAT-ATCATCTACAACTTTCATGCAGGACTCCAAAG
1 TGATTCAAGTGTCTCATAAAAGGTTATTTTATGATC-T-T-CAACTTTCATGCAGGACTCCAAAG
* * *
71494 CTAAATTTAATGTTTCAAGTAT-AAAAAATGCTTC-CAAAAATTAACTTTTTTCGGTTAGCGAGA
63 CTAAATTTAATGTTTCAAGTATCAAAAAA-GCTTCTGAAAAATTAACTTGTTTCGGTTAACGAGA
* * *
71557 ATGAATGGTCCACTTAATAGTACATAATTTTTGCTCCAGATGTCCGATTGAGG
127 ATGAATGATCCACTTAATAGTACATAACTTTTGCTCCAGATGTCCGATTGAGC
** * * * * **
71610 TGATTCAAGTGTCTGTTAAAAGGTTGTTTTGTGATCTTCAACTTTTATGTAGGACTTGAAAGCTA
1 TGATTCAAGTGTCTCATAAAAGGTTATTTTATGATCTTCAACTTTCATGCAGGACTCCAAAGCTA
* * * * * *
71675 AATTTGATTTTTTAAATACCAAAAATGCTTCTGAAAAATT
66 AATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAAAAATT
71715 TATATTTTAG
Statistics
Matches: 235, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
177 3 0.01
178 69 0.29
179 32 0.14
180 126 0.54
181 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (179 bp):
TGATTCAAGTGTCTCATAAAAGGTTATTTTATGATCTTCAACTTTCATGCAGGACTCCAAAGCTA
AATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAAAAATTAACTTGTTTCGGTTAACGAGAATGA
ATGATCCACTTAATAGTACATAACTTTTGCTCCAGATGTCCGATTGAGC
Found at i:81634 original size:11 final size:12
Alignment explanation
Indices: 81618--81650 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
81608 TAATGAACCA
81618 TAAACGAAT-TT
1 TAAACGAATATT
*
81629 TAAACGAGTATT
1 TAAACGAATATT
81641 TAAACGAATA
1 TAAACGAATA
81651 ATAAACGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (12 bp):
TAAACGAATATT
Found at i:81667 original size:23 final size:23
Alignment explanation
Indices: 81617--81667 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
81607 TTAATGAACC
**
81617 ATAAACGAATTTTAAACGAGTAT
1 ATAAACGAATAATAAACGAGTAT
*
81640 TTAAACGAATAATAAACGAGCTA-
1 ATAAACGAATAATAAACGAG-TAT
81663 ATAAA
1 ATAAA
81668 TGAACATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (23 bp):
ATAAACGAATAATAAACGAGTAT
Found at i:83689 original size:105 final size:106
Alignment explanation
Indices: 83509--83770 Score: 404
Period size: 107 Copynumber: 2.5 Consensus size: 106
83499 TAATTTTCTA
* * **
83509 ACCCTTAAAAGAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
83572 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
83612 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
83677 TTTCTAAAACCCTATAATAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
83719 ACCCTTAAAATAAAAATAAAATCTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
83771 AGACTAAACT
Statistics
Matches: 145, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 26 0.18
104 15 0.10
105 36 0.25
107 68 0.47
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Done.