Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006036.1 Corchorus capsularis cultivar CVL-1 contig06054, 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: 7793
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Found at i:642 original size:40 final size:40
Alignment explanation
Indices: 580--660 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
570 ACTTGGTCCT
* * *
580 CCTAATAATGAAGGAAATAAATTAAATTCAGGTTTAGCCC
1 CCTAATAATGAAGGAAAGAAATTAAATCCAAGTTTAGCCC
* *
620 CCTAATAATTAAGGTAAGAAATTAAATCCAAGTTTAGCCC
1 CCTAATAATGAAGGAAAGAAATTAAATCCAAGTTTAGCCC
660 C
1 C
661 AAGTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (40 bp):
CCTAATAATGAAGGAAAGAAATTAAATCCAAGTTTAGCCC
Found at i:1120 original size:2 final size:2
Alignment explanation
Indices: 1113--1139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1103 CTATATTGTT
1113 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 T
1140 TCTCTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3090 original size:53 final size:53
Alignment explanation
Indices: 2966--3081 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
2956 ATGGAAACCA
* * ** *
2966 TCGTTATTCATGTAGGAGATTGGTGGTGTTTACGAATTTATCACGTGGGACTC
1 TCGTTCTTCATGGAGGAGATCAGCGGTGTTTACGAATTTATCACGTGGGACTC
** *
3019 TCGTTCTTCATGGAGGAGATCAGCGGTGTTTATTAATTTATCATGTGGGACTC
1 TCGTTCTTCATGGAGGAGATCAGCGGTGTTTACGAATTTATCACGTGGGACTC
3072 TCGTTCTTCA
1 TCGTTCTTCA
3082 CATGGGAGAC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.39
Consensus pattern (53 bp):
TCGTTCTTCATGGAGGAGATCAGCGGTGTTTACGAATTTATCACGTGGGACTC
Found at i:3442 original size:16 final size:15
Alignment explanation
Indices: 3421--3476 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
3411 TAGGCAATTT
3421 TTTCGGGTCATTCGAG
1 TTTCGGGTCATTCG-G
3437 TTTCGGGTCATAT-GG
1 TTTCGGGTCAT-TCGG
* *
3452 GTTCGGGTTATTCGG
1 TTTCGGGTCATTCGG
3467 TTTTCGGGTC
1 -TTTCGGGTC
3477 TCGGGTCATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.03
15 12 0.36
16 19 0.58
17 1 0.03
ACGTcount: A:0.09, C:0.16, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTCGGGTCATTCGG
Found at i:3481 original size:23 final size:23
Alignment explanation
Indices: 3450--3499 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3440 CGGGTCATAT
* * *
3450 GGGT-TCGGGTTATTCGGTTTTC
1 GGGTCTCGGGTCATACGGGTTTC
3472 GGGTCTCGGGTCATACGGGTTTC
1 GGGTCTCGGGTCATACGGGTTTC
3495 GGGTC
1 GGGTC
3500 ATTTGGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.06, C:0.18, G:0.40, T:0.36
Consensus pattern (23 bp):
GGGTCTCGGGTCATACGGGTTTC
Found at i:3490 original size:16 final size:16
Alignment explanation
Indices: 3471--3546 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
3461 ATTCGGTTTT
3471 CGGGTCTCGGGTCATA
1 CGGGTCTCGGGTCATA
*
3487 CGGGTTTCGGGTCAT-
1 CGGGTCTCGGGTCATA
** *
3502 TTGGTACTCGGGTCATT
1 CGGGT-CTCGGGTCATA
* *
3519 CGGGTTTTGGGTC-TA
1 CGGGTCTCGGGTCATA
*
3534 CTAGGTCTCGGGT
1 C-GGGTCTCGGGT
3547 TGGGTGGGTT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
15 5 0.11
16 37 0.82
17 3 0.07
ACGTcount: A:0.09, C:0.20, G:0.37, T:0.34
Consensus pattern (16 bp):
CGGGTCTCGGGTCATA
Found at i:3500 original size:54 final size:54
Alignment explanation
Indices: 3423--3532 Score: 143
Period size: 54 Copynumber: 2.0 Consensus size: 54
3413 GGCAATTTTT
* *
3423 TCGGGTCATTCGAGTTTCGGGTCATATGGGT-TCGGGTTATTC-GGTTTTCGGGTC
1 TCGGGTCATACGAGTTTCGGGTCAT-TGGGTATCGGGTCATTCGGGTTTT-GGGTC
* *
3477 TCGGGTCATACGGGTTTCGGGTCATTTGGTACTCGGGTCATTCGGGTTTTGGGTC
1 TCGGGTCATACGAGTTTCGGGTCATTGGGTA-TCGGGTCATTCGGGTTTTGGGTC
3532 T
1 T
3533 ACTAGGTCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 4 0.08
54 23 0.47
55 16 0.33
56 6 0.12
ACGTcount: A:0.09, C:0.17, G:0.35, T:0.38
Consensus pattern (54 bp):
TCGGGTCATACGAGTTTCGGGTCATTGGGTATCGGGTCATTCGGGTTTTGGGTC
Found at i:3513 original size:39 final size:38
Alignment explanation
Indices: 3439--3515 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
3429 CATTCGAGTT
* * **
3439 TCGGGTCATATGGGTTCGGGTTATTCGGTTTTCGGGTC
1 TCGGGTCATACGGGTTCGGGTCATTCGGTACTCGGGTC
*
3477 TCGGGTCATACGGGTTTCGGGTCATTTGGTACTCGGGTC
1 TCGGGTCATACGGG-TTCGGGTCATTCGGTACTCGGGTC
3516 ATTCGGGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 13 0.39
39 20 0.61
ACGTcount: A:0.09, C:0.18, G:0.36, T:0.36
Consensus pattern (38 bp):
TCGGGTCATACGGGTTCGGGTCATTCGGTACTCGGGTC
Found at i:3544 original size:32 final size:31
Alignment explanation
Indices: 3473--3546 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
3463 TCGGTTTTCG
* *
3473 GGTCTCGGGTCATACGGGTTTCGGGTCATTT
1 GGTCTCGGGTCATACGGGTTTCGGGTCACTA
* *
3504 GGTACTCGGGTCATTCGGGTTTTGGGTCTACTA
1 GGT-CTCGGGTCATACGGGTTTCGGGTC-ACTA
3537 GGTCTCGGGT
1 GGTCTCGGGT
3547 TGGGTGGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 29 0.78
33 5 0.14
ACGTcount: A:0.09, C:0.19, G:0.36, T:0.35
Consensus pattern (31 bp):
GGTCTCGGGTCATACGGGTTTCGGGTCACTA
Found at i:3588 original size:16 final size:16
Alignment explanation
Indices: 3567--3600 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3557 CGGGTTTTGA
*
3567 TTTCGGGTCACTTGGG
1 TTTCGGGTCAATTGGG
3583 TTTCGGGTCAATTGGG
1 TTTCGGGTCAATTGGG
3599 TT
1 TT
3601 AGCATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (16 bp):
TTTCGGGTCAATTGGG
Found at i:4380 original size:16 final size:16
Alignment explanation
Indices: 4359--4494 Score: 141
Period size: 16 Copynumber: 8.5 Consensus size: 16
4349 GGTTAACTTC
* *
4359 TCGGGTTATTCGAGTT
1 TCGGGTCATTCGGGTT
*
4375 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
*
4391 TCGGGTCATTCGGATT
1 TCGGGTCATTCGGGTT
*
4407 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
4423 TCGGGTCA-TCTGCGTT
1 TCGGGTCATTC-GGGTT
* * *
4439 ACGGGTCATTCCGGTC
1 TCGGGTCATTCGGGTT
4455 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
4471 GCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
4487 TCGGGTCA
1 TCGGGTCA
4495 GGCGGGTCCG
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
15 4 0.04
16 89 0.92
17 4 0.04
ACGTcount: A:0.10, C:0.22, G:0.35, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:4395 original size:32 final size:31
Alignment explanation
Indices: 4376--4494 Score: 168
Period size: 32 Copynumber: 3.7 Consensus size: 31
4366 ATTCGAGTTT
4376 CGGGTCATTCGGGTCTCGGGTCAT-TCGGATTA
1 CGGGTCATTCGGGTCTCGGGTCATCT-GG-TTA
*
4408 CGGGTCATTCGGGTTTCGGGTCATCTGCGTTA
1 CGGGTCATTCGGGTCTCGGGTCATCTG-GTTA
* *
4440 CGGGTCATTCCGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATCT-GGTTA
4472 CGGGTCATTCGGGTCTCGGGTCA
1 CGGGTCATTCGGGTCTCGGGTCA
4495 GGCGGGTCCG
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
32 76 0.96
33 3 0.04
ACGTcount: A:0.09, C:0.24, G:0.36, T:0.31
Consensus pattern (31 bp):
CGGGTCATTCGGGTCTCGGGTCATCTGGTTA
Found at i:4412 original size:48 final size:48
Alignment explanation
Indices: 4357--4494 Score: 160
Period size: 48 Copynumber: 2.9 Consensus size: 48
4347 CGGGTTAACT
* *
4357 TCTCGGGTTATTCGAGTTTCGGGTCATTCGGGTCTCGGGTCATT-CGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATTCGGGTCTCGGGTCATTCCGG
*
4404 AT-TACGGGTCATTCGGGTTTCGGGTCA-TCTGCGT-TACGGGTCATTCCGG
1 -TCT-CGGGTCATTCGGGTTTCGGGTCATTC-GGGTCT-CGGGTCATTCCGG
*
4453 TCTCGGGTCA-TCTGGGTTGCGGGTCATTCGGGTCTCGGGTCA
1 TCTCGGGTCATTC-GGGTTTCGGGTCATTCGGGTCTCGGGTCA
4495 GGCGGGTCCG
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
47 6 0.08
48 64 0.83
49 7 0.09
ACGTcount: A:0.09, C:0.22, G:0.35, T:0.33
Consensus pattern (48 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATTCGGGTCTCGGGTCATTCCGG
Found at i:4500 original size:16 final size:15
Alignment explanation
Indices: 4375--4508 Score: 96
Period size: 16 Copynumber: 8.5 Consensus size: 15
4365 TATTCGAGTT
4375 TCGGGTCATTCGGGTC
1 TCGGGTCA-TCGGGTC
*
4391 TCGGGTCATTCGGAT-
1 TCGGGTCA-TCGGGTC
*
4406 TACGGGTCATTCGGGTT
1 T-CGGGTCA-TCGGGTC
*
4423 TCGGGTCATCTGCGT-
1 TCGGGTCATC-GGGTC
*
4438 TACGGGTCATTCCGGTC
1 T-CGGGTCA-TCGGGTC
4455 TCGGGTCATCTGGGT-
1 TCGGGTCATC-GGGTC
4470 TGCGGGTCATTCGGGTC
1 T-CGGGTCA-TCGGGTC
*
4487 TCGGGTCAGGCGGGTC
1 TCGGGTCA-TCGGGTC
4503 -CGGGTC
1 TCGGGTC
4509 GTTTACTTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
15 13 0.13
16 80 0.80
17 7 0.07
ACGTcount: A:0.08, C:0.24, G:0.38, T:0.30
Consensus pattern (15 bp):
TCGGGTCATCGGGTC
Found at i:4795 original size:54 final size:54
Alignment explanation
Indices: 4721--4959 Score: 284
Period size: 54 Copynumber: 4.4 Consensus size: 54
4711 CCATCCCAAC
* * * * *
4721 GAGTCTCTTGGCG-GGACGAACATGCACTCTTGACGCTCTGCCATCCCAACGAGA
1 GAGTCTCTTGGTGAGG-CGAACGTCCACTCTTGGCGCTCTGCCATCCCAACGAGG
* *
4775 GAGTCTCTTGGTGAGGCGAACGTCCACTCTTGGCACTCTTCCATCCCAACGAGG
1 GAGTCTCTTGGTGAGGCGAACGTCCACTCTTGGCGCTCTGCCATCCCAACGAGG
* * * *
4829 GAGTCTCTTGGAG-GGACGAACGTACACCCTTGGCGCTCTGCTATCCCAACGAGG
1 GAGTCTCTTGGTGAGG-CGAACGTCCACTCTTGGCGCTCTGCCATCCCAACGAGG
* * * * *
4883 GAGTCTCTTAGTGAGACGAACGTCCACTCTTGGCGTTCTTCCATCCCAACGACG
1 GAGTCTCTTGGTGAGGCGAACGTCCACTCTTGGCGCTCTGCCATCCCAACGAGG
* *
4937 GAGTCTCTTGGGGAGACGAACGT
1 GAGTCTCTTGGTGAGGCGAACGT
4960 GCCATCCCAA
Statistics
Matches: 158, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.01
54 153 0.97
55 3 0.02
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.23
Consensus pattern (54 bp):
GAGTCTCTTGGTGAGGCGAACGTCCACTCTTGGCGCTCTGCCATCCCAACGAGG
Found at i:4910 original size:108 final size:107
Alignment explanation
Indices: 4721--4959 Score: 352
Period size: 108 Copynumber: 2.2 Consensus size: 107
4711 CCATCCCAAC
* * * *
4721 GAGTCTCTTGGCGGGACGAACATGCACTCTTGACGCTCTGCCATCCCAACGAGAGAGTCTCTTGG
1 GAGTCTCTTGG-GGGACGAACGTACACCCTTGACGCTCTGCCATCCCAACGAGAGAGTCTCTTAG
* *
4786 TGAGGCGAACGTCCACTCTTGGCACTCTTCCATCCCAACGAGG
65 TGAGACGAACGTCCACTCTTGGCACTCTTCCATCCCAACGACG
* * *
4829 GAGTCTCTTGGAGGGACGAACGTACACCCTTGGCGCTCTGCTATCCCAACGAGGGAGTCTCTTAG
1 GAGTCTCTTGG-GGGACGAACGTACACCCTTGACGCTCTGCCATCCCAACGAGAGAGTCTCTTAG
**
4894 TGAGACGAACGTCCACTCTTGGCGTTCTTCCATCCCAACGACG
65 TGAGACGAACGTCCACTCTTGGCACTCTTCCATCCCAACGACG
4937 GAGTCTCTTGGGGAGACGAACGT
1 GAGTCTCTTGGGG-GACGAACGT
4960 GCCATCCCAA
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 2 0.02
108 116 0.98
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.23
Consensus pattern (107 bp):
GAGTCTCTTGGGGGACGAACGTACACCCTTGACGCTCTGCCATCCCAACGAGAGAGTCTCTTAGT
GAGACGAACGTCCACTCTTGGCACTCTTCCATCCCAACGACG
Found at i:4978 original size:38 final size:38
Alignment explanation
Indices: 4923--5035 Score: 181
Period size: 38 Copynumber: 3.0 Consensus size: 38
4913 TGGCGTTCTT
* *
4923 CCATCCCAACGACGGAGTCTCTTGGGGAGACGAACGTG
1 CCATCCCAACGAGGGAGTCTCTTGGCGAGACGAACGTG
*
4961 CCATCCCAACGAGGGAGTCTCTTGGCGAGACGAACATG
1 CCATCCCAACGAGGGAGTCTCTTGGCGAGACGAACGTG
* *
4999 GCATCCCAACGAGGGAGTCTCTTGGTGAGACGAACGT
1 CCATCCCAACGAGGGAGTCTCTTGGCGAGACGAACGT
5036 CCACCCTTAG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 69 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (38 bp):
CCATCCCAACGAGGGAGTCTCTTGGCGAGACGAACGTG
Found at i:5449 original size:76 final size:76
Alignment explanation
Indices: 5322--5545 Score: 304
Period size: 76 Copynumber: 2.9 Consensus size: 76
5312 GTTCTTGGCG
* * * * *
5322 CTCAGCCATCGGATGAGTGGCGTCTACTTGGATGCTCGGCCTCATTTAGAGTGAAACGAGGGCGT
1 CTCAGCCATCGGATGAGTGGCGTCTGCTTGGACGCTCGGCCTCATTTAGAGTGAAACGGGGGTGC
*
5387 CAGTCTAGATA
66 CAGTCTAGACA
* ** * * *
5398 CTCAGCCATCGGATAAGTGTTGTCTGCTTGGACGCTTGGCCTCATTCAGAGTTAAACGGGGGTGC
1 CTCAGCCATCGGATGAGTGGCGTCTGCTTGGACGCTCGGCCTCATTTAGAGTGAAACGGGGGTGC
*
5463 CAGTCTAGGCA
66 CAGTCTAGACA
* * *
5474 CCCAACCGTCGGATGAGTGGCGTCTGCTTGGACGCTCGGCCTCATTTAGAGTGAAACGGGGGTGC
1 CTCAGCCATCGGATGAGTGGCGTCTGCTTGGACGCTCGGCCTCATTTAGAGTGAAACGGGGGTGC
5539 CAGTCTA
66 CAGTCTA
5546 AGCACCCGTC
Statistics
Matches: 126, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 126 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (76 bp):
CTCAGCCATCGGATGAGTGGCGTCTGCTTGGACGCTCGGCCTCATTTAGAGTGAAACGGGGGTGC
CAGTCTAGACA
Found at i:7118 original size:11 final size:11
Alignment explanation
Indices: 7102--7144 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
7092 TATACTATAT
7102 CTAATTAATAG
1 CTAATTAATAG
*
7113 CTAATTAATAT
1 CTAATTAATAG
7124 CTAATTAATAG
1 CTAATTAATAG
*
7135 TTAATTAATA
1 CTAATTAATA
7145 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:7123 original size:22 final size:22
Alignment explanation
Indices: 7098--7144 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
7088 CCATTATACT
7098 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
7120 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
7142 ATA
1 ATA
7145 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Done.