Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011918.1 Corchorus capsularis cultivar CVL-1 contig11939, 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: 23753
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1413 original size:65 final size:65
Alignment explanation
Indices: 1332--1462 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
1322 GAGTCCTAAT
* *
1332 ATTATCAGCAAGAAATTAAGAATAACATTAAAAAGGATATATAAGGAAACCAAATACCGTAAAAG
1 ATTATCAGCAAGAAATTAAGAAAAACATTAAAAAGGATATACAAGGAAACCAAATACCGTAAAAG
1397 ATTATCAGCAAGAAATTAAGAAAAACATTAAAAAGGATATACAAGGAAACCAAATACCGTAAAAG
1 ATTATCAGCAAGAAATTAAGAAAAACATTAAAAAGGATATACAAGGAAACCAAATACCGTAAAAG
1462 A
1 A
1463 GAAATGGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.18
Consensus pattern (65 bp):
ATTATCAGCAAGAAATTAAGAAAAACATTAAAAAGGATATACAAGGAAACCAAATACCGTAAAAG
Found at i:1908 original size:5 final size:5
Alignment explanation
Indices: 1892--1926 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1882 AGGTGTTCAT
*
1892 GGGTC GGATC GGGTC GGGTC GGGTC GGGTC GGGTC
1 GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC
1927 CAAGCTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.03, C:0.20, G:0.57, T:0.20
Consensus pattern (5 bp):
GGGTC
Found at i:2476 original size:64 final size:64
Alignment explanation
Indices: 2408--2657 Score: 279
Period size: 64 Copynumber: 4.0 Consensus size: 64
2398 GAGATTTCAC
* *
2408 TGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTTGCTAATGTAGCTAA
1 TGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCGTTTCGCTAATGTAGCTAA
* * ** *
2472 TGGGTTTGTTTGTTGGGGAAGAGGTTAG-CGTTTCGATA-ATGTAGC-TAAT--C--ATGTTAGC
1 TGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTC-ATAGAT-TAGCGT-TTCGCTAATG-TAGC
2530 TAA
62 TAA
* * *
2533 T--G--TGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAA
1 TGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCGTTTCGCTAATGTAGCTAA
* *
2593 TGGGTTTGTTTGTTGGGGAAGATGTTTGTTGGCTCATAGATTAGCGTTTCGATAATGTAGCTAA
1 TGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCGTTTCGCTAATGTAGCTAA
2657 T
1 T
2658 CATGTTAGCT
Statistics
Matches: 154, Mismatches: 17, Indels: 30
0.77 0.08 0.15
Matches are distributed among these distances:
57 28 0.18
58 6 0.04
59 1 0.01
60 11 0.07
61 11 0.07
62 2 0.01
63 6 0.04
64 89 0.58
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.40
Consensus pattern (64 bp):
TGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCGTTTCGCTAATGTAGCTAA
Found at i:2565 original size:121 final size:126
Alignment explanation
Indices: 2413--2734 Score: 447
Period size: 121 Copynumber: 2.5 Consensus size: 126
2403 TTCACTGGGT
* * *
2413 TTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTTGCTAATGTAGCTAATGGGTT
1 TTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAATGGGTT
2478 TGTTTGTTGGGGAAGA-G-G-TTAGCGTTTCGATAATGTAGCTAATCATGTTAGCTAAT-G
66 TGTTTGTTGGGGAAGATGAGATTAGCGTTTCGATAATGTAGCTAATCATGTTAGCTAATGG
2535 -TGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAATGGGTT
1 TTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAATGGGTT
2599 TGTTTGTTGGGGAAGATGTTTGTTGGCTCATAGATTAGCGTTTCGATAATGTAGCTAATCATGTT
66 TGTTTGTTGGGGAAGA-------T-G-----AGATTAGCGTTTCGATAATGTAGCTAATCATGTT
2664 AGCTAATGGG
118 AGCTAAT-GG
2674 TTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAAT
1 -TTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAAT
2735 CATGTAGTGG
Statistics
Matches: 177, Mismatches: 3, Indels: 21
0.88 0.01 0.10
Matches are distributed among these distances:
121 77 0.44
130 1 0.01
136 1 0.01
137 38 0.21
139 1 0.01
141 59 0.33
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.39
Consensus pattern (126 bp):
TTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGTAGCTAATGGGTT
TGTTTGTTGGGGAAGATGAGATTAGCGTTTCGATAATGTAGCTAATCATGTTAGCTAATGG
Found at i:2674 original size:77 final size:77
Alignment explanation
Indices: 2586--2739 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
2576 TTCGGTAATG
* *
2586 TAGCTAATGGGTTTGTTTGTTGGGGAAGATGTTTGTTGGCTCATAGATTAGCGTTTCGATAATGT
1 TAGCTAATGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCATTTCGATAATGT
2651 AGCTAATCATGT
66 AGCTAATCATGT
* *
2663 TAGCTAATGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTAATGT
1 TAGCTAATGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCATTTCGATAATGT
2728 AGCTAATCATGT
66 AGCTAATCATGT
2740 AGTGGTGTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.40
Consensus pattern (77 bp):
TAGCTAATGGGTTTGTTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCATTTCGATAATGT
AGCTAATCATGT
Found at i:3273 original size:22 final size:22
Alignment explanation
Indices: 3243--3284 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3233 AATTACTCAA
3243 TAATACTTATGTTCTATGTGGT
1 TAATACTTATGTTCTATGTGGT
*
3265 TAATCCTTATGTTCTATGTG
1 TAATACTTATGTTCTATGTG
3285 ATATGTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (22 bp):
TAATACTTATGTTCTATGTGGT
Found at i:13757 original size:21 final size:21
Alignment explanation
Indices: 13717--13764 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
13707 AACACTTCTA
13717 ATAAAATTACTAAATAAAC-T
1 ATAAAATTACTAAATAAACTT
*
13737 ATAAAAGTTACT-GATAGAACTT
1 ATAAAA-TTACTAAATA-AACTT
13759 ATAAAA
1 ATAAAA
13765 AAGTTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 8 0.33
22 7 0.29
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (21 bp):
ATAAAATTACTAAATAAACTT
Found at i:13806 original size:22 final size:22
Alignment explanation
Indices: 13776--13836 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
13766 AGTTCATAAG
*
13776 GTTATTGAAAAAACTTATAA-C
1 GTTACTGAAAAAACTTATAACC
13797 GTTACATG-AAAAACTTATAACC
1 GTTAC-TGAAAAAACTTATAACC
*
13819 GTTACTAGAAAAAGCTTA
1 GTTACT-GAAAAAACTTA
13837 CAAAGTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 17 0.50
22 9 0.26
23 8 0.24
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (22 bp):
GTTACTGAAAAAACTTATAACC
Found at i:15059 original size:13 final size:13
Alignment explanation
Indices: 15041--15068 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15031 ATACTCTACG
15041 TGAAGGTAATTTT
1 TGAAGGTAATTTT
15054 TGAAGGTAATTTT
1 TGAAGGTAATTTT
15067 TG
1 TG
15069 TGCAGATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (13 bp):
TGAAGGTAATTTT
Found at i:15360 original size:67 final size:67
Alignment explanation
Indices: 15252--15398 Score: 276
Period size: 67 Copynumber: 2.2 Consensus size: 67
15242 CTTTTCCTTC
*
15252 CTCTCTCTTTCTGTCAATAGGTCAAGCACCGCAAATAAAGTAAATGGTAGTAATATGTAAGTCTT
1 CTCTCTCTTTTTGTCAATAGGTCAAGCACCGCAAATAAAGTAAATGGTAGTAATATGTAAGTCTT
15317 GT
66 GT
15319 CTCTCTCTTTTTGTCAATAGGTCAAGCACCGCAAATAAAGTAAATGGTAGTAATATGTAAGTCTT
1 CTCTCTCTTTTTGTCAATAGGTCAAGCACCGCAAATAAAGTAAATGGTAGTAATATGTAAGTCTT
15384 GT
66 GT
15386 CTCTCTCATTTTT
1 CTCTCTC-TTTTT
15399 TTTAATGTAA
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
67 73 0.94
68 5 0.06
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (67 bp):
CTCTCTCTTTTTGTCAATAGGTCAAGCACCGCAAATAAAGTAAATGGTAGTAATATGTAAGTCTT
GT
Done.