Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016483.1 Corchorus capsularis cultivar CVL-1 contig16504, 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: 4321
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:205 original size:22 final size:22
Alignment explanation
Indices: 158--623 Score: 191
Period size: 22 Copynumber: 21.4 Consensus size: 22
148 TTACGGAGTA
* *
158 ATCAAAATTTC--ATGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
178 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
200 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
222 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
244 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
266 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
* *
288 AACAAAATTTCATAATTAA-GTT
1 ATCAAAATTTCAT-ATGAAGGTT
** *
310 ATCAAAAAATCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
332 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * **
348 ATCAAGATTTCATAAGAAATTT
1 ATCAAAATTTCATATGAAGGTT
* * *
370 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
393 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
416 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
438 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
460 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
482 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
504 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
526 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
548 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
571 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
593 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
616 -TCAAAATT
1 ATCAAAATT
624 CCTTAAGGAG
Statistics
Matches: 338, Mismatches: 75, Indels: 64
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 13 0.04
21 16 0.05
22 227 0.67
23 67 0.20
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:244 original size:44 final size:44
Alignment explanation
Indices: 177--735 Score: 230
Period size: 44 Copynumber: 12.8 Consensus size: 44
167 TCATGGAGGA
*
177 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
* * *
221 TTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-T-TAGT
* * * * * *
266 -ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATTAAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
** *
309 TATCAAAAAATCATAGGAAGGTTATCAAAA-TT--T-G--TAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
* ** * **
347 TATCAAGATTTCATAAGAAATTTATCAAAATTTTATAG-GGAGGTT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTA-G-T
* * * **
392 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG-CGAGGT
1 TATCAAAATTTCATAAGAAG-GTTATCAAAATTTCATAGTTTA-GT
* * * *
437 TATCACAATTTCAT-AG-TGTGATTATCAAAATTTCAGAGTGT-GAT
1 TATCAAAATTTCATAAGAAG-G-TTATCAAAATTTCATAGTTTAG-T
* * * * * *** *
481 TA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGGT
1 TATC-AA-AATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * * * *
525 TATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-TTAGT
** *
570 TATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATA-TTGAGGT
1 TATCAAAATTTCA-TAAGAAGGTTATCAAAATTTCATAGTTTA-GT
* * * * ** *
614 CT-TCAAAATTCCTTAAGGAGGTTAACCGAATTTCATAAGGTTA--
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCAT-AGTTTAGT
** * * * * *
657 -AAAAAAATTT-ATAA-AATGGTTCTCGAAATTCCATAGTGTCGT
1 TATCAAAATTTCATAAGAA-GGTTATCAAAATTTCATAGTTTAGT
*
699 TATTAAAATTTCAT-AGAAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAAG-AAGGTTATCAAAATTTCATA
736 ATGGGGTCAT
Statistics
Matches: 380, Mismatches: 98, Indels: 74
0.69 0.18 0.13
Matches are distributed among these distances:
38 27 0.07
39 2 0.01
40 4 0.01
41 17 0.04
42 9 0.02
43 21 0.06
44 199 0.52
45 71 0.19
46 30 0.08
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
Found at i:594 original size:45 final size:45
Alignment explanation
Indices: 521--606 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
511 TTTCATAACG
* * *
521 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
566 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
607 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:2078 original size:23 final size:23
Alignment explanation
Indices: 2047--2094 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2037 CAGGCGGTTT
*
2047 TCTCAGGTCATTCGGGTTTCGGG
1 TCTCAGGTCATTCGGGTCTCGGG
* *
2070 TCTCGGGTCATTTGGGTCTCGGG
1 TCTCAGGTCATTCGGGTCTCGGG
2093 TC
1 TC
2095 ATTCGGGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.06, C:0.23, G:0.35, T:0.35
Consensus pattern (23 bp):
TCTCAGGTCATTCGGGTCTCGGG
Found at i:2086 original size:16 final size:16
Alignment explanation
Indices: 2067--2126 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
2057 TTCGGGTTTC
2067 GGGTCTCGGGTCATTT
1 GGGTCTCGGGTCATTT
*
2083 GGGTCTCGGGTCATTC
1 GGGTCTCGGGTCATTT
2099 GGGT-TCCGGGTCATTT
1 GGGTCT-CGGGTCATTT
2115 GGGTCTCGGGTC
1 GGGTCTCGGGTC
2127 TACCGGATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.03
16 38 0.95
17 1 0.03
ACGTcount: A:0.05, C:0.22, G:0.40, T:0.33
Consensus pattern (16 bp):
GGGTCTCGGGTCATTT
Found at i:2101 original size:32 final size:32
Alignment explanation
Indices: 2064--2126 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2054 TCATTCGGGT
2064 TTCGGG-TCTCGGGTCATTTGGGTCTCGGGTCA
1 TTCGGGTTC-CGGGTCATTTGGGTCTCGGGTCA
2096 TTCGGGTTCCGGGTCATTTGGGTCTCGGGTC
1 TTCGGGTTCCGGGTCATTTGGGTCTCGGGTC
2127 TACCGGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.05, C:0.22, G:0.38, T:0.35
Consensus pattern (32 bp):
TTCGGGTTCCGGGTCATTTGGGTCTCGGGTCA
Found at i:2141 original size:32 final size:33
Alignment explanation
Indices: 2070--2141 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
2060 GGGTTTCGGG
* * *
2070 TCTCGGGTCATTTGGGTCTCGGGTCATTCGGGT
1 TCTCGGGTCATTTGGGTCTCGGGTCATACCGGA
2103 TC-CGGGTCATTTGGGTCTCGGGTC-TACCGGA
1 TCTCGGGTCATTTGGGTCTCGGGTCATACCGGA
2134 TCTCGGGT
1 TCTCGGGT
2142 TGGGCGGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 6 0.17
32 27 0.77
33 2 0.06
ACGTcount: A:0.07, C:0.24, G:0.36, T:0.33
Consensus pattern (33 bp):
TCTCGGGTCATTTGGGTCTCGGGTCATACCGGA
Found at i:2991 original size:16 final size:16
Alignment explanation
Indices: 2970--3096 Score: 100
Period size: 16 Copynumber: 7.9 Consensus size: 16
2960 GGTTAACTTC
*
2970 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
*
2986 TCGGGTCATAT-GGGTC
1 TCGGGTCAT-TCGGGTT
*
3002 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
3018 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
3034 TCGAGTCA-TCTGGATT
1 TCGGGTCATTC-GGGTT
* * *
3050 ACGGGTTATTTGGGTCT
1 TCGGGTCATTCGGGT-T
3067 T-GGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
3082 GCGGGTCACTCGGGT
1 TCGGGTCATTCGGGT
3097 CGAGCGGGTT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
15 5 0.06
16 77 0.89
17 5 0.06
ACGTcount: A:0.09, C:0.18, G:0.37, T:0.35
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:3385 original size:13 final size:13
Alignment explanation
Indices: 3362--3401 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
3352 CGTCGTTTTG
3362 TATAA-TATATAT
1 TATAATTATATAT
3374 TATAATTATATAT
1 TATAATTATATAT
3387 TATATATATATATAT
1 TATA-AT-TATATAT
3402 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 2 0.08
15 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATAATTATATAT
Found at i:3424 original size:9 final size:9
Alignment explanation
Indices: 3396--3435 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
3386 TTATATATAT
3396 ATATATAAA
1 ATATATAAA
*
3405 ATA-AAAAA
1 ATATATAAA
3413 ATATATAAA
1 ATATATAAA
*
3422 ATATTTAAA
1 ATATATAAA
3431 ATATA
1 ATATA
3436 AATACCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATATAAA
Found at i:4303 original size:2 final size:2
Alignment explanation
Indices: 4296--4321 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4286 ACTTTGAGAG
4296 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.