Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000177.1 Corchorus capsularis cultivar CVL-1 contig00177, 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: 3493
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:29 original size:19 final size:19
Alignment explanation
Indices: 1--40 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1 TTCAGGGAGGATATCAAAA
1 TTCAGGGAGGATATCAAAA
*
20 TTCAGTGAGGATATCAAAA
1 TTCAGGGAGGATATCAAAA
39 TT
1 TT
41 TCATATGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (19 bp):
TTCAGGGAGGATATCAAAA
Found at i:59 original size:22 final size:22
Alignment explanation
Indices: 31--589 Score: 125
Period size: 22 Copynumber: 25.7 Consensus size: 22
21 TCAGTGAGGA
31 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
53 TATCAAATTTTAATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
75 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
97 TA-CAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
117 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
140 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
162 TATCAAAAAATCATAAGGAA-CT
1 TATCAAAATTTCAT-ATGAAGGT
* *
184 TATTAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
200 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
222 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
245 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
*
268 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
290 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
312 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
334 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
356 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
378 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
400 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
423 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
445 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
467 CT-TCAAAATTCCTTA-GAGAGGT
1 -TATCAAAATTTCATATGA-AGGT
* *
489 TAAT-AAAATTTCATAAGAAAGT
1 T-ATCAAAATTTCATATGAAGGT
* * *
511 T-TAAAAAATTT-ATA-AAATGAT
1 TAT-CAAAATTTCATATGAA-GGT
* ** * **
532 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
*
554 TATCAAAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
575 TATCAAAATTTCATA
1 TATCAAAATTTCATA
590 ATGGGATCAT
Statistics
Matches: 391, Mismatches: 101, Indels: 91
0.67 0.17 0.16
Matches are distributed among these distances:
16 9 0.02
18 2 0.01
20 15 0.04
21 51 0.13
22 236 0.60
23 72 0.18
24 6 0.02
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:167 original size:44 final size:44
Alignment explanation
Indices: 4--589 Score: 218
Period size: 44 Copynumber: 13.5 Consensus size: 44
1 TTC
*
4 AGGGAGGA-TATCAAAA-TTC--AGTGAGGATATCAAAATTTCAT
1 AGGGA-GATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * * *
45 ATGAAGGTTATCAAATTTTAATAGTTTA-GTTTTCAAAATTTCAT
1 AGGGAGATTATCAAAATTTCATAG-TGAGGTTATCAAAATTTCAT
* *
89 AAGAGG-G-TTA-CAAAATTTCATAGT-ATGTAGATCAAAATTTCAT
1 -AG-GGAGATTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCAT
* * **
132 AGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCAT
1 AGGGAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * *
176 AAGGA-ACTTATTAAAA-TT--T-GT-A-GTTATCAAGATTTCAT
1 AGGGAGA-TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * *
214 A-AGAAAGTTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTAT
1 AGGGAGA-TTATCAAAATTTCATAGTGAGG-TTATCAAAATTTCAT
** * *
259 AGAAAGATTTATCAAAATTTCATAGCGAGGTTATCACAATTTCAT
1 AGGGAGA-TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * *
304 AGTGTGATTATCAAAATTTTAAAGTGTGATTA-CTAACAA-TTCAT
1 AGGGAGATTATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCAT
* * * * * * ** * * *
348 ATGGAGGTTTTTAAATTTTTATAAAGTGGTTATCAATATATCAT
1 AGGGAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * *
392 ATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAAAATTTCAT
1 AGGGAGATTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCAT
* * * *
437 TGGGA-AGTTATCAAAATTTCATATTGAGGTCT-TCAAAATTCCTT
1 AGGGAGA-TTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCAT
* * ** * *
481 AGAGAGGTTAAT-AAAATTTCATAAGAAAGTTTA-AAAAATTT-AT
1 AGGGAGATT-ATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCAT
** * ** * *
524 A-AAATGATTCTTGAAATTCCATAGT-ACCGTTATCAAAATTTCAT
1 AGGGA-GATTATCAAAATTTCATAGTGA-GGTTATCAAAATTTCAT
*
568 A-GGAGGTTATCAAAATTTCATA
1 AGGGAGATTATCAAAATTTCATA
590 ATGGGATCAT
Statistics
Matches: 398, Mismatches: 108, Indels: 76
0.68 0.19 0.13
Matches are distributed among these distances:
37 2 0.01
38 23 0.06
39 3 0.01
40 2 0.01
41 16 0.04
42 17 0.04
43 65 0.16
44 165 0.41
45 81 0.20
46 24 0.06
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (44 bp):
AGGGAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
Found at i:252 original size:23 final size:23
Alignment explanation
Indices: 221--324 Score: 95
Period size: 23 Copynumber: 4.6 Consensus size: 23
211 CATAAGAAAG
*
221 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAGAGGT
* * *
244 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAGAGGT
* *
267 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGAGAGGT
* * * * *
289 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGAGAGGT
311 TTATCAAAATTTTA
1 TTATCAAAATTTTA
325 AAGTGTGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
21 1 0.02
22 29 0.44
23 36 0.55
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAGAGGT
Found at i:447 original size:45 final size:45
Alignment explanation
Indices: 374--459 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
364 TTTTATAAAG
* * *
374 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
419 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
460 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
Done.