Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005515.1 Corchorus capsularis cultivar CVL-1 contig05533, 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: 7050
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:180 original size:21 final size:22
Alignment explanation
Indices: 79--183 Score: 86
Period size: 22 Copynumber: 4.8 Consensus size: 22
69 TCTCAAAGCG
* **
79 AGGTTATCAAAATTACATAATG
1 AGGTTATCAAAATTTCATAAAA
* * * *
101 TGATTATCAGAATTTCAT-AGA
1 AGGTTATCAAAATTTCATAAAA
* * * *
122 GGGTTCAACAAAATTTTATAAAG
1 AGGTT-ATCAAAATTTCATAAAA
145 AGGTTATCAAAATTTCATAAAA
1 AGGTTATCAAAATTTCATAAAA
*
167 AGGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCA
184 AAATGTGATT
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
21 4 0.06
22 54 0.86
23 5 0.08
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAAA
Found at i:315 original size:20 final size:20
Alignment explanation
Indices: 281--343 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 20
271 AACTTTTATT
*
281 ATGGAGTAT-TCAAAATTTC
1 ATGGAGGATATCAAAATTTC
300 ATGGAGGATATCAAAATTTC
1 ATGGAGGATATCAAAATTTC
* *
320 ATATGAAGGTTATCAAAATTTC
1 --ATGGAGGATATCAAAATTTC
342 AT
1 AT
344 AGTTTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 8 0.21
20 12 0.32
22 18 0.47
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGGAGGATATCAAAATTTC
Found at i:336 original size:22 final size:22
Alignment explanation
Indices: 290--886 Score: 224
Period size: 22 Copynumber: 27.6 Consensus size: 22
280 TATGGAGTAT
* *
290 TCAAAATTTC--ATGGAGGATA
1 TCAAAATTTCATATGAAGGTTA
310 TCAAAATTTCATATGAAGGTTA
1 TCAAAATTTCATATGAAGGTTA
** *
332 TCAAAATTTCATAGTTTA-GTTT
1 TCAAAATTTCATA-TGAAGGTTA
* *
354 TCAAAATTTCACAAG-AGAGTTA
1 TCAAAATTTCATATGAAG-GTTA
* * **
376 TCAAAATTTCATA-GTATGAGA
1 TCAAAATTTCATATGAAGGTTA
* * *
397 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATATGAAGGTTA
*
419 ACAAAATTTCATAATG-AGGTTA
1 TCAAAATTTCAT-ATGAAGGTTA
** * *
441 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATATGAAGGTTA
*
463 TCAAAA--T--T-TGTA-GTTA
1 TCAAAATTTCATATGAAGGTTA
* * *
479 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATATGAAGGTTA
* * *
501 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATATGAAGG-TTA
* * *
524 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATATGAAG-GTTA
* * *
547 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATATGAAG-GTTA
570 TCAAAATTTCATA-GCAAGGTTA
1 TCAAAATTTCATATG-AAGGTTA
* * *
592 TCAAAATTTTATAGTG-TGATTA
1 TCAAAATTTCATA-TGAAGGTTA
* * *
614 TCAAAATTTCAGAGTG-TGATTA
1 TCAAAATTTCATA-TGAAGGTTA
*
636 -CTAACAA-TTCATAT-AGAGGTTT
1 TC-AA-AATTTCATATGA-AGGTTA
* * * *
658 TTAAATTTTCATAACG-TGGTTA
1 TCAAAATTTCAT-ATGAAGGTTA
* * *
680 TCAATATATCATATGAAAGTTA
1 TCAAAATTTCATATGAAGGTTA
* * **
702 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-TGAAGGTTA
*
725 TCAAAATTTCATTTGGAA-GTTA
1 TCAAAATTTCATAT-GAAGGTTA
*
747 TCAAAATTTCATATTGAA--TTCT
1 TCAAAATTTCATA-TGAAGGTT-A
*
769 TCGAAA-TTC-T-TG-AGGTTA
1 TCAAAATTTCATATGAAGGTTA
* * *
787 ACCAAATTTCATAAGAAGGTTA
1 TCAAAATTTCATATGAAGGTTA
** ** * *
809 AAAAAATTT-ATAAAAAGGCTC
1 TCAAAATTTCATATGAAGGTTA
* * **
830 TCGAAATTCCATA-GTATCGTTA
1 TCAAAATTTCATATG-AAGGTTA
* *
852 TTAAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATATGAAGGTTA
874 TCAAAATTTCATA
1 TCAAAATTTCATA
887 ATGAGATCAT
Statistics
Matches: 438, Mismatches: 97, Indels: 82
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 8 0.02
19 5 0.01
20 15 0.03
21 45 0.10
22 265 0.61
23 87 0.20
24 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATATGAAGGTTA
Found at i:526 original size:23 final size:23
Alignment explanation
Indices: 476--605 Score: 165
Period size: 23 Copynumber: 5.7 Consensus size: 23
466 AAATTTGTAG
* * * *
476 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAGGAAGGT
*
498 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
*
521 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGGT
*
544 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGGT
* *
567 TTATCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTTATAGGAAGGT
589 TTATCAAAATTTTATAG
1 TTATCAAAATTTTATAG
606 TGTGATTATC
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
22 33 0.34
23 63 0.66
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:745 original size:45 final size:45
Alignment explanation
Indices: 674--759 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
664 TTTCATAACG
* *
674 TGGTTATCAATATATCATATGAAAGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGAAAGTTATCAAAATCTCATAGTGT
* * * *
719 TGGTTATCAAAATTTCATTTGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATATGAAAGTTATCAAAATCTCATA
760 TTGAATTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGAAAGTTATCAAAATCTCATAGTGT
Found at i:6211 original size:2 final size:2
Alignment explanation
Indices: 6204--6230 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6194 CGATACATAC
6204 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6231 CATAATATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6431 original size:18 final size:19
Alignment explanation
Indices: 6410--6447 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6400 TCAAAACTCG
*
6410 ATCGAGCTCGAG-TCGAGT
1 ATCGAACTCGAGCTCGAGT
6428 ATCGAACTCGAGCTCGAGT
1 ATCGAACTCGAGCTCGAGT
6447 A
1 A
6448 GCTCACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (19 bp):
ATCGAACTCGAGCTCGAGT
Found at i:6445 original size:30 final size:32
Alignment explanation
Indices: 6376--6445 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 32
6366 GATACTCGAT
6376 TCGAGC-CGAGCTCGAGCTCGATAATCAAAAC
1 TCGAGCTCGAGCTCGAGCTCGATAATCAAAAC
*
6407 TCGA--TCGAGCTCGAG-TCGAGT-ATC-GAAC
1 TCGAGCTCGAGCTCGAGCTCGA-TAATCAAAAC
6435 TCGAGCTCGAG
1 TCGAGCTCGAG
6446 TAGCTCACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
28 7 0.21
29 7 0.21
30 16 0.47
31 4 0.12
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (32 bp):
TCGAGCTCGAGCTCGAGCTCGATAATCAAAAC
Found at i:6801 original size:3 final size:3
Alignment explanation
Indices: 6788--6834 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
6778 TTTGCTATAT
6788 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6835 CAAGCATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.