Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011790.1 Corchorus capsularis cultivar CVL-1 contig11811, 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: 3446
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:37 original size:22 final size:21
Alignment explanation
Indices: 3--131 Score: 109
Period size: 22 Copynumber: 5.9 Consensus size: 21
1 TG
*
3 TCATAGCGAGGTTATAAGAATT
1 TCATAGTGAGGTTATAA-AATT
* *
25 TCATAGTGTGGTTAACAAAATT
1 TCATAGTGAGGTT-ATAAAATT
*
47 TCATTAG-GAGGTTACTAATATT
1 TCA-TAGTGAGGTTA-TAAAATT
* *
69 TCATGGGGAGGTTATCAAAATT
1 TCATAGTGAGGTTAT-AAAATT
* *
91 TTATAGTGTGGTTATCAAAATT
1 TCATAGTGAGGTTAT-AAAATT
113 TCATA-TGAAGGTTATAAAA
1 TCATAGTG-AGGTTATAAAA
132 GTCTCAATTT
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
21 10 0.11
22 71 0.82
23 6 0.07
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (21 bp):
TCATAGTGAGGTTATAAAATT
Found at i:297 original size:21 final size:22
Alignment explanation
Indices: 137--300 Score: 84
Period size: 22 Copynumber: 7.3 Consensus size: 22
127 TAAAAGTCTC
* *
137 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
157 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
177 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
*
199 AATTTCATAAAAATCGGATTATCAAA
1 AATTTCATAAAGA--GG-TTATC-AA
* * * *
225 ATTTATTTCATAGAGGGGTCAACAA
1 A---ATTTCATAAAGAGGTTATCAA
* *
250 TATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
272 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
294 ATTTTCA
1 AATTTCA
301 AATGTGATTA
Statistics
Matches: 105, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.01
20 19 0.18
21 9 0.09
22 52 0.50
24 1 0.01
25 7 0.07
26 5 0.05
27 2 0.02
29 9 0.09
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:433 original size:22 final size:22
Alignment explanation
Indices: 405--852 Score: 169
Period size: 22 Copynumber: 20.4 Consensus size: 22
395 TTACGGAGTA
405 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
427 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
449 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
471 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
493 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
* *
515 AACAAAATTTCATAATTAA-GTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
537 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
559 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * **
575 ATCAAGATTTCATAAGAAATTT
1 ATCAAAATTTCATATGAAGGTT
* * *
597 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
620 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
643 ATCAAAATTTCATAGTG-AGGTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
665 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
687 ATCAAAATTTCAGA-GTATGATT
1 ATCAAAATTTCATATG-AAGGTT
* *
709 ATTAACAA-TTCATATGGAGGTT
1 ATCAA-AATTTCATATGAAGGTT
* * * *
731 TTTAAATTTTCATA--ACGTGATT
1 ATCAAAATTTCATATGAAG-G-TT
* * *
753 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
775 ATCAACATCTCATAGTGTGTTGGTT
1 ATCAAAATTTCATA---TGAAGGTT
800 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
822 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
845 -TCAAAATT
1 ATCAAAATT
853 CCTTAAGGAG
Statistics
Matches: 318, Mismatches: 75, Indels: 66
0.69 0.16 0.14
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 4 0.01
21 11 0.03
22 220 0.69
23 50 0.16
24 3 0.01
25 17 0.05
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:454 original size:44 final size:44
Alignment explanation
Indices: 405--835 Score: 221
Period size: 44 Copynumber: 9.8 Consensus size: 44
395 TTACGGAGTA
405 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTT
* * * *
449 TTCAAAATTTCACAAGAGGGTTATCAAAATTTCATAGTATGTAG--
1 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAGTT
* * * * * *
493 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATTAAGTT
1 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTT
** * *
537 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G--TAGTT
1 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTT
* * ** * **
575 ATCAAGATTTCATAAGAAATTTATCAAAATTTTATAG-GGAGGTTT
1 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-G-TT
* * * *
620 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG-TGAGGTT
1 ATCAAAATTTCATATGAAG-GTTATCAAAATTTCATAGTTTA-GTT
* * * * *
665 ATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTAT-GATT
1 ATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAGTTTAG-TT
* * * * * *
709 ATTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACG-TGA-TT
1 ATCAA-AATTTCATATGAAGGTTATCAAAATTTCAT-A-GTTTAGTT
* * * * * *
753 ATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTGTTGGTT
1 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATA--GT-TTAGTT
800 ATCAAAATTTCAT-TGGGAA-GTTATCAAAATTTCATA
1 ATCAAAATTTCATAT--GAAGGTTATCAAAATTTCATA
836 TTGAGGTCTT
Statistics
Matches: 293, Mismatches: 67, Indels: 51
0.71 0.16 0.12
Matches are distributed among these distances:
38 26 0.09
39 2 0.01
41 2 0.01
42 3 0.01
43 9 0.03
44 157 0.54
45 36 0.12
46 28 0.10
47 28 0.10
48 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTT
Found at i:1727 original size:22 final size:22
Alignment explanation
Indices: 1696--1753 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1686 TTGTCACATT
*
1696 TAACTACACTATGAAATTTTGG
1 TAACTTCACTATGAAATTTTGG
1718 TAACTTCACTATGAAATTTTGG
1 TAACTTCACTATGAAATTTTGG
* *
1740 TAACCTCCCTATGA
1 TAACTTCACTATGA
1754 CTTGCTCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (22 bp):
TAACTTCACTATGAAATTTTGG
Done.