Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001014.1 Corchorus capsularis cultivar CVL-1 contig01014, 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: 1898
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Found at i:169 original size:19 final size:19
Alignment explanation
Indices: 154--192 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
144 TACTATTATT
154 TTTTGAATTTAATATTTTA
1 TTTTGAATTTAATATTTTA
* *
173 TTTTTAATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
193 AATGTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTGAATTTAATATTTTA
Found at i:191 original size:20 final size:20
Alignment explanation
Indices: 153--192 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
143 TTACTATTAT
153 TTTTTGAATTTAATATTTTA
1 TTTTTGAATTTAATATTTTA
*
173 TTTTT-AATTTCAATTTTTTA
1 TTTTTGAATTT-AATATTTTA
193 AATGTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTGAATTTAATATTTTA
Found at i:383 original size:22 final size:22
Alignment explanation
Indices: 355--529 Score: 97
Period size: 22 Copynumber: 7.9 Consensus size: 22
345 TGTCTCTGTG
355 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
377 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
400 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
421 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* *
444 -AGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * **
465 TGGTTACCAAACTTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
487 TCAGATTATTAAAATTTCTTAAGA
1 T--GGTTATCAAAATTTCATAAGA
* **
511 AGGTTATTGAAATTTCATA
1 TGGTTATCAAAATTTCATA
530 GTGTGGTGAT
Statistics
Matches: 111, Mismatches: 32, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
20 2 0.02
22 90 0.81
23 4 0.04
24 15 0.14
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:425 original size:44 final size:44
Alignment explanation
Indices: 356--482 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
346 GTCTCTGTGT
* ** *
356 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-ATGGA
*
400 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
* *
444 AGTTATCAAAATTTCATAGTGTGGTTACCAAACTTTCAT
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAT
483 GGGATCAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 3 0.04
44 70 0.96
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
Found at i:470 original size:66 final size:66
Alignment explanation
Indices: 352--475 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
342 TCTTGTCTCT
* * * * *
352 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCAT
417 A
66 A
* *
418 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCAT-AGTGTGGTTACCAAA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGAG-GAGGTTACCAAA
476 CTTTCATGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
65 2 0.04
66 45 0.92
67 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCAT
A
Found at i:624 original size:22 final size:22
Alignment explanation
Indices: 599--925 Score: 102
Period size: 22 Copynumber: 14.5 Consensus size: 22
589 AGGTTATAAG
*
599 AATTTCATAGTGTGATTAACAA
1 AATTTCATAGTGTGATTATCAA
* *
621 AATTTAATAG-GAGATTA-CTATA
1 AATTTCATAGTGTGATTATC-A-A
* * *
643 ATATTTCATAGGGAGGTTATCAA
1 A-ATTTCATAGTGTGATTATCAA
666 AATTTCATAGTGT-AGTTATCAA
1 AATTTCATAGTGTGA-TTATCAA
**
688 AATTTTTTAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * * *
710 ATTTTCATA-TGAAGGTTATAAAA
1 AATTTCATAGTG-TGATTAT-CAA
* * *
733 GTCTCAATTTCATA-AG-GAGTACCAA
1 -----AATTTCATAGTGTGATTATCAA
* **
758 AATTTGATAAAAG-G-TTATC-A
1 AATTTCAT-AGTGTGATTATCAA
** * *
778 AATCCCATAGAGTGATTATCGA
1 AATTTCATAGTGTGATTATCAA
* *
800 AATTTCCATAGAGATCGAATTATTAA
1 AATTT-CATAGTG-T-G-ATTATCAA
*
826 AATTT-ATAG-GAAGATTATCAA
1 AATTTCATAGTG-TGATTATCAA
*
847 ACTTTCATAGTGTTG-TTATCAA
1 AATTTCATAGTG-TGATTATCAA
* * *
869 AATTTTTTCAAAGCGAGATTATCAA
1 AA---TTTCATAGTGTGATTATCAA
* *
894 AATTACATAATGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
916 AATTTCATAG
1 AATTTCATAG
926 AAGGGTCAAC
Statistics
Matches: 228, Mismatches: 48, Indels: 58
0.68 0.14 0.17
Matches are distributed among these distances:
19 3 0.01
20 15 0.07
21 29 0.13
22 100 0.44
23 24 0.11
24 13 0.06
25 21 0.09
26 14 0.06
28 9 0.04
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAA
Found at i:976 original size:22 final size:22
Alignment explanation
Indices: 887--982 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
877 CAAAGCGAGA
* * * *
887 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
909 TTATCAAAATTTCATAGAAG-GG
1 TTATCAAAATTTCATA-AAGAGG
* * * *
931 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
953 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
975 TTATCAAA
1 TTATCAAA
983 TTAATTTTCA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
21 2 0.03
22 57 0.93
23 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:1125 original size:20 final size:21
Alignment explanation
Indices: 1100--1151 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1090 TTATGGAGTA
*
1100 ATCAAAATTTCTA-GGAGGAT
1 ATCAAAATTTCTATGAAGGAT
* * *
1120 ATCAAATTTTATATGAAGGTT
1 ATCAAAATTTCTATGAAGGAT
1141 ATCAAAATTTC
1 ATCAAAATTTC
1152 ATAGTAGCAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (21 bp):
ATCAAAATTTCTATGAAGGAT
Found at i:1385 original size:22 final size:21
Alignment explanation
Indices: 1357--1578 Score: 127
Period size: 22 Copynumber: 10.3 Consensus size: 21
1347 TAGTTTTCAG
1357 AATTTCATAAGAGGATTATCAA
1 AATTTCATAAGAGG-TTATCAA
* * *
1379 AATTTCATAGGGAGATTAACAA
1 AATTTCATA-AGAGGTTATCAA
1401 AATTTCATAATGAGGTTATCAA
1 AATTTCATAA-GAGGTTATCAA
* * *
1423 ACA-ATCATAGGGACGTTATCAA
1 A-ATTTCATA-AGAGGTTATCAA
*
1445 AA-TT-GT---A-GTTATCAA
1 AATTTCATAAGAGGTTATCAA
* *
1460 GATTTGATAAGGAGGTTATCAA
1 AATTTCATAA-GAGGTTATCAA
* *
1482 AATTTTATAGGGAGGTTTATCAA
1 AATTTCATA-AGAGG-TTATCAA
* *
1505 AATTTTATAGGATGGTTTATCAA
1 AATTTCATAAGA-GG-TTATCAA
* *
1528 AATTTCATAGCGAGGTTATCAT
1 AATTTCATA-AGAGGTTATCAA
*
1550 AATTTCAT-AGTGTGATTATCAA
1 AATTTCATAAGAG-G-TTATCAA
1572 AATTTCA
1 AATTTCA
1579 AAGTGTGATT
Statistics
Matches: 161, Mismatches: 22, Indels: 34
0.74 0.10 0.16
Matches are distributed among these distances:
15 9 0.06
16 3 0.02
17 1 0.01
20 3 0.02
21 4 0.02
22 99 0.61
23 40 0.25
24 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
AATTTCATAAGAGGTTATCAA
Found at i:1406 original size:44 final size:43
Alignment explanation
Indices: 1357--1578 Score: 165
Period size: 44 Copynumber: 5.2 Consensus size: 43
1347 TAGTTTTCAG
*
1357 AATTTCATAAGAGGATTATCAAAATTTCATAGGGAGATTAACAA
1 AATTTCATAAGAGG-TTATCAAAATTTCATAGGGAGATTATCAA
*
1401 AATTTCATAATGAGGTTATCAAACA-ATCATAGGGACG-TTATCAA
1 AATTTCATAA-GAGGTTATCAAA-ATTTCATAGGGA-GATTATCAA
* * * * *
1445 AA-TT-GT---A-GTTATCAAGATTTGATAAGGAGGTTATCAA
1 AATTTCATAAGAGGTTATCAAAATTTCATAGGGAGATTATCAA
* * * *
1482 AATTTTATAGGGAGGTTTATCAAAATTTTATA-GGATGGTTTATCAA
1 AATTTCATA-AGAGG-TTATCAAAATTTCATAGGGA--GATTATCAA
* * * *
1528 AATTTCATAGCGAGGTTATCATAATTTCATAGTGTGATTATCAA
1 AATTTCATA-AGAGGTTATCAAAATTTCATAGGGAGATTATCAA
1572 AATTTCA
1 AATTTCA
1579 AAGTGTGATT
Statistics
Matches: 144, Mismatches: 18, Indels: 32
0.74 0.09 0.16
Matches are distributed among these distances:
36 2 0.01
37 24 0.17
38 3 0.02
39 1 0.01
42 1 0.01
43 3 0.02
44 54 0.38
45 34 0.24
46 22 0.15
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (43 bp):
AATTTCATAAGAGGTTATCAAAATTTCATAGGGAGATTATCAA
Found at i:1505 original size:23 final size:22
Alignment explanation
Indices: 1452--1757 Score: 161
Period size: 22 Copynumber: 13.8 Consensus size: 22
1442 CAAAATTGTA
* * *
1452 GTTATCAAGATTTGATAAGGAG
1 GTTATCAAAATTTCATAGGGAG
*
1474 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGGGAG
*
1496 GTTTATCAAAATTTTATA-GGATG
1 G-TTATCAAAATTTCATAGGGA-G
*
1519 GTTTATCAAAATTTCATAGCGAG
1 G-TTATCAAAATTTCATAGGGAG
* * *
1542 GTTATCATAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGGGAG
* * * *
1564 ATTATCAAAATTTCAAAGTGTG
1 GTTATCAAAATTTCATAGGGAG
* * * *
1586 ATTA-CAAACAATTCATATGCAG
1 GTTATCAAA-ATTTCATAGGGAG
* ** *
1608 GTT-TCTAAATTTTCATAACGTG
1 GTTATC-AAAATTTCATAGGGAG
* *
1630 GTTATCAATATATT-ATATGGAG
1 GTTATCAAAAT-TTCATAGGGAG
* * * **
1652 GCTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAG-GGAG
* * *
1675 GTTATTAAAATTTCATTGGGAA
1 GTTATCAAAATTTCATAGGGAG
* *
1697 GTTATCAACATTTCATAGTGAG
1 GTTATCAAAATTTCATAGGGAG
* ** * *
1719 ATCCTCAAAATTCCTTAGGGAG
1 GTTATCAAAATTTCATAGGGAG
* *
1741 GTTAACAAGATTTCATA
1 GTTATCAAAATTTCATA
1758 AAAAGGTTAA
Statistics
Matches: 212, Mismatches: 62, Indels: 20
0.72 0.21 0.07
Matches are distributed among these distances:
21 5 0.02
22 147 0.69
23 58 0.27
24 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:1547 original size:45 final size:44
Alignment explanation
Indices: 1452--1578 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 44
1442 CAAAATTGTA
* * * *
1452 GTTATCAAGATTTGATAAGGA-GGTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCAT-AGGATGGTTATCAAAATTTCATAGCGAG
*
1496 GTTTATCAAAATTTTATAGGATGGTTTATCAAAATTTCATAGCGAG
1 G-TTATCAAAATTTCATAGGATGG-TTATCAAAATTTCATAGCGAG
* *
1542 GTTATCATAATTTCATAGTG-TGATTATCAAAATTTCA
1 GTTATCAAAATTTCATAG-GATGGTTATCAAAATTTCA
1579 AAGTGTGATT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
44 19 0.26
45 32 0.44
46 21 0.29
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGGATGGTTATCAAAATTTCATAGCGAG
Found at i:1767 original size:22 final size:22
Alignment explanation
Indices: 1739--1787 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1729 TTCCTTAGGG
* * *
1739 AGGTTAACAAGATTTCATAAAA
1 AGGTTAACAAAAATTAATAAAA
1761 AGGTTAACAAAAATTAATAAAA
1 AGGTTAACAAAAATTAATAAAA
1783 AGGTT
1 AGGTT
1788 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (22 bp):
AGGTTAACAAAAATTAATAAAA
Done.