Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014260.1 Corchorus capsularis cultivar CVL-1 contig14281, 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: 40667
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:362 original size:19 final size:19
Alignment explanation
Indices: 338--376 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
328 AAGACACCAT
338 TACACCAAATGTTGATCAA
1 TACACCAAATGTTGATCAA
357 TACACCAAATGTTGATCAA
1 TACACCAAATGTTGATCAA
376 T
1 T
377 CTTTCACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (19 bp):
TACACCAAATGTTGATCAA
Found at i:2402 original size:2 final size:2
Alignment explanation
Indices: 2355--2383 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2345 ATTTGATCTA
2355 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2384 CCTTATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13773 original size:2 final size:2
Alignment explanation
Indices: 13766--13806 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
13756 ATTAAATAAA
* *
13766 AT AT AT AT AT -T CT AT -T AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13806 A
1 A
13807 CTAGTCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14515 original size:70 final size:71
Alignment explanation
Indices: 14439--14593 Score: 235
Period size: 70 Copynumber: 2.2 Consensus size: 71
14429 TAACTAAAAT
* * * *
14439 AGTAAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
1 AGTAAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
14503 TAGTTG
66 TAGTTG
*
14509 AGT-AAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
14573 TAGTTG
66 TAGTTG
*
14579 AGTAAAACTA-TAAAA
1 AGTAAAAATAGTAAAA
14594 ACCTAAACAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
69 5 0.06
70 67 0.87
71 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.36
Consensus pattern (71 bp):
AGTAAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
TAGTTG
Found at i:14876 original size:70 final size:70
Alignment explanation
Indices: 14783--14933 Score: 234
Period size: 70 Copynumber: 2.2 Consensus size: 70
14773 TAAAATAGTA
* * * *
14783 AAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGT
1 AAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGT
14847 TGAGT
66 TGAGT
*
14852 AAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGT
1 AAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGT
14917 TGAGT
66 TGAGT
14922 AAAACTA-TAAAA
1 AAAA-TAGTAAAA
14934 ACCTAAACAA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 5 0.07
70 68 0.91
71 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (70 bp):
AAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGT
TGAGT
Found at i:14973 original size:340 final size:336
Alignment explanation
Indices: 14357--15032 Score: 1300
Period size: 340 Copynumber: 2.0 Consensus size: 336
14347 CTTATTTTAG
14357 AAAAAAATTGTAAAAGTTTAAACAATGTCATTCAAGAAATATATTTTAAAAAAATAATATATCAA
1 AAAAAAATTGTAAAAGTTTAAACAATGTCATTCAAGAAATATATTTTAAAAAAATAATATATCAA
14422 TTTTTTTTAACTAAAATAGTAAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTAT
66 TTTTTTTTAACTAAAATAGTAAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTAT
14487 ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTA
131 ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTA
14552 ATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGACAATTTAGAA
196 ATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGACAATTTAGAA
14617 ATATATTTAACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAA
261 ATATATTTAACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAA
14682 TATAGTATAGA
326 TATAGTATAGA
14693 AAAAAAATTGTAAAAGTTTAAACAATGTCATTCAAGAAATATA-TTTAAAAAAACTAATATATCA
1 AAAAAAATTGTAAAAGTTTAAACAATGTCATTCAAGAAATATATTTTAAAAAAA-TAATATATCA
14757 AGTTTTTTTTTTAAACTAAAATAGTAAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTA
65 A---TTTTTTTT-AACTAAAATAGTAAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTA
14822 ATTATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTAT
126 ATTATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTAT
14887 ATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGACAATT
191 ATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGACAATT
14952 TAGAAATATATTTAACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGCTGAACGTACTT
256 TAGAAATATATTTAACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGCTGAACGTACTT
15017 TTTAATATAGTATAGA
321 TTTAATATAGTATAGA
15033 TATAGATATA
Statistics
Matches: 335, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
335 10 0.03
336 54 0.16
339 8 0.02
340 263 0.79
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (336 bp):
AAAAAAATTGTAAAAGTTTAAACAATGTCATTCAAGAAATATATTTTAAAAAAATAATATATCAA
TTTTTTTTAACTAAAATAGTAAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTAT
ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTA
ATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGACAATTTAGAA
ATATATTTAACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAA
TATAGTATAGA
Found at i:15750 original size:15 final size:15
Alignment explanation
Indices: 15730--15758 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15720 TTAAAGGTGT
15730 TTAGACATGTTCCTG
1 TTAGACATGTTCCTG
15745 TTAGACATGTTCCT
1 TTAGACATGTTCCT
15759 CTTTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (15 bp):
TTAGACATGTTCCTG
Found at i:21457 original size:25 final size:25
Alignment explanation
Indices: 21429--21477 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
21419 TGGTTTAGAC
21429 TTTAGTTTTACGACAGACTCTATGT
1 TTTAGTTTTACGACAGACTCTATGT
* **
21454 TTTAGTTTTATGGTAGACTCTATG
1 TTTAGTTTTACGACAGACTCTATG
21478 ACTTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (25 bp):
TTTAGTTTTACGACAGACTCTATGT
Found at i:23174 original size:13 final size:13
Alignment explanation
Indices: 23156--23182 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23146 AGGGAATGTA
23156 ACATTCCCATACC
1 ACATTCCCATACC
23169 ACATTCCCATACC
1 ACATTCCCATACC
23182 A
1 A
23183 TGACTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (13 bp):
ACATTCCCATACC
Found at i:25029 original size:17 final size:17
Alignment explanation
Indices: 24990--25022 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24980 CTAGGGACAC
*
24990 GTGGCGTGATTTGGTGA
1 GTGGGGTGATTTGGTGA
25007 GTGGGGTGATTTGGTG
1 GTGGGGTGATTTGGTG
25023 GTTGGGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.52, T:0.36
Consensus pattern (17 bp):
GTGGGGTGATTTGGTGA
Found at i:25557 original size:25 final size:26
Alignment explanation
Indices: 25502--25557 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
25492 CTTGATCTAC
* * *
25502 TTTTTTTTGAATGGCAAAGTAAATGA
1 TTTTTTTTGAAAGACAAAGTAAAGGA
25528 TTTTTTTTGAAAGACAAAGTAAAGGA
1 TTTTTTTTGAAAGACAAAGTAAAGGA
25554 TTTT
1 TTTT
25558 ATTAACAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43
Consensus pattern (26 bp):
TTTTTTTTGAAAGACAAAGTAAAGGA
Found at i:25567 original size:26 final size:26
Alignment explanation
Indices: 25516--25567 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
25506 TTTTGAATGG
* * *
25516 CAAAGTAAATGATTTTTTTTGAAAGA
1 CAAAGTAAAGGATTTTTATTAAAAGA
25542 CAAAGTAAAGGA-TTTTATTAACAAGA
1 CAAAGTAAAGGATTTTTATTAA-AAGA
25568 AACTGGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (26 bp):
CAAAGTAAAGGATTTTTATTAAAAGA
Found at i:29206 original size:41 final size:41
Alignment explanation
Indices: 29149--29413 Score: 341
Period size: 41 Copynumber: 6.4 Consensus size: 41
29139 TTTTCGTTTG
* *
29149 TTCAAGATCAAGTCATCGAGAACCTTGAATTAAGTTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
29190 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** * *
29231 TTCAAGATTGAGTCATCGAGATCCTTAAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
29272 TTCAAGAACAAGTCATCGAGACCCTTGAATTGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATT-AA--ATTATCAA
* *
29316 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * * *
29357 TTCAAGGTCAAGTCGTCAAGACCCTTGAATTAAATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
29398 TTGAAGACCAGGTCAT
1 TTCAAGATCAAGTCAT
29414 TTGACCCGAA
Statistics
Matches: 200, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
41 160 0.80
42 2 0.01
43 2 0.01
44 36 0.18
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:29388 original size:126 final size:123
Alignment explanation
Indices: 29149--29413 Score: 341
Period size: 126 Copynumber: 2.1 Consensus size: 123
29139 TTTTCGTTTG
* * ** *
29149 TTCAAGATCAAGTCATCGAGAACCTTGAATTAAGTTATCAATTCAAGATTGAGTCATCGAGACCC
1 TTCAAGAACAAGTCATCGAGAACCTTGAATTAAATTATCAATTCAAGATCAAGTCATCAAGACCC
** * *
29214 TTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGATCCTTAAATTAAATTATCAA
66 TTGAATTAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTAAATTAAATTATCAA
* *
29272 TTCAAGAACAAGTCATCGAGACCCTTGAATTGAATTATTATCAATTCAAGATCAAGTCGTCAAGA
1 TTCAAGAACAAGTCATCGAGAACCTTGAATT-AA--ATTATCAATTCAAGATCAAGTCATCAAGA
* * * *
29337 CCCTTGAATTAAATTATCAATTCAAGGTCAAGTCGTCAAGACCCTTGAATTAAATTGTCAA
63 CCCTTGAATTAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTAAATTAAATTATCAA
* * *
29398 TTGAAGACCAGGTCAT
1 TTCAAGAACAAGTCAT
29414 TTGACCCGAA
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
123 29 0.24
124 2 0.02
126 90 0.74
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (123 bp):
TTCAAGAACAAGTCATCGAGAACCTTGAATTAAATTATCAATTCAAGATCAAGTCATCAAGACCC
TTGAATTAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTAAATTAAATTATCAA
Done.