Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012543.1 Corchorus capsularis cultivar CVL-1 contig12564, 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: 49282
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:20700 original size:2 final size:2
Alignment explanation
Indices: 20695--20719 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20685 AAAAAAAGAA
20695 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 A
20720 AATTGAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25352 original size:31 final size:31
Alignment explanation
Indices: 25276--25372 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
25266 CAAAAAGTCG
*
25276 TGCCACATGTACCAAAAAGTGACA--TGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGACA
* *
25305 CGCCACGTGTACCAAAAAGTGACACGTGACA
1 TGCCACATGTACCAAAAAGTGACACGTGACA
** * * *
25336 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGACA
25367 TGCCAC
1 TGCCAC
25373 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.39
31 34 0.61
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGACA
Found at i:30536 original size:9 final size:9
Alignment explanation
Indices: 30522--30552 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
30512 AGCAAAAAAA
30522 AAAAGAAAG
1 AAAAGAAAG
30531 AAAAGAAAAG
1 AAAAG-AAAG
30541 AAAAGAAAG
1 AAAAGAAAG
30550 AAA
1 AAA
30553 GGCAAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:30539 original size:14 final size:13
Alignment explanation
Indices: 30515--30552 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
30505 GAACAGTAGC
30515 AAAAAAA-AAAAG
1 AAAAAAAGAAAAG
30527 AAAGAAAAGAAAAG
1 AAA-AAAAGAAAAG
30541 AAAAGAAAGAAA
1 AAAA-AAAGAAA
30553 GGCAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.13
13 5 0.22
14 15 0.65
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:36043 original size:14 final size:14
Alignment explanation
Indices: 36024--36067 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
36014 ACGTTGTTTC
*
36024 AAAAAAAATGAAAA
1 AAAAAAAACGAAAA
* *
36038 AAAAAAAAGGAATA
1 AAAAAAAACGAAAA
*
36052 AACAAAAACGAAAA
1 AAAAAAAACGAAAA
36066 AA
1 AA
36068 CGGACAGGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.82, C:0.05, G:0.09, T:0.05
Consensus pattern (14 bp):
AAAAAAAACGAAAA
Found at i:37734 original size:145 final size:145
Alignment explanation
Indices: 37468--37753 Score: 491
Period size: 145 Copynumber: 2.0 Consensus size: 145
37458 ATACTTACTA
* *
37468 CATATTATTTTTGTAGAAATGTGAAATTACTTAACAGTCCTTCCAACTTTTAATTTGGTGAGACC
1 CATATTATTTTTGTAGAAACGTGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACC
** *
37533 TTATCGCCCCGTTTTAGTAATTTTATACAAACCATTAATTAACACTTAATTAAAAGAGTTATAAA
66 TTATCGCCCAATTTTAGTAATTTTATACAAACCATTAATTAACACTTAATTAAAAGAATTATAAA
37598 ACCAAACCATTTTTT
131 ACCAAACCATTTTTT
* *
37613 CATATTATTTTTGTAGTAACGTGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGAGC
1 CATATTATTTTTGTAGAAACGTGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACC
* *
37678 TTATCGCCCAATTTTAGTAATTTTTTACAAACCATTAATTAACACTTAATTGAAAGAATTATAAA
66 TTATCGCCCAATTTTAGTAATTTTATACAAACCATTAATTAACACTTAATTAAAAGAATTATAAA
37743 ACCAAACCATT
131 ACCAAACCATT
37754 AACTCGAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
145 132 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (145 bp):
CATATTATTTTTGTAGAAACGTGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACC
TTATCGCCCAATTTTAGTAATTTTATACAAACCATTAATTAACACTTAATTAAAAGAATTATAAA
ACCAAACCATTTTTT
Found at i:39712 original size:2 final size:2
Alignment explanation
Indices: 39705--39730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39695 ATAATCACCC
39705 AT 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
39731 TTGTTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40452 original size:19 final size:18
Alignment explanation
Indices: 40424--40460 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
40414 CCATGTGTCC
40424 TTTTTGTACACGTGGCAT
1 TTTTTGTACACGTGGCAT
40442 TTTTTGATACACGTGGCAT
1 TTTTTG-TACACGTGGCAT
40461 GCCACGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (18 bp):
TTTTTGTACACGTGGCAT
Found at i:43132 original size:241 final size:243
Alignment explanation
Indices: 42648--43137 Score: 604
Period size: 241 Copynumber: 2.0 Consensus size: 243
42638 GTTATAAATC
* **
42648 TAAATACAATTCTTTCAACTAAACTAATCCGATATCTGGTAATCATTGGGTTCCGATTAATATGA
1 TAAATACAATTCTTTCAACTAAACTAATCCGATATCTGATAATCATTGGGTTCAAATTAATATGA
* * *
42713 AGTAATCAAGCGTGTGAACATCTAGGGTTGAATTCGAAATTGAGTTAATATAGAGCAAATTTTAC
66 AG--ATCAAGCATGCGAACATCTAGGGTTGAAATCGAAATTGAGTTAATATAGAGCAAA--TTAC
*
42778 TTTGCTCAAATTTGCAAATTAAGTAAATAAATAGTACCTCTAAAGCATATGAGTGGAAGAAAGTT
127 TTTGCTCAAATTTGC-AA-TAAGTAAATAAATAGTACCTATAAAGCATATGAGTGGAAGAAAGTT
*
42843 AAGTTTTGGTTCCTAGGGAACACTTGAGAGCAACTTTTTGATCTTTGATCTAATA
190 AAATTTTGGTTCCTAGGG-ACACTTGAGAGCAACTTTTTGATCTTTGATCTAATA
* *
42898 TAAATACAA-TCTTCATCAACTAAACTAATCCGATATCTGATAGTCATTGGGTTCAAATTAATCT
1 TAAATACAATTCTT--TCAACTAAACTAATCCGATATCTGATAATCATTGGGTTCAAATTAATAT
* * * *
42962 TAAG-TCAAGCCATGACGGACATTTAGGGTTGAAATCGAAATT-AGGTTGATATAGAGC-AA-T-
64 GAAGATCAAG-CATG-CGAACATCTAGGGTTGAAATCGAAATTGA-GTTAATATAGAGCAAATTA
* * * * *
43022 CTTTGCTTAAATTTGC-A-AAGT-AATTAATAGTACCTATATAGCATATGGGTGTAAGAAAGTTT
126 CTTTGCTCAAATTTGCAATAAGTAAATAAATAGTACCTATAAAGCATATGAGTGGAAGAAAG-TT
43084 AAATTTTGGTTCCCTATGGG-CACTTGAGAGCAACTTTTTGATCTTTGATCTAAT
190 AAATTTTGGTT-CCTA-GGGACACTTGAGAGCAACTTTTTGATCTTTGATCTAAT
43138 CTACTAAATC
Statistics
Matches: 213, Mismatches: 19, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
240 33 0.15
241 50 0.23
242 4 0.02
243 4 0.02
245 15 0.07
246 1 0.00
248 5 0.02
249 10 0.05
250 44 0.21
251 47 0.22
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (243 bp):
TAAATACAATTCTTTCAACTAAACTAATCCGATATCTGATAATCATTGGGTTCAAATTAATATGA
AGATCAAGCATGCGAACATCTAGGGTTGAAATCGAAATTGAGTTAATATAGAGCAAATTACTTTG
CTCAAATTTGCAATAAGTAAATAAATAGTACCTATAAAGCATATGAGTGGAAGAAAGTTAAATTT
TGGTTCCTAGGGACACTTGAGAGCAACTTTTTGATCTTTGATCTAATA
Found at i:47139 original size:46 final size:46
Alignment explanation
Indices: 47086--47173 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
47076 CATTTCAATC
*
47086 ACAATCTATACTTTCATGTATTAAAGAATTTCATTGTAACTAAATG
1 ACAATCTATACTTTCATGTATTAAAGAATTTCATTATAACTAAATG
47132 ACAATCTATACTTTCATGTATTAAAGAATTTCATTATAACTA
1 ACAATCTATACTTTCATGTATTAAAGAATTTCATTATAACTA
47174 TAACTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (46 bp):
ACAATCTATACTTTCATGTATTAAAGAATTTCATTATAACTAAATG
Found at i:48210 original size:22 final size:22
Alignment explanation
Indices: 48185--48229 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
48175 CTTTCCTACA
48185 TGGTTTAATCTAGTATAGTTTT
1 TGGTTTAATCTAGTATAGTTTT
48207 TGGTTTAATCTAGTATAGTTTT
1 TGGTTTAATCTAGTATAGTTTT
48229 T
1 T
48230 TTAAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (22 bp):
TGGTTTAATCTAGTATAGTTTT
Found at i:48765 original size:30 final size:30
Alignment explanation
Indices: 48729--48787 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
48719 TCCATAATCA
* *
48729 AAAGAAAGTAGACACTTATCTCAAAAAAAG
1 AAAGAAAGTAGACACTTACCTAAAAAAAAG
48759 AAAGAAAGTAGACACTTACCTAAAAAAAA
1 AAAGAAAGTAGACACTTACCTAAAAAAAA
48788 AGTAGACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.15
Consensus pattern (30 bp):
AAAGAAAGTAGACACTTACCTAAAAAAAAG
Found at i:49271 original size:15 final size:15
Alignment explanation
Indices: 49253--49281 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49243 AAAACCAGAG
49253 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
49268 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
49282 C
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Done.