Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015343.1 Corchorus olitorius cultivar O-4 contig15376, 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: 67103
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3115 original size:45 final size:45
Alignment explanation
Indices: 3051--3150 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
3041 AAGAGGTGTA
* *
3051 AATGGTCCTGTACCACCAATGCCAAATCTACCTTCCCCACGGATG
1 AATGGTCCTGTACCACCAATGCCAAATCTACCATCACCACGGATG
* * *
3096 AATGGTCCTGTTCCACCAATGCCCAATCTTCCATCACCACGGATG
1 AATGGTCCTGTACCACCAATGCCAAATCTACCATCACCACGGATG
*
3141 AATGGGCCTG
1 AATGGTCCTG
3151 CACTTTTACC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (45 bp):
AATGGTCCTGTACCACCAATGCCAAATCTACCATCACCACGGATG
Found at i:15181 original size:41 final size:41
Alignment explanation
Indices: 15123--15211 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
15113 CATGTAGGAT
15123 GTGGCTTTGTGCATTCCTCCCCTTTTGTTTTCCTTAGTTCA
1 GTGGCTTTGTGCATTCCTCCCCTTTTGTTTTCCTTAGTTCA
**
15164 GTGGCTTTGTGTTTTCCTCCCCTTTTGTTTTCCTTAGTTCA
1 GTGGCTTTGTGCATTCCTCCCCTTTTGTTTTCCTTAGTTCA
*
15205 GTTGCTT
1 GTGGCTT
15212 ATTCTTGCAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.06, C:0.25, G:0.18, T:0.52
Consensus pattern (41 bp):
GTGGCTTTGTGCATTCCTCCCCTTTTGTTTTCCTTAGTTCA
Found at i:21826 original size:43 final size:42
Alignment explanation
Indices: 21778--21885 Score: 171
Period size: 42 Copynumber: 2.5 Consensus size: 42
21768 TAATGGCCGA
21778 GAACGTGAAAGGGTAAAAACCGGGGATATCCCTTCCGGACCAG
1 GAACGTGAAAGGGT-AAAACCGGGGATATCCCTTCCGGACCAG
* * *
21821 GAACGTGAAAGGGTAAAACTGGCGATATCCCTTCTGGACCAG
1 GAACGTGAAAGGGTAAAACCGGGGATATCCCTTCCGGACCAG
*
21863 GAACGTGAAAGGGTTAAACCGGG
1 GAACGTGAAAGGGTAAAACCGGG
21886 TGAAATCTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 45 0.76
43 14 0.24
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.16
Consensus pattern (42 bp):
GAACGTGAAAGGGTAAAACCGGGGATATCCCTTCCGGACCAG
Found at i:32180 original size:17 final size:18
Alignment explanation
Indices: 32158--32193 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
32148 GTTGTAACAA
32158 TTTTTTCTTTCTT-TTTT
1 TTTTTTCTTTCTTCTTTT
*
32175 TTTTTTGTTTCTTCTTTT
1 TTTTTTCTTTCTTCTTTT
32193 T
1 T
32194 ATTTGTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTTTCTTTCTTCTTTT
Found at i:32198 original size:17 final size:17
Alignment explanation
Indices: 32165--32200 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
32155 CAATTTTTTC
* *
32165 TTTCTTTTTTTTTTTTG
1 TTTCTTCTTTTTATTTG
32182 TTTCTTCTTTTTATTTG
1 TTTCTTCTTTTTATTTG
32199 TT
1 TT
32201 ATGTAAGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.08, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTCTTCTTTTTATTTG
Found at i:33318 original size:10 final size:11
Alignment explanation
Indices: 33293--33336 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
33283 TATTAAGATT
*
33293 AAAAACAGGAC
1 AAAAACAGAAC
33304 AAAAACAGAAC
1 AAAAACAGAAC
*
33315 AAAAACAGAGC
1 AAAAACAGAAC
33326 -AAAACAGAAC
1 AAAAACAGAAC
33336 A
1 A
33337 GACAGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.68, C:0.18, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAACAGAAC
Found at i:52389 original size:6 final size:7
Alignment explanation
Indices: 52374--52403 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
52364 ACTGTTAGAT
52374 AAAAGAA
1 AAAAGAA
52381 AAAAGAA
1 AAAAGAA
52388 AAAAGAA
1 AAAAGAA
*
52395 AAAACAA
1 AAAAGAA
52402 AA
1 AA
52404 CTTGTAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:56334 original size:2 final size:2
Alignment explanation
Indices: 56327--56361 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56317 CATCTGTCAT
56327 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
56362 TTTTTGTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:57811 original size:38 final size:38
Alignment explanation
Indices: 57768--57846 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
57758 AAAGTCTTCC
57768 TGATAAATAAACTTTTGAAAGATCGAATTAATATTATT
1 TGATAAATAAACTTTTGAAAGATCGAATTAATATTATT
57806 TGATAAATAAACTTTTGAAAGATCGAATTAATATTATT
1 TGATAAATAAACTTTTGAAAGATCGAATTAATATTATT
57844 TGA
1 TGA
57847 AAGATCGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.39
Consensus pattern (38 bp):
TGATAAATAAACTTTTGAAAGATCGAATTAATATTATT
Found at i:62065 original size:22 final size:22
Alignment explanation
Indices: 62037--62079 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62027 TTTTTCTTAT
*
62037 CTTTCTCATTTCTT-CTTTTTCA
1 CTTTCTC-TCTCTTCCTTTTTCA
62059 CTTTCTCTCTCTTCCTTTTTC
1 CTTTCTCTCTCTTCCTTTTTC
62080 TCTCTCGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.63
Consensus pattern (22 bp):
CTTTCTCTCTCTTCCTTTTTCA
Found at i:66323 original size:44 final size:45
Alignment explanation
Indices: 66257--66357 Score: 186
Period size: 44 Copynumber: 2.3 Consensus size: 45
66247 TTGTGCACTC
66257 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
1 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
66302 GGCAATCATGG-GCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
1 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
*
66346 GGCAGTCATGGA
1 GGCAATCATGGA
66358 TTCCAACTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
44 43 0.80
45 11 0.20
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (45 bp):
GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
Found at i:67078 original size:2 final size:2
Alignment explanation
Indices: 67073--67103 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67063 CTCCCCCCCC
67073 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Done.