Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017376.1 Corchorus olitorius cultivar O-4 contig17409, 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: 48304
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1304 original size:24 final size:24
Alignment explanation
Indices: 1277--1337 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
1267 TTTTAACCAA
1277 TTTATGTTGATTGTTTGCGGATTT
1 TTTATGTTGATTGTTTGCGGATTT
*
1301 TTTATGTTGATTGTTTGTGGATTT
1 TTTATGTTGATTGTTTGCGGATTT
1325 TTTATGTTGATTG
1 TTTATGTTGATTG
1338 CTTGGGTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.13, C:0.02, G:0.25, T:0.61
Consensus pattern (24 bp):
TTTATGTTGATTGTTTGCGGATTT
Found at i:1457 original size:13 final size:13
Alignment explanation
Indices: 1436--1465 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1426 CATTGTGTGG
*
1436 ATTTTTGTGGGTA
1 ATTTGTGTGGGTA
1449 ATTTGTGTGGGTA
1 ATTTGTGTGGGTA
1462 ATTT
1 ATTT
1466 CGGCTATGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (13 bp):
ATTTGTGTGGGTA
Found at i:4151 original size:51 final size:50
Alignment explanation
Indices: 4075--4175 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 50
4065 CCTCGTCAAG
4075 TAACTAAAAAGAAAAATACTACTAATAGTTTTTTCTTTTATACAAGGAATA
1 TAACTAAAAAGAAAAATACTACTAATAG-TTTTTCTTTTATACAAGGAATA
4126 TAACTAAAAAGAAAAATACTACTAATAGTTTTTCTTTTATACAAGGAATA
1 TAACTAAAAAGAAAAATACTACTAATAGTTTTTCTTTTATACAAGGAATA
4176 AAATTATCAG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 22 0.44
51 28 0.56
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (50 bp):
TAACTAAAAAGAAAAATACTACTAATAGTTTTTCTTTTATACAAGGAATA
Found at i:4321 original size:21 final size:21
Alignment explanation
Indices: 4295--4343 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
4285 GTAACTAAAT
*
4295 CCACATAAAGTGGTACAAAAC
1 CCACATAAAGTGGCACAAAAC
4316 CCACATAAAGTGGCACAAAAC
1 CCACATAAAGTGGCACAAAAC
*
4337 TCACATA
1 CCACATA
4344 CTATTGAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.27, G:0.12, T:0.14
Consensus pattern (21 bp):
CCACATAAAGTGGCACAAAAC
Found at i:6294 original size:15 final size:14
Alignment explanation
Indices: 6274--6308 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
6264 AATTATTCTG
6274 ATTGTAATAAGGTT
1 ATTGTAATAAGGTT
6288 AATTGTAATAAGGTT
1 -ATTGTAATAAGGTT
6303 ATTGTA
1 ATTGTA
6309 CTCCTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (14 bp):
ATTGTAATAAGGTT
Found at i:7455 original size:27 final size:29
Alignment explanation
Indices: 7395--7456 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
7385 TAGTCCGTAG
* **
7395 CAATTTATATAATATTTATTCTTATTTGG
1 CAATTTATATAATATTTATTCATATTTAA
7424 CAATTTATATAATATTTA-T-ATATTTAA
1 CAATTTATATAATATTTATTCATATTTAA
*
7451 TAATTT
1 CAATTT
7457 TGGCTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.34
28 1 0.03
29 18 0.62
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (29 bp):
CAATTTATATAATATTTATTCATATTTAA
Found at i:22142 original size:7 final size:7
Alignment explanation
Indices: 22091--22141 Score: 93
Period size: 7 Copynumber: 7.3 Consensus size: 7
22081 TGGTTTTTTT
22091 AATGTGA
1 AATGTGA
22098 AATGTGA
1 AATGTGA
22105 AATGTGA
1 AATGTGA
22112 AATGTGA
1 AATGTGA
22119 AATGTGA
1 AATGTGA
22126 AATGTGA
1 AATGTGA
*
22133 AAAGTGA
1 AATGTGA
22140 AA
1 AA
22142 ATTGAAAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.25
Consensus pattern (7 bp):
AATGTGA
Found at i:22147 original size:14 final size:14
Alignment explanation
Indices: 22094--22153 Score: 86
Period size: 14 Copynumber: 4.3 Consensus size: 14
22084 TTTTTTTAAT
*
22094 GTGAAATGTGAAAT
1 GTGAAATGTGAAAA
*
22108 GTGAAATGTGAAAT
1 GTGAAATGTGAAAA
22122 GTGAAATGTGAAAA
1 GTGAAATGTGAAAA
22136 GTGAAAAT-TGAAAA
1 GTG-AAATGTGAAAA
22150 GTGA
1 GTGA
22154 GTGATGGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
13 1 0.02
14 39 0.89
15 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (14 bp):
GTGAAATGTGAAAA
Found at i:28508 original size:11 final size:11
Alignment explanation
Indices: 28494--28527 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
28484 TAATCCTAAC
28494 CTTTTTCTTTT
1 CTTTTTCTTTT
28505 CTTTTTCTTTTT
1 CTTTTTC-TTTT
28517 CTTTTTCTTTT
1 CTTTTTCTTTT
28528 ATTACTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:28510 original size:6 final size:6
Alignment explanation
Indices: 28494--28527 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
28484 TAATCCTAAC
28494 CTTTTT C-TTTT CTTTTT CTTTTT CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
28528 ATTACTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:38834 original size:31 final size:31
Alignment explanation
Indices: 38796--38860 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
38786 CCACATCAGC
38796 AAGGGACTGATTTGTCCCAAAAGAAAAACAT
1 AAGGGACTGATTTGTCCCAAAAGAAAAACAT
**
38827 AAGGGACTTTTTTGTCCCAAAAGAAAAACAT
1 AAGGGACTGATTTGTCCCAAAAGAAAAACAT
38858 AAG
1 AAG
38861 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (31 bp):
AAGGGACTGATTTGTCCCAAAAGAAAAACAT
Found at i:38869 original size:31 final size:31
Alignment explanation
Indices: 38806--38875 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
38796 AAGGGACTGA
*
38806 TTTGTCCCAAAAGAAAAACATAAGGGACTTT
1 TTTGTCCCAAAAGAAAAACATAAGGAACTTT
* *
38837 TTTGTCCCAAAAGAAAAACATAAGTAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGAACTTT
38868 TTTGTCCC
1 TTTGTCCC
38876 TATAAGAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGAACTTT
Found at i:39677 original size:127 final size:125
Alignment explanation
Indices: 39496--39735 Score: 333
Period size: 127 Copynumber: 1.9 Consensus size: 125
39486 CTTATTTTTC
**
39496 AAATATATTTCTTAAATACCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATACCATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
39561 ATTTAATCAAA-TCTAATATAT-TTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
66 ATTTAATCAAATTC-AATAT-TCTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
* * * ** *
39621 AAATATATTTTCTTAAATGA-TATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATT
1 AAATATA-TTTCTTAAAT-ACCATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATT
*
39685 TTTATTTAATGAAATTCAATATTCTTATAACTATTTTATTTTTACCATTTT
63 TTTATTTAATCAAATTCAATATTCTTATAACTATTTTATTTTTACCATTTT
39736 TTTAGGGAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
125 7 0.07
126 14 0.14
127 78 0.77
128 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (125 bp):
AAATATATTTCTTAAATACCATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAATTCAATATTCTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
Found at i:39965 original size:32 final size:31
Alignment explanation
Indices: 39882--39964 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
39872 ACTAAATACT
*
39882 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
39913 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
*
39944 AAAAAAATCACTTATGTTTTT
1 AAAAAAATCCCTTATGTTTTT
39965 TTTCGGGGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:43339 original size:105 final size:102
Alignment explanation
Indices: 43230--43433 Score: 329
Period size: 105 Copynumber: 2.0 Consensus size: 102
43220 TTGCTTAAAT
* *
43230 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATAAGTA
1 TTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-A--A
43295 CTATTTTATTTTTACCATTTTACT-ATTTTAATTAAAATGC
63 CTATTTTATTTTTACCATTTTACTAATTTT-ATTAAAATGC
*
43335 TTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
43400 TTTTATTTTTATCATTTTACTAATTTTATTAAAA
66 TTTTATTTTTACCATTTTACTAATTTTATTAAAA
43434 AATTTAGATA
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
102 30 0.32
103 5 0.05
104 1 0.01
105 58 0.62
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (102 bp):
TTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTTATTAAAATGC
Found at i:43412 original size:23 final size:23
Alignment explanation
Indices: 43386--43429 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
43376 TTAAATCTAA
*
43386 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
43409 TATCATTTTACTAATTTTATT
1 TATCATTATACTAATTTTATT
43430 AAAAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Found at i:46728 original size:33 final size:33
Alignment explanation
Indices: 46691--46756 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
46681 CTCTCTTCCA
46691 AGACTTTTGTTATATGAACTAGATCTCTCCCGG
1 AGACTTTTGTTATATGAACTAGATCTCTCCCGG
46724 AGACTTTTGTTATATGAACTAGATCTCTCCCGG
1 AGACTTTTGTTATATGAACTAGATCTCTCCCGG
46757 CACGCTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (33 bp):
AGACTTTTGTTATATGAACTAGATCTCTCCCGG
Done.