Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017050.1 Corchorus olitorius cultivar O-4 contig17083, 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: 51501
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Found at i:658 original size:18 final size:18
Alignment explanation
Indices: 623--659 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
613 TAATTAAAAT
*
623 TTAAAATTTCCAACTTAA
1 TTAAAATTTCCAAATTAA
*
641 TTAAAATTTCTAAATTAA
1 TTAAAATTTCCAAATTAA
659 T
1 T
660 ATAGAGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATTTCCAAATTAA
Found at i:2548 original size:17 final size:20
Alignment explanation
Indices: 2526--2565 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
2516 AATGTTGAAG
2526 TTATAACCT-TA-A-TTTTT
1 TTATAACCTCTATAGTTTTT
2543 TTATAACCTCTATAGTTTTT
1 TTATAACCTCTATAGTTTTT
2563 TTA
1 TTA
2566 GTAATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 1 0.05
20 8 0.40
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (20 bp):
TTATAACCTCTATAGTTTTT
Found at i:2871 original size:20 final size:21
Alignment explanation
Indices: 2846--2886 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2836 ATTGATAAGA
2846 GTATAGCATTTTTA-TAATAT
1 GTATAGCATTTTTATTAATAT
*
2866 GTATAGCTTTTTTATTAATAT
1 GTATAGCATTTTTATTAATAT
2887 TTTTATTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (21 bp):
GTATAGCATTTTTATTAATAT
Found at i:4637 original size:29 final size:29
Alignment explanation
Indices: 4571--4638 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
4561 GTTTGAACGT
* *
4571 TTTGTCCCCTGAACTTCAATTTTGGACAT
1 TTTGTCCCCTAAACTTCAATTTTGGACAG
*
4600 TTTATCCCCTAAACTTCAATTTTGGGAC-G
1 TTTGTCCCCTAAACTTCAATTTT-GGACAG
*
4629 TTTGCCCCCT
1 TTTGTCCCCT
4639 TAGGCTAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (29 bp):
TTTGTCCCCTAAACTTCAATTTTGGACAG
Found at i:5705 original size:119 final size:120
Alignment explanation
Indices: 5425--5719 Score: 511
Period size: 120 Copynumber: 2.5 Consensus size: 120
5415 CAATTAAATA
*
5425 TAACTTGTTGACGAAGTTATTATATAGATGCATTTTCAATTTTTTGAAATTAATATGATTAAGAA
1 TAACTTGTTGACGAAGTTATTATATAGATGCATTTTCAATTCTTTGAAATTAATATGATTAAGAA
* * * *
5490 ACAATTGGAATTAAGTGGTGAGAAAATCAAAAGTTTTTTTATTCCTTTTCAACAT
66 ACAATTGGAATTAAATAGTAAGAAAATCAAAAGCTTTTTTATTCCTTTTCAACAT
5545 TAACTTGTTGACGAAGTTATTATATAGATGCATTTTCAATTCTTTGAAATTAATATGATTAAGAA
1 TAACTTGTTGACGAAGTTATTATATAGATGCATTTTCAATTCTTTGAAATTAATATGATTAAGAA
5610 ACAATTGGAATTAAATAGTAAGAAAATCAAAAGCTTTTTT-TTCCTTTTCAACAT
66 ACAATTGGAATTAAATAGTAAGAAAATCAAAAGCTTTTTTATTCCTTTTCAACAT
* * *
5664 TAACTTGTTGACAAAGTTATTATATAGATGCATTTTCAATTCATTGAAACTAATAT
1 TAACTTGTTGACGAAGTTATTATATAGATGCATTTTCAATTCTTTGAAATTAATAT
5720 TTTTTTTTAG
Statistics
Matches: 167, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
119 67 0.40
120 100 0.60
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (120 bp):
TAACTTGTTGACGAAGTTATTATATAGATGCATTTTCAATTCTTTGAAATTAATATGATTAAGAA
ACAATTGGAATTAAATAGTAAGAAAATCAAAAGCTTTTTTATTCCTTTTCAACAT
Found at i:11196 original size:29 final size:30
Alignment explanation
Indices: 11163--11227 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
11153 AGAAGTGCAA
11163 GATGATAATTA-TTTCATGAATTTTATTTG
1 GATGATAATTATTTTCATGAATTTTATTTG
11192 GATGATAATTATTTTCATGAATTTTATTTG
1 GATGATAATTATTTTCATGAATTTTATTTG
11222 GATGAT
1 GATGAT
11228 GGATTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (30 bp):
GATGATAATTATTTTCATGAATTTTATTTG
Found at i:11203 original size:15 final size:16
Alignment explanation
Indices: 11163--11227 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 16
11153 AGAAGTGCAA
11163 GATGATA-ATTATTT-
1 GATGATATATTATTTG
* *
11177 CATGA-ATTTTATTTG
1 GATGATATATTATTTG
*
11192 GATGATA-ATTATTTT
1 GATGATATATTATTTG
* *
11207 CATGA-ATTTTATTTG
1 GATGATATATTATTTG
11222 GATGAT
1 GATGAT
11228 GGATTTGATA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.30
15 24 0.65
16 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (16 bp):
GATGATATATTATTTG
Found at i:11325 original size:29 final size:29
Alignment explanation
Indices: 11283--11338 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
11273 CCTTGCATGG
* *
11283 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTATGGTGTTGAT
11312 TGTTGAAAACTTGTAATTATGGTGTTG
1 TGTTGAAAACTTGTAATTATGGTGTTG
11339 TAAACTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.29, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTATGGTGTTGAT
Found at i:11846 original size:29 final size:29
Alignment explanation
Indices: 11804--11861 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
11794 GGTAAACCTC
11804 CAAATTTAATATATCATCAGAATAAAGTT
1 CAAATTTAATATATCATCAGAATAAAGTT
* * *
11833 CAAATTTAGTATATGATCATAATAAAGTT
1 CAAATTTAATATATCATCAGAATAAAGTT
11862 TTAGAAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
CAAATTTAATATATCATCAGAATAAAGTT
Found at i:12300 original size:13 final size:14
Alignment explanation
Indices: 12269--12307 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
12259 GCTCAACACT
12269 AACTGACTCGAAAA
1 AACTGACTCGAAAA
*
12283 AACTGACTC-AACA
1 AACTGACTCGAAAA
12296 AACTGACT-GAAA
1 AACTGACTCGAAA
12308 CCCGACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (14 bp):
AACTGACTCGAAAA
Found at i:12544 original size:1 final size:1
Alignment explanation
Indices: 12540--12564 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12530 TCTTTTTCCC
12540 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12565 GACATATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20553 original size:22 final size:21
Alignment explanation
Indices: 20508--20553 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
20498 AAAATCAGGG
**
20508 TTTTCTTTTTATTTTTTTCCT
1 TTTTCTTTTTATTTTTTAACT
20529 TTTTCCTTTTTATTTTTTAA-T
1 TTTT-CTTTTTATTTTTTAACT
20550 TTTT
1 TTTT
20554 GTTCTTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTATTTTTTAACT
Found at i:22070 original size:3 final size:3
Alignment explanation
Indices: 22055--22140 Score: 156
Period size: 3 Copynumber: 29.0 Consensus size: 3
22045 TTAAAGGGGT
*
22055 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22141 ATTAGTAGAA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39281 original size:58 final size:58
Alignment explanation
Indices: 39214--39325 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
39204 AGTACTCCAT
* **
39214 TTTAAGTTCGAGATGTAAAGATGTGACAACTACCACAAATAAAAGGAAGCAACACAAG
1 TTTAAGTTCGAAATGTAAAGATGTGACAACTAAAACAAATAAAAGGAAGCAACACAAG
* * *
39272 TTTAAGTTCGAAATTTATAGTTGTGACAACTAAAACAAATAAAAGGAAGCAACA
1 TTTAAGTTCGAAATGTAAAGATGTGACAACTAAAACAAATAAAAGGAAGCAACA
39326 AACGAGACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.22
Consensus pattern (58 bp):
TTTAAGTTCGAAATGTAAAGATGTGACAACTAAAACAAATAAAAGGAAGCAACACAAG
Found at i:49033 original size:25 final size:25
Alignment explanation
Indices: 49005--49052 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
48995 TCAAAATAAA
*
49005 CAGAAACTAATCAGAATTCAGAAAT
1 CAGAAACCAATCAGAATTCAGAAAT
*
49030 CAGAATCCAATCAGAATTCAGAA
1 CAGAAACCAATCAGAATTCAGAA
49053 TCCATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (25 bp):
CAGAAACCAATCAGAATTCAGAAAT
Found at i:49043 original size:18 final size:18
Alignment explanation
Indices: 49022--49056 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49012 TAATCAGAAT
49022 TCAGAAATCAGAATCCAA
1 TCAGAAATCAGAATCCAA
*
49040 TCAGAATTCAGAATCCA
1 TCAGAAATCAGAATCCA
49057 TATTTCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (18 bp):
TCAGAAATCAGAATCCAA
Done.