Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018079.1 Corchorus olitorius cultivar O-4 contig18112, 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: 28573
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:34 original size:12 final size:12
Alignment explanation
Indices: 19--64 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
9 TTTTTAATCT
19 TTTTATATTTTC
1 TTTTATATTTTC
31 TTTTA-A-TTTC
1 TTTTATATTTTC
*
41 TTTTAAGATTTTC
1 TTTT-ATATTTTC
*
54 TTTTATCTTTT
1 TTTTATATTTT
65 AATAAGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 11 0.38
13 8 0.28
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTATATTTTC
Found at i:525 original size:9 final size:10
Alignment explanation
Indices: 501--525 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
491 TGTGGTTGTA
501 ATTTTTTACT
1 ATTTTTTACT
511 ATTTTTTACT
1 ATTTTTTACT
521 ATTTT
1 ATTTT
526 AACACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTTACT
Found at i:1648 original size:22 final size:22
Alignment explanation
Indices: 1594--1650 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
1584 ACTATTTTTC
1594 AAAA-ATGCACATTAACGAGAT
1 AAAACATGCACATTAACGAGAT
*
1615 -AAACTAAAGCACATTAA-GAGACT
1 AAAAC--ATGCACATTAACGAGA-T
1638 AAAACATGCACAT
1 AAAACATGCACAT
1651 CCTAGACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
20 3 0.10
22 11 0.38
23 11 0.38
24 4 0.14
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (22 bp):
AAAACATGCACATTAACGAGAT
Found at i:16154 original size:11 final size:11
Alignment explanation
Indices: 16134--16168 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
16124 TTGACAGCGC
16134 AACAAAAACAA
1 AACAAAAACAA
*
16145 AACGAAAACAA
1 AACAAAAACAA
16156 AACAAAAACAA
1 AACAAAAACAA
16167 AA
1 AA
16169 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:20659 original size:21 final size:21
Alignment explanation
Indices: 20635--20702 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
20625 AAATTCTCTA
20635 TAAATTAAGAAATACTCAACT
1 TAAATTAAGAAATACTCAACT
* * **
20656 TAAATCATAGAAA-ATTC-TTT
1 TAAATTA-AGAAATACTCAACT
20676 GTAAATTAAGAAATACTCAACT
1 -TAAATTAAGAAATACTCAACT
*
20698 CAAAT
1 TAAAT
20703 CCTGATCCTT
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
20 6 0.18
21 22 0.65
22 6 0.18
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (21 bp):
TAAATTAAGAAATACTCAACT
Found at i:20682 original size:42 final size:42
Alignment explanation
Indices: 20623--20703 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
20613 GCTAAGTCTT
*
20623 GAAAATTCTCTATAAATTAAGAAATACTCAACTTAAATCATA
1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
* *
20665 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATC
20704 CTGATCCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
Found at i:20839 original size:55 final size:56
Alignment explanation
Indices: 20769--20881 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
20759 TTTATTTTGT
*
20769 AGAATAATTAAGTAGAGATA-GGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
*
20824 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACGTTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
20880 AG
1 AG
20882 GAAACGGATA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 20 0.36
56 35 0.64
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:21825 original size:29 final size:30
Alignment explanation
Indices: 21765--21840 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
21755 TTGACACAAA
* *
21765 TTGTAAATAGAGGGACCAAATTGATAGATT
1 TTGTAAGTAGAGGGACCAAATTGATACATT
* * *
21795 TTGT-AGTAGGGGGACCAAATTGATCCCTT
1 TTGTAAGTAGAGGGACCAAATTGATACATT
21824 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
21841 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACCAAATTGATACATT
Found at i:23334 original size:24 final size:25
Alignment explanation
Indices: 23307--23362 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
23297 TCATCTTTCA
* *
23307 TCTTTTTTCTCCTTTTCTTTGTT-T
1 TCTTTTTTCTCCTTTCCTTTGTTAG
*
23331 TCTTTCTTCTCCTTTCCTTTGTTAG
1 TCTTTTTTCTCCTTTCCTTTGTTAG
23356 TCTTTTT
1 TCTTTTT
23363 CTTGTACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.70
Consensus pattern (25 bp):
TCTTTTTTCTCCTTTCCTTTGTTAG
Found at i:24954 original size:6 final size:6
Alignment explanation
Indices: 24943--24977 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
24933 TTTATTTATG
*
24943 ATATTT ATATTT ATATTT ATATTT GATAATT ATAT
1 ATATTT ATATTT ATATTT ATATTT -ATATTT ATAT
24978 ACTTTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:24960 original size:12 final size:13
Alignment explanation
Indices: 24941--24977 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
24931 TTTTTATTTA
24941 TGATATTTATATT
1 TGATATTTATATT
24954 T-ATATTTATATT
1 TGATATTTATATT
*
24966 TGATAATTATAT
1 TGATATTTATAT
24978 ACTTTTTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (13 bp):
TGATATTTATATT
Found at i:26967 original size:25 final size:25
Alignment explanation
Indices: 26939--26987 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
26929 ACTATATAGC
26939 TTTTTAAGT-AATTTTAAATAAGAAT
1 TTTTTAA-TCAATTTTAAATAAGAAT
26964 TTTTTAATCAATTTTAAATAAGAA
1 TTTTTAATCAATTTTAAATAAGAA
26988 AATTGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTTTAATCAATTTTAAATAAGAAT
Found at i:28478 original size:2 final size:2
Alignment explanation
Indices: 28471--28506 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28461 AGCACTAGTG
28471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28507 CACACACTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.