Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023702.1 Corchorus olitorius cultivar O-4 contig23735, 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: 26642
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Found at i:315 original size:22 final size:21
Alignment explanation
Indices: 270--317 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
260 CGCCCCTCCA
*
270 TGATTTTAGATGTTGTTGGGT
1 TGATTTTAGATGTTGTTGGAT
* *
291 TGATTTTTGATGTTGTTTTGAT
1 TGATTTTAGATGTTG-TTGGAT
313 TGATT
1 TGATT
318 AAGGTTGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (21 bp):
TGATTTTAGATGTTGTTGGAT
Found at i:2593 original size:15 final size:15
Alignment explanation
Indices: 2561--2590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2551 TAAATTTCAA
2561 TAAAATAAAATATAT
1 TAAAATAAAATATAT
2576 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
2590 T
1 T
2591 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:5020 original size:2 final size:2
Alignment explanation
Indices: 5013--5048 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5003 ATGATGGGAA
5013 AT AT AT AT AT 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 AT AT AT AT AT
5049 TCATTTAATC
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):
AT
Found at i:5586 original size:21 final size:21
Alignment explanation
Indices: 5560--5599 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5550 CGGGGGTAAA
5560 CGTTCCTTTCTCCTTTCTAAC
1 CGTTCCTTTCTCCTTTCTAAC
5581 CGTTCCTTTCTCCTTTCTA
1 CGTTCCTTTCTCCTTTCTA
5600 TGGTATGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.38, G:0.05, T:0.50
Consensus pattern (21 bp):
CGTTCCTTTCTCCTTTCTAAC
Found at i:5630 original size:16 final size:14
Alignment explanation
Indices: 5600--5626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5590 CTCCTTTCTA
5600 TGGTATGTGTATTC
1 TGGTATGTGTATTC
5614 TGGTATGTGTATT
1 TGGTATGTGTATT
5627 TTCTCTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.30, T:0.52
Consensus pattern (14 bp):
TGGTATGTGTATTC
Found at i:5998 original size:2 final size:2
Alignment explanation
Indices: 5991--6016 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5981 AACTTAAGTA
5991 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
6017 TAATTTATTT
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:6749 original size:2 final size:2
Alignment explanation
Indices: 6742--6771 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6732 AATGATGAAT
*
6742 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6772 AAATATTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:9147 original size:46 final size:46
Alignment explanation
Indices: 9080--9172 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
9070 TAAAATCTTG
*
9080 TGTAATTTTATCGATTAAGTTATAAGGTTAGTTTGGAAAAGATTTA
1 TGTAATTTTATCGATTAAGTTAAAAGGTTAGTTTGGAAAAGATTTA
* *
9126 TGTAATTTTATCGATTAAGTTAAAAGGTTAGTTTGGAGAGGATTTA
1 TGTAATTTTATCGATTAAGTTAAAAGGTTAGTTTGGAAAAGATTTA
9172 T
1 T
9173 CCATATGTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (46 bp):
TGTAATTTTATCGATTAAGTTAAAAGGTTAGTTTGGAAAAGATTTA
Found at i:12565 original size:2 final size:2
Alignment explanation
Indices: 12558--12589 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12548 ATGATGAATA
12558 AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12590 TGGAACTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12925 original size:29 final size:29
Alignment explanation
Indices: 12857--13057 Score: 277
Period size: 29 Copynumber: 7.1 Consensus size: 29
12847 AATTGATCAA
*
12857 TTGCACA-CTCAGGGGTATTTTGGTCA--T
1 TTGCACATC-CAGGGGCATTTTGGTCATTT
*
12884 TTGCACATCCAGGGGCATTTTGGACATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTT
*
12913 TTGCACATTCAGGGGCATTTTGGTCA--T
1 TTGCACATCCAGGGGCATTTTGGTCATTT
* *
12940 TTGCACATCCTGGGGCATTTTGGCCATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTT
*
12969 TTGCACATCCTGGGGCATTTTGGTCATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTT
*
12998 TTGCACATCCAAGGGCATTTTGGTCATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTT
* *
13027 TTGCGCATCCAGGGGCATTTTGGTTATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTT
13056 TT
1 TT
13058 TGCATGCTCT
Statistics
Matches: 156, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
27 46 0.29
28 1 0.01
29 109 0.70
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (29 bp):
TTGCACATCCAGGGGCATTTTGGTCATTT
Found at i:12943 original size:56 final size:56
Alignment explanation
Indices: 12857--13055 Score: 283
Period size: 56 Copynumber: 3.5 Consensus size: 56
12847 AATTGATCAA
*
12857 TTGCACA-CTCAGGGGTATTTTGGTCATTTGCACATCCAGGGGCATTTTGGACATTT
1 TTGCACATC-CAGGGGCATTTTGGTCATTTGCACATCCAGGGGCATTTTGGACATTT
* * *
12913 TTGCACATTCAGGGGCATTTTGGTCATTTGCACATCCTGGGGCATTTTGGCCATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTTGCACATCCAGGGGCATTTTGGACATTT
* * *
12969 TTGCACATCCTGGGGCATTTTGGTCATTTTTGCACATCCAAGGGCATTTTGGTCATTT
1 TTGCACATCCAGGGGCATTTTGGTCA--TTTGCACATCCAGGGGCATTTTGGACATTT
* *
13027 TTGCGCATCCAGGGGCATTTTGGTTATTT
1 TTGCACATCCAGGGGCATTTTGGTCATTT
13056 TTTGCATGCT
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
56 78 0.61
58 50 0.39
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (56 bp):
TTGCACATCCAGGGGCATTTTGGTCATTTGCACATCCAGGGGCATTTTGGACATTT
Found at i:12998 original size:85 final size:86
Alignment explanation
Indices: 12857--13049 Score: 268
Period size: 85 Copynumber: 2.3 Consensus size: 86
12847 AATTGATCAA
* *
12857 TTGCACA-CTCAGGGGTATTTTGGTCA--TTTGCACATCCAGGGGCATTTTGGACATTTTTGCAC
1 TTGCACATC-CAGGGGCATTTTGGCCATTTTTGCACATCCAGGGGCATTTTGGACATTTTTGCAC
* *
12919 ATTCAGGGGCATTTTGGTCA-T
65 ATCCAAGGGCATTTTGGTCATT
* * *
12940 TTGCACATCCTGGGGCATTTTGGCCATTTTTGCACATCCTGGGGCATTTTGGTCATTTTTGCACA
1 TTGCACATCCAGGGGCATTTTGGCCATTTTTGCACATCCAGGGGCATTTTGGACATTTTTGCACA
13005 TCCAAGGGCATTTTGGTCATTT
66 TCCAAGGGCATTTTGGTCA-TT
*
13027 TTGCGCATCCAGGGGCATTTTGG
1 TTGCACATCCAGGGGCATTTTGG
13050 TTATTTTTTG
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
83 21 0.22
84 1 0.01
85 52 0.54
87 22 0.23
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (86 bp):
TTGCACATCCAGGGGCATTTTGGCCATTTTTGCACATCCAGGGGCATTTTGGACATTTTTGCACA
TCCAAGGGCATTTTGGTCATT
Found at i:20758 original size:19 final size:19
Alignment explanation
Indices: 20734--20777 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
20724 GGCTTGAGCC
*
20734 AACCGGCTTGGTCGGTCCG
1 AACCGGCTTGGTCGGACCG
*
20753 AACCGGCTTGGTTGGACCG
1 AACCGGCTTGGTCGGACCG
20772 AACCGG
1 AACCGG
20778 TTTGACCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.18
Consensus pattern (19 bp):
AACCGGCTTGGTCGGACCG
Done.