Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022045.1 Corchorus olitorius cultivar O-4 contig22078, 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: 49486
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:562 original size:23 final size:23
Alignment explanation
Indices: 535--578 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
525 TTGAAGAATG
535 AAGGAGA-AAGAAAAAGAAAATAA
1 AAGGAGAGAAG-AAAAGAAAATAA
558 AAGGAGAGAAGAAAAGAAAAT
1 AAGGAGAGAAGAAAAGAAAAT
579 GGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAGGAGAGAAGAAAAGAAAATAA
Found at i:571 original size:18 final size:19
Alignment explanation
Indices: 548--593 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
538 GAGAAAGAAA
548 AAGAAAATAAAA-GGAGAG
1 AAGAAAATAAAATGGAGAG
*
566 AAGAAAAGAAAATGGAGAG
1 AAGAAAATAAAATGGAGAG
*
585 AAAAAAATA
1 AAGAAAATA
594 TAATTAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.07
Consensus pattern (19 bp):
AAGAAAATAAAATGGAGAG
Found at i:589 original size:17 final size:18
Alignment explanation
Indices: 548--590 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
538 GAGAAAGAAA
*
548 AAGAAAATAAAAGGAGAG
1 AAGAAAAGAAAAGGAGAG
566 AAGAAAAGAAAATGGAGAG
1 AAGAAAAGAAAA-GGAGAG
585 AA-AAAA
1 AAGAAAA
591 ATATAATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (18 bp):
AAGAAAAGAAAAGGAGAG
Found at i:1139 original size:57 final size:58
Alignment explanation
Indices: 1043--1167 Score: 227
Period size: 57 Copynumber: 2.2 Consensus size: 58
1033 TACCAACAAA
*
1043 CAAATCA-TATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTC
1 CAAATCAGGATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTC
1100 C-AATCAGGATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTC
1 CAAATCAGGATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTC
1157 CAAATCAGGAT
1 CAAATCAGGAT
1168 TAATGAGGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
56 5 0.08
57 51 0.78
58 9 0.14
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (58 bp):
CAAATCAGGATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTC
Found at i:8499 original size:14 final size:14
Alignment explanation
Indices: 8470--8514 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
8460 TAACATGAAT
8470 TCTCATCTC-CCT-C
1 TCTC-TCTCTCCTCC
8483 TCTCTCTCTCCTCC
1 TCTCTCTCTCCTCC
8497 TCTCTCTCT-CTCC
1 TCTCTCTCTCCTCC
8510 -CTCTC
1 TCTCTC
8515 ACACTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.30
13 11 0.37
14 10 0.33
ACGTcount: A:0.02, C:0.56, G:0.00, T:0.42
Consensus pattern (14 bp):
TCTCTCTCTCCTCC
Found at i:8500 original size:16 final size:16
Alignment explanation
Indices: 8479--8509 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8469 TTCTCATCTC
8479 CCTCTCTCTCTCTCCT
1 CCTCTCTCTCTCTCCT
8495 CCTCTCTCTCTCTCC
1 CCTCTCTCTCTCTCC
8510 CTCTCACACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (16 bp):
CCTCTCTCTCTCTCCT
Found at i:14958 original size:1 final size:1
Alignment explanation
Indices: 14952--14984 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
14942 GGTAGCAAAG
*
14952 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14985 AGTGATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:16477 original size:14 final size:13
Alignment explanation
Indices: 16441--16479 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
16431 TAAAACTTTT
*
16441 TATTTTTTTAATA
1 TATTTTTTAAATA
*
16454 TATTTCTTAAATA
1 TATTTTTTAAATA
16467 TCATTTTTTAAAT
1 T-ATTTTTTAAAT
16480 TTTTTTATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTTTAAATA
Found at i:19109 original size:40 final size:38
Alignment explanation
Indices: 19055--19138 Score: 141
Period size: 40 Copynumber: 2.2 Consensus size: 38
19045 GTTTTATCAC
19055 CTTTGAGAGATTGCCCTTGTGTTACATGTGCTTAGGGA
1 CTTTGAGAGATTGCCCTTGTGTTACATGTGCTTAGGGA
*
19093 CTTTGAGAGAGGTTGCCCTTGTGTTATATGTGCTTAGGGA
1 CTTTGAGAGA--TTGCCCTTGTGTTACATGTGCTTAGGGA
19133 CTTTGA
1 CTTTGA
19139 TTATTGGGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
38 10 0.23
40 33 0.77
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.38
Consensus pattern (38 bp):
CTTTGAGAGATTGCCCTTGTGTTACATGTGCTTAGGGA
Found at i:20345 original size:152 final size:150
Alignment explanation
Indices: 20174--20460 Score: 443
Period size: 152 Copynumber: 1.9 Consensus size: 150
20164 TTTTAATTAA
* *
20174 TTTATTTTTACCATTTTACTATTTTTCATTGAAAA-CTAGGATGTATTAAAA-TATTTTAATGTA
1 TTTATTTTTACCATTTTACTATTTTTCATT-AAAATCTAGGATATATTAAAACT-TTTTAATATA
*
20237 CAGTTTTATTCTACTAAAAACTCTATTTTCATCTAATTAAATTCAATATTTTTTATAATTATTTT
64 CAGTTTTATTCTACT-AAAACTCTATTTTCATCTAATTAAATTCAATA-TTTCTATAATTATTTT
20302 ATTTTTACCATTTTAATTTAAGAG
127 ATTTTTACCATTTTAATTTAAGAG
** * **
20326 TTTATTTTTATGATTTTACTATTTTTCATTAAAATCTTGGATATATTAAAACTTTTTAATATGTA
1 TTTATTTTTACCATTTTACTATTTTTCATTAAAATCTAGGATATATTAAAACTTTTTAATATACA
*
20391 GTTTTATTCTACTAAAACTCTATTTTCATTTAATTAAATTCAATATTTCTATAATTATTTTATTT
66 GTTTTATTCTACTAAAACTCTATTTTCATCTAATTAAATTCAATATTTCTATAATTATTTTATTT
20456 TTACC
131 TTACC
20461 CTTGTACTTT
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
150 24 0.19
151 35 0.28
152 64 0.52
153 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (150 bp):
TTTATTTTTACCATTTTACTATTTTTCATTAAAATCTAGGATATATTAAAACTTTTTAATATACA
GTTTTATTCTACTAAAACTCTATTTTCATCTAATTAAATTCAATATTTCTATAATTATTTTATTT
TTACCATTTTAATTTAAGAG
Found at i:20524 original size:151 final size:152
Alignment explanation
Indices: 20175--20499 Score: 410
Period size: 152 Copynumber: 2.2 Consensus size: 152
20165 TTTAATTAAT
** * * * * **
20175 TTATTTTTACCATTTTACTATTTTTCATTGAAAA-CTAGGATGTATTAAAA-TATTTTAATGTAC
1 TTATTTTTATGATTTGACTATTTTTCATT-AAAATCTAGAATATATTAAAACT-TTTTAATATGT
*
20238 AGTTTTATTCTACTAAAAACTCTATTTTCATCTAATTAAATTCAATATTTTTTATAATTATTTTA
64 AGTTTTATTCTACTAAAAACTCTATTTTCATCTAATTAAATTCAATATTTTCTATAATTATTTTA
* * *
20303 TTTTTACCATTTTAATTTAAGAGT
129 TTTTTACCATTGTAATTTAAAAGG
* * *
20327 TTATTTTTATGATTTTACTATTTTTCATTAAAATCTTGGATATATTAAAACTTTTTAATATGTAG
1 TTATTTTTATGATTTGACTATTTTTCATTAAAATCTAGAATATATTAAAACTTTTTAATATGTAG
*
20392 TTTTATTCTACT-AAAACTCTATTTTCATTTAATTAAATTCAATA-TTTCTATAATTATTTTATT
66 TTTTATTCTACTAAAAACTCTATTTTCATCTAATTAAATTCAATATTTTCTATAATTATTTTATT
* *
20455 TTTACCCTTGTACTTTAAAAGG
131 TTTACCATTGTAATTTAAAAGG
*
20477 TTATTGTTTCT-ATTTGA-TATTTT
1 TTATT-TTTATGATTTGACTATTTT
20500 AATGTATTGT
Statistics
Matches: 154, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
149 6 0.04
150 45 0.29
151 39 0.25
152 63 0.41
153 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.53
Consensus pattern (152 bp):
TTATTTTTATGATTTGACTATTTTTCATTAAAATCTAGAATATATTAAAACTTTTTAATATGTAG
TTTTATTCTACTAAAAACTCTATTTTCATCTAATTAAATTCAATATTTTCTATAATTATTTTATT
TTTACCATTGTAATTTAAAAGG
Found at i:20752 original size:16 final size:15
Alignment explanation
Indices: 20727--20768 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
20717 AGGTTCGTTT
*
20727 ATTT-GGGTTAGGTCA
1 ATTTCGGGTTAGG-AA
20742 ATTTCGGGTTAAGGAA
1 ATTTCGGGTT-AGGAA
20758 ATTTCGGGTTA
1 ATTTCGGGTTA
20769 ATTTTCGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 16 0.67
17 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (15 bp):
ATTTCGGGTTAGGAA
Found at i:22005 original size:30 final size:29
Alignment explanation
Indices: 21965--22042 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
21955 CGTCCACAAA
* *
21965 GGGCTTATTTGACTGTTTTTAAGAGTTCGG
1 GGGCTTATTTGGCTGTTTTT-AGAGTTCAG
* * **
21995 GGGTTTATTTGGCGGTAATTAGAGTTCAG
1 GGGCTTATTTGGCTGTTTTTAGAGTTCAG
22024 GGGCTTATTTGGCTGTTTT
1 GGGCTTATTTGGCTGTTTT
22043 GTGTAAGCTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.15, C:0.09, G:0.32, T:0.44
Consensus pattern (29 bp):
GGGCTTATTTGGCTGTTTTTAGAGTTCAG
Found at i:32956 original size:19 final size:19
Alignment explanation
Indices: 32924--32969 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
32914 AAAAGTTCTT
32924 AAACAAAAATTAAAATTAA
1 AAACAAAAATTAAAATTAA
*
32943 AAACAGAAAA-TAAATTTAA
1 AAACA-AAAATTAAAATTAA
32962 AAA-AAAAA
1 AAACAAAAA
32970 CCGCAAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 1 0.04
19 16 0.64
20 4 0.16
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (19 bp):
AAACAAAAATTAAAATTAA
Found at i:33089 original size:18 final size:18
Alignment explanation
Indices: 33066--33101 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
33056 GTCAATCCAC
33066 TAATTAAGTAATGTAATT
1 TAATTAAGTAATGTAATT
33084 TAATTAAGTAATGTAATT
1 TAATTAAGTAATGTAATT
33102 AAAGCACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
TAATTAAGTAATGTAATT
Found at i:36143 original size:19 final size:18
Alignment explanation
Indices: 36106--36145 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
36096 CTCTTGAAAA
*
36106 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
36124 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
36143 AAT
1 AAT
36146 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Done.