Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023402.1 Corchorus olitorius cultivar O-4 contig23435, 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: 7361
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:958 original size:10 final size:10
Alignment explanation
Indices: 937--965 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
927 TTAAAAAAGG
937 AAATAAAA-T
1 AAATAAAATT
946 AAATAAAATT
1 AAATAAAATT
956 AAATAAAATT
1 AAATAAAATT
966 GTTAATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAAAATT
Found at i:2991 original size:14 final size:13
Alignment explanation
Indices: 2975--3039 Score: 87
Period size: 14 Copynumber: 4.8 Consensus size: 13
2965 ATAAAAGATT
2975 TTTTCAAAAATGA
1 TTTTCAAAAATGA
2988 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
3002 TTTTCAAGAAATGA
1 TTTTCAA-AAATGA
3016 TTTTCAAAAATGA
1 TTTTCAAAAATGA
3029 GTTTTCAAAAA
1 -TTTTCAAAAA
3040 GGTTTTGAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.31
14 31 0.65
15 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:3694 original size:17 final size:15
Alignment explanation
Indices: 3659--3714 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 15
3649 GAATCAATCT
3659 AAAGAAAAAAAAAAG
1 AAAGAAAAAAAAAAG
3674 -AAGAAAAAGAAAAAG
1 AAAGAAAAA-AAAAAG
*
3689 CAAAGAAAAATCAAAAG
1 -AAAGAAAAA-AAAAAG
3706 AAAGAAAAA
1 AAAGAAAAA
3715 TCAAAAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 8 0.22
15 6 0.17
16 9 0.25
17 13 0.36
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:3709 original size:16 final size:16
Alignment explanation
Indices: 3659--3721 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
3649 GAATCAATCT
3659 AAAGAAAAA-AAAAAG
1 AAAGAAAAATAAAAAG
*
3674 -AAGAAAAAGAAAAAG
1 AAAGAAAAATAAAAAG
*
3689 CAAAGAAAAATCAAAAG
1 -AAAGAAAAATAAAAAG
*
3706 AAAGAAAAATCAAAAG
1 AAAGAAAAATAAAAAG
3722 GAAAAGGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
14 8 0.19
15 6 0.14
16 16 0.37
17 13 0.30
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAGAAAAATAAAAAG
Found at i:3725 original size:17 final size:17
Alignment explanation
Indices: 3674--3725 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
3664 AAAAAAAAAG
** *
3674 AAGAAAAAGAAAAAGCA
1 AAGAAAAATCAAAAGGA
3691 AAGAAAAATCAAAA-GA
1 AAGAAAAATCAAAAGGA
3707 AAGAAAAATCAAAAGGA
1 AAGAAAAATCAAAAGGA
3724 AA
1 AA
3726 AGGTTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (17 bp):
AAGAAAAATCAAAAGGA
Found at i:3993 original size:87 final size:87
Alignment explanation
Indices: 3847--4102 Score: 415
Period size: 87 Copynumber: 2.9 Consensus size: 87
3837 TGTTTGAAGG
3847 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
1 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
3912 TTGGAGGAAGATTTGGGAAATA
66 TTGGAGGAAGATTTGGGAAATA
*
3934 TTTCTTAAGATGAGAAACTTATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
1 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
*
3999 TTGGAGGAAGATTTGAGAAATA
66 TTGGAGGAAGATTTGGGAAATA
* * * * *
4021 TTTCTTAAGGTGGGAAGCTGAT-CATGAACCATCAATTGAGTTGGGAATATCAATACATGATCAA
1 TTTCTTAAGATGAGAAACTGATCCA-GAAACATCAATTGAGTTGGGAATATCAATGCATGATCAA
* *
4085 ATTGGAAGAAGGTTTGGG
65 ATTGGAGGAAGATTTGGG
4103 GCATCAATCG
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
86 2 0.01
87 155 0.99
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (87 bp):
TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
TTGGAGGAAGATTTGGGAAATA
Found at i:4992 original size:37 final size:37
Alignment explanation
Indices: 4873--5151 Score: 285
Period size: 37 Copynumber: 7.5 Consensus size: 37
4863 TCAAGATTTT
*
4873 TGTTTAGGTGTCTTATCAAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTCATC-AAATCCTTATTTAAGGTCCC
* *
4911 TGTTTAGGTGTCTCACCAAAATCCTTATTTAAGATCCC
1 TGTTTAGGTGTCTCATC-AAATCCTTATTTAAGGTCCC
* *
4949 TG-TTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTCATCAAATCCTTATTTAAGGTCCC
* * * * * *
4985 TATTTAGGCGTCTCATCAAAACCTTGTTCAAGGTCCT
1 TGTTTAGGTGTCTCATCAAATCCTTATTTAAGGTCCC
* *
5022 TGTTT-GGATGTCTCATCAAAACCTTGTTTAAGGTCCC
1 TGTTTAGG-TGTCTCATCAAATCCTTATTTAAGGTCCC
* * * * * * *
5059 TTTTTAGCTGTCTCATCAAA-CCTTGTTCAAGATTCT
1 TGTTTAGGTGTCTCATCAAATCCTTATTTAAGGTCCC
* * **
5095 TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTATC
1 TGTTTAGGTGTCTCATCAAATCCTTATTTAAGGTCCC
*
5132 TGTTTAGGTGTCTCTTCAAA
1 TGTTTAGGTGTCTCATCAAA
5152 ATCCCAGTTT
Statistics
Matches: 199, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
36 50 0.25
37 111 0.56
38 38 0.19
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (37 bp):
TGTTTAGGTGTCTCATCAAATCCTTATTTAAGGTCCC
Found at i:4992 original size:74 final size:73
Alignment explanation
Indices: 4845--5152 Score: 375
Period size: 74 Copynumber: 4.2 Consensus size: 73
4835 ACAAAATTCA
**
4845 GTCTCATCAAAACCTTGTTCAAGATTTTTGTTTAGGTGTCTTATCAAAATCCTTATTTAAGGTCC
1 GTCTCATCAAAACCTTGTTCAAGATCCTTG-TTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
4910 CTGTTTAGGT
64 CTGTTTAGGT
* * * * *
4920 GTCTCACCAAAATCCTTATTTAAGATCCCTGTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAA-CCTTGTTCAAGATCCTTGTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* *
4985 TATTTAGGC
65 TGTTTAGGT
* * * * *
4994 GTCTCATCAAAACCTTGTTCAAGGTCCTTGTTTGGATGTCTCATCAAAACCTTGTTTAAGGTCCC
1 GTCTCATCAAAACCTTGTTCAAGATCCTTGTTAGG-TGTCTTATCAAATCCTTATTTAAGGTCCC
* *
5059 TTTTTAGCT
65 TGTTTAGGT
* * **
5068 GTCTCATC-AAACCTTGTTCAAGATTCTTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTATC
1 GTCTCATCAAAACCTTGTTCAAGATCCTTG-TTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
5132 TGTTTAGGT
65 TGTTTAGGT
*
5141 GTCTCTTCAAAA
1 GTCTCATCAAAA
5153 TCCCAGTTTA
Statistics
Matches: 195, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
73 74 0.38
74 84 0.43
75 24 0.12
76 13 0.07
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (73 bp):
GTCTCATCAAAACCTTGTTCAAGATCCTTGTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCT
GTTTAGGT
Found at i:5645 original size:215 final size:217
Alignment explanation
Indices: 5251--5671 Score: 620
Period size: 215 Copynumber: 1.9 Consensus size: 217
5241 TTTCTCTAGA
* *
5251 AAGTTGATCTTAAGTTGATCCTGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
1 AAGTTGATCTTAAGATGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
* *
5316 AAGATGACCCAGTGTGGTTTTTCATGGAAATTTTCAGAGATCTAAGTTGATCTTAAGATGACCCA
66 AAGATGACCCAGTGTGGTTTTTCATAGAAATTTTCAAAGATCTAAGTTGATCTTAAGATGACCCA
* * * * *
5381 GTGTGGTTTTTCATGGAAATTTTCAGAGATCTAAGTTGATCTTAAGTTGA-CTCAGTGTGGTC-T
131 GTGTGGTCTTCCATAGAAATTTTCAAAAATCTAAGTTGATCTTAAGTTGATC-CAGTGTGGTCAT
*
5444 TTCATAGAAGTTTTTCAGAGATCT
195 TCCA-AGAAGTTTTTCAGAGATCT
*
5468 AAGTTGATCTTCAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
1 AAGTTGATCTTAAGATGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
* * *
5532 AAGATGA-CCAGTGTGGTCTTTT-ATAGAAGCTTTT-AAAGGTCTAAGTTGATCTTCAGATGACC
66 AAGATGACCCAGTGTGGT-TTTTCATAGAA-ATTTTCAAAGATCTAAGTTGATCTTAAGATGACC
* *
5594 CTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCTAAGTTGATCTTAAGTTGATCCAGTGTGGTCA
129 CAGTGTGGTCTTCCATAGAAATTTTCAAAAATCTAAGTTGATCTTAAGTTGATCCAGTGTGGTCA
5659 TTCCAAGAAGTTT
194 TTCCAAGAAGTTT
5672 ACGATGATCA
Statistics
Matches: 184, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
215 103 0.56
216 65 0.35
217 16 0.09
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (217 bp):
AAGTTGATCTTAAGATGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
AAGATGACCCAGTGTGGTTTTTCATAGAAATTTTCAAAGATCTAAGTTGATCTTAAGATGACCCA
GTGTGGTCTTCCATAGAAATTTTCAAAAATCTAAGTTGATCTTAAGTTGATCCAGTGTGGTCATT
CCAAGAAGTTTTTCAGAGATCT
Found at i:5691 original size:54 final size:54
Alignment explanation
Indices: 5251--5671 Score: 580
Period size: 54 Copynumber: 7.8 Consensus size: 54
5241 TTTCTCTAGA
* * *
5251 AAGTTGATCTTAAGTTGATCCTGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
5305 AAGTTGATCTTAAGATGACCCAGTGTGGTTTTTCATGGAAATTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
5359 AAGTTGATCTTAAGATGACCCAGTGTGGTTTTTCATGGAAATTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
5413 AAGTTGATCTTAAGTTGACTCAGTGTGGTCTTTCATAGAAGTTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
*
5468 AAGTTGATCTTCAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
5521 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTTATAGAAGCTTTT-AAAGGTCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
* * * * *
5574 AAGTTGATCTTCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
5628 AAGTTGATCTTAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTC-TTTCATAGAAGTTT
5672 ACGATGATCA
Statistics
Matches: 334, Mismatches: 28, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
53 78 0.23
54 222 0.66
55 34 0.10
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (54 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
Found at i:5761 original size:55 final size:55
Alignment explanation
Indices: 5645--5764 Score: 131
Period size: 55 Copynumber: 2.2 Consensus size: 55
5635 TCTTAAGTTG
* *
5645 ATCCAGTGTGGTCATTCCAAGAAGTTTACGATGATCAGAGTTGATCTCTAAACTA
1 ATCCAGTGCGGTCATTCCAAGAAGTTTACCATGATCAGAGTTGATCTCTAAACTA
** *
5700 GCCCAGTGCGGTCATTCCAAGAAAGGTTT-CCATGATCA-AGGTTGAAT-TCTTAA-TA
1 ATCCAGTGCGGTCATTCCAAG-AA-GTTTACCATGATCAGA-GTTG-ATCTCTAAACTA
5755 ATCCAGTGCG
1 ATCCAGTGCG
5765 ATTAATTAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
55 29 0.54
56 19 0.35
57 6 0.11
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (55 bp):
ATCCAGTGCGGTCATTCCAAGAAGTTTACCATGATCAGAGTTGATCTCTAAACTA
Found at i:5835 original size:33 final size:33
Alignment explanation
Indices: 5779--5852 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
5769 ATTAAGAAGG
* * * * *
5779 TCAAAATTTGCATTTCATTTCAAAATTCAAAGT
1 TCAAAATCTACATATCATATCAAAACTCAAAGT
5812 TCAAAATCTACATATCATATCAAAACTCAAAGT
1 TCAAAATCTACATATCATATCAAAACTCAAAGT
5845 TCAAAATC
1 TCAAAATC
5853 CACAGTTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (33 bp):
TCAAAATCTACATATCATATCAAAACTCAAAGT
Found at i:6154 original size:7 final size:7
Alignment explanation
Indices: 5988--6139 Score: 178
Period size: 7 Copynumber: 21.4 Consensus size: 7
5978 ATTTCATTAC
5988 TCAAAAT
1 TCAAAAT
5995 TCAAAAT
1 TCAAAAT
6002 TCAAAAT
1 TCAAAAT
*
6009 TCAAAAAA
1 TC-AAAAT
*
6017 TCAAAAA
1 TCAAAAT
*
6024 TCAAAAA
1 TCAAAAT
6031 TCAAAAT
1 TCAAAAT
6038 TCAAAAT
1 TCAAAAT
*
6045 TCAAAAAA
1 TC-AAAAT
*
6053 TCAAAAA
1 TCAAAAT
6060 TCAAAAT
1 TCAAAAT
6067 TCAAAAT
1 TCAAAAT
6074 TCAAAAT
1 TCAAAAT
*
6081 TCAAAAC
1 TCAAAAT
*
6088 TCAAAAC
1 TCAAAAT
*
6095 TCAAAAC
1 TCAAAAT
*
6102 TCAAAAC
1 TCAAAAT
* *
6109 TCAGAAC
1 TCAAAAT
6116 TCAAAAT
1 TCAAAAT
*
6123 TCAAAAC
1 TCAAAAT
6130 TCAAAAT
1 TCAAAAT
6137 TCA
1 TCA
6140 TGGCTCAAAA
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
7 121 0.91
8 12 0.09
ACGTcount: A:0.60, C:0.18, G:0.01, T:0.21
Consensus pattern (7 bp):
TCAAAAT
Done.