Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017232.1 Corchorus olitorius cultivar O-4 contig17265, 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: 29878
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:392 original size:102 final size:103
Alignment explanation
Indices: 271--474 Score: 286
Period size: 105 Copynumber: 2.0 Consensus size: 103
261 ATCTAAGTTT
* *
271 TTTTAATTAAATTAGTAAAATGATAAAAATAAAATAGGTA-TA-AGGGTATTAGATTTAATAAAA
1 TTTTAATTAAAATAGTAAAATGATAAAAATAAAATA-GTACTATAGGATATTAGATTTAATAAAA
* * *
334 TAAAAATAGAGTTTTTAGTTGAGTAAATCTATAAAAGTA
65 GAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTA
* * * *
373 TTTTAATTAAAATATTAAAATGGTAAAAATAAAATAGTACTTATTTGGATATTAGATTTAATTAA
1 TTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGTAC-TA-TAGGATATTAGATTTAATAAA
438 AGAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAA
64 AGAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAA
475 ATTTAAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
101 3 0.03
102 33 0.37
103 2 0.02
105 51 0.57
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.36
Consensus pattern (103 bp):
TTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGTACTATAGGATATTAGATTTAATAAAAG
AAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTA
Found at i:9126 original size:31 final size:31
Alignment explanation
Indices: 9052--9152 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
9042 CCTCCATAAG
* * *
9052 GGGGTAAAATGTCTTGAATTTGAAAAGTTCAA
1 GGGGCAAAATGTCATGAATTTG-GAAGTTCAA
* * * *
9084 TGGACAAAATGTCATGAATTTGGGAGTTAAA
1 GGGGCAAAATGTCATGAATTTGGAAGTTCAA
* *
9115 GGGGCAAAATGTCCTG-ATTT-GAAGTTCAT
1 GGGGCAAAATGTCATGAATTTGGAAGTTCAA
9144 GGGGCAAAA
1 GGGGCAAAA
9153 GATCCTTGAC
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 15 0.27
30 4 0.07
31 19 0.34
32 18 0.32
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (31 bp):
GGGGCAAAATGTCATGAATTTGGAAGTTCAA
Found at i:10920 original size:16 final size:16
Alignment explanation
Indices: 10899--10939 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
10889 CTAAGCACAT
*
10899 TATATATAAAAAGTAA
1 TATATATAAAAAATAA
10915 TATATA-AAGAAAATAA
1 TATATATAA-AAAATAA
10931 T-TATATAAA
1 TATATATAAA
10940 TAAAAATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TATATATAAAAAATAA
Found at i:10935 original size:17 final size:16
Alignment explanation
Indices: 10897--10944 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
10887 AACTAAGCAC
*
10897 ATTATATATAAAAAGTA
1 ATTATATA-AAAAAATA
10914 A-TATATAAAGAAAATA
1 ATTATATAAA-AAAATA
10930 ATTATATAAATAAAA
1 ATTATATAAA-AAAA
10945 ATGACTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
ATTATATAAAAAAATA
Found at i:11867 original size:6 final size:6
Alignment explanation
Indices: 11856--11881 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11846 GCTTATTAAG
11856 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
11882 TAAATAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:12031 original size:35 final size:34
Alignment explanation
Indices: 11947--12043 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 34
11937 TAATAGGGTA
**
11947 AATAGATAATAATAATAAATAGATAGGGAAGTAAAT
1 AATAGATAATAATAATAAATAGATA--GAAAAAAAT
* *
11983 AATAAAT-ACAATAATAAATAGATA-AAAAAAAGT
1 AATAGATAATAATAATAAATAGATAGAAAAAAA-T
* *
12016 AGATAGATAATAATAAAAAATAAATAGA
1 A-ATAGATAATAATAATAAATAGATAGA
12044 TAAGGAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
32 5 0.10
33 2 0.04
34 5 0.10
35 30 0.61
36 7 0.14
ACGTcount: A:0.65, C:0.01, G:0.11, T:0.23
Consensus pattern (34 bp):
AATAGATAATAATAATAAATAGATAGAAAAAAAT
Found at i:12033 original size:21 final size:21
Alignment explanation
Indices: 11995--12046 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
11985 TAAATACAAT
* *
11995 AATAAATAGATAAAAAAAAGTA
1 AATAGATA-ATAAAAAAAAATA
* *
12017 GATAGATAATAATAAAAAATA
1 AATAGATAATAAAAAAAAATA
12038 AATAGATAA
1 AATAGATAA
12047 GGAAAATAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (21 bp):
AATAGATAATAAAAAAAAATA
Found at i:13486 original size:53 final size:54
Alignment explanation
Indices: 13397--13770 Score: 485
Period size: 54 Copynumber: 7.0 Consensus size: 54
13387 CTTTCTTTAA
*
13397 AACGACCGCACTGGATCAAAT-TGGAGATTAACTCTGATCATCG-AAACTTCTTGG
1 AACGACCGCACTGGATC--ATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
* *
13451 AACGACCGCACTAGATCAAT-TGGAGATCAACTCTGATCATCGAAAACTTCTTGA
1 AACGACCGCACTGGATC-ATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
* * *
13505 AACGACCACACTGGATCATCTGGAGATCAACTATGATCAT-GAAAAACTTCTTAG
1 AACGACCGCACTGGATCATCTGGAGATCAACTCTGATCATCG-AAAACTTCTTGG
* *
13559 AACGACCGCACTGGATCATCTGGAGATCAACTCTAATCATTGAAAACTTCTTGG
1 AACGACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
* * **
13613 AATGACCACACTGGATCATCTGG-GATCAACTCTGATCAAAGAAAACTTCTTGG
1 AACGACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
* * * **
13666 AATGACCGCACTGGGTCATCTAG-GATCAACTCTGATCAAAGAAAACTTCTTGG
1 AACGACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
*
13719 AATGACCGCACTGGATCATCTAGG-GATCAACTCTGATCATCG-AAACTTCTTG
1 AACGACCGCACTGGATCATCT-GGAGATCAACTCTGATCATCGAAAACTTCTTG
13771 AAAGGAGATC
Statistics
Matches: 291, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
53 134 0.46
54 156 0.54
55 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (54 bp):
AACGACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
Found at i:13694 original size:43 final size:45
Alignment explanation
Indices: 13646--13748 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 45
13636 GATCAACTCT
*
13646 GATCAAAGAAAACTTCTTGGAATGACCGCACTGGGTCATCTAGGATCAA
1 GATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGG----A
13695 CTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGG-
1 ----GATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGA
13743 GATCAA
1 GATCAA
13749 CTCTGATCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
44 6 0.12
53 43 0.88
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (45 bp):
GATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGA
Found at i:13807 original size:35 final size:35
Alignment explanation
Indices: 13743--14089 Score: 552
Period size: 35 Copynumber: 9.9 Consensus size: 35
13733 ATCATCTAGG
13743 GATCAACTCTGATCATCG-AAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
* *
13777 GATCAATTCTGATCATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
*
13812 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGT
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
* *
13847 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
* * * *
13882 GATCAACTATGATCTTCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
* *
13917 GATCAACTCTGATCATCAAAAACTTCTTGAAAGCA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
*
13952 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
*
13987 GATCAACTCTGATCATCGAAAACTTCTTGAAAGCA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
*
14022 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
14057 GATCAACTCTGATCATCGAAAACTTCTATGAAA
1 GATCAACTCTGATCATCGAAAACTTCT-TGAAA
14090 TACCACACTA
Statistics
Matches: 290, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
34 17 0.06
35 268 0.92
36 5 0.02
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
Found at i:29151 original size:16 final size:16
Alignment explanation
Indices: 29127--29162 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29117 TGGTAATTAA
*
29127 TAATTACAATTGATCC
1 TAATCACAATTGATCC
*
29143 TAATCACAATTGATTC
1 TAATCACAATTGATCC
29159 TAAT
1 TAAT
29163 TAGTCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (16 bp):
TAATCACAATTGATCC
Done.