Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023420.1 Corchorus olitorius cultivar O-4 contig23453, 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: 16688
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:3202 original size:21 final size:21
Alignment explanation
Indices: 3178--3248 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
3168 CTTAGGCAAT
*
3178 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
3199 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3220 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
3241 TCCAATGA
1 TCCAATGA
3249 TCTTCTAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 3 0.07
21 43 0.93
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:3902 original size:13 final size:13
Alignment explanation
Indices: 3884--3933 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
3874 TTTTTCATCA
*
3884 TTTTTCCTTTCTC
1 TTTTTCTTTTCTC
*
3897 TTTTTCTTTTTTC
1 TTTTTCTTTTCTC
*
3910 GTTTTCTTTTCTTC
1 TTTTTCTTTTC-TC
*
3924 TTCTTCTTTT
1 TTTTTCTTTT
3934 TTTTTTAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:3925 original size:27 final size:26
Alignment explanation
Indices: 3885--3935 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
3875 TTTTCATCAT
*
3885 TTTTCCTTTCTCTTTTTCTTTTTTCG
1 TTTTCCTTTCTCTTCTTCTTTTTTCG
*
3911 TTTTCTTTTCTTCTTCTTCTTTTTT
1 TTTTCCTTTC-TCTTCTTCTTTTTT
3936 TTTTAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTCCTTTCTCTTCTTCTTTTTTCG
Found at i:14059 original size:30 final size:30
Alignment explanation
Indices: 14023--14326 Score: 425
Period size: 30 Copynumber: 10.1 Consensus size: 30
14013 ACTGATGAAA
* * *
14023 CAATGATCCTAAACCAGGGTTTAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
14053 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
14083 CAATGATCCTCAACCAGGATTAAAGTAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
14113 CAATGATCCTCAACCAGGATGAAAATGAAA-
1 CAATGATCCTCAACCAGGATTAAAAT-AAAG
*
14143 CAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * * *
14173 CAAAT-ATCCTAAACTAGGATGAAAATAAAA
1 C-AATGATCCTCAACCAGGATTAAAATAAAG
* *
14203 CAATGATCCTCAACCAGGATTAAAGTAAGG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
14233 CAATGATCCTCAACCAGGATGAAAATGAAA-
1 CAATGATCCTCAACCAGGATTAAAAT-AAAG
*
14263 CAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
14293 CAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
14323 CAAT
1 CAAT
14327 AAAGGAATGA
Statistics
Matches: 243, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
29 9 0.04
30 227 0.93
31 7 0.03
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (30 bp):
CAATGATCCTCAACCAGGATTAAAATAAAG
Found at i:14169 original size:120 final size:120
Alignment explanation
Indices: 14017--14326 Score: 514
Period size: 120 Copynumber: 2.6 Consensus size: 120
14007 GGATTAACTG
* * * *
14017 ATGAAACAATGATCCTAAACCAGGGTTTAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
1 ATGAAACAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
14082 GCAATGATCCTCAACCAGGATTAAAGTAAAGCAATGATCCTCAACCAGGATGAAA
66 GCAATGATCCTCAACCAGGATTAAAGTAAAGCAATGATCCTCAACCAGGATGAAA
* * *
14137 ATGAAACAACGATCCTCAACCAGGATTAAAATAAAGCAAAT-ATCCTAAACTAGGATGAAAATAA
1 ATGAAACAACGATCCTCAACCAGGATTAAAATAAAGC-AATGATCCTCAACCAGGATTAAAATAA
* *
14201 AACAATGATCCTCAACCAGGATTAAAGTAAGGCAATGATCCTCAACCAGGATGAAA
65 AGCAATGATCCTCAACCAGGATTAAAGTAAAGCAATGATCCTCAACCAGGATGAAA
*
14257 ATGAAACAACGATCCTCAACCAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAA
1 ATGAAACAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
14322 GCAAT
66 GCAAT
14327 AAAGGAATGA
Statistics
Matches: 174, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
119 2 0.01
120 169 0.97
121 3 0.02
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.19
Consensus pattern (120 bp):
ATGAAACAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
GCAATGATCCTCAACCAGGATTAAAGTAAAGCAATGATCCTCAACCAGGATGAAA
Found at i:14368 original size:38 final size:38
Alignment explanation
Indices: 14286--14359 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
14276 CCAGGATTAA
* *
14286 AATAAAGCAACGATCCTCAACCAGGATTAAAATAAAGC
1 AATAAAGCAACGATCCTAAACCAGGATCAAAATAAAGC
* * *
14324 AATAAAGGAATGATCCTAAACCAGGATCGAAATAAA
1 AATAAAGCAACGATCCTAAACCAGGATCAAAATAAA
14360 CTGATAAAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.16
Consensus pattern (38 bp):
AATAAAGCAACGATCCTAAACCAGGATCAAAATAAAGC
Found at i:14743 original size:139 final size:139
Alignment explanation
Indices: 14467--14752 Score: 502
Period size: 139 Copynumber: 2.1 Consensus size: 139
14457 TCAGAATTAA
* * * * *
14467 TACCTGGAGGTTTCTGAAATTGTGCTCGGAGAACTTATCATTTGCCCTAAGGACATATCAATGTA
1 TACCCGGAGGTTTCTAAAATTGTGCCCAGAGAACTTATCAGTTGCCCTAAGGACATATCAATGTA
14532 AACTCTCGATGGAGACCTTCACCAAGGATTTTAAACTTAAACATGAATCTTTTATGAAAAACTTA
66 AACTCTCGATGGAGACCTTCACCAAGGATTTTAAACTTAAACATGAATCTTTTATGAAAAACTTA
14597 ATAAAATGG
131 ATAAAATGG
14606 TACCCGGAGGTTTCTAAAATTGTGCCCAGAGAACTTATCAGTTGCCCTAAGGACATATCAATGTA
1 TACCCGGAGGTTTCTAAAATTGTGCCCAGAGAACTTATCAGTTGCCCTAAGGACATATCAATGTA
*
14671 AACTCTGGATGGAGACCTTCACCAAGGATTTTTAAACTTAAACATGAATCTTTTATGAAAAACTT
66 AACTCTCGATGGAGACCTTCACCAAGGA-TTTTAAACTTAAACATGAATCTTTTATGAAAAACTT
14736 AAT-AAATGG
130 AATAAAATGG
14745 TACCCGGA
1 TACCCGGA
14753 CCGGAGGACT
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
139 101 0.72
140 39 0.28
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (139 bp):
TACCCGGAGGTTTCTAAAATTGTGCCCAGAGAACTTATCAGTTGCCCTAAGGACATATCAATGTA
AACTCTCGATGGAGACCTTCACCAAGGATTTTAAACTTAAACATGAATCTTTTATGAAAAACTTA
ATAAAATGG
Found at i:15151 original size:170 final size:169
Alignment explanation
Indices: 14753--15270 Score: 869
Period size: 170 Copynumber: 3.1 Consensus size: 169
14743 GGTACCCGGA
14753 CCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATG
1 CCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATG
*
14818 CAAACTTTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAA-TTTTGATG-AAAACT
66 CAAACTCTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACT
* * * * * *
14881 TTATAAAATGAAATGATACCCGGAGGTTTTATCAATTGC
131 TGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGC
** * * *
14920 TTGGAGGACTTATCAGAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGACTTACCAATG
1 CCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATG
*
14985 CAAACTCTGAATTGAGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACT
66 CAAACTCTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACT
15050 TAGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGC
131 T-GATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGC
15090 CCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATG
1 CCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATG
* * *
15155 CAAACTCTGAATAGTGACCTTGAACAAGGATTTTAAACTTAAACATGAACATTTGATGAAAAACT
66 CAAACTCTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACT
15220 TGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGC
131 TGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGC
15259 CCGGAGGACTTA
1 CCGGAGGACTTA
15271 CCAACGCAAA
Statistics
Matches: 326, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
167 107 0.33
168 8 0.02
169 57 0.17
170 154 0.47
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (169 bp):
CCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATG
CAAACTCTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACT
TGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGC
Found at i:15356 original size:122 final size:122
Alignment explanation
Indices: 15134--15372 Score: 338
Period size: 122 Copynumber: 2.0 Consensus size: 122
15124 TCTGAATTTG
* * * *
15134 TGCCCGGAGGACTTACCAATGCAAACTCTGAATAGTGACCTTGAACAAGGATTTTAAACTTAAAC
1 TGCCCGGAGGACTTACCAACGCAAACTCTAAATAGAGACCTTGAACAAGGATTTTAAACTTAAAA
* * *
15199 ATGAACATTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGAT
66 AAGAACATTTGATGAAAAACTTGATAAAATCAAATGATACCCGGAGGTTTTACCGAT
* *
15256 TGCCCGGAGGACTTACCAACGCAAACTCTAAATAGAGACCTTGACCAAGGATTTT-AGCTTAAAA
1 TGCCCGGAGGACTTACCAACGCAAACTCTAAATAGAGACCTTGAACAAGGATTTTAAACTT-AAA
* * *
15320 AAAGAA-TTTTTAGTGAAAAACTTGATAAAATGAAATGATACCCGGAGGTTTTA
65 AAAGAACATTTGA-TGAAAAACTTGATAAAATCAAATGATACCCGGAGGTTTTA
15373 TCAAATGGAA
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
121 8 0.08
122 95 0.92
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (122 bp):
TGCCCGGAGGACTTACCAACGCAAACTCTAAATAGAGACCTTGAACAAGGATTTTAAACTTAAAA
AAGAACATTTGATGAAAAACTTGATAAAATCAAATGATACCCGGAGGTTTTACCGAT
Done.