Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011302.1 Corchorus capsularis cultivar CVL-1 contig11323, 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, 975
Length: 1625
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Found at i:138 original size:21 final size:21
Alignment explanation
Indices: 114--179 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
104 ATGTACAGAA
114 TACTATAGCGAATGCTATACG
1 TACTATAGCGAATGCTATACG
** *
135 TACTATTAATGAAT-AT-TA--
1 TACTA-TAGCGAATGCTATACG
153 TACTATAGCGAATGCTATACG
1 TACTATAGCGAATGCTATACG
174 TACTAT
1 TACTAT
180 TAATGAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
19 2 0.06
20 2 0.06
21 12 0.35
22 6 0.18
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (21 bp):
TACTATAGCGAATGCTATACG
Found at i:154 original size:22 final size:21
Alignment explanation
Indices: 129--189 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
119 TAGCGAATGC
129 TATACGTACTATTAATGAATA
1 TATACGTACTATTAATGAATA
** *
150 T-TA--TACTA-TAGCGAATGC
1 TATACGTACTATTAATGAAT-A
168 TATACGTACTATTAATGAATA
1 TATACGTACTATTAATGAATA
189 T
1 T
190 TATTGCTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 2 0.07
20 2 0.07
21 7 0.24
22 6 0.21
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (21 bp):
TATACGTACTATTAATGAATA
Found at i:156 original size:39 final size:39
Alignment explanation
Indices: 113--192 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
103 AATGTACAGA
113 ATACTATAGCGAATGCTATACGTACTATTAATGAATATT
1 ATACTATAGCGAATGCTATACGTACTATTAATGAATATT
152 ATACTATAGCGAATGCTATACGTACTATTAATGAATATT
1 ATACTATAGCGAATGCTATACGTACTATTAATGAATATT
191 AT
1 AT
193 TGCTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (39 bp):
ATACTATAGCGAATGCTATACGTACTATTAATGAATATT
Found at i:418 original size:103 final size:102
Alignment explanation
Indices: 239--447 Score: 339
Period size: 103 Copynumber: 2.0 Consensus size: 102
229 TTAATATTAA
* * *
239 ATTAAACCTACTATTAATTTTATGAGCAAGATCCTCATTGAGCGCCACATGGCATTTGGTTTCTT
1 ATTAAACCTACTATTAATTTTATGAGCAAGACCCTCATTGAGCGCCACATGACATTTAGTTTCTT
*
304 TGACAAGTGTCAATAGTTAATTTTCTAATGTTTTGTTT
66 TGACAAGTGTCAATAGTTAA-TTTCTAATGTTTTATTT
* *
342 ATTAAACCTACTATTAATTTTATGTA-CAAGACCCTCATTGAGTGCCACTTGACATTTAGTTTCT
1 ATTAAACCTACTATTAATTTTATG-AGCAAGACCCTCATTGAGCGCCACATGACATTTAGTTTCT
406 TTGACAAGTGTCAATAGTTAATTTCTAATGTTTTATTT
65 TTGACAAGTGTCAATAGTTAATTTCTAATGTTTTATTT
444 ATTA
1 ATTA
448 TATTTTTATT
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
102 20 0.20
103 78 0.79
104 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (102 bp):
ATTAAACCTACTATTAATTTTATGAGCAAGACCCTCATTGAGCGCCACATGACATTTAGTTTCTT
TGACAAGTGTCAATAGTTAATTTCTAATGTTTTATTT
Found at i:548 original size:11 final size:11
Alignment explanation
Indices: 505--542 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
495 TTCCTATATA
*
505 AAATAAATTAT
1 AAATTAATTAT
516 CAAA-TAATTAT
1 -AAATTAATTAT
527 AAATTAATTAT
1 AAATTAATTAT
538 AAATT
1 AAATT
543 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:904 original size:27 final size:27
Alignment explanation
Indices: 873--981 Score: 76
Period size: 27 Copynumber: 4.0 Consensus size: 27
863 TAACTGAATT
873 TTTCTTAAAAGAATTTATAAAATAAAA
1 TTTCTTAAAAGAATTTATAAAATAAAA
** * * *
900 TTTCTTAATTGAATTTTCTTAAA-AGAA
1 TTTCTTAAAAGAA-TTTATAAAATAAAA
* * * * * * * *
927 TTTATAAAATAAAATTTCTTAACTGAAT
1 TTTCTTAAA-AGAATTTATAAAATAAAA
955 TTTCTTAAAAGAATTTATAAAATAAAA
1 TTTCTTAAAAGAATTTATAAAATAAAA
982 CAGCCGCACG
Statistics
Matches: 57, Mismatches: 22, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
27 40 0.70
28 17 0.30
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.41
Consensus pattern (27 bp):
TTTCTTAAAAGAATTTATAAAATAAAA
Found at i:917 original size:14 final size:14
Alignment explanation
Indices: 858--970 Score: 77
Period size: 14 Copynumber: 8.1 Consensus size: 14
848 CAAAATTTCA
*
858 TTTCTTAACTGAATT
1 TTTCTTAAATGAA-T
*
873 TTTCTTAAAAGAA-
1 TTTCTTAAATGAAT
* * * *
886 TTTATAAAATAAAA
1 TTTCTTAAATGAAT
*
900 TTTCTTAATTGAAT
1 TTTCTTAAATGAAT
*
914 TTTCTTAAAAGAA-
1 TTTCTTAAATGAAT
* * * *
927 TTTATAAAATAAAA
1 TTTCTTAAATGAAT
*
941 TTTCTTAACTGAAT
1 TTTCTTAAATGAAT
*
955 TTTCTTAAAAGAAT
1 TTTCTTAAATGAAT
969 TT
1 TT
971 ATAAAATAAA
Statistics
Matches: 72, Mismatches: 24, Indels: 5
0.71 0.24 0.05
Matches are distributed among these distances:
13 18 0.25
14 43 0.60
15 11 0.15
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (14 bp):
TTTCTTAAATGAAT
Found at i:929 original size:41 final size:41
Alignment explanation
Indices: 857--981 Score: 232
Period size: 41 Copynumber: 3.0 Consensus size: 41
847 ACAAAATTTC
857 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
*
899 ATTTCTTAATTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
940 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
981 A
1 A
982 CAGCCGCACG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
41 68 0.84
42 13 0.16
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (41 bp):
ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
Found at i:1119 original size:11 final size:11
Alignment explanation
Indices: 1076--1113 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1066 TTCCTATATA
*
1076 AAATAAATTAT
1 AAATTAATTAT
1087 CAAA-TAATTAT
1 -AAATTAATTAT
1098 AAATTAATTAT
1 AAATTAATTAT
1109 AAATT
1 AAATT
1114 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.