Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007041.1 Corchorus capsularis cultivar CVL-1 contig07062, 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: 47180
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1550 original size:11 final size:11
Alignment explanation
Indices: 1534--1571 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1524 GCAATTGCAG
1534 AAACATAATCA
1 AAACATAATCA
1545 AAACATAATCA
1 AAACATAATCA
1556 AAACAT-ATGCA
1 AAACATAAT-CA
1567 AAACA
1 AAACA
1572 AGCATTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.63, C:0.18, G:0.03, T:0.16
Consensus pattern (11 bp):
AAACATAATCA
Found at i:8300 original size:21 final size:21
Alignment explanation
Indices: 8274--8314 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8264 TCTTGAAGGC
*
8274 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGATCAA
**
8295 TTGAAGAGTATTGAAGATCA
1 TTGAAGACCATTGAAGATCA
8315 TAAGCCAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGACCATTGAAGATCAA
Found at i:12251 original size:39 final size:38
Alignment explanation
Indices: 12208--12324 Score: 135
Period size: 39 Copynumber: 3.0 Consensus size: 38
12198 AGGCATTTCT
12208 CTCTCCCCAAAGTCCCAAACACATATAACACAGGGGCAA
1 CTCT-CCCAAAGTCCCAAACACATATAACACAGGGGCAA
* * *
12247 CTCTCTCAAAGTCCTCAAACACATATAACACAGAGGCAT
1 CTCTCCCAAAGTCC-CAAACACATATAACACAGGGGCAA
* * * * *
12286 CTGTACTAAAATCCCTAAACACATATAACACAAGGGCAA
1 CTCTCCCAAAGTCCC-AAACACATATAACACAGGGGCAA
12325 TTTTCTTCTC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 10 0.15
39 55 0.85
ACGTcount: A:0.41, C:0.31, G:0.11, T:0.17
Consensus pattern (38 bp):
CTCTCCCAAAGTCCCAAACACATATAACACAGGGGCAA
Found at i:15200 original size:11 final size:10
Alignment explanation
Indices: 15182--15215 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
15172 GAAGTTTGTG
15182 TTTTGAAGAT
1 TTTTGAAGAT
15192 TTCTTGAAGAT
1 TT-TTGAAGAT
15203 ATTTTGAAGAT
1 -TTTTGAAGAT
15214 TT
1 TT
15216 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:21929 original size:11 final size:10
Alignment explanation
Indices: 21911--21944 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
21901 GAAGTTTGTG
21911 TTTTGAAGAT
1 TTTTGAAGAT
21921 TTCTTGAAGAT
1 TT-TTGAAGAT
21932 ATTTTGAAGAT
1 -TTTTGAAGAT
21943 TT
1 TT
21945 GAAGATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:32699 original size:21 final size:21
Alignment explanation
Indices: 32673--32713 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32663 TCTTGAAGGC
*
32673 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGATCAA
**
32694 TTGAAGAGTATTGAAGATCA
1 TTGAAGACCATTGAAGATCA
32714 TAAGCCAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGACCATTGAAGATCAA
Found at i:35406 original size:21 final size:21
Alignment explanation
Indices: 35367--35406 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35357 TTTGCACATG
* **
35367 TGGTTCACCACATTGAAGTGA
1 TGGTTAACCACATCCAAGTGA
35388 TGGTTAACCACATCCAAGT
1 TGGTTAACCACATCCAAGT
35407 CTTGGGCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TGGTTAACCACATCCAAGTGA
Found at i:43244 original size:15 final size:17
Alignment explanation
Indices: 43214--43245 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
43204 TGGCCCTTAG
43214 ATTTTATATATTTATTT
1 ATTTTATATATTTATTT
43231 ATTTTAT-T-TTTATTT
1 ATTTTATATATTTATTT
43246 GGGATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTATATATTTATTT
Found at i:43854 original size:37 final size:38
Alignment explanation
Indices: 43771--43865 Score: 131
Period size: 40 Copynumber: 2.5 Consensus size: 38
43761 AGCAACTCCA
*
43771 AAAGAAGACTTTTGGAAAATAAATGTTTTTAACAAATCC
1 AAAGAAGACTTTTGGAAAATAAAAG-TTTTAACAAATCC
*
43810 GAAAGAAGACTTTTGGAAAATAAAAG-TTTGA-AAATCC
1 -AAAGAAGACTTTTGGAAAATAAAAGTTTTAACAAATCC
43847 AAGAGAAGACTTTTGGAAA
1 AA-AGAAGACTTTTGGAAA
43866 TTAATAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
36 2 0.04
37 22 0.42
38 4 0.08
40 24 0.46
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.26
Consensus pattern (38 bp):
AAAGAAGACTTTTGGAAAATAAAAGTTTTAACAAATCC
Done.