Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009363.1 Corchorus capsularis cultivar CVL-1 contig09384, 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: 28471
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6352 original size:30 final size:29
Alignment explanation
Indices: 6303--6368 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 29
6293 TAATAATTTT
*
6303 TATTTTAAATTAATTAAATGCCACGTGG-
1 TATTTTTAATTAATTAAATGCCACGTGGC
6331 TATTTTTAATTAATTTTAAATGCCACGTGGC
1 TATTTTTAATTAA--TTAAATGCCACGTGGC
6362 TATTTTT
1 TATTTTT
6369 TGTCAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 12 0.35
30 15 0.44
31 7 0.21
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (29 bp):
TATTTTTAATTAATTAAATGCCACGTGGC
Found at i:17723 original size:13 final size:13
Alignment explanation
Indices: 17705--17731 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17695 AAAGATGGAA
17705 TAAAATTTGTTTT
1 TAAAATTTGTTTT
17718 TAAAATTTGTTTT
1 TAAAATTTGTTTT
17731 T
1 T
17732 TTTTTCAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TAAAATTTGTTTT
Found at i:17928 original size:39 final size:44
Alignment explanation
Indices: 17829--17942 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 44
17819 ACATTTTCAA
**
17829 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGATTTTCT
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGATAGTCT
*
17873 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAA-TAA-A-AGT-T
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGATAGTCT
*
17913 TTTAAG-AAATCCAAAAGAAGATTTTGGAAA
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAA
17943 TTAATAAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
39 23 0.35
40 7 0.11
41 1 0.02
42 1 0.02
43 2 0.03
44 32 0.48
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (44 bp):
TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGATAGTCT
Found at i:19269 original size:15 final size:15
Alignment explanation
Indices: 19233--19271 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
19223 ATTTGGTATA
* *
19233 AACTTCATCTTCTTC
1 AACTTCTTCATCTTC
19248 AACTTCTTCATCTTC
1 AACTTCTTCATCTTC
*
19263 ATCTTCTTC
1 AACTTCTTC
19272 GACCTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (15 bp):
AACTTCTTCATCTTC
Found at i:26935 original size:37 final size:36
Alignment explanation
Indices: 26893--27011 Score: 118
Period size: 37 Copynumber: 3.3 Consensus size: 36
26883 TAATTACTGG
*
26893 TTTACTGATTACTGTCACTTTGACTCTGAATTATCAA
1 TTTACTGATTACTATCACTTTGACTCT-AATTATCAA
* * * * *
26930 CTTACTGATTAATCTC-CTTTTACT-TAATTA-CTGA
1 TTTACTGATTACTATCACTTTGACTCTAATTATC-AA
* *
26964 TTTACTGATTACTATTACCTTGACTCTTAATTATCAA
1 TTTACTGATTACTATCACTTTGACTC-TAATTATCAA
27001 TTTACTGATTA
1 TTTACTGATTA
27012 ATTTTTCTAC
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
33 1 0.02
34 18 0.28
35 7 0.11
36 7 0.11
37 31 0.48
38 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTACTGATTACTATCACTTTGACTCTAATTATCAA
Found at i:26948 original size:71 final size:71
Alignment explanation
Indices: 26863--27013 Score: 239
Period size: 71 Copynumber: 2.1 Consensus size: 71
26853 TACCTTAACT
* * * *
26863 CTGATTAATTTCCTTTTACTTAATTACTGGTTTACTGATTACTGTCACTTTGACTCTGAATTATC
1 CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTGAATTATC
26928 AACTTA
66 AACTTA
* *
26934 CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTATC
1 CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTGAATTATC
*
26999 AATTTA
66 AACTTA
27005 CTGATTAAT
1 CTGATTAAT
27014 TTTTCTACCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (71 bp):
CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTGAATTATC
AACTTA
Found at i:27161 original size:38 final size:39
Alignment explanation
Indices: 27068--27161 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 39
27058 ACCCTTACTT
* * * **
27068 ACTGATTGCTACTTTTACTTCTTCTCTTAGTTATCAATTT
1 ACTGATTACTACTTTTACTTC-TCTCTTAATTACCAATGG
* *
27108 ACTGATTAATCCTTTTACTTC-CTCTTAATTACCAATGG
1 ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATGG
*
27146 ACTGATTACTTCTTTT
1 ACTGATTACTACTTTT
27162 TCTTTTCACT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 27 0.60
40 18 0.40
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.49
Consensus pattern (39 bp):
ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATGG
Done.