Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006708.1 Corchorus capsularis cultivar CVL-1 contig06729, 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: 25090
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:312 original size:19 final size:21
Alignment explanation
Indices: 276--317 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
266 TTTCTTCTAT
276 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
296 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
316 TT
1 TT
318 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:8996 original size:40 final size:40
Alignment explanation
Indices: 8952--9032 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
8942 GCTAGGTTTG
8952 CACGTATCTGTGTCGAAGTGGATTTACAAAAGCCCTTGCT
1 CACGTATCTGTGTCGAAGTGGATTTACAAAAGCCCTTGCT
8992 CACGTATCTGTGTCGAAGTGGATTTACAAAAGCCCTTGCT
1 CACGTATCTGTGTCGAAGTGGATTTACAAAAGCCCTTGCT
9032 C
1 C
9033 TCTAAAGTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (40 bp):
CACGTATCTGTGTCGAAGTGGATTTACAAAAGCCCTTGCT
Found at i:22092 original size:7 final size:7
Alignment explanation
Indices: 22080--22106 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
22070 TATATGGAGG
22080 TAGTGAC
1 TAGTGAC
22087 TAGTGAC
1 TAGTGAC
22094 TAGTGAC
1 TAGTGAC
22101 TAGTGA
1 TAGTGA
22107 GGTACTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (7 bp):
TAGTGAC
Found at i:22767 original size:30 final size:30
Alignment explanation
Indices: 22731--22794 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
22721 ATTTAGGATT
** *
22731 AAAAATATAAGCGAATT-ATTTCATTTTTTC
1 AAAAATATAAGC-AATTGAAGTCATTTTTAC
*
22761 AAAAATATTAGCAATTGAAGTCATTTTTAC
1 AAAAATATAAGCAATTGAAGTCATTTTTAC
22791 AAAA
1 AAAA
22795 TTGTGGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (30 bp):
AAAAATATAAGCAATTGAAGTCATTTTTAC
Found at i:24319 original size:12 final size:12
Alignment explanation
Indices: 24302--24381 Score: 133
Period size: 12 Copynumber: 6.5 Consensus size: 12
24292 CATCGATACC
24302 TCGATATATCCG
1 TCGATATATCCG
24314 TCGATATATCCG
1 TCGATATATCCG
24326 TCGATATATCCG
1 TCGATATATCCG
24338 TTCGATATATCCG
1 -TCGATATATCCG
24351 TCGATATATCCG
1 TCGATATATCCG
*
24363 TTCGATATATTCG
1 -TCGATATATCCG
24376 TCGATA
1 TCGATA
24382 CCTGTATTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
12 42 0.65
13 23 0.35
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:24348 original size:25 final size:25
Alignment explanation
Indices: 24302--24381 Score: 144
Period size: 25 Copynumber: 3.2 Consensus size: 25
24292 CATCGATACC
24302 TCGATATATCCG-TCGATATATCCG
1 TCGATATATCCGTTCGATATATCCG
24326 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCGTTCGATATATCCG
*
24351 TCGATATATCCGTTCGATATATTCG
1 TCGATATATCCGTTCGATATATCCG
24376 TCGATA
1 TCGATA
24382 CCTGTATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 12 0.22
25 42 0.78
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (25 bp):
TCGATATATCCGTTCGATATATCCG
Found at i:24352 original size:37 final size:37
Alignment explanation
Indices: 24303--24381 Score: 133
Period size: 37 Copynumber: 2.1 Consensus size: 37
24293 ATCGATACCT
24303 CGATATATCCGTCGATATATCCGTCGATATATCCGTT
1 CGATATATCCGTCGATATATCCGTCGATATATCCGTT
*
24340 CGATATATCCGTCGATATATCCGTTCGATATATTCG-T
1 CGATATATCCGTCGATATATCCG-TCGATATATCCGTT
24377 CGATA
1 CGATA
24382 CCTGTATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 29 0.73
38 11 0.28
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (37 bp):
CGATATATCCGTCGATATATCCGTCGATATATCCGTT
Found at i:24695 original size:36 final size:34
Alignment explanation
Indices: 24603--24701 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 34
24593 AAAATGAGGT
*
24603 TATTTTCCAGAAAATGTAATATTTTCTGTTGTTTGG
1 TATTTTCC-GAAAAT-TAATATTTTCTGTTGTTTGC
**
24639 T-TGTTT-CGAAAAAAAATATTTTCTGTTGTTTGAC
1 TAT-TTTCCGAAAATTAATATTTTCTGTTGTTTG-C
*
24673 TATTTTCCGGAAAATTAGTATTTTTCTGT
1 TATTTTCC-GAAAATTAATA-TTTTCTGT
24702 GAAGAATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
33 18 0.35
34 9 0.18
35 4 0.08
36 12 0.24
37 8 0.16
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.49
Consensus pattern (34 bp):
TATTTTCCGAAAATTAATATTTTCTGTTGTTTGC
Found at i:24769 original size:16 final size:16
Alignment explanation
Indices: 24736--24780 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
24726 GATTATATAT
* *
24736 AAAAATCAAACTATATA
1 AAAAAT-AAAATACATA
24753 AAAAATAAAATACATA
1 AAAAATAAAATACATA
*
24769 AAATATAAAATA
1 AAAAATAAAATA
24781 TTACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATACATA
Found at i:24989 original size:21 final size:21
Alignment explanation
Indices: 24963--25004 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24953 AGACTAATAT
24963 CTTGGCCTAATAACAATTAAA
1 CTTGGCCTAATAACAATTAAA
* *
24984 CTTGGCCTGATAATAATTAAA
1 CTTGGCCTAATAACAATTAAA
25005 AGTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (21 bp):
CTTGGCCTAATAACAATTAAA
Found at i:25022 original size:2 final size:2
Alignment explanation
Indices: 25010--25046 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
25000 TTAAAAGTTC
25010 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25047 CCTACATCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.