Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013399.1 Corchorus capsularis cultivar CVL-1 contig13420, 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: 11773
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2683 original size:51 final size:50
Alignment explanation
Indices: 2546--2693 Score: 219
Period size: 50 Copynumber: 3.0 Consensus size: 50
2536 CCAGCCTTAT
* *
2546 CGTTCCCGTTCACCCC-TTTCAGCCTTCCCATTCTTCCCGTTCACCTTGC
1 CGTTTCCGTTCACCCCTTTTCGGCCTTCCCATTCTTCCCGTTCACCTTGC
* *
2595 C-ATTCTCGTTCACCCCTTTTCGGCCTTCCCATTCTTCCCATTCACCTTGC
1 CGTTTC-CGTTCACCCCTTTTCGGCCTTCCCATTCTTCCCGTTCACCTTGC
*
2645 CGTTTCCGTTCACTCCCTTTTCGGCCTTCCCGTTCTTCCCGTTCACCTT
1 CGTTTCCGTTCAC-CCCTTTTCGGCCTTCCCATTCTTCCCGTTCACCTT
2694 CAGTGGAGTT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
48 2 0.02
49 11 0.12
50 39 0.44
51 36 0.41
ACGTcount: A:0.07, C:0.45, G:0.10, T:0.38
Consensus pattern (50 bp):
CGTTTCCGTTCACCCCTTTTCGGCCTTCCCATTCTTCCCGTTCACCTTGC
Found at i:4178 original size:2 final size:2
Alignment explanation
Indices: 4171--4196 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4161 AATAATAGAT
4171 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4197 ACTATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6068 original size:50 final size:51
Alignment explanation
Indices: 6008--6112 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
5998 CCATTCCCAG
*
6008 CCTTGCCGTTCCCGTTCA-CCCCTTTTCGACCTTCTCGTTCTTCCCGTTCA
1 CCTTGCCGTTCCCGTTCACCCCCTTTTCGACCTTCCCGTTCTTCCCGTTCA
* * * *
6058 CCTTGTCGTTCCCGTTCACCCCCTTTTCGGCTTTCCCGTTTTTCCCGTTCA
1 CCTTGCCGTTCCCGTTCACCCCCTTTTCGACCTTCCCGTTCTTCCCGTTCA
6109 CCTT
1 CCTT
6113 CAGTGGAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 17 0.35
51 32 0.65
ACGTcount: A:0.05, C:0.43, G:0.12, T:0.40
Consensus pattern (51 bp):
CCTTGCCGTTCCCGTTCACCCCCTTTTCGACCTTCCCGTTCTTCCCGTTCA
Found at i:8215 original size:48 final size:49
Alignment explanation
Indices: 8153--8298 Score: 179
Period size: 48 Copynumber: 3.0 Consensus size: 49
8143 ATTTGGTGAC
* *
8153 CTCACCAGGTGAGTATTGTACAAGATGAGTATCT-CACCAGGTGAGTA-T
1 CTCACCAGGTGAGTATTGTACCAGGTGAGTAT-TGCACCAGGTGAGTATT
* *
8201 CTCACCAGGTGAGTATTGCACCAGGTGAGTATTGCACTAGGTGAGTATT
1 CTCACCAGGTGAGTATTGTACCAGGTGAGTATTGCACCAGGTGAGTATT
* * * *
8250 TTTACCAGGTGAGTGTTTGTACCAGGTGAGTATTTGTACCAGGTGAGTA
1 CTCACCAGGTGAGT-ATTGTACCAGGTGAGTA-TTGCACCAGGTGAGTA
8299 GGGTAGGAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.01
48 41 0.49
49 13 0.15
50 15 0.18
51 14 0.17
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (49 bp):
CTCACCAGGTGAGTATTGTACCAGGTGAGTATTGCACCAGGTGAGTATT
Found at i:8261 original size:17 final size:16
Alignment explanation
Indices: 8155--8298 Score: 148
Period size: 16 Copynumber: 8.8 Consensus size: 16
8145 TTGGTGACCT
8155 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* * *
8171 TACAAGATGAGTATCT-
1 CACCAGGTGAGTAT-TG
8187 CACCAGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
8203 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
8219 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* *
8235 CACTAGGTGAGTATTTT
1 CACCAGGTGAGTA-TTG
* *
8252 TACCAGGTGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
8269 TACCAGGTGAGTATTTG
1 CACCAGGTGAGTA-TTG
*
8286 TACCAGGTGAGTA
1 CACCAGGTGAGTA
8299 GGGTAGGAAC
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.01
16 66 0.60
17 43 0.39
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:9270 original size:27 final size:27
Alignment explanation
Indices: 9232--9452 Score: 160
Period size: 27 Copynumber: 7.8 Consensus size: 27
9222 CTGGTGCGTG
* **
9232 GCACTAGGGGAGTCCCT-CCCTTGGTGC
1 GCACTGGGGGAGTGTCTCCCCTT-GTGC
*
9259 GCACTGGGGGAGTGTCTCCCCTGGTGCCAC
1 GCACTGGGGGAGTGTCTCCCCTTGTG---C
9289 GCACTTGGGGGAGTGTCTCCCCTTGTGC
1 GCAC-TGGGGGAGTGTCTCCCCTTGTGC
*
9317 GCACTTGGGGAGTGTCTCCCCTTGTGC
1 GCACTGGGGGAGTGTCTCCCCTTGTGC
* **
9344 GCCCTGGGGGAGCATCTCCCCTGGTGGTGC
1 GCACTGGGGGAGTGTCTCCCCT--T-GTGC
* * * *
9374 ACATTTGGGGAGTGTCTCCCCTGGTGC
1 GCACTGGGGGAGTGTCTCCCCTTGTGC
* **
9401 GCCTCACCTGGGGGATTAACT-CCCTTGGTGC
1 G---CA-CTGGGGGAGTGTCTCCCCTT-GTGC
*
9432 GC-CTTGGGGAGTGTCTCCCCT
1 GCACTGGGGGAGTGTCTCCCCT
9453 AGCGACTAAT
Statistics
Matches: 152, Mismatches: 28, Indels: 28
0.73 0.13 0.13
Matches are distributed among these distances:
26 10 0.07
27 65 0.43
28 10 0.07
29 1 0.01
30 31 0.20
31 35 0.23
ACGTcount: A:0.09, C:0.31, G:0.34, T:0.25
Consensus pattern (27 bp):
GCACTGGGGGAGTGTCTCCCCTTGTGC
Found at i:9285 original size:57 final size:57
Alignment explanation
Indices: 9216--9452 Score: 236
Period size: 57 Copynumber: 4.1 Consensus size: 57
9206 GGGAATTGGT
* * * *
9216 TCTCCCCTGGTGCGTGGCACTAGGGGAGTCCCT-CCCTTGGTGCGCACTGGGGGAGTG
1 TCTCCCCTGGTGCG-CGCACTGGGGGAGTCTCTCCCCTTGGTGCGCACTTGGGGAGTG
* *
9273 TCTCCCCTGGTGCCACGCACTTGGGGGAGTGTCTCCCCTT-GTGCGCACTTGGGGAGTG
1 TCTCCCCTGGTG-CGCGCAC-TGGGGGAGTCTCTCCCCTTGGTGCGCACTTGGGGAGTG
* * *
9331 TCTCCCCTTGTGCGC-C-CTGGGGGAG-CATCTCCCCTGGTGGTGCACATTTGGGGAGTG
1 TCTCCCCTGGTGCGCGCACTGGGGGAGTC-TCTCCCCT--TGGTGCGCACTTGGGGAGTG
* * **
9388 TCTCCCCTGGTGCGCCTCACCTGGGGGATTAACT-CCCTTGGTGCGC-CTTGGGGAGTG
1 TCTCCCCTGGTGCG-CGCA-CTGGGGGAGTCTCTCCCCTTGGTGCGCACTTGGGGAGTG
9445 TCTCCCCT
1 TCTCCCCT
9453 AGCGACTAAT
Statistics
Matches: 151, Mismatches: 17, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
54 16 0.11
55 1 0.01
56 2 0.01
57 65 0.43
58 47 0.31
59 6 0.04
60 4 0.03
61 10 0.07
ACGTcount: A:0.08, C:0.32, G:0.34, T:0.26
Consensus pattern (57 bp):
TCTCCCCTGGTGCGCGCACTGGGGGAGTCTCTCCCCTTGGTGCGCACTTGGGGAGTG
Found at i:9362 original size:85 final size:84
Alignment explanation
Indices: 9216--9402 Score: 216
Period size: 85 Copynumber: 2.2 Consensus size: 84
9206 GGGAATTGGT
**
9216 TCTCCCCTGGTGCGTGGCACTAGGGGAGTCCCTCCCTTGGTGCGCACTGGGGGAGTGTCTCCCCT
1 TCTCCCCTGGTGC---GCACTAGGGGAGTCCCTCCCTTGGTGCGCACTGGGGGAGCATCTCCCCT
9281 GGTGCCACGCAC-TTGGGGGAGTG
63 GGTG--ACGCACATTGGGGGAGTG
* * ** *
9304 TCTCCCCTTGTGCGCACTTGGGGAGTGTCTCCCCTT-GTGCGCCCTGGGGGAGCATCTCCCCTGG
1 TCTCCCCTGGTGCGCACTAGGGGAGTCCCT-CCCTTGGTGCGCACTGGGGGAGCATCTCCCCTGG
** *
9368 TGGTGCACATTTGGGGAGTG
65 TGACGCACATTGGGGGAGTG
9388 TCTCCCCTGGTGCGC
1 TCTCCCCTGGTGCGC
9403 CTCACCTGGG
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
83 4 0.05
84 24 0.28
85 41 0.48
86 5 0.06
88 12 0.14
ACGTcount: A:0.08, C:0.32, G:0.35, T:0.25
Consensus pattern (84 bp):
TCTCCCCTGGTGCGCACTAGGGGAGTCCCTCCCTTGGTGCGCACTGGGGGAGCATCTCCCCTGGT
GACGCACATTGGGGGAGTG
Found at i:9566 original size:30 final size:31
Alignment explanation
Indices: 9516--9574 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
9506 TCTCCCTTGG
*
9516 CACTTGGGGGAGTCTCTCCCCTGGTGCGCGGA
1 CACTGGGGGGAG-CTCTCCCCTGGTGCGCGGA
9548 CACTGGGGGGAG-TCTCCCCTGGTGCGC
1 CACTGGGGGGAGCTCTCCCCTGGTGCGC
9575 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 15 0.58
32 11 0.42
ACGTcount: A:0.08, C:0.32, G:0.39, T:0.20
Consensus pattern (31 bp):
CACTGGGGGGAGCTCTCCCCTGGTGCGCGGA
Found at i:9657 original size:29 final size:29
Alignment explanation
Indices: 9614--9713 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
9604 TTGGGAGTTT
* *
9614 CTCCCTTGGTTGCGCTGACACTGGGGGAGC
1 CTCCCCTGG-TGCGCGGACACTGGGGGAGC
9644 CTCCCCTGGTGCGCGGACACTGGGGGAGC
1 CTCCCCTGGTGCGCGGACACTGGGGGAGC
* * **
9673 CTCCCCTCGTGCGCGGACACT-GGGAAAT
1 CTCCCCTGGTGCGCGGACACTGGGGGAGC
9701 CTCCCCTGGTGCG
1 CTCCCCTGGTGCG
9714 TCCCCTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
28 16 0.25
29 39 0.62
30 8 0.13
ACGTcount: A:0.11, C:0.35, G:0.35, T:0.19
Consensus pattern (29 bp):
CTCCCCTGGTGCGCGGACACTGGGGGAGC
Found at i:11465 original size:12 final size:12
Alignment explanation
Indices: 11432--11466 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
11422 AAAGTGACCA
11432 CCCAAGAGAAAT
1 CCCAAGAGAAAT
11444 CCC-AGAAGAAAT
1 CCCAAG-AGAAAT
11456 CCCAAGAGAAA
1 CCCAAGAGAAA
11467 CAGCAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.51, C:0.26, G:0.17, T:0.06
Consensus pattern (12 bp):
CCCAAGAGAAAT
Found at i:11558 original size:2 final size:2
Alignment explanation
Indices: 11553--11577 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11543 AAACACGCAT
11553 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11578 CTATGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.