Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013562.1 Corchorus olitorius cultivar O-4 contig13595, 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: 11648
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:3389 original size:17 final size:19
Alignment explanation
Indices: 3367--3401 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3357 TTGTTACCGT
3367 AAATC-TAT-AAATTAGTG
1 AAATCTTATCAAATTAGTG
3384 AAATCTTATCAAATTAGT
1 AAATCTTATCAAATTAGT
3402 CAATTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (19 bp):
AAATCTTATCAAATTAGTG
Found at i:4257 original size:9 final size:9
Alignment explanation
Indices: 4242--4285 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
4232 CCTCCGCCTC
4242 CTCCTCTTT
1 CTCCTCTTT
*
4251 CTTCTCTTT
1 CTCCTCTTT
4260 CTCCTCTTT
1 CTCCTCTTT
*
4269 CTCCTCCTT
1 CTCCTCTTT
4278 CTCCTCTT
1 CTCCTCTT
4286 CCTTCTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (9 bp):
CTCCTCTTT
Found at i:4265 original size:18 final size:18
Alignment explanation
Indices: 4242--4306 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
4232 CCTCCGCCTC
4242 CTCCTCTTTCTTCTCTTT
1 CTCCTCTTTCTTCTCTTT
* *
4260 CTCCTCTTTCTCCTCCTT
1 CTCCTCTTTCTTCTCTTT
*
4278 CTCCTCTTCCTTCTTCTTCTT
1 CTCCTCTTTCTTC-TC-T-TT
4299 CTCCTCTT
1 CTCCTCTT
4307 CGCCCTCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 27 0.69
19 2 0.05
21 10 0.26
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (18 bp):
CTCCTCTTTCTTCTCTTT
Found at i:4273 original size:39 final size:39
Alignment explanation
Indices: 4230--4306 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
4220 TCTTCTTCAA
*
4230 CTCCTCCGCCTCCTCCTCTTTCTTC-TCTTTCTCCTCTTT
1 CTCCTCCGCCTCCTCCTCCTTCTTCTTC-TTCTCCTCTTT
** *
4269 CTCCTCCTTCTCCTCTTCCTTCTTCTTCTTCTCCTCTT
1 CTCCTCCGCCTCCTCCTCCTTCTTCTTCTTCTCCTCTT
4307 CGCCCTCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.00, C:0.48, G:0.01, T:0.51
Consensus pattern (39 bp):
CTCCTCCGCCTCCTCCTCCTTCTTCTTCTTCTCCTCTTT
Found at i:4314 original size:39 final size:39
Alignment explanation
Indices: 4239--4316 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
4229 ACTCCTCCGC
* *
4239 CTCCTCCTCTTTCTTCTCTTTCTCCTCTTTCTCCTCCTT
1 CTCCTCCTCCTTCTTCTCTTTCTCCTCTTTCCCCTCCTT
*
4278 CTCCTCTTCCTTCTTCT-TCTTCTCCTC-TTCGCCCTCCTT
1 CTCCTCCTCCTTCTTCTCT-TTCTCCTCTTTC-CCCTCCTT
4317 ATCTTACTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.00, C:0.47, G:0.01, T:0.51
Consensus pattern (39 bp):
CTCCTCCTCCTTCTTCTCTTTCTCCTCTTTCCCCTCCTT
Found at i:5107 original size:7 final size:7
Alignment explanation
Indices: 5087--5130 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
5077 AACAACGTTC
*
5087 TATATAA
1 TATATAG
5094 TATATAG
1 TATATAG
5101 TATATAG
1 TATATAG
5108 TAT-T-G
1 TATATAG
5113 CTATATAG
1 -TATATAG
5121 TATATAG
1 TATATAG
5128 TAT
1 TAT
5131 TGCTAAGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 1 0.03
6 4 0.12
7 27 0.82
8 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.45
Consensus pattern (7 bp):
TATATAG
Found at i:5119 original size:20 final size:20
Alignment explanation
Indices: 5094--5135 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5084 TTCTATATAA
5094 TATATAGTATATAGTATTGC
1 TATATAGTATATAGTATTGC
5114 TATATAGTATATAGTATTGC
1 TATATAGTATATAGTATTGC
5134 TA
1 TA
5136 AGTTCTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (20 bp):
TATATAGTATATAGTATTGC
Found at i:9357 original size:30 final size:31
Alignment explanation
Indices: 9315--9395 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
9305 TTGAGAAGTT
9315 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGAGGAAAAAG-A
* *
9345 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
1 TGGTAAGGTTTGTGA-AAGTTGAGGAAAAAGA
9375 TGGTAAGGTTTG-GAAAGTTGA
1 TGGTAAGGTTTGTGAAAGTTGA
9396 AAAGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 5 0.11
30 25 0.57
31 14 0.32
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (31 bp):
TGGTAAGGTTTGTGAAAGTTGAGGAAAAAGA
Found at i:11434 original size:11 final size:11
Alignment explanation
Indices: 11418--11466 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
11408 GAAGTTCGTG
11418 TTTGAAGACCA
1 TTTGAAGACCA
*
11429 TTTGAAGACTTA
1 TTTGAAGAC-CA
11441 TTTGAAGA-C-
1 TTTGAAGACCA
11450 -TTGAAGACCA
1 TTTGAAGACCA
11460 -TTGAAGA
1 TTTGAAGA
11467 TTTATTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 7 0.21
11 9 0.27
12 9 0.27
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:11445 original size:12 final size:12
Alignment explanation
Indices: 11418--11451 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11408 GAAGTTCGTG
*
11418 TTTGAAGAC-CA
1 TTTGAAGACTTA
11429 TTTGAAGACTTA
1 TTTGAAGACTTA
11441 TTTGAAGACTT
1 TTTGAAGACTT
11452 GAAGACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTTA
Found at i:11466 original size:30 final size:31
Alignment explanation
Indices: 11419--11478 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
11409 AAGTTCGTGT
*
11419 TTGAAGACCATTTGAAGACTTATTTGAAGAC
1 TTGAAGACCATTTGAAGACTTATTTCAAGAC
*
11450 TTGAAGACCA-TTGAAGATTTATTTCAAGA
1 TTGAAGACCATTTGAAGACTTATTTCAAGA
11479 GGAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (31 bp):
TTGAAGACCATTTGAAGACTTATTTCAAGAC
Done.