Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012732.1 Corchorus olitorius cultivar O-4 contig12765, 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: 7572
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:2624 original size:21 final size:21
Alignment explanation
Indices: 2598--2649 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2588 CCATTCACCA
2598 TGCCACCACCGG-TCAAGCCCG
1 TGCCACCACCGGCT-AAGCCCG
*
2619 TGCCACCACCGGCTATGCCCG
1 TGCCACCACCGGCTAAGCCCG
*
2640 TGCCATCACC
1 TGCCACCACC
2650 ATTCAGTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.13
Consensus pattern (21 bp):
TGCCACCACCGGCTAAGCCCG
Found at i:4495 original size:11 final size:11
Alignment explanation
Indices: 4479--4527 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
4469 GAAGTTCGTG
4479 TTTGAAGACCA
1 TTTGAAGACCA
**
4490 TTTGAAGATAA
1 TTTGAAGACCA
4501 TTTGAAGA-C-
1 TTTGAAGACCA
4510 TTTGAAGACCA
1 TTTGAAGACCA
4521 -TTGAAGA
1 TTTGAAGA
4528 TTTATTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:5926 original size:15 final size:15
Alignment explanation
Indices: 5906--5937 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5896 TTGTTTCCAA
*
5906 GTTTAATTGTTTTCT
1 GTTTAATTGCTTTCT
5921 GTTTAATTGCTTTCT
1 GTTTAATTGCTTTCT
5936 GT
1 GT
5938 CAACCTCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.62
Consensus pattern (15 bp):
GTTTAATTGCTTTCT
Found at i:7272 original size:2 final size:2
Alignment explanation
Indices: 7265--7294 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7255 GGGCCTTTGT
*
7265 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7295 GATAGGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7392 original size:52 final size:54
Alignment explanation
Indices: 7310--7412 Score: 147
Period size: 52 Copynumber: 1.9 Consensus size: 54
7300 GAATTTGGTG
*
7310 GCAAGGCCCATGTGTATGTATTATGAGCCTTTGCCCCAAAGAGAAATGCCTTAATA
1 GCAAGGCCCA-GTGTA-GTATTATGAGCCTTTGCCACAAAGAGAAATGCCTTAATA
* *
7366 GCAAGGCCCA-TGTA-TATTATGAGCCTTTGCCATAAGGAGAAATGCCT
1 GCAAGGCCCAGTGTAGTATTATGAGCCTTTGCCACAAAGAGAAATGCCT
7413 CTGTGTTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 30 0.68
54 4 0.09
56 10 0.23
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (54 bp):
GCAAGGCCCAGTGTAGTATTATGAGCCTTTGCCACAAAGAGAAATGCCTTAATA
Found at i:7495 original size:41 final size:41
Alignment explanation
Indices: 7405--7566 Score: 236
Period size: 43 Copynumber: 3.9 Consensus size: 41
7395 CCATAAGGAG
*
7405 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
*
7446 AGAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATAT
1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-AT
*
7489 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
*
7530 AAAGGTGCCCCTGTGTTATATATGTGTTTGGGGACTT
1 AAA--TGCCCCTGTGTTATATATGTGTTTGAGGACTT
7567 GAATAT
Statistics
Matches: 109, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
41 39 0.36
42 4 0.04
43 66 0.61
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.41
Consensus pattern (41 bp):
AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
Found at i:7519 original size:84 final size:84
Alignment explanation
Indices: 7405--7566 Score: 306
Period size: 84 Copynumber: 1.9 Consensus size: 84
7395 CCATAAGGAG
*
7405 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
7470 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
*
7489 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
7554 TGTTTGGGGACTT
66 TGTTTGGGGACTT
7567 GAATAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.41
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Done.