Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024771.1 Corchorus olitorius cultivar O-4 contig24804, 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: 16964
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2321 original size:12 final size:12
Alignment explanation
Indices: 2300--2340 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
2290 TACCCTATGT
*
2300 AAACACGACACG
1 AAACATGACACG
2312 AAACATGACACG
1 AAACATGACACG
2324 AAACATGACACG
1 AAACATGACACG
2336 AAACA
1 AAACA
2341 CGAATTGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.54, C:0.27, G:0.15, T:0.05
Consensus pattern (12 bp):
AAACATGACACG
Found at i:6702 original size:20 final size:21
Alignment explanation
Indices: 6667--6705 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6657 GCAAAACTTT
*
6667 TCAAAATCGGTTTAATTTGGA
1 TCAAAATCGATTTAATTTGGA
6688 TCAAAATC-ATTTAATTTG
1 TCAAAATCGATTTAATTTG
6706 ATCTATTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (21 bp):
TCAAAATCGATTTAATTTGGA
Found at i:8848 original size:31 final size:30
Alignment explanation
Indices: 8810--8891 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 30
8800 CCCTTTTTGC
* *
8810 CCCCCTAAACTTGTACGATTTTGACATTGTA
1 CCCCCTAAACTTGTAAG-TTTGGACATTGTA
* * *
8841 CCCCCTAAACTT-TAAGTTTGGATATTTTG
1 CCCCCTAAACTTGTAAGTTTGGACATTGTA
*
8870 CCCCCTAAACTTGCAA-TTTGGA
1 CCCCCTAAACTTGTAAGTTTGGA
8892 ACCATTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 27 0.61
30 5 0.11
31 12 0.27
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (30 bp):
CCCCCTAAACTTGTAAGTTTGGACATTGTA
Found at i:8881 original size:29 final size:31
Alignment explanation
Indices: 8804--8882 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
8794 TTAATGCCCT
* *
8804 TTTTGCCCCCCTAAACTTGTACGATTTTGACA
1 TTTTG-CCCCCTAAACTTGTAAGATTTGGACA
* * *
8836 TTGTACCCCCTAAACTT-TAAG-TTTGGATA
1 TTTTGCCCCCTAAACTTGTAAGATTTGGACA
8865 TTTTGCCCCCTAAACTTG
1 TTTTGCCCCCTAAACTTG
8883 CAATTTGGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 21 0.54
30 3 0.08
31 12 0.31
32 3 0.08
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.38
Consensus pattern (31 bp):
TTTTGCCCCCTAAACTTGTAAGATTTGGACA
Found at i:9761 original size:13 final size:13
Alignment explanation
Indices: 9743--9769 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9733 AAAAAATTAC
9743 ATAGTTGGCTTAG
1 ATAGTTGGCTTAG
9756 ATAGTTGGCTTAG
1 ATAGTTGGCTTAG
9769 A
1 A
9770 GTGCAAGCAA
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:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (13 bp):
ATAGTTGGCTTAG
Found at i:13190 original size:22 final size:22
Alignment explanation
Indices: 13165--13211 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
13155 GTAGTTATAA
13165 TTAATAGTGTTTGTATTTTCTT
1 TTAATAGTGTTTGTATTTTCTT
13187 TTAATAGTGTTTGTATTTTCTT
1 TTAATAGTGTTTGTATTTTCTT
13209 TTA
1 TTA
13212 CTAATTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.64
Consensus pattern (22 bp):
TTAATAGTGTTTGTATTTTCTT
Done.