Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018348.1 Corchorus olitorius cultivar O-4 contig18381, 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: 23077
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:395 original size:16 final size:15
Alignment explanation
Indices: 374--416 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
364 TTACTTTGTT
374 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
390 TTGTTTTTCTGTTTAA
1 TTG-TTTTCTGTTTAA
406 TTGTTTTCTGT
1 TTGTTTTCTGT
417 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4191 original size:53 final size:54
Alignment explanation
Indices: 4124--4230 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 54
4114 TTAATTAAAA
* *
4124 ATTATCATACTATATTACTAAGGGTATTCTAGTATTTCAATAATTAAAATTTTT
1 ATTATAATACTATATTACTAAGGGTATTCTAGTAATTCAATAATTAAAATTTTT
*
4178 ATTATAATA-TATATTACTAAGGGTATTTTAGTAATTCAATAATTAAAATTTTT
1 ATTATAATACTATATTACTAAGGGTATTCTAGTAATTCAATAATTAAAATTTTT
4231 GAGTTCGTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
53 42 0.84
54 8 0.16
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (54 bp):
ATTATAATACTATATTACTAAGGGTATTCTAGTAATTCAATAATTAAAATTTTT
Found at i:5614 original size:16 final size:17
Alignment explanation
Indices: 5579--5614 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5569 TCCCTCTTCT
5579 GTCCTACGTACTCCTTAA
1 GTCCTACGTACT-CTTAA
5597 GTCCTACGTACT-TTAA
1 GTCCTACGTACTCTTAA
5613 GT
1 GT
5615 TCTTCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
18 12 0.67
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (17 bp):
GTCCTACGTACTCTTAA
Found at i:10538 original size:12 final size:11
Alignment explanation
Indices: 10521--10551 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
10511 CGGTTGGTTT
10521 TCGGTTTTTTAG
1 TCGGTTTTTT-G
10533 TCGGTTTTTTG
1 TCGGTTTTTTG
10544 TCGGTTTT
1 TCGGTTTT
10552 AATTTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.03, C:0.10, G:0.26, T:0.61
Consensus pattern (11 bp):
TCGGTTTTTTG
Found at i:15486 original size:61 final size:61
Alignment explanation
Indices: 15391--15513 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
15381 ATCAATCCGA
*
15391 AGGTAATTTGGATTCTGGATGTATCATTGGTTGCCTTTGGTCGAGGGAGACTAGAGTCTCT
1 AGGTAATTTGGATTCTGGATGTATCATTGGTTGCCTTTGGTCGAGGGAGACTAGACTCTCT
15452 AGGTAATTTGGATTCTGGATGTATCATTGGTTGCCTTTGGTCGAGGGAGACTAGACTCTCT
1 AGGTAATTTGGATTCTGGATGTATCATTGGTTGCCTTTGGTCGAGGGAGACTAGACTCTCT
15513 A
1 A
15514 TGCAACCAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (61 bp):
AGGTAATTTGGATTCTGGATGTATCATTGGTTGCCTTTGGTCGAGGGAGACTAGACTCTCT
Found at i:16661 original size:17 final size:17
Alignment explanation
Indices: 16636--16671 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16626 GGGTTAGAGG
16636 AAGGGAAATAAAATAAC
1 AAGGGAAATAAAATAAC
* *
16653 AAGGTAAATAAGATAAC
1 AAGGGAAATAAAATAAC
16670 AA
1 AA
16672 TCCACACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.17, T:0.14
Consensus pattern (17 bp):
AAGGGAAATAAAATAAC
Done.