Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012861.1 Corchorus olitorius cultivar O-4 contig12894, 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: 11325
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:376 original size:15 final size:15
Alignment explanation
Indices: 346--387 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
336 TTACTTTGTT
346 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
362 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
377 TTGTTTTCTGT
1 TTGTTTTCTGT
388 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:5240 original size:83 final size:84
Alignment explanation
Indices: 5151--5319 Score: 304
Period size: 83 Copynumber: 2.0 Consensus size: 84
5141 TATGGTTGAT
5151 AGGATAATTTTATGTTTTTTCACTTTGAAATAATATGCTTCTTCAAATGTAGAATTGATTGATA-
1 AGGATAATTTTATGTTTTTTCACTTTGAAATAATATGCTTCTTCAAATGTAGAATTGATTGATAG
*
5215 AGTGTTGCAATGCAGGGCA
66 AGTGCTGCAATGCAGGGCA
*
5234 AGGATAATTTTCTGTTTTTTCACTTTGAAATAATATGCTTCTTCAAATGTAGAATTGATTGATAT
1 AGGATAATTTTATGTTTTTTCACTTTGAAATAATATGCTTCTTCAAATGTAGAATTGATTGATA-
5299 GAGTGCTGCAATGCAGGGCA
65 GAGTGCTGCAATGCAGGGCA
5319 A
1 A
5320 TTTGGGGTGG
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
83 63 0.77
85 19 0.23
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (84 bp):
AGGATAATTTTATGTTTTTTCACTTTGAAATAATATGCTTCTTCAAATGTAGAATTGATTGATAG
AGTGCTGCAATGCAGGGCA
Found at i:6168 original size:22 final size:22
Alignment explanation
Indices: 6137--6217 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
6127 TGAATATTTT
*
6137 TATAAAATTTCGATAATTACCC
1 TATAAAATTTTGATAATTACCC
* ** *
6159 TATTAAATTTTGATAACCACCA
1 TATAAAATTTTGATAATTACCC
*
6181 TATGAAATTTTGATAATTA-CC
1 TATAAAATTTTGATAATTACCC
*
6202 TATAAAATTGTGATAA
1 TATAAAATTTTGATAA
6218 ACTCCATAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 15 0.31
22 33 0.69
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (22 bp):
TATAAAATTTTGATAATTACCC
Found at i:6217 original size:43 final size:44
Alignment explanation
Indices: 6141--6239 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 44
6131 TATTTTTATA
* * * * *
6141 AAATTTCGATAATTACCCTATTAAATTTTGATAACCACCATATG
1 AAATTTTGATAATTACCCTATAAAATTGTGATAAACACCATAAG
*
6185 AAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCATAAG
1 AAATTTTGATAATTACCCTATAAAATTGTGATAAACACCATAAG
6228 AAATTTTGATAA
1 AAATTTTGATAA
6240 CCTAACTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 35 0.71
44 14 0.29
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAATTACCCTATAAAATTGTGATAAACACCATAAG
Found at i:6252 original size:22 final size:22
Alignment explanation
Indices: 6157--6293 Score: 104
Period size: 22 Copynumber: 6.3 Consensus size: 22
6147 CGATAATTAC
*
6157 CCTATTAAATTTTGATAACC-A
1 CCTATGAAATTTTGATAACCTA
*
6178 CCATATGAAATTTTGATAA-TTA
1 CC-TATGAAATTTTGATAACCTA
* * *
6200 CCTATAAAATTGTGATAAACT-
1 CCTATGAAATTTTGATAACCTA
*
6221 CCATAAGAAATTTTGATAACCTA
1 CC-TATGAAATTTTGATAACCTA
* * * *
6244 ACTATGAAATTTTAATAAACTTT
1 CCTATGAAATTTTGAT-AACCTA
* *
6267 TCTAT-AAATTTTG-TAACCTT
1 CCTATGAAATTTTGATAACCTA
6287 CCTATGA
1 CCTATGA
6294 TTTTTTATAA
Statistics
Matches: 91, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
20 9 0.10
21 20 0.22
22 53 0.58
23 9 0.10
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTA
Found at i:7959 original size:35 final size:35
Alignment explanation
Indices: 7913--7982 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
7903 GGATACCAAA
7913 ATTACAAATGCAATGATCATATATTTATCATCATC
1 ATTACAAATGCAATGATCATATATTTATCATCATC
7948 ATTACAAATGCAATGATCATATATTTATCATCATC
1 ATTACAAATGCAATGATCATATATTTATCATCATC
7983 GTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (35 bp):
ATTACAAATGCAATGATCATATATTTATCATCATC
Done.