Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017917.1 Corchorus olitorius cultivar O-4 contig17950, 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: 28469
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2154 original size:76 final size:76
Alignment explanation
Indices: 2019--2167 Score: 171
Period size: 76 Copynumber: 2.0 Consensus size: 76
2009 AAGGACCCCG
*
2019 ACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAAAACCCA-AGTG
1 ACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAAAACCCAGA-TG
2083 GGCAGTGTCACA
65 GGCAGTGTCACA
* * * **
2095 ACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCAGA
1 ACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAAAACCCAGA
*
2157 TGGGCTGTGTC
63 TGGGCAGTGTC
2168 TTAGCTCATC
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
75 4 0.06
76 51 0.82
77 7 0.11
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.25
Consensus pattern (76 bp):
ACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAAAACCCAGATGG
GCAGTGTCACA
Found at i:4572 original size:2 final size:2
Alignment explanation
Indices: 4565--4589 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4555 AGTAAATTCA
4565 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4590 AAAGAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6329 original size:21 final size:19
Alignment explanation
Indices: 6295--6338 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
6285 TTTCCCCAAT
*
6295 TTTTGAAAAAAATTTCGGA
1 TTTTGAAAAAAATTTCGAA
6314 TTTTGAAGATAAAATTTCGAA
1 TTTTGAA-A-AAAATTTCGAA
6335 TTTT
1 TTTT
6339 TCAAAACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 14 0.64
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTTGAAAAAAATTTCGAA
Found at i:11483 original size:31 final size:31
Alignment explanation
Indices: 11442--11588 Score: 170
Period size: 31 Copynumber: 4.7 Consensus size: 31
11432 GACGTGGCAT
* **
11442 GCCACATGTACCAAAAAGCAACATGTAGCAC
1 GCCACGTGTACCAAAAAGTGACATGTAGCAC
11473 GCCACGTGTACCAAAAAGTGACATG-AGGCAC
1 GCCACGTGTACCAAAAAGTGACATGTA-GCAC
*
11504 GCCACGTGTACCAAAAAGTGACATGTATCAC
1 GCCACGTGTACCAAAAAGTGACATGTAGCAC
* * * *
11535 GCCATGTGTACCCAAAAGTGACATGTGGCAT
1 GCCACGTGTACCAAAAAGTGACATGTAGCAC
* ** *
11566 GCCATGTGTTTCAAAAACTGACA
1 GCCACGTGTACCAAAAAGTGACA
11589 CATGGCATGC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
30 1 0.01
31 99 0.98
32 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGTGACATGTAGCAC
Found at i:11544 original size:62 final size:62
Alignment explanation
Indices: 11437--11588 Score: 196
Period size: 62 Copynumber: 2.5 Consensus size: 62
11427 TGTTCGACGT
* **
11437 GGCATGCCACATGTACCAAAAAGCAACATGTAGCACGCCACGTGTACCAAAAAGTGACATGA
1 GGCATGCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGTGACATGA
* * * * *
11499 GGCACGCCACGTGTACCAAAAAGTGACATGTATCACGCCATGTGTACCCAAAAGTGACATGT
1 GGCATGCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGTGACATGA
* ** *
11561 GGCATGCCATGTGTTTCAAAAACTGACA
1 GGCATGCCACGTGTACCAAAAAGTGACA
11589 CATGGCATGC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (62 bp):
GGCATGCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGTGACATGA
Found at i:17967 original size:42 final size:42
Alignment explanation
Indices: 17920--18007 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
17910 TTCTAAAACA
17920 AAAGTAATGTCATAATCTGCAATGCAAAAGATTGGATCTGAG
1 AAAGTAATGTCATAATCTGCAATGCAAAAGATTGGATCTGAG
*
17962 AAAGTAATGTCATAATCTGGAATGCAAAAGATTGGATCTGAG
1 AAAGTAATGTCATAATCTGCAATGCAAAAGATTGGATCTGAG
18004 AAAG
1 AAAG
18008 ATCACACATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (42 bp):
AAAGTAATGTCATAATCTGCAATGCAAAAGATTGGATCTGAG
Found at i:26456 original size:15 final size:14
Alignment explanation
Indices: 26427--26455 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26417 TGTTTTGGTG
26427 TAAGTAAAATTTTT
1 TAAGTAAAATTTTT
26441 TAAGTAAAATTTTT
1 TAAGTAAAATTTTT
26455 T
1 T
26456 TTCGGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAAGTAAAATTTTT
Done.