Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009544.1 Corchorus olitorius cultivar O-4 contig09576, 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: 25249
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:249 original size:29 final size:28
Alignment explanation
Indices: 210--265 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
200 GTTATTCCAC
*
210 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
239 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
266 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:3267 original size:20 final size:20
Alignment explanation
Indices: 3234--3272 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3224 CATAAATGAA
*
3234 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
3254 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
3273 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:4256 original size:31 final size:31
Alignment explanation
Indices: 4188--4245 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
4178 TATCATCTTT
*
4188 TAATTTGTTTAATTTAAGGCTTTCATTTTAA
1 TAATTTGTTTAATTTAAGGCTTTAATTTTAA
* *
4219 TTATTTGTTTAATTTAATGC-TTAATTT
1 TAATTTGTTTAATTTAAGGCTTTAATTT
4246 GTTGTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.59
Consensus pattern (31 bp):
TAATTTGTTTAATTTAAGGCTTTAATTTTAA
Found at i:14711 original size:19 final size:20
Alignment explanation
Indices: 14673--14719 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
14663 GAAATTCTAT
14673 TACACTCAAAAAAGATATCAA
1 TACAC-CAAAAAAGATATCAA
* *
14694 TACACCAAAATAGA-ATCAT
1 TACACCAAAAAAGATATCAA
14713 TACACCA
1 TACACCA
14720 TATGTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 8 0.33
21 5 0.21
ACGTcount: A:0.53, C:0.23, G:0.04, T:0.19
Consensus pattern (20 bp):
TACACCAAAAAAGATATCAA
Found at i:17358 original size:13 final size:13
Alignment explanation
Indices: 17340--17380 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
17330 TACTTCAGTG
17340 ACAAAAAAACAAA
1 ACAAAAAAACAAA
17353 ACAAAAAAACAAA
1 ACAAAAAAACAAA
17366 A-ATCAAAAAACAAA
1 ACA--AAAAAACAAA
17380 A
1 A
17381 AATGAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 11 0.42
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (13 bp):
ACAAAAAAACAAA
Found at i:17360 original size:7 final size:7
Alignment explanation
Indices: 17343--17382 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
17333 TTCAGTGACA
17343 AAAAAAC
1 AAAAAAC
*
17350 AAAACA-
1 AAAAAAC
17356 AAAAAAC
1 AAAAAAC
*
17363 AAAAATC
1 AAAAAAC
17370 AAAAAAC
1 AAAAAAC
17377 AAAAAA
1 AAAAAA
17383 TGAATTACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAAAAC
Found at i:17381 original size:14 final size:14
Alignment explanation
Indices: 17340--17381 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
17330 TACTTCAGTG
17340 ACAAAAAAAC-AAA
1 ACAAAAAAACAAAA
17353 ACAAAAAAACAAAA
1 ACAAAAAAACAAAA
17367 ATC-AAAAAACAAAA
1 A-CAAAAAAACAAAA
17381 A
1 A
17382 ATGAATTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.37
14 16 0.59
15 1 0.04
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (14 bp):
ACAAAAAAACAAAA
Done.