Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002138.1 Hibiscus syriacus cultivar Beakdansim tig00004372_pilon, 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: 71310
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10138 original size:31 final size:31
Alignment explanation
Indices: 10100--10161 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
10090 ATTATCATGA
10100 ATTACTCATCTCCTTTCATTAACTCTCTTGT
1 ATTACTCATCTCCTTTCATTAACTCTCTTGT
10131 ATTACTCATCTCCTTTCATTAACTCTCTTGT
1 ATTACTCATCTCCTTTCATTAACTCTCTTGT
10162 GTCCTAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.29, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTACTCATCTCCTTTCATTAACTCTCTTGT
Found at i:11014 original size:2 final size:2
Alignment explanation
Indices: 11009--11037 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10999 TGCAAAAAAG
11009 AT AT 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 AT AT A
11038 GTGTTGGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14643 original size:2 final size:2
Alignment explanation
Indices: 14593--14628 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14583 CCTCAATTTC
14593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14629 CTAAAGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24252 original size:3 final size:3
Alignment explanation
Indices: 24246--24306 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
24236 TATGATGATG
24246 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24294 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
24307 AAGAGAGGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31494 original size:29 final size:29
Alignment explanation
Indices: 31452--31510 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
31442 ATTTTCACCT
31452 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
31481 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
31510 A
1 A
31511 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:36183 original size:29 final size:29
Alignment explanation
Indices: 36138--36196 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
36128 ATTTTCACCT
36138 AACTAAATTGATATAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
*
36167 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
36196 A
1 A
36197 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAAGCAATGACATCAA
Found at i:42157 original size:16 final size:16
Alignment explanation
Indices: 42133--42165 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42123 TATCGCCGAC
*
42133 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
42149 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
42165 C
1 C
42166 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:44970 original size:14 final size:16
Alignment explanation
Indices: 44951--44983 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
44941 TAAAATTATT
44951 TTTAATAT-TTAA-TA
1 TTTAATATATTAATTA
44965 TTTAATATATTAATTA
1 TTTAATATATTAATTA
44981 TTT
1 TTT
44984 TATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATATATTAATTA
Found at i:45022 original size:16 final size:17
Alignment explanation
Indices: 44996--45036 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
44986 TAATTTTATG
44996 TTGTGAAAAATAT-ATTA
1 TTGT-AAAAATATAATTA
45013 TTGTAAAAATATAATTA
1 TTGTAAAAATATAATTA
45030 TT-TAAAA
1 TTGTAAAA
45037 TGATATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
TTGTAAAAATATAATTA
Found at i:62675 original size:38 final size:38
Alignment explanation
Indices: 62618--62693 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
62608 TTAGATGATG
*
62618 ACACTTGTAATCATCTGATTGGATAGAAATAAACAAAA
1 ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
* *
62656 ACACGTGTAATCATTTGATTGGATAGAAATTAACAAAA
1 ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
62694 GAAGAAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (38 bp):
ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
Done.