Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001501.1 Hibiscus syriacus cultivar Beakdansim tig00002945_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: 52815
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:1016 original size:21 final size:21
Alignment explanation
Indices: 991--1034 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
981 TTATCAGGCA
* *
991 ATACAATGCTTATATATATAT
1 ATACAATGCTCACATATATAT
1012 ATACAATGCTCACATATATAT
1 ATACAATGCTCACATATATAT
1033 AT
1 AT
1035 CCATAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (21 bp):
ATACAATGCTCACATATATAT
Found at i:4572 original size:18 final size:20
Alignment explanation
Indices: 4548--4605 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 20
4538 CTGAATATTT
4548 GTCCCGAAGGACCAC-TATA
1 GTCCCGAAGGACCACGTATA
4567 -TCCCGAAGGACCACTGTATA
1 GTCCCGAAGGACCAC-GTATA
*
4587 TGTCCCGAAGGACCGCGTA
1 -GTCCCGAAGGACCACGTA
4606 GACCCTCGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 14 0.41
20 4 0.12
21 3 0.09
22 13 0.38
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.17
Consensus pattern (20 bp):
GTCCCGAAGGACCACGTATA
Found at i:9717 original size:12 final size:12
Alignment explanation
Indices: 9699--9744 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
9689 ACTATACGGT
9699 ATGAACAGTACC
1 ATGAACAGTACC
* *
9711 GTGAACAGTTCC
1 ATGAACAGTACC
*
9723 ATGAACAGTGCC
1 ATGAACAGTACC
*
9735 ATGAGCAGTA
1 ATGAACAGTA
9745 AAAACTTTCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:13399 original size:19 final size:19
Alignment explanation
Indices: 13377--13434 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
13367 TTATCAGGCA
13377 ATACAATGCTTACATGTAT
1 ATACAATGCTTACATGTAT
13396 ATACAATGCTTACATGTAT
1 ATACAATGCTTACATGTAT
* *
13415 ATACAATGCTCACATATAT
1 ATACAATGCTTACATGTAT
13434 A
1 A
13435 CATCCATCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (19 bp):
ATACAATGCTTACATGTAT
Found at i:13967 original size:4 final size:4
Alignment explanation
Indices: 13958--13984 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13948 AAATGCATGT
13958 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
13985 CATAGTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:18092 original size:16 final size:17
Alignment explanation
Indices: 18071--18113 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
18061 ATGTAAAAAT
18071 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
18087 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
18104 AAATATTTAA
1 AAATATTTAA
18114 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:21116 original size:23 final size:24
Alignment explanation
Indices: 21088--21138 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
21078 CAGCAGAAAT
*
21088 AATAAAATAA-AAGAACAAAATAA
1 AATAAAATAAGAACAACAAAATAA
**
21111 AAT-AAATAAGCTCAACAAAATAA
1 AATAAAATAAGAACAACAAAATAA
21134 AATAA
1 AATAA
21139 TACTTGCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 6 0.26
23 16 0.70
24 1 0.04
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.16
Consensus pattern (24 bp):
AATAAAATAAGAACAACAAAATAA
Found at i:49182 original size:19 final size:19
Alignment explanation
Indices: 49158--49205 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
49148 ATGTATTTTA
49158 TGCACCGATGCACAGGTAG
1 TGCACCGATGCACAGGTAG
49177 TGCACCGATGCACAGGTAG
1 TGCACCGATGCACAGGTAG
*
49196 TGCATCGATG
1 TGCACCGATG
49206 TACCGATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (19 bp):
TGCACCGATGCACAGGTAG
Done.