Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 19
Found at i:3281634 original size:10 final size:8
Alignment explanation
Indices: 3281597--3281646 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
3281587 GACCCGACAT
3281597 GTTGACCC
1 GTTGACCC
3281605 GTTGA-CC
1 GTTGACCC
3281612 GTTGACCC
1 GTTGACCC
3281620 GTTGACCGGC
1 GTTGACC--C
3281630 GTTGACCACC
1 GTTGA-C-CC
3281640 GTTGACC
1 GTTGACC
3281647 AAAACTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.19
8 15 0.41
9 1 0.03
10 12 0.32
11 1 0.03
12 1 0.03
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (8 bp):
GTTGACCC
Found at i:3284179 original size:24 final size:24
Alignment explanation
Indices: 3284061--3284176 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
3284051 TTCGATTTGA
*
3284061 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
3284085 ATTCTGATATGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
*
3284109 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
3284133 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
3284157 AGTT-TGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
3284177 CTGATTTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 1 0.01
24 78 0.95
25 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:3296646 original size:17 final size:17
Alignment explanation
Indices: 3296620--3296660 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3296610 TGTGAATAGG
*
3296620 ATTACCGGGAATGTTAC
1 ATTACTGGGAATGTTAC
3296637 ATTACTGGGAATGTTAC
1 ATTACTGGGAATGTTAC
3296654 ATTACTG
1 ATTACTG
3296661 TGTTTGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (17 bp):
ATTACTGGGAATGTTAC
Found at i:3296799 original size:15 final size:15
Alignment explanation
Indices: 3296781--3296854 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
3296771 GTGAAATTCT
3296781 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
3296796 AATTATTTATATAAA
1 AATTATTTAAATAAA
* **
3296811 AGTTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
3296824 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
3296838 AATTATTTATATAAA
1 AATTATTTAAATAAA
3296853 AA
1 AA
3296855 ATCATCGATA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 5 0.11
14 6 0.14
15 30 0.68
16 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:3296831 original size:42 final size:42
Alignment explanation
Indices: 3296780--3296870 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
3296770 AGTGAAATTC
**
3296780 TAAT-TATTTAAATAAAAATTATTTATATAAAAGTTCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
3296821 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
3296863 TAATATAT
1 TAATATAT
3296871 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (42 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
Done.