Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005313.1 Hibiscus syriacus cultivar Beakdansim tig00012028_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: 182071
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
File 2 of 2
Found at i:168819 original size:2 final size:2
Alignment explanation
Indices: 168734--168804 Score: 69
Period size: 2 Copynumber: 37.5 Consensus size: 2
168724 ATGTAATAAA
168734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
168774 AA AC AA AG AT GT A- AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
168805 AATACGTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
1 4 0.07
2 54 0.93
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:170471 original size:6 final size:6
Alignment explanation
Indices: 170455--170511 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
170445 ACCCACCTTA
*
170455 TTTTC- TTTTCT TTTTCT TTTT-T TCTTT-T TTCTCTTT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TT-T-TCT TTTTCT TTTTCT
170503 TTTT-T TTTT
1 TTTTCT TTTT
170512 TTTCTAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
5 13 0.28
6 28 0.61
7 2 0.04
8 3 0.07
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:170478 original size:8 final size:8
Alignment explanation
Indices: 170465--170514 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
170455 TTTTCTTTTC
170465 TTTTTCTT
1 TTTTTCTT
170473 TTTTTCTT
1 TTTTTCTT
170481 TTTTCTCTT
1 TTTT-TCTT
170490 TTTTTC--
1 TTTTTCTT
170496 TTTTTCTT
1 TTTTTCTT
170504 TTTTT-TT
1 TTTTTCTT
170511 TTTT
1 TTTT
170515 CTAATTTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 19 0.49
9 8 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:170479 original size:14 final size:14
Alignment explanation
Indices: 170460--170516 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
170450 CCTTATTTTC
170460 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
170474 TTTTCTTTTTTCTCTTT
1 TTTTC--TTTT-TCTTT
170491 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
*
170505 TTTTTTTTTTCT
1 TTTTCTTTTTCT
170517 AATTTAGGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
14 21 0.54
15 4 0.10
16 4 0.10
17 10 0.26
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:172647 original size:22 final size:22
Alignment explanation
Indices: 172605--172647 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
172595 TGTTTGAGTT
**
172605 TTCGTGTAGCCCAAACTAAGTC
1 TTCGTGTAGCCCAAAAAAAGTC
172627 TTCGTGTAGCCCAAAAAAAGT
1 TTCGTGTAGCCCAAAAAAAGT
172648 ATAACAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (22 bp):
TTCGTGTAGCCCAAAAAAAGTC
Found at i:175774 original size:46 final size:46
Alignment explanation
Indices: 175702--175795 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
175692 TGCTAGGGCA
*
175702 TGGCTCAATGGATTACCTTCCGGATCGATAATTTCTTGGGCTGACT
1 TGGCTCAATGGATTACCTTCCAGATCGATAATTTCTTGGGCTGACT
175748 TGGCTCAATGGATTACCTTCCAGATCGATAATTTCTTGGGCTGACT
1 TGGCTCAATGGATTACCTTCCAGATCGATAATTTCTTGGGCTGACT
175794 TG
1 TG
175796 TACAAAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (46 bp):
TGGCTCAATGGATTACCTTCCAGATCGATAATTTCTTGGGCTGACT
Done.