Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004827.1 Hibiscus syriacus cultivar Beakdansim tig00010872_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: 62841
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:23647 original size:6 final size:6
Alignment explanation
Indices: 23636--23672 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
23626 TCCATAGCGT
* *
23636 CTGCAA CTGCAA CTGCGA CTGCGA CTGCGA CTGCGA C
1 CTGCGA CTGCGA CTGCGA CTGCGA CTGCGA CTGCGA C
23673 GACCCTGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (6 bp):
CTGCGA
Found at i:24413 original size:20 final size:20
Alignment explanation
Indices: 24390--24430 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24380 AATTTGAATC
24390 TCCTTACCATCCTTCTCCAT
1 TCCTTACCATCCTTCTCCAT
24410 TCCTTACCATCCTTCTCCAT
1 TCCTTACCATCCTTCTCCAT
24430 T
1 T
24431 GGTACGCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.44, G:0.00, T:0.41
Consensus pattern (20 bp):
TCCTTACCATCCTTCTCCAT
Found at i:36761 original size:2 final size:2
Alignment explanation
Indices: 36754--36780 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36744 GAAAGCTGCG
36754 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
36781 TGTGTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52436 original size:2 final size:2
Alignment explanation
Indices: 52429--52462 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
52419 TAATTCAATA
52429 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
52463 TAAGGCATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52587 original size:3 final size:3
Alignment explanation
Indices: 52579--52635 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
52569 ACACCTACAT
52579 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
52627 ATA ATA ATA
1 ATA ATA ATA
52636 TATATATCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53648 original size:21 final size:21
Alignment explanation
Indices: 53624--53665 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
53614 AGTTTATTTT
53624 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
*
53645 TAAACTTTGTTTTAATTATCG
1 TAAACTTTGTTTCAATTATCG
53666 AACTTGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
TAAACTTTGTTTCAATTATCG
Found at i:54179 original size:15 final size:15
Alignment explanation
Indices: 54159--54194 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54149 TTGAACCGGT
* *
54159 TTTTTTTAAATCTGA
1 TTTTTTAAAATCTAA
54174 TTTTTTAAAATCTAA
1 TTTTTTAAAATCTAA
54189 TTTTTT
1 TTTTTT
54195 GACTAGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTTTAAAATCTAA
Done.