Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007335.1 Hibiscus syriacus cultivar Beakdansim tig00019629_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: 48945
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:612 original size:35 final size:35
Alignment explanation
Indices: 563--665 Score: 163
Period size: 35 Copynumber: 2.9 Consensus size: 35
553 TTGATAATGA
*
563 CTCAAATTAGGTTATCCCACTAGTATTGAAAATATG
1 CTCAAATTAGGTTATCCCACTAGTATTGAAAATA-C
*
599 CT-AAATTAGGTTATCCCACTAGTATTGCAAATAC
1 CTCAAATTAGGTTATCCCACTAGTATTGAAAATAC
*
633 CTCAAATTAGGTTATCCCACTAGTATTGTAAAT
1 CTCAAATTAGGTTATCCCACTAGTATTGAAAAT
666 GACGATTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 2 0.03
35 59 0.94
36 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (35 bp):
CTCAAATTAGGTTATCCCACTAGTATTGAAAATAC
Found at i:12906 original size:14 final size:15
Alignment explanation
Indices: 12880--12913 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12870 GGGCATGGCG
*
12880 AATAATAAATTAAGA
1 AATAATAAATTAAAA
12895 AATAAT-AATTAAAA
1 AATAATAAATTAAAA
12909 AATAA
1 AATAA
12914 AGATAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAATAAATTAAAA
Found at i:30763 original size:5 final size:5
Alignment explanation
Indices: 30755--31766 Score: 1943
Period size: 5 Copynumber: 203.8 Consensus size: 5
30745 AACATAACAT
30755 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
30805 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
30855 AATAC AATAC AATAC AATAC AATAC -ATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
30904 -ATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
30953 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31003 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31053 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31103 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31153 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC -A-AC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31201 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC -A-AC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31249 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31299 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31349 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31399 AATAC AATAC AATAC AATAC AATAC AATAC AATAC -ATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31448 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31498 AATAC AATAC -A-AC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31546 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31596 AATAC AATAC AATAC AATAC AATAC AATACAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AAT--AC AATAC AATAC AATAC AATAC
31648 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31698 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
31748 AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATA
31767 TAATTAAAAT
Statistics
Matches: 996, Mismatches: 0, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
3 6 0.01
4 18 0.02
5 967 0.97
7 5 0.01
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAC
Found at i:32657 original size:23 final size:23
Alignment explanation
Indices: 32631--32701 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
32621 ATCTCTATTT
32631 ATGAAAAATAGTTAAGTCTTTTC
1 ATGAAAAATAGTTAAGTCTTTTC
* *
32654 ATGAAAAATAGTTAAATCATTTC
1 ATGAAAAATAGTTAAGTCTTTTC
** *
32677 ACCCAAAAA-AGTCAAGTCTTTTC
1 A-TGAAAAATAGTTAAGTCTTTTC
32700 AT
1 AT
32702 TTTAACCTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 34 0.87
24 5 0.13
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (23 bp):
ATGAAAAATAGTTAAGTCTTTTC
Found at i:37986 original size:22 final size:23
Alignment explanation
Indices: 37932--37987 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
37922 AAATTAGTTA
** *
37932 AAGTCTTTTCATGAAAAATAGTT
1 AAGTCTTTTCACCAAAAATAGTC
* *
37955 AATTCATTTCACCAAAAA-AGTC
1 AAGTCTTTTCACCAAAAATAGTC
37977 AAGTCTTTTCA
1 AAGTCTTTTCA
37988 TGTTAACATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
AAGTCTTTTCACCAAAAATAGTC
Done.