Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006807.1 Hibiscus syriacus cultivar Beakdansim tig00017276_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: 56441
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1656 original size:15 final size:16
Alignment explanation
Indices: 1630--1660 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1620 TTATTCACCT
1630 TTGGGGGAATTCCTTA
1 TTGGGGGAATTCCTTA
1646 TTGGGGG-ATTCCTTA
1 TTGGGGGAATTCCTTA
1661 CTCTAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.16, C:0.13, G:0.32, T:0.39
Consensus pattern (16 bp):
TTGGGGGAATTCCTTA
Found at i:31966 original size:12 final size:12
Alignment explanation
Indices: 31946--32003 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
31936 GATACATGAC
31946 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
31958 CTGATTTCTGAT
1 CTGAATTCTGTT
*
31970 CTGGATTCTGTT
1 CTGAATTCTGTT
31982 CTGAATTCTGTT
1 CTGAATTCTGTT
*
31994 TTGAATTCTG
1 CTGAATTCTG
32004 ATATCTCCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:32001 original size:24 final size:24
Alignment explanation
Indices: 31923--32003 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
31913 ATTTCCGACT
* * *
31923 TGAATTCTGTTATG-ATACATGACC
1 TGAATTCTGTTCTGAATTC-TGATC
*
31947 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGAATTCTGATC
* * *
31971 TGGATTCTGTTCTGAATTCTGTTT
1 TGAATTCTGTTCTGAATTCTGATC
31995 TGAATTCTG
1 TGAATTCTG
32004 ATATCTCCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGAATTCTGATC
Found at i:42889 original size:15 final size:15
Alignment explanation
Indices: 42861--42900 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
42851 TTTTATTTAT
42861 TTAATATATTTAATA
1 TTAATATATTTAATA
42876 TTAAT-TATTATAATA
1 TTAATATATT-TAATA
42891 -TAATA-ATTTA
1 TTAATATATTTA
42901 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 11 0.48
15 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATATTTAATA
Found at i:42998 original size:22 final size:21
Alignment explanation
Indices: 42973--43015 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
42963 TGGGTTGATT
42973 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
42995 TTAAGATTTAAACCTAAAATA
1 TTAAAATATAAACATAAAATA
43016 ATACCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:44179 original size:34 final size:35
Alignment explanation
Indices: 44120--44188 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
44110 AATATTGACA
* * *
44120 AAAAATAATTGTCGTCGCAACTCACCAACTAAGAC
1 AAAAATAATTATCGTCACAAATCACCAACTAAGAC
44155 AAAAA-AATTATCGTCACAAATCACCAACTAAGAC
1 AAAAATAATTATCGTCACAAATCACCAACTAAGAC
44189 TATTGACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.19
Consensus pattern (35 bp):
AAAAATAATTATCGTCACAAATCACCAACTAAGAC
Found at i:44694 original size:19 final size:18
Alignment explanation
Indices: 44670--44749 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 18
44660 AAACCGAAAC
44670 CGGTTTTATCGGTTCGGTT
1 CGGTTTT-TCGGTTCGGTT
****
44689 CGGTTTTTTAAAT-GGTT
1 CGGTTTTTCGGTTCGGTT
*
44706 CGGGTTTTTTGGTTCGGTT
1 C-GGTTTTTCGGTTCGGTT
*
44725 CGGTTTTTCGGTT--TTT
1 CGGTTTTTCGGTTCGGTT
44741 CGGTTTTTC
1 CGGTTTTTC
44750 AATGAAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
16 11 0.22
17 5 0.10
18 22 0.44
19 12 0.24
ACGTcount: A:0.05, C:0.12, G:0.29, T:0.54
Consensus pattern (18 bp):
CGGTTTTTCGGTTCGGTT
Found at i:44747 original size:7 final size:8
Alignment explanation
Indices: 44723--44749 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
44713 TTTGGTTCGG
44723 TTCGGTTT
1 TTCGGTTT
44731 TTCGGTTT
1 TTCGGTTT
44739 TTCGGTTT
1 TTCGGTTT
44747 TTC
1 TTC
44750 AATGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.22, T:0.63
Consensus pattern (8 bp):
TTCGGTTT
Found at i:53537 original size:30 final size:30
Alignment explanation
Indices: 53503--53603 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 30
53493 AGAAGTTAGT
53503 TGGGATGTTCTTCTATGTTTCTTAGCCATG
1 TGGGATGTTCTTCTATGTTTCTTAGCCATG
* * * * *
53533 TGGGATTGTTTTGTTCTCATATTTTCTCTTTAGACTTT
1 TGGGA-TG--TT-CT-TC-TATGTT-TC-TTAGCCATG
53571 TGGGATGTTCTTCTATGTTTCTTAGCCATG
1 TGGGATGTTCTTCTATGTTTCTTAGCCATG
53601 TGG
1 TGG
53604 AATTGTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
30 14 0.26
31 4 0.08
32 5 0.09
33 4 0.08
34 2 0.04
35 4 0.08
36 5 0.09
37 4 0.08
38 11 0.21
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (30 bp):
TGGGATGTTCTTCTATGTTTCTTAGCCATG
Done.