Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000269.1 Hibiscus syriacus cultivar Beakdansim tig00000495_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: 52443
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6056 original size:21 final size:21
Alignment explanation
Indices: 6030--6071 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6020 GGAACCTATT
6030 GGTCTTATCTACATCAGCACA
1 GGTCTTATCTACATCAGCACA
6051 GGTCTTATCTACATCAGCACA
1 GGTCTTATCTACATCAGCACA
6072 ACCATGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
GGTCTTATCTACATCAGCACA
Found at i:13004 original size:18 final size:18
Alignment explanation
Indices: 12981--13017 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12971 TACAATATGG
12981 CCAGATTTTGCACTACGA
1 CCAGATTTTGCACTACGA
12999 CCAGATTTTGCACTACGA
1 CCAGATTTTGCACTACGA
13017 C
1 C
13018 GTAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (18 bp):
CCAGATTTTGCACTACGA
Found at i:21736 original size:51 final size:51
Alignment explanation
Indices: 21660--21758 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
21650 CCACATTTTT
* *
21660 TTGTGGAGTGTCGACACAGGAAGTGAGGTGGACTATTCCGTTTTCCTGTTG
1 TTGTGGAGTGTCGACACAAGAAGTGAGGTGGACTATTCAGTTTTCCTGTTG
*
21711 TTGTGGTGTGTCGACACAAGAAGTGAGGTGGACTATTCAGTTTTCCTG
1 TTGTGGAGTGTCGACACAAGAAGTGAGGTGGACTATTCAGTTTTCCTG
21759 GAAGAAAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.32, T:0.33
Consensus pattern (51 bp):
TTGTGGAGTGTCGACACAAGAAGTGAGGTGGACTATTCAGTTTTCCTGTTG
Found at i:23841 original size:17 final size:17
Alignment explanation
Indices: 23821--23858 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
23811 CAGAAGCGGC
*
23821 ACTGTGAGGAGAGAAGT
1 ACTGAGAGGAGAGAAGT
*
23838 ACTGAGAGGAGAGCAGT
1 ACTGAGAGGAGAGAAGT
23855 ACTG
1 ACTG
23859 GGAGAAGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.39, T:0.16
Consensus pattern (17 bp):
ACTGAGAGGAGAGAAGT
Found at i:23867 original size:17 final size:17
Alignment explanation
Indices: 23830--23870 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
23820 CACTGTGAGG
* *
23830 AGAGAAGTACTGAGAGG
1 AGAGCAGTACTGAGAGA
*
23847 AGAGCAGTACTGGGAGA
1 AGAGCAGTACTGAGAGA
23864 AGAGCAG
1 AGAGCAG
23871 CGTTGTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.41, T:0.10
Consensus pattern (17 bp):
AGAGCAGTACTGAGAGA
Found at i:24566 original size:27 final size:27
Alignment explanation
Indices: 24536--24589 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
24526 ACCTCTCTTA
24536 ATATGCCTAATGACCACACCCCTATTT
1 ATATGCCTAATGACCACACCCCTATTT
24563 ATATGCCTAATGACCACACCCCTATTT
1 ATATGCCTAATGACCACACCCCTATTT
24590 CTCACTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (27 bp):
ATATGCCTAATGACCACACCCCTATTT
Found at i:30958 original size:24 final size:22
Alignment explanation
Indices: 30913--30961 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
30903 TGTTGGGGCA
*
30913 GTTTGACCCGTTGACCCGACCC
1 GTTTGACCCGTTGACCCAACCC
30935 GTTTGACCCGGTTTGACCCAACCC
1 GTTTGACCC-G-TTGACCCAACCC
30959 GTT
1 GTT
30962 CAGCGTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 1 0.04
24 14 0.58
ACGTcount: A:0.14, C:0.37, G:0.22, T:0.27
Consensus pattern (22 bp):
GTTTGACCCGTTGACCCAACCC
Found at i:33029 original size:38 final size:38
Alignment explanation
Indices: 32966--33054 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
32956 ATTTTGTTCG
32966 GGTCGGGTCGGG-TTTTTTAAGTGTGATATTCAGGTC-
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
*
33002 GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
33041 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
33055 CGGGTTTAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 1 0.02
37 11 0.22
38 36 0.73
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.37
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
Found at i:33626 original size:16 final size:18
Alignment explanation
Indices: 33601--33646 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
33591 TATGGAATTG
33601 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
*
33617 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
33635 GATTCCAATTCC
1 GATTCCAATTCC
33647 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:34475 original size:23 final size:25
Alignment explanation
Indices: 34448--34507 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 25
34438 GAATGTTTTA
*
34448 TCTGATTTTC-GATTTGAATT-TGT
1 TCTGATTTTCTGATCTGAATTCTGT
*
34471 TCTGA-TATCTGATCTGAATTCTGT
1 TCTGATTTTCTGATCTGAATTCTGT
*
34495 TTTGA-TTTCTGAT
1 TCTGATTTTCTGAT
34508 ATCTCCGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 14 0.45
24 14 0.45
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (25 bp):
TCTGATTTTCTGATCTGAATTCTGT
Found at i:34500 original size:24 final size:23
Alignment explanation
Indices: 34462--34507 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
34452 ATTTTCGATT
34462 TGAATTTGTTCTGATATCTGATC
1 TGAATTTGTTCTGATATCTGATC
* *
34485 TGAATTCTGTTTTGATTTCTGAT
1 TGAATT-TGTTCTGATATCTGAT
34508 ATCTCCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (23 bp):
TGAATTTGTTCTGATATCTGATC
Found at i:36533 original size:32 final size:32
Alignment explanation
Indices: 36482--36544 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
36472 TGACCCAGTT
*
36482 TTGACCCGACCCGTTTGACCC-GCTTTGACCTG
1 TTGACCCGACCCGTGTGACCCAG-TTTGACCTG
* *
36514 TTGACCTGACTCGTGTGACCCAGTTTGACCT
1 TTGACCCGACCCGTGTGACCCAGTTTGACCT
36545 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.14, C:0.33, G:0.22, T:0.30
Consensus pattern (32 bp):
TTGACCCGACCCGTGTGACCCAGTTTGACCTG
Found at i:38847 original size:24 final size:24
Alignment explanation
Indices: 38819--38881 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
38809 GAATGTTTTA
*
38819 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCCGATATGAATTCTGT
* *
38843 TCTGATATCTGATATGAATTCTGT
1 TCTGATTTCCGATATGAATTCTGT
* *
38867 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
38882 CTCTGTTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.51
Consensus pattern (24 bp):
TCTGATTTCCGATATGAATTCTGT
Found at i:41916 original size:20 final size:19
Alignment explanation
Indices: 41888--41931 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41878 ATTATAAAAT
* * *
41888 TTAAAATTATTATTTTTTCA
1 TTAATATTATT-TTTATTAA
41908 TTAATATTATTTTTATTAA
1 TTAATATTATTTTTATTAA
41927 TTAAT
1 TTAAT
41932 TATATTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATATTATTTTTATTAA
Found at i:41933 original size:17 final size:17
Alignment explanation
Indices: 41892--41934 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
41882 TAAAATTTAA
41892 AATTATTATTTTTTCATT
1 AATTATTA-TTTTTCATT
41910 AA-TATTATTTTT-ATT
1 AATTATTATTTTTCATT
41925 AATTAATTAT
1 AATT-ATTAT
41935 ATTATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 10 0.43
18 2 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTATTATTTTTCATT
Found at i:42026 original size:59 final size:59
Alignment explanation
Indices: 41963--42076 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
41953 ATGATCTTAA
* **
41963 TTTTAAATTAATCC-CTAAACTTTTTAATGTTTTAATTTCATCCCTAATA-TATGATATAC
1 TTTTAAATTAATCCTCAAAACTTTAAAAT-TTTTAATTTCATCCCTAA-ACTATGATATAC
*
42022 TTTTAAATTAGTCCTCAAAACTTTAAAATTTTTAATTTCATCCCTAAACTATGAT
1 TTTTAAATTAATCCTCAAAACTTTAAAATTTTTAATTTCATCCCTAAACTATGAT
42077 TTTTATTCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 1 0.02
59 37 0.76
60 11 0.22
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.46
Consensus pattern (59 bp):
TTTTAAATTAATCCTCAAAACTTTAAAATTTTTAATTTCATCCCTAAACTATGATATAC
Done.