Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007295.1 Hibiscus syriacus cultivar Beakdansim tig00019407_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: 56845
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2386 original size:10 final size:10
Alignment explanation
Indices: 2379--2404 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2369 ACTAAATGTC
2379 ATGCAATGAA
1 ATGCAATGAA
2389 ATGCAATGAA
1 ATGCAATGAA
2399 ATGCAA
1 ATGCAA
2405 ACTAAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (10 bp):
ATGCAATGAA
Found at i:3906 original size:20 final size:21
Alignment explanation
Indices: 3883--3926 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3873 GAGAAAAAGT
3883 AAAAGTTAA-AATGAAATAGA
1 AAAAGTTAAGAATGAAATAGA
*
3903 AAAAGTTAAGGATGAAATAGA
1 AAAAGTTAAGAATGAAATAGA
3924 AAA
1 AAA
3927 TAAAAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (21 bp):
AAAAGTTAAGAATGAAATAGA
Found at i:3920 original size:26 final size:25
Alignment explanation
Indices: 3865--3938 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 25
3855 AGAAGATGAA
* * *
3865 GAAATGAAGAGAAAAAGTAAAAGTT
1 GAAATGAAAAGAAAAAGTTAAAGAT
* *
3890 AAAATGAAATAGAAAAAGTTAAGGAT
1 GAAATGAAA-AGAAAAAGTTAAAGAT
*
3916 GAAATAGAAAATAAAAAGTTAAA
1 GAAAT-GAAAAGAAAAAGTTAAA
3939 AAATTGATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 7 0.18
26 28 0.72
27 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.18
Consensus pattern (25 bp):
GAAATGAAAAGAAAAAGTTAAAGAT
Found at i:10962 original size:25 final size:25
Alignment explanation
Indices: 10934--10990 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
10924 CACGAACCAC
10934 CTTAGCT-CGCTAGCTCCTCTCGACG
1 CTTAGCTAC-CTAGCTCCTCTCGACG
10959 CTTAGCTACCTAGCTCCTCTCGACG
1 CTTAGCTACCTAGCTCCTCTCGACG
10984 CTTAGCT
1 CTTAGCT
10991 TACCACTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.14, C:0.39, G:0.18, T:0.30
Consensus pattern (25 bp):
CTTAGCTACCTAGCTCCTCTCGACG
Found at i:14083 original size:18 final size:18
Alignment explanation
Indices: 14060--14105 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
14050 CAAAAGTAAG
14060 ACGAGGTGGGGATAGAAC
1 ACGAGGTGGGGATAGAAC
14078 ACGAGGTGGGGATAGAAC
1 ACGAGGTGGGGATAGAAC
14096 ACGAGG-GGGG
1 ACGAGGTGGGG
14106 TGGTAGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.30, C:0.11, G:0.50, T:0.09
Consensus pattern (18 bp):
ACGAGGTGGGGATAGAAC
Found at i:20457 original size:20 final size:20
Alignment explanation
Indices: 20428--20466 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20418 ATTTCACTAC
*
20428 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
20448 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
20467 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:38104 original size:1 final size:1
Alignment explanation
Indices: 38100--38158 Score: 64
Period size: 1 Copynumber: 59.0 Consensus size: 1
38090 TTTTTGGCTC
* *** * *
38100 TTTTTTTTGTTTTTTTTTTGCCTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38159 GAGAAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:38107 original size:13 final size:12
Alignment explanation
Indices: 38089--38152 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 12
38079 AAATTTTGGC
*
38089 TTTTTTGGCTCT
1 TTTTTTTGCTCT
*
38101 TTTTTTTG-TTT
1 TTTTTTTGCTCT
38112 TTTTTTTGC-CT
1 TTTTTTTGCTCT
** *
38123 TTTTTTTTTTTT
1 TTTTTTTGCTCT
38135 TTTTTTTG-T-T
1 TTTTTTTGCTCT
38145 TTTTTTTG
1 TTTTTTTG
38153 TTTTTTGAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
10 9 0.21
11 19 0.44
12 15 0.35
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (12 bp):
TTTTTTTGCTCT
Found at i:38113 original size:10 final size:10
Alignment explanation
Indices: 38100--38158 Score: 73
Period size: 10 Copynumber: 5.5 Consensus size: 10
38090 TTTTTGGCTC
38100 TTTTTTTTGTT
1 TTTTTTTTG-T
38111 TTTTTTTTGCCTT
1 TTTTTTTTG---T
*
38124 TTTTTTTTTT
1 TTTTTTTTGT
38134 TTTTTTTTGT
1 TTTTTTTTGT
38144 TTTTTTTTGT
1 TTTTTTTTGT
38154 TTTTT
1 TTTTT
38159 GAGAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
10 25 0.57
11 9 0.20
13 10 0.23
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:38114 original size:22 final size:21
Alignment explanation
Indices: 38089--38158 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 21
38079 AAATTTTGGC
38089 TTTTTTGGCTCTTTTTTTTGTTTT
1 TTTTTTGGCT-TTTTTTTTG--TT
* *
38113 TTTTTTGCCTTTTTTTTTTTTT
1 TTTTTTGGC-TTTTTTTTTGTT
*
38135 TTTTTTTG-TTTTTTTTTGTT
1 TTTTTTGGCTTTTTTTTTGTT
38155 TTTT
1 TTTT
38159 GAGAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 15 0.38
22 8 0.20
24 16 0.40
25 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.86
Consensus pattern (21 bp):
TTTTTTGGCTTTTTTTTTGTT
Found at i:38126 original size:23 final size:22
Alignment explanation
Indices: 38089--38158 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 22
38079 AAATTTTGGC
*
38089 TTTTTTGGCTCTTTTTTTTGTTT
1 TTTTTTTGCT-TTTTTTTTGTTT
*
38112 TTTTTTTGCCTTTTTTTTTTTTT
1 TTTTTTTG-CTTTTTTTTTGTTT
38135 TTTTTTTG-TTTTTTTTTGTTT
1 TTTTTTTGCTTTTTTTTTGTTT
38156 TTT
1 TTT
38159 GAGAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.35
23 26 0.60
24 2 0.05
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.86
Consensus pattern (22 bp):
TTTTTTTGCTTTTTTTTTGTTT
Found at i:45107 original size:44 final size:47
Alignment explanation
Indices: 44986--45113 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 47
44976 ATATAAATTT
* *
44986 CTTACC-TTTTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* ** *
45032 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTT-TTTTTTTCAATATA
1 CTTACCATTT--AATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* *
45080 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
45114 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
44 19 0.28
45 3 0.04
46 6 0.09
47 5 0.07
48 17 0.25
49 19 0.28
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (47 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
Found at i:49197 original size:18 final size:18
Alignment explanation
Indices: 49156--49200 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
49146 TTTTCATCTC
*
49156 TCATTTTTTTCTCTTTTT
1 TCATTTTTTTCTCTGTTT
49174 TC-TTTTCTTTCTC-GTTT
1 TCATTTT-TTTCTCTGTTT
49191 TCATTTTTTT
1 TCATTTTTTT
49201 TCTTCTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (18 bp):
TCATTTTTTTCTCTGTTT
Found at i:49202 original size:18 final size:18
Alignment explanation
Indices: 49159--49203 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
49149 TCATCTCTCA
*
49159 TTTTTTTCTCTTTTTTCT
1 TTTTTTTCTCTGTTTTCT
*
49177 TTTCTTTCTC-GTTTTCAT
1 TTTTTTTCTCTGTTTTC-T
49195 TTTTTTTCT
1 TTTTTTTCT
49204 TCTTCTTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTTCTCTGTTTTCT
Found at i:49217 original size:37 final size:35
Alignment explanation
Indices: 49146--49234 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 35
49136 GAAATATTTT
*
49146 TTTTCATCTCTCATTTTTTTCTCTTTTTTCTTTTC-
1 TTTTCAT-TTTCATTTTTTTCTCTTTTTTCTTTTCA
*
49181 TTTCTCGTTTTCATTTTTTT-TCTTCTTCTTCGTTTTCA
1 TTT-TCATTTTCATTTTTTTCTCTT-TT-TTC-TTTTCA
49219 TTTTCATTTTC-TTTTT
1 TTTTCATTTTCATTTTT
49235 CTATATTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
34 4 0.09
35 16 0.35
36 11 0.24
37 12 0.26
38 3 0.07
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.72
Consensus pattern (35 bp):
TTTTCATTTTCATTTTTTTCTCTTTTTTCTTTTCA
Found at i:49228 original size:27 final size:26
Alignment explanation
Indices: 49171--49236 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
49161 TTTTTCTCTT
49171 TTTTCTTTTC-T-TTC-TCGTTTTCA
1 TTTTCTTTTCTTCTTCTTCGTTTTCA
49194 TTTT-TTTTCTTCTTCTTCGTTTTCA
1 TTTTCTTTTCTTCTTCTTCGTTTTCA
*
49219 TTTTCATTTTCTTTTTCT
1 TTTTC-TTTTCTTCTTCT
49237 ATATTTTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 5 0.14
23 5 0.14
24 3 0.08
25 13 0.35
27 11 0.30
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.73
Consensus pattern (26 bp):
TTTTCTTTTCTTCTTCTTCGTTTTCA
Found at i:49243 original size:27 final size:27
Alignment explanation
Indices: 49188--49267 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
49178 TTCTTTCTCG
* *
49188 TTTTCATTTT--TTTTCTTCTTCTTCG
1 TTTTCATTTTCATTTTCTTTTTCTTCA
49213 TTTTCATTTTCATTTTCTTTTTCTAT-A
1 TTTTCATTTTCATTTTCTTTTTCT-TCA
* *
49240 TTTTCTTTTTCTATTTTTTTTCTTCTTC
1 TTTTCATTTTC-ATTTTCTTT-TTCTTC
49268 TTATAATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 10 0.22
27 21 0.47
28 10 0.22
29 4 0.09
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.74
Consensus pattern (27 bp):
TTTTCATTTTCATTTTCTTTTTCTTCA
Found at i:52208 original size:47 final size:49
Alignment explanation
Indices: 52084--52215 Score: 130
Period size: 47 Copynumber: 2.8 Consensus size: 49
52074 ATATAAATTT
* *
52084 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA-TT-TTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTGTTTACCAAAATA
** ** *
52130 CTTACCATTTAAAATTCCATAAGCTGGTAAGCTTATTTGTTTTTCAATATA
1 CTTACCATTT--AATTCCATAAGCTCATAAGCTTATTTGTTTACCAAAATA
* *
52181 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTTG
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTG
52216 CATGGTTACT
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
46 6 0.09
47 26 0.37
49 19 0.27
50 4 0.06
51 15 0.21
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTGTTTACCAAAATA
Done.