Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005547.1 Hibiscus syriacus cultivar Beakdansim tig00012841_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: 56440
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1796 original size:2 final size:2
Alignment explanation
Indices: 1789--1826 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1779 CGTTGAGATA
*
1789 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1827 TCGAGTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2306 original size:25 final size:26
Alignment explanation
Indices: 2262--2313 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
2252 AGAAAAATTA
2262 TTTGAAGATAATGATAAGTGTGAAAG
1 TTTGAAGATAATGATAAGTGTGAAAG
2288 TTTGAAGAT-ATGATAAGTGTGAAAG
1 TTTGAAGATAATGATAAGTGTGAAAG
2313 T
1 T
2314 CACATGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (26 bp):
TTTGAAGATAATGATAAGTGTGAAAG
Found at i:11733 original size:30 final size:29
Alignment explanation
Indices: 11695--11756 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
11685 TTGATATTTC
*
11695 AACAGTTCATCATCGTCTTTTTGAAGTTG
1 AACAGTTCATCATCGTCTTTTTGAAGCTG
11724 AACATGTTCATCATCGTCTTTTTGAAGCTG
1 AACA-GTTCATCATCGTCTTTTTGAAGCTG
11754 AAC
1 AAC
11757 CTATCCCTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (29 bp):
AACAGTTCATCATCGTCTTTTTGAAGCTG
Found at i:12436 original size:22 final size:22
Alignment explanation
Indices: 12406--12463 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
12396 ATTTTTATAC
*
12406 AAAAGAAAAAAAAAAGAC-TAA
1 AAAATAAAAAAAAAAGACATAA
* *
12427 TAAAATAAAATAAAATGACATAA
1 -AAAATAAAAAAAAAAGACATAA
*
12450 ATAAATAAATAAAA
1 A-AAATAAAAAAAA
12464 CATGCAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAATAAAAAAAAAAGACATAA
Found at i:12484 original size:2 final size:2
Alignment explanation
Indices: 12477--12598 Score: 244
Period size: 2 Copynumber: 61.0 Consensus size: 2
12467 GCAAAAACAA
12477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12599 GATAAAATTT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 120 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13671 original size:2 final size:2
Alignment explanation
Indices: 13662--13700 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
13652 ATATAACAAA
13662 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13701 TTCGTTTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30848 original size:27 final size:27
Alignment explanation
Indices: 30818--30871 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
30808 TACCATCATT
30818 TCAAAGTTGCTAAAGCCGAAAAGACCA
1 TCAAAGTTGCTAAAGCCGAAAAGACCA
30845 TCAAAGTTGCTAAAGCCGAAAAGACCA
1 TCAAAGTTGCTAAAGCCGAAAAGACCA
30872 GCAATAGAAG
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:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (27 bp):
TCAAAGTTGCTAAAGCCGAAAAGACCA
Found at i:46890 original size:54 final size:55
Alignment explanation
Indices: 46816--47220 Score: 323
Period size: 51 Copynumber: 7.7 Consensus size: 55
46806 TCAGACAACA
* * * * * *
46816 GGTTCGCTCCCTATTCCTTCATGGAGTAGA-AACTCGTACAATCTTTTGCCTACG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATACG
* * * *
46870 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAA-AATCTTCTGCAAACG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATACG
* * *
46924 GGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAC-ATC--TT-CAAACG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATACG
* * *
46975 GGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAC-ATC--TT-C-GACTG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATAC-G
* * * * *
47026 GGTTTGCTCCCTTTTTCTTCAGGGAGTATAGAACTC-AAAAATCTTCTT-CTTACG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTT-TTGCATACG
* * * * *
47080 GGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAA-AATC--TT-CAAACG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATACG
* ** * * *
47131 GGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAAC-ATC--TT-CAAACG
1 GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATACG
* *
47182 GGTTCGCTCCTTCTTTCATT-AAGGAGAATAGAACTCGAA
1 GGTTCGCTCCCTCTTTC-TTCAAGGAGTATAGAACTCGAA
47221 TATCTTCAAC
Statistics
Matches: 304, Mismatches: 36, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
50 4 0.01
51 174 0.57
52 3 0.01
54 113 0.37
55 10 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (55 bp):
GGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAACAATCTTTTGCATACG
Found at i:46994 original size:51 final size:51
Alignment explanation
Indices: 46867--47229 Score: 442
Period size: 51 Copynumber: 7.0 Consensus size: 51
46857 TCTTTTGCCT
* * * * *
46867 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-T-T-CAA
46921 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
46972 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * * * * **
47022 ACTGGGTTTGCTCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTT
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTC--GAA-CATCTTCAA
* * *
47077 ACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
** *
47128 ACGGGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * *
47179 ACGGGTTCGCTCCTTCTTTCATTAAGGAGAATAGAACTCGAATATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
47230 CAATCGTGTC
Statistics
Matches: 272, Mismatches: 30, Indels: 17
0.85 0.09 0.05
Matches are distributed among these distances:
50 2 0.01
51 180 0.66
52 7 0.03
53 7 0.03
54 74 0.27
55 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (51 bp):
ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
Found at i:47005 original size:105 final size:105
Alignment explanation
Indices: 46867--47227 Score: 441
Period size: 105 Copynumber: 3.5 Consensus size: 105
46857 TCTTTTGCCT
* * * *
46867 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACGGGTTCGCT
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTGCAAACGGGTTCGCT
46932 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
66 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* *
46972 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G---ACTGGGTTTGC
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTGCAAAC-GGGTTCGC
* * * * **
47033 TCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTT
65 T-CCTTCTTTCTTTAAGGAGTATAGAACTC--GAA-CATCTTCAA
* *
47077 ACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATC-T-T-CAAACGGGTTCGCT
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTGCAAACGGGTTCGCT
** *
47139 CCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAA
66 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * *
47179 ACGGGTTCGCTCCTTCTTTCATTAAGGAGAATAGAACTCGAATATCTTC
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC
47228 AACAATCGTG
Statistics
Matches: 214, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
101 2 0.01
102 76 0.36
103 7 0.03
104 8 0.04
105 119 0.56
106 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (105 bp):
ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTGCAAACGGGTTCGCT
CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
Found at i:47058 original size:156 final size:156
Alignment explanation
Indices: 46867--47227 Score: 521
Period size: 156 Copynumber: 2.3 Consensus size: 156
46857 TCTTTTGCCT
* *
46867 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACGGGTTCGCT
1 ACGGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTGCAAACGGGTTCGCT
* * * **
46932 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
66 CCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTAA
* *
46997 GGAGTATAGAACTCGAACATCTTC-G
131 AGAGTATAGAACTCGAACATCTTCAA
* * * **
47022 ACTGGGTTTGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGC
1 AC-GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTGCAAACGGGTTCGC
47087 TCCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTA
65 TCCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTA
47152 AAGAGTATAGAACTCGAACATCTTCAA
130 AAGAGTATAGAACTCGAACATCTTCAA
* * *
47179 ACGGGTTCGCT-CCTTCTTTCATT-AAGGAGAATAGAACTCGAATATCTTC
1 ACGGGTTCGCTCCCTT-TTTC-TTCAGGGAGTATAGAACTCGAAAATCTTC
47228 AACAATCGTG
Statistics
Matches: 183, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
155 6 0.03
156 173 0.95
157 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (156 bp):
ACGGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTGCAAACGGGTTCGCT
CCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTAA
AGAGTATAGAACTCGAACATCTTCAA
Found at i:47262 original size:156 final size:154
Alignment explanation
Indices: 46867--47284 Score: 495
Period size: 156 Copynumber: 2.7 Consensus size: 154
46857 TCTTTTGCCT
* * * *
46867 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACGGGTTCGCT
1 ACGGGTTCGCTCCTTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTACAATCGGGTTCGCT
* **
46932 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
66 CCTTCTTTCTTTAA-GAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTAA
* *
46997 GGAGTATAGAACTCGAACATCTTCG
130 AGAGTATAGAACTCGAACATCTTCA
* * * *
47022 ACTGGGTTTGCTCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTC-TTACGGGTTC
1 AC-GGGTTCGCT-CCTTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTACAAT-CGGGTTC
*
47085 GCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTT
63 GCTCCTTCTTTCTTT-AAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTT
47150 TAAAGAGTATAGAACTCGAACATCTTCAA
127 TAAAGAGTATAGAACTCGAACATCTTC-A
* * * * *
47179 ACGGGTTCGCTCCTTCTTTCATT-AAGGAGAATAGAACTCGAATATCTTCAACAATCGTG-TCTG
1 ACGGGTTCGCTCCTTCTTTC-TTCAGGGAGTATAGAACTCGAAAATCTTCTACAATCGGGTTC-G
* * * *
47242 CTCCCTATTTCTTCAGAGAGTAT-GAGACTCGAACGATCTTCAA
64 CTCCTTCTTTCTTTA-AGAGTATAGA-ACTCGAA-AATCTTCAA
47285 CGATTGTTGG
Statistics
Matches: 224, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
155 11 0.05
156 195 0.87
157 18 0.08
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (154 bp):
ACGGGTTCGCTCCTTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTACAATCGGGTTCGCT
CCTTCTTTCTTTAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTAAA
GAGTATAGAACTCGAACATCTTCA
Done.