Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005772.1 Hibiscus syriacus cultivar Beakdansim tig00013511_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: 58435
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:16749 original size:37 final size:37
Alignment explanation
Indices: 16701--16851 Score: 180
Period size: 37 Copynumber: 4.1 Consensus size: 37
16691 CTAGTTTTAT
* * *
16701 ATCAATGAAATTCATAACCAACAATAGTAACCCCTAT
1 ATCAATGAAATTCATATCCAACAATACTAACCCCTAC
* *
16738 ATCAATAAAATTCATATCCAACAA-ACTAACCCATAC
1 ATCAATGAAATTCATATCCAACAATACTAACCCCTAC
* *
16774 ATCAATGGAATTCATATCCAACAATACTAACTCCTAC
1 ATCAATGAAATTCATATCCAACAATACTAACCCCTAC
* * * * *
16811 ATCAATGTAATTCATATCTAATAACACTAA-CTCTAC
1 ATCAATGAAATTCATATCCAACAATACTAACCCCTAC
16847 ATCAA
1 ATCAA
16852 AGGAATAACT
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
36 40 0.41
37 58 0.59
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.26
Consensus pattern (37 bp):
ATCAATGAAATTCATATCCAACAATACTAACCCCTAC
Found at i:16788 original size:73 final size:73
Alignment explanation
Indices: 16701--16857 Score: 199
Period size: 73 Copynumber: 2.2 Consensus size: 73
16691 CTAGTTTTAT
* * *
16701 ATCAATGAAATTCATAACCAACAATAGTAACCCCTATATCAATAAAATTCATATCCAACAA-ACT
1 ATCAATGGAATTCATAACCAACAATACTAACCCCTACATCAATAAAATTCATATCCAACAACACT
16765 AACCCATAC
66 AACCC-TAC
* * ** * *
16774 ATCAATGGAATTCATATCCAACAATACTAACTCCTACATCAATGTAATTCATATCTAATAACACT
1 ATCAATGGAATTCATAACCAACAATACTAACCCCTACATCAATAAAATTCATATCCAACAACACT
*
16839 AACTCTAC
66 AACCCTAC
*
16847 ATCAAAGGAAT
1 ATCAATGGAAT
16858 AACTTTATTA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 65 0.90
74 7 0.10
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.26
Consensus pattern (73 bp):
ATCAATGGAATTCATAACCAACAATACTAACCCCTACATCAATAAAATTCATATCCAACAACACT
AACCCTAC
Found at i:26599 original size:26 final size:27
Alignment explanation
Indices: 26553--26606 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
26543 AATTAATGGA
* *
26553 AAATAATAAAAAAATGATTAATCAATG
1 AAATAATAAAAAAATAATTAATAAATG
26580 AAAT-ATAAAAAAA-AACTTAATAAATG
1 AAATAATAAAAAAATAA-TTAATAAATG
26606 A
1 A
26607 GATTATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 19 0.79
27 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.24
Consensus pattern (27 bp):
AAATAATAAAAAAATAATTAATAAATG
Found at i:31522 original size:90 final size:90
Alignment explanation
Indices: 31369--31548 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
31359 CTTGATGGAG
31369 AGTCACTTTACGACTACTGGGATCAGTTTAAGAAGTTATGTTCTAGTTGCCCAAAACATGGGTTA
1 AGTCACTTTACGACTACTGGGATCAGTTTAAGAAGTTATGTTCTAGTTGCCCAAAACATGGGTTA
31434 ACTGAACAAACAATACTTCAATACT
66 ACTGAACAAACAATACTTCAATACT
31459 AGTCACTTTACGACTACTGGGATCAGTTTAAGAAGTTATGTTCTAGTTGCCCAAAACATGGGTTA
1 AGTCACTTTACGACTACTGGGATCAGTTTAAGAAGTTATGTTCTAGTTGCCCAAAACATGGGTTA
*
31524 ACTGAACAAACAATACTTTAATACT
66 ACTGAACAAACAATACTTCAATACT
31549 TTTATGAAGG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (90 bp):
AGTCACTTTACGACTACTGGGATCAGTTTAAGAAGTTATGTTCTAGTTGCCCAAAACATGGGTTA
ACTGAACAAACAATACTTCAATACT
Found at i:34735 original size:23 final size:25
Alignment explanation
Indices: 34705--34758 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
34695 GCTCCATCAG
*
34705 GAAAAAAGAT-AAAAAAATA-GTTC
1 GAAAAAAGATAAAAAAAAGATGTTC
34728 GAAAAAAGATAAAAAAAAGATGTTC
1 GAAAAAAGATAAAAAAAAGATGTTC
34753 GAAAAA
1 GAAAAA
34759 TAAAGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 10 0.36
24 8 0.29
25 10 0.36
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.15
Consensus pattern (25 bp):
GAAAAAAGATAAAAAAAAGATGTTC
Found at i:34743 original size:11 final size:11
Alignment explanation
Indices: 34706--34748 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
34696 CTCCATCAGG
34706 AAAAAAGATAA
1 AAAAAAGATAA
* **
34717 AAAAATAGTTCG
1 AAAAA-AGATAA
34729 AAAAAAGATAA
1 AAAAAAGATAA
34740 AAAAAAGAT
1 AAAAAAGAT
34749 GTTCGAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (11 bp):
AAAAAAGATAA
Found at i:34743 original size:25 final size:23
Alignment explanation
Indices: 34705--34758 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
34695 GCTCCATCAG
34705 GAAAAAAGATAAAAAA-ATAGTTC
1 GAAAAAAGATAAAAAAGAT-GTTC
34728 GAAAAAAGATAAAAAAAAGATGTTC
1 GAAAAAAGAT--AAAAAAGATGTTC
34753 GAAAAA
1 GAAAAA
34759 TAAAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.36
25 16 0.57
26 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.15
Consensus pattern (23 bp):
GAAAAAAGATAAAAAAGATGTTC
Found at i:36891 original size:20 final size:20
Alignment explanation
Indices: 36854--36891 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36844 CTCAAAATCA
*
36854 TTTTTTAAAATATTATTTTG
1 TTTTTTAAAATATAATTTTG
*
36874 TTTTTTAAAATCTAATTT
1 TTTTTTAAAATATAATTT
36892 ACTTTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTTTAAAATATAATTTTG
Found at i:38745 original size:22 final size:22
Alignment explanation
Indices: 38703--38771 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
38693 GAACCTGGAA
* *
38703 AATAAAATAAATA-AATA-AAT
1 AATATAATAAATATATTATAAT
38723 AATATAATAAATATATTATAAT
1 AATATAATAAATATATTATAAT
*
38745 -ATATATATATATATATTATAA-
1 AATATA-ATAAATATATTATAAT
38766 AATATA
1 AATATA
38772 TTTTCCGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.29
21 8 0.19
22 22 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATAATAAATATATTATAAT
Found at i:38772 original size:22 final size:22
Alignment explanation
Indices: 38723--38853 Score: 81
Period size: 22 Copynumber: 5.8 Consensus size: 22
38713 ATAAATAAAT
*
38723 AATATA-ATAAATATATTATAA
1 AATATATATATATATATTATAA
*
38744 TATATATATATATATATTATAA
1 AATATATATATATATATTATAA
* * * *
38766 AATATATTTTCCGAAAACTATAATATAT
1 AATATA-TAT----ATA-TATATTATAA
* * *
38794 AACATATATATATATTTTAAAA
1 AATATATATATATATATTATAA
*
38816 AACTATATA-ATATAT-TTAAAA
1 AA-TATATATATATATATTATAA
38837 AATATAT-TATATATATT
1 AATATATATATATATATT
38854 TTCAAAAGCT
Statistics
Matches: 85, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
20 11 0.13
21 15 0.18
22 33 0.39
23 9 0.11
27 4 0.05
28 13 0.15
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
AATATATATATATATATTATAA
Found at i:38836 original size:20 final size:21
Alignment explanation
Indices: 38797--38850 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
38787 AATATATAAC
38797 ATATAT-ATATATTTTAAAAAA
1 ATATATAATATA-TTTAAAAAA
*
38818 CTATATAATATATTT-AAAAA
1 ATATATAATATATTTAAAAAA
*
38838 ATATATTATATAT
1 ATATATAATATAT
38851 ATTTTCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.55
21 8 0.28
22 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATAATATATTTAAAAAA
Found at i:38854 original size:22 final size:21
Alignment explanation
Indices: 38797--38854 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
38787 AATATATAAC
38797 ATATATATATAT-TTTAAAAA
1 ATATATATATATATTTAAAAA
38817 ACTATATA-ATATATTTAAAAA
1 A-TATATATATATATTTAAAAA
38838 ATATATTATATATATTT
1 ATATA-TATATATATTT
38855 TCAAAAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.26
21 17 0.50
22 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATATATATATTTAAAAA
Found at i:38860 original size:22 final size:21
Alignment explanation
Indices: 38798--38875 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
38788 ATATATAACA
38798 TATATATATATTTTAAAAAAC
1 TATATATATATTTTAAAAAAC
*
38819 TATATA-ATATATTTAAAAAATA
1 TATATATATAT-TTTAAAAAA-C
* *
38841 TATTATATATATTTTCAAAAGC
1 TA-TATATATATTTTAAAAAAC
*
38863 TTTATAT-TATTTT
1 TATATATATATTTT
38876 TTTGAATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 10 0.21
21 20 0.42
22 3 0.06
23 11 0.23
24 4 0.08
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (21 bp):
TATATATATATTTTAAAAAAC
Found at i:38921 original size:2 final size:2
Alignment explanation
Indices: 38881--38906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38871 ATTTTTTTGA
38881 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
38907 TCAAAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40907 original size:41 final size:41
Alignment explanation
Indices: 40826--40913 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 41
40816 GAACTCTCAA
* * *
40826 TTTTTCCTAAAGCTCCCTTTGTGGGTTTTCACTCTGAGTTT
1 TTTTTCCTAAAGCGCCCTTTGCGGGTTTTCACTCTAAGTTT
*
40867 TTTTTACCTAGAGCGCCCTTTGCGGGTTTTCACT-TAAGTTT
1 TTTTT-CCTAAAGCGCCCTTTGCGGGTTTTCACTCTAAGTTT
40908 TTTTTC
1 TTTTTC
40914 TTTTTTTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 1 0.02
41 16 0.38
42 25 0.60
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (41 bp):
TTTTTCCTAAAGCGCCCTTTGCGGGTTTTCACTCTAAGTTT
Found at i:50874 original size:6 final size:6
Alignment explanation
Indices: 50855--50891 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
50845 CCTTTTTCAG
*
50855 AAAATA AAATTA AAAATA AAAATAA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA
50892 GTTAAGGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:50882 original size:13 final size:13
Alignment explanation
Indices: 50855--50891 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
50845 CCTTTTTCAG
*
50855 AAAAT-AAAATTA
1 AAAATAAAAATAA
50867 AAAATAAAAATAA
1 AAAATAAAAATAA
50880 AAAATAAAAATA
1 AAAATAAAAATA
50892 GTTAAGGTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:52240 original size:28 final size:27
Alignment explanation
Indices: 52195--52258 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
52185 AAAATAAATA
52195 TATAATAT-AATATATTTTCCAAAAAC
1 TATAATATAAATATATTTTCCAAAAAC
* ***
52221 TATAATATAACATATTTTTTTTTAAAAC
1 TATAATATAA-ATATATTTTCCAAAAAC
52249 TATTAATATA
1 TA-TAATATA
52259 CTTAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 8 0.26
27 1 0.03
28 15 0.48
29 7 0.23
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (27 bp):
TATAATATAAATATATTTTCCAAAAAC
Found at i:52296 original size:27 final size:26
Alignment explanation
Indices: 52266--52325 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
52256 ATACTTAAAA
* *
52266 ATATATTATATATTTTTTTCAAAAATT
1 ATATATTATATA-TATTTTCAAAAACT
*
52293 ATATAATATATATATTTTCAAAAACT
1 ATATATTATATATATTTTCAAAAACT
52319 ATATATT
1 ATATATT
52326 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATATTATATATATTTTCAAAAACT
Done.