Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007546.1 Hibiscus syriacus cultivar Beakdansim tig00021148_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: 86152
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4711 original size:17 final size:19
Alignment explanation
Indices: 4683--4717 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4673 TCAAATGAAA
4683 TAAAGAAGATAAA-AAAAG
1 TAAAGAAGATAAAGAAAAG
4701 TAAAG-AGATAAAGAAAA
1 TAAAGAAGATAAAGAAAA
4718 ATAATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (19 bp):
TAAAGAAGATAAAGAAAAG
Found at i:19396 original size:13 final size:13
Alignment explanation
Indices: 19378--19404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19368 AAATTCATGA
19378 GAATTTCTCGTAT
1 GAATTTCTCGTAT
19391 GAATTTCTCGTAT
1 GAATTTCTCGTAT
19404 G
1 G
19405 GATTATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (13 bp):
GAATTTCTCGTAT
Found at i:25783 original size:2 final size:2
Alignment explanation
Indices: 25776--25806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25766 ATTTTTATTT
25776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25807 TCTTTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25859 original size:37 final size:34
Alignment explanation
Indices: 25818--25936 Score: 98
Period size: 39 Copynumber: 3.3 Consensus size: 34
25808 CTTTTTTCTC
25818 AAAACATTTTTGACAAAGTATAATATATAATTTTCAG
1 AAAACATTTTTGA-AAA-TATAATATATAATTTTC-G
* *
25855 AAAACGGTTTTTTGAAAATATATATTGTATAATTTT-G
1 AAAAC--ATTTTTGAAAATATA-A-TATATAATTTTCG
* *
25892 AAAACATTTTT-AAAAAATATATAATATATAGTTTCG
1 AAAACATTTTTGAAAATATA-AT-ATATA-ATTTTCG
25928 AAAACATTT
1 AAAACATTT
25937 ATATGTTATA
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
33 1 0.01
34 13 0.19
35 9 0.13
36 10 0.14
37 15 0.22
38 4 0.06
39 17 0.25
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (34 bp):
AAAACATTTTTGAAAATATAATATATAATTTTCG
Found at i:25979 original size:39 final size:37
Alignment explanation
Indices: 25927--26018 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 37
25917 ATATAGTTTC
* *
25927 GAAAACATTTATATGTTATATAGTTTTTAAAAGTCATTTT
1 GAAAA-ATATATATGATATATAGTTTTTAAAA--CATTTT
*
25967 GAAAAATATATATAATATATAGTTTTTAAAACATTTT
1 GAAAAATATATATGATATATAGTTTTTAAAACATTTT
26004 -AAAAATTATATATGA
1 GAAAAA-TATATATGA
26019 AAACATTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 5 0.11
37 14 0.30
39 23 0.49
40 5 0.11
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
GAAAAATATATATGATATATAGTTTTTAAAACATTTT
Found at i:26110 original size:34 final size:34
Alignment explanation
Indices: 26012--26111 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
26002 TTAAAAATTA
26012 TATATGAAAACATTTTGAAAAT-TATA-ATATATAGT
1 TATAT-AAAACATTTTGAAAATATATATA-ATATA-T
* *
26047 TTTA-AAAACATTTTTGAAAACAT-T-T-ATATAT
1 TATATAAAACA-TTTTGAAAATATATATAATATAT
*
26078 TATATAAGACATTTTGAAAATATATATAATATAT
1 TATATAAAACATTTTGAAAATATATATAATATAT
26112 ACTTTTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
31 15 0.28
32 11 0.21
33 7 0.13
34 16 0.30
35 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (34 bp):
TATATAAAACATTTTGAAAATATATATAATATAT
Found at i:26134 original size:40 final size:39
Alignment explanation
Indices: 26089--26239 Score: 137
Period size: 38 Copynumber: 3.9 Consensus size: 39
26079 ATATAAGACA
*
26089 TTTTGAAAATATATATAATATATACTTTTTAAAAAAATAT
1 TTTTGAAAATATATATAATATATA-TTTTTAAAAAAACAT
** * * * *
26129 TTTTGAAGTTATATATATTGTATATTTTT-TAAAAACGT
1 TTTTGAAAATATATATAATATATATTTTTAAAAAAACAT
* * *
26167 TTCTGAAAATACATATAATATATAGTTTTAAAAAAAACA-
1 TTTTGAAAATATATATAATATATA-TTTTTAAAAAAACAT
* * *
26206 TTTTGAAAAGT-TATATATTATATGTTTTTGAAAA
1 TTTTGAAAA-TATATATAATATATATTTTTAAAAA
26240 CTTTTTATAT
Statistics
Matches: 86, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
38 32 0.37
39 27 0.31
40 27 0.31
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
TTTTGAAAATATATATAATATATATTTTTAAAAAAACAT
Found at i:36089 original size:23 final size:23
Alignment explanation
Indices: 36063--36107 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
36053 TCACAAACAT
**
36063 GTTCGTTTGGTATTAGTTTATAC
1 GTTCGTTTAATATTAGTTTATAC
*
36086 GTTCGTTTAATATTCGTTTATA
1 GTTCGTTTAATATTAGTTTATA
36108 TCTTCACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (23 bp):
GTTCGTTTAATATTAGTTTATAC
Found at i:53786 original size:28 final size:28
Alignment explanation
Indices: 53718--53822 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 28
53708 ATATAATCAA
53718 TTATATTATAATAATATA-AGATATTATATTTT
1 TTATATT-TAATAATATATA-ATA--AT-TTTT
53750 TTAT-TTTAATAATATATAATAATTTTT
1 TTATATTTAATAATATATAATAATTTTT
53777 TTATATTTAATAATGA-ATAAT-ATTATTT
1 TTATATTTAATAAT-ATATAATAATT-TTT
* *
53805 ATATATTTAA-AACATATA
1 TTATATTTAATAATATATA
53823 CTAGTAAAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
26 1 0.02
27 16 0.24
28 28 0.42
29 1 0.02
30 13 0.20
31 3 0.05
32 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (28 bp):
TTATATTTAATAATATATAATAATTTTT
Found at i:53848 original size:23 final size:23
Alignment explanation
Indices: 53807--53868 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
53797 TATTATTTAT
*
53807 ATATTTAAAACATATACTAGTAAAG
1 ATATTT-AAA-ATATACTAATAAAG
* *
53832 ATATTTAAAATATACTAATTAAT
1 ATATTTAAAATATACTAATAAAG
*
53855 ATTTTTAAAATATA
1 ATATTTAAAATATA
53869 ATATAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.73
24 3 0.09
25 6 0.18
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATTTAAAATATACTAATAAAG
Found at i:54196 original size:29 final size:30
Alignment explanation
Indices: 54159--54231 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
54149 TTCTAGAAAT
54159 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
54188 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
54218 GTAATTCATTTTCC
1 GTAATTCATTTTCC
54232 GGAAAACTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:54231 original size:15 final size:15
Alignment explanation
Indices: 54159--54231 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
54149 TTCTAGAAAT
54159 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
54174 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
54188 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
54203 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
54218 GTAATTCATTTTCC
1 GTAATTCATTTTCC
54232 GGAAAACTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:67757 original size:45 final size:47
Alignment explanation
Indices: 67691--67804 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 47
67681 CCACGTAGGG
* * * *
67691 TATAGCGCGGATCAAGTACCGC-GCTATACC-TCCTG-CATAATTTTA
1 TATAGCGCGGGTCAGGTACCGCAAC-ATACCTTACTGACATAATTTTA
*
67736 TATAGTGCGGGTCAGGTACCGCAACATACCTTTACTGACATAATTTTA
1 TATAGCGCGGGTCAGGTACCGCAACATACC-TTACTGACATAATTTTA
*
67784 TATAGCGCGGGGCAGGTACCG
1 TATAGCGCGGGTCAGGTACCG
67805 TGTTTTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
45 24 0.41
46 1 0.02
47 4 0.07
48 29 0.50
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (47 bp):
TATAGCGCGGGTCAGGTACCGCAACATACCTTACTGACATAATTTTA
Found at i:68555 original size:45 final size:47
Alignment explanation
Indices: 68460--68557 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 47
68450 ATGCCCCGCA
* *
68460 CTATATAAAATTATGTCAGTAAAGGTATGTCGCGGTACCTGACTCGCG
1 CTATATAAAATTATGTCAG-AAAGATATGTCGCGGTACCTAACTCGCG
*
68508 CTATATAAAATTATG-CAG-GAGATATAGT-GCGGTACCTAA-TCTGCG
1 CTATATAAAATTATGTCAGAAAGATAT-GTCGCGGTACCTAACTC-GCG
68553 CTATA
1 CTATA
68558 CCCCTACGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 2 0.04
45 23 0.51
46 2 0.04
47 3 0.07
48 15 0.33
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (47 bp):
CTATATAAAATTATGTCAGAAAGATATGTCGCGGTACCTAACTCGCG
Found at i:68673 original size:50 final size:49
Alignment explanation
Indices: 68590--68688 Score: 112
Period size: 50 Copynumber: 2.0 Consensus size: 49
68580 CTACAGGGGC
* * * *
68590 CGCGCTATACCCACGTAGTGTCAACTCACCGTATAGCGCGGTGCAGGGA
1 CGCGCTATACCCACGTAGTGCCAACTCAACGTATAACGCGATGCAGGGA
*
68639 CGCGCTATACCCCACGT-GTTGCC-ACATCAACGTATAACGCGATGTAGGGA
1 CGCGCTATA-CCCACGTAG-TGCCAAC-TCAACGTATAACGCGATGCAGGGA
68689 ATGCGCTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
49 12 0.29
50 30 0.71
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.19
Consensus pattern (49 bp):
CGCGCTATACCCACGTAGTGCCAACTCAACGTATAACGCGATGCAGGGA
Found at i:68943 original size:2 final size:2
Alignment explanation
Indices: 68936--68967 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
68926 TTCTCCATTC
68936 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
68968 TACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70848 original size:9 final size:9
Alignment explanation
Indices: 70834--70858 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
70824 TAAATTGTAA
70834 AAAAAATAT
1 AAAAAATAT
70843 AAAAAATAT
1 AAAAAATAT
70852 AAAAAAT
1 AAAAAAT
70859 GCAAGACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:77763 original size:6 final size:6
Alignment explanation
Indices: 77752--77788 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
77742 CGCGCGGGAT
*
77752 ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
77789 GCCGAGCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:81832 original size:6 final size:6
Alignment explanation
Indices: 81821--82005 Score: 370
Period size: 6 Copynumber: 30.8 Consensus size: 6
81811 CACGTATTAT
81821 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
81869 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
81917 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
81965 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
82006 GCCGAGCCAC
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 179 1.00
ACGTcount: A:0.34, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:82013 original size:5 final size:5
Alignment explanation
Indices: 82003--82083 Score: 81
Period size: 5 Copynumber: 15.8 Consensus size: 5
81993 ACCACGACCA
* *
82003 CGAGC CGAGCC ACGAGC CGAGC CGAGC CGAGC CGAGC CGAGA CGAGA CGAGC
1 CGAGC CGAG-C -CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* * * * *
82055 CGAGA CGAGA CGAGA CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
82084 ACGGACGGCG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
5 65 0.92
6 2 0.03
7 4 0.06
ACGTcount: A:0.30, C:0.31, G:0.40, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:82084 original size:5 final size:5
Alignment explanation
Indices: 82014--82090 Score: 93
Period size: 5 Copynumber: 15.6 Consensus size: 5
82004 GAGCCGAGCC
* * * * * *
82014 ACGAG CCGAG CCGAG CCGAG CCGAG CCGAG ACGAG ACGAG CCGAG ACGAG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG
82064 ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACG
82091 GCGGCGGCGG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
4 4 0.06
5 64 0.94
ACGTcount: A:0.31, C:0.29, G:0.40, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:82086 original size:15 final size:15
Alignment explanation
Indices: 82002--82083 Score: 110
Period size: 15 Copynumber: 5.3 Consensus size: 15
81992 GACCACGACC
82002 ACGAGCCGAGCCACGAG
1 ACGAGCCGAG--ACGAG
* *
82019 CCGAGCCGAGCCGAG
1 ACGAGCCGAGACGAG
*
82034 CCGAGCCGAGACGAG
1 ACGAGCCGAGACGAG
82049 ACGAGCCGAGACGAG
1 ACGAGCCGAGACGAG
*
82064 ACGAGACGAGACGAG
1 ACGAGCCGAGACGAG
82079 ACGAG
1 ACGAG
82084 ACGGACGGCG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
15 51 0.85
17 9 0.15
ACGTcount: A:0.30, C:0.30, G:0.39, T:0.00
Consensus pattern (15 bp):
ACGAGCCGAGACGAG
Found at i:85643 original size:31 final size:30
Alignment explanation
Indices: 85608--85702 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
85598 ATTATATGAT
85608 ATTATTTTATTATATTCTTTAATTATTAAAA
1 ATTATTTTATTATA-TCTTTAATTATTAAAA
*** * *
85639 ATTATAAAATAATAT-TTTAAATA-TAAAA
1 ATTATTTTATTATATCTTTAATTATTAAAA
*
85667 TATTATTTTATTGA-ATCTTTTGATTATTAAAA
1 -ATTATTTTATT-ATATC-TTTAATTATTAAAA
85699 ATTA
1 ATTA
85703 CAAAATTATT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 5 0.10
29 16 0.33
30 2 0.04
31 20 0.42
32 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTATTTTATTATATCTTTAATTATTAAAA
Found at i:86103 original size:60 final size:60
Alignment explanation
Indices: 86008--86121 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
85998 TAATCAAGTT
* * * * * *
86008 ATTATTTTATAATTTTTAATATTTAAAAGACTTAATAAATTAATATCTTATAATTAAAAG
1 ATTATTTTATAAATTTTAATAGTTAAAAGAATTAATAAAATAACACCTTATAATTAAAAG
** *
86068 ATTATTTTATAAATTTTAATAGTTATGATAATTAATAAAATAACACCTTATAAT
1 ATTATTTTATAAATTTTAATAGTTAAAAGAATTAATAAAATAACACCTTATAAT
86122 ATAAGTATCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (60 bp):
ATTATTTTATAAATTTTAATAGTTAAAAGAATTAATAAAATAACACCTTATAATTAAAAG
Done.