Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001616.1 Hibiscus syriacus cultivar Beakdansim tig00003209_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: 59648
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:303 original size:21 final size:21
Alignment explanation
Indices: 215--309 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
205 ATATGGTATA
*
215 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
236 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
257 AA-CCTGGCGGGCTAGGAATTT
1 AACCCT-GCGGGCTAGGAATGT
*
278 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
299 AACCCCTGCGG
1 AA-CCCTGCGG
310 AATGGCATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
20 3 0.04
21 53 0.79
22 11 0.16
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:338 original size:21 final size:21
Alignment explanation
Indices: 312--359 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
302 CCCTGCGGAA
*
312 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
333 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
354 GGGCAT
1 TGGCAT
360 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2093 original size:32 final size:32
Alignment explanation
Indices: 2057--2176 Score: 76
Period size: 32 Copynumber: 3.8 Consensus size: 32
2047 ATTAGCAAAA
2057 AAATAATAATTCTAAATAAATAATAATTATAT
1 AAATAATAATTCTAAATAAATAATAATTATAT
* *
2089 AAAT-AT-ATTTTAATAATAAAATAAT-ATTACAT
1 AAATAATAATTCT-A-AAT-AAATAATAATTATAT
* * *
2121 AAATATATTAA-TATAAA-AAATAATAACTATTT
1 AAATA-A-TAATTCTAAATAAATAATAATTATAT
*
2153 AAA-AA-AATACTAACATAAA-AATAA
1 AAATAATAATTCTAA-ATAAATAATAA
2177 ATTTCTTACC
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
28 2 0.03
29 3 0.04
30 11 0.16
31 14 0.20
32 24 0.35
33 9 0.13
34 2 0.03
35 3 0.04
36 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (32 bp):
AAATAATAATTCTAAATAAATAATAATTATAT
Found at i:2132 original size:30 final size:32
Alignment explanation
Indices: 2069--2145 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
2059 ATAATAATTC
*
2069 TAAATAAATAATAATTATATAAATATATTTTAATA
1 TAAA-AAATAAT-ATTACATAAATATA-TTTAATA
*
2104 -ATAAAATAATATTACATAAATATA-TTAATA
1 TAAAAAATAATATTACATAAATATATTTAATA
2134 TAAAAAATAATA
1 TAAAAAATAATA
2146 ACTATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 6 0.16
31 10 0.26
32 13 0.34
33 7 0.18
34 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATATTACATAAATATATTTAATA
Found at i:2787 original size:7 final size:7
Alignment explanation
Indices: 2775--2800 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2765 AACAGCTACA
2775 TTACAAT
1 TTACAAT
2782 TTACAAT
1 TTACAAT
2789 TTACAAT
1 TTACAAT
2796 TTACA
1 TTACA
2801 CACATCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (7 bp):
TTACAAT
Found at i:6918 original size:37 final size:39
Alignment explanation
Indices: 6860--6944 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 39
6850 TCCCATTATC
*
6860 ATTTTTC-AACAAACATCTACCAAACTTTGAA-A-AATT
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAACATAATT
* *
6896 ATTTTTCAAAGAAACATTTACCAAACTTTGAACATCATT
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAACATAATT
6935 -TTTTTCAAAG
1 ATTTTTCAAAG
6945 TTGGTTGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 7 0.16
37 22 0.51
38 11 0.26
39 3 0.07
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (39 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAACATAATT
Found at i:7022 original size:23 final size:23
Alignment explanation
Indices: 6992--7038 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
6982 TTAAAAACTG
6992 ATTTTTTTCAACATGTCTGCCAA
1 ATTTTTTTCAACATGTCTGCCAA
7015 ATTTTTTTCAACATGTCTGCCAA
1 ATTTTTTTCAACATGTCTGCCAA
7038 A
1 A
7039 CTTTGAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (23 bp):
ATTTTTTTCAACATGTCTGCCAA
Found at i:17768 original size:22 final size:22
Alignment explanation
Indices: 17736--17799 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
17726 AGGGGTAGAA
17736 TTGAAAT-GTTTAAAAATTAAT
1 TTGAAATAGTTTAAAAATTAAT
* *
17757 TT-ATAATAGTTTAAAGATAAAT
1 TTGA-AATAGTTTAAAAATTAAT
17779 TTGAAATA-TTTAAAAACTTAA
1 TTGAAATAGTTTAAAAA-TTAA
17800 AGACCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 21 0.60
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (22 bp):
TTGAAATAGTTTAAAAATTAAT
Found at i:21088 original size:12 final size:14
Alignment explanation
Indices: 21071--21107 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
21061 AGAAATGGAT
21071 GCTGCTGCAAA-A-
1 GCTGCTGCAAAGAG
21083 GCTGCTGCACAAGAG
1 GCTGCTGCA-AAGAG
21098 GCTGCTGCAA
1 GCTGCTGCAA
21108 GGAGTGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (14 bp):
GCTGCTGCAAAGAG
Found at i:23269 original size:29 final size:29
Alignment explanation
Indices: 23204--23270 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
23194 TTTTATGTTG
* ***
23204 AAAAACGAATTTAAATTTATAAAATTTTA
1 AAAAACGAATTTAAAGTTATAAAATAAAA
** *
23233 AAGGACGAATTTGAAGTTATAAAATAAAA
1 AAAAACGAATTTAAAGTTATAAAATAAAA
23262 AAAAACGAA
1 AAAAACGAA
23271 AATATAATTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.27
Consensus pattern (29 bp):
AAAAACGAATTTAAAGTTATAAAATAAAA
Found at i:29674 original size:51 final size:50
Alignment explanation
Indices: 29598--30056 Score: 575
Period size: 51 Copynumber: 9.0 Consensus size: 50
29588 ACATTAACAT
*
29598 CTGTTGTGGTAGCTGAGTATATGTTTGGGAACCAATTTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
* * * *
29649 CTGTTGTGGTAGTAGAGTAAATGTTT-GGATATCAATGTTTCCAACTTGCTT
1 CTGTTGTGGTAGT-GAGTATATGTTTGGGA-ACCAATGTTTCCACCTTGCTG
* *
29700 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCATTGTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
* * *
29751 CTGATGTGGTAGCAGAGTATATGTTTGGGAA-TATATGTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCA-ATGTTTCCACCTTGCTG
* * *
29802 CTGTTGTGGTAGCTGAGAATATGTTTGGGATCCATTGTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
* * *
29853 CTGATGTGGTAGCAGAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
*
29904 CTGTTGTGGTAGATGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
* * *
29955 CTGTTGCGGTAGCTGAGTATATGTTTGGGATCCAAAGTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
* *
30006 CTGTTGAGGTAGTTGAGTATATGTTTGGG-ACTTCGA-GTTTCCACCTTGCTG
1 CTGTTGTGGTAG-TGAGTATATGTTTGGGAAC--CAATGTTTCCACCTTGCTG
30057 AGTCTGCGCC
Statistics
Matches: 360, Mismatches: 40, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
50 6 0.02
51 347 0.96
52 7 0.02
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (50 bp):
CTGTTGTGGTAGTGAGTATATGTTTGGGAACCAATGTTTCCACCTTGCTG
Found at i:29775 original size:102 final size:102
Alignment explanation
Indices: 29598--30056 Score: 678
Period size: 102 Copynumber: 4.5 Consensus size: 102
29588 ACATTAACAT
* * *
29598 CTGTTGTGGTAGCTGAGTATATGTTTGGGAACCAATT-TTTCCACCTTGCTGCTGTTGTGGTAGT
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCC-ATTGTTTCCACCTTGCTGCTGATGTGGTAGC
* * *
29662 AGAGTAAATGTTT-GGATATCAATGTTTCCAACTTGCTT
65 AGAGTATATGTTTGGGA-ATCAATGTTTCCACCTTGCTG
29700 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCATTGTTTCCACCTTGCTGCTGATGTGGTAGCA
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCATTGTTTCCACCTTGCTGCTGATGTGGTAGCA
29765 GAGTATATGTTTGGGAAT-ATATGTTTCCACCTTGCTG
66 GAGTATATGTTTGGGAATCA-ATGTTTCCACCTTGCTG
*
29802 CTGTTGTGGTAGCTGAGAATATGTTTGGGATCCATTGTTTCCACCTTGCTGCTGATGTGGTAGCA
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCATTGTTTCCACCTTGCTGCTGATGTGGTAGCA
29867 GAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTG
66 GAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTG
* * * * *
29904 CTGTTGTGGTAGATGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGCTGTTGCGGTAGCT
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCATTGTTTCCACCTTGCTGCTGATGTGGTAGCA
*
29969 GAGTATATGTTTGGG-ATCCAAAGTTTCCACCTTGCTG
66 GAGTATATGTTTGGGAAT-CAATGTTTCCACCTTGCTG
* * *
30006 CTGTTGAGGTAGTTGAGTATATGTTTGGGACTTCGA--GTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGA--TCCATTGTTTCCACCTTGCTG
30057 AGTCTGCGCC
Statistics
Matches: 333, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
101 6 0.02
102 320 0.96
103 4 0.01
104 3 0.01
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (102 bp):
CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCATTGTTTCCACCTTGCTGCTGATGTGGTAGCA
GAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTG
Found at i:30718 original size:3 final size:3
Alignment explanation
Indices: 30704--30733 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30694 GATTCAACGA
*
30704 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30734 TCCACAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:34669 original size:18 final size:18
Alignment explanation
Indices: 34646--34690 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
34636 GTATCTCCGC
34646 TAGAGTGTCAAGTACAAA
1 TAGAGTGTCAAGTACAAA
34664 TAGAGTGTCAAGTACAAA
1 TAGAGTGTCAAGTACAAA
34682 TAGAGTGTC
1 TAGAGTGTC
34691 CTGTTTAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
TAGAGTGTCAAGTACAAA
Found at i:39797 original size:16 final size:16
Alignment explanation
Indices: 39776--39825 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
39766 AATAAATAAA
39776 TTTAAATTTATAAAAC
1 TTTAAATTTATAAAAC
*
39792 TTTAAAATTAT-AAAC
1 TTTAAATTTATAAAAC
*
39807 -TTAAATTTATAAAAT
1 TTTAAATTTATAAAAC
39822 TTTA
1 TTTA
39826 TGAGATGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 9 0.31
15 7 0.24
16 13 0.45
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAAATTTATAAAAC
Found at i:39816 original size:14 final size:14
Alignment explanation
Indices: 39771--39819 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
39761 GTTAGAATAA
*
39771 ATAAATTTAAATTT
1 ATAAACTTAAATTT
*
39785 ATAAAACTTTAAAATT
1 AT-AAAC-TTAAATTT
39801 ATAAACTTAAATTT
1 ATAAACTTAAATTT
39815 ATAAA
1 ATAAA
39820 ATTTTATGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 14 0.47
15 7 0.23
16 9 0.30
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAACTTAAATTT
Found at i:40205 original size:21 final size:21
Alignment explanation
Indices: 40179--40223 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40169 AAATTATAAA
* * * *
40179 TTTTATTATTCAATTTTCTTT
1 TTTTATCATTAAAATTTATTT
40200 TTTTATCATTAAAATTTATTT
1 TTTTATCATTAAAATTTATTT
40221 TTT
1 TTT
40224 ACTTTGTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATCATTAAAATTTATTT
Found at i:49435 original size:29 final size:29
Alignment explanation
Indices: 49394--49458 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
49384 GAGGAGCAGG
49394 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
49423 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
49452 CGGAGTG
1 AGGAGTG
49459 GCGACCTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:49466 original size:25 final size:27
Alignment explanation
Indices: 49402--49466 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
49392 GGAGGAGTGC
49402 ATGGCGACCTACAAGGTCGCCAGGAGTG
1 ATGGCGACCTACAAGGTCGCCAGGAG-G
*
49430 CATGGCGACCTACAAGGTCGCCCGGA-G
1 -ATGGCGACCTACAAGGTCGCCAGGAGG
49457 -TGGCGACCTA
1 ATGGCGACCTA
49467 TGCTGGGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 10 0.29
27 1 0.03
29 24 0.69
ACGTcount: A:0.23, C:0.29, G:0.34, T:0.14
Consensus pattern (27 bp):
ATGGCGACCTACAAGGTCGCCAGGAGG
Found at i:54761 original size:21 final size:21
Alignment explanation
Indices: 54737--54801 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
54727 AGCAAAATTA
*
54737 TGCATCGATGCACTGCTACAG
1 TGCATCGATGTACTGCTACAG
54758 TGCATCGATGTACTGCTACAG
1 TGCATCGATGTACTGCTACAG
54779 TGCATCGATGTACTGCTACAG
1 TGCATCGATGTACTGCTACAG
54800 TG
1 TG
54802 ATTTTCGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
TGCATCGATGTACTGCTACAG
Done.