Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003770.1 Hibiscus syriacus cultivar Beakdansim tig00008074_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: 62981
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:6105 original size:26 final size:27
Alignment explanation
Indices: 6050--6127 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
6040 ATTTGATTTT
* *
6050 AATTTTAATATCAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
6075 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
6101 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
6127 A
1 A
6128 TTTTTAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
24 15 0.33
25 5 0.11
26 17 0.38
27 1 0.02
28 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:6128 original size:40 final size:36
Alignment explanation
Indices: 6080--6162 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 36
6070 AAATAAATTA
*
6080 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAA-TTTTTAA-A-TAAATTA-A-ATATTAATTTTT
6120 AATATTAATTTTTAAATAAATTAAATATTAATTTTT
1 AATATTAATTTTTAAATAAATTAAATATTAATTTTT
6156 AATATTA
1 AATATTA
6163 TATTATAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 7 0.17
36 12 0.29
37 6 0.15
38 1 0.02
39 7 0.17
40 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
AATATTAATTTTTAAATAAATTAAATATTAATTTTT
Found at i:6161 original size:62 final size:64
Alignment explanation
Indices: 6034--6188 Score: 248
Period size: 62 Copynumber: 2.5 Consensus size: 64
6024 ATATTAATTT
*
6034 TATTATATT-T-GATTTTAATTTTAATATCAATTTTTTAAATAAATTAAATATTAATTTTTTAA
1 TATTATATTATAGATATTAATTTTAATATCAATTTTTTAAATAAATTAAATATTAATTTTTTAA
*
6096 TATTATATTATAGATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAA-TTTTTAA
1 TATTATATTATAGATATTAATTTTAATATCAATTTTTTAAATAAATTAAATATTAATTTTTTAA
6158 TATTATATTATAGATATTTAATTTT-ATATCA
1 TATTATATTATAGATA-TTAATTTTAATATCA
6189 TATAAATTAT
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
62 37 0.43
63 32 0.37
64 18 0.21
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (64 bp):
TATTATATTATAGATATTAATTTTAATATCAATTTTTTAAATAAATTAAATATTAATTTTTTAA
Found at i:6238 original size:20 final size:19
Alignment explanation
Indices: 6178--6239 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
6168 TAGATATTTA
*
6178 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
6197 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
6215 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
6235 ATTTT
1 ATTTT
6240 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:6453 original size:19 final size:19
Alignment explanation
Indices: 6433--6473 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
6423 AAATAAAAAT
6433 AATCATAAAATAATTTTATA
1 AATCATAAAAT-ATTTTATA
* *
6453 AATTATAAAATATTTTCTA
1 AATCATAAAATATTTTATA
6472 AA
1 AA
6474 AATATCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AATCATAAAATATTTTATA
Found at i:6730 original size:31 final size:31
Alignment explanation
Indices: 6693--6752 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6683 TAGTTGTATG
* *
6693 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
6724 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
6753 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:32870 original size:14 final size:14
Alignment explanation
Indices: 32853--32879 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32843 TTTATTATAA
32853 TTATATTTTTATTT
1 TTATATTTTTATTT
32867 TTATATTTTTATT
1 TTATATTTTTATT
32880 ACAGTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATATTTTTATTT
Found at i:36458 original size:16 final size:16
Alignment explanation
Indices: 36437--36468 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
36427 TTTTGCTTCT
36437 GGAACACATTCAATTA
1 GGAACACATTCAATTA
36453 GGAACACATTCAATTA
1 GGAACACATTCAATTA
36469 AAGACATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
GGAACACATTCAATTA
Found at i:37800 original size:28 final size:28
Alignment explanation
Indices: 37760--37818 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
37750 GTGATAATAT
37760 GGCGTATCTTTTAAGCTTCTGGTTCAAA
1 GGCGTATCTTTTAAGCTTCTGGTTCAAA
37788 GGCGTATCTTTTAAGCTTCTGGTTCAAA
1 GGCGTATCTTTTAAGCTTCTGGTTCAAA
37816 GGC
1 GGC
37819 TTAAACGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (28 bp):
GGCGTATCTTTTAAGCTTCTGGTTCAAA
Found at i:41731 original size:29 final size:29
Alignment explanation
Indices: 41697--41755 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
41687 CCTAAATTAA
41697 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
41726 TTTGATGTCATTTCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
41755 T
1 T
41756 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:45894 original size:16 final size:16
Alignment explanation
Indices: 45873--45914 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
45863 GCTGATTATG
45873 CAGGAGATCATGACAC
1 CAGGAGATCATGACAC
45889 CAGGAGATCATGACAC
1 CAGGAGATCATGACAC
45905 CAGGAGATCA
1 CAGGAGATCA
45915 ACAACTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (16 bp):
CAGGAGATCATGACAC
Found at i:46431 original size:29 final size:29
Alignment explanation
Indices: 46395--46453 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
46385 CATAAATTAA
46395 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
46424 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
46453 T
1 T
46454 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:48695 original size:21 final size:20
Alignment explanation
Indices: 48655--48696 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
48645 CCAACTTACA
*
48655 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
48675 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
48696 A
1 A
48697 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:53371 original size:21 final size:21
Alignment explanation
Indices: 53345--53389 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53335 ATGATTTGGG
* *
53345 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
53366 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
53387 CAA
1 CAA
53390 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:54317 original size:30 final size:31
Alignment explanation
Indices: 54254--54337 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
54244 AGGGTCGAGG
*
54254 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
54285 GTTTACCTATGTTCTTCGGAACATAT-GACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
54315 GTTTACCTATG-TCTTCGGAACAT
1 GTTTACCTATGTTCTTCGGAACAT
54338 TGTTACGGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 12 0.23
30 15 0.29
31 25 0.48
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:57443 original size:21 final size:21
Alignment explanation
Indices: 57417--57461 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57407 GATTTATGGG
* *
57417 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
57438 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
57459 CAA
1 CAA
57462 ACAACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:57832 original size:18 final size:16
Alignment explanation
Indices: 57811--57850 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
57801 TGATTATACG
57811 TATATGAATGACATGAAT
1 TATATGAATG-CATG-AT
*
57829 TATATGTATGCATGAT
1 TATATGAATGCATGAT
57845 TATATG
1 TATATG
57851 TGTTAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (16 bp):
TATATGAATGCATGAT
Found at i:57848 original size:16 final size:18
Alignment explanation
Indices: 57811--57851 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
57801 TGATTATACG
*
57811 TATATGAATGACATGAAT
1 TATATGTATGACATGAAT
57829 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
57845 TATATGT
1 TATATGT
57852 GTTAACATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:58359 original size:31 final size:31
Alignment explanation
Indices: 58321--58475 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
58311 AGGGTCGAGG
*
58321 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
58352 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
58383 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
58414 GTTTACCTATGTCCTTCGGGA-ATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
58444 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
58475 G
1 G
58476 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 25 0.22
31 88 0.78
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:61125 original size:6 final size:6
Alignment explanation
Indices: 61114--61150 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
61104 GTAATATTAT
61114 ATTCTG ATTCTGAG ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCT--G ATTCTG ATTCTG ATTCTG ATTCT
61151 CATCCAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 23 0.79
8 6 0.21
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
ATTCTG
Done.