Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006987.1 Hibiscus syriacus cultivar Beakdansim tig00018016_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: 75606
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4193 original size:24 final size:25
Alignment explanation
Indices: 4161--4212 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
4151 GAAGTGAACT
4161 ATTTTAACATTT-T-TTTGTTACAAA
1 ATTTTAACATTTATATTTGTTA-AAA
4185 ATTTTAACATTTATATTTGTTAAAA
1 ATTTTAACATTTATATTTGTTAAAA
4210 ATT
1 ATT
4213 ATGAGTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 12 0.46
25 7 0.27
26 7 0.27
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTTTAACATTTATATTTGTTAAAA
Found at i:4774 original size:19 final size:19
Alignment explanation
Indices: 4750--4787 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4740 GTAGAATAAA
4750 GTTTAATAATACACAAACT
1 GTTTAATAATACACAAACT
*
4769 GTTTAATAATATACAAACT
1 GTTTAATAATACACAAACT
4788 CAACTCAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (19 bp):
GTTTAATAATACACAAACT
Found at i:7582 original size:6 final size:6
Alignment explanation
Indices: 7571--7881 Score: 496
Period size: 6 Copynumber: 51.3 Consensus size: 6
7561 TCAAGATCCC
* * *
7571 ATATGT ATATGT ATATGT ATATGT ATATCAT ATGCATGC ATATGT ATATGC
1 ATATGT ATATGT ATATGT ATATGT ATAT-GT AT--ATGT ATATGT ATATGT
* * * * * * *
7622 ATATGC ATATGC ATATGC ATATGC ATATGC ATATGC ATATGC ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
*
7670 ATATGC ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
7718 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
7766 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
7814 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
7862 ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT AT
7882 GTACGCATGC
Statistics
Matches: 294, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
6 287 0.98
7 3 0.01
8 2 0.01
9 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.46
Consensus pattern (6 bp):
ATATGT
Found at i:17652 original size:2 final size:2
Alignment explanation
Indices: 17645--17674 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17635 AATATTTTTA
17645 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
17675 TAATGGAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20756 original size:18 final size:19
Alignment explanation
Indices: 20727--20764 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
20717 AAGAGATTTG
20727 TTTTGAAGTTTTTCAAAAA
1 TTTTGAAGTTTTTCAAAAA
*
20746 TTTTG-AGTTTTTTAAAAA
1 TTTTGAAGTTTTTCAAAAA
20764 T
1 T
20765 ATATATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTGAAGTTTTTCAAAAA
Found at i:28049 original size:4 final size:4
Alignment explanation
Indices: 28042--28068 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28032 CATACATACA
28042 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
28069 ATATTTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:28211 original size:4 final size:4
Alignment explanation
Indices: 28202--28232 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
28192 AAAGAAGCTT
28202 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
28233 TGTATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:28216 original size:181 final size:180
Alignment explanation
Indices: 27907--28245 Score: 597
Period size: 181 Copynumber: 1.9 Consensus size: 180
27897 ATTTTAGGAG
* *
27907 TATATATATAATAAATCAATAAAGAATAACTAAATCTCCTCCTAGGCATGTTGGTCTTTCCTATT
1 TATATATAGAATAAATCAATAAAGAATAACTAAATCTCCTCCTAGGCATGTTGGTCTTTCCTACT
* *
27972 TTCCTTGTACATTTCTTGATTCAATTAAGAGCTAACTACAAAGAAGCTTATACATATATACATAC
66 TTCCTTGTACACTTCTTGATTCAATTAAGAGCTAACTACAAAGAAGCTTATACATACATACATAC
** **
28037 ATACATATGTATGTATGTATGTATGTATGTATATATTTACTATACATATA
131 ATACATACATACATATGTATGTATGTATGTATATATTTACTATACATATA
28087 TATATATAGAATAAATCAATAAAGAATAACTAAATCTCCTCCTCAGGCATGTTGGTCTTTCCTAC
1 TATATATAGAATAAATCAATAAAGAATAACTAAATCTCCTCCT-AGGCATGTTGGTCTTTCCTAC
28152 TTTCCTTGTACACTTCTTGATTCAATTAAGAGCTAACTACAAAGAAGCTTATACATACATACATA
65 TTTCCTTGTACACTTCTTGATTCAATTAAGAGCTAACTACAAAGAAGCTTATACATACATACATA
28217 CATACATACATACATATGTATGTATGTAT
130 CATACATACATACATATGTATGTATGTAT
28246 ATTCTACATA
Statistics
Matches: 150, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
180 42 0.28
181 108 0.72
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (180 bp):
TATATATAGAATAAATCAATAAAGAATAACTAAATCTCCTCCTAGGCATGTTGGTCTTTCCTACT
TTCCTTGTACACTTCTTGATTCAATTAAGAGCTAACTACAAAGAAGCTTATACATACATACATAC
ATACATACATACATATGTATGTATGTATGTATATATTTACTATACATATA
Found at i:31764 original size:23 final size:23
Alignment explanation
Indices: 31706--31773 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
31696 TTTTCAATAA
31706 CTCTGTCTTTATGACACGTCTTCTT
1 CTCTGTCTTTATGACACGT-TT-TT
31731 -T-TG-CTTCTATGACACGTTTTT
1 CTCTGTCTT-TATGACACGTTTTT
*
31752 CTCTGTCTTTATGACATGTTTT
1 CTCTGTCTTTATGACACGTTTT
31774 CGGTCGTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 2 0.05
22 6 0.16
23 26 0.68
24 4 0.11
ACGTcount: A:0.13, C:0.22, G:0.13, T:0.51
Consensus pattern (23 bp):
CTCTGTCTTTATGACACGTTTTT
Found at i:32925 original size:21 final size:20
Alignment explanation
Indices: 32892--32934 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
32882 TTTTGTCATT
*
32892 ATTTTTTCCGATTTTTCAAG
1 ATTTTTTCCGATTATTCAAG
* *
32912 ATTTTATTCTGATTATTCTAG
1 ATTTT-TTCCGATTATTCAAG
32933 AT
1 AT
32935 AAATCGATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (20 bp):
ATTTTTTCCGATTATTCAAG
Found at i:35179 original size:16 final size:18
Alignment explanation
Indices: 35147--35181 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
35137 ATGTAAAAAC
35147 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
35165 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
35181 A
1 A
35182 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:35815 original size:35 final size:36
Alignment explanation
Indices: 35745--35844 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 36
35735 GTGCTTGTGG
* * *
35745 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
35782 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
* *
35817 ATCATATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
35845 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.47
36 11 0.20
37 18 0.33
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:37305 original size:16 final size:16
Alignment explanation
Indices: 37260--37310 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
37250 AAATTAAAAT
37260 TTTAAGTATTAAAATAA
1 TTTAAGTATT-AAATAA
* *
37277 ATTAA-AATT-AATAA
1 TTTAAGTATTAAATAA
*
37291 TTTAAGTATTAAATAG
1 TTTAAGTATTAAATAA
37307 TTTA
1 TTTA
37311 CCCTTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 9 0.33
15 3 0.11
16 11 0.41
17 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTAAGTATTAAATAA
Found at i:40359 original size:16 final size:16
Alignment explanation
Indices: 40340--40373 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40330 CAATATACAA
40340 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
40356 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
40372 AT
1 AT
40374 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:40446 original size:16 final size:18
Alignment explanation
Indices: 40414--40447 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
40404 TATTAATGTA
40414 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
40432 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
40448 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:41159 original size:128 final size:123
Alignment explanation
Indices: 40912--41165 Score: 361
Period size: 124 Copynumber: 2.0 Consensus size: 123
40902 AATTTTCTTC
* *
40912 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTACACATGTCAGATCCTG
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTACACATGTCAGATCCTA
* *
40977 GTTAAATGATTAATTTATTAAATTTTATTAATTAGGACCAAATTGATAGCATATATAAA
66 ATTAAATGATTAATTTATTAAATTCTATTAATTAGGACCAAATTGATA-CATATATAAA
* * *
41036 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCA--TG-T-ACACATGTCAGAT
41101 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT---TATATAAA
62 CCTAATTAAATGATTAATTTATTAAATTCTA-TTAA-TTAGGACCAAATTGATACATATATAAA
41162 TAAT
1 TAAT
41166 AAAGACTGAA
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
124 41 0.35
126 14 0.12
127 1 0.01
128 41 0.35
129 4 0.03
130 16 0.14
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (123 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTACACATGTCAGATCCTA
ATTAAATGATTAATTTATTAAATTCTATTAATTAGGACCAAATTGATACATATATAAA
Found at i:41600 original size:35 final size:35
Alignment explanation
Indices: 41550--41625 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
41540 AATTGGATTG
* *
41550 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
41585 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
41620 AATTGA
1 AATTGA
41626 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:45314 original size:21 final size:20
Alignment explanation
Indices: 45294--45330 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
45284 TGTGATTTAA
45294 AAAATTATA-TTTAAAAATT
1 AAAATTATATTTTAAAAATT
45313 AAAATTATATTTTAAAAA
1 AAAATTATATTTTAAAAA
45331 ATATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTATATTTTAAAAATT
Found at i:59041 original size:31 final size:31
Alignment explanation
Indices: 58979--59079 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 31
58969 CACATTGTGC
* * *
58979 GAAATAAACAATTTAACGGTTTAGTGGTATAATT
1 GAAATAAA-AA-TTAA-AGTTTAATGATATAATT
*
59013 GAAATAAAAATTAAAGTTTAATGTTATAATT
1 GAAATAAAAATTAAAGTTTAATGATATAATT
* *
59044 G--AT-AAAATTAAAAGCTTAATGATATAAAT
1 GAAATAAAAATT-AAAGTTTAATGATATAATT
*
59073 GATATAA
1 GAAATAA
59080 TGCCTAAAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.11
29 19 0.33
31 17 0.30
32 5 0.09
33 2 0.04
34 8 0.14
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.35
Consensus pattern (31 bp):
GAAATAAAAATTAAAGTTTAATGATATAATT
Found at i:61545 original size:8 final size:8
Alignment explanation
Indices: 61519--61561 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
61509 ACCTGATTGA
61519 CAAAATTT
1 CAAAATTT
61527 CAAAAATATTT
1 C--AAA-ATTT
61538 CAAAATTTT
1 CAAAA-TTT
61547 CAAAATTT
1 CAAAATTT
61555 CAAAATT
1 CAAAATT
61562 GATAGAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 12 0.39
9 11 0.35
10 3 0.10
11 5 0.16
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (8 bp):
CAAAATTT
Found at i:62047 original size:14 final size:14
Alignment explanation
Indices: 62028--62056 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62018 ATAATATTTC
62028 TTTATTTAAACTCA
1 TTTATTTAAACTCA
62042 TTTATTTAAACTCA
1 TTTATTTAAACTCA
62056 T
1 T
62057 CACGTCGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTATTTAAACTCA
Found at i:63531 original size:23 final size:23
Alignment explanation
Indices: 63458--63516 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
63448 TGTGACATGT
63458 TCTATGCCTTTATGACATATTTA
1 TCTATGCCTTTATGACATATTTA
*
63481 TCTATGTCTTTATGACATATTTA
1 TCTATGCCTTTATGACATATTTA
*
63504 TCTCTGCCTTTAT
1 TCTATGCCTTTAT
63517 TGCATGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (23 bp):
TCTATGCCTTTATGACATATTTA
Found at i:64026 original size:23 final size:24
Alignment explanation
Indices: 63997--64043 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
63987 AAAACTAGTT
63997 AATTTCTAT-AAAAAATTGAATTG
1 AATTTCTATAAAAAAATTGAATTG
64020 AATTTCTATAAAAAAATTGAATTG
1 AATTTCTATAAAAAAATTGAATTG
64044 CGATATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
AATTTCTATAAAAAAATTGAATTG
Found at i:64057 original size:24 final size:24
Alignment explanation
Indices: 64001--64060 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
63991 CTAGTTAATT
*
64001 TCTAT-AAAAAATTGAATTGAATT
1 TCTATAAAAAAATTGAATTGAATA
*
64024 TCTATAAAAAAATTGAATTGCGATA
1 TCTATAAAAAAATTGAATTG-AATA
64049 T-TATGAAAAAAA
1 TCTAT-AAAAAAA
64061 AGTAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 17 0.53
25 10 0.31
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (24 bp):
TCTATAAAAAAATTGAATTGAATA
Done.