Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000386.1 Hibiscus syriacus cultivar Beakdansim tig00000710_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: 55068
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:598 original size:12 final size:12
Alignment explanation
Indices: 583--620 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
573 ATGATGTTTT
583 ATTTGATTTCTG
1 ATTTGATTTCTG
*
595 ATTTGAATTCTG
1 ATTTGATTTCTG
607 -TTATGATTTCTG
1 ATT-TGATTTCTG
619 AT
1 AT
621 CTGAATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 19 0.86
13 1 0.05
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.55
Consensus pattern (12 bp):
ATTTGATTTCTG
Found at i:615 original size:24 final size:24
Alignment explanation
Indices: 586--642 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
576 ATGTTTTATT
* *
586 TGATTTCTGATTTGAATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTGA
* *
610 TGATTTCTGATCTGAATTTTGTGC
1 TGATTTCTGATCTGAATTCTGTGA
634 TGATTTCTG
1 TGATTTCTG
643 GTGGATTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.19, T:0.53
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTGA
Found at i:1954 original size:20 final size:19
Alignment explanation
Indices: 1929--1978 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
1919 TAAATTGAAT
1929 TTATTCAAAGTCTTCAAAAA
1 TTATTCAAAGTCTTC-AAAA
1949 TTATTCAAAGTCTTCAAAA
1 TTATTCAAAGTCTTCAAAA
*
1968 TAATTCAAAGT
1 TTATTCAAAGT
1979 GCAAACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (19 bp):
TTATTCAAAGTCTTCAAAA
Found at i:1973 original size:19 final size:20
Alignment explanation
Indices: 1931--1978 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
1921 AATTGAATTT
*
1931 ATTCAAAGTCTTCAAAAATT
1 ATTCAAAGTCTTCAAAAATA
1951 ATTCAAAGTCTTC-AAAATA
1 ATTCAAAGTCTTCAAAAATA
1970 ATTCAAAGT
1 ATTCAAAGT
1979 GCAAACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTCAAAGTCTTCAAAAATA
Found at i:2141 original size:21 final size:20
Alignment explanation
Indices: 2095--2158 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
2085 TGGCTCAAAG
* * * *
2095 GATCGATTCCTTAGCAAAAG
1 GATCGATCCCTTTGAAAAAT
*
2115 GATCGATCCCTTTGACCAAAT
1 GATCGATCCCTTTGA-AAAAT
*
2136 GATCGATCCCCTTGAAAAAT
1 GATCGATCCCTTTGAAAAAT
2156 GAT
1 GAT
2159 TAATCCCTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (20 bp):
GATCGATCCCTTTGAAAAAT
Found at i:2157 original size:20 final size:21
Alignment explanation
Indices: 2109--2158 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2099 GATTCCTTAG
* *
2109 CAAAAGGATCGATCCCTTTGA
1 CAAAATGATCGATCCCCTTGA
*
2130 CCAAATGATCGATCCCCTTGA
1 CAAAATGATCGATCCCCTTGA
2151 -AAAATGAT
1 CAAAATGAT
2159 TAATCCCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (21 bp):
CAAAATGATCGATCCCCTTGA
Found at i:3505 original size:20 final size:19
Alignment explanation
Indices: 3462--3508 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3452 AATAATTTTC
*
3462 TTTTGAAAGTAAAAATGGA
1 TTTTGAAAGTAAAAATGAA
* *
3481 CTTTGAAAGTCAAAATGAAA
1 TTTTGAAAGTAAAAATG-AA
3501 TTTTGAAA
1 TTTTGAAA
3509 AAAGATTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.32
Consensus pattern (19 bp):
TTTTGAAAGTAAAAATGAA
Found at i:5552 original size:24 final size:25
Alignment explanation
Indices: 5509--5560 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5499 TTCGTGGTAT
*
5509 AAAGAAATAAAAGAAATGAAAGGGA
1 AAAGAAATAAAACAAATGAAAGGGA
* *
5534 AAAGAAA-AAAACAATTGAAATGGA
1 AAAGAAATAAAACAAATGAAAGGGA
5558 AAA
1 AAA
5561 TATTGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (25 bp):
AAAGAAATAAAACAAATGAAAGGGA
Found at i:17017 original size:3 final size:3
Alignment explanation
Indices: 17011--17077 Score: 59
Period size: 3 Copynumber: 22.0 Consensus size: 3
17001 TATAATAATA
*
17011 TAT TAT TAT TAAT TA- TAT ATGT TAT TAT TAT TAT TAT TA- TAT TAAT
1 TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT
*
17057 TA- TAT ATAT TAT TAT AAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT
17078 AAATATTACA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
2 6 0.11
3 36 0.68
4 11 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:17039 original size:22 final size:22
Alignment explanation
Indices: 17011--17072 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
17001 TATAATAATA
17011 TATTATTATTAATTA-TATATGT
1 TATTATTATT-ATTATTATATGT
17033 TATTATTATTATTATTATAT-T
1 TATTATTATTATTATTATATGT
*
17054 AATTA-TATATATTATTATA
1 TATTATTAT-TATTATTATA
17073 ATTATAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 3 0.08
21 19 0.51
22 15 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTATTATTATTATTATATGT
Found at i:17058 original size:33 final size:34
Alignment explanation
Indices: 17000--17077 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 34
16990 TTCCAAGTTT
* *
17000 TTATAATAATATATTATTATTAATTATATATGTTA
1 TTATAATTAT-TATTATTATTAATTATATATATTA
*
17035 TTATTATTATTATTA-TATTAATTATATATATTA
1 TTATAATTATTATTATTATTAATTATATATATTA
17068 TTATAATTAT
1 TTATAATTAT
17078 AAATATTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 26 0.67
34 5 0.13
35 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
TTATAATTATTATTATTATTAATTATATATATTA
Found at i:18410 original size:27 final size:28
Alignment explanation
Indices: 18380--18450 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
18370 TCATATAGTT
*
18380 TTAATATTAAATATTATACTAG-AATTA
1 TTAATATTAAATATTAAACTAGTAATTA
* *
18407 TTAATATT-AATATTAAATTAGTCATTA
1 TTAATATTAAATATTAAACTAGTAATTA
*
18434 TTTATATTAAATTATTA
1 TTAATATTAAA-TATTA
18451 GTAAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 11 0.30
27 19 0.51
28 2 0.05
29 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
TTAATATTAAATATTAAACTAGTAATTA
Found at i:21749 original size:24 final size:24
Alignment explanation
Indices: 21717--21772 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
21707 CTATTCTTTC
21717 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
21741 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
21765 GCTTCAAT
1 GCTTCAAT
21773 GGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:29078 original size:24 final size:24
Alignment explanation
Indices: 29020--29082 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
29010 CGTTCGTGAA
*
29020 CGTTCGGTTATGTTCGTTTATATT
1 CGTTCAGTTATGTTCGTTTATATT
* *
29044 CGTTCGGTTATGTTCGTTTATGCTT
1 CGTTCAGTTATGTTCGTTTAT-ATT
*
29069 -GTTCATTTATGTTC
1 CGTTCAGTTATGTTC
29083 ACTGGAGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATT
Found at i:30072 original size:16 final size:16
Alignment explanation
Indices: 30051--30083 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30041 AAAAAAAATT
30051 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
30067 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
30083 T
1 T
30084 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:32720 original size:20 final size:19
Alignment explanation
Indices: 32679--32725 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
32669 AATGATTCTC
*
32679 TTTTGAAAGCAAAATTGGA
1 TTTTGAAAGCAAAATTGAA
32698 TTTTGAAGAGCAAAA-TGAAA
1 TTTTGAA-AGCAAAATTG-AA
32718 TTTTGAAA
1 TTTTGAAA
32726 AATGATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (19 bp):
TTTTGAAAGCAAAATTGAA
Found at i:33804 original size:25 final size:25
Alignment explanation
Indices: 33775--33824 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
33765 TAGGATTGAA
33775 AAATTCAATTTCAAGAATGAAAAAG
1 AAATTCAATTTCAAGAATGAAAAAG
33800 AAATTCAATTTCAAGAATGAAAAAG
1 AAATTCAATTTCAAGAATGAAAAAG
33825 TTGGAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (25 bp):
AAATTCAATTTCAAGAATGAAAAAG
Found at i:34400 original size:21 final size:22
Alignment explanation
Indices: 34360--34401 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
34350 ATTTAAAAAT
*
34360 ATTAAAGGAAGTATCGATACTC
1 ATTAAAGGAAGTACCGATACTC
*
34382 ATTAAAGG-AGTGCCGATACT
1 ATTAAAGGAAGTACCGATACT
34402 ACCTTTCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
ATTAAAGGAAGTACCGATACTC
Found at i:38026 original size:21 final size:20
Alignment explanation
Indices: 37983--38022 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
37973 ATTCCAAATT
37983 TAATAAGGGTATCGATACCC
1 TAATAAGGGTATCGATACCC
*
38003 TAATGAGGGTATCGATACCC
1 TAATAAGGGTATCGATACCC
38023 CTAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (20 bp):
TAATAAGGGTATCGATACCC
Found at i:38539 original size:22 final size:20
Alignment explanation
Indices: 38489--38552 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 20
38479 AGTCGAGGGT
38489 TTCATAGGTCTTCCGGGACAA
1 TTCATAGGTCTT-CGGGACAA
* *
38510 CTCATAGGTCATTTGGGACATA
1 TTCATAGGTC-TTCGGGACA-A
38532 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGT-CTTCGGGACAA
38553 ATTTCATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 16 0.44
22 19 0.53
23 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (20 bp):
TTCATAGGTCTTCGGGACAA
Found at i:47035 original size:41 final size:42
Alignment explanation
Indices: 46989--47083 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 42
46979 TTTTCTTATA
* * *
46989 AAATAAAATAAAATTATATC-AAGTTTGATTATGCTCAATTTT
1 AAATAAAATAAAATAAAATCAAAGTTT-ATTATACTCAATTTT
47031 -AATAATAA-AAAATAAAATCAAAGTTTATTATACTCAATTTT
1 AAATAA-AATAAAATAAAATCAAAGTTTATTATACTCAATTTT
*
47072 AAATAAATTAAA
1 AAATAAAATAAA
47084 TTTAAATCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
41 29 0.64
42 16 0.36
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (42 bp):
AAATAAAATAAAATAAAATCAAAGTTTATTATACTCAATTTT
Found at i:52085 original size:8 final size:8
Alignment explanation
Indices: 52068--52112 Score: 51
Period size: 7 Copynumber: 6.0 Consensus size: 8
52058 TTTTCATCCC
52068 AAAA-ATT
1 AAAATATT
52075 AAAATATT
1 AAAATATT
52083 AAAATATT
1 AAAATATT
*
52091 -GAATATT
1 AAAATATT
*
52098 AAAA-AAT
1 AAAATATT
52105 AAAATATT
1 AAAATATT
52113 TTATATTCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
7 16 0.52
8 15 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:52110 original size:15 final size:15
Alignment explanation
Indices: 52068--52112 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
52058 TTTTCATCCC
*
52068 AAAAATTAAAATATT
1 AAAAAATAAAATATT
* **
52083 AAAATATTGAATATT
1 AAAAAATAAAATATT
52098 AAAAAATAAAATATT
1 AAAAAATAAAATATT
52113 TTATATTCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAAAATAAAATATT
Done.