Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001748.1 Hibiscus syriacus cultivar Beakdansim tig00003538_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: 70692
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:2713 original size:7 final size:7
Alignment explanation
Indices: 2703--2754 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
2693 TAAATTTCTT
2703 ATTTAAA
1 ATTTAAA
2710 ATTTATAA
1 ATTTA-AA
2718 ATTTAAA
1 ATTTAAA
2725 A-TT--A
1 ATTTAAA
2729 ATTT-AA
1 ATTTAAA
2735 ATTTAAA
1 ATTTAAA
*
2742 ATAT-AA
1 ATTTAAA
2748 ATTTAAA
1 ATTTAAA
2755 TTGACTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 12 0.32
7 15 0.39
8 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:2713 original size:14 final size:15
Alignment explanation
Indices: 2703--2754 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 15
2693 TAAATTTCTT
2703 ATTTAAAATTTATAA
1 ATTTAAAATTTATAA
*
2718 ATTTAAAATTAATTTAA
1 ATTTAAAATT--TATAA
2735 ATTTAAAA--TATAA
1 ATTTAAAATTTATAA
2748 ATTTAAA
1 ATTTAAA
2755 TTGACTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 11 0.33
15 10 0.30
17 12 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTAAAATTTATAA
Found at i:2733 original size:19 final size:18
Alignment explanation
Indices: 2715--2756 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 18
2705 TTAAAATTTA
2715 TAAATTTAAAAT-TAATT
1 TAAATTTAAAATATAATT
2732 TAAATTTAAAATATAAATT
1 TAAATTTAAAATAT-AATT
2751 TAAATT
1 TAAATT
2757 GACTAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 1 0.04
19 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTTAAAATATAATT
Found at i:2755 original size:6 final size:6
Alignment explanation
Indices: 2715--2756 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2705 TTAAAATTTA
* *
2715 TAAATT TAAAAT T-AATT TAAATT TAAAATA TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
2757 GACTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.70
7 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:3130 original size:14 final size:14
Alignment explanation
Indices: 3111--3142 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3101 AAAGCTATAG
3111 TATTATCATAAATT
1 TATTATCATAAATT
*
3125 TATTATCATAACTT
1 TATTATCATAAATT
3139 TATT
1 TATT
3143 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:4075 original size:158 final size:152
Alignment explanation
Indices: 3792--4106 Score: 413
Period size: 159 Copynumber: 2.0 Consensus size: 152
3782 TAATAAAAAT
* *
3792 AATT-ATTTATATTAATTTGAAAAAAATTGTGACGTGCATCACAAGTAGACATGTCATTAGCATC
1 AATTGATTTATATTAATTTGAAAAAAATTGTGACGTGCATCACAAGCAGACATGCCATTAGCATC
* * *
3856 TCCATCCACATGTTCTTGCTTAGTCAACTACAAAAATTGACCGTTATTTGACTAACGATTTTTAT
66 TCCATCCACATGTTCTTGCTTAGTCAAATACAAAAATTGACCGTTAATTGACTAACGATTTTGAT
*
3921 CTAACGAGGGTATTTTTTTGACCCA
131 CCAACGA-GGTA-TTTTTT-ACCCA
* * *
3946 AATTGATTTATAATTAATTTGAAAAAAAATTGTTGACGTGGCATCACACGCGGACGTGCCACGTT
1 AATTGATTTAT-ATTAATTTG-AAAAAAATTG-TGACGT-GCATCACAAGCAGACATGCCA--TT
* * *
4011 AGCATCTCCCT-C-CATGTTCTTGCTTAGTCAAATATAAGAATTGA-CGTTAATTGACTAACGAT
60 AGCATCTCCATCCACATGTTCTTGCTTAGTCAAATACAAAAATTGACCGTTAATTGACTAACGAT
4073 TTTGATCCAACGAGGTATTTTTTACCCA
125 TTTGATCCAACGAGGTATTTTTTACCCA
4101 AATTGA
1 AATTGA
4107 AACATTAAGG
Statistics
Matches: 142, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
154 4 0.03
155 17 0.12
156 15 0.11
157 14 0.10
158 34 0.24
159 45 0.32
160 1 0.01
161 12 0.08
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (152 bp):
AATTGATTTATATTAATTTGAAAAAAATTGTGACGTGCATCACAAGCAGACATGCCATTAGCATC
TCCATCCACATGTTCTTGCTTAGTCAAATACAAAAATTGACCGTTAATTGACTAACGATTTTGAT
CCAACGAGGTATTTTTTACCCA
Found at i:10549 original size:2 final size:2
Alignment explanation
Indices: 10542--10569 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10532 AAATACTAAC
10542 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
10570 GTACAGATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11325 original size:46 final size:46
Alignment explanation
Indices: 11270--11396 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
11260 GTAAGCATGC
11270 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
11316 AACTAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
11362 AAATAAGCTTACGAGCTTATAGG-A-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTAT-GGTATTAAATGGTAAG
11397 AAATTTTATA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
45 11 0.14
46 63 0.83
47 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
Found at i:13694 original size:13 final size:13
Alignment explanation
Indices: 13676--13716 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
13666 AAATATATAT
13676 AAGAAAAAAA-AA
1 AAGAAAAAAAGAA
13688 GAAGAAAAAAAGAA
1 -AAGAAAAAAAGAA
*
13702 AAGAAAAAGAGAA
1 AAGAAAAAAAGAA
13715 AA
1 AA
13717 ATGATGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 24 0.92
14 2 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:13700 original size:21 final size:21
Alignment explanation
Indices: 13676--13717 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13666 AAATATATAT
13676 AAGAAAA-AAAAAGAAGAAAAA
1 AAGAAAAGAAAAAG-AGAAAAA
13697 AAGAAAAGAAAAAGAGAAAAA
1 AAGAAAAGAAAAAGAGAAAAA
13718 TGATGAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (21 bp):
AAGAAAAGAAAAAGAGAAAAA
Found at i:17603 original size:46 final size:46
Alignment explanation
Indices: 17548--17674 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
17538 GTAAGCATTC
17548 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
17594 AACTAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* * *
17640 AAATAAGCTTACAAGCTAATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAG
17675 AATTTTATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 11 0.15
46 63 0.85
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
Found at i:19388 original size:46 final size:46
Alignment explanation
Indices: 19333--19459 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
19323 GTTAGCATGC
19333 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
19379 AACTAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
19425 AAATAAGCTTACGAGCTTATAGG-A-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTAT-GGTATTAAATGGTAAG
19460 AAATTTTATA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
45 11 0.14
46 63 0.83
47 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
Found at i:21790 original size:17 final size:17
Alignment explanation
Indices: 21770--21815 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
21760 ATAAGAGCTA
21770 AAAAAATATAATAT-AAG
1 AAAAAA-ATAATATGAAG
* *
21787 AAAAAAAGAAAATGAAG
1 AAAAAAATAATATGAAG
21804 AAAAAAATAATA
1 AAAAAAATAATA
21816 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AAAAAAATAATATGAAG
Found at i:21834 original size:16 final size:16
Alignment explanation
Indices: 21790--21839 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
21780 ATATAAGAAA
21790 AAAAGAAAATGAAGAAA-
1 AAAAGAAAA-GAA-AAAG
* *
21807 AAAATAATAGAAAAAG
1 AAAAGAAAAGAAAAAG
21823 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
21839 A
1 A
21840 GAAAAATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 3 0.11
16 18 0.64
17 7 0.25
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:25798 original size:46 final size:46
Alignment explanation
Indices: 25743--25869 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
25733 GTAATCATGC
*
25743 AAATAAGCTTACGAGCTTATGGTATTAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
25789 AACTAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
25835 AAATAAGCTTACGAGCTAATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAG
25870 AATTTTATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 11 0.15
46 63 0.85
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
Found at i:29544 original size:54 final size:54
Alignment explanation
Indices: 29481--29625 Score: 200
Period size: 54 Copynumber: 2.7 Consensus size: 54
29471 GTACTTTCAG
* * *
29481 CACTATGTGTGCAACCCACGAAATTCATAATGAGTTTATGAATGACCATCTCGA
1 CACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATGAATGACCATATCGA
* * *
29535 CACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATGGATGACCGTATCGG
1 CACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATGAATGACCATATCGA
* * * *
29589 CAGTATGTGTGCAATCTATGGAATTCATAATAAGTTT
1 CACTATGTGTGCAACCCATGAAATTCATAATAAGTTT
29626 GTGTATTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (54 bp):
CACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATGAATGACCATATCGA
Found at i:36723 original size:54 final size:54
Alignment explanation
Indices: 36654--36803 Score: 185
Period size: 54 Copynumber: 2.8 Consensus size: 54
36644 TCGTATTAGT
* *
36654 ACTATATGTGCAACCCACGGAATTCATAATGAGTTTATGAATGAACGAATC-AGC
1 ACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGAACGAATCGA-C
* ** * *
36708 ACTATGTGTGTAACCCACATAATTCATAATAAGTTTATGAATGACCGTATCGAC
1 ACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGAACGAATCGAC
* * * *
36762 ACTATGTGTGCAATCTATGGAATTCATAATAAGTTTGTGAAT
1 ACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAAT
36804 TTCCATTTCG
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 80 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (54 bp):
ACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGAACGAATCGAC
Found at i:53438 original size:11 final size:10
Alignment explanation
Indices: 53424--53498 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 10
53414 CATTAAATGA
53424 ATTTAAAATTC
1 ATTT-AAATTC
53435 ATTT-AATT-
1 ATTTAAATTC
* *
53443 AATTAAATGC
1 ATTTAAATTC
53453 ATTTTAAATTC
1 A-TTTAAATTC
53464 ATTT-AATT-
1 ATTTAAATTC
* *
53472 AGTTAAATGC
1 ATTTAAATTC
53482 ATTTTAAATTC
1 A-TTTAAATTC
53493 ATTTAA
1 ATTTAA
53499 TTAGTTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
8 6 0.12
9 14 0.28
10 10 0.20
11 20 0.40
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (10 bp):
ATTTAAATTC
Found at i:53451 original size:29 final size:29
Alignment explanation
Indices: 53415--53509 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 29
53405 GGAATTTCTC
* *
53415 ATTAAATGAATTTAAAATTCATTTAATTA
1 ATTAAATGCATTTTAAATTCATTTAATTA
53444 ATTAAATGCATTTTAAATTCATTTAATTA
1 ATTAAATGCATTTTAAATTCATTTAATTA
*
53473 GTTAAATGCATTTTAAATTCATTTAATTA
1 ATTAAATGCATTTTAAATTCATTTAATTA
*
53502 GTTAAATG
1 ATTAAATG
53510 TTAAGTGTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
ATTAAATGCATTTTAAATTCATTTAATTA
Found at i:56396 original size:15 final size:15
Alignment explanation
Indices: 56378--56421 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
56368 GAGAGTATAT
56378 ATATTGTGAGTACAA
1 ATATTGTGAGTACAA
56393 ATATTGTGAGTATC-A
1 ATATTGTGAGTA-CAA
*
56408 ATATTATGAGTACA
1 ATATTGTGAGTACA
56422 GTACCAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (15 bp):
ATATTGTGAGTACAA
Found at i:63181 original size:20 final size:21
Alignment explanation
Indices: 63156--63200 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
63146 GTAATTTGGC
63156 TTTGGGGT-TTAGCGTTGTAA
1 TTTGGGGTCTTAGCGTTGTAA
* *
63176 TTT-GGGTCTTCGGGTTGTAA
1 TTTGGGGTCTTAGCGTTGTAA
63196 TTTGG
1 TTTGG
63201 ACCTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.11, C:0.07, G:0.36, T:0.47
Consensus pattern (21 bp):
TTTGGGGTCTTAGCGTTGTAA
Found at i:63477 original size:35 final size:35
Alignment explanation
Indices: 63438--63504 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
63428 TGATATATTC
** *
63438 TTGCTTCACTACTCTTTTTTGAATGCTTGATTGCA
1 TTGCTTCACTACTCTTTTAAGAAGGCTTGATTGCA
*
63473 TTGCTTTACTACTCTTTTAAGAAGGCTTGATT
1 TTGCTTCACTACTCTTTTAAGAAGGCTTGATT
63505 TGTATTGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (35 bp):
TTGCTTCACTACTCTTTTAAGAAGGCTTGATTGCA
Found at i:66260 original size:20 final size:20
Alignment explanation
Indices: 66235--66274 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
66225 TGATTTTCTT
66235 ACTGATATTGCCATCAAATC
1 ACTGATATTGCCATCAAATC
66255 ACTGATATTGCCATCAAATC
1 ACTGATATTGCCATCAAATC
66275 CTCATCAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (20 bp):
ACTGATATTGCCATCAAATC
Done.