Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003554.1 Hibiscus syriacus cultivar Beakdansim tig00007499_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: 75821
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:1647 original size:36 final size:37
Alignment explanation
Indices: 1576--1648 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
1566 TTTTTTTAAC
*
1576 AAATTGAAAAATATTTATATATTTTCTTTAAAAAATT
1 AAATTCAAAAATATTTATATATTTTCTTTAAAAAATT
*
1613 AAATTCAAAAAT-TTTATATAATTTT-TTTACAAAATT
1 AAATTCAAAAATATTTATAT-ATTTTCTTTAAAAAATT
1649 GAAAATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
AAATTCAAAAATATTTATATATTTTCTTTAAAAAATT
Found at i:2655 original size:2 final size:2
Alignment explanation
Indices: 2648--2675 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2638 AGCCTTTTGA
2648 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
2676 GAAAAACGAT
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:3429 original size:16 final size:17
Alignment explanation
Indices: 3408--3439 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3398 TGGCCTAAAC
3408 AATTAGAAA-TATTTAG
1 AATTAGAAATTATTTAG
3424 AATTAGAAATTATTTA
1 AATTAGAAATTATTTA
3440 ACCTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
AATTAGAAATTATTTAG
Found at i:8750 original size:2 final size:2
Alignment explanation
Indices: 8708--8732 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8698 GTTGAAGATA
8708 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8733 ACTATTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23096 original size:3 final size:3
Alignment explanation
Indices: 23088--23113 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23078 TTAAGACACA
23088 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
23114 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40163 original size:16 final size:15
Alignment explanation
Indices: 40110--40166 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
40100 ATTAATAAAA
*
40110 TTAAACTTTATTTATC
1 TTAAA-TTTATTTATT
40126 TTAATATTTATTTACTTT
1 TTAA-ATTTATTTA--TT
40144 TTAAATCTTATTTATT
1 TTAAAT-TTATTTATT
40160 TTAAATT
1 TTAAATT
40167 AAAGAATTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 20 0.56
17 3 0.08
18 12 0.33
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAAATTTATTTATT
Found at i:43349 original size:3 final size:3
Alignment explanation
Indices: 43343--43375 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
43333 ATAAAAGGAG
43343 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
43376 AGAGGAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43749 original size:6 final size:6
Alignment explanation
Indices: 43738--43769 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
43728 CTCCATTCCT
43738 CTGCAG CTGCAG CTGCAG CTGCAG CCTGCAG C
1 CTGCAG CTGCAG CTGCAG CTGCAG -CTGCAG C
43770 AGCTATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.38, G:0.31, T:0.16
Consensus pattern (6 bp):
CTGCAG
Found at i:44743 original size:36 final size:35
Alignment explanation
Indices: 44707--44774 Score: 84
Period size: 37 Copynumber: 1.9 Consensus size: 35
44697 TTCTAATATA
44707 AATTTTA-AAAAATAAAAAAATAAATATTAAATTAT
1 AATTTTATAAAAATAAAAAAAT-AATATTAAATTAT
* * *
44742 AATTTTATTAAAAATGAATAAATATTATTAAAT
1 AATTTTA-TAAAAATAAAAAAATAATATTAAAT
44775 GTTGTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 7 0.25
36 9 0.32
37 12 0.43
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (35 bp):
AATTTTATAAAAATAAAAAAATAATATTAAATTAT
Found at i:44792 original size:30 final size:31
Alignment explanation
Indices: 44719--44792 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
44709 TTTTAAAAAA
*
44719 TAAAAA-AATAAATATTAAATTATAATTTTAT
1 TAAAAATAATAAATATT-AATTATAATGTTAT
*
44750 TAAAAATGAATAAATATT-ATTA-AATGTTGT
1 TAAAAAT-AATAAATATTAATTATAATGTTAT
44780 TAAAAAATAATAA
1 T-AAAAATAATAA
44793 TTAATGGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 12 0.32
31 16 0.42
33 10 0.26
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (31 bp):
TAAAAATAATAAATATTAATTATAATGTTAT
Found at i:45726 original size:41 final size:40
Alignment explanation
Indices: 45681--45790 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 40
45671 ATTCACGTTG
* *
45681 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
* *
45722 CATTTCGTGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
45763 CATTTCGCGTTGCGATAGTTGAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAATCGC
45791 AACGCGATCT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
40 7 0.11
41 54 0.87
42 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:45772 original size:20 final size:20
Alignment explanation
Indices: 45706--45778 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
45696 TAGTTGAAAA
*
45706 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
45726 TCGTGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
45747 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
45767 TCGCGTTGCGAT
1 TCGCGTTGCGAT
45779 AGTTGAAATC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.11, C:0.21, G:0.27, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:45790 original size:20 final size:21
Alignment explanation
Indices: 45685--45790 Score: 58
Period size: 20 Copynumber: 5.2 Consensus size: 21
45675 ACGTTGCATT
*
45685 TCGCATTGCGATAGTT-GAAAA
1 TCGCGTTGCGATAGTTCG-AAA
** * **
45706 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* * *
45726 TCGTGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
45747 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
45767 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
45787 TCGC
1 TCGC
45791 AACGCGATCT
Statistics
Matches: 59, Mismatches: 23, Indels: 7
0.66 0.26 0.08
Matches are distributed among these distances:
20 33 0.56
21 26 0.44
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:45843 original size:21 final size:21
Alignment explanation
Indices: 45819--45884 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
45809 GCAAATTCGC
45819 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** * *
45840 GTTGAAAATCGCGTTGTGGT-
1 GTTGCATTTCGCGTTGCGATA
* *
45860 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
45881 GTTG
1 GTTG
45885 AAAATCGCGT
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:45851 original size:41 final size:41
Alignment explanation
Indices: 45806--45892 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
45796 GATCTCCATT
*
45806 ATCGCAAAT-TCGCGTTGCATTTCGCGTTGCGATAGTTGAAA
1 ATCGC-AATGTCGCGTTCCATTTCGCGTTGCGATAGTTGAAA
** * **
45847 ATCGCGTTGTGGTTTTCCATTTCGCGTTGCGATAGTTGAAA
1 ATCGCAATGTCGCGTTCCATTTCGCGTTGCGATAGTTGAAA
45888 ATCGC
1 ATCGC
45893 GTTACGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCAATGTCGCGTTCCATTTCGCGTTGCGATAGTTGAAA
Found at i:45894 original size:21 final size:21
Alignment explanation
Indices: 45827--45900 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
45817 GCGTTGCATT
45827 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * * ** **
45848 TCGCGTTGTGGT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
45868 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
45889 TCGCGTTACGAT
1 TCGCGTTGCGAT
45901 TTTGTTGGTC
Statistics
Matches: 37, Mismatches: 15, Indels: 2
0.69 0.28 0.04
Matches are distributed among these distances:
20 13 0.35
21 24 0.65
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:46069 original size:12 final size:14
Alignment explanation
Indices: 46039--46070 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
46029 CAAACCATGA
46039 AATTTATACAAACT
1 AATTTATACAAACT
46053 AATTTATA-AAA-T
1 AATTTATACAAACT
46065 AATTTA
1 AATTTA
46071 CGTATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATACAAACT
Found at i:49648 original size:25 final size:26
Alignment explanation
Indices: 49597--49649 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
49587 TTATATATAT
**
49597 AATCCCCAAACTTTTTGAAAATTTTAA
1 AATCCCCAAAC-TTTTGAAAACCTTAA
49624 AATCCCCAAAC-TTTGAAAACCTTAA
1 AATCCCCAAACTTTTGAAAACCTTAA
49649 A
1 A
49650 TCTAATCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
27 11 0.46
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (26 bp):
AATCCCCAAACTTTTGAAAACCTTAA
Found at i:60718 original size:16 final size:16
Alignment explanation
Indices: 60697--60729 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
60687 GATGGGATAC
60697 GGAAGTTACAGTTATA
1 GGAAGTTACAGTTATA
60713 GGAAGTTACAGTTATA
1 GGAAGTTACAGTTATA
60729 G
1 G
60730 TCTAACTATT
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:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (16 bp):
GGAAGTTACAGTTATA
Found at i:73543 original size:29 final size:29
Alignment explanation
Indices: 73510--73622 Score: 174
Period size: 29 Copynumber: 3.9 Consensus size: 29
73500 GACAACCAAC
*
73510 ATAGGTCGCCATGCACGGCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
*
73539 ATAGGTCGCCATGCACGCACGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
*
73568 ATAGGTCGCCATGCACGCCCGACGTCC-T
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
*
73596 ATAAGATCGCCATGCACGCCCGGCGTC
1 AT-AGGTCGCCATGCACGCCCGGCGTC
73623 ATACGTTCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
28 3 0.04
29 74 0.96
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:73762 original size:36 final size:36
Alignment explanation
Indices: 73715--73861 Score: 133
Period size: 45 Copynumber: 4.0 Consensus size: 36
73705 CCCCAATCTC
73715 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGT
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGT
* * *
73751 CCCATGCATGAACCGATCCTTGGTCGTGCACGATCTCCCCAATCT
1 CCCATGCATGAACCGATCCTT-G--GT---CG--C-CCCGAGTGT
*
73796 CCCATGCATGAAACGATCCTTGGTCG-CCCGAGTG-
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGT
*
73830 -CCATGCATGAACC--TCCTTGGTCTCCCCGAGTG
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
73862 CATGGCACGA
Statistics
Matches: 92, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
31 9 0.10
32 8 0.09
33 12 0.13
35 5 0.05
36 21 0.23
37 1 0.01
39 4 0.04
42 4 0.04
44 2 0.02
45 26 0.28
ACGTcount: A:0.18, C:0.36, G:0.22, T:0.23
Consensus pattern (36 bp):
CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGT
Found at i:73817 original size:81 final size:77
Alignment explanation
Indices: 73701--73851 Score: 241
Period size: 81 Copynumber: 1.9 Consensus size: 77
73691 CCTACACACA
*
73701 ATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGTCCCATGCATGAACCG
1 ATCTCCCCAATCTCCCCATGCATGAAACGATCCTTGGTCG-CCCGAGTG--CCATGCATGAACC-
73766 ATCCTTGGTCGTGCACG
62 -TCCTTGGTCGTGCACG
73783 ATCTCCCCAATCT-CCCATGCATGAAACGATCCTTGGTCGCCCGAGTGCCATGCATGAACCTCCT
1 ATCTCCCCAATCTCCCCATGCATGAAACGATCCTTGGTCGCCCGAGTGCCATGCATGAACCTCCT
73847 TGGTC
66 TGGTC
73852 TCCCCGAGTG
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
76 9 0.13
78 13 0.19
80 8 0.12
81 25 0.37
82 13 0.19
ACGTcount: A:0.19, C:0.37, G:0.20, T:0.24
Consensus pattern (77 bp):
ATCTCCCCAATCTCCCCATGCATGAAACGATCCTTGGTCGCCCGAGTGCCATGCATGAACCTCCT
TGGTCGTGCACG
Found at i:73850 original size:31 final size:34
Alignment explanation
Indices: 73797--73862 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 34
73787 CCCCAATCTC
*
73797 CCATGCATGAAACGATCCTTGGTC-GCCCGAGTG
1 CCATGCATGAAACGATCCTTGGTCTCCCCGAGTG
*
73830 CCATGCATG-AAC-CTCCTTGGTCTCCCCGAGTG
1 CCATGCATGAAACGATCCTTGGTCTCCCCGAGTG
73862 C
1 C
73863 ATGGCACGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 9 0.30
32 12 0.40
33 9 0.30
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.23
Consensus pattern (34 bp):
CCATGCATGAAACGATCCTTGGTCTCCCCGAGTG
Found at i:73922 original size:29 final size:29
Alignment explanation
Indices: 73890--73969 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
73880 GTCGCCCCGA
* *
73890 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTAGGC
73919 GTGCATGGCGACCTCTTTGGTCGTTAGGC
1 GTGCATGGCGACCTCTTTGGTCGTTAGGC
*
73948 GTGCATGACGACCTCTTTGGTC
1 GTGCATGGCGACCTCTTTGGTC
73970 ACTGTACAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.10, C:0.26, G:0.34, T:0.30
Consensus pattern (29 bp):
GTGCATGGCGACCTCTTTGGTCGTTAGGC
Done.