Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007309.1 Hibiscus syriacus cultivar Beakdansim tig00019471_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: 85778
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:523 original size:13 final size:13
Alignment explanation
Indices: 505--529 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
495 GTCACATCAA
505 TTTTTTTTTGCTT
1 TTTTTTTTTGCTT
518 TTTTTTTTTGCT
1 TTTTTTTTTGCT
530 ATAAAGAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTGCTT
Found at i:1759 original size:89 final size:88
Alignment explanation
Indices: 1587--1763 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 88
1577 AAATCTTAAA
* *
1587 ACAACTTTAAATATCAACAACTAGTTGGTGTAGTCGAATGAGGCACTAAATCTCTTAAGTAAGGT
1 ACAACTTTAAATATCAACAACTAGTTGGTCTAGTCGAATGAGACACTAAATCTCTTAAGTAAGGT
1652 TAATGGTTTGAATCCTGATGATT
66 TAATGGTTTGAATCCTGATGATT
* *
1675 ACAACTTTTAAAATATCAACAACTAGTTGGTCTAGTCGATTGAGACACTAGATC-CATT-AGTAA
1 ACAAC-TTT-AAATATCAACAACTAGTTGGTCTAGTCGAATGAGACACTAAATCTC-TTAAGTAA
1738 GGTTAATGGTTTGAATCCTGATGATT
63 GGTTAATGGTTTGAATCCTGATGATT
1764 GTGTGAATGG
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
88 5 0.06
89 35 0.43
90 42 0.51
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (88 bp):
ACAACTTTAAATATCAACAACTAGTTGGTCTAGTCGAATGAGACACTAAATCTCTTAAGTAAGGT
TAATGGTTTGAATCCTGATGATT
Found at i:15996 original size:15 final size:12
Alignment explanation
Indices: 15962--15989 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
15952 ACTCACAGCT
15962 AAATAAACCACC
1 AAATAAACCACC
15974 AAATAAACCACC
1 AAATAAACCACC
15986 AAAT
1 AAAT
15990 GGTAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.11
Consensus pattern (12 bp):
AAATAAACCACC
Found at i:26851 original size:12 final size:12
Alignment explanation
Indices: 26834--26859 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26824 GTTTATCCTA
26834 AATTAATAAATG
1 AATTAATAAATG
26846 AATTAATAAATG
1 AATTAATAAATG
26858 AA
1 AA
26860 AGAGAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AATTAATAAATG
Found at i:32356 original size:38 final size:38
Alignment explanation
Indices: 32278--32394 Score: 154
Period size: 38 Copynumber: 3.2 Consensus size: 38
32268 CCTAAACCCA
* *
32278 AACCCGACCTGAATATCACACTT-AAAAAATCT---CG
1 AACCCGACCCGAATATCACACTTAAAAAAACCTGACCG
*
32312 -ATCCGACCCGAATATCACACTTAAAAAAACCTGACCG
1 AACCCGACCCGAATATCACACTTAAAAAAACCTGACCG
*
32349 AACCCGACCCGAATATCACACTTAAAAAAACCCGACCCG
1 AACCCGACCCGAATATCACACTTAAAAAAACCTGA-CCG
32388 AACCCGA
1 AACCCGA
32395 AATTTAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
33 20 0.28
34 8 0.11
37 2 0.03
38 32 0.44
39 10 0.14
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (38 bp):
AACCCGACCCGAATATCACACTTAAAAAAACCTGACCG
Found at i:32387 original size:33 final size:33
Alignment explanation
Indices: 32279--32395 Score: 144
Period size: 33 Copynumber: 3.4 Consensus size: 33
32269 CTAAACCCAA
* * *
32279 ACCCGACCTGAATATCACACTTAAAAAATCTCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
32312 ATCCGACCCGAATATCACACTTAAAAAAACCTGACCG
1 ACCCGACCCGAATATCACACTTAAAAAAA-C---CCG
32349 AACCCGACCCGAATATCACACTTAAAAAAACCCG
1 -ACCCGACCCGAATATCACACTTAAAAAAACCCG
32383 ACCCGAACCCGAA
1 ACCCG-ACCCGAA
32396 ATTTAAAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
33 31 0.42
34 11 0.15
37 3 0.04
38 28 0.38
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:35234 original size:20 final size:20
Alignment explanation
Indices: 35211--35252 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
35201 TTTATTTTAA
*
35211 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAGTCCTG
35231 TTCTATTCAATTTAGTCCTG
1 TTCTATTCAATTTAGTCCTG
35251 TT
1 TT
35253 GCGGCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (20 bp):
TTCTATTCAATTTAGTCCTG
Found at i:38971 original size:32 final size:31
Alignment explanation
Indices: 38915--38997 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
38905 GGTGTTAACG
** * **
38915 AGTTAAGGGCCAAATTATAGATCAAAGTCAA
1 AGTTAAGGGCCAAATTGCATATCAAAACCAA
38946 AGTTAAAGGGCCAAATTGCATATCAAAACCAA
1 AGTT-AAGGGCCAAATTGCATATCAAAACCAA
* *
38978 AGTTAGGGGCCATATTGCAT
1 AGTTAAGGGCCAAATTGCAT
38998 CTACTAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 18 0.41
32 26 0.59
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (31 bp):
AGTTAAGGGCCAAATTGCATATCAAAACCAA
Found at i:49788 original size:75 final size:75
Alignment explanation
Indices: 49703--49860 Score: 239
Period size: 75 Copynumber: 2.1 Consensus size: 75
49693 CGTTTTAGTT
* **
49703 TTGGG-TTTTTGTTTAAAGA-CCTCGTTTCTTCTTGAAATCTGAATTAGGGTTTTGGTTCCGTGG
1 TTGGGATTTTTGTTTAAAGAGACT-GTTTCTTCTTGAAATCTGAATTAGGGTTTTGGTTCCAAGG
49766 CTTGTTGGATG
65 CTTGTTGGATG
*
49777 TTGGGATTTTTGTTTAAAGAGACTGTTTCTTCTTGAAATCTGAATTAGGGTTTTGGTTTCAAGGC
1 TTGGGATTTTTGTTTAAAGAGACTGTTTCTTCTTGAAATCTGAATTAGGGTTTTGGTTCCAAGGC
*
49842 TTGTTGGTTG
66 TTGTTGGATG
*
49852 TTTGGATTT
1 TTGGGATTT
49861 AATGGATTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 5 0.07
75 69 0.91
76 2 0.03
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.47
Consensus pattern (75 bp):
TTGGGATTTTTGTTTAAAGAGACTGTTTCTTCTTGAAATCTGAATTAGGGTTTTGGTTCCAAGGC
TTGTTGGATG
Found at i:54734 original size:14 final size:14
Alignment explanation
Indices: 54712--54783 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
54702 GATTCGAGTT
54712 TGAGGTCTTGTATA
1 TGAGGTCTTGTATA
* *
54726 TGCGGTCTTG-AGTT
1 TGAGGTCTTGTA-TA
54740 TGAGGTCTTGTATA
1 TGAGGTCTTGTATA
* * *
54754 CGTGGTCTCAAGT-T-
1 TGAGGTCT--TGTATA
54768 TGAGGTCTTGTATA
1 TGAGGTCTTGTATA
54782 TG
1 TG
54784 CGGAACATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
12 2 0.05
13 2 0.05
14 34 0.81
15 2 0.05
16 2 0.05
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.42
Consensus pattern (14 bp):
TGAGGTCTTGTATA
Found at i:54739 original size:28 final size:28
Alignment explanation
Indices: 54705--54786 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
54695 TAAATAAGAT
54705 TCGAGTTTGAGGTCTTGTATATGCGGTC
1 TCGAGTTTGAGGTCTTGTATATGCGGTC
* * *
54733 TTGAGTTTGAGGTCTTGTATACGTGGTC
1 TCGAGTTTGAGGTCTTGTATATGCGGTC
*
54761 TCAAGTTTGAGGTCTTGTATATGCGG
1 TCGAGTTTGAGGTCTTGTATATGCGG
54787 AACATTTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (28 bp):
TCGAGTTTGAGGTCTTGTATATGCGGTC
Found at i:55060 original size:2 final size:2
Alignment explanation
Indices: 55053--55082 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55043 TATAACCATA
55053 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
55083 GTGATATACA
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:57660 original size:31 final size:32
Alignment explanation
Indices: 57623--57708 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 32
57613 GTCGGGTTGA
*
57623 GTCGGGTCAGGTCAATATCGGATCGGTTGATT
1 GTCGGGTCAGGTCAATATCAGATCGGTTGATT
**
57655 -TCGGGTC-GGATCAA-ATCAGATATGTTGATT
1 GTCGGGTCAGG-TCAATATCAGATCGGTTGATT
* *
57685 GTCGGGTCAAGTCAATATCCGATC
1 GTCGGGTCAGGTCAATATCAGATC
57709 AATTATTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
30 15 0.34
31 22 0.50
32 7 0.16
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (32 bp):
GTCGGGTCAGGTCAATATCAGATCGGTTGATT
Found at i:63806 original size:16 final size:16
Alignment explanation
Indices: 63785--63817 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
63775 CAGGAAATTG
63785 CCTATAAAACCTCCAT
1 CCTATAAAACCTCCAT
63801 CCTATAAAACCTCCAT
1 CCTATAAAACCTCCAT
63817 C
1 C
63818 TTGGTGAGGA
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:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
CCTATAAAACCTCCAT
Found at i:66882 original size:19 final size:19
Alignment explanation
Indices: 66858--66903 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
66848 AAATGAAGAT
*
66858 TTTTAAAGTTTTAGGTTT-A
1 TTTTAAAATTTT-GGTTTCA
*
66877 TTTTAAAATTTTTGTTTCA
1 TTTTAAAATTTTGGTTTCA
66896 TTTTAAAA
1 TTTTAAAA
66904 ATATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTTTGGTTTCA
Found at i:66889 original size:20 final size:19
Alignment explanation
Indices: 66856--66903 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
66846 TAAAATGAAG
*
66856 ATTTTTAAAGTTTTAGGTTT-
1 ATTTTAAAAGTTTT--GTTTC
*
66876 ATTTTAAAATTTTTGTTTC
1 ATTTTAAAAGTTTTGTTTC
66895 ATTTTAAAA
1 ATTTTAAAA
66904 ATATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTTAAAAGTTTTGTTTC
Found at i:71320 original size:22 final size:22
Alignment explanation
Indices: 71292--71343 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
71282 TTTATATAGT
71292 ACGAATTTGTCACATTGAGATG
1 ACGAATTTGTCACATTGAGATG
*
71314 ACGAATTTGTCACATTGAGGTG
1 ACGAATTTGTCACATTGAGATG
*
71336 ACAAATTT
1 ACGAATTT
71344 TAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (22 bp):
ACGAATTTGTCACATTGAGATG
Found at i:74115 original size:30 final size:30
Alignment explanation
Indices: 74062--74120 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
74052 AAAGAACCAG
* * ** *
74062 CGGTTCACACTGGTTTTGTCGGTTTTCAGT
1 CGGTTCACACCGATTTTACCGGTTCTCAGT
74092 CGGTTCACACCGATTTTACCGGTTCTCAG
1 CGGTTCACACCGATTTTACCGGTTCTCAG
74121 CTGGTTCTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.37
Consensus pattern (30 bp):
CGGTTCACACCGATTTTACCGGTTCTCAGT
Found at i:74127 original size:30 final size:30
Alignment explanation
Indices: 74059--74127 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
74049 AAAAAAGAAC
* * ** *
74059 CAGC-GGTTCACACTGGTTTTGTCGGTTTT
1 CAGCTGGTTCACACCGATTTTACCGGTTCT
74088 CAG-TCGGTTCACACCGATTTTACCGGTTCT
1 CAGCT-GGTTCACACCGATTTTACCGGTTCT
74118 CAGCTGGTTC
1 CAGCTGGTTC
74128 TACTGGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 3 0.09
30 28 0.88
31 1 0.03
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.36
Consensus pattern (30 bp):
CAGCTGGTTCACACCGATTTTACCGGTTCT
Found at i:75901 original size:29 final size:28
Alignment explanation
Indices: 75823--75902 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
75813 AACTGAAACG
*
75823 AAAATCAAAGTTCAGTGCTATAATTGAC
1 AAAATTAAAGTTCAGTGCTATAATTGAC
*
75851 AAAATTAAAGTTCAGTGCTATAATTGGC
1 AAAATTAAAGTTCAGTGCTATAATTGAC
* *
75879 AAAATTAAAAGTTTAGTGGTATAA
1 AAAATT-AAAGTTCAGTGCTATAA
75903 ATGAGACAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 32 0.68
29 15 0.32
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (28 bp):
AAAATTAAAGTTCAGTGCTATAATTGAC
Found at i:79415 original size:4 final size:4
Alignment explanation
Indices: 79378--79408 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
79368 TATGTATATA
79378 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
79409 ATGTATGATT
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:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:82870 original size:18 final size:18
Alignment explanation
Indices: 82845--82891 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
82835 TGCACACACA
82845 CATACATACATGCATGCT
1 CATACATACATGCATGCT
*
82863 CGTACATACATGCATGCT
1 CATACATACATGCATGCT
*
82881 CATGCATACAT
1 CATACATACAT
82892 ATAACTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.28
Consensus pattern (18 bp):
CATACATACATGCATGCT
Found at i:82890 original size:22 final size:20
Alignment explanation
Indices: 82826--82892 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 20
82816 CATGGATATG
** * *
82826 ATACATACATGCACACACAC
1 ATACATACATGCATGCTCGC
82846 ATACATACATGCATGCTCG-
1 ATACATACATGCATGCTCGC
82865 -TACATACATGCATGCTCATGC
1 ATACATACATGCATGCTC--GC
82886 ATACATA
1 ATACATA
82893 TAACTAACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 17 0.44
20 16 0.41
22 6 0.15
ACGTcount: A:0.37, C:0.28, G:0.10, T:0.24
Consensus pattern (20 bp):
ATACATACATGCATGCTCGC
Found at i:83553 original size:4 final size:4
Alignment explanation
Indices: 83546--83583 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
83536 AATTATTAAA
*
83546 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
83584 TAACTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Done.