Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002400.1 Hibiscus syriacus cultivar Beakdansim tig00004910_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: 74259
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:5072 original size:33 final size:33
Alignment explanation
Indices: 5030--5095 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5020 ACGACAAGCT
5030 ATCCGTCAACAGTTCAATACTCTTCGAGTGGCA
1 ATCCGTCAACAGTTCAATACTCTTCGAGTGGCA
5063 ATCCGTCAACAGTTCAATACTCTTCGAGTGGCA
1 ATCCGTCAACAGTTCAATACTCTTCGAGTGGCA
5096 GAAACGCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (33 bp):
ATCCGTCAACAGTTCAATACTCTTCGAGTGGCA
Found at i:8483 original size:22 final size:22
Alignment explanation
Indices: 8455--8502 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
8445 GTTATTTAGT
8455 TTTTATTTTTATCACTCACTTA
1 TTTTATTTTTATCACTCACTTA
*
8477 TTTTATTTTTATCACTCATTTA
1 TTTTATTTTTATCACTCACTTA
8499 TTTT
1 TTTT
8503 GGTCGCGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATTTTTATCACTCACTTA
Found at i:8485 original size:28 final size:32
Alignment explanation
Indices: 8430--8488 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
8420 AAATTGTTAA
*
8430 TTTAGTCACTCACTTGTTATTTAGTTTTTATT
1 TTTAGTCACTCACTTGATATTTAGTTTTTATT
8462 TTTA-TCACTCACTT-AT-TTTA-TTTTTAT
1 TTTAGTCACTCACTTGATATTTAGTTTTTAT
8489 CACTCATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 4 0.15
30 1 0.04
31 10 0.38
32 4 0.15
ACGTcount: A:0.20, C:0.14, G:0.05, T:0.61
Consensus pattern (32 bp):
TTTAGTCACTCACTTGATATTTAGTTTTTATT
Found at i:18684 original size:2 final size:2
Alignment explanation
Indices: 18677--18736 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
18667 GATTCGGTTC
18677 AT AT AT AT AT AT 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 AT AT AT AT AT AT
18719 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
18737 CGTATTAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18890 original size:10 final size:11
Alignment explanation
Indices: 18869--18896 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18859 TTCTTATTAG
18869 TTTTATGTTTT
1 TTTTATGTTTT
18880 TTTTATGTTTT
1 TTTTATGTTTT
18891 TTTTAT
1 TTTTAT
18897 TTATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.82
Consensus pattern (11 bp):
TTTTATGTTTT
Found at i:24129 original size:16 final size:15
Alignment explanation
Indices: 24080--24139 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
24070 ATATTTTAAT
*
24080 TATTTATAATTTTAAA
1 TATTTA-AATTTAAAA
* *
24096 TATCTAAATTAAAAA
1 TATTTAAATTTAAAA
24111 TATTTAAATTTAAATA
1 TATTTAAATTTAAA-A
**
24127 TATGAAAATTTAA
1 TATTTAAATTTAA
24140 TTTTTTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 19 0.53
16 17 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
TATTTAAATTTAAAA
Found at i:39420 original size:30 final size:30
Alignment explanation
Indices: 39384--39440 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
39374 CCAACTACTT
39384 CTCCAAATGGTACTGCAGCTGCCCCAACTA
1 CTCCAAATGGTACTGCAGCTGCCCCAACTA
39414 CTCCAAATGGTACTGCAGCTGCCCCAA
1 CTCCAAATGGTACTGCAGCTGCCCCAA
39441 GATCACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.19
Consensus pattern (30 bp):
CTCCAAATGGTACTGCAGCTGCCCCAACTA
Found at i:39450 original size:30 final size:30
Alignment explanation
Indices: 39386--39453 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
39376 AACTACTTCT
* *
39386 CCAAATGGTACTGCAGCTGCCCCAACTACT
1 CCAAATGGTACTGCAGCTGCCCCAAATACA
39416 CCAAATGGTACTGCAGCTGCCCCAAGAT-CA
1 CCAAATGGTACTGCAGCTGCCCCAA-ATACA
39446 CCAAATGG
1 CCAAATGG
39454 ACAGCCTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.18
Consensus pattern (30 bp):
CCAAATGGTACTGCAGCTGCCCCAAATACA
Found at i:43828 original size:56 final size:56
Alignment explanation
Indices: 43701--44203 Score: 318
Period size: 51 Copynumber: 9.6 Consensus size: 56
43691 TGACGAGCCT
* *
43701 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * * *
43756 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
43812 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * * ** **
43867 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAA-CGAACTAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* ** **
43918 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * * ** **
43969 GCTCCCTATTCATTCAGAGAGTATAGGGCT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
44020 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
44071 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
44122 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* *
44173 GCTCCCTATTCTTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
44204 AATCTTCAAC
Statistics
Matches: 416, Mismatches: 26, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
51 294 0.71
55 71 0.17
56 51 0.12
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (56 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
Found at i:43923 original size:51 final size:51
Alignment explanation
Indices: 43808--44219 Score: 671
Period size: 51 Copynumber: 8.0 Consensus size: 51
43798 AATAAAACGG
* * * ** **
43808 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
43863 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
43914 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
43965 GTCCGCTCCCTATTCATTCAGAGAGTATAGGGCTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
44016 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
44067 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
44118 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
44169 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
44220 ATTTGCTTCA
Statistics
Matches: 342, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 311 0.91
55 31 0.09
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:43991 original size:102 final size:102
Alignment explanation
Indices: 43701--44219 Score: 673
Period size: 102 Copynumber: 5.0 Consensus size: 102
43691 TGACGAGCCT
* * * * *
43701 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAACGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACGAACTTGTCCGCTCCCTA
* * ** **
43764 TTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
60 TTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACTTGTCC
* * ** **
43812 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCCCTATT
* * *
43877 CTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTAGTCC
62 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
43918 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
*
43983 CAGAGAGTATAGGGCTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
44020 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
44085 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* *
44122 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
44187 CAGAGAGTATAGGACTCAATCTTCAACGAACTT
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTT
44220 ATTTGCTTCA
Statistics
Matches: 374, Mismatches: 28, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
102 260 0.70
106 36 0.10
107 10 0.03
110 2 0.01
111 65 0.17
112 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (102 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:45393 original size:26 final size:24
Alignment explanation
Indices: 45359--45413 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 24
45349 TTATTTCTCT
45359 TTTTCCATTTTTCTCTTTTTCTTTC
1 TTTTCCATTTTT-TCTTTTTCTTTC
*
45384 ATTTTCCATTTTTTCTTTTTTTTTC
1 -TTTTCCATTTTTTCTTTTTCTTTC
45409 TTTTC
1 TTTTC
45414 GTTTTTCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 5 0.18
25 11 0.39
26 12 0.43
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTCCATTTTTTCTTTTTCTTTC
Found at i:45413 original size:34 final size:34
Alignment explanation
Indices: 45366--45438 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
45356 TCTTTTTCCA
* *
45366 TTTTTCTCTTTTTCTTTCATTTTC-CATTTTTTCTT
1 TTTTTCTCTTTTTCGTT--TTTCCACATTTTTTCTT
*
45401 TTTTTTTC-TTTTCGTTTTTCCATCATTTTTTCTT
1 TTTTTCTCTTTTTCGTTTTTCCA-CATTTTTTCTT
45435 TTTT
1 TTTT
45439 CACATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
32 4 0.12
34 22 0.67
35 7 0.21
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.75
Consensus pattern (34 bp):
TTTTTCTCTTTTTCGTTTTTCCACATTTTTTCTT
Found at i:45468 original size:19 final size:18
Alignment explanation
Indices: 45424--45473 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
45414 GTTTTTCCAT
45424 CATTTTTTCTT-TTTTCA
1 CATTTTTTCTTCTTTTCA
*
45441 CATTTTTTCTTCTTTTCT
1 CATTTTTTCTTCTTTTCA
*
45459 CTTTTATTTCTTCTT
1 CATTT-TTTCTTCTT
45474 CAAGCAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.38
18 9 0.31
19 9 0.31
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (18 bp):
CATTTTTTCTTCTTTTCA
Found at i:48964 original size:2 final size:2
Alignment explanation
Indices: 48957--48988 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
48947 GAAAGAAAAG
48957 AT 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 AT
48989 GGGAGGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55198 original size:45 final size:46
Alignment explanation
Indices: 55132--55227 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
55122 GTTATCCACA
*
55132 AAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC-TTATTCAG
1 AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTC-G
* *
55178 AAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
55224 AAAA
1 AAAA
55228 AACGAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 27 0.60
46 12 0.27
47 6 0.13
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (46 bp):
AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:59069 original size:26 final size:25
Alignment explanation
Indices: 59017--59102 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 25
59007 ATTCATTTCA
*
59017 CCTAAATCCATAAAACTTCAA-CTAAAC
1 CCTAAA-CCATAAATC-TCAATC-AAAC
59044 CCTAAACCATAAATCTCAATCAAAAC
1 CCTAAACCATAAATCTCAATC-AAAC
* * *
59070 CATTAACC-TAAAATCACAATCAAAC
1 CCTAAACCAT-AAATCTCAATCAAAC
*
59095 CTTAAACC
1 CCTAAACC
59103 TCATAACTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
25 15 0.30
26 29 0.58
27 6 0.12
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (25 bp):
CCTAAACCATAAATCTCAATCAAAC
Found at i:59102 original size:25 final size:27
Alignment explanation
Indices: 59040--59108 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
59030 AACTTCAACT
* *
59040 AAACCCTAAACC-ATAAATCTCAATCA
1 AAACCTTAAACCTATAAATCACAATCA
59066 AAACCATT-AACCTA-AAATCACAATC-
1 AAACC-TTAAACCTATAAATCACAATCA
59091 AAACCTTAAACCTCATAA
1 AAACCTTAAACCT-ATAA
59109 CTAGGGCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 2 0.06
25 10 0.28
26 20 0.56
27 4 0.11
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (27 bp):
AAACCTTAAACCTATAAATCACAATCA
Found at i:68950 original size:90 final size:90
Alignment explanation
Indices: 68793--68971 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
68783 TAATAAAAGG
* * * * *
68793 TAACAAACATGATTCTAATATCATAATGATGACTTTTATCGTCTGTTTATCAAGAGTTTTTCAAT
1 TAACAAAAATGATTCAAATATCAAAATGATGAATTTTATCGTCTGTTTATCAAGAATTTTTCAAT
*
68858 GATTGTAACCCTTATGACTAAGTTA
66 GATTGTAACCCCTATGACTAAGTTA
* *
68883 TAACAAAAATGATTCAAATATCAAAATGATGAATTTTATCGTCTGTTTGTCAAGAATTTTTCGAT
1 TAACAAAAATGATTCAAATATCAAAATGATGAATTTTATCGTCTGTTTATCAAGAATTTTTCAAT
*
68948 GATTGTAGCCCCTATGACTAAGTT
66 GATTGTAACCCCTATGACTAAGTT
68972 GTTATAAATA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (90 bp):
TAACAAAAATGATTCAAATATCAAAATGATGAATTTTATCGTCTGTTTATCAAGAATTTTTCAAT
GATTGTAACCCCTATGACTAAGTTA
Done.