Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002740.1 Hibiscus syriacus cultivar Beakdansim tig00005650_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: 58431
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:994 original size:39 final size:39
Alignment explanation
Indices: 952--1084 Score: 126
Period size: 39 Copynumber: 3.3 Consensus size: 39
942 TATTTAAAAT
* * *
952 TATTTAAACTAAAATACCTAAATCAGAGATAAAATATAT
1 TATTTAAAATAAAATACCTAAATCAAAGATAAAATATAA
* * * *
991 TATTTAAAATAATAT-CCTAAATCCTAA-TTAAAACACTTAAAAA
1 TATTTAAAATAAAATACCTAAAT-CAAAGAT-AAA-A--T-ATAA
*
1034 TATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
1 TATTTAAAATAAAATACCTAAATCAAAGATAAAATATAA
1073 TATTTAAAATAA
1 TATTTAAAATAA
1085 TATATTAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
38 8 0.11
39 33 0.45
40 2 0.03
42 2 0.03
43 22 0.30
44 7 0.09
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (39 bp):
TATTTAAAATAAAATACCTAAATCAAAGATAAAATATAA
Found at i:1012 original size:82 final size:82
Alignment explanation
Indices: 926--1087 Score: 261
Period size: 82 Copynumber: 2.0 Consensus size: 82
916 AATAAAGAAA
* * * * * * *
926 TAAATCCTAATTAAAATATTTAAAATTATTTAAACTAAAATACCTAAATCAGAGATAAAATATAT
1 TAAATCCTAATTAAAACACTTAAAAATATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
991 TATTTAAAATAATATCC
66 TATTTAAAATAATATCC
1008 TAAATCCTAATTAAAACACTTAAAAATATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAACACTTAAAAATATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
1073 TATTTAAAATAATAT
66 TATTTAAAATAATAT
1088 ATTAAATATG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (82 bp):
TAAATCCTAATTAAAACACTTAAAAATATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
TATTTAAAATAATATCC
Found at i:5904 original size:16 final size:16
Alignment explanation
Indices: 5880--5910 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5870 CGTGTAGGCT
*
5880 CTTCCAAGAACCTGGG
1 CTTCAAAGAACCTGGG
5896 CTTCAAAGAACCTGG
1 CTTCAAAGAACCTGG
5911 ACAAAAGGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (16 bp):
CTTCAAAGAACCTGGG
Found at i:11945 original size:26 final size:26
Alignment explanation
Indices: 11900--11949 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
11890 TATTGGGAGA
* *
11900 AAGCTAGAATGATTTGGGATGATTTTG
1 AAGCTAGAATGAGTTAGGAT-ATTTTG
11927 AAGCTA-AATGAGTTAGGATATTT
1 AAGCTAGAATGAGTTAGGATATTT
11950 ATAGTTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 11 0.52
27 6 0.29
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (26 bp):
AAGCTAGAATGAGTTAGGATATTTTG
Found at i:16245 original size:57 final size:58
Alignment explanation
Indices: 16158--16276 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 58
16148 CCCTCGACTA
16158 TTAATAGTTACAAAATAGTCATTCGACTATTCATATATTTCAAACTCATATTTTTTCG
1 TTAATAGTTACAAAATAGTCATTCGACTATTCATATATTTCAAACTCATATTTTTTCG
* *
16216 TTAATAGTTAC-AAATGGTCATTCGACTATTCATATATTTTAAACTCATATTTTTTCG
1 TTAATAGTTACAAAATAGTCATTCGACTATTCATATATTTCAAACTCATATTTTTTCG
16273 TTAA
1 TTAA
16277 AAATTTGATT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 48 0.81
58 11 0.19
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (58 bp):
TTAATAGTTACAAAATAGTCATTCGACTATTCATATATTTCAAACTCATATTTTTTCG
Found at i:17841 original size:25 final size:25
Alignment explanation
Indices: 17809--17856 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17799 GAGTTGAATT
*
17809 TTTTTGAGCTTAAATCTAACTTTAA
1 TTTTTGAGCTTAAATCGAACTTTAA
* *
17834 TTTTTGAGTTTAATTCGAACTTT
1 TTTTTGAGCTTAAATCGAACTTT
17857 GATAGTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (25 bp):
TTTTTGAGCTTAAATCGAACTTTAA
Found at i:21027 original size:12 final size:12
Alignment explanation
Indices: 21010--21049 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
21000 TACAGCAGCC
21010 CCCCCTTAGCAG
1 CCCCCTTAGCAG
21022 CCCCCTTAGCAG
1 CCCCCTTAGCAG
21034 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
21047 CCC
1 CCC
21050 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:21038 original size:13 final size:13
Alignment explanation
Indices: 21003--21049 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
20993 AAAAAATTAC
21003 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
21017 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
21029 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
21042 AGCAGCCC
1 AGCAGCCC
21050 ATGTGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.38
13 15 0.47
14 5 0.16
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:24338 original size:15 final size:16
Alignment explanation
Indices: 24310--24341 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
24300 AAAATCTTTC
24310 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
24326 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
24341 T
1 T
24342 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:47075 original size:31 final size:30
Alignment explanation
Indices: 47004--47077 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
46994 AATGTTTGTA
*
47004 TTGTATTGTAATGTAATGTAGGAGTTAATGT
1 TTGTATT-TAATGTAATGTAGGAGTTAATCT
* * *
47035 TTCTAATTTAATGTGATGTATGAGTTAATACT
1 TTGT-ATTTAATGTAATGTAGGAGTTAAT-CT
47067 TTGTATTTAAT
1 TTGTATTTAAT
47078 AAAAATTATC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (30 bp):
TTGTATTTAATGTAATGTAGGAGTTAATCT
Found at i:48888 original size:18 final size:18
Alignment explanation
Indices: 48856--48893 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
48846 TTATCTTAAT
*
48856 ATATCAATATTATAATTA
1 ATATCAATATTATAAATA
48874 ATAT-AATATTAATAAATA
1 ATATCAATATT-ATAAATA
48892 AT
1 AT
48894 GATTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATCAATATTATAAATA
Found at i:50808 original size:23 final size:23
Alignment explanation
Indices: 50779--50837 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
50769 CGTATAAATG
50779 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* * *
50802 CATCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTA
50825 CACCGAAGTGCCA
1 CACCGAAGTGCCA
50838 TATAAAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:54074 original size:107 final size:107
Alignment explanation
Indices: 53895--54094 Score: 310
Period size: 107 Copynumber: 1.9 Consensus size: 107
53885 TCTGTTTCTT
* * * *
53895 CTTCACTACTCTTTCTTGAAGACTGAGAATGATTGACTTGATGAGAATCTAATTTCACTACTCTT
1 CTTCACTACTCTTCCGTGAAGACTGAAAATGATTGACTTGATAAGAATCTAATTTCACTACTCTT
53960 CCATGAAGATCAGATTCAAGGTTGAACTGGCTTCTGCTTTTG
66 CCATGAAGATCAGATTCAAGGTTGAACTGGCTTCTGCTTTTG
* * *
54002 CTTCACTACTCTTCCGTGAAGACTGAAAATGATTGTCTTGATAAGGATCTAATTTCACTACTTTT
1 CTTCACTACTCTTCCGTGAAGACTGAAAATGATTGACTTGATAAGAATCTAATTTCACTACTCTT
* * *
54067 TCGTGAAGATCATATTCAAGGTTGAACT
66 CCATGAAGATCAGATTCAAGGTTGAACT
54095 TGGTTCCACT
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 83 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (107 bp):
CTTCACTACTCTTCCGTGAAGACTGAAAATGATTGACTTGATAAGAATCTAATTTCACTACTCTT
CCATGAAGATCAGATTCAAGGTTGAACTGGCTTCTGCTTTTG
Found at i:54203 original size:20 final size:20
Alignment explanation
Indices: 54178--54267 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
54168 ACTCAAGGAA
*
54178 TTTACAAATTACCTGGAGGC
1 TTTACAAATTACCCGGAGGC
*
54198 TTTACAAATTACCCAGAGGC
1 TTTACAAATTACCCGGAGGC
*
54218 TTTACAAATGACCCGGAGGC
1 TTTACAAATTACCCGGAGGC
* * *
54238 TTTACAAATGACCCGAAGGT
1 TTTACAAATTACCCGGAGGC
54258 TTTACAAATT
1 TTTACAAATT
54268 CATGTGAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (20 bp):
TTTACAAATTACCCGGAGGC
Done.