Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009255.1 Hibiscus syriacus cultivar Beakdansim tig00112903_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: 84075
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:844 original size:41 final size:41
Alignment explanation
Indices: 787--916 Score: 181
Period size: 41 Copynumber: 3.2 Consensus size: 41
777 ATTCTGCATG
*
787 GAAGAAAACAGAAACTTGAAGCATATTTGCAAGAATGTAAT
1 GAAGAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
* *
828 GAAGAAAACAGAAACTTGAAGCATCTTTGCAAGAATGCAAC
1 GAAGAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
* * * *
869 GGA-AAAACAGAAACTTGAGGCGTCTTTGCTAGAATGTAAT
1 GAAGAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
*
909 GAGGAAAA
1 GAAGAAAA
917 ATCTAGACTC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 33 0.43
41 44 0.57
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (41 bp):
GAAGAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
Found at i:11925 original size:18 final size:18
Alignment explanation
Indices: 11902--11973 Score: 135
Period size: 18 Copynumber: 4.0 Consensus size: 18
11892 ATTTGAATAA
11902 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
*
11920 TTGAATCAAATATAAAAT
1 TTGAATCGAATATAAAAT
11938 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
11956 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
11974 CTTAAAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:20334 original size:18 final size:18
Alignment explanation
Indices: 20311--20346 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20301 ATTCAAATAA
20311 TTGAATCGAAAATAAAAT
1 TTGAATCGAAAATAAAAT
*
20329 TTGAATCGAATATAAAAT
1 TTGAATCGAAAATAAAAT
20347 CTTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (18 bp):
TTGAATCGAAAATAAAAT
Found at i:24659 original size:4 final size:4
Alignment explanation
Indices: 24611--24640 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
24601 AAAATAATCA
*
24611 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
24641 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29076 original size:18 final size:18
Alignment explanation
Indices: 29039--29073 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29029 ATGTACTATG
*
29039 ATATATGTGATATTCTTT
1 ATATATGTGATATGCTTT
29057 ATATAT-TGATATGCTTT
1 ATATATGTGATATGCTTT
29074 TATTTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (18 bp):
ATATATGTGATATGCTTT
Found at i:29271 original size:2 final size:2
Alignment explanation
Indices: 29266--29302 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
29256 TATATATATA
* *
29266 TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG CG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
29303 TAATGATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.05, G:0.49, T:0.46
Consensus pattern (2 bp):
TG
Found at i:29807 original size:38 final size:38
Alignment explanation
Indices: 29756--29829 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
29746 TTAAACCAAG
* *
29756 CATGTTTTGAATTGAAAAGTGTATACATACCACTAGAT
1 CATGTTTTAAATTGAAAAGTGTATACATACAACTAGAT
* *
29794 CATGTTTTAAATTGAAAATTTTATACATACAACTAG
1 CATGTTTTAAATTGAAAAGTGTATACATACAACTAG
29830 GATATCATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (38 bp):
CATGTTTTAAATTGAAAAGTGTATACATACAACTAGAT
Found at i:36195 original size:15 final size:15
Alignment explanation
Indices: 36175--36205 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36165 TTAATTTTGA
36175 TGAAAAGTCAAATTT
1 TGAAAAGTCAAATTT
*
36190 TGAAAAGTCATATTT
1 TGAAAAGTCAAATTT
36205 T
1 T
36206 ATCTTTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (15 bp):
TGAAAAGTCAAATTT
Found at i:40205 original size:20 final size:20
Alignment explanation
Indices: 40189--40232 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
40179 CGACCCGCCC
40189 CGACCTGGTTTGACCCGACA
1 CGACCTGGTTTGACCCGACA
* *
40209 TGACCTGGTTTGA-CCGATA
1 CGACCTGGTTTGACCCGACA
40228 CGACC
1 CGACC
40233 CGACTTCCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (20 bp):
CGACCTGGTTTGACCCGACA
Found at i:46375 original size:117 final size:119
Alignment explanation
Indices: 46227--46440 Score: 299
Period size: 117 Copynumber: 1.8 Consensus size: 119
46217 ATTTTCTTTT
** *
46227 GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTTAAAAA
1 GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATAATGAAAAAGGAGTTAGAGATTTTAAAAA
*
46292 TGAAATGTGAAA-TCTTTGAAAAAG-AAATTTTCGAACTAAACAAACTTCTTCTA
66 TGAAATGTGAAAGT-ATTGAAAAAGAAAATTTTCGAACTAAACAAACTTCTTCTA
* * * * * *
46345 GAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATAATGAAGAAGGATTTAGAGATTTTAAAAA
1 GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATAATGAAAAAGGAGTTAGAGATTTTAAAAA
*
46409 TGAAATTTGAAAGTATTGAAAAAGAAAATTTT
66 TGAAATGTGAAAGTATTGAAAAAGAAAATTTT
46441 GATTTGAAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
117 71 0.86
118 12 0.14
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (119 bp):
GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATAATGAAAAAGGAGTTAGAGATTTTAAAAA
TGAAATGTGAAAGTATTGAAAAAGAAAATTTTCGAACTAAACAAACTTCTTCTA
Found at i:47502 original size:16 final size:16
Alignment explanation
Indices: 47477--47507 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47467 AGAGGATTGC
*
47477 CAAAGCTAAAATTTGA
1 CAAAGATAAAATTTGA
47493 CAAAGATAAAATTTG
1 CAAAGATAAAATTTG
47508 TGATGTATGT
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:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (16 bp):
CAAAGATAAAATTTGA
Found at i:54682 original size:15 final size:15
Alignment explanation
Indices: 54649--54690 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
54639 GAAAATCAAG
* * *
54649 AATAAAGATTAAGAT
1 AATAAAGAATAAAAC
54664 AATAAAGAATAAAAC
1 AATAAAGAATAAAAC
54679 AATAAA-AATAAA
1 AATAAAGAATAAA
54691 TAAAGACGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (15 bp):
AATAAAGAATAAAAC
Found at i:66359 original size:12 final size:12
Alignment explanation
Indices: 66342--66367 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
66332 CGAGTTTGTC
66342 TTTTTCATTTGA
1 TTTTTCATTTGA
66354 TTTTTCATTTGA
1 TTTTTCATTTGA
66366 TT
1 TT
66368 ATCAATATAT
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:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTCATTTGA
Found at i:67254 original size:98 final size:97
Alignment explanation
Indices: 67078--67280 Score: 241
Period size: 98 Copynumber: 2.1 Consensus size: 97
67068 TAATTTACGA
* * * * * *
67078 CATAAAATTACGACACACAAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGCAG
1 CATAAATTTACGACACACAAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAA
*
67143 CGTAAGTCGTAAAT-GTAAGTCATAAATGCGTGT
66 CGTAAGTCATAAATAGT--GTCATAAATGCGTGT
* *
67176 CATAAATTTATGACACACAAATGTGTGTCATCTTCATTT-ATGACGAGGGCTTCAATGACGCGCA
1 CATAAATTTACGACACACAAATGTGTGTCATCTT-ATTTAATGACGAGGGCTTCAATGACACGCA
* *
67240 ATGTGCA-TCATAAATACGTGTCATAAATGCGTGT
65 ACGT-AAGTCATAAATA-GTGTCATAAATGCGTGT
67274 CATAAAT
1 CATAAAT
67281 GCGCGTCATA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
98 84 0.93
99 4 0.04
100 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (97 bp):
CATAAATTTACGACACACAAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAA
CGTAAGTCATAAATAGTGTCATAAATGCGTGT
Found at i:67265 original size:13 final size:13
Alignment explanation
Indices: 67247--67290 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
67237 GCAATGTGCA
*
67247 TCATAAATACGTG
1 TCATAAATGCGTG
67260 TCATAAATGCGTG
1 TCATAAATGCGTG
*
67273 TCATAAATGCGCG
1 TCATAAATGCGTG
67286 TCATA
1 TCATA
67291 GATGTATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:73151 original size:18 final size:19
Alignment explanation
Indices: 73116--73158 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
73106 TGAATAGATA
*
73116 AATAAATATATAAATAATG
1 AATAAAAATATAAATAATG
73135 AATAAAAATAT-AATAATG
1 AATAAAAATATAAATAATG
73153 AATAAA
1 AATAAA
73159 GTAGATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AATAAAAATATAAATAATG
Found at i:75271 original size:46 final size:46
Alignment explanation
Indices: 75202--75531 Score: 536
Period size: 46 Copynumber: 7.2 Consensus size: 46
75192 TATATAATCT
* *
75202 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTAGCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
75247 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
75293 CTTACCATCTAATACCATAAGATCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
75339 CTTACCATTTAATACCATAAGCTAGTAAGCTTATTTTACCAATACA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
75385 CTTTCCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
75431 TTTACCATTTAATAGCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
75477 CTTACCATTTAATACCATAAGTTCTTAAGCTTATTTTACCAATACA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
75523 CTTGCCATT
1 CTTACCATT
75532 ATTCTATAAC
Statistics
Matches: 264, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 10 0.04
46 254 0.96
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:75731 original size:61 final size:61
Alignment explanation
Indices: 75622--75736 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
75612 GTAGTACTAA
* *
75622 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCAGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCGTGCCCACC
* * * * *
75683 ACCTACACTAAGCTTACGCTATAGTGCTACTCCGGACATGATATATAAGGTCGT
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCGT
75737 ATCCACCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCGTGCCCACC
Found at i:77632 original size:13 final size:13
Alignment explanation
Indices: 77600--77646 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
77590 AACGGTCAAC
77600 GGTCAACGGGTCG
1 GGTCAACGGGTCG
77613 GGT---CGGGTCG
1 GGTCAACGGGTCG
77623 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
77636 GGTAAACGGGT
1 GGTCAACGGGT
77647 AAACGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:77679 original size:10 final size:10
Alignment explanation
Indices: 77662--77713 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
77652 GGTCGTGACA
77662 GGTC-AAACC
1 GGTCAAAACC
77671 GGTCAAAACC
1 GGTCAAAACC
*
77681 GATTCAAAACC
1 G-GTCAAAACC
*
77692 GGT-TAAACC
1 GGTCAAAACC
77701 GGTCAAAACC
1 GGTCAAAACC
77711 GGT
1 GGT
77714 TTCCAGCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 12 0.33
10 15 0.42
11 9 0.25
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (10 bp):
GGTCAAAACC
Done.