Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007972.1 Hibiscus syriacus cultivar Beakdansim tig00110409_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: 115004
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:102519 original size:30 final size:30
Alignment explanation
Indices: 102478--102539 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
102468 ACATAAGAAC
*
102478 AGTTGCCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
102508 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
102538 AG
1 AG
102540 GTTCTTCGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:107661 original size:135 final size:135
Alignment explanation
Indices: 107458--107796 Score: 357
Period size: 135 Copynumber: 2.5 Consensus size: 135
107448 TATCACCTTT
* * * * * *
107458 AGATGGCC-AGAACTCTTCATCACGTTTGAGTCA-TGTCATCAC-CTAACCT-GATCTCCCCATC
1 AGATGGCCAAGAACTCTTCATCACGTATGAGT-AGTGTCATCACTC-GA-CTAAATTTCCTCATT
** * * * * *
107519 ACATAGGAGTTGTGTCAACCTTTGATAACCAGTC-GTCCTCATCGCATAGGAATCGAGTTACCAT
63 ATGTAGGAGTTATGTCAACCATTGATAACCA-ACAGTCCTCATCGCATAGGAACCAAGTTACCAT
* *
107583 CCTTCTTAA
127 ACTTCTAAA
107592 AGATGGCCAAGAACTCTTCATCACGTATGAGTAGTGTCATCACTCGACTAAATTTCCTCATTATG
1 AGATGGCCAAGAACTCTTCATCACGTATGAGTAGTGTCATCACTCGACTAAATTTCCTCATTATG
* * * *
107657 TAGGAGTTATGTCAACCATTGATAACCAACAGTCTTCATCGCGTAGGAACCAAGTTATCATATTT
66 TAGGAGTTATGTCAACCATTGATAACCAACAGTCCTCATCGCATAGGAACCAAGTTACCATACTT
107722 CTAAA
131 CTAAA
** * * * * *
107727 AGATGGAAAAGAACTCTTCATCACGTATGAGCAGTTTCATCCCTTGACTATATCTT-CTCATTAT
1 AGATGGCCAAGAACTCTTCATCACGTATGAGTAGTGTCATCACTCGACTAAAT-TTCCTCATTAT
107791 GTAGGA
65 GTAGGA
107797 TTCTTGTTAC
Statistics
Matches: 173, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
134 12 0.07
135 158 0.91
136 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (135 bp):
AGATGGCCAAGAACTCTTCATCACGTATGAGTAGTGTCATCACTCGACTAAATTTCCTCATTATG
TAGGAGTTATGTCAACCATTGATAACCAACAGTCCTCATCGCATAGGAACCAAGTTACCATACTT
CTAAA
Found at i:108825 original size:14 final size:14
Alignment explanation
Indices: 108798--108831 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
108788 CACAACAAGA
*
108798 AGCGCCGGCTATACC
1 AGCG-CGGCCATACC
108813 AGCGCGGCCATACC
1 AGCGCGGCCATACC
108827 AGCGC
1 AGCGC
108832 CGCTAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.21, C:0.41, G:0.29, T:0.09
Consensus pattern (14 bp):
AGCGCGGCCATACC
Found at i:108971 original size:43 final size:43
Alignment explanation
Indices: 108841--109125 Score: 315
Period size: 43 Copynumber: 6.7 Consensus size: 43
108831 CCGCTAATGT
* * * * *
108841 TAGCGGCGTTTGTGAAATAAAAACGCCACAAAAAGTCAAGATCTA
1 TAGCGGCGTTTTTG-GATACAAACGCCGCAAAAGGTC-AGATCTA
* *
108886 TAGCAGCGTTTTT-GAAACAAACGCCGC-AAAGGTCAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
*
108927 TAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* * * * * ** *
108970 TAGCAGCGATTTTGTATACAAACGCCACGAAACTTCAGATCTG
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* * * *
109013 TAGAGGCATTTTTGGATACAAATGCCGCAAAAGGTCAGATCTG
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* *
109056 TAGCGGCGTTTTTGGATACAAACGTCGCAAAAGGTCAGATCTG
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* *
109099 TAGCGGCGGTTTTGGA-ACAAACACCGC
1 TAGCGGCGTTTTTGGATACAAACGCCGC
109126 TAATTACCAT
Statistics
Matches: 204, Mismatches: 34, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
41 19 0.09
42 27 0.13
43 147 0.72
45 11 0.05
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
Found at i:110055 original size:58 final size:59
Alignment explanation
Indices: 109965--110077 Score: 192
Period size: 58 Copynumber: 1.9 Consensus size: 59
109955 CTGTACAAGA
*
109965 ATAGCAGTAATGAATAAAAAGTTCGCTATAAATTTAACCAATAT-GTTTTAAATGATAC
1 ATAGCAGTAATGAATAAAAAGTTCGCTATAAATTTAACCAAGATGGTTTTAAATGATAC
* *
110023 ATAGCAGTAATGAATACAAAGTTCGTTATAAATTTAACCAAGATGGTTTTAAATG
1 ATAGCAGTAATGAATAAAAAGTTCGCTATAAATTTAACCAAGATGGTTTTAAATG
110078 GTCAGTGACG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 41 0.80
59 10 0.20
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (59 bp):
ATAGCAGTAATGAATAAAAAGTTCGCTATAAATTTAACCAAGATGGTTTTAAATGATAC
Found at i:113051 original size:40 final size:41
Alignment explanation
Indices: 113003--113509 Score: 558
Period size: 40 Copynumber: 12.6 Consensus size: 41
112993 ACAACTTGCA
113003 GCGTTTGTAAAAAAACGCCACTAAAG-ACGAGTCTATAGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
*
113043 GCGCTTGT-AAAAAA--CCACTAAAG-ACGAGTCTATA-CG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
* * * * * *
113079 GCATTTGTATAAAAACGCCACTAAAGTGCAAGCCTATTGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
*
113120 GCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGAG
1 GCGTTTGTAAA-A-AAACGCCACTAAAGTACGAGTCTATAGCG
* *
113163 GCGTTTGTATAAAAAAAAGCCACTAATGTACGAGTCTATAGCG
1 GCGTTTG--TAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
* * * *
113206 GCGTTTGT-ACAAAACGCCACTAAAGTACAAGCCTATTGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
*
113246 GCGTTTATAAACACAAACGCCACTAAAGTACGAGTCTATAGC-
1 GCGTTTGTAAA-A-AAACGCCACTAAAGTACGAGTCTATAGCG
* *
113288 GCGTTTGTATAAAAACGCCACT-AAGTACAAGTCTATAGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
* * * *
113328 GCGTTTAT-ATAAAACGCCACTAAAGTAGGCGTCTATAGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
* * * * *
113368 GCGTTTGT-ATAAAACACCGCAAAAGTACTA--CTATAGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
*
113406 GCGTTTGTATAAAAACGCCACT-AAGTACGAGTCTATAGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
* * * *
113446 CCATTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGCG
1 GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
* *
113487 G-GTTTGTATAAAAACGCCGCTAA
1 GCGTTTGTAAAAAAACGCCACTAA
113510 CGTTACCATT
Statistics
Matches: 391, Mismatches: 58, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
36 8 0.02
37 25 0.06
38 23 0.06
39 50 0.13
40 148 0.38
41 32 0.08
42 11 0.03
43 89 0.23
44 1 0.00
45 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (41 bp):
GCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAGCG
Found at i:113237 original size:126 final size:124
Alignment explanation
Indices: 112998--113494 Score: 598
Period size: 126 Copynumber: 4.1 Consensus size: 124
112988 AAGAGACAAC
* *
112998 TTGCAGCGTTTGTAAA-A-AAACGCCACTAAAG-ACGAGTCTATAGCGGCGCTTG--TAAAAAA-
1 TTGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAAG
*
113057 CCACTAAAG-ACGAGTCTATA-CGGCATTTGTATAAAAACGCCACTAAAGTGCAAGCCTA
66 CCACT-AAGTACGAGTCTATAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGCCTA
*
113115 TTGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGAGGCGTTTGTATAAAAAAA
1 TTGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT--AAAAA
* *
113180 AGCCACTAATGTACGAGTCTATAGCGGCGTTTGTA-CAAAACGCCACTAAAGTACAAGCCTA
64 AGCCACTAA-GTACGAGTCTATAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGCCTA
* *
113241 TTGCGGCGTTTATAAACACAAACGCCACTAAAGTACGAGTCTATAGC-GCGTTTGTATAAAAACG
1 TTGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAAG
* * * *** *
113305 CCACTAAGTACAAGTCTATAGCGGCGTTTATAT-AAAACGCCACTAAAGTAGGCGTCTA
66 CCACTAAGTACGAGTCTATAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGCCTA
* * * * *
113363 TAGCGGCGTTTGTATAAAAC-ACCG-CA--AAAGTACTA--CTATAGCGGCGTTTGTATAAAAAC
1 TTGCGGCGTTTGTA-AACACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAA
* * * *
113422 GCCACTAAGTACGAGTCTATAGCGCCATTTGTATAAAAATGCCACTAAAGTACGAGTCTA
65 GCCACTAAGTACGAGTCTATAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGCCTA
*
113482 TAGCGG-GTTTGTA
1 TTGCGGCGTTTGTA
113495 TAAAAACGCC
Statistics
Matches: 338, Mismatches: 27, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
117 22 0.07
118 54 0.16
119 50 0.15
120 19 0.06
121 2 0.01
122 60 0.18
123 17 0.05
124 8 0.02
125 16 0.05
126 80 0.24
127 10 0.03
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (124 bp):
TTGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAAG
CCACTAAGTACGAGTCTATAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGCCTA
Done.