Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008972.1 Hibiscus syriacus cultivar Beakdansim tig00112318_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: 36668
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:341 original size:103 final size:105
Alignment explanation
Indices: 1--781 Score: 1259
Period size: 103 Copynumber: 7.6 Consensus size: 105
1 TTGAACTTACGTTGTCTGGAAG-CCAATATCCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 TTGAACTTACGTTGTCTGG-AGTCCAATAT-CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
65 GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
64 GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* **
107 TTGAACTT-TGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGA
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
171 GAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
211 TTG-ACTTGCGTTGTCTGGAGTCC-ATATCCTTCGTTGTGAAGTTGAACTTGGCTCTGAAATTGA
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
274 G-GATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
313 TTGAACTTACG-TGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGGAATTGGCTCTGAAATTGA
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
377 AAAATG-TTGTTTGA-AACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
416 TTGAACTTACGTTGTCTGGAATCCAATATCCTTCGTT-TGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
480 GAAATGTTTGTTGACAACCA-CGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* **
519 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGA
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
584 GAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
624 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-TGAAATTGGCTCTGAAA-TGA
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
687 AAAATGTTGGTTGACAACCAGCGGTCCC-T--TCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
724 TTGAACTTACGTTGTCTGGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
782 GGTAAAACTG
Statistics
Matches: 633, Mismatches: 30, Indels: 29
0.91 0.04 0.04
Matches are distributed among these distances:
100 49 0.08
101 14 0.02
102 52 0.08
103 242 0.38
104 190 0.30
105 78 0.12
106 8 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
Found at i:11011 original size:10 final size:10
Alignment explanation
Indices: 10986--11019 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
10976 AACGTTAGTA
*
10986 AAATAGAAAT
1 AAATAAAAAT
*
10996 AGATAAAAAT
1 AAATAAAAAT
11006 AAATAAAAAT
1 AAATAAAAAT
11016 AAAT
1 AAAT
11020 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:12483 original size:2 final size:2
Alignment explanation
Indices: 12476--12510 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12466 AAAAATTCAA
12476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12511 GTAAATACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12493 original size:250 final size:244
Alignment explanation
Indices: 12007--12485 Score: 854
Period size: 250 Copynumber: 1.9 Consensus size: 244
11997 ATGCAAGGAA
* *
12007 AAATACGAAAATTCAAATGAGGAAAAAGGAAAGAAATGGAAAAAATATAAACAAATAAATAAAAA
1 AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGAAAAAAATATAAACAAATAAATAAAAA
12072 TATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGACATGAGTAGTATATATATAATAAA
66 TATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGACATGAGTAG-ATATATATAATAAA
12137 ATAACATATAAATAAAGGAAAATAGGTAATGTATATATATATATATATATAAACATAAGAATATA
130 ATAACATATAAATAAAGGAAAATAGGTAATG-----ATATATATATATATAAACATAAGAATATA
12202 ATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
190 ATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
12257 AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGAAAAAAATATAAACAAATAAATAAAAA
1 AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGAAAAAAATATAAACAAATAAATAAAAA
* *
12322 TGTATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGATATGAGTAG-TATATATAATAAAA
66 TATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGACATGAGTAGATATATATAATAAAA
12386 TAACATATAAATAAAGGAAAATAGGTAATG-TATATATATATATAAACATAAGAATATAATACAA
131 TAACATATAAATAAAGGAAAATAGGTAATGATATATATATATATAAACATAAGAATATAATACAA
12450 TATAGCGTAAACAAATAAAAATTCAAATATATATAT
196 TATAGCGTAAACAAATAAAAATTCAAATATATATAT
12486 ATATATATAT
Statistics
Matches: 225, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
242 70 0.31
248 44 0.20
250 111 0.49
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.24
Consensus pattern (244 bp):
AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGAAAAAAATATAAACAAATAAATAAAAA
TATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGACATGAGTAGATATATATAATAAAA
TAACATATAAATAAAGGAAAATAGGTAATGATATATATATATATAAACATAAGAATATAATACAA
TATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
Found at i:14141 original size:23 final size:23
Alignment explanation
Indices: 14111--14160 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
14101 ACAAGTATAT
*
14111 GATCTATTGATCGAACTAATCTA
1 GATCTATTGATCGAACTAATCCA
14134 GATCTATTGATCGAACTAATCCA
1 GATCTATTGATCGAACTAATCCA
14157 GATC
1 GATC
14161 AGATTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (23 bp):
GATCTATTGATCGAACTAATCCA
Found at i:21111 original size:25 final size:26
Alignment explanation
Indices: 21083--21138 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
21073 AAATAATTTT
*
21083 ATATTATGAATTTAATATTAAT-AAA
1 ATATTATGAATATAATATTAATCAAA
* * *
21108 ATATT-TTAATATCATTTTAATCAAA
1 ATATTATGAATATAATATTAATCAAA
21133 ATATTA
1 ATATTA
21139 ATTATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTATGAATATAATATTAATCAAA
Found at i:21183 original size:40 final size:40
Alignment explanation
Indices: 21097--21183 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
21087 TATGAATTTA
* *
21097 ATATTAATAAAATATTTTAATATCATTTTAATCAAAATATT
1 ATATTATTAAAATATTTAAATATCATTTT-ATCAAAATATT
*
21138 A-ATTATTAAAATATTTAAAATAT-ATTTT-TTAATAATATT
1 ATATTATTAAAATATTT-AAATATCATTTTATCAA-AATATT
21177 ATATTAT
1 ATATTAT
21184 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 3 0.08
39 7 0.17
40 24 0.60
41 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (40 bp):
ATATTATTAAAATATTTAAATATCATTTTATCAAAATATT
Found at i:21191 original size:22 final size:23
Alignment explanation
Indices: 21133--21193 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
21123 TTTAATCAAA
*
21133 ATATTA-ATTATTAA-AATATTT
1 ATATTATATTTTTAATAATATTT
* *
21154 AAAATATATTTTTTAATAATA-TT
1 ATATTATA-TTTTTAATAATATTT
21177 ATATTATATTTTTAATA
1 ATATTATATTTTTAATA
21194 TTATAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.12
22 10 0.31
23 14 0.44
24 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATATTTTTAATAATATTT
Found at i:23276 original size:129 final size:129
Alignment explanation
Indices: 23079--23312 Score: 441
Period size: 129 Copynumber: 1.8 Consensus size: 129
23069 AGTATAACTC
23079 CTATAAACCACAGCCAGATCAAGAGAAAGAGAAGCCAATGCCAGAAGAGACAGAAAAGACTGGTT
1 CTATAAACCACAGCCAGATCAAGAGAAAGAGAAGCCAATGCCAGAAGAGACAGAAAAGACTGGTT
23144 ATAGCACAAAACCAGTCTATCAACCACAACCAGAAAAGCCTGATTATAACACCAAGCCAAATTA
66 ATAGCACAAAACCAGTCTATCAACCACAACCAGAAAAGCCTGATTATAACACCAAGCCAAATTA
* * *
23208 CTATGAACCACAGCCAGATCAAGAGAAAGAGAAGCCAATGCCAGAAGAGAGAGAAAAGTCTGGTT
1 CTATAAACCACAGCCAGATCAAGAGAAAGAGAAGCCAATGCCAGAAGAGACAGAAAAGACTGGTT
23273 ATAGCACAAAACCAGTCTATCAACCACAACCAGAAAAGCC
66 ATAGCACAAAACCAGTCTATCAACCACAACCAGAAAAGCC
23313 AGAGTCAAAG
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 102 1.00
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (129 bp):
CTATAAACCACAGCCAGATCAAGAGAAAGAGAAGCCAATGCCAGAAGAGACAGAAAAGACTGGTT
ATAGCACAAAACCAGTCTATCAACCACAACCAGAAAAGCCTGATTATAACACCAAGCCAAATTA
Found at i:23717 original size:150 final size:150
Alignment explanation
Indices: 23175--23690 Score: 872
Period size: 150 Copynumber: 3.4 Consensus size: 150
23165 AACCACAACC
* * * * *
23175 AGAAAAGCCTGATTAT-AACACCAAGCCAAATTACTATGAACCACAGCCAGATCAAGAGAAAGAG
1 AGAAAAGCCTGATTATGGA-ACCAAGCCAAATTACTATAAACCACAGCCAG---AAGACAAGGAA
* * * *
23239 AAGCCAATGCCAGAAGAGAGAGAAAAGTCTGGTTATAGCACAAAACCAGTCTATCAACCACAACC
62 AAACCAATGCCAGAAGAGACAGAAAAGCCAGGTTATAGCACAAAACCAGTCTATCAACCACAACC
*
23304 AGAAAAGCCAGAGTCAAAGCAGGA
127 AGAAAAGGCAGAGTCAAAGCAGGA
*
23328 AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATCAACCACAGCCAGAAGACAAGGAAAAAC
1 AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATAAACCACAGCCAGAAGACAAGGAAAAAC
23393 CAATGCCAGAAGAGACAGAAAAGCCAGGTTATAGCACAAAACCAGTCTATCAACCACAACCAGAA
66 CAATGCCAGAAGAGACAGAAAAGCCAGGTTATAGCACAAAACCAGTCTATCAACCACAACCAGAA
*
23458 AAGGTAGAGTCAAAGCAGGA
131 AAGGCAGAGTCAAAGCAGGA
23478 AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATAAACCACAGCCAGAAGACAAGGAAAAAC
1 AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATAAACCACAGCCAGAAGACAAGGAAAAAC
*
23543 CAATGCCAGAAGAGACAGAAAAGCCAGGTTATAGCACAAAACCAGTCTATCAACCACAACTAGAA
66 CAATGCCAGAAGAGACAGAAAAGCCAGGTTATAGCACAAAACCAGTCTATCAACCACAACCAGAA
23608 AAGGCAGAGTCAAAGCAGGA
131 AAGGCAGAGTCAAAGCAGGA
23628 AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATAAACCACAGCCAGAAGACAAGGAAAA
1 AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATAAACCACAGCCAGAAGACAAGGAAAA
23691 CCCAGAAACA
Statistics
Matches: 348, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
150 301 0.86
153 46 0.13
154 1 0.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (150 bp):
AGAAAAGCCTGATTATGGAACCAAGCCAAATTACTATAAACCACAGCCAGAAGACAAGGAAAAAC
CAATGCCAGAAGAGACAGAAAAGCCAGGTTATAGCACAAAACCAGTCTATCAACCACAACCAGAA
AAGGCAGAGTCAAAGCAGGA
Found at i:23910 original size:2 final size:2
Alignment explanation
Indices: 23903--23933 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23893 AAACTATTTG
23903 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
23934 ATTTAAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27726 original size:229 final size:231
Alignment explanation
Indices: 27305--27783 Score: 698
Period size: 229 Copynumber: 2.1 Consensus size: 231
27295 TGAATTAGAA
* * *
27305 ACCCGA-CTCGACCCAAAATAATAATAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG
1 ACCCGACCT-GACCCGAAATAATAATAAAAATTATTTTTATTCAATAAAAACACTAACTTAATTG
* * * *
27369 GAAAAATATATATAGAGAGAGAGGTATTATTGTTATTATTCCTAAATATATAAGGTAAAATTATA
65 AAAAAAAAAATATAGAGAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATA
* * * *
27434 TATTTTTTGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAC
130 TATTATAT--GTCGGGCCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCAAATATCAC
* *
27499 ACTTAAAAAAACCGACTCGATCCGACCAAAATAAAGTTTC
193 ACTTAAAAAAACAGAC-CGACCCGACCAAAATAAAGTTTC
27539 ACCCGACCTGACCCGAAATAATAA-AAAAA-TATTTTTATTCAATAAAAACACTAACTTAATTGA
1 ACCCGACCTGACCCGAAATAATAATAAAAATTATTTTTATTCAATAAAAACACTAACTTAATTGA
* * *
27602 AAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATA
66 AAAAAAAAA-TATAGAGAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATA
* *
27667 TA-TATAT-TCGGGCCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCAAATATCACTC
130 TATTATATGTCGGGCCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCAAATATCACAC
*
27730 TTAAAAAAGCAGACCGACCCGACCAAAATAAAGTTTC
195 TTAAAAAAACAGACCGACCCGACCAAAATAAAGTTTC
*
27767 ACCCGACCCGACCCGAA
1 ACCCGACCTGACCCGAA
27784 TATATGAATT
Statistics
Matches: 223, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
228 38 0.17
229 64 0.29
232 41 0.18
233 58 0.26
234 20 0.09
235 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (231 bp):
ACCCGACCTGACCCGAAATAATAATAAAAATTATTTTTATTCAATAAAAACACTAACTTAATTGA
AAAAAAAAATATAGAGAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATAT
ATTATATGTCGGGCCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCAAATATCACACT
TAAAAAAACAGACCGACCCGACCAAAATAAAGTTTC
Found at i:30468 original size:14 final size:14
Alignment explanation
Indices: 30446--30485 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
30436 AAATCTCAAA
*
30446 CAACTATCATATCT
1 CAACAATCATATCT
*
30460 CAACCATCATATCT
1 CAACAATCATATCT
30474 CAACAATCATAT
1 CAACAATCATAT
30486 TAATGTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (14 bp):
CAACAATCATATCT
Found at i:30689 original size:60 final size:60
Alignment explanation
Indices: 30562--30695 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
30552 AATAGTCGGG
** *
30562 TGACCATTTTGT-ACTTTTAATAGTCGATAGACTTAACAAAGTAATATTATATAGGTGAA
1 TGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAGTAATACCATATAGGTCAA
* * * *
30621 TGATCATTTTGTAACTTTTAATAGTCGA-AGGACTTAATAAAGTAGTACCCTATA-GTCAA
1 TGACCATTTTGTAACTTTTAATAGTCGATA-GACTTAACAAAGTAATACCATATAGGTCAA
30680 TGGACCATTTGTGTAA
1 T-GACCATTT-TGTAA
30696 TTTACCCTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 17 0.27
60 41 0.65
61 5 0.08
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAGTAATACCATATAGGTCAA
Done.