Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005647.1 Hibiscus syriacus cultivar Beakdansim tig00013175_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: 56632
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2270 original size:33 final size:33
Alignment explanation
Indices: 2191--2294 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2181 ATACAATCTG
* *
2191 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2227 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2260 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2293 TC
1 TC
2295 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:6652 original size:24 final size:24
Alignment explanation
Indices: 6598--6652 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
6588 AAAAAATCAG
*
6598 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
6621 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
6645 AAAAGAAA
1 AAAAGAAA
6653 GAAAGAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:12418 original size:14 final size:14
Alignment explanation
Indices: 12399--12430 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12389 CGAATCTGCC
12399 GATGAAGCTTGAAT
1 GATGAAGCTTGAAT
12413 GATGAAGCTTGAAT
1 GATGAAGCTTGAAT
12427 GATG
1 GATG
12431 TATTTGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28
Consensus pattern (14 bp):
GATGAAGCTTGAAT
Found at i:17178 original size:90 final size:91
Alignment explanation
Indices: 17019--17200 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
17009 CCTAGAACAC
* * *
17019 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATA
* *
17084 AAGAGTTCTCTCCCTATTCGGCTAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
17110 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCACCAAGATA
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATA
17174 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
17200 C
1 C
17201 ATCATTTCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 61 0.76
91 19 0.24
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATA
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:21557 original size:90 final size:91
Alignment explanation
Indices: 21403--21584 Score: 285
Period size: 90 Copynumber: 2.0 Consensus size: 91
21393 CCTAAAACAC
*
21403 CCATGTGCTTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCTTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
21468 AAGAGTTCTCTCCATATTCGGCCAAG
66 AAGAGCTCTCTCCATATTCGGCCAAG
* * * * *
21494 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCTTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
21558 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCATATTCGGCCAAG
21584 C
1 C
21585 ATCATTTCTC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 63 0.76
91 20 0.24
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (91 bp):
CCATGTGCTTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCATATTCGGCCAAG
Found at i:22672 original size:18 final size:17
Alignment explanation
Indices: 22649--22683 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
22639 TAGGTTAGGG
22649 TAGAAAGAATAGAAGAAA
1 TAGAAAG-ATAGAAGAAA
*
22667 TAGAAAGGTAGAAGAAA
1 TAGAAAGATAGAAGAAA
22684 GGATTCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
TAGAAAGATAGAAGAAA
Found at i:33443 original size:26 final size:26
Alignment explanation
Indices: 33414--33492 Score: 149
Period size: 26 Copynumber: 3.0 Consensus size: 26
33404 AGGTTGTCAA
33414 CAGAGTGTTATCAACGTTGTTGAGAG
1 CAGAGTGTTATCAACGTTGTTGAGAG
*
33440 CAGAGTGTTATCAACATTGTTGAGAG
1 CAGAGTGTTATCAACGTTGTTGAGAG
33466 CAGAGTGTTATCAACGTTGTTGAGAG
1 CAGAGTGTTATCAACGTTGTTGAGAG
33492 C
1 C
33493 CATCATAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (26 bp):
CAGAGTGTTATCAACGTTGTTGAGAG
Found at i:35350 original size:11 final size:11
Alignment explanation
Indices: 35331--35362 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
35321 CATGCCAACA
35331 CCATCACCATT
1 CCATCACCATT
*
35342 CCATTACCATT
1 CCATCACCATT
35353 CCATCACCAT
1 CCATCACCAT
35363 AAAAACATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (11 bp):
CCATCACCATT
Found at i:37295 original size:23 final size:23
Alignment explanation
Indices: 37269--37312 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
37259 GCTTGGTTTT
* * *
37269 ATGGTGAATATGGAGATTCATTA
1 ATGGTAAAAATGGAAATTCATTA
37292 ATGGTAAAAATGGAAATTCAT
1 ATGGTAAAAATGGAAATTCAT
37313 ATTGGATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (23 bp):
ATGGTAAAAATGGAAATTCATTA
Found at i:38865 original size:59 final size:59
Alignment explanation
Indices: 38766--38894 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
38756 CAGCAGGCTG
** * *
38766 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
38825 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
*
38884 CATACTCGGGA
1 CATATTCGGGA
38895 TTGCACTACA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:39024 original size:44 final size:44
Alignment explanation
Indices: 38975--39078 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
38965 TGGTGTATGG
* *
38975 TTATGGA-ATAATGGCAAGTGTATTAGTAAAATAAGCTTACTAGC
1 TTATGGATA-AATGGCAAGTATATTAGTAAAATAAGCTTACGAGC
* *
39019 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGCAAGTATATTAGTAAAATAAGCTTACGAGC
39063 TTATGGTATTAAATGG
1 TTATGG-A-TAAATGG
39079 TAAAATATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
44 44 0.83
45 2 0.04
46 7 0.13
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.34
Consensus pattern (44 bp):
TTATGGATAAATGGCAAGTATATTAGTAAAATAAGCTTACGAGC
Found at i:39751 original size:23 final size:23
Alignment explanation
Indices: 39725--39777 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
39715 AACACACACA
39725 CAAAGAATCTCACAATTTCACTC
1 CAAAGAATCTCACAATTTCACTC
39748 CAAAGAATCTCACAATTTCACTC
1 CAAAGAATCTCACAATTTCACTC
39771 CAAAGAA
1 CAAAGAA
39778 ATCAGAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.23
Consensus pattern (23 bp):
CAAAGAATCTCACAATTTCACTC
Found at i:39792 original size:23 final size:23
Alignment explanation
Indices: 39725--39793 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
39715 AACACACACA
* *
39725 CAAAGAATCTCACAATTTCACTC
1 CAAAGAATATCACAATTGCACTC
* *
39748 CAAAGAATCTCACAATTTCACTC
1 CAAAGAATATCACAATTGCACTC
*
39771 CAAAGAA-ATCAGAATTGGCACTC
1 CAAAGAATATCACAATT-GCACTC
39794 AATCACACTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
22 7 0.17
23 35 0.83
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.23
Consensus pattern (23 bp):
CAAAGAATATCACAATTGCACTC
Found at i:41318 original size:2 final size:2
Alignment explanation
Indices: 41301--41334 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
41291 TCATAATAAC
*
41301 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41335 GAAAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44849 original size:18 final size:18
Alignment explanation
Indices: 44834--44872 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
44824 ATGAGATGAG
*
44834 AAGATTATAAATGATGGC
1 AAGATTACAAATGATGGC
*
44852 ATGATTACAAATGATGGC
1 AAGATTACAAATGATGGC
44870 AAG
1 AAG
44873 CCTCTCAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (18 bp):
AAGATTACAAATGATGGC
Found at i:46452 original size:5 final size:5
Alignment explanation
Indices: 46395--46451 Score: 84
Period size: 5 Copynumber: 12.0 Consensus size: 5
46385 AAATCAAAAA
*
46395 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTCT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
46444 -TTTT -TTTT
1 CTTTT CTTTT
46452 TGTAATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
4 11 0.22
5 38 0.78
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
CTTTT
Found at i:46460 original size:23 final size:23
Alignment explanation
Indices: 46411--46473 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
46401 TTTTCTTTTC
* **
46411 TTTTCTTTTCTTTTCTTTTCTTCT
1 TTTTCTTTT-TTTTTTTTTCTAAT
*
46435 TTTTCTTTTTTTTTTTTTGTAAT
1 TTTTCTTTTTTTTTTTTTCTAAT
**
46458 TTTTGATTTTTTTTTT
1 TTTTCTTTTTTTTTTT
46474 AATTTTTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 24 0.73
24 9 0.27
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.83
Consensus pattern (23 bp):
TTTTCTTTTTTTTTTTTTCTAAT
Found at i:46482 original size:20 final size:20
Alignment explanation
Indices: 46444--46480 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46434 TTTTTCTTTT
46444 TTTTTTTTTGTAATTTTTGA
1 TTTTTTTTTGTAATTTTTGA
46464 TTTTTTTTT-TAATTTTT
1 TTTTTTTTTGTAATTTTT
46481 TGGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTGTAATTTTTGA
Found at i:54775 original size:32 final size:31
Alignment explanation
Indices: 54714--54798 Score: 75
Period size: 32 Copynumber: 2.6 Consensus size: 31
54704 CTAAGTCACC
* *
54714 TATTTCTTTTTTTTCATTTCCTTTTCTTAAGT
1 TATTTCTTTTTTTTCATTT-CATTCCTTAAGT
**
54746 TATTTCTTTCTTTTTCATTAT-ATTCCTTAAAC
1 TATTTCTTT-TTTTTCATT-TCATTCCTTAAGT
54778 TA-TTCTTTTATTTTCCATTTC
1 TATTTCTTTT-TTTT-CATTTC
54799 TTTTTTCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
30 1 0.02
31 11 0.25
32 22 0.50
33 9 0.20
34 1 0.02
ACGTcount: A:0.16, C:0.18, G:0.01, T:0.65
Consensus pattern (31 bp):
TATTTCTTTTTTTTCATTTCATTCCTTAAGT
Found at i:54801 original size:16 final size:17
Alignment explanation
Indices: 54780--54812 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54770 CCTTAAACTA
54780 TTCTTTTAT-TTTCCAT
1 TTCTTTTATCTTTCCAT
*
54796 TTCTTTTTTCTTTCCAT
1 TTCTTTTATCTTTCCAT
54813 CCTAACGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTTTATCTTTCCAT
Done.