Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003431.1 Hibiscus syriacus cultivar Beakdansim tig00007229_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: 57118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:999 original size:15 final size:15
Alignment explanation
Indices: 975--1019 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
965 CCAGAAAAAA
* *
975 AAATATTTAAATTAT
1 AAATAATTAATTTAT
*
990 AAATTATTAATTTAT
1 AAATAATTAATTTAT
*
1005 CAATAATTAATTTAT
1 AAATAATTAATTTAT
1020 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATAATTAATTTAT
Found at i:4330 original size:16 final size:16
Alignment explanation
Indices: 4311--4382 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
4301 AATTAAATTA
4311 TTAAT-TTTAGTTTATT
1 TTAATATTTA-TTTATT
4327 TTAATATTTATTTA-T
1 TTAATATTTATTTATT
* *
4342 TTAA-ATCATATGTAATAT
1 TTAATAT-TTAT-TTAT-T
*
4360 TTAATTTTTATTTTATT
1 TTAATATTTA-TTTATT
4377 TTAATA
1 TTAATA
4383 CTTGTAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
14 2 0.05
15 8 0.19
16 11 0.26
17 10 0.23
18 10 0.23
19 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAATATTTATTTATT
Found at i:4648 original size:21 final size:21
Alignment explanation
Indices: 4602--4642 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4592 TAAATACTAA
*
4602 AAAAATTAAAATTGATAGTTT
1 AAAAATTAAAATTCATAGTTT
4623 AAAAATT-AAATTCATAGTTT
1 AAAAATTAAAATTCATAGTTT
4643 TTAAAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAAATTAAAATTCATAGTTT
Found at i:5263 original size:17 final size:16
Alignment explanation
Indices: 5241--5287 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
5231 TATTTTGTGC
5241 TTAATTTATTTAAGTAT
1 TTAATTTATTTAA-TAT
5258 TTAATTTATTTAATAT
1 TTAATTTATTTAATAT
* *
5274 TTTATTTAATTAAT
1 TTAATTTATTTAAT
5288 TTTTTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTAATTTATTTAATAT
Found at i:14708 original size:20 final size:20
Alignment explanation
Indices: 14680--14734 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
14670 ATAATGTTAT
14680 CAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
* *
14700 CAGGATATCTACACCATAGA
1 CAGGGTATCTATACCATAGA
*
14720 CAGGGTATATATACC
1 CAGGGTATCTATACC
14735 TCAGTTAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:15708 original size:43 final size:43
Alignment explanation
Indices: 15481--15752 Score: 131
Period size: 43 Copynumber: 6.3 Consensus size: 43
15471 GCCGCTAAAG
* * * * *** *
15481 TTAGCGGCGTTTTTTTTAAAAAACGCCGCAATATGTTACAACAT
1 TTAGCGACGTTTTCTCT-AAAAACGCCGCAATAGGTTTTGATAT
* * * * * *
15525 ATAGCGGCGTTTTCT-GAACAAACGTCGCAATAGGATTTGTTAT
1 TTAGCGACGTTTTCTCTAA-AAACGCCGCAATAGGTTTTGATAT
* ** * ** *
15568 TTAGCGGCGTTTGTC-AGAAAAAGGCCGCAATAGGCGTTGATGT
1 TTAGCGACGTTT-TCTCTAAAAACGCCGCAATAGGTTTTGATAT
* * * *
15611 TTAACGACGTTTTTTCTAAAAACGCCGCAA-ATGGTTTTGAGAA
1 TTAGCGACGTTTTCTCTAAAAACGCCGCAATA-GGTTTTGATAT
* * *
15654 GTAGCGGCGTTTTACT-TAAAATCGCCGCAATAGGTTTTGATAT
1 TTAGCGACGTTTT-CTCTAAAAACGCCGCAATAGGTTTTGATAT
* * * * * * *
15697 TTTGCGACGTTTT-TCTCAAAAATGCCGCAGTAAGTTATGTTTT
1 TTAGCGACGTTTTCTCT-AAAAACGCCGCAATAGGTTTTGATAT
*
15740 TTAGCGGCGTTTT
1 TTAGCGACGTTTT
15753 TATCGAAAAC
Statistics
Matches: 171, Mismatches: 48, Indels: 19
0.72 0.20 0.08
Matches are distributed among these distances:
41 1 0.01
42 5 0.03
43 145 0.85
44 20 0.12
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (43 bp):
TTAGCGACGTTTTCTCTAAAAACGCCGCAATAGGTTTTGATAT
Found at i:15837 original size:44 final size:43
Alignment explanation
Indices: 15786--15905 Score: 143
Period size: 44 Copynumber: 2.7 Consensus size: 43
15776 TTGAGAATTA
15786 GCGGCGTTTCTAGTGCAAAAACGCCGCTAAATGCATGGTATATT
1 GCGGCGTTTCTAGTGC-AAAACGCCGCTAAATGCATGGTATATT
** **
15830 GCGGCGTTTCTAGTATACAAACGCCGCTAAATGTTTGGTATATT
1 GCGGCGTTTCTAGTGCA-AAACGCCGCTAAATGCATGGTATATT
* *
15874 GCGACATTTCTAGTTTGC-AAACGCCGCTAAAT
1 GCGGCGTTTCTAG--TGCAAAACGCCGCTAAAT
15906 AACACAGGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 63 0.97
46 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTCTAGTGCAAAACGCCGCTAAATGCATGGTATATT
Found at i:20083 original size:52 final size:52
Alignment explanation
Indices: 20020--20178 Score: 300
Period size: 52 Copynumber: 3.1 Consensus size: 52
20010 TAACAACAAA
20020 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
* *
20072 ATACATTATAATTTAGAAACATTAAAGTACTTATGCGTAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
20124 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
20176 ATA
1 ATA
20179 TTGTTCAGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:22490 original size:31 final size:31
Alignment explanation
Indices: 22448--22603 Score: 228
Period size: 31 Copynumber: 5.0 Consensus size: 31
22438 AGGGTCGAGG
*
22448 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
22479 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
22510 GTTTACCTA-GATTCTTCGGGACATATGGACT
1 GTTTACCTATG-TTCTTCGGGACATATGGACT
*
22541 GTTTACCTTTGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
22572 GATTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
22603 G
1 G
22604 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
30 2 0.02
31 111 0.97
32 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:22863 original size:18 final size:18
Alignment explanation
Indices: 22840--22974 Score: 105
Period size: 18 Copynumber: 7.5 Consensus size: 18
22830 AATATTAATA
*
22840 CATGATAGTGATAGAGAT
1 CATGATAATGATAGAGAT
**
22858 CATGATAATGATATCGAT
1 CATGATAATGATAGAGAT
* *
22876 GATAATAATGATAGAGAT
1 CATGATAATGATAGAGAT
*
22894 CATGATAATGATATTA-AT
1 CATGATAATGATA-GAGAT
** *
22912 GTTGA-AAGAGATAGAGAT
1 CATGATAA-TGATAGAGAT
**
22930 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
*
22948 -GTGGATAATGATAGAGAT
1 CAT-GATAATGATAGAGAT
*
22966 TATGATAAT
1 CATGATAAT
22975 ATTATTGACG
Statistics
Matches: 88, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
17 4 0.05
18 80 0.91
19 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:22889 original size:36 final size:36
Alignment explanation
Indices: 22848--22982 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
22838 TACATGATAG
*
22848 TGATAGAGATCATGATAATGATATCGATGAT-AATAA
1 TGATAGAGATCATGATAATGATATTGATG-TGAATAA
*
22884 TGATAGAGATCATGATAATGATATTAATGTTGAA-AGA
1 TGATAGAGATCATGATAATGATATTGATG-TGAATA-A
*
22921 -GATAGAGATCATGATAATGATATTGATGTGGATAA
1 TGATAGAGATCATGATAATGATATTGATGTGAATAA
*
22956 TGATAGAGATTATGATAAT-ATTATTGA
1 TGATAGAGATCATGATAATGA-TATTGA
22983 CGTTGTTAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
35 5 0.06
36 80 0.91
37 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (36 bp):
TGATAGAGATCATGATAATGATATTGATGTGAATAA
Found at i:39382 original size:30 final size:30
Alignment explanation
Indices: 39316--39384 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
39306 ATTTGAGTAC
* * * *
39316 TATGAGCTGCTATAGGTGTTGTGAGGTAAT
1 TATGAGTTGCCATAGGTGCTGTGAGCTAAT
39346 TATGAGTTGCCATAGGTGCTGTGAGCTAAT
1 TATGAGTTGCCATAGGTGCTGTGAGCTAAT
39376 TATGAGTTG
1 TATGAGTTG
39385 TCATGCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (30 bp):
TATGAGTTGCCATAGGTGCTGTGAGCTAAT
Found at i:40391 original size:18 final size:18
Alignment explanation
Indices: 40368--40406 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40358 CCAATAAAAA
*
40368 TTATATTGTATTAAA-ATT
1 TTATATT-TATCAAATATT
40386 TTATATTTATCAAATATT
1 TTATATTTATCAAATATT
40404 TTA
1 TTA
40407 ATTATATCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTATATTTATCAAATATT
Found at i:44969 original size:18 final size:19
Alignment explanation
Indices: 44948--44996 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
44938 TTTTTGTTGG
* *
44948 TAAAAAAATTATGAT-TTT
1 TAAAAAAATTATGATAATC
* *
44966 TAAAATAATTATTATAATC
1 TAAAAAAATTATGATAATC
44985 TAAAAAAATTAT
1 TAAAAAAATTAT
44997 AAACAAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAAAAATTATGATAATC
Done.