Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004651.1 Hibiscus syriacus cultivar Beakdansim tig00010425_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: 39986
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:11490 original size:8 final size:8
Alignment explanation
Indices: 11473--11648 Score: 64
Period size: 8 Copynumber: 21.1 Consensus size: 8
11463 CTTAAAGAAT
*
11473 AAATGGAA
1 AAATGAAA
11481 AAATGAAAAA
1 AAATG--AAA
11491 AAATGAAA
1 AAATGAAA
*
11499 AAAAGAAGA
1 AAATGAA-A
11508 AAA--AAGA
1 AAATGAA-A
11515 AAA-G-AA
1 AAATGAAA
11521 AAATGAGAA
1 AAATGA-AA
11530 AAATGAAAA
1 AAATG-AAA
*
11539 ATGAAGGAAA
1 A--AATGAAA
11549 AAATGAAA
1 AAATGAAA
**
11557 AGAAAAAAA
1 A-AATGAAA
*
11566 GAAAT-AGA
1 -AAATGAAA
**
11574 AAATGGGA
1 AAATGAAA
11582 AAATGGAAGA
1 AAAT-GAA-A
*
11592 AAA--AAG
1 AAATGAAA
11598 AAATGAAA
1 AAATGAAA
11606 AAATGATGAA
1 AAATGA--AA
11616 AAATG-AA
1 AAATGAAA
11623 AAATGAAA
1 AAATGAAA
11631 AAATAGAGAA
1 AAAT-GA-AA
11641 AAAT-AAA
1 AAATGAAA
11648 A
1 A
11649 GGGGGTTCAA
Statistics
Matches: 133, Mismatches: 13, Indels: 45
0.70 0.07 0.24
Matches are distributed among these distances:
6 7 0.05
7 25 0.19
8 44 0.33
9 24 0.18
10 30 0.23
11 3 0.02
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:11494 original size:10 final size:10
Alignment explanation
Indices: 11479--11539 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
11469 GAATAAATGG
11479 AAAAATGAAA
1 AAAAATGAAA
11489 AAAAATG-AA
1 AAAAATGAAA
11498 AAAAA-GAAGA
1 AAAAATGAA-A
11508 AAAAA-GAAAA
1 AAAAATG-AAA
*
11518 GAAAAATG-AG
1 -AAAAATGAAA
11528 AAAAATGAAA
1 AAAAATGAAA
11538 AA
1 AA
11540 TGAAGGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
8 1 0.02
9 15 0.35
10 19 0.44
11 7 0.16
12 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.07
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:11549 original size:39 final size:40
Alignment explanation
Indices: 11479--11642 Score: 163
Period size: 39 Copynumber: 4.0 Consensus size: 40
11469 GAATAAATGG
* *
11479 AAAAATGAAAAAAAATGAAAAAAAGAAGAAAAAAGAAAAG-
1 AAAAATGAAGAAAAATG-AAAAATGAAGAAAAAAGAAAAGA
11519 AAAAATG-AGAAAAATGAAAAATGAAGGAAAAAATGAAAAGA
1 AAAAATGAAGAAAAATGAAAAATGAA-GAAAAAA-GAAAAGA
* * * *
11560 AAAAAAGAAATAGAAAATGGGAAAATGGAAGAAAAAAGAAATGA
1 AAAAATG-AAGA-AAAAT-GAAAAAT-GAAGAAAAAAGAAAAGA
*
11604 AAAAATGATGAAAAATGAAAAATGAA-AAAATAGAGAAAA
1 AAAAATGAAGAAAAATGAAAAATGAAGAAAA-A-AGAAAA
11643 ATAAAAGGGG
Statistics
Matches: 103, Mismatches: 11, Indels: 19
0.77 0.08 0.14
Matches are distributed among these distances:
38 8 0.08
39 19 0.18
40 17 0.17
41 17 0.17
42 5 0.05
43 4 0.04
44 17 0.17
45 13 0.13
46 3 0.03
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (40 bp):
AAAAATGAAGAAAAATGAAAAATGAAGAAAAAAGAAAAGA
Found at i:11632 original size:25 final size:24
Alignment explanation
Indices: 11589--11648 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
11579 GGAAAATGGA
*
11589 AGAAAAA-AGAAATGAAAAAAT-G
1 AGAAAAATAAAAATGAAAAAATAG
11611 ATGAAAAATGAAAAATGAAAAAATAG
1 A-GAAAAAT-AAAAATGAAAAAATAG
11637 AGAAAAATAAAA
1 AGAAAAATAAAA
11649 GGGGGTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 6 0.18
24 4 0.12
25 20 0.61
26 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (24 bp):
AGAAAAATAAAAATGAAAAAATAG
Found at i:12693 original size:16 final size:17
Alignment explanation
Indices: 12672--12705 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12662 CAGGTTCCCA
12672 AAGATAGTGAAG-ATTG
1 AAGATAGTGAAGCATTG
*
12688 AAGATATTGAAGCATTG
1 AAGATAGTGAAGCATTG
12705 A
1 A
12706 GATGAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (17 bp):
AAGATAGTGAAGCATTG
Found at i:13085 original size:55 final size:55
Alignment explanation
Indices: 13019--13411 Score: 456
Period size: 55 Copynumber: 7.1 Consensus size: 55
13009 AGATTAAGTC
* * ** *
13019 CTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCATTGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
*
13074 CTATACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTT
*
13129 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTATTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTT
* * ** * *
13184 CTATACTCTCAGAAGAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
*
13239 CTATACTCTTTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTT
* * *
13294 CTATACTCCCTGAACGG-ATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAG-T
1 CTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
* * * * * * ** *
13348 CTTATACTCACTAAATGAATAGGGAGCAGACACGTTTACCGAAGATTGTTTGAG-T
1 C-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
13403 CTTATACTC
1 C-TATACTC
13412 CTTAAAAGAA
Statistics
Matches: 300, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
54 5 0.02
55 291 0.97
56 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (55 bp):
CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
Found at i:13394 original size:165 final size:165
Alignment explanation
Indices: 13015--13449 Score: 533
Period size: 165 Copynumber: 2.6 Consensus size: 165
13005 TTGAAGATTA
* * * * *
13015 AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCATTGAAGATTGTTCGAGTTCTATAC
1 AGTCTTATACTCTCTAAATGAATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTCTATAC
* * *
13080 TCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
66 TCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
*
13145 AATAGAGAGCGGACCCGTTTTATGAAGATTATTCG
131 AATAGAGAGCAGACCCGTTTTATGAAGATTATTCG
* * * *
13180 AGT-TCTATACTCTC-AGAA-GAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCGAGTTCTA
1 AGTCT-TATACTCTCTA-AATG-AATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTCTA
13242 TACTCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGA
63 TACTCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGA
* *
13307 ACGG-ATAGGGAGCAGACCCG-TTTATTGAAGATTGTTCG
128 A-GGAATAGAGAGCAGACCCGTTTTA-TGAAGATTATTCG
* ** *
13345 AGTCTTATACTCACTAAATGAATAGGGAGCAGACACGTTTACCGAAGATTGTTTGAG-TCTTATA
1 AGTCTTATACTCTCTAAATGAATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTC-TATA
* * * * **
13409 CTCCTTAAAAGAATAGGGAGAAGACCCGTTATT-TGAAGATT
65 CTCTTTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGATT
13450 TTTCAAGTCT
Statistics
Matches: 231, Mismatches: 29, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
164 7 0.03
165 217 0.94
166 7 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (165 bp):
AGTCTTATACTCTCTAAATGAATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTCTATAC
TCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
AATAGAGAGCAGACCCGTTTTATGAAGATTATTCG
Found at i:13412 original size:110 final size:110
Alignment explanation
Indices: 13015--13460 Score: 469
Period size: 110 Copynumber: 4.1 Consensus size: 110
13005 TTGAAGATTA
* * * *
13015 AGTC-CTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCATTGAAGATTGTTCGAGTTCTAT
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTA-TGAAGATTGTTCGAGTTCTAT
* * *
13078 ACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGTTCG
65 ACTCCCTGAA-GAATAGAGAGCAGACCCGTTTAT-TGAAGATTGTTCG
* *
13125 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTATA
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATA
* * * * *
13189 CTCTCAGAAGAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCG
66 CTCCCTGAAG-AATAGAGAGCAGACCCGTTTATTGAAGATTGTTCG
* *
13235 AGT-TCTATACTCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATA
* *
13299 CTCCCTGAACGGATAGGGAGCAGACCCGTTTATTGAAGATTGTTCG
66 CTCCCTGAA-GAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCG
* * * * * * *
13345 AGTCT-TATACTCACTAAATGAATAGGGAGCAGACACG-TTTACCGAAGATTGTTTGAG-TCTTA
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTA-TGAAGATTGTTCGAGTTC-TA
* * * * * *
13407 TACTCCTTAAAAGAATAGGGAGAAGACCCG-TTATTTGAAGATTTTTCA
64 TACTCCCT-GAAGAATAGAGAGCAGACCCGTTTA-TTGAAGATTGTTCG
13455 AGTCTC
1 AGTCTC
13461 GTTTATCCAG
Statistics
Matches: 290, Mismatches: 35, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
109 10 0.03
110 272 0.94
111 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (110 bp):
AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATA
CTCCCTGAAGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCG
Found at i:13459 original size:55 final size:56
Alignment explanation
Indices: 13034--13460 Score: 344
Period size: 55 Copynumber: 7.8 Consensus size: 56
13024 CTCTCTGAAT
* ** * * *
13034 GAATAGGGAGCGGACAAGTTCATTGAAGATTGTTCGAGT-TCTATACT-CTCTGAAG
1 GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCT-TAAAA
* * * * *
13089 GAATAGAGAGCGGACCCATTT-TATGAAGATTGTTCGAGT-TCTATACT-CTCTGAAG
1 GAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTCGAGTCTCTATACTCCT-TAAAA
* * * * *
13144 GAATAGAGAGCGGACCCGTTT-TATGAAGATTATTCGAGT-TCTATACT-CTCAGAA
1 GAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* * * * * * *
13198 GAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTTTGAAG
1 G-AATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* * * * *
13254 GAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGT-TCTATACTCCCTGAAC
1 GAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* *
13309 GGATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCT-TATACTCAC-TAAAT
1 GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTC-CTTAAAA
* ** *
13364 GAATAGGGAGCAGACACGTTTACCGAAGATTGTTTGAGTCT-TATACTCCTTAAAA
1 GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* * *
13419 GAATAGGGAGAAGACCCG-TTATTTGAAGATTTTTCAAGTCTC
1 GAATAGGGAGCAGACCCGTTTA-TTGAAGATTGTTCGAGTCTC
13461 GTTTATCCAG
Statistics
Matches: 317, Mismatches: 44, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
54 8 0.03
55 302 0.95
56 7 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (56 bp):
GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
Found at i:17286 original size:24 final size:24
Alignment explanation
Indices: 17259--17329 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
17249 CACCACAACT
*
17259 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
17283 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
17307 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
17330 TATAAGATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 13 0.32
24 28 0.68
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:23513 original size:24 final size:24
Alignment explanation
Indices: 23486--23553 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
23476 CACCACAGCT
*
23486 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* * * *
23510 CGTAGAATTTGCACTGAATTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
23534 CGTAGAAA-TGCACCGTAGTG
1 CGTAGAAATTGCACCGAAGTG
23554 TCATATAAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 9 0.26
24 26 0.74
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:31696 original size:37 final size:35
Alignment explanation
Indices: 31589--31697 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 35
31579 ATTATCCTTA
*
31589 TTATATATTTATTTTT-TAACAAGTTAAAAAAT-AAAT
1 TTATATATTT-TTTTTATAA-AA-TTAAAATATAAAAT
* * *
31625 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAAT
1 TTATATATTTTTTTTATAAAA-TTAAAAT-ATAAAAT
31662 TTATATAATTTTTTTTATAAAATTGAAAATATAAAA
1 TTATAT-ATTTTTTTTATAAAATT-AAAATATAAAA
31698 ATATTTAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
35 11 0.18
36 14 0.23
37 18 0.30
38 17 0.28
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (35 bp):
TTATATATTTTTTTTATAAAATTAAAATATAAAAT
Found at i:31699 original size:38 final size:37
Alignment explanation
Indices: 31621--31697 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
31611 GTTAAAAAAT
* *
31621 AAATTTATATATTTTCTTTAAAAAATTTAAATTCATA
1 AAATTTATATATTTTCTTTAAAAAATTGAAAATCATA
* *
31658 AAATTTATATAATTTTTTTTATAAAATTGAAAAT-ATA
1 AAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATA
31695 AAA
1 AAA
31698 ATATTTAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
AAATTTATATATTTTCTTTAAAAAATTGAAAATCATA
Found at i:37725 original size:16 final size:16
Alignment explanation
Indices: 37704--37735 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37694 CAGCACTGTA
37704 CAGCTGAATGGTAAAT
1 CAGCTGAATGGTAAAT
37720 CAGCTGAATGGTAAAT
1 CAGCTGAATGGTAAAT
37736 AAGCGTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (16 bp):
CAGCTGAATGGTAAAT
Found at i:38104 original size:20 final size:20
Alignment explanation
Indices: 38068--38105 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38058 CATTGGGATA
*
38068 TTTTAATAACTTGAAATATT
1 TTTTAATAACTTAAAATATT
38088 TTTTAATAA-TATAAAATA
1 TTTTAATAACT-TAAAATA
38106 GCTCTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTTAATAACTTAAAATATT
Done.