Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007502.1 Hibiscus syriacus cultivar Beakdansim tig00020805_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: 50691
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7566 original size:22 final size:23
Alignment explanation
Indices: 7529--7575 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
7519 AACCCTAAAT
7529 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
7552 AAGCCC-ATAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
7574 AA
1 AA
7576 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:19314 original size:15 final size:16
Alignment explanation
Indices: 19294--19327 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19284 ATTTTTTATT
19294 ATTATTT-AATATAAA
1 ATTATTTAAATATAAA
19309 ATTATTTAAAATATAAA
1 ATTATTT-AAATATAAA
19326 AT
1 AT
19328 AAAAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATTTAAATATAAA
Found at i:24795 original size:20 final size:20
Alignment explanation
Indices: 24759--24796 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24749 CCTGACTTGT
**
24759 TTGGAAGACCTGTAAATCAG
1 TTGGAAGACCTAAAAATCAG
24779 TTGGAAGACCTAAAAATC
1 TTGGAAGACCTAAAAATC
24797 GGTTCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (20 bp):
TTGGAAGACCTAAAAATCAG
Found at i:34874 original size:34 final size:33
Alignment explanation
Indices: 34815--34880 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
34805 TTCTTGAGAG
*
34815 TTGTTTTCTCCTTTTTATCAAGAGAGAATTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAATTGTTA
*
34849 TTGTTTTCTCCTTGTTAGATC-GAGAGAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAATTGT
34881 AATTCATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 23 0.82
35 2 0.07
36 3 0.11
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAATTGTTA
Found at i:39827 original size:31 final size:31
Alignment explanation
Indices: 39784--39862 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
39774 TCATTTAAAT
*
39784 GAACGAATATGAACAAACTATACTCCTTAAG
1 GAACGAACATGAACAAACTATACTCCTTAAG
* * *
39815 GAACGAACATGAACAAGCTATATTCCTTAAT
1 GAACGAACATGAACAAACTATACTCCTTAAG
39846 GAACGAACATGAACAAA
1 GAACGAACATGAACAAA
39863 AATTTTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (31 bp):
GAACGAACATGAACAAACTATACTCCTTAAG
Found at i:42351 original size:8 final size:7
Alignment explanation
Indices: 42332--42363 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
42322 ATAATCACAA
42332 ATTTTTT
1 ATTTTTT
42339 ATTTTTT
1 ATTTTTT
42346 ATTTTTT
1 ATTTTTT
42353 ATTTTATT
1 ATTTT-TT
42361 ATT
1 ATT
42364 AAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Found at i:46845 original size:108 final size:106
Alignment explanation
Indices: 46653--46857 Score: 304
Period size: 108 Copynumber: 1.9 Consensus size: 106
46643 GCGCAGGGCC
* * * * * *
46653 CCCAAAAAATACCCAAAAAAGTATATATGGTGGCGTTTTTCAATAAACGCCACTATAGATGGATC
1 CCCAAAAAATACCCAAAAAAATATATATAGTAGCGTTTTTCAATAAACACCACTATAAATGGACC
46718 TATTGCGACGTTTATTAAAAAAACGCCACTATTATTGTGCAG
66 TATTGCGACGTTTATTAAAAAAA-GCCACTATTATTGTGCAG
*
46760 CCCAAAAAATGCCCAAAAAATATATATATAGTAGCGTTTTTCAATAAACACCACTATAAATGGAC
1 CCCAAAAAATACCCAAAAAA-ATATATATAGTAGCGTTTTTCAATAAACACCACTATAAATGGAC
*
46825 CTATTTCGACGTTT-TATAAAAAAAGCCACTATT
65 CTATTGCGACGTTTAT-TAAAAAAAGCCACTATT
46858 GTTGCCCCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 29 0.33
108 59 0.67
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (106 bp):
CCCAAAAAATACCCAAAAAAATATATATAGTAGCGTTTTTCAATAAACACCACTATAAATGGACC
TATTGCGACGTTTATTAAAAAAAGCCACTATTATTGTGCAG
Found at i:49846 original size:19 final size:20
Alignment explanation
Indices: 49765--49854 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 20
49755 AACGCGATTT
* *
49765 TGAAAAATGTATTGCGATAG
1 TGAAAAACGTGTTGCGATAG
* * *
49785 T-TAAAATGTGTTGCGAGAG
1 TGAAAAACGTGTTGCGATAG
*
49804 TTTGAAAAACGTGTTGTTTTGATAG
1 --TGAAAAACGTGTTG---CGATAG
49829 TGAAAAA-GTGTTGCGATAG
1 TGAAAAACGTGTTGCGATAG
49848 TGAAAAA
1 TGAAAAA
49855 TCCAAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
19 27 0.48
20 1 0.02
21 1 0.02
22 16 0.29
23 7 0.12
25 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (20 bp):
TGAAAAACGTGTTGCGATAG
Found at i:50411 original size:19 final size:19
Alignment explanation
Indices: 50387--50423 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50377 TGCGATACTG
*
50387 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
50406 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
50424 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Done.