Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002157.1 Hibiscus syriacus cultivar Beakdansim tig00004404_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: 75982
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:912 original size:2 final size:2
Alignment explanation
Indices: 905--932 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
895 TGGTAGTGAT
905 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
933 GTAGTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29886 original size:22 final size:23
Alignment explanation
Indices: 29835--29888 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
29825 TATCTAAATT
29835 ATTA-ATTTTGATTTTTTTAATA
1 ATTATATTTTGATTTTTTTAATA
*
29857 TTTAATATTTT-ATTTTTTTGAA-A
1 ATT-ATATTTTGATTTTTTT-AATA
29880 ATTATATTT
1 ATTATATTT
29889 GACATTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 8 0.30
23 12 0.44
24 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
ATTATATTTTGATTTTTTTAATA
Found at i:30741 original size:90 final size:89
Alignment explanation
Indices: 30588--30767 Score: 288
Period size: 90 Copynumber: 2.0 Consensus size: 89
30578 TTTTTGTGAA
* * * *
30588 AAAAATTGTTAAAATAATTTTGTAATGCTCCGAATCCCGGATTAGTAGTTCGGGTCAACCCGAGA
1 AAAAATTGTTAAAATAATTTTGTAATGATCCAAATCCCGGATTAATAGTTCAGGTCAACCCGAGA
*
30653 CCCAACTTAAAGGATTTATTAAAAT
66 -CCAACCTAAAGGATTTATTAAAAT
* *
30678 AAAAATTGTTAAAATAATTTTGTAATGATCCAAATCCTGGATTAATAGTTCAGGTCAATCCGAGA
1 AAAAATTGTTAAAATAATTTTGTAATGATCCAAATCCCGGATTAATAGTTCAGGTCAACCCGAGA
30743 CCAACCTAAAGGATTTATTAAAAT
66 CCAACCTAAAGGATTTATTAAAAT
30767 A
1 A
30768 GTTTGAACCA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 24 0.29
90 59 0.71
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (89 bp):
AAAAATTGTTAAAATAATTTTGTAATGATCCAAATCCCGGATTAATAGTTCAGGTCAACCCGAGA
CCAACCTAAAGGATTTATTAAAAT
Found at i:39872 original size:57 final size:57
Alignment explanation
Indices: 39784--39898 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
39774 CCCCGCCATG
39784 TCCATGCTTCCTCCTCTTTGGCACCTATTTTTCTTATTAAATTATTTTAACCCTTGT
1 TCCATGCTTCCTCCTCTTTGGCACCTATTTTTCTTATTAAATTATTTTAACCCTTGT
39841 TCCATGCTTCCTCCTCTTTGGCACCTATTTTTCTTATTAAATTATTTTAACCCTTGT
1 TCCATGCTTCCTCCTCTTTGGCACCTATTTTTCTTATTAAATTATTTTAACCCTTGT
39898 T
1 T
39899 AGTTTTAGCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (57 bp):
TCCATGCTTCCTCCTCTTTGGCACCTATTTTTCTTATTAAATTATTTTAACCCTTGT
Found at i:43238 original size:21 final size:22
Alignment explanation
Indices: 43213--43253 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43203 AATTTCAACA
*
43213 ATTATT-TTACTAAAAAAACTT
1 ATTATTATAACTAAAAAAACTT
*
43234 ATTATTATAATTAAAAAAAC
1 ATTATTATAACTAAAAAAAC
43254 AACCCTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTATTATAACTAAAAAAACTT
Found at i:45237 original size:22 final size:22
Alignment explanation
Indices: 45170--45228 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
45160 TCGAGGGTTC
*
45170 TATGTGGTCATGCGGGATAAAT
1 TATGTGGTCATTCGGGATAAAT
45192 TATGTGGTCATTCGGGATAAAT
1 TATGTGGTCATTCGGGATAAAT
45214 TATGTGGTCATTCGG
1 TATGTGGTCATTCGG
45229 TGCAAATTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.36
Consensus pattern (22 bp):
TATGTGGTCATTCGGGATAAAT
Found at i:45885 original size:12 final size:13
Alignment explanation
Indices: 45870--45901 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
45860 ATCAAAGCAG
45870 AATTCAGAACA-A
1 AATTCAGAACATA
45882 AATTCAGAACATA
1 AATTCAGAACATA
45895 AA-TCAGA
1 AATTCAGA
45902 TAAAATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (13 bp):
AATTCAGAACATA
Found at i:48241 original size:20 final size:21
Alignment explanation
Indices: 48216--48254 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
48206 AAAGAGAATG
48216 TTTTTTTTT-G-TTTTATACA
1 TTTTTTTTTAGTTTTTATACA
48235 TTTTTTTTTAGTTTTTATAC
1 TTTTTTTTTAGTTTTTATAC
48255 CAAATCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTTTTTAGTTTTTATACA
Found at i:56070 original size:22 final size:22
Alignment explanation
Indices: 56042--56087 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
56032 TTGGAACCCG
*
56042 TCAGGTTCGGGTTCCATCCCCA
1 TCAGGTTCGAGTTCCATCCCCA
*
56064 TCAGGTTCGAGTTTCATCCCCA
1 TCAGGTTCGAGTTCCATCCCCA
56086 TC
1 TC
56088 CCTAATCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.30
Consensus pattern (22 bp):
TCAGGTTCGAGTTCCATCCCCA
Found at i:64381 original size:19 final size:18
Alignment explanation
Indices: 64333--64384 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
64323 ATTTAAGTCA
64333 TATTTTAT-AAATTAAAT
1 TATTTTATAAAATTAAAT
* *
64350 TTTATTTAAAAAATTAAAT
1 TAT-TTTATAAAATTAAAT
64369 TAATTTTATAAAATTA
1 T-ATTTTATAAAATTA
64385 CGAGTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 4 0.14
19 21 0.75
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTATAAAATTAAAT
Found at i:65345 original size:2 final size:2
Alignment explanation
Indices: 65338--65369 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
65328 ATGTTTTGTA
65338 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65370 TATGTCTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:74016 original size:29 final size:27
Alignment explanation
Indices: 73962--74017 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
73952 GTTATTTGAA
* *
73962 TTAAATGTTTTCAAAATATAATTAAAT
1 TTAAATATTTTCAAAAAATAATTAAAT
73989 TTAAATATTTTCAAAAAATATATATAAAT
1 TTAAATATTTTCAAAAAATA-AT-TAAAT
74018 CAATCTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
TTAAATATTTTCAAAAAATAATTAAAT
Done.