Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000441.1 Hibiscus syriacus cultivar Beakdansim tig00000805_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: 39798
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:68 original size:28 final size:29
Alignment explanation
Indices: 33--93 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
23 AAGGATAGTG
*
33 GTCAGC-AAAGAAAAATGCAATGGCAAGT
1 GTCAGCAAAAGAAAAATGCAATGGAAAGT
61 GTCAGCAAAAGAAAAATGCAATGGAAAGT
1 GTCAGCAAAAGAAAAATGCAATGGAAAGT
90 -TCAG
1 GTCAG
94 ATTTATGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.48, C:0.13, G:0.25, T:0.15
Consensus pattern (29 bp):
GTCAGCAAAAGAAAAATGCAATGGAAAGT
Found at i:4255 original size:18 final size:18
Alignment explanation
Indices: 4232--4277 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
4222 TTAATATAAG
4232 GAAGTTGAATTCATGCTT
1 GAAGTTGAATTCATGCTT
4250 GAAGTTGAATTCATGCTT
1 GAAGTTGAATTCATGCTT
*
4268 GAAATTGAAT
1 GAAGTTGAAT
4278 GAAAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (18 bp):
GAAGTTGAATTCATGCTT
Found at i:6551 original size:18 final size:18
Alignment explanation
Indices: 6175--6538 Score: 469
Period size: 18 Copynumber: 20.2 Consensus size: 18
6165 AATTCTAAAT
*
6175 ATTTACAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
6193 ATTTTCAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
*
6211 ATTTTCAGTTATCATATG
1 ATTTTCAGTTATCAGATG
*
6229 ATTTTCAGTTATTAGATG
1 ATTTTCAGTTATCAGATG
* * *
6247 ATTTACAATTATTAGATG
1 ATTTTCAGTTATCAGATG
6265 ATTTTCAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
* *
6283 ATTTTTAGTTATCAAATG
1 ATTTTCAGTTATCAGATG
*
6301 ATTTTCAATTATCAGATG
1 ATTTTCAGTTATCAGATG
*
6319 ATTTACAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
*
6337 ATTTTTAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
*
6355 ATTTTCGGTTATCAGATG
1 ATTTTCAGTTATCAGATG
*
6373 ATTTACAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
6391 ATTTAT-AGTTATCAGATG
1 ATTT-TCAGTTATCAGATG
*
6409 ATTTTCAGTTATCAGATT
1 ATTTTCAGTTATCAGATG
* * * *
6427 ATTTACAATTATCAAATC
1 ATTTTCAGTTATCAGATG
* * *
6445 ATTTTTAGTTATCAAATC
1 ATTTTCAGTTATCAGATG
* * *
6463 ATTTACAATTATCAAATG
1 ATTTTCAGTTATCAGATG
*
6481 ATTTTCAGTTATCATATG
1 ATTTTCAGTTATCAGATG
*
6499 ATTTTCAGTTATCATATG
1 ATTTTCAGTTATCAGATG
*
6517 ATTTACAGTTATCAGATG
1 ATTTTCAGTTATCAGATG
6535 ATTT
1 ATTT
6539 ACAATTATTA
Statistics
Matches: 304, Mismatches: 40, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
17 1 0.00
18 303 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (18 bp):
ATTTTCAGTTATCAGATG
Found at i:15776 original size:15 final size:15
Alignment explanation
Indices: 15756--15794 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
15746 GAAAATCAAG
15756 AATAAAGATTAAGAC
1 AATAAAGATTAAGAC
* *
15771 AATAAAGAATAAGAT
1 AATAAAGATTAAGAC
15786 AATAAAGAT
1 AATAAAGAT
15795 AAATTAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.03, G:0.13, T:0.21
Consensus pattern (15 bp):
AATAAAGATTAAGAC
Found at i:28041 original size:29 final size:31
Alignment explanation
Indices: 27974--28047 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 31
27964 TTATTATTCA
27974 TTAATTATTATTTTTCAACAACAATTAATAAT
1 TTAA-TATTATTTTTCAACAACAATTAATAAT
* *
28006 TT-TTATTCATTTTT-AATAA-AATTAA-AAT
1 TTAATATT-ATTTTTCAACAACAATTAATAAT
28034 TTAATATTTATTTT
1 TTAATA-TTATTTT
28048 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
28 5 0.14
29 13 0.36
30 10 0.28
31 6 0.17
32 2 0.06
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAATATTATTTTTCAACAACAATTAATAAT
Found at i:37923 original size:33 final size:33
Alignment explanation
Indices: 37872--37940 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
37862 ATTAAGCTAG
* *
37872 TTATAAAATTATTATAATCAATTTTATATTTAAT
1 TTATAAAATTATTATAATCAATATTAAATTT-AT
* *
37906 TTATATAATT-TTTTAATCAATATTAAATTTAT
1 TTATAAAATTATTATAATCAATATTAAATTTAT
37938 TTA
1 TTA
37941 AAATATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 5 0.16
33 17 0.55
34 9 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (33 bp):
TTATAAAATTATTATAATCAATATTAAATTTAT
Found at i:38166 original size:23 final size:24
Alignment explanation
Indices: 38124--38173 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
38114 CAGTCTAAAT
38124 AAATATTTTAAATTTAATTTTT-A
1 AAATATTTTAAATTTAATTTTTCA
*
38147 AAATATTTT-AATATTGATTTTTCA
1 AAATATTTTAAAT-TTAATTTTTCA
38171 AAA
1 AAA
38174 CATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 3 0.12
23 17 0.71
24 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATATTTTAAATTTAATTTTTCA
Found at i:39506 original size:13 final size:13
Alignment explanation
Indices: 39488--39514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39478 GACTTACTAT
39488 ATAAAATTATTTA
1 ATAAAATTATTTA
39501 ATAAAATTATTTA
1 ATAAAATTATTTA
39514 A
1 A
39515 ATAATGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Done.