Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004511.1 Hibiscus syriacus cultivar Beakdansim tig00009950_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: 60969
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:3217 original size:26 final size:26
Alignment explanation
Indices: 3181--3248 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
3171 ATGAACCCAC
*
3181 ATGCAAGGCACATGGGGGCTGGTCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
3207 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
**
3233 ATGCAAAACACATGGG
1 ATGCAAGGCACATGGG
3249 TGTTCTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.34, T:0.18
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGCTGATCAT
Found at i:6166 original size:90 final size:90
Alignment explanation
Indices: 6013--6176 Score: 267
Period size: 90 Copynumber: 1.8 Consensus size: 90
6003 CCTAACACTC
* * *
6013 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACACTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
6078 ATTTAATTATTTGGAATTTAATAAT
66 ATTTAATTATTTGGAATTTAATAAT
* *
6103 CCTTTTATATCCAAGTTACACTAATCATA-TCGTGGATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACACTAATCATATTAG-GGATTTTATTATTTCAAATTAATTAAATCTA
6167 TATTTAATTA
65 TATTTAATTA
6177 ATTAAAATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
89 2 0.03
90 66 0.97
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACACTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTATTTGGAATTTAATAAT
Found at i:12932 original size:90 final size:90
Alignment explanation
Indices: 12779--12956 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
12769 CCTAACGCAC
* * *
12779 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
12844 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
12869 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
12934 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
12957 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:14946 original size:17 final size:16
Alignment explanation
Indices: 14915--14949 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
14905 AACAAAAAGC
14915 AACAAAAAAAAAAGAA
1 AACAAAAAAAAAAGAA
*
14931 AACAAAAGAGAAAAGAA
1 AACAAAA-AAAAAAGAA
14948 AA
1 AA
14950 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAAAGAA
Found at i:25860 original size:90 final size:90
Alignment explanation
Indices: 25707--25884 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
25697 CCTAACGTAC
* * * *
25707 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTTAAATTAATTTAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
25772 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
25797 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
25862 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
25885 TTCGGGATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:42090 original size:19 final size:20
Alignment explanation
Indices: 42066--42118 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
42056 TTTGGCTAAG
*
42066 ATCATGTATCTTCATT-AAA
1 ATCATGTATTTTCATTAAAA
42085 ATCATGTATTTTCATTAAAA
1 ATCATGTATTTTCATTAAAA
42105 ATCATGTATTTTCA
1 ATCATGTATTTTCA
42119 AAGGGGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
ATCATGTATTTTCATTAAAA
Found at i:54527 original size:28 final size:28
Alignment explanation
Indices: 54496--54563 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
54486 GTTAATTTAA
54496 TAAATGAACTAGTTTAATTAACGAAGCC
1 TAAATGAACTAGTTTAATTAACGAAGCC
54524 TAAATGAACTAGTTTAATTAACGAAGCC
1 TAAATGAACTAGTTTAATTAACGAAGCC
**
54552 TAAGCGAACTAG
1 TAAATGAACTAG
54564 ATGATTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (28 bp):
TAAATGAACTAGTTTAATTAACGAAGCC
Found at i:54572 original size:28 final size:28
Alignment explanation
Indices: 54496--54572 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
54486 GTTAATTTAA
* * *
54496 TAAATGAACTAGTTTAATTAACGAAGCC
1 TAAACGAACTAGATGAATTAACGAAGCC
* * *
54524 TAAATGAACTAGTTTAATTAACGAAGCC
1 TAAACGAACTAGATGAATTAACGAAGCC
* *
54552 TAAGCGAACTAGATGATTTAA
1 TAAACGAACTAGATGAATTAA
54573 ATGCAATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (28 bp):
TAAACGAACTAGATGAATTAACGAAGCC
Done.