Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007380.1 Hibiscus syriacus cultivar Beakdansim tig00019830_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: 57240
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:78 original size:20 final size:18
Alignment explanation
Indices: 36--100 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
26 CTGTAGGTTT
36 GCACACATAGTGCCTGTA
1 GCACACATAGTGCCTGTA
*
54 GCACACATAGTTCCTGTA
1 GCACACATAGTGCCTGTA
*
72 GCACACATAGTGCATGTA
1 GCACACATAGTGCCTGTA
*
90 GTACACATAGT
1 GCACACATAGT
101 ACTAATATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (18 bp):
GCACACATAGTGCCTGTA
Found at i:18309 original size:21 final size:21
Alignment explanation
Indices: 18285--18329 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18275 CAGTAAGGCA
* *
18285 TTTGTTAAAGCCATTAAATCT
1 TTTGCTAAAGCCATAAAATCT
* *
18306 TTTGCTGAGGCCATAAAATCT
1 TTTGCTAAAGCCATAAAATCT
18327 TTT
1 TTT
18330 AGTGAAGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (21 bp):
TTTGCTAAAGCCATAAAATCT
Found at i:20690 original size:15 final size:15
Alignment explanation
Indices: 20670--20701 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20660 TAAGCGCGTA
20670 AGTCCAAGTCCATAT
1 AGTCCAAGTCCATAT
20685 AGTCCAAGTCCATAT
1 AGTCCAAGTCCATAT
20700 AG
1 AG
20702 CTTACCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (15 bp):
AGTCCAAGTCCATAT
Found at i:25401 original size:15 final size:15
Alignment explanation
Indices: 25381--25409 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25371 AATTATGACC
25381 ATCAACATCATCAGA
1 ATCAACATCATCAGA
25396 ATCAACATCATCAG
1 ATCAACATCATCAG
25410 CAGCCTTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (15 bp):
ATCAACATCATCAGA
Found at i:38033 original size:117 final size:117
Alignment explanation
Indices: 37824--38057 Score: 342
Period size: 117 Copynumber: 2.0 Consensus size: 117
37814 ACATGATAAA
* * * *
37824 TACACAATACAGGAAGTTGCATCTATCTGGCATACATCATTTCTTGCATGGATTACAAGTATTCG
1 TACACAATACAAGAAGATACATCTATCCGGCATACATCATTTCTTGCATGGATTACAAGTATTCG
* * * *
37889 ATTTGAGTACAAATCACTTTCAAAAAGGGAGGATGATACATGCATGACTAGG
66 ATTTAAGGAAAAATCACTTTCAAAAAGGGAGGATGATACATACATGACTAGG
* * *
37941 TACACAATACAAGAAGATACATCTATCCGGCGTACATCATTTCTTTCATGGATTACAAGTCTTCG
1 TACACAATACAAGAAGATACATCTATCCGGCATACATCATTTCTTGCATGGATTACAAGTATTCG
* * *
38006 ATTTAAGGAAAAATTACTTTCATAAAGGGAGGATGATATATACATGACTAGG
66 ATTTAAGGAAAAATCACTTTCAAAAAGGGAGGATGATACATACATGACTAGG
38058 CTCCAGTTCA
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 103 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (117 bp):
TACACAATACAAGAAGATACATCTATCCGGCATACATCATTTCTTGCATGGATTACAAGTATTCG
ATTTAAGGAAAAATCACTTTCAAAAAGGGAGGATGATACATACATGACTAGG
Found at i:49150 original size:22 final size:22
Alignment explanation
Indices: 49122--49172 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
49112 AGTTGAGGGT
*
49122 TTCATAGGTCCTTTGGGACATA
1 TTCATAGGTCCTTTGGGACAAA
49144 TTCATAGGTCCTTTGGGACAAA
1 TTCATAGGTCCTTTGGGACAAA
49166 TCTCATA
1 T-TCATA
49173 TGCCACTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (22 bp):
TTCATAGGTCCTTTGGGACAAA
Found at i:54591 original size:16 final size:16
Alignment explanation
Indices: 54570--54600 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54560 TTTGGAAATG
54570 TTGTGTATGATCAATC
1 TTGTGTATGATCAATC
54586 TTGTGTATGATCAAT
1 TTGTGTATGATCAAT
54601 TTATAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (16 bp):
TTGTGTATGATCAATC
Found at i:55960 original size:22 final size:22
Alignment explanation
Indices: 55919--55960 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55909 AATCGAGGGT
* *
55919 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCATTCAGGACATA
*
55941 TTCATAGGTCATTCATGACA
1 TTCATAGGTCATTCAGGACA
55961 ATTTGCAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
TTCATAGGTCATTCAGGACATA
Done.