Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002729.1 Hibiscus syriacus cultivar Beakdansim tig00005626_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: 69017
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6242 original size:18 final size:20
Alignment explanation
Indices: 6205--6244 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6195 GCAGAGGCTC
6205 AATAAATATAGTCATCTGAT
1 AATAAATATAGTCATCTGAT
*
6225 AATAAATTTAG-C-TCTGAT
1 AATAAATATAGTCATCTGAT
6243 AA
1 AA
6245 GTAACATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AATAAATATAGTCATCTGAT
Found at i:18996 original size:146 final size:147
Alignment explanation
Indices: 18731--19023 Score: 473
Period size: 146 Copynumber: 2.0 Consensus size: 147
18721 TTTGAAATTA
* *
18731 CTTTCGAAAAGTGATTTTTAAAAGTGAAGTAGAAAATATTTTTTTAAATTTGTTTTATTAAAAGT
1 CTTTCGAAAAGTGATTCTTAAAAGTGAAGTAGAAAATATATTTTTAAATTTGTTTTATTAAAAGT
* *
18796 AAAGTTTAAAATTTAATTATTTGAGATTATTGTTAAAAAATGATTTGAAGAGATAAAATATTCGT
66 AAAGTTCAAAATTTAATTATTTGAGATTATTGTTAAAAAATGATTTGAAGAGATAAAATATTCAT
*
18861 TTTAGATATTATGTTGT
131 TTTAAATATTATGTTGT
* * *
18878 CTTTCGAAAATTGATTCTTAAAAGTGACGTAGAAAATA-ATTTTTAATTTTGTTTTATTAAAAGT
1 CTTTCGAAAAGTGATTCTTAAAAGTGAAGTAGAAAATATATTTTTAAATTTGTTTTATTAAAAGT
* *
18942 AGAGTTCAAAATTTAATTGA-TTGAGATTATTGTTAAAAAGTGATTTGAAGAGATAAAATATTCA
66 AAAGTTCAAAATTTAATT-ATTTGAGATTATTGTTAAAAAATGATTTGAAGAGATAAAATATTCA
19006 TTTTAAATATTATGTTGT
130 TTTTAAATATTATGTTGT
19024 AAATTAAAAA
Statistics
Matches: 135, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
146 99 0.73
147 36 0.27
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.43
Consensus pattern (147 bp):
CTTTCGAAAAGTGATTCTTAAAAGTGAAGTAGAAAATATATTTTTAAATTTGTTTTATTAAAAGT
AAAGTTCAAAATTTAATTATTTGAGATTATTGTTAAAAAATGATTTGAAGAGATAAAATATTCAT
TTTAAATATTATGTTGT
Found at i:24772 original size:20 final size:20
Alignment explanation
Indices: 24749--24787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24739 AATTCACCAC
*
24749 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
24769 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
24788 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:32787 original size:20 final size:20
Alignment explanation
Indices: 32758--32795 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32748 ATTTCACCAC
*
32758 ATGCAACTATATGCTCCTTA
1 ATGCAACTATATGATCCTTA
*
32778 ATGCATCTATATGATCCT
1 ATGCAACTATATGATCCT
32796 ATATGAGCTC
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:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGCAACTATATGATCCTTA
Found at i:41052 original size:30 final size:30
Alignment explanation
Indices: 41016--41076 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
41006 AGTCGAGGGT
41016 TACCTATGTCCTTCGGAACATATGGACAGG
1 TACCTATGTCCTTCGGAACATATGGACAGG
* *
41046 TACCTATGTTCTTCGGAACATATGGATAGG
1 TACCTATGTCCTTCGGAACATATGGACAGG
41076 T
1 T
41077 CCTTTGGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (30 bp):
TACCTATGTCCTTCGGAACATATGGACAGG
Found at i:41863 original size:23 final size:24
Alignment explanation
Indices: 41833--41881 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
41823 TTTTAACTGT
41833 TAAAAAA-TAAAAAAATA-TATCA
1 TAAAAAATTAAAAAAATATTATCA
*
41855 TAAATAAATTTTAAAAAATATTATCA
1 TAAA-AAA-TTAAAAAAATATTATCA
41881 T
1 T
41882 TACATTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.18
23 3 0.14
25 9 0.41
26 6 0.27
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAAATTAAAAAAATATTATCA
Found at i:44075 original size:21 final size:21
Alignment explanation
Indices: 44049--44090 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
44039 CTATAGACCG
44049 GTAGTCTCTTTGATAAAAAAC
1 GTAGTCTCTTTGATAAAAAAC
44070 GTAGTCTCTTTGATAAAAAAC
1 GTAGTCTCTTTGATAAAAAAC
44091 CTGATGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
GTAGTCTCTTTGATAAAAAAC
Found at i:51434 original size:59 final size:59
Alignment explanation
Indices: 51371--51501 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
51361 TTGGGAACCG
* * * * * *
51371 ATTTAGAATGAAGATCATTGTTTAGGGATGAAATTGAAATA-TCAAAAGTTTAA-GAACTA
1 ATTTAGAATGAAG-TCATAGTATAGGGATAAAATTAAAACATTCAAAAATTTAATG-ACTA
51430 ATTTAGAATGATAGTCATAGTATAGGGATAAAATTAAAACATTCAAAAATTTAATGACTA
1 ATTTAGAATGA-AGTCATAGTATAGGGATAAAATTAAAACATTCAAAAATTTAATGACTA
* *
51490 ATATAAAATGAA
1 ATTTAGAATGAA
51502 AGTTGTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 34 0.56
60 26 0.43
61 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.31
Consensus pattern (59 bp):
ATTTAGAATGAAGTCATAGTATAGGGATAAAATTAAAACATTCAAAAATTTAATGACTA
Found at i:54389 original size:21 final size:21
Alignment explanation
Indices: 54365--54446 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
54355 ACTTAAACCC
54365 TAACACATAAACCCTAAATCT
1 TAACACATAAACCCTAAATCT
54386 TAACACAT-AACCCTAAA-CT
1 TAACACATAAACCCTAAATCT
* * *
54405 CTAA-ACTTTAAACCTTAAATCC
1 -TAACAC-ATAAACCCTAAATCT
* *
54427 TATCACATAAACTCTAAATC
1 TAACACATAAACCCTAAATC
54447 CTAAACCCTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
19 4 0.08
20 13 0.27
21 29 0.59
22 3 0.06
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (21 bp):
TAACACATAAACCCTAAATCT
Found at i:54743 original size:14 final size:14
Alignment explanation
Indices: 54726--54766 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54716 TTTATTCATC
54726 AATAATGTATTTTT
1 AATAATGTATTTTT
54740 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
54751 AATAATGTAATTTT
1 AATAATGTATTTTT
54765 AA
1 AA
54767 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Done.