Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002300.1 Hibiscus syriacus cultivar Beakdansim tig00004680_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: 56887
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:5181 original size:70 final size:70
Alignment explanation
Indices: 5057--5233 Score: 237
Period size: 70 Copynumber: 2.5 Consensus size: 70
5047 GCAAACCCGA
* * * *
5057 TTTAGCACTAAAGTGTATATAAAGGATACTTAGTGCAGGTGGTTAGCATAACCTTATGTGTCATA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTCAGCACAACCTTATGTGTCATA
*
5122 TTCGG
66 TTCAG
* * ** * *
5127 TTTAGCACTGTAGTGTATATAAAGGACACTTAGTGCAGGTGGTCGGTGCGACCTTGTGTGTCATA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTCAGCACAACCTTATGTGTCATA
5192 TTCAG
66 TTCAG
* *
5197 TTCAGCACTATAGTGTATAAAAAGGACACTTAGTGCA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCA
5234 TATGTTGCAT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 93 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (70 bp):
TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTCAGCACAACCTTATGTGTCATA
TTCAG
Found at i:5781 original size:22 final size:24
Alignment explanation
Indices: 5738--5782 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
5728 TGAATAAATA
**
5738 TTATTATATTAAATTATCTTTTAT
1 TTATTATATTAAATTAGATTTTAT
5762 TTATTA-ATT-AATTAGATTTTA
1 TTATTATATTAAATTAGATTTTA
5783 AATTTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATTATATTAAATTAGATTTTAT
Found at i:12185 original size:29 final size:31
Alignment explanation
Indices: 12143--12207 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
12133 TTGGCTAGTA
* * *
12143 ACCAAAATATAAATTT-T-AAAATTTTAATG
1 ACCAAAATACAAATTTGTAAAAAGTTTAAGG
*
12172 ACCAAATTACAAATTTGTAAAAAGTTTAAGG
1 ACCAAAATACAAATTTGTAAAAAGTTTAAGG
12203 ACCAA
1 ACCAA
12208 TATGGTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 15 0.50
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (31 bp):
ACCAAAATACAAATTTGTAAAAAGTTTAAGG
Found at i:15024 original size:69 final size:71
Alignment explanation
Indices: 14912--15098 Score: 240
Period size: 69 Copynumber: 2.7 Consensus size: 71
14902 GTATACCCGA
*
14912 TTTAGCACTATAGTGTATATAAAGGAT-ATATAGTGCAGGTTGTGGGCATA-ACCTTATGTGTCA
1 TTTAGCACTATAGTGTATATAAAGGATAAT-TAGTGCAGATTGTGGGCATACACCTTATGTGTCA
14975 TATTC-G
65 TATTCAG
* * *
14981 TTTAGCATTGTAGTGTATATAAAGGATAATTAGTGCAGATTGT-GG-ATACGACCTTGTGTGTCA
1 TTTAGCACTATAGTGTATATAAAGGATAATTAGTGCAGATTGTGGGCATAC-ACCTTATGTGTCA
15044 TATTCAG
65 TATTCAG
* * * * *
15051 TTTAGCACTATAGTGTATAAAAAGGACACTTAGTGCATATGGTGGGCA
1 TTTAGCACTATAGTGTATATAAAGGATAATTAGTGCAGATTGTGGGCA
15099 CGTCCTGATG
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
67 3 0.03
68 2 0.02
69 54 0.53
70 39 0.39
71 2 0.02
72 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (71 bp):
TTTAGCACTATAGTGTATATAAAGGATAATTAGTGCAGATTGTGGGCATACACCTTATGTGTCAT
ATTCAG
Found at i:16215 original size:5 final size:5
Alignment explanation
Indices: 16184--16230 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
16174 GGAATGGATT
*
16184 AATGA AATAAGA AATGA AA-GA AA-GA AATGA AATGA TATGA AATGA AA
1 AATGA AAT--GA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AA
16231 GGGATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 8 0.22
5 24 0.65
7 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (5 bp):
AATGA
Found at i:21378 original size:19 final size:19
Alignment explanation
Indices: 21354--21403 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
21344 AGAAAGAATG
21354 AAAGAAAATGAAACGAAAT
1 AAAGAAAATGAAACGAAAT
* *
21373 AAAGAAAATAAAATGAAAT
1 AAAGAAAATGAAACGAAAT
*
21392 AAATAAAATGAA
1 AAAGAAAATGAA
21404 GATAACTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (19 bp):
AAAGAAAATGAAACGAAAT
Found at i:21395 original size:14 final size:15
Alignment explanation
Indices: 21369--21408 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
21359 AAATGAAACG
*
21369 AAATAAAGA-AAATA
1 AAATGAAGATAAATA
21383 AAATGAA-ATAAATA
1 AAATGAAGATAAATA
21397 AAATGAAGATAA
1 AAATGAAGATAA
21409 CTTACAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (15 bp):
AAATGAAGATAAATA
Found at i:27850 original size:13 final size:13
Alignment explanation
Indices: 27832--27862 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
27822 AACTCGTATT
27832 GGGTTGTGTGTGC
1 GGGTTGTGTGTGC
27845 GGGTTGTGTGTGC
1 GGGTTGTGTGTGC
27858 GGGTT
1 GGGTT
27863 ATGGGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.55, T:0.39
Consensus pattern (13 bp):
GGGTTGTGTGTGC
Found at i:29011 original size:15 final size:15
Alignment explanation
Indices: 28974--29022 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
28964 ACAACGCAAC
*
28974 AAAGAAACAGAAA-A
1 AAAGAAAAAGAAAGA
*
28988 GAA-AAAAAGAAAGA
1 AAAGAAAAAGAAAGA
29002 AAAGAAAAAGAAAGA
1 AAAGAAAAAGAAAGA
*
29017 AGAGAA
1 AAAGAA
29023 GCTTACCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 8 0.28
14 5 0.17
15 16 0.55
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAGA
Found at i:31101 original size:9 final size:9
Alignment explanation
Indices: 31087--31111 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31077 TTACATGTAA
31087 ATTTAAATT
1 ATTTAAATT
31096 ATTTAAATT
1 ATTTAAATT
31105 ATTTAAA
1 ATTTAAA
31112 AGAATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:35290 original size:24 final size:24
Alignment explanation
Indices: 35254--35306 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
35244 CTACACTCTT
35254 GCCTACCGCAATGACTATGGCATG
1 GCCTACCGCAATGACTATGGCATG
*
35278 GCCTACCGTAATGACTATGGCATG
1 GCCTACCGCAATGACTATGGCATG
*
35302 ACCTA
1 GCCTA
35307 TCATCCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (24 bp):
GCCTACCGCAATGACTATGGCATG
Found at i:41550 original size:70 final size:70
Alignment explanation
Indices: 41426--41602 Score: 237
Period size: 70 Copynumber: 2.5 Consensus size: 70
41416 GCAAACCCGA
* * * *
41426 TTTAGCACTAAAGTGTATATAAAGGATACTTAGTGCAGGTGGTTAGCATAACCTTATGTGTCATA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTCAGCACAACCTTATGTGTCATA
*
41491 TTCGG
66 TTCAG
* * ** * *
41496 TTTAGCACTGTAGTGTATATAAAGGACACTTAGTGCAGGTGGTCGGTGCGACCTTGTGTGTCATA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTCAGCACAACCTTATGTGTCATA
41561 TTCAG
66 TTCAG
* *
41566 TTCAGCACTATAGTGTATAAAAAGGACACTTAGTGCA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCA
41603 TATGTTGCAT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 93 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (70 bp):
TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTCAGCACAACCTTATGTGTCATA
TTCAG
Found at i:42149 original size:22 final size:24
Alignment explanation
Indices: 42106--42150 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
42096 TGAATAAATA
**
42106 TTATTATATTAAATTATCTTTTAT
1 TTATTATATTAAATTAGATTTTAT
42130 TTATTA-ATT-AATTAGATTTTA
1 TTATTATATTAAATTAGATTTTA
42151 AATTTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATTATATTAAATTAGATTTTAT
Found at i:48360 original size:29 final size:31
Alignment explanation
Indices: 48318--48382 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
48308 TTGGCTAGTA
* * *
48318 ACCAAAATATAAATTT-T-AAAATTTTAATG
1 ACCAAAATACAAATTTGTAAAAAGTTTAAGG
*
48347 ACCAAATTACAAATTTGTAAAAAGTTTAAGG
1 ACCAAAATACAAATTTGTAAAAAGTTTAAGG
48378 ACCAA
1 ACCAA
48383 TATGGTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 15 0.50
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (31 bp):
ACCAAAATACAAATTTGTAAAAAGTTTAAGG
Found at i:51190 original size:69 final size:71
Alignment explanation
Indices: 51078--51264 Score: 240
Period size: 69 Copynumber: 2.7 Consensus size: 71
51068 GTATACCCGA
*
51078 TTTAGCACTATAGTGTATATAAAGGAT-ATATAGTGCAGGTTGTGGGCATA-ACCTTATGTGTCA
1 TTTAGCACTATAGTGTATATAAAGGATAAT-TAGTGCAGATTGTGGGCATACACCTTATGTGTCA
51141 TATTC-G
65 TATTCAG
* * *
51147 TTTAGCATTGTAGTGTATATAAAGGATAATTAGTGCAGATTGT-GG-ATACGACCTTGTGTGTCA
1 TTTAGCACTATAGTGTATATAAAGGATAATTAGTGCAGATTGTGGGCATAC-ACCTTATGTGTCA
51210 TATTCAG
65 TATTCAG
* * * * *
51217 TTTAGCACTATAGTGTATAAAAAGGACACTTAGTGCATATGGTGGGCA
1 TTTAGCACTATAGTGTATATAAAGGATAATTAGTGCAGATTGTGGGCA
51265 CGTCCTGATG
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
67 3 0.03
68 2 0.02
69 54 0.53
70 39 0.39
71 2 0.02
72 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (71 bp):
TTTAGCACTATAGTGTATATAAAGGATAATTAGTGCAGATTGTGGGCATACACCTTATGTGTCAT
ATTCAG
Found at i:52374 original size:5 final size:5
Alignment explanation
Indices: 52343--52389 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
52333 GGAATGGATT
*
52343 AATGA AATAAGA AATGA AA-GA AA-GA AATGA AATGA TATGA AATGA AA
1 AATGA AAT--GA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AA
52390 GGGATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 8 0.22
5 24 0.65
7 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (5 bp):
AATGA
Done.