Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009500.1 Hibiscus syriacus cultivar Beakdansim tig00115000_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: 51618
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:2207 original size:2 final size:2
Alignment explanation
Indices: 2200--2225 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2190 TTAATTCTTG
2200 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2226 TATTTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2260 original size:18 final size:18
Alignment explanation
Indices: 2222--2261 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2212 ATATATATAT
*
2222 ATATTATTTTTCTGAAAA
1 ATATTATTTTTATGAAAA
2240 ATATTATTTTTAT-AAATA
1 ATATTATTTTTATGAAA-A
2258 ATAT
1 ATAT
2262 AAAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTATTTTTATGAAAA
Found at i:5705 original size:29 final size:31
Alignment explanation
Indices: 5663--5720 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
5653 TTGAAAAATA
*
5663 ATTATATATTATTA-AA-ATAAAAGAATAAT
1 ATTATATATCATTATAATATAAAAGAATAAT
*
5692 ATTATATATCATTATAATATTAAAGAATA
1 ATTATATATCATTATAATATAAAAGAATA
5721 TAATATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 2 0.08
31 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (31 bp):
ATTATATATCATTATAATATAAAAGAATAAT
Found at i:6205 original size:18 final size:18
Alignment explanation
Indices: 6167--6206 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6157 ATATATATAT
*
6167 ATATTATTTTTCTGAAAA
1 ATATTATTTTTATGAAAA
6185 ATATTATTTTTAT-AAATA
1 ATATTATTTTTATGAAA-A
6203 ATAT
1 ATAT
6207 AAAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTATTTTTATGAAAA
Found at i:16153 original size:5 final size:5
Alignment explanation
Indices: 16143--16204 Score: 60
Period size: 5 Copynumber: 13.2 Consensus size: 5
16133 AACGGTCAAC
* * *
16143 GGTCG GGTCG GGTCG GGTC- GGTC- GGTCG GGTAG GTTC- GGT-T GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
*
16189 GGTTG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG G
16205 ACCGGTTCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 13 0.28
5 34 0.72
ACGTcount: A:0.02, C:0.16, G:0.56, T:0.26
Consensus pattern (5 bp):
GGTCG
Found at i:16171 original size:18 final size:18
Alignment explanation
Indices: 16142--16204 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
16132 CAACGGTCAA
*
16142 CGGTCGGGTCGGGTCGGGT
1 CGGTC-GGTCGGGTAGGGT
*
16161 CGGTCGGTCGGGTAGGTT
1 CGGTCGGTCGGGTAGGGT
* *
16179 CGGTTGGTCGGGTTGGGT
1 CGGTCGGTCGGGTAGGGT
16197 CGGGTCGG
1 C-GGTCGG
16205 ACCGGTTCAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
18 27 0.73
19 10 0.27
ACGTcount: A:0.02, C:0.17, G:0.56, T:0.25
Consensus pattern (18 bp):
CGGTCGGTCGGGTAGGGT
Found at i:17122 original size:2 final size:2
Alignment explanation
Indices: 17117--17159 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
17107 AGAAAAAATA
17117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17159 A
1 A
17160 AGAATAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23119 original size:2 final size:2
Alignment explanation
Indices: 23112--23144 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
23102 TTTCTTGGAA
23112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
23145 TTTTATAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27743 original size:23 final size:23
Alignment explanation
Indices: 27699--27743 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
27689 GATGGTTTAA
* *
27699 TTATTTCATTTTTAAATGCAAAT
1 TTATTTCATTTATAAATACAAAT
* *
27722 TTATTTTATTTATAATTACAAA
1 TTATTTCATTTATAAATACAAA
27744 ATAATTCATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATTTCATTTATAAATACAAAT
Found at i:32249 original size:2 final size:2
Alignment explanation
Indices: 32244--32268 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32234 AAAAATATCT
32244 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32269 TTCCAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33656 original size:31 final size:29
Alignment explanation
Indices: 33589--33657 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
33579 AAATCATTAA
* *
33589 ATATTATTAAAATAAAAGTATAATATTAT
1 ATATTATTAAAATAAAAGAATAATAATAT
*
33618 ATATTATTATAATATTAAAGAAT-ATAATAT
1 ATATTATTA-AA-ATAAAAGAATAATAATAT
33648 CATATTATTA
1 -ATATTATTA
33658 GAATTATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.26
30 8 0.24
31 17 0.50
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
ATATTATTAAAATAAAAGAATAATAATAT
Found at i:35210 original size:2 final size:2
Alignment explanation
Indices: 35205--35233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35195 AAAAATATCT
35205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35234 TTCCAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36622 original size:31 final size:29
Alignment explanation
Indices: 36555--36623 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
36545 AAATCATTAA
* *
36555 ATATTATTAAAATAAAAGTATAATATTAT
1 ATATTATTAAAATAAAAGAATAATAATAT
*
36584 ATATTATTATAATATTAAAGAAT-ATAATAT
1 ATATTATTA-AA-ATAAAAGAATAATAATAT
36614 CATATTATTA
1 -ATATTATTA
36624 GAATTATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.26
30 8 0.24
31 17 0.50
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
ATATTATTAAAATAAAAGAATAATAATAT
Found at i:38175 original size:2 final size:2
Alignment explanation
Indices: 38170--38196 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38160 AAAAATATCT
38170 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38197 TTCCAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39583 original size:28 final size:26
Alignment explanation
Indices: 39513--39583 Score: 70
Period size: 30 Copynumber: 2.5 Consensus size: 26
39503 AAATCATTAA
* * *
39513 ATATTATTAAAATAAAAGTATATATT
1 ATATTATTAAATTAAAAATATATATC
39539 ATATTATTATAATATTAAAGAATATATATC
1 ATATTA-T-TAA-ATTAAA-AATATATATC
39569 ATATTATTAGAATTA
1 ATATTATTA-AATTA
39584 TGAGTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 6 0.16
27 1 0.03
28 9 0.24
29 7 0.19
30 14 0.38
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATTATTAAATTAAAAATATATATC
Found at i:40038 original size:18 final size:19
Alignment explanation
Indices: 39999--40040 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
39989 ATATATATAT
*
39999 ATATATATTTTTCTGAAAA
1 ATATATATTTTTATGAAAA
40018 ATAT-TATTTTTAT-AAATA
1 ATATATATTTTTATGAAA-A
40036 ATATA
1 ATATA
40041 AAAGTCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.15
18 13 0.65
19 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATATTTTTATGAAAA
Found at i:48763 original size:2 final size:2
Alignment explanation
Indices: 48758--48782 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48748 AAAAATATCT
48758 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
48783 TTCCAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49893 original size:22 final size:22
Alignment explanation
Indices: 49847--49893 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
49837 ATATTAATTT
*
49847 TATTGAATTTTTTAATAAATTA
1 TATTGAATTTTTTAATAAATAA
*
49869 TATT-AATTTTTTATTATAATAA
1 TATTGAATTTTTTAATA-AATAA
49891 TAT
1 TAT
49894 ATTCTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTGAATTTTTTAATAAATAA
Found at i:50064 original size:21 final size:20
Alignment explanation
Indices: 50036--50076 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
50026 AGTTTTGTAA
* *
50036 TTTATGAATAATAGTATATT
1 TTTATGAAAAATAATATATT
50056 TTTATTGAAAAATAATATATT
1 TTTA-TGAAAAATAATATATT
50077 ATTAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTATGAAAAATAATATATT
Found at i:50100 original size:26 final size:30
Alignment explanation
Indices: 50066--50137 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
50056 TTTATTGAAA
*
50066 AATAATATATTATTA-AA-A-TAAAG-TAT
1 AATATTATATTATTATAATATTAAAGATAT
*
50092 AATATTATATCATTATAATATTAAAGAATAT
1 AATATTATATTATTATAATATTAAAG-ATAT
*
50123 AATATCATATTATTA
1 AATATTATATTATTA
50138 GAATTATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.35
27 2 0.05
28 1 0.03
29 5 0.14
31 16 0.43
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
AATATTATATTATTATAATATTAAAGATAT
Done.