Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002878.1 Hibiscus syriacus cultivar Beakdansim tig00005932_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: 44072
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:12539 original size:19 final size:19
Alignment explanation
Indices: 12493--12545 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
12483 CTACCCTAAG
*
12493 AGTATCGATACTCCTACAAA
1 AGTATCGATACT-TTACAAA
* * *
12513 AGTTTCGATACTTTATATA
1 AGTATCGATACTTTACAAA
*
12532 AGTATCGATGCTTT
1 AGTATCGATACTTT
12546 TAAACATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (19 bp):
AGTATCGATACTTTACAAA
Found at i:16091 original size:24 final size:24
Alignment explanation
Indices: 16064--16116 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
16054 GCTGCCCAGC
*
16064 GCAACCAACAAGATTCAGCAGCTA
1 GCAAACAACAAGATTCAGCAGCTA
*
16088 GCAAACAACAAGCTTCAGCAGCTA
1 GCAAACAACAAGATTCAGCAGCTA
*
16112 ACAAA
1 GCAAA
16117 AGTCACCGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.11
Consensus pattern (24 bp):
GCAAACAACAAGATTCAGCAGCTA
Found at i:21182 original size:24 final size:24
Alignment explanation
Indices: 21131--21182 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
21121 ATGTCCATTA
*
21131 TTTTTTCTGCTCTTACTGGCACGCT
1 TTTTTTCTGCTCTTACTGGCAC-AT
*
21156 TTTTTCTCTGCTCTTAGTGGCA-AT
1 TTTTT-TCTGCTCTTACTGGCACAT
21180 TTT
1 TTT
21183 ATCTTTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 5 0.21
26 15 0.62
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.52
Consensus pattern (24 bp):
TTTTTTCTGCTCTTACTGGCACAT
Found at i:36448 original size:14 final size:14
Alignment explanation
Indices: 36429--36456 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36419 GACATAAACA
36429 AACATAACCGAACG
1 AACATAACCGAACG
36443 AACATAACCGAACG
1 AACATAACCGAACG
36457 TTCACGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.14, T:0.07
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:37772 original size:23 final size:23
Alignment explanation
Indices: 37746--37793 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
37736 ATAAAGTACA
*
37746 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
37769 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
37792 AT
1 AT
37794 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:38536 original size:18 final size:18
Alignment explanation
Indices: 38513--38549 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38503 CGAAATATAT
38513 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
38531 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
38549 A
1 A
38550 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:38779 original size:23 final size:23
Alignment explanation
Indices: 38753--38817 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
38743 ATGCGAGATA
38753 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
38776 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
38799 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
38818 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:39200 original size:21 final size:20
Alignment explanation
Indices: 39170--39223 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
39160 GATAGACACT
*
39170 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
39191 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
39214 TTACATTATA
1 TTACATTATA
39224 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:39211 original size:23 final size:23
Alignment explanation
Indices: 39185--39247 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
39175 ATATAACCAT
39185 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
39208 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
39231 TACCTATTACATCATAT
1 TACCTATTACATTATAT
39248 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:39622 original size:21 final size:20
Alignment explanation
Indices: 39592--39645 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
39582 GATAGACACT
*
39592 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
39613 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
39636 TTACATTATA
1 TTACATTATA
39646 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:39633 original size:23 final size:23
Alignment explanation
Indices: 39607--39669 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
39597 ATATAACCAT
39607 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
39630 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
39653 TACCTATTACATCATAT
1 TACCTATTACATTATAT
39670 GTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:40045 original size:21 final size:20
Alignment explanation
Indices: 40015--40068 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
40005 GATAGACACT
*
40015 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
40036 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
40059 TTACATTATA
1 TTACATTATA
40069 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:40056 original size:23 final size:23
Alignment explanation
Indices: 40030--40092 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
40020 ATATAACCAT
40030 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
40053 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
40076 TACCTATTACATCATAT
1 TACCTATTACATTATAT
40093 GTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:40462 original size:21 final size:20
Alignment explanation
Indices: 40432--40485 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
40422 GATAGACACT
*
40432 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
40453 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
40476 TTACATTATA
1 TTACATTATA
40486 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:40473 original size:23 final size:23
Alignment explanation
Indices: 40447--40509 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
40437 ATATAACCAT
40447 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
40470 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
40493 TACCTATTACATCATAT
1 TACCTATTACATTATAT
40510 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:40508 original size:417 final size:426
Alignment explanation
Indices: 38755--40607 Score: 3439
Period size: 429 Copynumber: 4.4 Consensus size: 426
38745 GCGAGATAGA
38755 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
38820 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
38885 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
38950 ATTTCATTTGCACAAAAAAATATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCAC--AAAAATATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAA-TTTT
39015 TAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
258 TAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
39080 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
323 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGA
39145 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
387 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
39185 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
39250 TTACCTATTAT-TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
39314 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
39379 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCAC-AAAAA-TATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
39444 AATTTAATAATAATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACT-AA--AA
259 AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
39505 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACA-TGAAAAAGTATGGACA
324 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACA
39569 CTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
389 CTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
39607 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATG-
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
39671 TTACCTA-T-TATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
39733 TGTAATTTATGTTTCAATTTTTTTAACA-TGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
39797 ATTTCA-TTGCACAAAAAATTATTTGATTGTTTTTTATATTTTATAAAATATTATTTAGAATTTT
196 ATTTCATTTGCAC-AAAAA-TATTTGATTG-TTTTTATATTTTATAAAATATTATTTAGAATTTT
39861 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
258 TAATTTAATAAT-A-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
39926 TAATATCTTAAAACTCACTCAAAAGATAACCTT-AATT-ATGTTTTCCACAGTGAAAAAGTATGG
321 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGG
39989 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
386 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
40030 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATG-
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
40094 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTT-AAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
40157 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
40222 ATTTCATTTGCAC-AAAA-A-TT-ATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAA
196 ATTTCATTTGCACAAAAATATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAA
40283 TTTAAT-AT-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
261 TTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
40346 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACACT
326 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACACT
40411 TTTATAAAAAGGATAGACACTTTACAATATAACCAT
391 TTTATAAAAAGGATAGACACTTTACAATATAACCAT
40447 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
40512 TTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
40576 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
40608 ACTGCGAATT
Statistics
Matches: 1403, Mismatches: 0, Indels: 51
0.96 0.00 0.04
Matches are distributed among these distances:
415 83 0.06
416 4 0.00
417 168 0.12
418 131 0.09
419 141 0.10
420 42 0.03
421 40 0.03
422 131 0.09
423 131 0.09
424 122 0.09
425 73 0.05
426 22 0.02
427 31 0.02
428 37 0.03
429 171 0.12
430 76 0.05
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (426 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAATATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAA
TTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACACT
TTTATAAAAAGGATAGACACTTTACAATATAACCAT
Found at i:41909 original size:33 final size:33
Alignment explanation
Indices: 41872--41937 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
41862 CATCTTAATA
*
41872 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
41905 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
41938 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:44041 original size:22 final size:22
Alignment explanation
Indices: 44015--44062 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
44005 TTTTTCAGAG
*
44015 GATAT-TTAGCTTATATTTCATC
1 GATATGTTA-CTTATATTTAATC
*
44037 GATATGTTATTTATATTTAATC
1 GATATGTTACTTATATTTAATC
44059 GATA
1 GATA
44063 CAAATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (22 bp):
GATATGTTACTTATATTTAATC
Done.