Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004425.1 Hibiscus syriacus cultivar Beakdansim tig00009703_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: 41953
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:20713 original size:23 final size:23
Alignment explanation
Indices: 20687--20757 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
20677 GAAAGTGTAC
20687 CGATGTATTCCTTGAATGTGCAT
1 CGATGTATTCCTTGAATGTGCAT
* *
20710 CGA--TA--CACTATGAACGTGCAC
1 CGATGTATTC-CT-TGAATGTGCAT
* *
20731 CGATGCATTCCTTGAATGTGTAT
1 CGATGTATTCCTTGAATGTGCAT
20754 CGAT
1 CGAT
20758 ACACTCAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 14 0.39
23 16 0.44
24 2 0.06
25 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
CGATGTATTCCTTGAATGTGCAT
Found at i:20723 original size:44 final size:44
Alignment explanation
Indices: 20660--20762 Score: 170
Period size: 44 Copynumber: 2.3 Consensus size: 44
20650 TTTGTGCACA
* *
20660 GTGCATCGATACACTATGAAAGTGTACCGATGTATTCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAT
*
20704 GTGCATCGATACACTATGAACGTGCACCGATGCATTCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAT
*
20748 GTGTATCGATACACT
1 GTGCATCGATACACT
20763 CAGCAGTGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAT
Found at i:20728 original size:21 final size:21
Alignment explanation
Indices: 20659--20734 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
20649 TTTTGTGCAC
*
20659 AGTGCATCGATACACTATGAA
1 AGTGCACCGATACACTATGAA
*
20680 AGTGTACCGATGTATTC-CT-TGAA
1 AGTGCACCGA--TA--CACTATGAA
* *
20703 TGTGCATCGATACACTATGAA
1 AGTGCACCGATACACTATGAA
*
20724 CGTGCACCGAT
1 AGTGCACCGAT
20735 GCATTCCTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
19 1 0.02
20 2 0.05
21 23 0.55
23 13 0.31
24 2 0.05
25 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTGCACCGATACACTATGAA
Found at i:26967 original size:90 final size:90
Alignment explanation
Indices: 26814--26989 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 90
26804 TAACATACCC
*
26814 TTTTATAGCCAAGTTACCCTAATCATATCTGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCTGGGATTTTATTATTTCAAATTAATTAAATCTATAT
* *
26879 TTAATTAATTAGAATTTAATAATCT
66 TTAATTAATTAAAATTAAATAATCT
* * * *
26904 TTTTATATCTAAGTTACCGTAATCATAT-TAGGGATTTTATTATTTTAAATTAATTAAATCTATA
1 TTTTATAGCCAAGTTACCCTAATCATATCT-GGGATTTTATTATTTCAAATTAATTAAATCTATA
26968 TTTAATTAATTAAAATTAAATA
65 TTTAATTAATTAAAATTAAATA
26990 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 1 0.01
90 77 0.99
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATCTGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTAAAATTAAATAATCT
Found at i:33039 original size:90 final size:90
Alignment explanation
Indices: 32886--33063 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
32876 CCTAACACAC
* * *
32886 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATCAATTAAATCTAT
1 CCTTTTATAGCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAAATCAATTAAATCTAT
*
32951 ATTTAATTAATTAAAATTCAATAAT
66 ATTTAATTAATTAAAATTAAATAAT
* * *
32976 CCTTTTATATCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAATTTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAAATCAATTAAATCTAT
*
33041 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTAAAATTAAATA
33064 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAAATCAATTAAATCTAT
ATTTAATTAATTAAAATTAAATAAT
Found at i:34764 original size:137 final size:137
Alignment explanation
Indices: 34523--35099 Score: 870
Period size: 137 Copynumber: 4.2 Consensus size: 137
34513 AACCAGACAC
*
34523 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAATCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* * * *
34588 CCTTAGATAGCCATAATTCCTCATCACAAAGGAATCGTGTTATCTCAATTATCTTTAAATATGGA
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
*
34653 CAGACAT
131 CAGACGT
* * * *
34660 CCTCATCACGAAGAAACAATGTCATCCACCAACCAGAACTCCTTATCATGTAGGAGCCGAGTCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* *
34725 CCTTAGATAGTCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGC
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
34790 CAGACGT
131 CAGACGT
*
34797 CCTCATCACGAATGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* *
34862 CCTTAGATAGCCAGAATTCCTCATCATGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGC
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
34927 CAGACGT
131 CAGACGT
* * * *
34934 CCTCATCACAAAGGAAC-ATGTCATCCATCGACCAGAACTTCTCATCACGTAGGAGTCGAGTCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* * * * * ** *
34998 CCTTTGATAGCCAGAATTCCTCATCGCGTAGGAACTGTGTTATCTCAATCATCCCTAAACAT-GA
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
35062 CCAGACGT
131 -CAGACGT
* *
35070 CCTCATCATGAAGGAACAATGTCATACACC
1 CCTCATCACGAAGGAACAATGTCATCCACC
35100 AATTTGATCT
Statistics
Matches: 400, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
135 1 0.00
136 119 0.30
137 280 0.70
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (137 bp):
CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
CAGACGT
Found at i:35266 original size:3 final size:3
Alignment explanation
Indices: 35258--35295 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
35248 CATCCCGTTT
* *
35258 TTA TTA TTA TTA -TA ATA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35296 CAAATAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:38866 original size:15 final size:17
Alignment explanation
Indices: 38829--38869 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
38819 ATTAAGGACT
38829 AATTG-AATACATATAA
1 AATTGAAATACATATAA
*
38845 AAGTGAAATAC-T-TAA
1 AATTGAAATACATATAA
38860 AATTGAAATA
1 AATTGAAATA
38870 AATTAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (17 bp):
AATTGAAATACATATAA
Found at i:38975 original size:2 final size:2
Alignment explanation
Indices: 38968--39258 Score: 98
Period size: 2 Copynumber: 146.5 Consensus size: 2
38958 TAAAAATAAA
* *
38968 AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
* * * *
39010 AT AA ACT AT AT TT AT -T AT AA ACT AT AT A- AT -T AT -T AT AT GCT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT -AT
* * * *
39051 AT AT AT AA AT -T AT GT TT AT AT GA- ACT AT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT A-T AT
* * * * * *
39092 GT AT AT AA ACT AT AT AGT AT AA ACT AT AA AA AGT AT AT AGT TT AT
1 AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT A-T AT AT A-T AT AT
* * *
39137 A- AT AT AT AT AT AT AT AA ACT AT AT AA AT AT AT AT -T TT AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
39177 AT -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
39216 ACT A- AT AT A- AGT A- AT CT AT AG AT -T AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39256 AT A
1 AT A
39259 GTTTATAGAA
Statistics
Matches: 213, Mismatches: 40, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
1 19 0.09
2 175 0.82
3 19 0.09
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:39010 original size:13 final size:13
Alignment explanation
Indices: 38963--39119 Score: 92
Period size: 13 Copynumber: 11.8 Consensus size: 13
38953 TTGAATAAAA
*
38963 ATAAAATATATAT
1 ATAAACTATATAT
*
38976 ATATA-TATA-AT
1 ATAAACTATATAT
* *
38987 AT-AAGTTTATAT
1 ATAAACTATATAT
38999 ATAAAC--TATAT
1 ATAAACTATATAT
39010 ATAAACTATATTTATT
1 ATAAACTATA--TA-T
39026 ATAAACTATATAATT
1 ATAAACTATAT-A-T
* *
39041 ATTATA-TGCTATAT
1 A-TAAACT-ATATAT
* *
39055 ATAAATTATGTTTAT
1 ATAAACTA--TATAT
*
39070 ATGAACTATATAT
1 ATAAACTATATAT
*
39083 ATAAACTATGTAT
1 ATAAACTATATAT
39096 ATAAACTATATAGT
1 ATAAACTATATA-T
39110 ATAAACTATA
1 ATAAACTATA
39120 AAAAGTATAT
Statistics
Matches: 114, Mismatches: 15, Indels: 29
0.72 0.09 0.18
Matches are distributed among these distances:
10 1 0.01
11 18 0.16
12 8 0.07
13 37 0.32
14 15 0.13
15 18 0.16
16 17 0.15
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (13 bp):
ATAAACTATATAT
Found at i:39047 original size:27 final size:28
Alignment explanation
Indices: 38975--39037 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
38965 AAAATATATA
38975 TATATATATAA-TATAAGTTTATATATAAAC
1 TATATATA-AACTAT-A-TTTATATATAAAC
39005 TATATATAAACTATATTTAT-TATAAAC
1 TATATATAAACTATATTTATATATAAAC
39032 TATATA
1 TATATA
39038 ATTATTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.41
28 5 0.16
29 3 0.09
30 11 0.34
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATATAAACTATATTTATATATAAAC
Found at i:39190 original size:39 final size:39
Alignment explanation
Indices: 39102--39209 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
39092 GTATATAAAC
* *
39102 TATATAGTATAAACTATAAAAAGTATATAGTTTATAATATA
1 TATATA-TATAAACTATATAAA-TATATATTTTATAATATA
39143 TATATATATAAACTATATAAATATATATTTTATAAT-TA
1 TATATATATAAACTATATAAATATATATTTTATAATATA
* * *
39181 TAATTTATATTAA-TATAGTATATATATAT
1 T-ATATATATAAACTATA-TAAATATATAT
39210 ATATATACTA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
38 7 0.12
39 33 0.55
40 14 0.23
41 6 0.10
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (39 bp):
TATATATATAAACTATATAAATATATATTTTATAATATA
Found at i:39539 original size:2 final size:2
Alignment explanation
Indices: 39532--39666 Score: 192
Period size: 2 Copynumber: 70.0 Consensus size: 2
39522 TATAAACTTG
* **
39532 TA TA TA TA TA TA AA CTA TA TA TA TA -A CC TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39574 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39615 TA -A TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39654 TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA
39667 AATAAAAACC
Statistics
Matches: 121, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
1 6 0.05
2 114 0.94
3 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39907 original size:56 final size:57
Alignment explanation
Indices: 39834--39942 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 57
39824 TAAACTATAT
* * *
39834 ATATAACTTATATTATATGTAT-TAA-AA-CTATGTATAGTATATATGAACTATACATA
1 ATATAACCTATAGTATATGTATATAACAATCTATGTAT-GT-TATATAAACTATACATA
*
39890 ATATAACCTATAGTATATGTATATAACAATCTATTTATGTTATATAAACTATA
1 ATATAACCTATAGTATATGTATATAACAATCTATGTATGTTATATAAACTATA
39943 TGTACCTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 20 0.43
57 15 0.33
58 4 0.09
59 7 0.15
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (57 bp):
ATATAACCTATAGTATATGTATATAACAATCTATGTATGTTATATAAACTATACATA
Found at i:40283 original size:26 final size:28
Alignment explanation
Indices: 40239--40297 Score: 95
Period size: 26 Copynumber: 2.2 Consensus size: 28
40229 TGTATTATAT
40239 TAATATAAGTTAATATTAATATTAATTA
1 TAATATAAGTTAATATTAATATTAATTA
*
40267 TAATATAA-TT-ATTTTAATATTAATTA
1 TAATATAAGTTAATATTAATATTAATTA
40293 TAATA
1 TAATA
40298 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 20 0.67
27 2 0.07
28 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TAATATAAGTTAATATTAATATTAATTA
Found at i:41077 original size:6 final size:6
Alignment explanation
Indices: 41062--41108 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
41052 ACTGAGCCTG
* *
41062 AACCTCA AACCTA AACCCA AACCCA ACCCCA AACCCA AACCCA AACC
1 AACC-CA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACC
41109 TGACACGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 32 0.89
7 4 0.11
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.04
Consensus pattern (6 bp):
AACCCA
Found at i:41094 original size:24 final size:24
Alignment explanation
Indices: 41062--41108 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41052 ACTGAGCCTG
* *
41062 AACCTCAAACCTAAACCCAAACCC
1 AACCCCAAACCCAAACCCAAACCC
41086 AACCCCAAACCCAAACCCAAACC
1 AACCCCAAACCCAAACCCAAACC
41109 TGACACGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.04
Consensus pattern (24 bp):
AACCCCAAACCCAAACCCAAACCC
Found at i:41121 original size:17 final size:17
Alignment explanation
Indices: 41099--41176 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
41089 CCCAAACCCA
41099 AACCCAAACCTG-ACACG
1 AACCCAAACCTGAAC-CG
* *
41116 AACCCATACCTGAAATCG
1 AACCCAAACCTG-AACCG
* * *
41134 TACCCGAACCTGAACCA
1 AACCCAAACCTGAACCG
* *
41151 AACCCAAACCCGAATCCA
1 AACCCAAACCTGAA-CCG
41169 AACCCAAA
1 AACCCAAA
41177 TTCAAACTCG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
17 25 0.52
18 22 0.46
19 1 0.02
ACGTcount: A:0.42, C:0.40, G:0.09, T:0.09
Consensus pattern (17 bp):
AACCCAAACCTGAACCG
Done.