Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009593.1 Hibiscus syriacus cultivar Beakdansim tig00116972_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: 57557
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2917 original size:29 final size:29
Alignment explanation
Indices: 2883--2941 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2873 CCAAAATTAA
2883 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2912 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2941 T
1 T
2942 AGCTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:3650 original size:2 final size:2
Alignment explanation
Indices: 3645--3673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3635 ACAGAGAAAA
3645 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3674 ACACAATCTG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20631 original size:3 final size:3
Alignment explanation
Indices: 20623--20666 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
20613 CTTTATCAAT
20623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20667 ATGAATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:22871 original size:21 final size:21
Alignment explanation
Indices: 22845--22889 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22835 GATTTCTGGG
* *
22845 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
22866 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
22887 CAA
1 CAA
22890 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:24258 original size:30 final size:30
Alignment explanation
Indices: 24183--24337 Score: 258
Period size: 30 Copynumber: 5.1 Consensus size: 30
24173 TCGAGACATA
24183 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
24214 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
24245 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
24275 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* **
24305 TGGACAGTTACCG-GGGTCTTGGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
24334 TGGA
1 TGGA
24338 TAGGTCCTTC
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 17 0.14
30 66 0.55
31 38 0.31
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:26830 original size:15 final size:15
Alignment explanation
Indices: 26806--26881 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
26796 AAACAAAACG
26806 ATAT-TGGTGACATT
1 ATATATGGTGACATT
*
26820 ATATATGGTGATAATT
1 ATATATGGTGA-CATT
* ** * *
26836 -TTTAGTTTTGCCACT
1 ATATA-TGGTGACATT
26851 ATA-ATGGTGACATT
1 ATATATGGTGACATT
*
26865 ATATATGGTGACGTT
1 ATATATGGTGACATT
26880 AT
1 AT
26882 GCATAATCAT
Statistics
Matches: 44, Mismatches: 13, Indels: 9
0.67 0.20 0.14
Matches are distributed among these distances:
14 13 0.30
15 24 0.55
16 7 0.16
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (15 bp):
ATATATGGTGACATT
Found at i:27201 original size:194 final size:193
Alignment explanation
Indices: 26872--27226 Score: 548
Period size: 194 Copynumber: 1.8 Consensus size: 193
26862 ATTATATATG
* *
26872 GTGACGTTATGCATAATCATCATTCATAATATTATTAGGTAACGGTATATTATGTCACTAAAAAT
1 GTGACGTTATGCATAAACATCATTCATAATATTATTAGGTAACGGTATATTATGCCACTAAAAAT
*** *
26937 GTGACAATATCTCTTTCGTCACATATAAGTTGATTTTAATACATTATTTTTGACAATATAAATTA
66 GTGACAATATCTCTTTCGTCACATATAAGTTGATTTTAATACATTATCCGTGACAATATAAATCA
**
27002 TCAATAACGAAATCTTATTTAATTTAGTGACGTAACCAACTGTCATAGAATATAAACTATAAA
131 TCAATAACGAAATCTTACATAATTTAGTGACGTAACCAACTGTCATAGAATATAAACTATAAA
* **
27065 GTGACGTTATGCATAAACGTCATTCATAATATTATTAGGTAACATTTATATTATGCCACTAAAAA
1 GTGACGTTATGCATAAACATCATTCATAATATTATTAGGTAAC-GGTATATTATGCCACTAAAAA
* * ** *
27130 TTTGACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATCCGTGACGATATAAATC
65 TGTGACAATATCTCTTTCGTCACATATAAGTTGATTTTAATACATTATCCGTGACAATATAAATC
*
27195 ATCAATAACGAAATTTTACATAATTTAGTGAC
130 ATCAATAACGAAATCTTACATAATTTAGTGAC
27227 ATAATTAGTT
Statistics
Matches: 144, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
193 41 0.28
194 103 0.72
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (193 bp):
GTGACGTTATGCATAAACATCATTCATAATATTATTAGGTAACGGTATATTATGCCACTAAAAAT
GTGACAATATCTCTTTCGTCACATATAAGTTGATTTTAATACATTATCCGTGACAATATAAATCA
TCAATAACGAAATCTTACATAATTTAGTGACGTAACCAACTGTCATAGAATATAAACTATAAA
Found at i:27297 original size:194 final size:193
Alignment explanation
Indices: 26896--27298 Score: 484
Period size: 194 Copynumber: 2.1 Consensus size: 193
26886 AATCATCATT
* *
26896 CATAATATTATTAGGTAACGGTATATTATGTCACTAAAAATGTGACAATATCTCTTTCGTCACAT
1 CATAATACTATTAGGTAACGGTATATTATGCCACTAAAAATGTGACAATATCTCTTTCGTCACAT
*** * **
26961 ATAAGTTGATTTTAATACATTATTTTTGACAATATAAATTATCAATAACGAAATCTTATTTAATT
66 ATAAGTTGATTTTAATACATTATCCGTGACAATATAAATCATCAATAACGAAATCTTACATAATT
* * * * *
27026 TAGTGACGTAACCAACTGTCATAGAATATAAACTATAAAGTGACGTTATGCATAAACGTCATT
131 TAGTGACATAACCAACTGTCATAGAATATAAACTATAAAGTGACATTATACATAAACGCCATC
* ** *
27089 CATAATATTATTAGGTAACATTTATATTATGCCACTAAAAATTTGACAATATCTCTTTCGTCACA
1 CATAATACTATTAGGTAAC-GGTATATTATGCCACTAAAAATGTGACAATATCTCTTTCGTCACA
* ** * *
27154 TATAGGTTGATTTTAATGTATTATCCGTGACGATATAAATCATCAATAACGAAATTTTACATAAT
65 TATAAGTTGATTTTAATACATTATCCGTGACAATATAAATCATCAATAACGAAATCTTACATAAT
** ** * * * * * *
27219 TTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGACATTATATATAAATGCCATC
130 TTAGTGACATAACCAACTGTCATAGAATATAAACTATAAAGTGACATTATACATAAACGCCATC
*
27283 CATGCA-ACTATTAGGT
1 CAT-AATACTATTAGGT
27299 GATGAAATAC
Statistics
Matches: 176, Mismatches: 32, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
193 19 0.11
194 156 0.89
195 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (193 bp):
CATAATACTATTAGGTAACGGTATATTATGCCACTAAAAATGTGACAATATCTCTTTCGTCACAT
ATAAGTTGATTTTAATACATTATCCGTGACAATATAAATCATCAATAACGAAATCTTACATAATT
TAGTGACATAACCAACTGTCATAGAATATAAACTATAAAGTGACATTATACATAAACGCCATC
Found at i:37110 original size:64 final size:65
Alignment explanation
Indices: 37042--37222 Score: 163
Period size: 64 Copynumber: 2.8 Consensus size: 65
37032 TTGGAACACT
*
37042 TGATGCATC-AGTGCACCAAGTATGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGC
1 TGATGCATCGA-TGCACCAAGTATGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGC
37105 C
65 C
***** * **
37106 TGATGCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTC
1 TGATGCATCGATGCACCAAGTATGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
* *** * **
37170 AGAGTGCATCGATGCATGGAG-AGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCACCAAGTA-TGCATCGATGCATCAAATGCATTCGATGTT
37223 CAATTAATTC
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
64 50 0.52
65 46 0.48
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGTATGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
Found at i:37194 original size:19 final size:19
Alignment explanation
Indices: 37170--37220 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
37160 GAAAATATTC
37170 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
37189 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
37208 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
37221 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:37196 original size:65 final size:65
Alignment explanation
Indices: 37064--37222 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
37054 GCACCAAGTA
* ****
37064 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGTCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGAG
* **
37128 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAGA
37192 G
65 G
* *
37193 TGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGAAATGCATTCGATGTT
37223 CAATTAATTC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
64 36 0.44
65 46 0.56
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGAG
Found at i:43693 original size:22 final size:21
Alignment explanation
Indices: 43651--43690 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43641 GAGTTTGTTT
*
43651 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
43672 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
43691 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:45704 original size:64 final size:64
Alignment explanation
Indices: 45634--45796 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 64
45624 CGGTGCACCA
45634 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTA-A-CGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC-AGAGCGCATCGATGCATG
*
45697 T
64 G
** * ** *
45698 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGCGCATCGATGCATGG
* * *
45763 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
45797 CAATTAATTC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 39 0.47
65 43 0.52
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGCGCATCGATGCATGG
Found at i:45768 original size:19 final size:19
Alignment explanation
Indices: 45744--45794 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
45734 GAAAATATTC
45744 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
45763 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
45782 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
45795 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:45836 original size:65 final size:65
Alignment explanation
Indices: 45638--45845 Score: 182
Period size: 65 Copynumber: 3.2 Consensus size: 65
45628 GCACCAAGTG
* * ** *
45638 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTA-A-CGCATCGATGCATGT-CT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTC-AGAGTGCATCGATGCATGTAC-
45700 TG-
63 TGA
* * * *
45702 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGTACTG
45765 A
65 A
* *
45766 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGTA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGTA
45828 CTGA
62 CTGA
45832 TGCATCGGTGCATG
1 TGCATCGGTGCATG
45846 CCTTTGAATA
Statistics
Matches: 121, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
62 3 0.02
63 9 0.07
64 50 0.41
65 57 0.47
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGTACTGA
Found at i:46807 original size:15 final size:16
Alignment explanation
Indices: 46776--46811 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
46766 TAACTTGTAA
*
46776 TTATATGTTTAATATT
1 TTATATGTTTAACATT
46792 TTATAT-TTTAACATT
1 TTATATGTTTAACATT
46807 TTATA
1 TTATA
46812 AATTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATATGTTTAACATT
Done.