Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004888.1 Hibiscus syriacus cultivar Beakdansim tig00011007_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: 52201
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:15486 original size:62 final size:62
Alignment explanation
Indices: 15389--15511 Score: 246
Period size: 62 Copynumber: 2.0 Consensus size: 62
15379 AAATTTTAGG
15389 ATTTACTCCCTTATTTTGTTTTGTTAAGCATATCAGCGGCTAAACCACCCCATCCAATTGGA
1 ATTTACTCCCTTATTTTGTTTTGTTAAGCATATCAGCGGCTAAACCACCCCATCCAATTGGA
15451 ATTTACTCCCTTATTTTGTTTTGTTAAGCATATCAGCGGCTAAACCACCCCATCCAATTGG
1 ATTTACTCCCTTATTTTGTTTTGTTAAGCATATCAGCGGCTAAACCACCCCATCCAATTGG
15512 TGGTCCAGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (62 bp):
ATTTACTCCCTTATTTTGTTTTGTTAAGCATATCAGCGGCTAAACCACCCCATCCAATTGGA
Found at i:16714 original size:17 final size:16
Alignment explanation
Indices: 16694--16740 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
16684 GTTCATTGAT
16694 TAAACTAGCTCATTCA
1 TAAACTAGCTCATTCA
* *
16710 GTAAACTAGTTCATTGA
1 -TAAACTAGCTCATTCA
16727 TCAAACTAGCTCAT
1 T-AAACTAGCTCAT
16741 AATTGTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (16 bp):
TAAACTAGCTCATTCA
Found at i:18824 original size:137 final size:136
Alignment explanation
Indices: 18600--18986 Score: 411
Period size: 135 Copynumber: 2.8 Consensus size: 136
18590 ACTAAAAGTA
* * * * * *
18600 GAGGCTCTAATTAATAA-CCTATTTAATTTTAATTAATTATGCAATTCGAATAATTAAAGTGGAA
1 GAGGCTTTAA-TATTAATCCTAATTAATTTTAATAAATTATG-AATTCGAATAATTAAATTAGAA
* * *
18664 CC-T-CGAAAAG-TGAGGACCAAATTAAGAATTCTCCTAATTTAAGGACTAAAGG-TGAAATTAG
64 CCTTGAGAAAAGCT-AGGACCAAATTAAGAATTCACCTAATTTAAGGA-TAAAGGACGAAATTAG
18725 GCCTAAGATG
127 GCCTAAGATG
*
18735 GAGGCTTTAATATTAATCCTAATTAATTTTAAAAAATTATTG-ATTCGAATAATTAAATTAGAAC
1 GAGGCTTTAATATTAATCCTAATTAATTTTAATAAATTA-TGAATTCGAATAATTAAATTAGAAC
*
18799 CTTGAGTAAAAGCTAGGACCAAATTAAGAATTCACCTAAATTAAGG----AGGACGAAATTAGGC
65 CTTGAG-AAAAGCTAGGACCAAATTAAGAATTCACCTAATTTAAGGATAAAGGACGAAATTAGGC
18860 CTAAGATG
129 CTAAGATG
* * **
18868 AAAGCTTTAATATTAATCCTAATTAATTTTAATCGATTATGACATGTCGAATAATT-AATTCAGA
1 GAGGCTTTAATATTAATCCTAATTAATTTTAATAAATTATGA-AT-TCGAATAATTAAATT-AGA
* * *
18932 ACCTCGAGCAAAAACGAGGA-CAAAGTTAAGAATTCACCTAAATTTAAGGAATAAA
63 ACCTTGAG-AAAAGCTAGGACCAAA-TTAAGAATTCACCT-AATTTAAGG-ATAAA
18987 TATGAATCGA
Statistics
Matches: 213, Mismatches: 21, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
132 5 0.02
133 52 0.24
134 36 0.17
135 72 0.34
136 11 0.05
137 35 0.16
138 1 0.00
141 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (136 bp):
GAGGCTTTAATATTAATCCTAATTAATTTTAATAAATTATGAATTCGAATAATTAAATTAGAACC
TTGAGAAAAGCTAGGACCAAATTAAGAATTCACCTAATTTAAGGATAAAGGACGAAATTAGGCCT
AAGATG
Found at i:20924 original size:6 final size:6
Alignment explanation
Indices: 20915--20956 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
20905 TTATTTGAAA
* * *
20915 TAATAA TAATAA TAATGT TAATAT TAATAT TAATAT TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
20957 ATATAAGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
TAATAT
Found at i:21328 original size:85 final size:85
Alignment explanation
Indices: 21222--21425 Score: 281
Period size: 85 Copynumber: 2.4 Consensus size: 85
21212 AATCAATCGT
* * *
21222 AGTGATGATTCTGATCCAACTCCTTATGTGATGGACGAGTAAAAATTATGATGTTGATCAAACTT
1 AGTGATGATT-TGATCCAACTCCTTATGTGATGGACGAGAAAAAATGATGATGTTGATCAAACTC
*
21287 CTTATG-TGATGGACGAGCGAA
65 CTTATGCT-ATGGACGAGCCAA
* *
21308 A-TGATGATGTTGATCTAACTCCTTATGTGATGGACGAGAAAAAATGATGATGTTGATCCAACTC
1 AGTGATGAT-TTGATCCAACTCCTTATGTGATGGACGAGAAAAAATGATGATGTTGATCAAACTC
*
21372 CTTATGCTATGGATGAGCCAA
65 CTTATGCTATGGACGAGCCAA
21393 AGTTGATGATTT--TCCAACTCCTTATGTGATGGA
1 AG-TGATGATTTGATCCAACTCCTTATGTGATGGA
21426 ATCGAGTTGA
Statistics
Matches: 106, Mismatches: 8, Indels: 10
0.85 0.06 0.08
Matches are distributed among these distances:
84 20 0.19
85 74 0.70
86 5 0.05
87 7 0.07
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (85 bp):
AGTGATGATTTGATCCAACTCCTTATGTGATGGACGAGAAAAAATGATGATGTTGATCAAACTCC
TTATGCTATGGACGAGCCAA
Found at i:21333 original size:42 final size:42
Alignment explanation
Indices: 21224--21425 Score: 234
Period size: 43 Copynumber: 4.8 Consensus size: 42
21214 TCAATCGTAG
*
21224 TGATGAT-TCTGATCCAACTCCTTATGTGATGGACGAGTAAAAA
1 TGATGATGT-TGATCCAACTCCTTATGTGATGGACGAG-CAAAA
* * * *
21267 TTATGATGTTGATCAAACTTCTTATGTGATGGACGAGCGAAA
1 TGATGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAA
* *
21309 TGATGATGTTGATCTAACTCCTTATGTGATGGACGAGAAAAAA
1 TGATGATGTTGATCCAACTCCTTATGTGATGGACGAG-CAAAA
* *
21352 TGATGATGTTGATCCAACTCCTTATGCT-ATGGATGAGCCAAAGT
1 TGATGATGTTGATCCAACTCCTTATG-TGATGGACGAG-CAAA-A
21396 TGATGAT-TT--TCCAACTCCTTATGTGATGGA
1 TGATGATGTTGATCCAACTCCTTATGTGATGGA
21426 ATCGAGTTGA
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.01
41 19 0.14
42 37 0.27
43 73 0.53
44 9 0.06
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (42 bp):
TGATGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAA
Found at i:21617 original size:117 final size:117
Alignment explanation
Indices: 21435--21783 Score: 527
Period size: 117 Copynumber: 3.0 Consensus size: 117
21425 AATCGAGTTG
* * *
21435 AGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCGCATTATG
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATG
* * * * *
21500 AACTATCTATTGAAAATGTTGATCCACTTCCTTCTATGATGGAATCGAACCA
66 AACTCTCCACTGGAAATGTTGATCCACCTCCTTCTATGATGGAATCGAACCA
* * *
21552 AGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCACTCATCGGATGAGTTCTTCTCTTTATG
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATG
* * *
21617 AACTCTCCACTGGAAATGCTGATCCACCTCCTTCTGTGATGAAATCGAACCA
66 AACTCTCCACTGGAAATGTTGATCCACCTCCTTCTATGATGGAATCGAACCA
* * *
21669 AGATTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATG
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATG
* *
21734 AACTCTCCACTGGAAATATTGATCAACCTCCTTCTATGATGGAATCGAAC
66 AACTCTCCACTGGAAATGTTGATCCACCTCCTTCTATGATGGAATCGAAC
21784 AAAGTGATGA
Statistics
Matches: 207, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 207 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (117 bp):
AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATG
AACTCTCCACTGGAAATGTTGATCCACCTCCTTCTATGATGGAATCGAACCA
Found at i:22577 original size:2 final size:2
Alignment explanation
Indices: 22570--22601 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22560 ACATACATAC
22570 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
22602 CATCATCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22786 original size:23 final size:23
Alignment explanation
Indices: 22764--22861 Score: 124
Period size: 23 Copynumber: 4.3 Consensus size: 23
22754 GAAGTGCCAT
* *
22764 GTAGAAATGTCCTGAAGGACCAT
1 GTAGAAATGTCCCGAAGGACCAC
* * *
22787 ATAGATATGTCCCGAAGGACCGC
1 GTAGAAATGTCCCGAAGGACCAC
*
22810 GTAGAAATATCCCGAAGGACCAC
1 GTAGAAATGTCCCGAAGGACCAC
* *
22833 GTAGAATTGTCCCGAAGGACCGC
1 GTAGAAATGTCCCGAAGGACCAC
22856 GTAGAA
1 GTAGAA
22862 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (23 bp):
GTAGAAATGTCCCGAAGGACCAC
Found at i:22827 original size:46 final size:46
Alignment explanation
Indices: 22764--22861 Score: 144
Period size: 46 Copynumber: 2.1 Consensus size: 46
22754 GAAGTGCCAT
* * *
22764 GTAGAAATGTCCTGAAGGACCATATAG-ATATGTCCCGAAGGACCGC
1 GTAGAAATATCCCGAAGGACCACATAGAAT-TGTCCCGAAGGACCGC
*
22810 GTAGAAATATCCCGAAGGACCACGTAGAATTGTCCCGAAGGACCGC
1 GTAGAAATATCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGC
22856 GTAGAA
1 GTAGAA
22862 CCCTCGACTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (46 bp):
GTAGAAATATCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGC
Found at i:23012 original size:43 final size:43
Alignment explanation
Indices: 22938--23069 Score: 156
Period size: 45 Copynumber: 3.0 Consensus size: 43
22928 TTATACCATT
*** * * *
22938 TCACATAGCTTATATCACATAAACGTATAATCACATAGATCAA
1 TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAA
*
22981 TCACATAGCTTATATCATATTTTCATGTAATCACATAGGTCAA
1 TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAA
* * *
23024 TGCCACATAGCTTATATCACGTTTTCAAGTAATCAAATAGGTCAA
1 T--CACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAA
23069 T
1 T
23070 ATCATATAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 37 0.49
45 39 0.51
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (43 bp):
TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAA
Found at i:25891 original size:33 final size:33
Alignment explanation
Indices: 25849--25912 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
25839 AGCTTTTGAA
25849 TATCAATGTCAATTTCAATTACAGAAAAGATAT
1 TATCAATGTCAATTTCAATTACAGAAAAGATAT
*
25882 TATCAATGTCAGTTTCAATTACAGAAAAGAT
1 TATCAATGTCAATTTCAATTACAGAAAAGAT
25913 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (33 bp):
TATCAATGTCAATTTCAATTACAGAAAAGATAT
Found at i:27453 original size:22 final size:23
Alignment explanation
Indices: 27428--27472 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
27418 GGCAGAAACT
27428 TTAACAAAGCTGAAAAC-ATAAA
1 TTAACAAAGCTGAAAACAATAAA
27450 TTAACAAAGCTGAAAACAATAAA
1 TTAACAAAGCTGAAAACAATAAA
27473 GAAATAAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.18
Consensus pattern (23 bp):
TTAACAAAGCTGAAAACAATAAA
Found at i:30281 original size:21 final size:22
Alignment explanation
Indices: 30249--30308 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
30239 ATAACTTGCA
*
30249 CCGAAGTG-CCACATA-TTTGTC
1 CCGAA-TGACCACATAGTTTATC
30270 CCGAATGACCACATAGTTTTATC
1 CCGAATGACCACATAG-TTTATC
* *
30293 CCTAATGAGCACATAG
1 CCGAATGACCACATAG
30309 AACCCTCGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.06
21 12 0.36
23 19 0.58
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (22 bp):
CCGAATGACCACATAGTTTATC
Found at i:38480 original size:36 final size:36
Alignment explanation
Indices: 38439--38514 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
38429 ATTTTCGGGA
*
38439 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
38475 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
38511 TTTT
1 TTTT
38515 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:38952 original size:15 final size:15
Alignment explanation
Indices: 38932--38961 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38922 TATCACAATC
38932 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
38947 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
38962 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:43475 original size:36 final size:36
Alignment explanation
Indices: 43434--43509 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
43424 ATTTTCGGGA
*
43434 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
43470 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
43506 TTTT
1 TTTT
43510 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:45736 original size:18 final size:18
Alignment explanation
Indices: 45713--45751 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
45703 GAAATAAGTT
45713 AATTAATC-AAATTAATTA
1 AATTAATCAAAATT-ATTA
45731 AATTAATCAAAATTATTA
1 AATTAATCAAAATTATTA
45749 AAT
1 AAT
45752 ATTTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAATCAAAATTATTA
Found at i:47137 original size:31 final size:31
Alignment explanation
Indices: 47102--47160 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
47092 GTTAGCACCG
* *
47102 AGGCACCTAAAATATTATCGTTTGTAACGTT
1 AGGCACCTAAAATATTAACGTTTATAACGTT
47133 AGGCACCTAAAATATTAACGTTTATAAC
1 AGGCACCTAAAATATTAACGTTTATAAC
47161 TTTAAGTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (31 bp):
AGGCACCTAAAATATTAACGTTTATAACGTT
Found at i:47621 original size:18 final size:18
Alignment explanation
Indices: 47598--47632 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47588 GAAATCGGTT
*
47598 AATTAATTGAATTAACTG
1 AATTAATTAAATTAACTG
47616 AATTAATTAAATTAACT
1 AATTAATTAAATTAACT
47633 TTAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
AATTAATTAAATTAACTG
Found at i:49767 original size:19 final size:20
Alignment explanation
Indices: 49743--49786 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
49733 CGCATCGGCA
49743 CGCATCGGATCGCATCA-AC
1 CGCATCGGATCGCATCAGAC
49762 CGCATCGGATCGCATCAGAC
1 CGCATCGGATCGCATCAGAC
49782 CGCAT
1 CGCAT
49787 TATGTACCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (20 bp):
CGCATCGGATCGCATCAGAC
Found at i:52066 original size:16 final size:16
Alignment explanation
Indices: 52047--52085 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
52037 ATTTAAAGAC
52047 AACTTAAGCTTTTCTT
1 AACTTAAGCTTTTCTT
52063 AACTTAAGCTTTTCTT
1 AACTTAAGCTTTTCTT
52079 AAGCTTA
1 AA-CTTA
52086 TTTATCACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (16 bp):
AACTTAAGCTTTTCTT
Done.