Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006659.1 Hibiscus syriacus cultivar Beakdansim tig00016475_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: 60488
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3117 original size:21 final size:23
Alignment explanation
Indices: 3091--3133 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
3081 AATTAAAACT
3091 TGGATTGATT-TTT-GATGTTTC
1 TGGATTGATTATTTGGATGTTTC
*
3112 TGGATTGTTTATTTGGATGTTT
1 TGGATTGATTATTTGGATGTTT
3134 GAACTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.14, C:0.02, G:0.26, T:0.58
Consensus pattern (23 bp):
TGGATTGATTATTTGGATGTTTC
Found at i:4858 original size:16 final size:16
Alignment explanation
Indices: 4837--4881 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4827 TTTTTGTGTG
*
4837 ATATAAATTATATTAT
1 ATATAAATTATATAAT
*
4853 ATATAAATAATATAAT
1 ATATAAATTATATAAT
*
4869 ATAATATATTATA
1 AT-ATAAATTATA
4882 AATTATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATTATATAAT
Found at i:5207 original size:23 final size:23
Alignment explanation
Indices: 5155--5207 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5145 AAAATAAGTT
*
5155 TGTCTTTGTGACACATTTATCTT
1 TGTCTTTGTGACACATTTATCTC
* *
5178 TGCCTTTGTGACACGTTTATCTC
1 TGTCTTTGTGACACATTTATCTC
5201 TGTCTTT
1 TGTCTTT
5208 TGATAGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (23 bp):
TGTCTTTGTGACACATTTATCTC
Found at i:5495 original size:14 final size:14
Alignment explanation
Indices: 5476--5503 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5466 GTTGGTATTC
5476 GTTATTTTGTTAGA
1 GTTATTTTGTTAGA
5490 GTTATTTTGTTAGA
1 GTTATTTTGTTAGA
5504 TTTTTTAACA
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:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (14 bp):
GTTATTTTGTTAGA
Found at i:18032 original size:115 final size:116
Alignment explanation
Indices: 17900--18115 Score: 346
Period size: 115 Copynumber: 1.9 Consensus size: 116
17890 TTTTTATTAT
**
17900 TTTTTTTAACTTTGTCTCATTTATTATTTATATGTTATTATGACTCAATATTATTT-AAAATTTT
1 TTTTTTTAAC-TTGTCTCATTTATTATTTATATGTTATTATGACTCAATATTATTTAAAAAAATT
* *
17964 ATTATTGATAAAAATATGAAAATTTTTATTTTAAAATGTTGATTTATTTTTGA
65 ATTATTGAT-AAAATATGAAAATCTGTATTTTAAAATGTTGATTTATTTTTGA
* *
18017 TTTTTTTAAC-TGTCTCATTTATTATTTATATTTTATTATGACTCATTATTATTTAAAAAAATTA
1 TTTTTTTAACTTGTCTCATTTATTATTTATATGTTATTATGACTCAATATTATTTAAAAAAATTA
18081 TTATTGATAAAATATGAAAATCTGTATTTTAAAAT
66 TTATTGATAAAATATGAAAATCTGTATTTTAAAAT
18116 TTTTAAATCA
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
115 67 0.73
116 15 0.16
117 10 0.11
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (116 bp):
TTTTTTTAACTTGTCTCATTTATTATTTATATGTTATTATGACTCAATATTATTTAAAAAAATTA
TTATTGATAAAATATGAAAATCTGTATTTTAAAATGTTGATTTATTTTTGA
Found at i:18050 original size:28 final size:28
Alignment explanation
Indices: 18005--18071 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
17995 TAAAATGTTG
* *
18005 ATTTATT-TTTGAT-TTTTTTAACTGTCTC
1 ATTTATTATTT-ATATTTTATAA-TGACTC
*
18033 ATTTATTATTTATATTTTATTATGACTC
1 ATTTATTATTTATATTTTATAATGACTC
18061 A-TTATTATTTA
1 ATTTATTATTTA
18072 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 10 0.29
28 15 0.44
29 9 0.26
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.63
Consensus pattern (28 bp):
ATTTATTATTTATATTTTATAATGACTC
Found at i:21604 original size:21 final size:22
Alignment explanation
Indices: 21563--21604 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21553 ATTAACATCT
*
21563 AAATTTTAAAATATTTCAAATA
1 AAATTTTAAAATATTTAAAATA
*
21585 AAATTTTAAATTA-TTAAAAT
1 AAATTTTAAAATATTTAAAAT
21605 TGTATCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTTTAAAATATTTAAAATA
Found at i:28894 original size:18 final size:18
Alignment explanation
Indices: 28871--28907 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28861 GAAAAAGCCA
28871 TTTTCATTCATATCATAT
1 TTTTCATTCATATCATAT
* *
28889 TTTTCATTTATTTCATAT
1 TTTTCATTCATATCATAT
28907 T
1 T
28908 CTTAACCCCA
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:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTCATTCATATCATAT
Found at i:30362 original size:36 final size:36
Alignment explanation
Indices: 30321--30396 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
30311 ATTTTCGGGA
*
30321 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
30357 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
30393 TTTT
1 TTTT
30397 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:30838 original size:12 final size:12
Alignment explanation
Indices: 30821--30845 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30811 TCACAATCGC
30821 GCAGGATTCCGG
1 GCAGGATTCCGG
30833 GCAGGATTCCGG
1 GCAGGATTCCGG
30845 G
1 G
30846 AGCACCGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (12 bp):
GCAGGATTCCGG
Found at i:35352 original size:36 final size:36
Alignment explanation
Indices: 35311--35386 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
35301 ATTTTCGGGA
*
35311 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
35347 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
35383 TTTT
1 TTTT
35387 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:38325 original size:19 final size:18
Alignment explanation
Indices: 38297--38332 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
38287 TTGATATTTG
38297 ACTTTATTTATAATTTTT
1 ACTTTATTTATAATTTTT
38315 ACTTCTATTTATAATTTT
1 ACTT-TATTTATAATTTT
38333 AAAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (18 bp):
ACTTTATTTATAATTTTT
Found at i:38332 original size:18 final size:17
Alignment explanation
Indices: 38292--38333 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
38282 GAGAATTGAT
*
38292 ATTTGACTTTATTTATA
1 ATTTTACTTTATTTATA
38309 ATTTTTACTTCTATTTATA
1 A-TTTTACTT-TATTTATA
38328 ATTTTA
1 ATTTTA
38334 AAATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 12 0.55
19 9 0.41
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTACTTTATTTATA
Found at i:38341 original size:18 final size:18
Alignment explanation
Indices: 38300--38342 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
38290 ATATTTGACT
* **
38300 TTATTTATAATTTTTACT
1 TTATTTATAATTTTAAAA
38318 TCTATTTATAATTTTAAAA
1 T-TATTTATAATTTTAAAA
38337 TTATTT
1 TTATTT
38343 TATATGTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTTATAATTTTAAAA
Found at i:38578 original size:46 final size:46
Alignment explanation
Indices: 38511--38649 Score: 278
Period size: 46 Copynumber: 3.0 Consensus size: 46
38501 AATATAGAGG
38511 TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
1 TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
38557 TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
1 TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
38603 TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
1 TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
38649 T
1 T
38650 GCTCTCACAC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 93 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (46 bp):
TCTATCTGCAGAGTTGCTTAAGGCTGAAATCTCTCATCGACTTACC
Found at i:47779 original size:21 final size:21
Alignment explanation
Indices: 47746--47785 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47736 TTCTACGTGG
*
47746 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
47767 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
47786 GGTACTTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:47876 original size:18 final size:18
Alignment explanation
Indices: 47855--47891 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
47845 CTTTCAGGAT
*
47855 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCATTCGGGAC
47873 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
47891 A
1 A
47892 AATATTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (18 bp):
ATAGTGGTCATTCGGGAC
Found at i:50109 original size:35 final size:35
Alignment explanation
Indices: 50049--50116 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
50039 GTTTTAAAGA
*
50049 TGGTAACGATACCGTCCTTATGGTATCGGTACCCT
1 TGGTAACGATACCGTCCTTATGGTATCGATACCCT
* *
50084 TGGTAACGATACTGTTCTTCA-GGTATCGATACC
1 TGGTAACGATACCGTCCTT-ATGGTATCGATACC
50117 TCATTAATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (35 bp):
TGGTAACGATACCGTCCTTATGGTATCGATACCCT
Found at i:57004 original size:20 final size:20
Alignment explanation
Indices: 56979--57052 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
56969 TCGTTTCAAA
56979 GATGGTATCGATACCGTCCT
1 GATGGTATCGATACCGTCCT
*
56999 GATGGTATCGATACCATCCT
1 GATGGTATCGATACCGTCCT
* * *
57019 GATGGTACCAATACCGTCTT
1 GATGGTATCGATACCGTCCT
*
57039 TATGGTATCGATAC
1 GATGGTATCGATAC
57053 TGTTCTTCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (20 bp):
GATGGTATCGATACCGTCCT
Found at i:57065 original size:20 final size:20
Alignment explanation
Indices: 57042--57112 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
57032 CCGTCTTTAT
57042 GGTATCGATACTGTTCTTCA
1 GGTATCGATACTGTTCTTCA
* *
57062 GGTATCGATATTGTTCTTTA
1 GGTATCGATACTGTTCTTCA
*
57082 GGTATCGATAATGTTCTTCA
1 GGTATCGATACTGTTCTTCA
57102 GGTATCGATAC
1 GGTATCGATAC
57113 CTTATGAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (20 bp):
GGTATCGATACTGTTCTTCA
Found at i:57086 original size:40 final size:41
Alignment explanation
Indices: 57035--57111 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
57025 ACCAATACCG
*
57035 TCTTTATGGTATCGATACTGTTCTTCAGGTATCGATATTGT
1 TCTTTATGGTATCGATAATGTTCTTCAGGTATCGATATTGT
57076 TCTTTA-GGTATCGATAATGTTCTTCAGGTATCGATA
1 TCTTTATGGTATCGATAATGTTCTTCAGGTATCGATA
57112 CCTTATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 29 0.83
41 6 0.17
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.44
Consensus pattern (41 bp):
TCTTTATGGTATCGATAATGTTCTTCAGGTATCGATATTGT
Done.