Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001161.1 Hibiscus syriacus cultivar Beakdansim tig00002316_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: 53588
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:8992 original size:31 final size:28
Alignment explanation
Indices: 8918--9008 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
8908 TATTAAACAA
8918 TTTAGGTACCTATTTTGACATAAAATAC
1 TTTAGGTACCTATTTTGACATAAAATAC
* *
8946 TATAGATACCTATTTTGATCGA-AAATATAAC
1 TTTAGGTACCTATTTTGA-C-ATAAA-AT-AC
* *
8977 TTTAGGTACTTATTTT-AGCAAAAAATA-
1 TTTAGGTACCTATTTTGA-CATAAAATAC
9004 TTTAG
1 TTTAG
9009 TACTTAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 5 0.10
28 17 0.33
29 7 0.13
30 8 0.15
31 15 0.29
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (28 bp):
TTTAGGTACCTATTTTGACATAAAATAC
Found at i:10855 original size:23 final size:23
Alignment explanation
Indices: 10824--10892 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
10814 CACCACAGCT
*
10824 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
10847 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
10870 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
10893 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:11079 original size:103 final size:103
Alignment explanation
Indices: 10908--11122 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
10898 TAATGTCCAT
* *
10908 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
10973 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
11011 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
11076 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
11114 AAGGACCAC
1 AAGGACCAC
11123 GTAGACCCTC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:13863 original size:18 final size:18
Alignment explanation
Indices: 13823--13875 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
13813 CCGCATAGAA
**
13823 ATGTCCCGAAGGAATACT
1 ATGTCCCGAAGGACCACT
*
13841 CTGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
13859 ATGTCCCCAAGGACCAC
1 ATGTCCCGAAGGACCAC
13876 ATAGAACCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:14108 original size:16 final size:17
Alignment explanation
Indices: 14087--14120 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
14077 TTATAATCAC
14087 TATCTC-ATGTTCATAT
1 TATCTCTATGTTCATAT
14103 TATCTCTTATGTTCATAT
1 TATCTC-TATGTTCATAT
14121 CATAGATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (17 bp):
TATCTCTATGTTCATAT
Found at i:18078 original size:16 final size:17
Alignment explanation
Indices: 18057--18090 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18047 CATAATCACA
18057 TATCTC-ATGTTCATAT
1 TATCTCTATGTTCATAT
18073 TATCTCTTATGTTCATAT
1 TATCTC-TATGTTCATAT
18091 CATAGATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (17 bp):
TATCTCTATGTTCATAT
Found at i:24984 original size:25 final size:25
Alignment explanation
Indices: 24949--24998 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
24939 TTTAGATAAT
24949 AGAACAGAATGTACAAACTATTAAG
1 AGAACAGAATGTACAAACTATTAAG
* *
24974 AGAACATAATGTACATACTATTAAG
1 AGAACAGAATGTACAAACTATTAAG
24999 CAATGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (25 bp):
AGAACAGAATGTACAAACTATTAAG
Found at i:27686 original size:75 final size:75
Alignment explanation
Indices: 27580--27763 Score: 253
Period size: 75 Copynumber: 2.5 Consensus size: 75
27570 ATTTTTTTAG
* *
27580 ACTTGATATTATGGTTTGAGTCTT-AAGATTTGACACTTTAATAGTATGATTTGATTATGGATTT
1 ACTTAATATTGTGGTTTGAGTCTTGAA-ATTTGACACTTTAATAGTATGATTTGATTATGGATTT
* *
27644 TATTATTCTAG
65 TACTATTCTAA
* * * * * *
27655 AGTTAATATTGTGGTTTGAATCTTGAAATTTGACATTTTAATATTGTGATTTGTTTATGGATTTT
1 ACTTAATATTGTGGTTTGAGTCTTGAAATTTGACACTTTAATAGTATGATTTGATTATGGATTTT
27720 ACTATTCTAA
66 ACTATTCTAA
*
27730 ACTTAATATTGTGGTTTGAGTCTTGATATTTGAC
1 ACTTAATATTGTGGTTTGAGTCTTGAAATTTGAC
27764 TTTATTTATG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 93 0.98
76 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (75 bp):
ACTTAATATTGTGGTTTGAGTCTTGAAATTTGACACTTTAATAGTATGATTTGATTATGGATTTT
ACTATTCTAA
Found at i:29831 original size:13 final size:13
Alignment explanation
Indices: 29810--29845 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
29800 CAACTGACCA
*
29810 CCGATAGCCACCG
1 CCGACAGCCACCG
29823 CCGACAGCCACCG
1 CCGACAGCCACCG
*
29836 CTGACAGCCA
1 CCGACAGCCA
29846 ATGGTGGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.25, C:0.47, G:0.22, T:0.06
Consensus pattern (13 bp):
CCGACAGCCACCG
Found at i:30618 original size:8 final size:9
Alignment explanation
Indices: 30607--30646 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
30597 AATAATAATA
30607 ATATTAT-T
1 ATATTATAT
30615 ATA-TATAT
1 ATATTATAT
30623 ATA-TATAT
1 ATATTATAT
30631 ATATATATAT
1 ATAT-TATAT
30641 ATATTA
1 ATATTA
30647 AAACGACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.10
8 15 0.52
9 2 0.07
10 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATTATAT
Found at i:30621 original size:2 final size:2
Alignment explanation
Indices: 30614--30644 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30604 ATAATATTAT
30614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30645 TAAAACGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40926 original size:11 final size:11
Alignment explanation
Indices: 40910--40967 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
40900 TTCGGGTTGT
*
40910 ATAATAATTTA
1 ATAATAATATA
40921 ATAATAATATA
1 ATAATAATATA
*
40932 ATAATATTAT-
1 ATAATAATATA
40942 ATAATATATATA
1 ATAATA-ATATA
40954 TATATATATATATA
1 -ATA-ATA-ATATA
40968 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
10 6 0.15
11 22 0.55
13 3 0.08
14 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATAATAATATA
Found at i:40950 original size:2 final size:2
Alignment explanation
Indices: 40927--40980 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
40917 TTTAATAATA
40927 AT AT A- AT A- AT AT -T AT AT A- 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 AT AT AT AT AT
40965 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
40981 TAAAAGGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.08
2 44 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43003 original size:38 final size:38
Alignment explanation
Indices: 42925--43011 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
42915 AGAGTAATAT
* *
42925 TATACTATTTAGGGATTTATATTCAATTCAAATTCAAA
1 TATATTATTTAGGAATTTATATTCAATTCAAATTCAAA
* * *
42963 TATGTTATTTAGGAATTTATATTCAATTGAAATAT-GAA
1 TATATTATTTAGGAATTTATATTCAATTCAAAT-TCAAA
43001 TATATTATTTA
1 TATATTATTTA
43012 TAAACTTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 41 0.98
39 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (38 bp):
TATATTATTTAGGAATTTATATTCAATTCAAATTCAAA
Found at i:43021 original size:38 final size:38
Alignment explanation
Indices: 42941--43023 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
42931 ATTTAGGGAT
* * *
42941 TTATATTCAATTCAAATTCAAATATGTTATTTAGGAAT
1 TTATATTCAATTCAAATTCAAATATATTATTTAGAAAC
* * *
42979 TTATATTCAATTGAAATAT-GAATATATTATTTATAAAC
1 TTATATTCAATTCAAAT-TCAAATATATTATTTAGAAAC
43017 TTATATT
1 TTATATT
43024 TGATTAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (38 bp):
TTATATTCAATTCAAATTCAAATATATTATTTAGAAAC
Found at i:50178 original size:3 final size:3
Alignment explanation
Indices: 50170--50195 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
50160 TAGTAATTAT
50170 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
50196 TAATGATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:50341 original size:30 final size:30
Alignment explanation
Indices: 50302--50360 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
50292 ATGATTGTAT
* *
50302 AAATTTTATTA-AAAAAATATTTTATATTTC
1 AAATATTATTATAAAAAA-ATTTTAAATTTC
*
50332 AAATATTATTATAAAAGAATTTTAAATTT
1 AAATATTATTATAAAAAAATTTTAAATTT
50361 GAAGAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AAATATTATTATAAAAAAATTTTAAATTTC
Done.