Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000874.1 Hibiscus syriacus cultivar Beakdansim tig00001689_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: 89610
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6900 original size:15 final size:15
Alignment explanation
Indices: 6880--6917 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
6870 GTTCCAGTCC
6880 CAGAAGAAACAAAGA
1 CAGAAGAAACAAAGA
6895 CAGAAGAAACAAAGA
1 CAGAAGAAACAAAGA
6910 CAGAAGAA
1 CAGAAGAA
6918 CTCCAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.66, C:0.13, G:0.21, T:0.00
Consensus pattern (15 bp):
CAGAAGAAACAAAGA
Found at i:31509 original size:106 final size:106
Alignment explanation
Indices: 31380--31827 Score: 668
Period size: 106 Copynumber: 4.2 Consensus size: 106
31370 GTATTGTTCC
* ** **
31380 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACA
* * * *
31444 ACCAGCCGT-CCTTACGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTT-CGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
31486 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACAA
* *
31551 CCAGGGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31592 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACA
31656 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
31698 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACAA
* *
31763 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
31804 GAGTCCAATATCCTTCGCTATGAA
1 GAGTCCAATATCCTTCGCTGTGAA
31828 ATTGGGAAGT
Statistics
Matches: 317, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
105 1 0.00
106 310 0.98
107 6 0.02
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:31896 original size:88 final size:88
Alignment explanation
Indices: 31738--31915 Score: 302
Period size: 88 Copynumber: 2.0 Consensus size: 88
31728 ATTGGCTCTA
* * *
31738 AAATTGGGAAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTAT
1 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTATAT
31803 GGAGTCCAATATCCTTCGCTATG
66 GGAGTCCAATATCCTTCGCTATG
*
31826 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTATCT
1 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTATAT
* *
31891 TGAGTCCAATATCCTTCGCTGTG
66 GGAGTCCAATATCCTTCGCTATG
31914 AA
1 AA
31916 GTTGAAATTG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (88 bp):
AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTATAT
GGAGTCCAATATCCTTCGCTATG
Found at i:32007 original size:105 final size:106
Alignment explanation
Indices: 31824--32449 Score: 1109
Period size: 105 Copynumber: 6.0 Consensus size: 106
31814 TCCTTCGCTA
* * *
31824 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTAT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
31889 CTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
31930 TGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
31994 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
32035 TGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
32099 CTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
32140 TGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
32204 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
32245 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
32309 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
32350 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
32414 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
32450 TACTCTCGAG
Statistics
Matches: 509, Mismatches: 10, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
104 2 0.00
105 491 0.96
106 16 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:50605 original size:30 final size:31
Alignment explanation
Indices: 50570--50633 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
50560 ATAAGTAAAA
*
50570 ATAAATTTATAAGTTATCTA-TTTTTATATG
1 ATAAATTTATAACTTATCTATTTTTTATATG
*
50600 ATAAATTTATAACTTATTTATTTTTTATATG
1 ATAAATTTATAACTTATCTATTTTTTATATG
50631 ATA
1 ATA
50634 CTTAAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
ATAAATTTATAACTTATCTATTTTTTATATG
Found at i:52719 original size:21 final size:21
Alignment explanation
Indices: 52695--52736 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
52685 TCATATAGCA
52695 AAATAATTCGTCATGACTGCT
1 AAATAATTCGTCATGACTGCT
*
52716 AAATAATTTGTCATGACTGCT
1 AAATAATTCGTCATGACTGCT
52737 GAATGAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATAATTCGTCATGACTGCT
Found at i:57067 original size:2 final size:2
Alignment explanation
Indices: 57062--57099 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
57052 TATAATATGA
57062 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
57100 GAGCATAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:60719 original size:19 final size:19
Alignment explanation
Indices: 60682--60721 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
60672 CCTATATATA
* **
60682 ATTCGATTTAATTGGATTC
1 ATTCAATTTAATTCAATTC
60701 ATTCAATTTAATTCAATTC
1 ATTCAATTTAATTCAATTC
60720 AT
1 AT
60722 GCTATTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTCAATTTAATTCAATTC
Found at i:67584 original size:13 final size:13
Alignment explanation
Indices: 67566--67591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67556 ATTAAATACT
67566 AGTAACATAATTG
1 AGTAACATAATTG
67579 AGTAACATAATTG
1 AGTAACATAATTG
67592 CTAACTAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AGTAACATAATTG
Found at i:81905 original size:17 final size:17
Alignment explanation
Indices: 81879--81916 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
81869 ACAAGGAATG
*
81879 AAAGTTCTTGTGGAGCA
1 AAAGTCCTTGTGGAGCA
81896 AAAGTCCTTGTGGAGCA
1 AAAGTCCTTGTGGAGCA
81913 AAAG
1 AAAG
81917 CTACTTCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (17 bp):
AAAGTCCTTGTGGAGCA
Found at i:88833 original size:57 final size:57
Alignment explanation
Indices: 88739--88849 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
88729 GTTTTGTAAC
* * *
88739 TTATAATTCTCAAGTGAAACAATGATGTAAAGTCTTATAAATAAATAGACTTGTCAT
1 TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGTCAT
* * * *
88796 TTATGATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATTAATAGATTTGT
1 TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGT
88850 AAAACGGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (57 bp):
TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGTCAT
Done.