Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009513.1 Hibiscus syriacus cultivar Beakdansim tig00115577_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: 16035
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.23
Found at i:8065 original size:94 final size:93
Alignment explanation
Indices: 7924--8288 Score: 311
Period size: 94 Copynumber: 4.0 Consensus size: 93
7914 GCACCCAGCG
** * *
7924 CTCGGTTCTGTGCGGCACT-CCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGTGTTGC
1 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGC
7988 CGATGGTGACCGAGGCCCCCGCACCAACT
66 CGATGGTGACCGA-GCCCCCGCACCAACT
*
8017 CTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCA-CCGT-GGGGGTTG-
1 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGC
* * * ****
8079 CGATGGTGA-CGAGACACCG-TCTGGGT
66 CGATGGTGACCGAGCCCCCGCACCAACT
* * * * *** * * *** * *
8105 -TGCCGAT-GGTGACGAG-AC-ACCGTCTGGCTTTGCCAATGG-TGACCGAGGCCACCCGCCTGG
1 CT-CGGTTCTGTG-CG-GCACTCCCG-CACCCGTGGCCTGGGGTTG-CCGAGG-CACCCGTCGGG
* * *
8165 GATTGCCGATGGTGACCGAGCCTCACGCACCAACG
60 GGTTGCCGATGGTGACCGAGCC-CCCGCACCAACT
8200 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGC
1 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGC
*
8265 CGATGGTGACCGAGGCCCCGCACC
66 CGATGGTGACCGAGCCCCCGCACC
8289 CGTGGCCTGG
Statistics
Matches: 201, Mismatches: 53, Indels: 36
0.69 0.18 0.12
Matches are distributed among these distances:
87 9 0.04
88 23 0.11
89 8 0.04
90 6 0.03
91 15 0.07
92 16 0.08
93 34 0.17
94 59 0.29
95 22 0.11
96 9 0.04
ACGTcount: A:0.13, C:0.34, G:0.35, T:0.18
Consensus pattern (93 bp):
CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGC
CGATGGTGACCGAGCCCCCGCACCAACT
Found at i:8184 original size:33 final size:29
Alignment explanation
Indices: 8073--8180 Score: 128
Period size: 29 Copynumber: 3.6 Consensus size: 29
8063 GGCACCGTGG
8073 GGGTTG-CGATGGTGACGAGACACCGTCT
1 GGGTTGCCGATGGTGACGAGACACCGTCT
8101 GGGTTGCCGATGGTGACGAGACACCGTCT
1 GGGTTGCCGATGGTGACGAGACACCGTCT
* * * *
8130 GGCTTTGCCAATGGTGACCGAGGCCACCCGCCT
1 GG-GTTGCCGATGGTGA-CGA-GACA-CCGTCT
8163 GGGATTGCCGATGGTGAC
1 GGG-TTGCCGATGGTGAC
8181 CGAGCCTCAC
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.09
29 24 0.35
30 12 0.18
31 3 0.04
32 4 0.06
33 19 0.28
ACGTcount: A:0.17, C:0.26, G:0.37, T:0.20
Consensus pattern (29 bp):
GGGTTGCCGATGGTGACGAGACACCGTCT
Found at i:8295 original size:62 final size:61
Alignment explanation
Indices: 8219--8349 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 61
8209 GTGCGGCACT
*
8219 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTG-CGATGGTGACCGAGGA
8281 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCGATGGTGACCGAGGA
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCGATGGTGACCGAGGA
8342 CCCGCACC
1 CCCGCACC
8350 AACTCTCGGC
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 23 0.34
62 45 0.66
ACGTcount: A:0.11, C:0.35, G:0.40, T:0.14
Consensus pattern (61 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCGATGGTGACCGAGGA
Found at i:8310 original size:30 final size:31
Alignment explanation
Indices: 8219--8315 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
8209 GTGCGGCACT
8219 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
**** * *
8250 CCCGTCGGGGGTTGCC-GATGG-TGACCGAGGC-
1 CCCG-CACCCGTGGCCTG-GGGTTG-CCGAGGCA
8281 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
8312 CCCG
1 CCCG
8316 TCGGGGGTTG
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
30 15 0.31
31 18 0.38
32 15 0.31
ACGTcount: A:0.09, C:0.37, G:0.40, T:0.13
Consensus pattern (31 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
Found at i:8442 original size:31 final size:31
Alignment explanation
Indices: 8400--8515 Score: 157
Period size: 31 Copynumber: 3.8 Consensus size: 31
8390 TGCCGAGCCA
* *
8400 CCGTCGGGGGTTGCCGATGGTGACCGAGACAC
1 CCGTCTGGGTTTGCCGATGGTGA-CGAGACAC
8432 CCGTCTGGGTTTG-CGATGGTGACG-GACAC
1 CCGTCTGGGTTTGCCGATGGTGACGAGACAC
*
8461 CCGTCTGGGTTTGCCGATGGTGACGAGGCCAC
1 CCGTCTGGGTTTGCCGATGGTGACGA-GACAC
*
8493 CCGCCTGGG-TTGCCGATGGTGAC
1 CCGTCTGGGTTTGCCGATGGTGAC
8516 CGAGCCTCAC
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
29 18 0.23
30 13 0.17
31 23 0.30
32 23 0.30
ACGTcount: A:0.13, C:0.28, G:0.39, T:0.21
Consensus pattern (31 bp):
CCGTCTGGGTTTGCCGATGGTGACGAGACAC
Found at i:8475 original size:61 final size:61
Alignment explanation
Indices: 8400--8515 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
8390 TGCCGAGCCA
*
8400 CCGTCGGGGGTTGCCGATGGTGACCGA-GACACCCGTCTGGGTTTG-CGATGGTGACGGACAC
1 CCGTCGGGGGTTGCCGATGGTGA-CGAGGACACCCGCCTGGG-TTGCCGATGGTGACGGACAC
* * *
8461 CCGTCTGGGTTTGCCGATGGTGACGAGGCCACCCGCCTGGGTTGCCGATGGTGAC
1 CCGTCGGGGGTTGCCGATGGTGACGAGGACACCCGCCTGGGTTGCCGATGGTGAC
8516 CGAGCCTCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 6 0.12
61 43 0.88
ACGTcount: A:0.13, C:0.28, G:0.39, T:0.21
Consensus pattern (61 bp):
CCGTCGGGGGTTGCCGATGGTGACGAGGACACCCGCCTGGGTTGCCGATGGTGACGGACAC
Found at i:8641 original size:33 final size:32
Alignment explanation
Indices: 8565--8652 Score: 106
Period size: 33 Copynumber: 2.8 Consensus size: 32
8555 CTCACCAATG
*
8565 GCCTGGGGTTGCCGATGGTGA-CGAGACACCC
1 GCCTGGGATTGCCGATGGTGACCGAGACACCC
** ** *
8596 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACACCC
8629 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
8653 GGGCTCACGC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 17 0.37
32 3 0.07
33 26 0.57
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (32 bp):
GCCTGGGATTGCCGATGGTGACCGAGACACCC
Done.