Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009558.1 Hibiscus syriacus cultivar Beakdansim tig00116557_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: 9614
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Found at i:7513 original size:31 final size:31
Alignment explanation
Indices: 7443--7572 Score: 190
Period size: 31 Copynumber: 4.2 Consensus size: 31
7433 GTGCGTGAGG
* *
7443 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGAC-GGT-GT
7475 CTCGGTCACCATCGGCAAACCCAGACGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGTGT
7506 CTCGGTCACCATCGGCAAACCCAGACGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGTGT
* * *
7537 CTCGGTCACCATCGGCAACCCCCGACGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGTGT
7568 CTCGG
1 CTCGG
7573 CAACCCCAGG
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
31 65 0.71
32 19 0.21
33 8 0.09
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (31 bp):
CTCGGTCACCATCGGCAAACCCAGACGGTGT
Found at i:7665 original size:32 final size:32
Alignment explanation
Indices: 7624--7728 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
7614 GAGTTGGGTG
7624 CGGGT-CCTCGGTCACCATCGGCAACCCCCGA
1 CGGGTGCCTCGGTCACCATCGGCAACCCCCGA
* * ****
7655 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG-
1 CGGGTGCCTCGGTC-ACCATC-GGCAACCCCCGA
7686 CGGG-GCCTCGGTCACCATCGGCAACCCCCGA
1 CGGGTGCCTCGGTCACCATCGGCAACCCCCGA
7717 CGGGTGCCTCGG
1 CGGGTGCCTCGG
7729 CAACCCCAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
30 16 0.29
31 17 0.31
32 22 0.40
ACGTcount: A:0.13, C:0.42, G:0.33, T:0.11
Consensus pattern (32 bp):
CGGGTGCCTCGGTCACCATCGGCAACCCCCGA
Found at i:7716 original size:62 final size:62
Alignment explanation
Indices: 7619--7750 Score: 255
Period size: 62 Copynumber: 2.1 Consensus size: 62
7609 GCCGAGAGTT
*
7619 GGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
7681 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
7743 GGGTGCGG
1 GGGTGCGG
7751 AGTGCCGCAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 69 1.00
ACGTcount: A:0.14, C:0.40, G:0.36, T:0.11
Consensus pattern (62 bp):
GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:7721 original size:93 final size:92
Alignment explanation
Indices: 7506--7728 Score: 229
Period size: 93 Copynumber: 2.4 Consensus size: 92
7496 CAGACGGTGT
*
7506 CTCGGTCACCATCGGCAAACCCAGACGGTGT-CTCGGTCACCATCGGCAACCCCCGACGGTGGCT
1 CTCGGTCACCATCGGCAAACCCAGACGG-GTCCTCGGTCACCATCGGCAACCCCCGACGGTGCCT
7570 CGGCAACCCCAGGCCACGGGTGCGGGAG
65 CGGCAACCCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
7598 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTCCTCGGTCACCATCGGCAACCCCCGAC-GGTG
7661 CCTCGGCAACCCCAGGCCACGGGTGCGGG-G
62 CCTCGGCAACCCCAGGCCACGGGTGCGGGAG
* *
7691 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGT-CCTCGG
7729 CAACCCCAGG
Statistics
Matches: 99, Mismatches: 23, Indels: 16
0.72 0.17 0.12
Matches are distributed among these distances:
91 1 0.01
92 8 0.08
93 45 0.45
94 44 0.44
95 1 0.01
ACGTcount: A:0.16, C:0.38, G:0.34, T:0.13
Consensus pattern (92 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTC
GGCAACCCCAGGCCACGGGTGCGGGAG
Found at i:7756 original size:32 final size:31
Alignment explanation
Indices: 7655--7756 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 31
7645 CAACCCCCGA
7655 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * ****
7686 CGGG-GCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
7716 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
7748 CGGAGTGCC
1 CGG-GTGCC
7757 GCACAGAACC
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
30 16 0.31
31 15 0.29
32 21 0.40
ACGTcount: A:0.14, C:0.40, G:0.36, T:0.10
Consensus pattern (31 bp):
CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
Found at i:7763 original size:155 final size:156
Alignment explanation
Indices: 7532--8000 Score: 623
Period size: 155 Copynumber: 3.0 Consensus size: 156
7522 AAACCCAGAC
* *
7532 GGTGTCTCGGTCACCATCGGCAACCCCCGAC-GGTGGCTCGGCAACCCCAGGCCACGGGTGCGGG
1 GGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
* *
7596 AGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTG
66 AGTGCCGCACAGAGCCGAGAGTTGGGTGCGGG-CCTCGGTCACCATCGGCAACCCCCGACGGGTG
*
7661 CCTCGGCAACCCCAGGCCACGGGTGCG
130 CCTCGGCAACCCCAGGCCACCGGTGCG
7688 GG-GCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGC-GG
1 GGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
* * * * * *
7751 AGTGCCGCACAGAACCGAGCGTT-GGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGT
66 AGTGCCGCACAGAGCCGAGAGTTGGGTGCG-G-GCCTCGGTCACCATCGGCAACCCCCGACGGGT
* * * *
7815 GGCCTCGGTC-ACCATC-GGCAAACCCAG-ACG
129 -GCCTCGG-CAACC-CCAGGC-CA-CCGGTGCG
*
7845 GGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
1 GGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
*
7910 AGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGCCTC-GTCACCATCGGCAACACCCGAC-GGTGC
66 AGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGC
* **
7973 CTCGGCAACCCCAGTCCATTGGTGCG
131 CTCGGCAACCCCAGGCCACCGGTGCG
7999 GG
1 GG
8001 AGTGCCGCAC
Statistics
Matches: 269, Mismatches: 30, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
153 1 0.00
154 13 0.05
155 88 0.33
156 48 0.18
157 25 0.09
158 64 0.24
159 24 0.09
160 6 0.02
ACGTcount: A:0.16, C:0.36, G:0.35, T:0.13
Consensus pattern (156 bp):
GGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
AGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGC
CTCGGCAACCCCAGGCCACCGGTGCG
Found at i:7859 original size:32 final size:32
Alignment explanation
Indices: 7785--7886 Score: 150
Period size: 32 Copynumber: 3.2 Consensus size: 32
7775 GTGCGTGAGG
* *
7785 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
*
7818 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
7850 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
7882 CTCGG
1 CTCGG
7887 CAACCCCAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 35 0.56
33 28 0.44
ACGTcount: A:0.17, C:0.38, G:0.30, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:8010 original size:91 final size:92
Alignment explanation
Indices: 7854--8031 Score: 286
Period size: 91 Copynumber: 1.9 Consensus size: 92
7844 GGGTGTCTCG
*
7854 GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
1 GTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
* *
7919 CAGAGCCGAGAGTTGGGTGCGGGCCTC
66 CAGAACCGAGAGCTGGGTGCGGGCCTC
* **
7946 GTCACCATCGGCAACACCCGAC-GGTGCCTCGGCAACCCCAGTCCATTGGTGCGGGAGTGCCGCA
1 GTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
*
8010 CAGAACCGAGCGCTGGGTGCGG
66 CAGAACCGAGAGCTGGGTGCGG
8032 CAGCCTCGCA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 58 0.73
92 21 0.27
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.12
Consensus pattern (92 bp):
GTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
CAGAACCGAGAGCTGGGTGCGGGCCTC
Done.