Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009529.1 Hibiscus syriacus cultivar Beakdansim tig00116143_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: 9381
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Found at i:8059 original size:33 final size:32
Alignment explanation
Indices: 8022--8103 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
8012 AGCCCCCGGT
*
8022 CATCGGCAATCCCAGGCGGGTGGCCTCGGTCAC
1 CATCGGCAAACCCAGGCGGGT-GCCTCGGTCAC
* ** *
8055 CATCGGCAAAACCATACGGGTGTCTCGGTCAC
1 CATCGGCAAACCCAGGCGGGTGCCTCGGTCAC
*
8087 CATCGGCAACCCCAGGC
1 CATCGGCAAACCCAGGC
8104 ATTGGTGAGG
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 23 0.57
33 17 0.43
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
CATCGGCAAACCCAGGCGGGTGCCTCGGTCAC
Found at i:8190 original size:32 final size:32
Alignment explanation
Indices: 8149--8280 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
8139 GTGCGTGAGG
* *
8149 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
8181 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
8213 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* *
8245 CTCGGTCACCATCGGC-AACCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
8276 CTCGG
1 CTCGG
8281 CAACCCAGGC
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
31 18 0.19
32 65 0.68
33 12 0.13
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:8432 original size:92 final size:92
Alignment explanation
Indices: 8206--8433 Score: 232
Period size: 92 Copynumber: 2.5 Consensus size: 92
8196 CAAACCCAGA
* * *
8206 CGGGTGTCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACG
1 CGGGAGTCCCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCGACG
*
8271 GGTGGCTCGGCAACCCAGGCCAGGGTG
66 GGTGCCTCGGCAACCCAGGCCAGGGTG
* * * * * ***** *
8298 CGGGAGTTCCGGACA-GAGCCG-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCG
1 CGGGAGTCCCGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAACCCCG
8360 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
63 ACGGGTGCCTCGGCAA-CCCAGGCCA-GGGTG
*
8392 CGGG-G-CCCGGTCACCATCGGCAAACCCCGACGGGTGCCTCGG
1 CGGGAGTCCCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGG
8434 CAACCCCAGG
Statistics
Matches: 102, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
90 1 0.01
91 6 0.06
92 69 0.68
93 16 0.16
94 10 0.10
ACGTcount: A:0.16, C:0.35, G:0.36, T:0.13
Consensus pattern (92 bp):
CGGGAGTCCCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCGACG
GGTGCCTCGGCAACCCAGGCCAGGGTG
Found at i:8439 original size:153 final size:154
Alignment explanation
Indices: 8247--8527 Score: 419
Period size: 153 Copynumber: 1.8 Consensus size: 154
8237 ACGGGTGTCT
* * *
8247 CGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAA-CCCAGGCCAGGGTGCGGGAGTTCCGGA
1 CGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAGGGTGCGGGAGTGCCGCA
* *
8311 CAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAA-CCCCGACGGGT-GCCTCG
66 CAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAATCCCAGACGGGTGGCCTCG
8372 GCAACCCCAGGCCACGGGTGCGGGGCC
128 GCAACCCCAGGCCACGGGTGCGGGGCC
*
8399 CGGTCACCATCGGCAAACCCCGACGGGTGCCTCGGCAACCCCAGGCCGGGGTGCGGGAGTGCCGC
1 CGGTCACCATCGGC-AACCCCGACGGGTGCCTCGGCAACCCCAGGCCAGGGTGCGGGAGTGCCGC
* *
8464 ACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
65 ACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGACGGGTGGCCTCGG
8528 TCACCTTGGC
Statistics
Matches: 115, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
152 14 0.12
153 46 0.40
154 46 0.40
155 9 0.08
ACGTcount: A:0.16, C:0.35, G:0.38, T:0.12
Consensus pattern (154 bp):
CGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAGGGTGCGGGAGTGCCGCA
CAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGACGGGTGGCCTCGGCA
ACCCCAGGCCACGGGTGCGGGGCC
Found at i:8451 original size:60 final size:62
Alignment explanation
Indices: 8325--8455 Score: 223
Period size: 61 Copynumber: 2.1 Consensus size: 62
8315 GCCGAGAGTT
8325 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
*
8387 GGGTGCGGGG-CC-CGGTCACCATCGGCAAACCCCGACGGGTGCCTCGGCAACCCCAGGCC-G
1 GGGTGCGGGGTCCTCGGTCACCATCGGC-AACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
8447 GGGTGCGGG
1 GGGTGCGGG
8456 AGTGCCGCAC
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
60 23 0.34
61 34 0.51
62 10 0.15
ACGTcount: A:0.14, C:0.38, G:0.38, T:0.10
Consensus pattern (62 bp):
GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:8551 original size:32 final size:32
Alignment explanation
Indices: 8490--8622 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
8480 GTGCGTGAGG
* *
8490 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
8523 CTCGGTCACC-TTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
8554 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
8586 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
8618 CTCGG
1 CTCGG
8623 CAACCCCAGG
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.12
32 68 0.76
33 10 0.11
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Done.