Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009504.1 Hibiscus syriacus cultivar Beakdansim tig00115095_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: 9229
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Found at i:347 original size:33 final size:32
Alignment explanation
Indices: 310--398 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
300 GCGTGAGCCC
*
310 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
343 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
375 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
399 CATTGGTGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.49
33 24 0.51
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:486 original size:32 final size:32
Alignment explanation
Indices: 445--577 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
435 GTGCGTGAGG
* *
445 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
477 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
509 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
541 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
573 CTCGG
1 CTCGG
578 CAACCCAGGC
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 83 0.87
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:738 original size:58 final size:58
Alignment explanation
Indices: 634--750 Score: 193
Period size: 58 Copynumber: 2.0 Consensus size: 58
624 GGTGCGGGGT
634 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGG
1 CCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCA-GGGTGCGG
694 CCTCGGTCACCATCGGCAA-CCCGACGGGTGCCTCGGGCAA-CCCAGGCCAGGGTGCGG
1 CCTCGGTCACCATCGGCAACCCCGACGGGTGCCTC-GGCAACCCCAGGCCAGGGTGCGG
751 GAGTGCCGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
57 8 0.14
58 24 0.43
59 5 0.09
60 19 0.34
ACGTcount: A:0.15, C:0.41, G:0.33, T:0.10
Consensus pattern (58 bp):
CCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAGGGTGCGG
Found at i:854 original size:65 final size:63
Alignment explanation
Indices: 785--917 Score: 185
Period size: 65 Copynumber: 2.1 Consensus size: 63
775 GTGCGTGAGG
* * * * *
785 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCATCGGC-AACCCAGACGGGTGC
* *
850 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCAGACGGGTGC
913 CTCGG
1 CTCGG
918 CAACCCAGGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 17 0.28
64 16 0.26
65 28 0.46
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (63 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCAGACGGGTGC
Found at i:859 original size:32 final size:32
Alignment explanation
Indices: 785--917 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
775 GTGCGTGAGG
* *
785 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
818 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
850 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
882 CTCGGTCACCATCGGC-AACCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
913 CTCGG
1 CTCGG
918 CAACCCAGGC
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 18 0.20
32 47 0.52
33 26 0.29
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:1012 original size:93 final size:94
Alignment explanation
Indices: 882--1064 Score: 289
Period size: 95 Copynumber: 2.0 Consensus size: 94
872 AGACGGGTGT
882 CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAA-CCCAGGCCACGGGTG-GGGAGTGCC
1 CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
* *
945 GCACAGAGCCGAGAGTTGGGTGCGGGGGC
66 GCACAGAACCGAGAGCTGGGTGCGGGGGC
* **
974 CTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAAC-CCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
*
1039 CGCACAGAACCGAGCGCTGGGTGCGG
65 CGCACAGAACCGAGAGCTGGGTGCGG
1065 CAGCCTCGCA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
92 19 0.23
93 20 0.24
94 12 0.15
95 31 0.38
ACGTcount: A:0.17, C:0.34, G:0.37, T:0.12
Consensus pattern (94 bp):
CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
GCACAGAACCGAGAGCTGGGTGCGGGGGC
Done.