Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009492.1 Hibiscus syriacus cultivar Beakdansim tig00114651_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: 11200
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.22
Found at i:8116 original size:30 final size:30
Alignment explanation
Indices: 8070--8189 Score: 158
Period size: 30 Copynumber: 4.0 Consensus size: 30
8060 GTGAGGCTCG
* *
8070 GTCACCATCGGCAACCCAGGCGGTGGCCTC
1 GTCACCATCGGCAACCCAGACGGTGGTCTC
8100 GGTCACCATC-GCAACCCAGACGGT-GTCTC
1 -GTCACCATCGGCAACCCAGACGGTGGTCTC
8129 GTCACCATCGGCAACCCAGACGG-GTGTCTC
1 GTCACCATCGGCAACCCAGACGGTG-GTCTC
*
8159 GTCACCATCGGCAACCCCCGACGGTGG-CTC
1 GTCACCATCGGCAA-CCCAGACGGTGGTCTC
8189 G
1 G
8190 GCAACCCCAG
Statistics
Matches: 81, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.11
29 17 0.21
30 36 0.44
31 18 0.22
32 1 0.01
ACGTcount: A:0.18, C:0.39, G:0.28, T:0.15
Consensus pattern (30 bp):
GTCACCATCGGCAACCCAGACGGTGGTCTC
Found at i:8173 original size:59 final size:60
Alignment explanation
Indices: 8064--8189 Score: 168
Period size: 59 Copynumber: 2.1 Consensus size: 60
8054 TGGTGCGTGA
*
8064 GGCTCGGTCACCATCGGCAACCCAGGCGGTGGCCTCGGTCACCATCGCAA-CCCAGACGGT
1 GGCTC-GTCACCATCGGCAACCCAGACGGTGGCCTCGGTCACCATCGCAACCCCAGACGGT
* * *
8124 GTCTCGTCACCATCGGCAACCCAGACGG-GTGTCTC-GTCACCATCGGCAACCCCCGACGGT
1 GGCTCGTCACCATCGGCAACCCAGACGGTG-GCCTCGGTCACCATC-GCAACCCCAGACGGT
8184 GGCTCG
1 GGCTCG
8190 GCAACCCCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
58 10 0.17
59 30 0.52
60 18 0.31
ACGTcount: A:0.17, C:0.39, G:0.29, T:0.15
Consensus pattern (60 bp):
GGCTCGTCACCATCGGCAACCCAGACGGTGGCCTCGGTCACCATCGCAACCCCAGACGGT
Found at i:8280 original size:32 final size:32
Alignment explanation
Indices: 8243--8342 Score: 100
Period size: 32 Copynumber: 3.2 Consensus size: 32
8233 TTGGGTGCGT
8243 CCTCGGTCACCATCGGCAACCCCCGACGGGTG
1 CCTCGGTCACCATCGGCAACCCCCGACGGGTG
* * ****
8275 CCTCGG-CAACC-CCAGGCCACGGGTG-CGGG-G
1 CCTCGGTC-ACCATC-GGCAACCCCCGACGGGTG
8305 CCTCGGTCACCATCGGCAACCCCCGACGGGTG
1 CCTCGGTCACCATCGGCAACCCCCGACGGGTG
8337 CCTCGG
1 CCTCGG
8343 CAACCCCAGG
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
30 16 0.32
31 12 0.24
32 22 0.44
ACGTcount: A:0.14, C:0.43, G:0.32, T:0.11
Consensus pattern (32 bp):
CCTCGGTCACCATCGGCAACCCCCGACGGGTG
Found at i:8309 original size:30 final size:31
Alignment explanation
Indices: 8269--8365 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 31
8259 CAACCCCCGA
8269 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * ****
8300 CGGG-GCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
8330 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
8362 CGGG
1 CGGG
8366 AGTGCCGCAC
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
30 16 0.33
31 16 0.33
32 16 0.33
ACGTcount: A:0.13, C:0.40, G:0.37, T:0.09
Consensus pattern (31 bp):
CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
Found at i:8319 original size:62 final size:62
Alignment explanation
Indices: 8243--8365 Score: 246
Period size: 62 Copynumber: 2.0 Consensus size: 62
8233 TTGGGTGCGT
8243 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGG
1 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGG
8305 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
1 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
8366 AGTGCCGCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.15, C:0.42, G:0.33, T:0.10
Consensus pattern (62 bp):
CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGG
Found at i:8392 original size:152 final size:154
Alignment explanation
Indices: 8159--8435 Score: 402
Period size: 154 Copynumber: 1.8 Consensus size: 154
8149 CGGGTGTCTC
* * *
8159 GTCACCATCGGCAACCCCCGACGGTGGCTCGGCAACCCCAGGCCACGGTGCGGAGTTCCGGACAG
1 GTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGGCCACGGTGCGGAGTGCCGCACAG
* * *
8224 AGCCGAGAGTTGGGTGC-G-TCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGGCAACC
66 AACCGAGAGTTGGGTGCTGAGCCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCGGCAACC
8286 CCAGGCCACGGGTGCGGGGCCTCG
131 CCAGGCCACGGGTGCGGGGCCTCG
8310 GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
1 GTCACCATCGGCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCAC-GGTGC-GGAGTGCCGCA
* * * *
8375 CAGAACCGAGCG-T-GGTGCTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
63 CAGAACCGAGAGTTGGGTGCTGAGCCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCGG
8436 TCACCATTGG
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
151 22 0.20
152 28 0.25
153 7 0.06
154 46 0.42
155 7 0.06
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (154 bp):
GTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGGCCACGGTGCGGAGTGCCGCACAG
AACCGAGAGTTGGGTGCTGAGCCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCGGCAACC
CCAGGCCACGGGTGCGGGGCCTCG
Found at i:8506 original size:32 final size:32
Alignment explanation
Indices: 8398--8533 Score: 170
Period size: 32 Copynumber: 4.3 Consensus size: 32
8388 GGTGCTGAGG
* *
8398 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
8431 CTCGGTCACCATTGGCAAAGCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
8462 CTC-GTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
8493 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
8525 CTCGG-CACC
1 CTCGGTCACC
8534 CCAGGCCACG
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
30 20 0.22
31 16 0.18
32 33 0.36
33 22 0.24
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:8672 original size:93 final size:93
Alignment explanation
Indices: 8295--8674 Score: 296
Period size: 93 Copynumber: 4.1 Consensus size: 93
8285 CCCAGGCCAC
*
8295 GGGTGC-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGC-ACCCCAGGCCACGG
*
8359 GTGCGGGAGTGCCGCACAGAACCGAGCG-T
65 GTGCGGGAGTGCCGCACA-AACCGAGAGCT
* * * * *** * *
8388 -GGTGCTGAGG-CTCGGTCACCATCGGCAATC-CCAGGCGGGTGGCCTCGGTCACCATTGGCAAA
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAA-CACCCGACGGGT-GCCTCGG-CACCCCAGGCCAC
*** * * * * * *
8450 GCCAGAC-GGTGT-CTCGTCACCATCGGCA-AACC
63 GGGTG-CGGGAGTGC-CG-CACAAACCG-AGAGCT
** * * * *
8482 CAG-ACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCACCCCAGGCCACGGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCACCCCAGGCCACGGG
* *
8546 TGCGGGAGTGCCGCACAAGCCGAGAGTT
66 TGCGGGAGTGCCGCACAAACCGAGAGCT
* **
8574 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCA-TCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGC-ACCCCAGGCCACGG
*
8638 GTGCGGGAGTGCCGCACAGAACCGAGCGCT
65 GTGCGGGAGTGCCGCACA-AACCGAGAGCT
8668 -GGTGCGG
1 GGGTGCGG
8675 CAGCCTCGCA
Statistics
Matches: 217, Mismatches: 52, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
91 1 0.00
92 41 0.19
93 116 0.53
94 32 0.15
95 27 0.12
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.13
Consensus pattern (93 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCACCCCAGGCCACGGG
TGCGGGAGTGCCGCACAAACCGAGAGCT
Done.