Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009468.1 Hibiscus syriacus cultivar Beakdansim tig00114122_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: 8952
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Found at i:8222 original size:33 final size:31
Alignment explanation
Indices: 8185--8271 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 31
8175 GCGTGAGCCC
8185 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAA-CCCAGGCGGGT-GCCT
* ** *
8218 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGC-AACCCAGGCGGGTGCCT
8250 CGGTCACCATC-GCAACCCAGGC
1 CGGTCACCATCGGCAACCCAGGC
8272 CATTGGTGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 6 0.13
31 2 0.04
32 14 0.30
33 22 0.48
34 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAACCCAGGCGGGTGCCT
Found at i:8387 original size:31 final size:32
Alignment explanation
Indices: 8321--8440 Score: 174
Period size: 31 Copynumber: 3.8 Consensus size: 32
8311 CGTGAGGCTC
* *
8321 GTCACCATCGGC-AACCCAGGCGGGTGGCCTCG
1 GTCACCATCGGCAAACCCAGACGGGT-GTCTCG
8353 GTCACCATC-GCAAACCCAGACGGGTGTCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGTCTCG
8384 GTCACCATCGGCAAACCCAGAC-GGTGTCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGTCTCG
* *
8415 GTCACCATCGGCAACCCCCGACGGGT
1 GTCACCATCGGCAAACCCAGACGGGT
8441 TGGCTCGGCA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
31 45 0.56
32 36 0.44
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (32 bp):
GTCACCATCGGCAAACCCAGACGGGTGTCTCG
Found at i:8438 original size:63 final size:63
Alignment explanation
Indices: 8321--8440 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
8311 CGTGAGGCTC
*
8321 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCG
1 GTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCG
* * *
8384 GTCACCATCGGCAAACCCAGAC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGT
1 GTCACCATCGGC-AACCCAGACGGGTGGCCTCGGTCACCATC-GCAAACCCAGACGGGT
8441 TGGCTCGGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
62 14 0.27
63 29 0.57
64 8 0.16
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (63 bp):
GTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCG
Found at i:8590 original size:61 final size:62
Alignment explanation
Indices: 8495--8622 Score: 224
Period size: 62 Copynumber: 2.1 Consensus size: 62
8485 CCCGAGAGTT
*
8495 GGGTGCGGGGTCCTCGTCACCATCGGCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
8556 GGGTGCGGGGGCCTCGGTCACCATC-GCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTC-GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
8618 GGGTG
1 GGGTG
8623 GGGAGTGCCG
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
61 26 0.41
62 38 0.59
ACGTcount: A:0.14, C:0.41, G:0.34, T:0.11
Consensus pattern (62 bp):
GGGTGCGGGGGCCTCGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:8727 original size:155 final size:155
Alignment explanation
Indices: 8346--8757 Score: 450
Period size: 155 Copynumber: 2.7 Consensus size: 155
8336 CCAGGCGGGT
* * *
8346 GGCCTCGGTCACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGAC-GGT
1 GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGT
*
8409 GTCTCGGTCACCATCGGCAACCCCCGACGGGTTGGCTCGGCAACCCCAGCCACGGGTGCGGGAGT
66 GTCTCGGTCACCATC-GCAACCCCCGACGGG-TGCCTCGGCAACCCCAGCCACGGGTGCGGGAGT
* *
8474 TCCGGACAGAGCCCGAGAGTTGGGTGCGG
129 GCCGCACAGA-CCCGAGAGTT-GGTGCGG
* * ** * * ***
8503 GGTCCTC-GTCACCATCGGCAACCCCCGAC-GGTGCCTCGG-CAACCCCAGGCCACGGGTG-CGG
1 GG-CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTC-ACCATAGGCAAAGCCAGACGG
* *
8564 GGGCCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTG-GGGAG
64 GTGTCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCA-GCCACGGGTGCGGGAG
*
8628 TGCCGCACAGA-CCGAGCGTT-GTGCGTG
128 TGCCGCACAGACCCGAGAGTTGGTGCG-G
* * *
8655 AGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGG
1 -GGCCTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCATAGGCAAAGCCAGACGG
* *
8719 GTGTCTCGGTCACCATCGCAAACCCCGAC-GGTGTCTCGG
64 GTGTCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGG
8758 TCACCATCGG
Statistics
Matches: 210, Mismatches: 33, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
151 8 0.04
152 20 0.10
153 13 0.06
154 25 0.12
155 59 0.28
156 27 0.13
157 44 0.21
158 14 0.07
ACGTcount: A:0.17, C:0.36, G:0.33, T:0.14
Consensus pattern (155 bp):
GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGT
GTCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGCCACGGGTGCGGGAGTGC
CGCACAGACCCGAGAGTTGGTGCGG
Found at i:8742 original size:342 final size:339
Alignment explanation
Indices: 8261--8889 Score: 1045
Period size: 342 Copynumber: 1.8 Consensus size: 339
8251 GGTCACCATC
**
8261 GCAACCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGTCAC
1 GCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGTCAC
8326 CATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCGGTCACCA
66 CATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCGGTCACCA
*
8391 TCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTTGGCTCGGCAACCCC
131 TCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGG-TGCCTC-GCAACCCC
* * *
8456 A-GCCACGGGTGCGGGAGTTCCGGACAGAGCCCGAGAGTTGGGTGCGGGGTCCTCGTCACCATCG
194 AGGCCAC-GGTGCGGGAGTGCCGCACAGAG-CCGAGAGTTGGGTGCGGGGGCCTCGTCACCATCG
*
8520 GCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGCA
257 GCAACACCC-ACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGCA
8584 ACCCCCGACGGGTGCCTCG
321 ACCCCCGACGGGTGCCTCG
8603 GCAACCCCAGGCCACGGGTG-GGGAGTGCCGCACAG-ACCGAGCGTT-GTGCGTGAGGCTCGGTC
1 GCAA-CCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTC-GTC
* *
8665 ACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCGGTC
64 ACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCA-TCGCAAACCCAGACGGGTGTCTCGGTC
*
8730 ACCATC-GCAAACCCCGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACC
127 ACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACC
8794 CCAGGCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGTCACCATCG
192 CCAGGCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGTCACCATCG
8859 GCAACACCCACGGGTGCCTCGGCAACCCCAG
257 GCAACACCCACGGGTGCCTCGGCAACCCCAG
8890 TCCATGGTGC
Statistics
Matches: 271, Mismatches: 10, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
338 2 0.01
339 60 0.22
340 42 0.15
341 34 0.13
342 89 0.33
343 44 0.16
ACGTcount: A:0.18, C:0.36, G:0.33, T:0.13
Consensus pattern (339 bp):
GCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGTCAC
CATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCGGTCACCA
TCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAG
GCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGTCACCATCGGCAA
CACCCACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGCAACCCC
CGACGGGTGCCTCG
Found at i:8754 original size:30 final size:32
Alignment explanation
Indices: 8658--8788 Score: 158
Period size: 33 Copynumber: 4.1 Consensus size: 32
8648 GTGCGTGAGG
* * *
8658 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
* *
8691 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
*
8723 CTCGGTCACCATC-GCAAACCCCGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
8753 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
8785 CTCG
1 CTCG
8789 CAACCCCAGG
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
30 18 0.21
31 21 0.24
32 21 0.24
33 26 0.30
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:8770 original size:62 final size:65
Alignment explanation
Indices: 8658--8788 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 65
8648 GTGCGTGAGG
* * * * *
8658 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
* * * *
8723 CTCGGTCACCATC-GCAAACCCCGAC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
8785 CTCG
1 CTCG
8789 CAACCCCAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 32 0.56
63 3 0.05
64 9 0.16
65 13 0.23
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (65 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
Done.