Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009514.1 Hibiscus syriacus cultivar Beakdansim tig00115601_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: 14812
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.23
Found at i:7832 original size:91 final size:93
Alignment explanation
Indices: 7665--7838 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 93
7655 TGCGAGGCTG
* *
7665 CCGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGTCCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
*
7730 GTCGGGTGTTGCCGATGGACCGAGGCCC
66 GTCGGGGGTTGCCGATGGACCGAGGCCC
* ** *
7758 CCGCACCCAACTCTCGG-CCTGTGCGGCACTCCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGTCCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
7821 GTCGGGGGTTGCCGATGG
66 GTCGGGGGTTGCCGATGG
7839 TGACCGAGAC
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
91 34 0.46
92 25 0.34
93 15 0.20
ACGTcount: A:0.11, C:0.38, G:0.34, T:0.16
Consensus pattern (93 bp):
CCGCACCCAACGCTCGGTCCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
GTCGGGGGTTGCCGATGGACCGAGGCCC
Found at i:7846 original size:32 final size:32
Alignment explanation
Indices: 7810--7943 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
7800 GCCTGGGTTG
* * *
7810 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
7842 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
7874 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
7906 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
7939 CCGAG
1 CCGAG
7944 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 64 0.70
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:8056 original size:63 final size:62
Alignment explanation
Indices: 7978--8111 Score: 250
Period size: 63 Copynumber: 2.1 Consensus size: 62
7968 GTGCGGCACT
*
7978 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTC-GGGGTTGCCGATGGTGACCGAGGAC
8041 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
8103 CCCGCACCC
1 CCCGCACCC
8112 AACTCTCGTC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 33 0.47
63 37 0.53
ACGTcount: A:0.10, C:0.37, G:0.39, T:0.13
Consensus pattern (62 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
Found at i:8070 original size:31 final size:31
Alignment explanation
Indices: 7978--8075 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
7968 GTGCGGCACT
7978 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
**** * * *
8009 CCCGTCGGGGGTTGCC-GATGG-TGACCGAGGCC
1 CCCG-CACCCGTGGCCTG-GGGTTG-CCGAGGCA
8041 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
8072 CCCG
1 CCCG
8076 TCGGGGTTGC
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.09, C:0.38, G:0.40, T:0.13
Consensus pattern (31 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCA
Found at i:8076 original size:190 final size:187
Alignment explanation
Indices: 7738--8100 Score: 477
Period size: 190 Copynumber: 1.9 Consensus size: 187
7728 CCGTCGGGTG
* *
7738 TTGCCGATGGACCGAGGCCCCCGCACCCAACTCTCGGCCTGTGCGGCACTCCCGCACCCGTGGCC
1 TTGCCGATGGACCGAGGCCCACGCACCCAACGCTCGGCCTGTGCGGCACTCCCGCACCCGTGGCC
*** *
7803 TGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGA
66 TGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGACACCCGTCCCCGTTGGCCGA
* *
7868 TGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
131 GGGTGACCGAGACACCCGTC-GGCGTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
*
7926 TTGCCGATGGTGACCGA-GCCTCACGCA-CCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGT
1 TTGCCGAT-G-GACCGAGGCC-CACGCACCCAACGCTCGG-CCTGTGCGGCACTCCCGCACCCGT
* *
7989 GGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGCCCCCG-CACCCG-T
62 GGCCT-GGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGACACCCGTC-CCCGTT
* * *
8052 GGCCTG-GGGTTG-CCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGG
125 GGCC-GAGGG-TGACCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGG
8101 ACCCCGCACC
Statistics
Matches: 153, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
188 8 0.05
189 34 0.22
190 59 0.39
191 52 0.34
ACGTcount: A:0.13, C:0.35, G:0.36, T:0.17
Consensus pattern (187 bp):
TTGCCGATGGACCGAGGCCCACGCACCCAACGCTCGGCCTGTGCGGCACTCCCGCACCCGTGGCC
TGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGACACCCGTCCCCGTTGGCCGA
GGGTGACCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:8099 original size:31 final size:32
Alignment explanation
Indices: 8001--8104 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 32
7991 CCTGGGGTTG
*
8001 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCAGGGGTTGCCGATGGTGA
* *** * *
8033 CCGAGGCCCCCG-CACCCGTGGCCTG-GGGTTG-
1 CCGAGGCACCCGTCAGGGGTTGCC-GATGG-TGA
8064 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCAGGGGTTGCCGATGGTGA
8095 CCGAGG-ACCC
1 CCGAGGCACCC
8105 CGCACCCAAC
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
30 7 0.13
31 32 0.59
32 15 0.28
ACGTcount: A:0.12, C:0.35, G:0.40, T:0.13
Consensus pattern (32 bp):
CCGAGGCACCCGTCAGGGGTTGCCGATGGTGA
Found at i:8137 original size:156 final size:156
Alignment explanation
Indices: 7906--8191 Score: 422
Period size: 156 Copynumber: 1.8 Consensus size: 156
7896 CCAATGGTGA
7906 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
* * *
7971 CGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCG
66 CCGAACTCCCGCACCCGTGGCCT-GGGTTGCCGAGCCACCCGTC-GGGGTTGCCGATGGTGACCG
8036 AGGCCCCCGCACCCGTGGCCTGGGGTTG
129 AGGCCCCCGCACCCGTGGCCTGGGGTTG
* * *
8064 CCGAGG-CACCCGTC-GGGGTTGCCGATGGTGACCGAGGACC-C-CGCACCCAACTCTC-GTCTC
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGA-G-CCTCACGCA-CCAACGCTCGGT-TC
8124 TGT-CCGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGAC
62 TGTGCCGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGAC
8188 CGAG
127 CGAG
8192 ACACCCTCTG
Statistics
Matches: 118, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
154 22 0.19
155 19 0.16
156 47 0.40
157 22 0.19
158 8 0.07
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.16
Consensus pattern (156 bp):
CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
CCGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGACCGAG
GCCCCCGCACCCGTGGCCTGGGGTTG
Found at i:8239 original size:32 final size:32
Alignment explanation
Indices: 8156--8285 Score: 187
Period size: 31 Copynumber: 4.2 Consensus size: 32
8146 GCCTGGGTTG
* *
8156 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
8187 CCGAGACACCC-TCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
8218 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
8250 CCGAGGCCACCCGCCT-GG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
8281 CCGAG
1 CCGAG
8286 CCTCACGCAC
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
30 3 0.03
31 54 0.59
32 26 0.28
33 9 0.10
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:8254 original size:63 final size:62
Alignment explanation
Indices: 8156--8285 Score: 183
Period size: 63 Copynumber: 2.1 Consensus size: 62
8146 GCCTGGGTTG
* *
8156 CCGAGCCACCCGTCGGGGTTGCCGATGGTGACCGA-GACACCC-TCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGGACACCCGCCT-GG-TTGCCGATGGTGA
* *
8218 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGTTGCCGATGGTGA
1 CCGAGACACCCGTC-GGGGTTGCCGATGGTGACCGAGGACACCCGCCTGGTTGCCGATGGTGA
8281 CCGAG
1 CCGAG
8286 CCTCACGCAC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 13 0.21
63 38 0.62
64 8 0.13
65 2 0.03
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (62 bp):
CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGGACACCCGCCTGGTTGCCGATGGTGA
Found at i:8408 original size:33 final size:32
Alignment explanation
Indices: 8331--8419 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
8321 CTCACCAATG
*
8331 GCCTGGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGATTGCCGATGGTGACCGAGACACCC
** ** *
8363 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACACCC
8396 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
8420 GCTCACGCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 21 0.45
33 26 0.55
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (32 bp):
GCCTGGGATTGCCGATGGTGACCGAGACACCC
Found at i:8435 original size:33 final size:32
Alignment explanation
Indices: 8371--8435 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
8361 CCGTATGGTT
*
8371 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACC-AGGCCACCCACCTGGGA
*
8404 TTGCCGATGGTGACC-GGCTCACGCACACTGGG
1 TTGCCGATGGTGACCAGGC-CACCCAC-CTGGG
8436 GCCTGATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 5 0.18
33 20 0.71
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.17
Consensus pattern (32 bp):
TTGCCGATGGTGACCAGGCCACCCACCTGGGA
Done.