Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003368.1 Hibiscus syriacus cultivar Beakdansim tig00007080_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: 76430
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:27959 original size:20 final size:21
Alignment explanation
Indices: 27934--27972 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27924 GGCTGCTGGA
27934 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
27954 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTGACCGGTTT
27973 GACCGGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTTC
Found at i:27970 original size:10 final size:9
Alignment explanation
Indices: 27935--28025 Score: 74
Period size: 10 Copynumber: 9.4 Consensus size: 9
27925 GCTGCTGGAA
27935 ACCGGTTTG
1 ACCGGTTTG
*
27944 ACCGGTTTTCA
1 ACCGG-TTT-G
27955 ACCGGTTCTG
1 ACCGGTT-TG
27965 ACCGGTTTG
1 ACCGGTTTG
*
27974 ACCGGTTTCA
1 ACCGGTTT-G
*
27984 ACCGGTTCG
1 ACCGGTTTG
*
27993 AACCGGTTTA
1 -ACCGGTTTG
*
28003 ACCGGTCTG
1 ACCGGTTTG
*
28012 AATCGGTTTG
1 -ACCGGTTTG
28022 ACCG
1 ACCG
28026 TTGACCCGAC
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 25 0.39
10 33 0.52
11 6 0.09
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:27979 original size:19 final size:20
Alignment explanation
Indices: 27934--28025 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 20
27924 GGCTGCTGGA
* *
27934 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
27954 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TGACCGGTTCTG
*
27974 -ACCGGTTTCAACCGGTTC-G
1 AACCGGTTT-GACCGGTTCTG
*
27993 AACCGGTTTAACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
28012 AATCGGTTTGACCG
1 AACCGGTTTGACCG
28026 TTGACCCGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.05
19 34 0.54
20 17 0.27
21 9 0.14
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:27997 original size:29 final size:30
Alignment explanation
Indices: 27934--28008 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
27924 GGCTGCTGGA
27934 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
27965 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
27993 AACCGGTTTAACCGGT
1 AACCGGTTTGACCGGT
28009 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.64
30 14 0.33
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:28049 original size:22 final size:22
Alignment explanation
Indices: 28021--28075 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
28011 GAATCGGTTT
28021 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
*
28043 GACCGTTGACCCGACCCGACCT
1 GACCGTTGACCCGACCCGACCC
28065 GACCGTTGACC
1 GACCGTTGACC
28076 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (22 bp):
GACCGTTGACCCGACCCGACCC
Found at i:28076 original size:7 final size:7
Alignment explanation
Indices: 28064--28088 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28054 CGACCCGACC
28064 TGACCGT
1 TGACCGT
28071 TGACCGT
1 TGACCGT
28078 TGACCGT
1 TGACCGT
28085 TGAC
1 TGAC
28089 TTTCTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
TGACCGT
Found at i:29042 original size:32 final size:31
Alignment explanation
Indices: 28958--29034 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
28948 CTAATGTGAC
* *
28958 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
28989 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
29021 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
29035 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:29060 original size:63 final size:63
Alignment explanation
Indices: 28958--29081 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
28948 CTAATGTGAC
* ** * *
28958 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
29021 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
29082 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:34194 original size:21 final size:21
Alignment explanation
Indices: 34169--34208 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34159 TGAAATATTA
*
34169 AAAAATATTAATGTTTTAGGT
1 AAAAATAATAATGTTTTAGGT
34190 AAAAATAATAATGTTTTAG
1 AAAAATAATAATGTTTTAG
34209 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAGGT
Found at i:45181 original size:20 final size:21
Alignment explanation
Indices: 45156--45194 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
45146 GGCTGCTGGA
45156 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
45176 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTGACCGGTTT
45195 GACCGGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTTC
Found at i:45192 original size:10 final size:9
Alignment explanation
Indices: 45157--45247 Score: 74
Period size: 10 Copynumber: 9.4 Consensus size: 9
45147 GCTGCTGGAA
45157 ACCGGTTTG
1 ACCGGTTTG
*
45166 ACCGGTTTTCA
1 ACCGG-TTT-G
45177 ACCGGTTCTG
1 ACCGGTT-TG
45187 ACCGGTTTG
1 ACCGGTTTG
*
45196 ACCGGTTTCA
1 ACCGGTTT-G
*
45206 ACCGGTTCG
1 ACCGGTTTG
*
45215 AACCGGTTTA
1 -ACCGGTTTG
*
45225 ACCGGTCTG
1 ACCGGTTTG
*
45234 AATCGGTTTG
1 -ACCGGTTTG
45244 ACCG
1 ACCG
45248 TTGACCCGAC
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 25 0.39
10 33 0.52
11 6 0.09
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:45201 original size:19 final size:20
Alignment explanation
Indices: 45156--45247 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 20
45146 GGCTGCTGGA
* *
45156 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
45176 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TGACCGGTTCTG
*
45196 -ACCGGTTTCAACCGGTTC-G
1 AACCGGTTT-GACCGGTTCTG
*
45215 AACCGGTTTAACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
45234 AATCGGTTTGACCG
1 AACCGGTTTGACCG
45248 TTGACCCGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.05
19 34 0.54
20 17 0.27
21 9 0.14
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:45219 original size:29 final size:30
Alignment explanation
Indices: 45156--45230 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
45146 GGCTGCTGGA
45156 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
45187 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
45215 AACCGGTTTAACCGGT
1 AACCGGTTTGACCGGT
45231 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.64
30 14 0.33
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:45271 original size:22 final size:22
Alignment explanation
Indices: 45243--45297 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
45233 GAATCGGTTT
45243 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
*
45265 GACCGTTGACCCGACCCGACCT
1 GACCGTTGACCCGACCCGACCC
45287 GACCGTTGACC
1 GACCGTTGACC
45298 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (22 bp):
GACCGTTGACCCGACCCGACCC
Found at i:45298 original size:7 final size:7
Alignment explanation
Indices: 45286--45310 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
45276 CGACCCGACC
45286 TGACCGT
1 TGACCGT
45293 TGACCGT
1 TGACCGT
45300 TGACCGT
1 TGACCGT
45307 TGAC
1 TGAC
45311 TTTCTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
TGACCGT
Found at i:46264 original size:32 final size:31
Alignment explanation
Indices: 46180--46256 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
46170 CTAATGTGAC
* *
46180 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
46211 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
46243 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
46257 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:46282 original size:63 final size:63
Alignment explanation
Indices: 46180--46303 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
46170 CTAATGTGAC
* ** * *
46180 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
46243 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
46304 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:51410 original size:21 final size:21
Alignment explanation
Indices: 51385--51424 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
51375 TGAAATATTA
*
51385 AAAAATATTAATGTTTTAGGT
1 AAAAATAATAATGTTTTAGGT
51406 AAAAATAATAATGTTTTAG
1 AAAAATAATAATGTTTTAG
51425 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAGGT
Found at i:62206 original size:56 final size:56
Alignment explanation
Indices: 62133--62241 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 56
62123 ATTTTACAGG
* ** * * *
62133 TAAAATGATTTTTTATTTTAATTTGATCTTTAAACTTTTAAATATTTTAATTTTTC
1 TAAAATGATTTTTTATTTTAAATCAATCCTCAAACTTTTAAACATTTTAATTTTTC
62189 TAAATATGA-TTTTTATTTTAAATCAATCCTCAAACTTTTAAACATTTTAATTT
1 TAAA-ATGATTTTTTATTTTAAATCAATCCTCAAACTTTTAAACATTTTAATTT
62242 CATCTACAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 42 0.91
57 4 0.09
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (56 bp):
TAAAATGATTTTTTATTTTAAATCAATCCTCAAACTTTTAAACATTTTAATTTTTC
Done.