Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006623.1 Hibiscus syriacus cultivar Beakdansim tig00016273_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: 62834
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:372 original size:17 final size:16
Alignment explanation
Indices: 326--373 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
316 TCCTCCATTA
326 TTTTTTTATATATTTAC
1 TTTTTTTATAT-TTTAC
343 TTTTTTTATTATTTTA-
1 TTTTTTTA-TATTTTAC
359 TTCATTTTTATATTT
1 TT--TTTTTATATTT
374 ACTGCTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.07
17 17 0.61
18 9 0.32
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTATATTTTAC
Found at i:12211 original size:13 final size:13
Alignment explanation
Indices: 12193--12240 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12183 AGGCATGAGA
12193 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
12206 ATGGTGAT-G-AT
1 ATGGTGATGGAAG
12217 ATAGGTGATGGAAG
1 AT-GGTGATGGAAG
*
12231 ATGGCGATGG
1 ATGGTGATGG
12241 TATAGGCGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.10
12 7 0.24
13 16 0.55
14 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.44, T:0.25
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:12223 original size:25 final size:25
Alignment explanation
Indices: 12195--12263 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
12185 GCATGAGAAT
12195 GGTGATGGAAGATGGTGATGATATA
1 GGTGATGGAAGATGGTGATGATATA
* *
12220 GGTGATGGAAGATGGCGATGGTATA
1 GGTGATGGAAGATGGTGATGATATA
* *
12245 GGCG-T-GAAAATGGTGATGA
1 GGTGATGGAAGATGGTGATGA
12264 ACAGATAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.29
24 1 0.03
25 26 0.68
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.25
Consensus pattern (25 bp):
GGTGATGGAAGATGGTGATGATATA
Found at i:16250 original size:35 final size:35
Alignment explanation
Indices: 16180--16297 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 35
16170 ATGGTAATGG
* *
16180 GATGGTAATAATATAGGTGTGAGAATGGTGATGGAA
1 GATGGTGATGATATAGGTGTGA-AATGGTGATGGAA
* *
16216 GATGTTGATGATATAGGTGTGATATGGTGATGGAA
1 GATGGTGATGATATAGGTGTGAAATGGTGATGGAA
* * *
16251 GATGGTGATTATATAGGCGTGAAAATGTTGATGGAA
1 GATGGTGATGATATAGGTGTG-AAATGGTGATGGAA
16287 GATGGTGATGA
1 GATGGTGATGA
16298 ACAAATAGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 30 0.42
36 41 0.58
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.31
Consensus pattern (35 bp):
GATGGTGATGATATAGGTGTGAAATGGTGATGGAA
Found at i:24148 original size:15 final size:13
Alignment explanation
Indices: 24137--24174 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
24127 AAAAAAAAGC
24137 AAAAACAAAAAAA
1 AAAAACAAAAAAA
*
24150 AACAA-AAAAAAA
1 AAAAACAAAAAAA
24162 AAAAACAAAAAAA
1 AAAAACAAAAAAA
24175 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:24148 original size:16 final size:15
Alignment explanation
Indices: 24127--24174 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
24117 CTATTTTTTT
*
24127 AAAAAAAAGCAAAAA
1 AAAAAAAAACAAAAA
24142 CAAAAAAAAACAAAAA
1 -AAAAAAAAACAAAAA
24158 AAAAAAAAACAAAAA
1 AAAAAAAAACAAAAA
24173 AA
1 AA
24175 GCCAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACAAAAA
Found at i:24192 original size:1 final size:1
Alignment explanation
Indices: 24127--24174 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
24117 CTATTTTTTT
** * * *
24127 AAAAAAAAGCAAAAACAAAAAAAAACAAAAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24175 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:54245 original size:21 final size:21
Alignment explanation
Indices: 54219--54266 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
54209 TGGGAGCGTT
54219 TGGTGCATCGATGCATAAGGC
1 TGGTGCATCGATGCATAAGGC
54240 TGGTGCATCGATGCATAAGGC
1 TGGTGCATCGATGCATAAGGC
*
54261 TAGTGC
1 TGGTGC
54267 GTCGGTACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
TGGTGCATCGATGCATAAGGC
Found at i:54402 original size:45 final size:46
Alignment explanation
Indices: 54333--54439 Score: 137
Period size: 45 Copynumber: 2.3 Consensus size: 46
54323 GGTGCACTAA
* * * *
54333 GAGTGCATCGATGCATGAAGTGCATTCGACG-TTTCA-AACAAGCCT
1 GAGTGCATCGATGCATCAAATGCATTCGACGTTTTCATAA-AAACAT
* *
54378 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAATAT
1 GAGTGCATCGATGCATCAAATGCATTCGACGTTTTCATAAAAACAT
54424 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
54440 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 28 0.52
46 24 0.44
47 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
GAGTGCATCGATGCATCAAATGCATTCGACGTTTTCATAAAAACAT
Found at i:60572 original size:24 final size:24
Alignment explanation
Indices: 60540--60587 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
60530 ATGATGAGCT
60540 TTTTCCTGCAAGAACCGTCACGGG
1 TTTTCCTGCAAGAACCGTCACGGG
60564 TTTTCCTGCAAGAACCGTCACGGG
1 TTTTCCTGCAAGAACCGTCACGGG
60588 CTAGCAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (24 bp):
TTTTCCTGCAAGAACCGTCACGGG
Done.