Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000977.1 Hibiscus syriacus cultivar Beakdansim tig00001953_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: 52265
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:9613 original size:18 final size:18
Alignment explanation
Indices: 9587--9621 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9577 CATGAAGTAT
9587 ATCAACCTCTTATTGAAA
1 ATCAACCTCTTATTGAAA
*
9605 ATCAGCCTCTTATTGAA
1 ATCAACCTCTTATTGAA
9622 GACGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCAACCTCTTATTGAAA
Found at i:11305 original size:76 final size:76
Alignment explanation
Indices: 11199--11350 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
11189 AAAACGTTGT
11199 CCAAAGTAGCTTTCACAATGTTTCGTGAGAGAGTGAATGTGTGTTTGCTGAAGAAATGAGAAGAA
1 CCAAAGTAGCTTTCACAATGTTTCGTGAGAGAGTGAATGTGTGTTTGCTGAAGAAATGAGAAGAA
11264 GAAGAAACAGG
66 GAAGAAACAGG
11275 CCAAAGTAGCTTTCACAATGTTTCGTGAGAGAGTGAATGTGTGTTTGCTGAAGAAATGAGAAGAA
1 CCAAAGTAGCTTTCACAATGTTTCGTGAGAGAGTGAATGTGTGTTTGCTGAAGAAATGAGAAGAA
11340 GAAGAAACAGG
66 GAAGAAACAGG
11351 GAGAATGTTG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (76 bp):
CCAAAGTAGCTTTCACAATGTTTCGTGAGAGAGTGAATGTGTGTTTGCTGAAGAAATGAGAAGAA
GAAGAAACAGG
Found at i:14703 original size:26 final size:26
Alignment explanation
Indices: 14646--14700 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
14636 TTTAAAAAAC
*
14646 AAACTTGAAAATAAAAGAAAAATAAA
1 AAACTTGAAAATAAAAGAAAAAGAAA
*
14672 AAACTTGAAAAGTAAAATAAAAGAGAAA
1 AAACTTGAAAA-TAAAAGAAAA-AGAAA
14700 A
1 A
14701 CTTTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.15
Consensus pattern (26 bp):
AAACTTGAAAATAAAAGAAAAAGAAA
Found at i:18746 original size:21 final size:21
Alignment explanation
Indices: 18722--18765 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
18712 GGAAGCCATT
18722 GATGAAAGATTGGAACTTTGG
1 GATGAAAGATTGGAACTTTGG
18743 GATGAAAGATTGGAACTTTGG
1 GATGAAAGATTGGAACTTTGG
18764 GA
1 GA
18766 AGATGAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (21 bp):
GATGAAAGATTGGAACTTTGG
Found at i:19194 original size:19 final size:20
Alignment explanation
Indices: 19170--19215 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19160 GTTTGAGTCT
19170 TGATTTTTGACAT-TATTTA
1 TGATTTTTGACATATATTTA
* *
19189 TGATTTTTTATATATATTTA
1 TGATTTTTGACATATATTTA
*
19209 TAATTTT
1 TGATTTT
19216 AAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
TGATTTTTGACATATATTTA
Found at i:19324 original size:12 final size:12
Alignment explanation
Indices: 19286--19325 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
19276 TTTCCCGTCC
19286 CCGTCCCCGTAT
1 CCGTCCCCGTAT
*
19298 CCATCCCCGTAT
1 CCGTCCCCGTAT
19310 CCGTCCCCGTAT
1 CCGTCCCCGTAT
19322 CCGT
1 CCGT
19326 ATCCGTGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.10, C:0.50, G:0.15, T:0.25
Consensus pattern (12 bp):
CCGTCCCCGTAT
Found at i:19325 original size:6 final size:6
Alignment explanation
Indices: 19316--19404 Score: 133
Period size: 6 Copynumber: 14.8 Consensus size: 6
19306 GTATCCGTCC
* *
19316 CCGTAT CCGTAT CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT
1 CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT
* * *
19364 CCGTGT CCGTGT CCGTGT CCGTAT CCGTAT CCGTAT CCGTG
1 CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT CCGTGT CCGTG
19405 CAACATAGCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.06, C:0.34, G:0.28, T:0.33
Consensus pattern (6 bp):
CCGTGT
Found at i:19325 original size:18 final size:18
Alignment explanation
Indices: 19304--19404 Score: 130
Period size: 18 Copynumber: 5.6 Consensus size: 18
19294 GTATCCATCC
** *
19304 CCGTATCCGTCCCCGTAT
1 CCGTATCCGTGTCCGTGT
19322 CCGTATCCGTGTCCGTGT
1 CCGTATCCGTGTCCGTGT
*
19340 CCGTGTCCGTGTCCGTGT
1 CCGTATCCGTGTCCGTGT
*
19358 CCGTGTCCGTGTCCGTGT
1 CCGTATCCGTGTCCGTGT
* * *
19376 CCGTGTCCGTATCCGTAT
1 CCGTATCCGTGTCCGTGT
19394 CCGTATCCGTG
1 CCGTATCCGTG
19405 CAACATAGCA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 75 1.00
ACGTcount: A:0.06, C:0.36, G:0.27, T:0.32
Consensus pattern (18 bp):
CCGTATCCGTGTCCGTGT
Found at i:21436 original size:16 final size:16
Alignment explanation
Indices: 21415--21446 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21405 AAGAAGATTC
21415 ACTTAGTGTGATATAA
1 ACTTAGTGTGATATAA
21431 ACTTAGTGTGATATAA
1 ACTTAGTGTGATATAA
21447 GTAATGTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
ACTTAGTGTGATATAA
Found at i:38436 original size:20 final size:20
Alignment explanation
Indices: 38407--38449 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
38397 ATTCCACCAC
38407 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
38427 ATGCATCTATGTGCTCCTAA
1 ATGCAACTATATGCTCCTAA
38447 ATG
1 ATG
38450 AGTTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:40604 original size:21 final size:20
Alignment explanation
Indices: 40576--40614 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40566 CACTGCAGGA
40576 ATTTATGG-TCTCGACAAAAT
1 ATTTATGGCT-TCGACAAAAT
40596 ATTTCATGGCTTCGACAAA
1 ATTT-ATGGCTTCGACAAA
40615 GACTTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTATGGCTTCGACAAAAT
Found at i:45188 original size:13 final size:14
Alignment explanation
Indices: 45170--45203 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
45160 ACACAGTTTC
*
45170 TTTTCCTTTAAA-A
1 TTTTCCCTTAAATA
45183 TTTTCCCTTAAATA
1 TTTTCCCTTAAATA
45197 TTTTCCC
1 TTTTCCC
45204 CTCAACGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTCCCTTAAATA
Done.