Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005096.1 Hibiscus syriacus cultivar Beakdansim tig00011459_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: 58192
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:5594 original size:12 final size:12
Alignment explanation
Indices: 5579--5604 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5569 CCAGGCAAGT
5579 GCAGCGGCACCA
1 GCAGCGGCACCA
5591 GCAGCGGCACCA
1 GCAGCGGCACCA
5603 GC
1 GC
5605 TCCGGCTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.35, T:0.00
Consensus pattern (12 bp):
GCAGCGGCACCA
Found at i:8604 original size:2 final size:2
Alignment explanation
Indices: 8591--8643 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
8581 ATTAATGTGT
*
8591 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8633 TA TA TA TA TA T
1 TA TA TA TA TA T
8644 TACATGTGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8894 original size:8 final size:9
Alignment explanation
Indices: 8881--8933 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
8871 TGACTGTCGA
8881 TTTTTTTCT
1 TTTTTTTCT
8890 TTTTTTTCT
1 TTTTTTTCT
8899 TTTTTATATCAT
1 TTTTT-T-TC-T
*
8911 ATATTTTT-T
1 -TTTTTTTCT
8920 TTTTTTTCT
1 TTTTTTTCT
8929 TTTTT
1 TTTTT
8934 AATAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 6 0.16
9 21 0.57
10 1 0.03
11 3 0.08
12 2 0.05
13 4 0.11
ACGTcount: A:0.09, C:0.08, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:12185 original size:24 final size:24
Alignment explanation
Indices: 12152--12199 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
12142 AGATCGGATC
*
12152 ATGTTTGCATTTAAGATGAGAAAT
1 ATGTTCGCATTTAAGATGAGAAAT
12176 ATGTTCGCATTTAAGATGAGAAAT
1 ATGTTCGCATTTAAGATGAGAAAT
12200 CTGTGACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (24 bp):
ATGTTCGCATTTAAGATGAGAAAT
Found at i:12446 original size:16 final size:14
Alignment explanation
Indices: 12411--12445 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
12401 ATATATATTT
*
12411 TATTTTATTATATA
1 TATTTTATTAAATA
12425 TATTTTATTAAATA
1 TATTTTATTAAATA
12439 TGATTTT
1 T-ATTTT
12446 TTTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATTTTATTAAATA
Found at i:17315 original size:15 final size:15
Alignment explanation
Indices: 17288--17323 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
17278 TGCAGGGAGA
17288 TTTCTGCTTTATTTG
1 TTTCTGCTTTATTTG
17303 TATTCTG-TTTATTTG
1 T-TTCTGCTTTATTTG
17318 TTTCTG
1 TTTCTG
17324 GTAATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.08, C:0.11, G:0.14, T:0.67
Consensus pattern (15 bp):
TTTCTGCTTTATTTG
Found at i:20291 original size:6 final size:6
Alignment explanation
Indices: 20282--20311 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
20272 TAAGGTTTAT
20282 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
20312 AACTTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
GTTTGA
Found at i:34766 original size:43 final size:42
Alignment explanation
Indices: 34610--34790 Score: 197
Period size: 43 Copynumber: 4.3 Consensus size: 42
34600 TAACGATATA
* * * * ** *
34610 TAGCGGCGTTTTTTCAACAACCGCCGCAAAAGGTGCTGATATT
1 TAGCGGCGTTTTTT-TACAAACGCAGCAATAGGTTTTGACATT
* *
34653 TAGCGGCG--TTTGTACAAACGCCGCAATAGGTTTTGACATT
1 TAGCGGCGTTTTTTTACAAACGCAGCAATAGGTTTTGACATT
*
34693 TCGCGGCGTTTTTTTACAAACGCAGCAATAGGTTTTGACATT
1 TAGCGGCGTTTTTTTACAAACGCAGCAATAGGTTTTGACATT
* *
34735 TAGCGGCGTTTGTTTTATAACCGTCA-CAATAGGTTTTGACATT
1 TAGCGGCGTTT-TTTTACAAACG-CAGCAATAGGTTTTGACATT
*
34778 TAGCGGTGTTTTT
1 TAGCGGCGTTTTT
34791 AGGATAAAAC
Statistics
Matches: 120, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 29 0.24
41 3 0.03
42 42 0.35
43 44 0.37
44 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (42 bp):
TAGCGGCGTTTTTTTACAAACGCAGCAATAGGTTTTGACATT
Found at i:41373 original size:40 final size:41
Alignment explanation
Indices: 41287--41378 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 41
41277 GTTTTTTGTT
* * * *
41287 AAAACGCCACTATATGTCCAATATATTGCAGCGTTTGTACAT
1 AAAACGCCACTAGA-GTACAATATATTGCAGCGTTTATACAA
*
41329 AAAACGCCACTAGA-TACAATAATATTGCGGCGTTTAT-CAA
1 AAAACGCCACTAGAGTACAAT-ATATTGCAGCGTTTATACAA
41369 AAAACGCCAC
1 AAAACGCCAC
41379 ACCATTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 17 0.39
41 14 0.32
42 13 0.30
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (41 bp):
AAAACGCCACTAGAGTACAATATATTGCAGCGTTTATACAA
Found at i:44668 original size:17 final size:17
Alignment explanation
Indices: 44646--44679 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44636 CACACATATA
*
44646 TTAATAATATAAAATTT
1 TTAATAAGATAAAATTT
*
44663 TTAATACGATAAAATTT
1 TTAATAAGATAAAATTT
44680 CATGGTAGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAATAAGATAAAATTT
Found at i:45067 original size:24 final size:23
Alignment explanation
Indices: 45026--45074 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
45016 ATTTTTTATA
*
45026 TATTATAATATTACATATTTAAT
1 TATTATAATATTACATATTAAAT
* *
45049 TATTAATAATTTTATATATTAAAT
1 TATT-ATAATATTACATATTAAAT
45073 TA
1 TA
45075 AACTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTATAATATTACATATTAAAT
Found at i:45199 original size:17 final size:17
Alignment explanation
Indices: 45163--45199 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
45153 TAAGTTTTAT
* *
45163 ATTTAAAAAAATTAACA
1 ATTTAAAAAAAATAAAA
45180 ATTTAAAAAAAATAAAA
1 ATTTAAAAAAAATAAAA
45197 ATT
1 ATT
45200 AGATACCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTTAAAAAAAATAAAA
Found at i:49163 original size:9 final size:9
Alignment explanation
Indices: 49149--49182 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
49139 TGGTTCGTGC
49149 TATTGTTAT
1 TATTGTTAT
49158 TATTGTTAT
1 TATTGTTAT
* *
49167 TGTTATTAT
1 TATTGTTAT
49176 TATTGTT
1 TATTGTT
49183 GTTGTTGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (9 bp):
TATTGTTAT
Found at i:49177 original size:18 final size:18
Alignment explanation
Indices: 49154--49188 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49144 CGTGCTATTG
49154 TTATTATTGTTATTGTTA
1 TTATTATTGTTATTGTTA
*
49172 TTATTATTGTTGTTGTT
1 TTATTATTGTTATTGTT
49189 GTTGTTGTTT
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:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTATTATTGTTATTGTTA
Found at i:49184 original size:15 final size:15
Alignment explanation
Indices: 49149--49185 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
49139 TGGTTCGTGC
*
49149 TATTGTTATTATTGT
1 TATTGTTATTATTAT
49164 TATTGTTATTATTAT
1 TATTGTTATTATTAT
*
49179 TGTTGTT
1 TATTGTT
49186 GTTGTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.68
Consensus pattern (15 bp):
TATTGTTATTATTAT
Done.