Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004052.1 Hibiscus syriacus cultivar Beakdansim tig00008864_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: 63989
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7238 original size:88 final size:88
Alignment explanation
Indices: 7089--7252 Score: 301
Period size: 88 Copynumber: 1.9 Consensus size: 88
7079 CCACAGTTAA
*
7089 GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGCCATGACAAA
1 GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGACATGACAAA
7154 ATGCTTTATGCGACATATTAATC
66 ATGCTTTATGCGACATATTAATC
* *
7177 GAATGGGACTAAGAGCATTTGACTTATTTGGTGCATTAACAAGTAATTTCCTTTGACATGACAAA
1 GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGACATGACAAA
7242 ATGCTTTATGC
66 ATGCTTTATGC
7253 TTGGTTTACT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (88 bp):
GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGACATGACAAA
ATGCTTTATGCGACATATTAATC
Found at i:14011 original size:17 final size:18
Alignment explanation
Indices: 13984--14017 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13974 TACTCAAATA
*
13984 ATAGTATAATTGATATAT
1 ATAGTATAATTAATATAT
14002 ATAG-ATAATTAATATA
1 ATAGTATAATTAATATA
14018 AGGATAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
ATAGTATAATTAATATAT
Found at i:14933 original size:2 final size:2
Alignment explanation
Indices: 14928--14966 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
14918 AAAATAGAAG
*
14928 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14967 CAATTTGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16466 original size:20 final size:19
Alignment explanation
Indices: 16416--16469 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
16406 CATTGGATTT
*
16416 TTGTTGAT-ATGGAAATGA
1 TTGTTGATGATGAAAATGA
16434 TTG-TGAATGGATGAAAATGA
1 TTGTTG-AT-GATGAAAATGA
16454 TGTGTTGATGATGAAA
1 T-TGTTGATGATGAAA
16470 TTATGCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
20 17 0.57
21 4 0.13
22 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (19 bp):
TTGTTGATGATGAAAATGA
Found at i:17425 original size:27 final size:26
Alignment explanation
Indices: 17386--17448 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
17376 GAACAAAAAT
*
17386 ATAATTTGCATAAACAGTGAGT-TTAAA
1 ATAA-TTGAATAAACA-TGAGTATTAAA
* *
17413 AGTTATTGAATAAATATGAGTATTAAA
1 A-TAATTGAATAAACATGAGTATTAAA
17440 ATAATTGAA
1 ATAATTGAA
17449 CAATAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 12 0.40
27 16 0.53
28 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (26 bp):
ATAATTGAATAAACATGAGTATTAAA
Found at i:25925 original size:18 final size:18
Alignment explanation
Indices: 25901--25942 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
25891 ATATTATCAA
*
25901 TAAAAAATATAAAAAATACT
1 TAAAACATAT-AAAAATA-T
25921 TAAAACATATAAAAATAT
1 TAAAACATATAAAAATAT
25939 TAAA
1 TAAA
25943 TGCTGTAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 7 0.33
20 9 0.43
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAACATATAAAAATAT
Found at i:46294 original size:12 final size:12
Alignment explanation
Indices: 46274--46317 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
46264 TTGTGCTGCG
*
46274 GTATGTATGCAT
1 GTATATATGCAT
*
46286 GTATATATGTAT
1 GTATATATGCAT
*
46298 GTATGTAT-CAT
1 GTATATATGCAT
46309 GTATATATG
1 GTATATATG
46318 TTAATGAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (12 bp):
GTATATATGCAT
Found at i:46296 original size:16 final size:16
Alignment explanation
Indices: 46275--46305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46265 TGTGCTGCGG
46275 TATGTATGCATGTATA
1 TATGTATGCATGTATA
*
46291 TATGTATGTATGTAT
1 TATGTATGCATGTAT
46306 CATGTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.48
Consensus pattern (16 bp):
TATGTATGCATGTATA
Found at i:46313 original size:23 final size:24
Alignment explanation
Indices: 46274--46318 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
46264 TTGTGCTGCG
46274 GTATGTATGCATGTATATATGTAT
1 GTATGTATGCATGTATATATGTAT
46298 GTATGTAT-CATGTATATATGT
1 GTATGTATGCATGTATATATGT
46319 TAATGAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (24 bp):
GTATGTATGCATGTATATATGTAT
Found at i:47295 original size:19 final size:19
Alignment explanation
Indices: 47263--47300 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
47253 GGGAGGTTTT
*
47263 AATTAATTTTATTAGTTAAA
1 AATTAATTTGATTA-TTAAA
47283 AATT-ATTTGATTATTAAA
1 AATTAATTTGATTATTAAA
47301 TATATTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AATTAATTTGATTATTAAA
Found at i:53361 original size:72 final size:72
Alignment explanation
Indices: 53256--53394 Score: 215
Period size: 72 Copynumber: 1.9 Consensus size: 72
53246 GCTGTACAAC
* *
53256 TTTTCCGAGACGGTTCTCGTAAACTCCTTTGATGGAGTTGTGGCGGAGCTTGATACCTTCGGGCT
1 TTTTCCGAGACGGTTCTCCTAAACTCCTTTGATGGAGTAGTGGCGGAGCTTGATACCTTCGGGCT
53321 GCTCACT
66 GCTCACT
* * * * *
53328 TTTTCTGAGATGGTTCTCCTAAATTCTTTTGATGGAGTAGTGGTGGAGCTTGATACCTTCGGGCT
1 TTTTCCGAGACGGTTCTCCTAAACTCCTTTGATGGAGTAGTGGCGGAGCTTGATACCTTCGGGCT
53393 GC
66 GC
53395 AAATGTGTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (72 bp):
TTTTCCGAGACGGTTCTCCTAAACTCCTTTGATGGAGTAGTGGCGGAGCTTGATACCTTCGGGCT
GCTCACT
Found at i:62394 original size:31 final size:31
Alignment explanation
Indices: 62356--62441 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 31
62346 GTTTCATAAG
*
62356 TTACAAAATGATCATTAAACTTACCAAACTA
1 TTACAAAATGGTCATTAAACTTACCAAACTA
* * * * *
62387 TTACAAAATGGCCGTTAAAACTGATCAAACTG
1 TTACAAAATGGTCATT-AAACTTACCAAACTA
*
62419 TTACAAAATGGTCTTTAAACTTA
1 TTACAAAATGGTCATTAAACTTA
62442 TCGAATTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (31 bp):
TTACAAAATGGTCATTAAACTTACCAAACTA
Done.