Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009430.1 Hibiscus syriacus cultivar Beakdansim tig00113413_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: 336544
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:304422 original size:59 final size:59
Alignment explanation
Indices: 304342--304455 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 59
304332 TTGGTTAGGA
* *
304342 TCATATTATCGTGTTTGCCTTTTCATTACGACAAGGAGGGTTCGATAGGACACTTGGGG
1 TCATATTATCGAGTTTACCTTTTCATTACGACAAGGAGGGTTCGATAGGACACTTGGGG
* * *
304401 TCATATTATCGAGTTTACCTTTTCATTACTACTAGGAGGGTTCGATATGACACTT
1 TCATATTATCGAGTTTACCTTTTCATTACGACAAGGAGGGTTCGATAGGACACTT
304456 ATCCATCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (59 bp):
TCATATTATCGAGTTTACCTTTTCATTACGACAAGGAGGGTTCGATAGGACACTTGGGG
Found at i:308660 original size:47 final size:47
Alignment explanation
Indices: 308563--308664 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 47
308553 GGATTTAGAT
*
308563 TTATTATTTTATTAGGAATTAAAGATGAGTTAAAACATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATT--A-ATGAGTTAAAACATGATTTTTAGTTA
308613 TTATTATTTTTATTAGGAATT-A-GAGTTAAAACATGATTAGTTT-GTTA
1 TTATTA-TTTTATTAGGAATTAATGAGTTAAAACATGATT--TTTAGTTA
308660 TTATT
1 TTATT
308665 TTATTCATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
46 15 0.31
47 10 0.21
48 3 0.06
50 6 0.12
51 14 0.29
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (47 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACATGATTTTTAGTTA
Found at i:308977 original size:59 final size:59
Alignment explanation
Indices: 308902--309014 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
308892 TGGTTAGAGC
*
308902 CATATTATCAACTTTACCTTTTCATTGCGACTAGGAGGGTTCTATAGGACACTTGGGGT
1 CATATTATCAACTTTACCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTGGGGT
* * * *
308961 CATATTATCGAGTTTACCTTTTCATTGCTATTAGGAGGGTTCGATAGGACACTT
1 CATATTATCAACTTTACCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTT
309015 ATCCATCTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (59 bp):
CATATTATCAACTTTACCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTGGGGT
Found at i:314961 original size:216 final size:216
Alignment explanation
Indices: 314582--315012 Score: 727
Period size: 216 Copynumber: 2.0 Consensus size: 216
314572 GATCTCGTTA
* *
314582 TGTTACTTTCTTGGAGTGATATATGAGGTTTCTTGCTTTGTTGAATTTTCTTTCTTTTATATTTA
1 TGTTACTTTCTTGGAGTGACATATGAAGTTTCTTGCTTTGTTGAATTTTCTTTCTTTTATATTTA
* *
314647 TTTTACTTTAAATGTTTCGTTGAGTGTTGTGATTTTCATCATATTTGAACCAGGACAATTTTTAA
66 TTTTACTTTAAATGTTTCGTTCAGTGTTGTGATTTTCAGCATATTTGAACCAGGACAATTTTTAA
* *
314712 GACCTAATTGTATGGTTATACGTCAGTCTTTAAGCACTGAAGATACGAAAAAAGCTTACATTCAA
131 GACCTAATTGTATGGTTATACGTCAGTCTTTAAGAACTGAAGATACGAAAAAAGCTGACATTCAA
314777 AGAACAAAATTACTTCATTCG
196 AGAACAAAATTACTTCATTCG
* * * *
314798 TGTTTCTTTCTTGGAGTGGCATGTGAAGTTTCTTGCTTTGTTGAATTTTCTTTCTTTTATTTTTA
1 TGTTACTTTCTTGGAGTGACATATGAAGTTTCTTGCTTTGTTGAATTTTCTTTCTTTTATATTTA
* * *
314863 TTTTACTTTTAATGTTTCGTTCAGTGTTGTGATTTTCAGGATATTTGAACCAGGACAATTTTTTA
66 TTTTACTTTAAATGTTTCGTTCAGTGTTGTGATTTTCAGCATATTTGAACCAGGACAATTTTTAA
314928 GACCTAATTGTATGGTTATACGTCAGTCTTTAAGAACTGAAGATACGAAAAAAGCTGACATTCAA
131 GACCTAATTGTATGGTTATACGTCAGTCTTTAAGAACTGAAGATACGAAAAAAGCTGACATTCAA
* *
314993 AGAACAAATTTATTTCATTC
196 AGAACAAAATTACTTCATTC
315013 CTGATGATAT
Statistics
Matches: 200, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 200 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (216 bp):
TGTTACTTTCTTGGAGTGACATATGAAGTTTCTTGCTTTGTTGAATTTTCTTTCTTTTATATTTA
TTTTACTTTAAATGTTTCGTTCAGTGTTGTGATTTTCAGCATATTTGAACCAGGACAATTTTTAA
GACCTAATTGTATGGTTATACGTCAGTCTTTAAGAACTGAAGATACGAAAAAAGCTGACATTCAA
AGAACAAAATTACTTCATTCG
Found at i:321310 original size:59 final size:59
Alignment explanation
Indices: 321230--321342 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
321220 TGGTTAGAGC
* *
321230 CATATTATCTACTTTGACTTTTCATTGCGACTAGGAGGGTT-TGATAGGACACTTGGGGT
1 CATATTATCAACTTTGACTTTTCATTGCGACTAGGAGGGTTCT-ATAGCACACTTGGGGT
* *
321289 CATATTATCAAGTTT-ACCTTTTCATTGTGACTAGGAGGGTTCTATAGCACACTT
1 CATATTATCAACTTTGA-CTTTTCATTGCGACTAGGAGGGTTCTATAGCACACTT
321343 ATCCATCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 1 0.02
59 46 0.96
60 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (59 bp):
CATATTATCAACTTTGACTTTTCATTGCGACTAGGAGGGTTCTATAGCACACTTGGGGT
Found at i:324846 original size:21 final size:23
Alignment explanation
Indices: 324822--324867 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
324812 AATATATGAT
324822 GATTTATTATCT-TTAGG-ATTA
1 GATTTATTATCTATTAGGAATTA
*
324843 GATTTATTATTTATTAGGAATTA
1 GATTTATTATCTATTAGGAATTA
324866 GA
1 GA
324868 GTTAAGACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (23 bp):
GATTTATTATCTATTAGGAATTA
Found at i:336417 original size:21 final size:21
Alignment explanation
Indices: 336388--336427 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
336378 AATATATGAT
336388 GATTCATTATCTT-TTAGGATA
1 GATTCATTAT-TTATTAGGATA
*
336409 GATTTATTATTTATTAGGA
1 GATTCATTATTTATTAGGA
336428 ATTAGAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (21 bp):
GATTCATTATTTATTAGGATA
Done.