Hello, As stated in the prior response, the chromFa.zip genomic is masked. The genomic version used for web Blat is unmasked.
I took both of your sequences (NM_182762 and the genomic fragment chr7:20140804-20141600), pasted them into the same query, and ran a web Blat. From the results, I can see that the NM_182762 sequence overlaps with multiple repeat masker regions. This may be causing the differences in scores, etc. in your output. However, the best hit is still in the same location for both plus they each have short high identity matches to other locations (using web Blat, but they are short and not significant, meaning = annotated repeats). Please see these Session links for the evidence: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Jennifer&hgS_otherUserSessionName=Re%3A%20%5BGenome%5D%20question%20about%20Genome%20data%20%2D%20seq%20one%20and%20two%20primary%20hits http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Jennifer&hgS_otherUserSessionName=Re%3A%20%5BGenome%5D%20question%20about%20Genome%20data%20%2D%20seq%20two%20repeat%20hit%20example Recommendations ... use unmasked genomic and follow these guidelines for an approximation (not exact duplication) of web Blat type results: http://genome.ucsc.edu/FAQ/FAQblat If I have failed to understand your question or have left parts unanswered, please let me know, after you have reviewed the data above. Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Wayne wrote: > Dear colleague, > > I did BLAT search for the following sequence > > > >> NM_182762 6276 >> > AACAAAGCGUGUGUUUUUGAUGGGAGGGAAAAUGAGGUAAUGGUGUGUGU > GUGUGUGUGUCUGUGUGUGUCUGUGUGUGUCUCUGUGUGUCUGUGUGUGU > GUGUCUGUGUGUGUGUGUCUGUGUGUGUGUGUGUGUGUGUGUAGGAAAGA > AAGAAUCUCAGAAAAGCAUUAUAUUAAUUUUCUUCAUGCUCAAAACCAGU > UUUUUUUUCCUGAUGAAAGCACAGCCUAACUGAUAACCAAGAUGGGUUUU > AUCCUCAAAUAUGUAUUUUUGUGUAUGUUUCAAAUACAAGUAUUAGGCUG > CUUUGUUCUUAGAAAGGAAAGAAAAAAGAAAAGUGCCCUCUCUCUCUUUC > AGUGUUAUUUUAAAUUUACUAAGUCAAAGCUGUUUGAAUAAUUACAUCAC > ACAGAUAUCUGGGUAAACUAGAGACUAUCAACAUGAUCAAGGCAGUGUUC > CCAGGAGGCAGCUAGAAAGAGGGGAAGCAAGCACACACCCUGUGGCCAGU > CACGGCUGCCCGCUUUCCACACCUGACCUCUUCAGUUCAUCAGUGGGGUU > CACCAGCAUCACCCCCAUUUUUCAUGGGGAGAAACUCAGAAGUGGAGAGA > ACGUCUGAGGCUACAUAGCCAGUACAAAGUAGGUUUUCUGCUUGAAAAAC > CUGUUUCUAUUUCUUUUUAAAAAAUCAUACUGCAUAACAGAAUAGUAAAA > ACAAAAUGCGUGUUAAGACUUACAGGGAAACAGUUGCCGUUUCAUUUUAA > GUGAGACUUGCUACUCUUUUUCAUCGUCUCUUGAAAGACUGACAGAAGGA > AAAUAUGACUUAUCAGAAAUCUGUUGUCUGCAUGCAUGGACCUAGUGUUU > UCAUCAGCUCCCUUCAGCAUCUUGGGACCUCUCUAAUCCUGCCUAAUUUG > GGACUUUUUCUGCAGGAUUGUAAUGUAAAAUAGUUCUUUAGCUCUUGGAG > AUUUUUAAUAAUACGAGUUAUUAAAAACCACCACCACCAGAAACUUGAUU > AACUUGAUUACCCUGUUGAGUAGAGAGGUCUUAACCACCGAAAACACUGA > UAUCUUUAUGUUGGCAUGCUCAUGCAAACACAUGUGUGUGUGUGUGUGUG > UGUGUGUGUGUGUGUGUGUACCACAGUGUUUUAUAAAGCACAGCCUAAUU > GAUUAUAUAGGACAAAAAUUGUAUAGGACCCUGGGUCAGUAUAAAUGCUA > AUGGCUGACAAAGUUCACAAAGAGAUGUAUUUUGCUUACUCCUCUGUUCA > AUCCUCUGGUUGCCUGCCAGUGUUUAUGUGUGUAUUUGGACAGACAUUCA > UUUAUUGUCAUUCAGUCAAUAGGUAGAGUAUAUGUGUCUAUUUUUUGGCA > GGCAUAUAGAUGCUUGAGGCUAAUGGGAAAAAACCAGCAUGAACUCUGAC > UUUAGUAGUGCUAAGUAAUAGAUAAUUUUAAAAAAUGACACCGUUAAAUA > GAAAAUGGCAUGCAUACUAACAGUUGCAAUGGAGAGGCUGUGAUGCUACG > AGAUAUAAACGUAGAGAUGCCAUCAUGUGAAACUGGAAGUGGGGGUGGGU > CAGGGAAAUUUGUUCUUGGAAAGAAAUAAUGAACCUCAAGGAAGAGUAGG > CAUUGUCCUGGUGUGGUGGGGUGUAAGCGGUGAUCCCACAAAGCACUGAA > GCUCUUAGAUGGGUGGGAGCUGAAUAGGUGCAGAUAGCAGGGGUGAAGGA > GUGAAAGGAUAAAAGAUUCAAGGUUGAGAUGAGGAUGGAGCAAGAAGAAG > CCACAUUAGGGCCAUUAAGGCUGCUAGAAUUUAGAAAGAAAACACACAGC > CUCAAAGAAAUGUGGGUAAGCCAAAGAAGGAUUUUGUUUUGGGAACCUGA > AUAAAAGAUGUCCAUUUGGCUAAAAAGUAAAAGCAGAAUCUUUUUAGGGC > UUUUAAUAUACCCACCCUGGGAUAUUUGGUAUGCUGGCAAUGGUAAUUCA > AAUUGGCGUUUAAGAAUAAUCUUGGCCGGGCGCGAUGGCUCAUGCCUGAA > AUCCCAGCACUUUGGGAGGCCGAGGCGGGCAGAUCACUAGGUCAGGAGAU > CGAGACCAUCCUGGCUAACGCGGUGAAACCCCGUCUCUACUAAAAAUACA > AAAAAUUAGCCGGGCGUGGUGGCAGGCGCCUGUAGUCCCAGCUACUCAGG > AGGCUGAGGCAGGAGAAUGGCGUGAACCCGGGAGGCGGAGCUUGCAGUGA > GCCGAGUUCAUGCCACUGCACUCCAGCCUGGGUGACAGGCUGUCUCAAAA > AAAAAAAAAGGAAUAAUCUGUACGGCUUUCAGUAUUUAUAUUUGAUUAUA > AGGGAACACAGCCUGACCAAAUAAUUAUGUAUACACAUUCAAGGACAGAA > UUUAUUUUAAUUAAAAAUAAAUUAUGAGAGAAGGAAAAAAAAGCACAGUU > UUUACUUUCAGAACACAGUCCUUUUUUGUGGUGAUUUUGCUUUCUUUAGA > ACAUUCUUGGAAUCUUAUUAACAUGUCAGCUAACCAGAGAAUUUUGGGAA > GGGAUAGUGGGGAUUAAUAACUGGGUUUUUCCAGGCUCCAAGAUCUAAGA > AGACAGAGAUCUUGUUAGCUGAUUAGUGUAGUAAGAUUAAAUAAAUAAUU > UAAGGUUUACAUUGCAUCAUGUAUUAUGAUUGUGAUUGAGAAUAAUAAGA > GUUUAAAAAAAUGAAAAACAAGAUCUCUGUAAUUUGAGGAUGAAACAAUG > GUUCUAAUAUUAAUACACACAAAUAUAUUUUAUAAUCUUGUAACAAAUCC > UUCCAGGGGAAAUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUGAGCCAGA > GUCUGGCUCUGUUGCCCAGACUGGAGUGCGGUGUUUCAAUCUUGACUCAC > UGCAACCUCCACCUCCUGGGUUCAAAAGAUCCUUCUGCCUCCGCCUCCCA > AGUAGCUGGGAUUACAGGCAUGCACCACCUUGUCCGGGUAAUUUUUGUAU > UUUUAGUGGAGACAAGGUUUUACCAUUUUGGCCAGACUGGUCUGGAACUC > CUGACCUCAGGUCAUCCACCUGCCUCGGCCUCCCAGAGUGCUAGGAUUAC > AGGCAUGAGCCACUGCUCCCAGCCUUCCAGAGGAAUUUUAAGCCCAUGUC > CAAACAUUCUGUUUGUAUAAAUAUAUUCUAAUUUUUAAAUAAAUAGUUUC > UACUUUUCUGAACUUUAUAUUUUUUCUUGCUAUAAUGGAUUUUCAUAAUC > AGAAAAGAUUAAAUUAGUAAUCAUGAAUUGCCUUCAAUAUUUGGCAGUAA > GUCAAUGAAAUAAUAAGGCACUUAUAUACCAUCUUUGACAUCAUUAAAAG > UAUCAAAUCCCAUUAAUCUAAAACUUCUUUAAGCAUUUUGAAAGCAGAAA > AUGUUUACAUGGUUCUUUCAGUUCCUCAGGCUUUUUGUCUAAUGAUGCGU > GACUUAGGAUAAGAUUUGAAUUAAGUGCCCAGCUUGAAACAUAAUAAUUU > UUCUGUAUAAGCCACAGAUCCUCUACCUCCUUUGUGUUAAAGCCUUUAUA > UGAAACAAUUAAGUAGAAGCAUUCAAUAGUGUGUCAUUAACUGUUCAUAC > UAAUAAAUGGAUACAGCACAUUUUCAUGGCCUGUAAUGUAGAACAUACUA > UAUAAAGUUCUCAGUUUGGGGAUGACUAGGUUUCUGGAAGGAAUAGAAUG > CUAAAUCAAUGGAUGGCAUUGGGCUGAGAAACACUGCUGCUACUAAUCAG > CCUUGAAUGUGUAAUGUGAACAUGCAAAAGAGAACAUGCAUACACUCAAA > UUUGUACAAUGCUAUAACUGGAAGUUGAAGGACUUGAAUUUUUAUAUUGU > GCUAUUGUUAUGUUUUCUGUAAUUGUUUAUAUCUAAGGAAUUUUUGAGGU > AAUAUAAAAGAAAAAGAGAAUAAUGAACAAUGAUGUCACUGGAGGGUUUU > UACAUUAAAUUAGAUCAUUUUUCUUCUUAUUCACAAUAAUAAUCUUAAUC > UUUAAGAAUUAAUUAUAAUUUAAUAUUAUAAUUCAUAAUCUUUAAGAAUU > AAUAAUUAUAAUUUAAUAUUAUAAUUAAUAAUCUUUAAGAAUUAAUAAAU > AUUAUAAUUAAUAAUCUUUAAGAAUUAAUAAUUACAAUUAAUAAUUAAUA > AUAAUCUUAAUCUUUAAGAAUUAAUAAUAAUCCUUAAUCGCAAUAAUAAU > CGCAAGGAGGAGAAGUAAGUCCCUCCUCCUUCUGUAUGAACUUUUCUCCC > ACAUGCUGCUGUAUGGUUUAGUGAGAGUGAAGUUCUAAAGAACAUAUGAU > UGGUGGGAUAAUCCAAAGACAUUUUUUCAGAAUCAAAUGGCAUGUCGAAG > GUUUGUUUCUUGCAUAUGUAUUUACUGGUCCACAGCACAAAAUAAAGUGA > CCACAUAUACAUAGGAAAGUUGAAUUUGUACACAUACAGCAUCUGAAAUG > UAUCUGAUGUUCAGCAUCAAGAUUUCACUGAACAUUGUAGAAAUGUGUAU > CUUUUGCAUGUAUAUUUUACAUUGAUUUUCUAUUUAUGUACAUCUAGAAA > GUUUUAACCCUAAUAAAUAGUUUUGUAAUUUUGAAUAAUAGUGUCAGUUU > AUAUGUGAGGGAGUAGAGACAGAGAGGUUAGCACUGGAUAAUAAUUAGUA > AGGCCAAAGGAGAAAAUUUCAUAGAAAAUAUUGUUGUUGUCAUAAUGAGU > ACAGCAUGAAAGGCUUCCUCUACAAGACACUAGUCAAAGAGUUGAGAGCU > GCGGUUUCUAAUCUUUGUCCAUUACUCCCUUACUCCCUAUGAGACUGUGG > ACCUGUCACUUGGCCUCUCUGGUCUUCAGUUUUCUCACCAGUAAAACAAG > GAACUUGAACCAAAUGACCUCUAGUGUUCCCCUUGGGUUUAAAUGUCUAU > AAAUGUUCAAUGACUAGAAUGUAUUGCGUUUUUCUUUAUUCUUUUUGCUU > UGAGAAAAGAGAAUGUGAUUUAAGAGUAAUAAUUUGAAUACCAAUUAUCC > ACAUUAAAAUUGUGUCCUCUAUGUGUAAGGCAUAGCACAUUUAGCACACA > UACAUAAGCACACUAAGCACCUUACAAAUAUCCUCAUUUAUUCUUUACAU > AAUCUUUUGAAAUUGAUUAUGUAAUACACACUGUUUUUGAACAAUUGGUG > ACUUCCAGCUGUUUAAAACAAACUACAGUAUGGUGCUUGAGUACUGACUU > AGGAGGUCAGCAUUGGUUUCACUAGGAGCUUCUCAAAGCACGCUGCCAAA > CAUGCUCCAGUCUCAUUGUCAAGGCCUUAGACCAGGCAAUCAUUACGGCA > GUGGUUCUUCAACUUCAGCAGCAGCAAAACGAUCUGGCGGGGGCUUGGUG > AAACAGACUGCUGGGCUCGACCACCAGAAUUUCUCAUUCAGAGGGUCUGG > CCUGAUCACUUGCAUUUCUAAUCACUUCCCAGGUGAUGCAGAUGUUUCUG > GUCCAGGGACCCCAGUUUGAGAACCACUGUAUUAAAAUUUCCUUCAUCUC > UAUAGAAAUGGAAAGAUUUUUUAUAAGUCCUCUAAUUUGCUUUAAGAUAA > AUGAGAUUUCACUUAAUUCUGUUGGAGAAAUUGUUUUAAAAAUUGUGCUA > AAGAACCGAAAAUCACUUUAUGUUAAGGCUCUAUUUAUAGCAAGUGAACU > UUUCAUGAGUUAAUAAAGGCCUACAAAAAUAAUUUUGACUGUGAAACUAA > UUAAAAUCUCUGUGUUUCAUUUAAAGCAUAAACAUAUUUGAAUAAAAAUA > GGUUAACAAUAAUUUGGGACAUGUAUUCAGUAUAAUUUUAAGAUAAUUUU > ACAAAAUAUAUGUAACAUUGCAUUUGUUUCUGUAAAAUAUCUUCGGAAAA > AGCCUUGUUUUCCCUAGUGUGUUAUUUGUUGAAUUUCUUGUUAAAUGUAU > UUUUUCCCAUUGAAAAAAAUGUUUUUAAUCAAUGUGAUCAAUACAGCUAU > CUAUAUGCCCUGCUUUCACUGUAGAAUUAGAAAGUGUUAAUAAGGUGAUC > GGAUGUUCUUUCUAAGGAUCAUAUUCCACAUUUAAAGAGAUGGUGACUGA > GAAGAGGUGGCAAGCUGAACCAUCUCACUUUGAGAUUGACGUAUCACGUU > UUAUCCUCUGCCAUCAUUUCCUUGUUAAUUGUUUUUCUUUGGGUGAUUGG > AAGAAUCUAUGGCUUCCUUUUCUCUGUUCUUAAAGAUAUCAAGACUCUGC > CCUUUUGUGACUGGAAGUAGAUUUUAAAUGUCCCUAAUGUUUAUAUGCUC > ACUUAAACUCAAUACAUGGAAUUUACUGGGGCAUUUAACUUGUUCAUGAA > AAUAGAGUGAGUCAUUGAAAAAUCAA > > > in http://genome.ucsc.edu/cgi-bin/hgBlat (choose version hg18, Mar. 2006) > and the result is: > BLAT Search Results > > ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO > STRAND START END SPAN > --------------------------------------------------------------------------------------------------- > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:20140804-20147092&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=20140803&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr7&l=20140803&r=20147092&db=hg18&hgsid=136019191> > NM_182762 6274 1 6276 6276 100.0% 7 - 20140804 > 20147092 6289 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:116084102-116084394&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=116084101&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr11&l=116084101&r=116084394&db=hg18&hgsid=136019191> > NM_182762 248 1975 2259 6276 94.0% 11 - 116084102 > 116084394 293 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:16094573-16094880&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=16094572&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr7&l=16094572&r=16094880&db=hg18&hgsid=136019191> > NM_182762 241 1958 2259 6276 92.3% 7 - 16094573 > 16094880 308 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr9:130722169-130722454&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=130722168&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr9&l=130722168&r=130722454&db=hg18&hgsid=136019191> > NM_182762 236 1978 2254 6276 93.5% 9 + 130722169 > 130722454 286 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr14:68970544-69164800&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=68970543&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr14&l=68970543&r=69164800&db=hg18&hgsid=136019191> > NM_182762 228 2767 3077 6276 87.2% 14 + 68970544 > 69164800 194257 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr15:40192421-40192715&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=40192420&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr15&l=40192420&r=40192715&db=hg18&hgsid=136019191> > NM_182762 225 1975 2259 6276 91.9% 15 + 40192421 > 40192715 295 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr16:84335668-84335949&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=84335667&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr16&l=84335667&r=84335949&db=hg18&hgsid=136019191> > NM_182762 224 1986 2259 6276 92.5% 16 + 84335668 > 84335949 282 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr19:8494734-8495483&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=8494733&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr19&l=8494733&r=8495483&db=hg18&hgsid=136019191> > NM_182762 212 2776 3063 6276 88.6% 19 - 8494734 > 8495483 750 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr2:43841003-43841454&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=43841002&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr2&l=43841002&r=43841454&db=hg18&hgsid=136019191> > NM_182762 210 2772 3074 6276 84.9% 2 + 43841003 > 43841454 452 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr14:23473150-23473433&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=23473149&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr14&l=23473149&r=23473433&db=hg18&hgsid=136019191> > NM_182762 208 2782 3064 6276 87.0% 14 - 23473150 > 23473433 284 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:66605236-66605548&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=66605235&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr11&l=66605235&r=66605548&db=hg18&hgsid=136019191> > NM_182762 206 2773 3075 6276 85.9% 11 - 66605236 > 66605548 313 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:36341922-36342215&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=36341921&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr7&l=36341921&r=36342215&db=hg18&hgsid=136019191> > NM_182762 205 2782 3075 6276 90.6% 7 - 36341922 > 36342215 294 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr17:17958281-17958582&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=17958280&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr17&l=17958280&r=17958582&db=hg18&hgsid=136019191> > NM_182762 205 2767 3066 6276 85.6% 17 + 17958281 > 17958582 302 > > However, when I did local BLAST research, I can not locate my query in the > same location in chromosome data (I downloaded Genome data from > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ > chromFa.zip<http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip>. > My local blast result showed that there is no perfect match in > chromosome > to my query). Furthermore, I tried to follow the BLAT result and locate my > query in chr7.fa manually. I found the sequence in position 20140804 is : > > TTGATTTTTCAATGACTCACTCTATTTTCATGAACAAGTTAAATGCC > CCAGTAAATTCCATGTATTGAGTTTAAGTGAGCATATAAACATTAGGGAC > ATTTAAAATCTACTTCCAGTCACAAAAGGGCAGAGTCTTGATATCTTTAA > GAACAGAGAAAAGGAAGCCATAGATTCTTCCAATCACCCAAAGAAAAACA > ATTAACAAGGAAATGATGGCAGAGGATAAAACGTGATACGTCAATCTCAA > AGTGAGATGGTTCAGCTTGCCACCTCTTCTCAGTCACCATCTCTTTAAAT > GTGGAATATGATCCTTAGAAAGAACATCCGATCACCTTATTAACACTTTC > TAATTCTACAGTGAAAGCAGGGCATATAGATAGCTGTATTGATCACATTG > ATTAAAAACATTTTTTTCAATGGGAAAAAATACATTTAACAAGAAATTCA > ACAAATAACACACTAGGGAAAACAAGGCTTTTTCCGAAGATATTTTACAG > AAACAAATGCAATGTTACATATATTTTGTAAAATTATCTTAAAATTATAC > TGAATACATGTCCCAAATTATTGTTAACCTATTTTTATTCAAATATGTTT > ATGCTTTAAATGAAACACAGAGATTTTAATTAGTTTCACAGTCAAAATTA > TTTTTGTAGGCCTTTATTAACTCATGAAAAGTTCACTTGCTATAAATAGA > GCCTTAACATAAAGTGATTTTCGGTTCTTTAGCACAATTTTTAAAACAAT > TTCTCCAACAGAATTAAGTGAAATCTCATTTATCTTAAAGCAAATTAGAG > > Obviously, this sequence is different from my query. > > So, my question is: Did I download the same version of genome data as used > in BLAT. If possible, could you please help me to explain why my local BLAST > result is different from your BLAT result? If I used the wrong data, could > you please tell me where to download the right one. > > Thanks beforehand. > > Regards > > Wayne > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
