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Human BLAT Search
| # BLAT Search Genome
Genome: | Assembly: | Query type: | Sort output: | Output type: |  |
Please paste in a query sequence to see where it is located in the the genome. Multiple sequences can be searched at once if separated by a line starting with > and the sequence name. |  |
>sequenza test 1 attgagagaa cagagaacat gacaagtact tctagctcag cactgctcca actactgaag 61 ctgattttca aggctactta aaaaaatctg cagcgtacat taatggattt ctgttgtgtt 121 taaattctcc acagattgta ttgtaaatat tttatgaagt agagcatatg tatatattta 181 tatatacgtg cacatacatt agtagcacta cctttggaag tctcagctct tgcttttcgg 241 gactgaagcc agttttgcat gataaaagtg gccttgttac gggagataat tgtgttctgt 301 tgggacttta gacaaaactc acctgcaaaa aactgacagg cattaactac tggaacttcc 361 aaataatgtg tttgctgatc gttttactct tcgcataaat attttaggaa gtgtatgaga 421 attttgcctt caggaacttt tctaacagcc aaagacagaa cttaacctct gcaagcaaga 481 ttcgtggaag atagtctcca ctttttaatg cactaagcaa tcggttgcta ggagcccatc 541 ctgggtcaga ggccgatccg cagaaccaga acgttttccc ctcctggact gttagtaact 601 tagtctccct cctcccctaa ccacccccgc ccccccccac cccccgcagt aataaaggcc 661 cctgaacgtg tatgttggtc tcccgggagc tgcttgctga agatccgcgc ccctgtcgcc 721 gtctggtagg agctgtttgc agggtcctaa ctcaatcggc ttgttgtgat gcgtatcccc 781 gtagatgcca gcacgagccg ccgcttcacg ccgccttcca ccgcgctgag cccaggcaag 841 atgagcgagg cgttgccgct gggcgccccg gacgccggcg ctgccctggc cggcaagctg 901 aggagcggcg accgcagcat ggtggaggtg ctggccgacc acccgggcga gctggtgcgc 961 accgacagcc ccaacttcct ctgctccgtg ctgcctacgc actggcgctg caacaagacc 1021 ctgcccatcg ctttcaaggt ggtggcccta ggggatgttc cagatggcac tctggtcact 1081 gtgatggctg gcaatgatga aaactactcg gctgagctga gaaatgctac cgcagccatg 1141 aagaaccagg ttgcaagatt taatgacctc aggtttgtcg gtcgaagtgg aagagggaaa 1201 agcttcactc tgaccatcac tgtcttcaca aacccaccgc aagtcgccac ctaccacaga 1261 gccatcaaaa tcacagtgga tgggccccga gaacctcgaa gacatcggca gaaactagat 1321 gatcagacca agcccgggag cttgtccttt tccgagcggc tcagtgaact ggagcagctg 1381 cggcgcacag ccatgagggt cagcccacac cacccagccc ccacgcccaa ccctcgtgcc 1441 tccctgaacc actccactgc ctttaaccct cagcctcaga gtcagatgca ggaggaagac 1501 acagcaccct ggagatgtta aggcagaagt cagttcttct gtccatccct ctccccagcc 1561 aggatagagc tatcttttcc atctcatcct cagaagagac tcagaagaaa gatgacagcc 1621 ctcagaatgc acgttatgag gaaggcagaa tgtgggtctg taattcctcc gtgtcccttc 1681 tccccctctg caaaccgtcg taacaataat agttcctaac acatgggaca attgtgagga 1741 ttaaatgagt tagcctgcag aaatcacttg atgcacagca catgggaagc attgtgtgta 1801 tttattaatc cttcacaaag tctttgagat atatttttat caaatattta gcatggatcc 1861 cggtacactt tcaatactta ataaatggtc aatgttattc tttttcacta tt>sequenza test 1 attgagagaa cagagaacat gacaagtact tctagctcag cactgctcca actactgaag 61 ctgattttca aggctactta aaaaaatctg cagcgtacat taatggattt ctgttgtgtt 121 taaattctcc acagattgta ttgtaaatat tttatgaagt agagcatatg tatatattta 181 tatatacgtg cacatacatt agtagcacta cctttggaag tctcagctct tgcttttcgg 241 gactgaagcc agttttgcat gataaaagtg gccttgttac gggagataat tgtgttctgt 301 tgggacttta gacaaaactc acctgcaaaa aactgacagg cattaactac tggaacttcc 361 aaataatgtg tttgctgatc gttttactct tcgcataaat attttaggaa gtgtatgaga 421 attttgcctt caggaacttt tctaacagcc aaagacagaa cttaacctct gcaagcaaga 481 ttcgtggaag atagtctcca ctttttaatg cactaagcaa tcggttgcta ggagcccatc 541 ctgggtcaga ggccgatccg cagaaccaga acgttttccc ctcctggact gttagtaact 601 tagtctccct cctcccctaa ccacccccgc ccccccccac cccccgcagt aataaaggcc 661 cctgaacgtg tatgttggtc tcccgggagc tgcttgctga agatccgcgc ccctgtcgcc 721 gtctggtagg agctgtttgc agggtcctaa ctcaatcggc ttgttgtgat gcgtatcccc 781 gtagatgcca gcacgagccg ccgcttcacg ccgccttcca ccgcgctgag cccaggcaag 841 atgagcgagg cgttgccgct gggcgccccg gacgccggcg ctgccctggc cggcaagctg 901 aggagcggcg accgcagcat ggtggaggtg ctggccgacc acccgggcga gctggtgcgc 961 accgacagcc ccaacttcct ctgctccgtg ctgcctacgc actggcgctg caacaagacc 1021 ctgcccatcg ctttcaaggt ggtggcccta ggggatgttc cagatggcac tctggtcact 1081 gtgatggctg gcaatgatga aaactactcg gctgagctga gaaatgctac cgcagccatg 1141 aagaaccagg ttgcaagatt taatgacctc aggtttgtcg gtcgaagtgg aagagggaaa 1201 agcttcactc tgaccatcac tgtcttcaca aacccaccgc aagtcgccac ctaccacaga 1261 gccatcaaaa tcacagtgga tgggccccga gaacctcgaa gacatcggca gaaactagat 1321 gatcagacca agcccgggag cttgtccttt tccgagcggc tcagtgaact ggagcagctg 1381 cggcgcacag ccatgagggt cagcccacac cacccagccc ccacgcccaa ccctcgtgcc 1441 tccctgaacc actccactgc ctttaaccct cagcctcaga gtcagatgca ggaggaagac 1501 acagcaccct ggagatgtta aggcagaagt cagttcttct gtccatccct ctccccagcc 1561 aggatagagc tatcttttcc atctcatcct cagaagagac tcagaagaaa gatgacagcc 1621 ctcagaatgc acgttatgag gaaggcagaa tgtgggtctg taattcctcc gtgtcccttc 1681 tccccctctg caaaccgtcg taacaataat agttcctaac acatgggaca attgtgagga 1741 ttaaatgagt tagcctgcag aaatcacttg atgcacagca catgggaagc attgtgtgta 1801 tttattaatc cttcacaaag tctttgagat atatttttat caaatattta gcatggatcc Rather than pasting a sequence, you can choose to upload a text file containing the sequence. Upload sequence: Only DNA sequences of 25,000 or fewer bases and protein or translated sequence of 5000 or fewer letters will be processed. Up to 25 sequences can be submitted at the same time. The total limit for multiple sequence submissions is 50,000 bases or 12,500 letters. BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats. The index takes up a bit less than a gigabyte of RAM. The genome itself is not kept in memory, allowing BLAT to deliver high performance on a reasonably priced Linux box. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment. Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little more than 2 gigabytes BLAT was written by Jim Kent. Like most of Jim's software interactive use on this web server is free to all. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available. Contact Jim for details. |