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added brute force algorithm
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RJain12 committed Aug 9, 2021
1 parent cb95d50 commit 3946579
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Showing 45 changed files with 1,419 additions and 42 deletions.
26 changes: 26 additions & 0 deletions benchmark_sequences/brute/AKT1_dna.fasta
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>NM_005163.2 Homo sapiens AKT serine/threonine kinase 1 (AKT1), transcript variant 1, mRNA
ATGAGTGATGTCGCCATAGTGAAAGAAGGGTGGTTACACAAACGGGGCGAATATATTAAG
ACTTGGCGTCCCAGGTACTTTCTGCTCAAAAATGATGGGACCTTTATTGGTTATAAAGAG
CGACCTCAAGATGTGGACCAGCGCGAAGCACCTCTCAACAATTTTTCTGTCGCGCAGTGC
CAGCTAATGAAAACCGAGAGACCTCGCCCCAACACGTTCATAATTAGGTGTTTACAGTGG
ACAACGGTCATCGAGCGGACTTTCCACGTCGAAACCCCAGAAGAGAGAGAGGAATGGACT
ACTGCTATACAGACGGTTGCCGATGGTTTAAAAAAACAAGAGGAGGAAGAGATGGACTTT
CGCTCCGGATCCCCTTCGGACAATAGCGGCGCAGAGGAAATGGAGGTGAGCCTGGCAAAG
CCAAAACACAGGGTGACCATGAACGAGTTCGAATACCTTAAACTATTAGGTAAGGGAACA
TTCGGTAAGGTAATACTTGTAAAAGAGAAAGCAACCGGTCGTTATTATGCGATGAAAATT
CTTAAGAAGGAGGTTATCGTCGCAAAGGATGAAGTTGCACACACCCTAACGGAAAACCGT
GTTTTGCAGAATTCAAGGCATCCGTTTTTAACCGCCTTAAAGTATAGTTTCCAAACGCAT
GACCGGTTATGTTTCGTGATGGAATATGCAAATGGGGGAGAGCTATTCTTTCATCTCTCC
CGAGAACGGGTGTTCAGCGAGGATCGTGCACGATTCTACGGCGCCGAAATTGTGAGTGCC
CTAGACTACCTTCATTCGGAAAAAAACGTCGTGTACCGCGACCTCAAGTTGGAGAACCTG
ATGCTGGATAAGGACGGTCACATTAAAATCACAGACTTCGGGCTTTGCAAAGAAGGGATC
AAGGACGGTGCAACGATGAAAACCTTCTGCGGCACCCCGGAATACCTGGCTCCTGAGGTG
CTGGAAGATAATGATTACGGACGTGCCGTAGACTGGTGGGGCTTGGGCGTTGTTATGTAT
GAGATGATGTGTGGTCGTCTGCCGTTTTATAACCAGGATCATGAAAAATTATTCGAGCTG
ATTCTGATGGAAGAAATTCGATTCCCCAGAACACTGGGCCCCGAAGCGAAATCTCTTCTT
AGCGGCCTCCTGAAAAAAGATCCAAAACAAAGGCTTGGTGGTGGAAGTGAGGATGCTAAG
GAAATCATGCAGCACCGGTTCTTTGCTGGCATCGTGTGGCAGCATGTCTACGAAAAGAAA
CTGAGCCCGCCGTTTAAGCCTCAAGTTACATCCGAGACCGATACCCGGTATTTCGATGAG
GAGTTTACGGCACAGATGATCACGATCACGCCTCCGGACCAGGATGATTCCATGGAATGT
GTTGACTCAGAGCGACGTCCTCATTTCCCTCAGTTTTCGTACTCGGCCAGTGGGACCGCC
TAA
10 changes: 10 additions & 0 deletions benchmark_sequences/brute/BIRC5_dna.fasta
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>NM_001012271.2 Homo sapiens baculoviral IAP repeat containing 5 (BIRC5), transcript variant 3, mRNA
ATGGGTGCCCCCACTTTGCCCCCTGCGTGGCAGCCGTTCTTGAAAGATCATCGTATTTCC
ACATTCAAAAACTGGCCATTCCTTGAAGGGTGCGCATGCACGCCGGAACGTATGGCGGAG
GCGGGCTTTATTCATTGTCCTACAGAAAACGAACCGGACTTGGCACAGTGTTTCTTTTGT
TTTAAAGAACTAGAAGGGTGGGAGCCAGATGATGATCCAATTGGCCCTGGAACTGTCGCT
TACGCGTGTAATACTTCCACCCTGGGCGGCAGAGGGGGCCGGATTACGCGGGAAGAACAT
AAAAAACATTCTTCGGGCTGTGCTTTTCTCAGCGTGAAAAAGCAGTTTGAAGAACTGACT
CTAGGTGAATTTTTAAAATTAGATCGTGAGCGTGCGAAAAACAAGATTGCCAAGGAAACT
AACAACAAAAAAAAGGAATTTGAAGAAACGGCTGAGAAAGTCCGCCGTGCGATAGAACAG
CTGGCGGCCATGGACTAG
40 changes: 40 additions & 0 deletions benchmark_sequences/brute/BRAF1_dna.fasta
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>NM_004333.6 Homo sapiens B-Raf proto-oncogene, serine/threonine kinase (BRAF), transcript variant 1, mRNA
ATGGCGGCATTGTCGGGAGGTGGTGGCGGCGGAGCTGAACCAGGCCAGGCGTTATTCAAC
GGTGATATGGAGCCTGAGGCGGGTGCGGGGGCCGGTGCCGCCGCATCATCGGCCGCGGAT
CCGGCTATTCCTGAAGAGGTGTGGAACATTAAGCAAATGATCAAGCTCACTCAGGAGCAT
ATCGAAGCGCTGCTGGATAAATTTGGTGGCGAACACAATCCACCGAGTATTTACTTAGAA
GCGTATGAAGAATATACTTCCAAACTTGATGCACTTCAACAACGTGAACAACAACTGCTG
GAGTCTCTCGGCAACGGAACAGACTTTTCAGTGTCCAGCTCGGCTTCAATGGATACGGTG
ACCTCGAGTTCCTCGAGCAGCTTGAGTGTGCTGCCTAGCTCACTGAGCGTGTTCCAGAAT
CCAACGGACGTAGCACGATCAAATCCCAAATCACCACAGAAGCCCATAGTGCGCGTTTTC
CTGCCCAACAAACAGCGGACTGTGGTCCCGGCGAGATGTGGGGTCACTGTTCGGGATTCA
CTAAAGAAAGCACTTATGATGCGAGGTCTCATCCCTGAATGTTGTGCGGTATACCGTATA
CAAGACGGTGAGAAAAAGCCGATTGGATGGGATACTGACATATCTTGGCTGACAGGAGAA
GAACTCCATGTCGAGGTCCTAGAGAACGTGCCTCTCACAACTCACAATTTCGTCCGCAAG
ACTTTTTTTACACTCGCTTTTTGTGACTTTTGCAGAAAACTGCTCTTCCAGGGGTTTCGG
TGTCAGACATGTGGCTATAAATTTCATCAGCGTTGTAGCACGGAGGTCCCCCTGATGTGC
GTAAATTACGACCAACTTGACCTGTTGTTCGTGTCTAAATTTTTCGAGCACCATCCTATT
CCACAGGAGGAGGCAAGCCTGGCAGAGACTGCGCTGACGTCCGGTTCCAGCCCATCTGCC
CCTGCGAGCGATAGCATAGGTCCTCAGATCCTTACTAGCCCAAGTCCTTCGAAATCTATT
CCTATCCCGCAACCTTTTCGACCTGCGGACGAAGATCATAGAAACCAGTTCGGCCAGCGC
GATCGATCCTCGAGCGCACCAAATGTACATATTAACACGATAGAGCCTGTCAACATTGAC
GACCTAATCCGAGACCAGGGGTTTCGCGGCGACGGAGGCAGTACCACGGGCTTGAGCGCG
ACCCCGCCTGCCTCGCTACCTGGCTCTCTCACAAATGTTAAGGCGTTGCAAAAAAGCCCG
GGCCCACAGCGCGAACGGAAATCTTCGTCGTCGAGCGAGGATAGGAACCGAATGAAAACC
CTAGGCCGGAGAGACTCAAGTGATGACTGGGAGATTCCCGATGGTCAGATCACCGTGGGC
CAGCGGATCGGGTCCGGATCTTTTGGAACTGTGTATAAAGGAAAATGGCATGGTGATGTC
GCTGTTAAAATGTTGAATGTCACTGCACCCACCCCTCAGCAGTTACAAGCGTTCAAAAAT
GAGGTAGGCGTTCTCCGAAAAACGCGACATGTGAATATCCTCTTATTTATGGGTTATAGC
ACGAAACCCCAGCTCGCCATCGTTACTCAGTGGTGCGAAGGGTCCTCTCTCTACCATCAC
CTCCACATTATCGAGACTAAATTCGAGATGATTAAATTAATCGATATAGCGCGACAGACA
GCCCAGGGGATGGACTATTTGCATGCTAAGTCCATCATCCACCGAGATCTCAAATCAAAT
AATATATTCCTCCATGAAGATCTTACGGTGAAGATTGGTGATTTCGGCCTGGCCACTGTG
AAGAGCCGGTGGTCCGGATCACATCAGTTTGAGCAACTTTCAGGTTCCATACTTTGGATG
GCGCCAGAAGTGATCAGAATGCAAGATAAAAACCCATATAGTTTCCAGTCAGACGTGTAT
GCATTTGGGATCGTTCTCTATGAACTTATGACTGGACAGTTGCCATACTCTAATATAAAT
AATCGGGATCAGATAATTTTCATGGTTGGTCGTGGCTACCTCTCACCCGATCTTTCAAAA
GTCAGATCAAATTGTCCCAAGGCGATGAAAAGATTGATGGCTGAATGCCTGAAGAAGAAA
AGGGATGAACGACCGCTGTTCCCTCAAATACTCGCATCTATCGAGCTGCTAGCCCGATCT
CTGCCGAAGATTCATCGTAGCGCGAGTGAGCCGTCGTTGAACCGCGCGGGATTCCAGACG
GAGGACTTCAGCTTATACGCCTGCGCATCGCCTAAAACACCGATCCAAGCGGGTGGGTAC
GGGGCCTTCCCGGTGCACTAG
10 changes: 10 additions & 0 deletions benchmark_sequences/brute/CAV1_dna.fasta
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>NM_001753.5 Homo sapiens caveolin 1 (CAV1), transcript variant 1, mRNA
ATGTCAGGAGGTAAGTATGTCGATTCTGAAGGTCATCTTTATACAGTCCCTATTCGTGAG
CAGGGCAATATTTATAAACCGAACAATAAAGCTATGGCTGATGAACTGTCGGAAAAGCAG
GTATATGACGCGCACACAAAGGAAATAGATCTGGTTAATCGTGACCCGAAACATCTGAAC
GATGACGTCGTCAAGATTGATTTTGAGGACGTAATAGCGGAGCCGGAGGGGACACATAGT
TTTGATGGCATATGGAAAGCCAGTTTTACAACCTTTACGGTGACGAAATACTGGTTCTAC
CGGTTACTTTCCGCACTATTTGGTATTCCTATGGCTCTTATCTGGGGCATCTATTTCGCG
ATCCTGAGCTTCTTACACATCTGGGCCGTAGTTCCGTGCATTAAGTCCTTCCTGATCGAG
ATCCAGTGTATTTCGAGAGTGTATTCGATTTATGTCCACACCGTTTGCGACCCACTGTTT
GAAGCAGTTGGAAAAATTTTCAGCAACGTACGTATTAATCTGCAGAAAGAGATCTGA
17 changes: 17 additions & 0 deletions benchmark_sequences/brute/CD80_dna.fasta
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>NM_009855.2 Mus musculus CD80 antigen (Cd80), transcript variant 2, mRNA
ATGGCTTGCAATTGTCAACTTATGCAGGATACTCCTTTGCTCAAATTCCCCTGTCCGCGT
CTTATCTTGTTATTTGTTCTCCTGATTCGTTTGAGTCAGGTTTCAAGCGACGTGGATGAG
CAACTATCCAAGTCCGTTAAAGACAAAGTTCTGCTTCCTTGCAGGTACAATAGTCCACAC
GAAGACGAAAGTGAGGATAGGATTTATTGGCAGAAGCATGATAAAGTTGTGCTGAGCGTA
ATCGCGGGCAAACTCAAAGTCTGGCCTGAGTACAAGAACCGCACTTTATATGATAATACC
ACCTACTCATTGATCATCCTTGGTCTAGTGTTGTCTGATAGGGGTACCTACTCCTGTGTG
GTTCAGAAGAAAGAACGTGGCACGTACGAGGTGAAACATCTCGCTTTAGTCAAACTTTCT
ATCAAAGCCGATTTCTCTACCCCCAATATTACAGAGTCAGGGAACCCTAGTGCTGATACA
AAGCGGATCACGTGCTTCGCTTCAGGGGGCTTTCCTAAACCGCGTTTTTCCTGGCTCGAA
AACGGGCGAGAATTACCAGGTATTAATACTACGATTAGTCAGGACCCAGAATCAGAACTG
TATACTATAAGCTCGCAACTGGACTTCAACACGACCCGTAACCACACCATTAAATGTTTA
ATCAAATACGGCGACGCGCACGTATCCGAGGACTTCACATGGGAGAAACCGCCAGAAGAT
CCGCCGGACAGCAAGAATACGCTTGTTCTTTTCGGCGCAGGCTTCGGAGCGGTTATTACT
GTGGTTGTGATCGTGGTAATCATCAAATGCTTCTGCAAACATCGTTCTTGCTTTCGTCGT
AACGAGGCGTCACGGGAAACAAATAACTCCCTGACTTTTGGCCCGGAAGAAGCACTGGCC
GAACAAACTGTGTTCTTATAG
16 changes: 16 additions & 0 deletions benchmark_sequences/brute/CDK1_dna.fasta
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>NM_001786.5 Homo sapiens cyclin dependent kinase 1 (CDK1), transcript variant 1, mRNA
ATGGAAGACTACACGAAAATCGAAAAGATCGGTGAGGGTACGTACGGCGTTGTTTACAAA
GGTCGCCATAAGACGACAGGCCAAGTGGTGGCGATGAAAAAGATCCGTTTGGAGAGCGAG
GAAGAAGGTGTTCCCTCTACGGCTATCAGGGAAATTAGTCTCCTGAAAGAGCTGAGGCAT
CCGAATATAGTTAGTTTACAAGATGTCTTGATGCAGGATTCTCGTCTGTACTTAATCTTT
GAATTTCTTTCTATGGACTTGAAAAAGTATTTAGACAGTATACCGCCCGGGCAGTATATG
GATAGTAGTTTGGTAAAAAGTTATTTGTACCAGATTTTACAGGGCATAGTGTTCTGCCAC
AGCCGACGTGTCCTCCACAGGGATTTGAAACCGCAGAACCTGCTGATAGACGATAAAGGA
ACGATAAAACTGGCTGATTTTGGCCTGGCACGTGCATTTGGTATACCCATAAGGGTCTAT
ACGCATGAGGTTGTGACCTTATGGTATAGGTCTCCCGAAGTCTTATTGGGGTCAGCCCGT
TACTCCACGCCCGTGGACATCTGGTCCATTGGAACAATATTTGCCGAGTTAGCCACGAAA
AAGCCGCTTTTCCATGGTGACAGTGAAATCGATCAATTGTTTCGTATTTTCCGTGCCTTG
GGTACCCCCAATAATGAAGTTTGGCCTGAAGTAGAGAGTCTGCAGGACTACAAAAATACC
TTTCCGAAATGGAAACCCGGCTCGCTGGCTAGCCATGTGAAAAACCTGGATGAAAATGGT
TTAGATTTACTCTCGAAAATGCTCATTTATGATCCAGCCAAAAGAATATCAGGAAAAATG
GCGTTAAACCATCCTTACTTTAACGACCTGGACAACCAGATTAAGAAAATGTAA
54 changes: 54 additions & 0 deletions benchmark_sequences/brute/CEBPZ_dna.fasta
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>NM_005760.3 Homo sapiens CCAAT enhancer binding protein zeta (CEBPZ), mRNA
ATGGCGGCCGTTAAAGAACCGCTTGAATTCCACGCAAAACGTCCGTGGAGACCTGAGGAG
GCAGTCGAAGACCCTGATGAGGAAGATGAAGACAATACGTCCGAGGCCGAGAATGGCTTC
AGCTTAGAAGAGGTGTTGCGCCTGGGCGGCACAAAGCAGGACTATCTAATGCTCGCTACA
CTAGATGAGAATGAGGAGGTTATTGACGGAGGGAAGAAGGGAGCCATAGATGACCTTCAG
CAAGGAGAACTGGAGGCATTCATTCAGAACCTGAATTTAGCGAAATATACAAAAGCTAGC
CTTGTAGAAGAAGACGAGCCAGCCGAAAAAGAAAACAGCAGCAAAAAAGAAGTAAAAATA
CCAAAAATCAACAATAAAAATACGGCAGAAAGCCAGCGCACTAGTGTAAACAAGGTGAAA
AACAAAAATCGTCCAGAACCGCACTCTGACGAAAACGGGAGCACTACACCGAAAGTTAAA
AAGGATAAACAGAACATTTTTGAGTTTTTCGAAAGGCAAACGCTCTTGCTGAGGCCTGGT
GGCAAATGGTACGATTTAGAGTACTCAAATGAATATTCTTTAAAGCCCCAACCGCAGGAC
GTTGTTTCGAAATACAAGACGTTGGCGCAAAAACTTTATCAACATGAGATTAATCTGTTC
AAGTCAAAGACAAATAGCCAAAAGGGTGCGTCCAGCACCTGGATGAAGGCAATCGTCTCG
TCCGGCACGCTCGGAGATCGGATGGCCGCCATGATACTCCTGATTCAGGATGATGCCGTT
CATACTTTGCAGTTCGTCGAAACCTTAGTAAACCTCGTTAAGAAAAAGGGCTCAAAACAA
CAATGCCTGATGGCGTTAGACACCTTTAAAGAATTACTAATTACGGATCTACTTCCAGAC
AACCGAAAGTTACGGATATTTAGCCAGCGCCCATTTGACAAGCTAGAGCAGCTGTCCAGT
GGAAATAAGGATTCTCGCGATCGTCGCCTGATCCTATGGTATTTCGAACATCAGTTGAAG
CACTTGGTTGCCGAGTTTGTACAAGTATTAGAAACCCTGAGTCATGACACCCTTGTAACA
ACCAAAACACGCGCTCTAACGGTTGCCCACGAACTCCTCTGCAACAAACCGGAGGAGGAA
AAGGCGTTACTAGTGCAAGTAGTTAATAAACTTGGCGACCCGCAGAACCGCATTGCGACC
AAGGCAAGCCACCTCCTCGAAACTCTACTTTGCAAGCACCCAAACATGAAGGGTGTTGTC
AGCGGTGAAGTCGAACGACTGCTTTTTAGATCCAATATCTCGTCTAAGGCTCAGTACTAC
GCAATCTGCTTCCTTAACCAGATGGCACTTTCCCATGAAGAGTCAGAGCTGGCCAATAAG
CTGATAACTGTATACTTTTGTTTCTTTCGTACCTGCGTTAAGAAGAAAGATGTGGAATCT
AAAATGTTGTCAGCCCTTTTGACCGGAGTTAACCGCGCGTACCCCTATAGCCAGACGGGT
GATGATAAGGTGCGAGAGCAGATTGACACGTTATTCAAGGTATTACATATTGTAAACTTC
AATACATCTGTTCAGGCCTTAATGCTCCTGTTCCAAGTAATGAACTCCCAGCAAACAATT
TCAGACCGATATTACACGGCGCTATATCGTAAGATGTTGGACCCGGGCCTGATGACCTGT
TCGAAACAAGCAATGTTTCTCAATCTGGTGTATAAGAGTCTGAAAGCTGATATAGTTTTA
CGTCGTGTTAAAGCGTTTGTAAAACGGCTGCTGCAGGTTACGTGTCAACAGATGCCTCCT
TTTATTTGTGGCGCGCTTTACCTAGTATCTGAAATTTTGAAGGCGAAACCGGGACTACGA
TCGCAGCTAGATGATCATCCGGAGTCTGATGATGAAGAAAACTTCATCGATGCAAACGAT
GACGAAGATATGGAGAAGTTTACGGACGCTGATAAAGAAACAGAAATCGTGAAAAAACTG
GAGACGGAGGAGACCGTGCCAGAAACTGACGTGGAAACGAAGAAACCCGAGGTCGCGAGC
TGGGTGCACTTCGATAATCTTAAGGGCGGCAAGCAGCTAAATAAGTATGACCCCTTTTCC
CGTAATCCGTTGTTCTGTGGTGCTGAGAATACCAGTTTGTGGGAGCTGAAAAAGCTTTCT
GTACATTTTCATCCTAGTGTAGCGCTGTTCGCTAAGACTATCCTTCAAGGTAACTACATT
CAGTATTCCGGCGACCCCTTGCAAGATTTCACGCTAATGCGTTTTCTCGATCGTTTCGTA
TATCGGAACCCTAAACCTCACAAGGGTAAGGAAAATACTGACTCGGTAGTCATGCAGCCC
AAGCGCAAACACTTTATTAAAGACATCCGTCACCTGCCTGTAAACTCGAAGGAATTTCTG
GCTAAGGAAGAGTCCCAAATCCCGGTAGACGAAGTGTTCTTCCACAGGTACTACAAAAAA
GTTGCAGTAAAGGAGAAACAAAAGAGAGACGCCGATGAAGAGTCAATTGAAGACGTAGAC
GATGAAGAGTTCGAAGAACTTATTGATACGTTCGAAGACGACAACTGTTTCTCATCTGGA
AAAGACGACATGGACTTCGCGGGCAACGTAAAAAAACGAACAAAGGGCGCGAAAGATAAT
ACCTTAGATGAGGATTCTGAAGGCTCAGATGACGAGCTGGGTAATCTCGACGATGATGAG
GTCTCTCTGGGATCCATGGACGATGAGGAATTTGCGGAAGTAGATGAAGATGGCGGCACG
TTTATGGATGTGCTAGATGATGAATCAGAATCTGTCCCAGAACTTGAGGTGCACTCCAAA
GTAAGTACAAAGAAGAGTAAAAGGAAAGGCACGGACGACTTCGACTTTGCAGGCTCCTTT
CAAGGTCCACGAAAGAAGAAGCGCAACTTAAACGATAGTAGTCTATTTGTATCCGCTGAA
GAGTTCGGCCACTTGCTGGATGAGAACATGGGATCGAAATTTGACAACATCGGGATGAAT
GCAATGGCTAACAAGGACAACGCGAGCTTGAAGCAATTAAGATGGGAAGCCGAGCGTGAC
GACTGGCTTCACAATCGTGACGCAAAATCCATTATCAAGAAAAAGAAGCATTTTAAAAAA
AAACGGATTAAAACTACACAAAAGACAAAGAAACAACGCAAATAG
23 changes: 23 additions & 0 deletions benchmark_sequences/brute/CLN3_dna.fasta
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>NM_000086.2 Homo sapiens CLN3 lysosomal/endosomal transmembrane protein, battenin (CLN3), transcript variant 2, mRNA
ATGGGAGGATGCGCTGGTTCCCGTCGCAGATTTTCGGATAGTGAAGGCGAGGAAACCGTA
CCAGAACCGCGCTTACCCCTCTTGGACCATCAAGGCGCCCACTGGAAGAATGCAGTTGGT
TTCTGGTTGTTGGGCCTGTGTAACAATTTCTCTTACGTTGTGATGTTATCGGCGGCACAC
GACATCCTGTCCCATAAAAGGACATCCGGCAATCAGAGCCATGTAGACCCGGGTCCGACT
CCCATTCCGCACAATAGCTCGAGCCGATTTGACTGCAACAGCGTATCTACAGCTGCCGTT
TTACTGGCTGATATCCTACCGACGTTAGTAATAAAACTGCTTGCGCCCCTGGGTCTCCAC
CTGTTACCGTATAGTCCGAGGGTGTTAGTATCAGGGATCTGCGCAGCCGGAAGCTTTGTA
TTAGTGGCGTTTTCGCATAGCGTGGGGACCTCCCTTTGTGGCGTGGTTTTTGCGTCAATC
AGCTCAGGCCTCGGCGAAGTTACGTTTTTGAGCCTTACCGCCTTCTATCCACGGGCCGTT
ATCTCTTGGTGGTCATCAGGTACCGGTGGAGCAGGTCTGCTGGGCGCACTGAGTTATCTA
GGACTCACCCAAGCCGGACTTTCTCCGCAGCAAACACTACTTTCCATGCTCGGTATTCCC
GCTCTCCTCCTCGCTTCCTATTTTCTTTTGTTGACCAGTCCGGAAGCCCAAGATCCGGGT
GGGGAGGAAGAAGCGGAAAGCGCTGCGCGTCAGCCTTTGATCCGCACAGAAGCACCTGAG
TCTAAACCGGGCTCTTCATCATCCCTAAGCCTGCGGGAACGCTGGACTGTGTTTAAAGGC
CTCCTATGGTACATTGTACCACTTGTGGTAGTCTATTTTGCTGAGTACTTTATTAACCAG
GGGCTATTCGAACTCCTTTTCTTTTGGAACACCTCCCTGTCCCATGCTCAACAGTATCGA
TGGTATCAGATGCTGTACCAGGCTGGCGTCTTCGCGTCGAGAAGCTCATTGAGATGCTGC
CGGATTAGGTTCACCTGGGCGTTGGCCCTGCTGCAGTGTCTTAATTTGGTTTTTCTACTG
GCGGATGTCTGGTTTGGTTTCCTTCCGAGCATATATCTGGTGTTTCTTATTATCTTATAT
GAAGGACTCTTGGGCGGCGCAGCGTATGTTAACACATTTCACAACATCGCTCTGGAGACA
TCAGACGAACATCGGGAATTCGCGATGGCTGCCACTTGTATAAGCGACACGTTAGGGATT
TCGCTGAGTGGTCTCTTAGCACTCCCTCTTCACGATTTTTTGTGCCAGCTATCATAA
18 changes: 18 additions & 0 deletions benchmark_sequences/brute/CREB1_dna.fasta
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>NM_004379.5 Homo sapiens cAMP responsive element binding protein 1 (CREB1), transcript variant 1, mRNA
ATGACCATGGAGAGTGGGGCAGAAAATCAGCAATCGGGAGATGCCGCCGTAACCGAAGCT
GAGAATCAACAAATGACCGTACAGGCACAACCCCAAATTGCAACCCTCGCCCAGGTAAGC
ATGCCTGCGGCGCACGCGACGTCCTCTGCACCGACCGTGACCCTAGTTCAGTTACCGAAT
GGCCAAACTGTCCAAGTCCACGGCGTTATCCAGGCAGCTCAGCCGTCCGTGATTCAGAGT
CCGCAGGTACAGACAGTGCAGATCAGTACTATTGCTGAAAGTGAGGATTCACAGGAGAGC
GTGGATTCAGTAACAGACTCGCAGAAAAGAAGAGAAATTTTATCGCGAAGGCCGTCGTAT
CGTAAGATATTGAATGATTTAAGCTCAGATGCTCCAGGTGTACCTAGAATCGAGGAAGAG
AAAAGTGAAGAGGAAACTAGTGCTCCGGCAATCACTACAGTGACAGTACCGACGCCGATT
TATCAAACCTCCTCGGGCCAATATATTGCCATTACGCAAGGAGGTGCCATTCAACTAGCA
AACAATGGTACCGATGGGGTGCAGGGGCTGCAGACCCTGACAATGACGAATGCAGCTGCG
ACCCAGCCGGGGACCACTATACTTCAATACGCCCAGACGACGGATGGGCAACAAATTCTT
GTTCCGAGTAATCAGGTTGTGGTGCAAGCGGCCTCGGGTGATGTGCAAACCTACCAGATA
CGTACAGCGCCAACTTCAACGATTGCCCCTGGAGTCGTCATGGCGTCAAGTCCTGCGCTC
CCGACACAACCTGCTGAAGAGGCTGCCCGTAAACGCGAGGTTAGACTGATGAAAAACCGT
GAAGCCGCTCGGGAATGTCGGCGCAAAAAGAAGGAATATGTTAAATGTCTTGAAAACCGG
GTGGCCGTCCTGGAGAATCAAAACAAAACCCTGATCGAAGAACTGAAAGCGCTGAAAGAT
CTCTACTGCCACAAATCCGACTAA
18 changes: 18 additions & 0 deletions benchmark_sequences/brute/CSNK1A1_dna.fasta
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>NM_001892.6 Homo sapiens casein kinase 1 alpha 1 (CSNK1A1), transcript variant 2, mRNA
ATGGCATCATCATCAGGCTCGAAAGCAGAATTTATTGTCGGCGGAAAATATAAGCTTGTT
CGCAAAATCGGTTCCGGCTCTTTCGGTGATATTTATCTCGCTATCAATATTACTAACGGT
GAGGAAGTTGCAGTGAAGCTGGAGAGTCAGAAGGCCCGCCATCCTCAGCTGCTTTATGAA
TCGAAATTGTACAAAATCCTGCAAGGAGGGGTGGGCATCCCGCACATTAGATGGTACGGC
CAAGAGAAAGATTACAACGTCCTTGTCATGGACTTACTGGGCCCGTCACTAGAAGATCTT
TTCAACTTCTGTAGCAGGCGTTTCACAATGAAGACAGTCTTGATGCTGGCAGACCAAATG
ATTAGCCGAATCGAGTATGTGCATACCAAAAACTTTATTCATCGTGATATAAAACCGGAT
AACTTCCTCATGGGCATCGGTCGCCACTGTAATAAACTGTTCCTCATAGACTTTGGCCTG
GCGAAAAAATATCGGGATAACCGAACTCGCCAACATATCCCTTACAGAGAAGATAAAAAC
TTAACGGGTACCGCTCGGTACGCGTCTATCAACGCACACCTAGGCATAGAACAATCACGA
AGGGACGATATGGAATCCTTGGGTTATGTACTTATGTACTTCAATAGGACCTCGCTGCCT
TGGCAGGGGCTCAAAGCGGCCACGAAGAAGCAGAAGTACGAGAAGATCAGTGAAAAAAAA
ATGAGTACGCCGGTAGAGGTACTGTGTAAGGGATTCCCAGCAGAGTTTGCGATGTACCTT
AACTATTGCCGAGGTCTTCGCTTCGAGGAAGCACCGGACTACATGTACCTGCGTCAGTTG
TTTCGGATTCTGTTTAGGACTCTGAATCACCAGTATGATTACACCTTCGATTGGACGATG
TTGAAGCAAAAAGCCGCCCAGCAGGCAGCGTCTAGTAGCGGTCAGGGTCAGCAAGCCCAA
ACTCCTACAGGGAAACAGACGGATAAAACCAAATCTAACATGAAGGGTTTCTAA
14 changes: 14 additions & 0 deletions benchmark_sequences/brute/EMG1_dna.fasta
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>NM_006331.8 Homo sapiens EMG1 N1-specific pseudouridine methyltransferase (EMG1), transcript variant 1, mRNA
ATGGCGGCGCCTTCTGACGGGTTCAAACCCCGCGAACGTTCGGGGGGCGAGCAGGCTCAG
GACTGGGACGCCCTGCCGCCGAAACGGCCGAGACTGGGCGCAGGTAACAAGATCGGCGGA
CGGCGTCTGATTGTCGTTCTAGAGGGCGCTTCTTTGGAGACAGTTAAGGTGGGTAAGACG
TATGAATTACTCAACTGCGATAAACACAAGTCGATACTACTAAAGAATGGTCGTGACCCG
GGCGAAGCCCGTCCGGACATTACACACCAGAGCCTGCTCATGCTGATGGATTCACCTCTG
AATCGGGCCGGACTTCTCCAGGTATATATCCACACCCAAAAAAATGTTCTTATTGAAGTG
AACCCGCAGACAAGGATCCCGAGAACGTTTGACCGCTTTTGCGGTCTCATGGTGCAATTG
CTCCATAAACTTAGTGTTCGCGCGGCTGACGGTCCGCAGAAACTACTGAAGGTGATTAAA
AATCCTGTAAGTGACCATTTTCCCGTGGGATGTATGAAAGTAGGTACCTCTTTCTCCATT
CCAGTAGTGTCAGATGTTAGAGAACTGGTTCCTAGTTCGGATCCGATTGTTTTTGTCGTA
GGCGCTTTTGCGCATGGTAAGGTTTCAGTAGAATACACAGAGAAGATGGTGTCTATCTCT
AACTACCCGCTTTCGGCGGCCTTAACGTGTGCCAAGCTAACAACCGCGTTTGAAGAAGTG
TGGGGGGTGATCTGA
18 changes: 18 additions & 0 deletions benchmark_sequences/brute/FALVAC-1_dna.fasta
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>U65407.1 Plasmodium falciparum apical membrane antigen 1 (AMA-1) gene, complete cds
ATGGCAAAGCATAAAAAACTCAAACAGCCGGGCGATGGGAATCCCTGGAGTCCATGTTCA
GTGACTTGCGGTAAGCCGAAGGATGAACTAGACTACGAAAACGACATAGAAAAGAAAATC
TGTAAAATGGAAAAATGCTCATCCGTATTCAACGTGGTTAATTCGAATTCAGGCTGCTTC
CGACATCTGGACGAGCGCGAAGAGTGCAAGTGCTTGCTGGAAGACAGTGGTTCCAACGGC
AAAAAGATTACGTGTGAATGTACGAAACCGGATTCGAAACCTATCGTTCAGTATGACAAC
TTCAACGCGAATCCGAACGCTAATCCTAATGCCAACCCTGATGGAAATTGCGAAGATATC
CCTCATGTTAACGAATTTAGTGCTATTGACCTCGGCAATGCAGAAAAATATGATAAAATG
GATGAACCACAGCACTACGGTAAATCCTTGACCCCGTTGGAGGAACTGTATAAACCAAAC
GATAAATCGTTATATCAATATATTAAAGCGAATAGCAAGTTTATCGGCATCACCGAACTG
TCAAACACGTTTATTAATAATGCCGGTCAGCATGGACATATGCACGGTAACGAAAGGGAA
GACGAACGCACCCTTACCAAGGAGTATGAGGATATTGTGTTGAAAGAGTTCACGTATATG
ATTAATTTCGGACGTGGACAGAACTACTGGGAACACCCCTACCAAAAGTCCGACCAGCCG
AAGCAATATGAGCAACACCTAACAGACTACGAAAAAATTAAGGAGGGCAAGCCGTTGGAT
AAATTCGGTAACATATACGATTATCACTATGAGCATAGCTCTCCGTCTTCTACAAAGTCG
AGCAGCCCGAGTAATGTGAAATCAGCGTCACTGGCAACCCGTTTAATGAAGAAGTTTAAA
GCCGAGATCAGGGATTTCTTTGGAATTAGTTACTATGAAAAAGTGCTAGCTAAATATAAA
GATGACCTGGAG
42 changes: 42 additions & 0 deletions benchmark_sequences/brute/FGFR4_dna.fasta
Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
>NM_002011.5 Homo sapiens fibroblast growth factor receptor 4 (FGFR4), transcript variant 1, mRNA
ATGAGATTACTGCTTGCCCTCCTCGGAGTTCTTCTATCGGTACCGGGGCCGCCGGTCCTT
TCCCTAGAGGCGAGTGAAGAAGTGGAACTAGAACCGTGCCTGGCGCCATCTTTGGAGCAA
CAAGAGCAGGAACTGACGGTCGCCCTTGGCCAACCGGTCAGGCTGTGTTGTGGCCGTGCT
GAGCGAGGCGGGCATTGGTATAAAGAAGGGTCTCGTCTCGCGCCCGCTGGTCGGGTTCGC
GGCTGGCGAGGTAGACTTGAAATTGCTAGTTTTCTCCCGGAAGATGCTGGCCGTTATCTG
TGCTTAGCTCGCGGTTCTATGATCGTGCTCCAGAACTTAACCCTGATAACTGGTGATTCG
TTGACTTCATCAAATGACGACGAGGATCCAAAATCCCATCGAGATCCTTCCAATCGACAC
TCGTATCCACAGCAGGCCCCTTACTGGACTCACCCCCAGCGGATGGAGAAAAAATTACAC
GCGGTTCCGGCAGGAAATACCGTTAAGTTTCGCTGCCCCGCGGCAGGTAACCCCACCCCA
ACTATAAGATGGTTAAAGGATGGCCAGGCCTTTCATGGCGAGAATCGCATTGGTGGGATC
CGCCTGAGGCACCAGCATTGGTCCCTGGTTATGGAATCTGTCGTTCCTTCCGACCGTGGA
ACATACACTTGTTTGGTGGAAAATGCAGTCGGTTCCATACGGTATAACTATCTTTTGGAC
GTGCTTGAGAGATCCCCTCACCGTCCTATCTTGCAGGCTGGTTTACCCGCTAATACGACA
GCAGTGGTCGGAAGTGACGTAGAGCTATTATGCAAAGTCTACTCTGACGCTCAACCGCAT
ATACAATGGCTTAAACATATCGTCATCAACGGGAGCTCGTTTGGGGCGGATGGGTTCCCT
TACGTTCAGGTGTTGAAAACAGCTGACATCAACTCAAGCGAGGTTGAGGTCCTTTACCTG
CGGAATGTCTCGGCGGAGGATGCCGGCGAGTATACCTGCCTAGCGGGGAACTCTATCGGA
CTAAGTTATCAGTCCGCATGGTTGACCGTGCTGCCAGAGGAAGATCCTACATGGACCGCC
GCTGCGCCAGAGGCTAGATATACGGATATCATTCTATACGCCTCAGGATCATTGGCCCTG
GCCGTGCTATTGCTACTCGCAGGTCTCTACCGAGGCCAAGCTTTACACGGTCGGCACCCT
CGCCCGCCGGCCACTGTACAGAAGCTCTCTCGCTTCCCTCTGGCGAGGCAATTTTCGCTC
GAGAGCGGAAGCTCAGGAAAATCGTCCTCGAGCCTCGTGAGAGGTGTCCGCCTGTCATCC
TCAGGCCCAGCGTTATTAGCTGGTTTAGTCTCCCTTGATCTGCCCCTGGATCCGCTATGG
GAATTTCCCAGGGACCGTCTGGTTCTGGGTAAACCACTCGGGGAGGGATGTTTCGGACAA
GTGGTTCGTGCCGAAGCTTTCGGCATGGACCCGGCCCGACCCGACCAGGCTTCAACGGTG
GCTGTCAAAATGTTAAAAGACAACGCGTCCGACAAAGACTTGGCCGATCTTGTTTCCGAG
ATGGAGGTTATGAAGCTTATTGGTCGCCATAAGAATATCATAAACCTTCTGGGTGTGTGC
ACTCAAGAAGGCCCTCTTTATGTAATTGTTGAGTGCGCCGCAAAAGGTAATCTCCGAGAA
TTTCTCCGCGCTAGACGGCCGCCTGGGCCCGATTTGAGCCCAGATGGCCCGCGGTCGTCT
GAGGGGCCTCTGAGCTTCCCGGTGCTCGTGTCCTGTGCATACCAAGTTGCGCGGGGGATG
CAATACCTTGAGAGCCGCAAATGTATCCACCGTGACCTAGCAGCGCGCAATGTCCTCGTC
ACAGAAGACAACGTCATGAAAATTGCAGACTTTGGGCTTGCTCGTGGTGTGCATCACATC
GATTACTACAAGAAAACCTCAAACGGCCGCTTACCAGTGAAATGGATGGCGCCGGAAGCC
CTTTTCGATCGTGTGTATACTCACCAATCTGATGTCTGGTCATTCGGTATCCTGCTATGG
GAAATATTTACACTGGGAGGAAGTCCCTACCCGGGGATTCCAGTCGAGGAATTATTCAGT
CTCTTACGCGAAGGCCATCGCATGGATCGGCCGCCTCATTGCCCTCCCGAACTCTACGGG
TTGATGCGAGAATGCTGGCACGCTGCACCGAGCCAGCGTCCGACATTCAAACAATTGGTG
GAGGCGCTCGATAAAGTCTTACTCGCCGTTAGTGAAGAATATTTAGATCTGCGGTTAACC
TTCGGGCCCTACAGCCCATCGGGGGGGGATGCTAGTAGTACTTGCAGTTCAAGTGATTCT
GTTTTTTCCCATGATCCGCTTCCTCTGGGTTCGAGCAGTTTTCCATTCGGGTCCGGTGTA
CAGACGTAG
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