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wilzbachwilzbach
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add vp_24 example
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‎snippets/data/VP24_Filoviridae/VP24_Filoviridae-alignment-annotation.gff

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##gff-version 3.2.1
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Bundibugyo_virus . Helix 23 31 . . . Name=Helix
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Bundibugyo_virus . Strand 37 43 . . . Name=Strand
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Bundibugyo_virus . Strand 45 49 . . . Name=Strand
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Bundibugyo_virus . Helix 54 58 . . . Name=Helix
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Bundibugyo_virus . Helix 70 80 . . . Name=Helix
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Bundibugyo_virus . Helix 85 88 . . . Name=Helix
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Bundibugyo_virus . Helix 90 126 . . . Name=Helix
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Bundibugyo_virus . Strand 127 127 . . . Name=Strand
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Bundibugyo_virus . Helix 128 128 . . . Name=Helix
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Bundibugyo_virus . Strand 134 134 . . . Name=Strand
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Bundibugyo_virus . Helix 139 166 . . . Name=Helix
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Bundibugyo_virus . Strand 167 170 . . . Name=Strand
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Bundibugyo_virus . Strand 178 181 . . . Name=Strand
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Bundibugyo_virus . Strand 187 192 . . . Name=Strand
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Bundibugyo_virus . Strand 196 202 . . . Name=Strand
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Bundibugyo_virus . Strand 217 222 . . . Name=Strand
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Bundibugyo_virus . Helix 225 226 . . . Name=Helix
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Bundibugyo_virus . Strand 238 242 . . . Name=Strand
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Bundibugyo_virus . Helix 243 245 . . . Name=Helix
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Sudan_ebolavirus . Helix 23 31 . . . Name=Helix
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Sudan_ebolavirus . Strand 37 42 . . . Name=Strand
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Sudan_ebolavirus . Strand 45 49 . . . Name=Strand
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Sudan_ebolavirus . Strand 54 58 . . . Name=Strand
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Sudan_ebolavirus . Helix 70 71 . . . Name=Helix
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Sudan_ebolavirus . Helix 73 79 . . . Name=Helix
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Sudan_ebolavirus . Helix 85 88 . . . Name=Helix
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Sudan_ebolavirus . Helix 90 125 . . . Name=Helix
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Sudan_ebolavirus . Strand 126 128 . . . Name=Strand
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Sudan_ebolavirus . Strand 133 135 . . . Name=Strand
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Sudan_ebolavirus . Helix 140 166 . . . Name=Helix
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Sudan_ebolavirus . Strand 167 170 . . . Name=Strand
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Sudan_ebolavirus . Strand 178 181 . . . Name=Strand
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Sudan_ebolavirus . Strand 187 192 . . . Name=Strand
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Sudan_ebolavirus . Strand 196 202 . . . Name=Strand
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Sudan_ebolavirus . Strand 217 222 . . . Name=Strand
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Sudan_ebolavirus . Helix 225 226 . . . Name=Helix
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Sudan_ebolavirus . Helix 238 246 . . . Name=Helix
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Reston_ebolavirus . Helix 23 31 . . . Name=Helix
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Reston_ebolavirus . Strand 37 42 . . . Name=Strand
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Reston_ebolavirus . Strand 45 49 . . . Name=Strand
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Reston_ebolavirus . Strand 54 55 . . . Name=Strand
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Reston_ebolavirus . Helix 56 56 . . . Name=Helix
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Reston_ebolavirus . Strand 57 58 . . . Name=Strand
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Reston_ebolavirus . Helix 70 71 . . . Name=Helix
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Reston_ebolavirus . Helix 73 79 . . . Name=Helix
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Reston_ebolavirus . Helix 85 88 . . . Name=Helix
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Reston_ebolavirus . Helix 90 125 . . . Name=Helix
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Reston_ebolavirus . Strand 126 128 . . . Name=Strand
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Reston_ebolavirus . Strand 134 135 . . . Name=Strand
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Reston_ebolavirus . Helix 140 166 . . . Name=Helix
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Reston_ebolavirus . Strand 167 170 . . . Name=Strand
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Reston_ebolavirus . Strand 178 181 . . . Name=Strand
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Reston_ebolavirus . Strand 187 192 . . . Name=Strand
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Reston_ebolavirus . Strand 196 202 . . . Name=Strand
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Reston_ebolavirus . Strand 217 222 . . . Name=Strand
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Reston_ebolavirus . Helix 225 226 . . . Name=Helix
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Reston_ebolavirus . Helix 238 247 . . . Name=Helix
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Zaire_ebolavirus . Helix 23 31 . . . Name=Helix
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Zaire_ebolavirus . Strand 38 42 . . . Name=Strand
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Zaire_ebolavirus . Strand 45 49 . . . Name=Strand
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Zaire_ebolavirus . Helix 54 58 . . . Name=Helix
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Zaire_ebolavirus . Helix 70 71 . . . Name=Helix
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Zaire_ebolavirus . Helix 73 80 . . . Name=Helix
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Zaire_ebolavirus . Helix 85 88 . . . Name=Helix
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Zaire_ebolavirus . Helix 90 126 . . . Name=Helix
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Zaire_ebolavirus . Strand 127 127 . . . Name=Strand
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Zaire_ebolavirus . Strand 134 134 . . . Name=Strand
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Zaire_ebolavirus . Helix 139 166 . . . Name=Helix
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Zaire_ebolavirus . Strand 167 170 . . . Name=Strand
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Zaire_ebolavirus . Strand 178 181 . . . Name=Strand
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Zaire_ebolavirus . Strand 187 192 . . . Name=Strand
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Zaire_ebolavirus . Strand 196 201 . . . Name=Strand
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Zaire_ebolavirus . Strand 217 221 . . . Name=Strand
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Zaire_ebolavirus . Helix 224 226 . . . Name=Helix
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Zaire_ebolavirus . Helix 238 247 . . . Name=Helix
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TaiForest_ebolavirus . Helix 23 31 . . . Name=Helix
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TaiForest_ebolavirus . Strand 38 42 . . . Name=Strand
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TaiForest_ebolavirus . Strand 45 49 . . . Name=Strand
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TaiForest_ebolavirus . Helix 54 58 . . . Name=Helix
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TaiForest_ebolavirus . Helix 70 71 . . . Name=Helix
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TaiForest_ebolavirus . Helix 73 80 . . . Name=Helix
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TaiForest_ebolavirus . Helix 85 88 . . . Name=Helix
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TaiForest_ebolavirus . Helix 90 126 . . . Name=Helix
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TaiForest_ebolavirus . Strand 127 127 . . . Name=Strand
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TaiForest_ebolavirus . Strand 133 135 . . . Name=Strand
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TaiForest_ebolavirus . Helix 139 166 . . . Name=Helix
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TaiForest_ebolavirus . Strand 167 170 . . . Name=Strand
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TaiForest_ebolavirus . Strand 178 181 . . . Name=Strand
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TaiForest_ebolavirus . Strand 187 192 . . . Name=Strand
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TaiForest_ebolavirus . Strand 196 202 . . . Name=Strand
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TaiForest_ebolavirus . Strand 217 221 . . . Name=Strand
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TaiForest_ebolavirus . Helix 224 227 . . . Name=Helix
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TaiForest_ebolavirus . Helix 238 247 . . . Name=Helix
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LakeVictoria_marburgvirus . Helix 23 31 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 37 42 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 45 49 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 54 55 . . . Name=Strand
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LakeVictoria_marburgvirus . Helix 56 56 . . . Name=Helix
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LakeVictoria_marburgvirus . Strand 57 59 . . . Name=Strand
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LakeVictoria_marburgvirus . Helix 70 71 . . . Name=Helix
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LakeVictoria_marburgvirus . Helix 73 80 . . . Name=Helix
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LakeVictoria_marburgvirus . Helix 85 101 . . . Name=Helix
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LakeVictoria_marburgvirus . Helix 105 123 . . . Name=Helix
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LakeVictoria_marburgvirus . Helix 125 125 . . . Name=Helix
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LakeVictoria_marburgvirus . Strand 126 128 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 133 135 . . . Name=Strand
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LakeVictoria_marburgvirus . Helix 139 166 . . . Name=Helix
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LakeVictoria_marburgvirus . Strand 167 170 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 178 181 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 187 192 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 196 202 . . . Name=Strand
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LakeVictoria_marburgvirus . Strand 219 224 . . . Name=Strand
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LakeVictoria_marburgvirus . Helix 226 228 . . . Name=Helix
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LakeVictoria_marburgvirus . Helix 241 248 . . . Name=Helix
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Lloviu_cuevavirus . Strand 8 8 . . . Name=Strand
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Lloviu_cuevavirus . Helix 23 31 . . . Name=Helix
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Lloviu_cuevavirus . Strand 37 42 . . . Name=Strand
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Lloviu_cuevavirus . Strand 45 49 . . . Name=Strand
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Lloviu_cuevavirus . Strand 54 54 . . . Name=Strand
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Lloviu_cuevavirus . Helix 55 56 . . . Name=Helix
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Lloviu_cuevavirus . Strand 57 58 . . . Name=Strand
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Lloviu_cuevavirus . Helix 70 71 . . . Name=Helix
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Lloviu_cuevavirus . Helix 73 80 . . . Name=Helix
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Lloviu_cuevavirus . Helix 85 88 . . . Name=Helix
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Lloviu_cuevavirus . Helix 90 125 . . . Name=Helix
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Lloviu_cuevavirus . Strand 126 128 . . . Name=Strand
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Lloviu_cuevavirus . Strand 133 135 . . . Name=Strand
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Lloviu_cuevavirus . Helix 140 166 . . . Name=Helix
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Lloviu_cuevavirus . Strand 167 170 . . . Name=Strand
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Lloviu_cuevavirus . Strand 178 181 . . . Name=Strand
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Lloviu_cuevavirus . Strand 187 192 . . . Name=Strand
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Lloviu_cuevavirus . Strand 196 201 . . . Name=Strand
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Lloviu_cuevavirus . Strand 217 222 . . . Name=Strand
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Lloviu_cuevavirus . Helix 225 226 . . . Name=Helix
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Lloviu_cuevavirus . Strand 240 242 . . . Name=Strand
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Lloviu_cuevavirus . Helix 243 243 . . . Name=Helix

‎snippets/data/VP24_Filoviridae/VP24_Filoviridae-alignment-clustal.aln

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CLUSTAL W (1.83) multiple sequence alignment
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Bundibugyo_virus MAKATGRYNLVSPKKDLERGLVLSDLCTFLVDQTIQGWRVTWVGIEFDIAQKGMALLHRL
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Reston_ebolavirus MAKATGRYNLVPPKKDMEKGVIFSDLCNFLITQTLQGWKVYWAGIEFDVSQKGMALLTRL
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Sudan_ebolavirus MAKATGRYNLVTPKRELEQGVVFSDLCNFLVTPTVQGWKVYWAGLEFDVNQKGITLLNRL
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TaiForest_ebolavirus MAKATGRYNLISPKKDLEKGLVLNDLCTLSVAQTVQGWKVTWAGIEFDVTQKGMALLHRL
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Zaire_ebolavirus MAKATGRYNLISPKKDLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLQRL
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LakeVictoria_marburgvirus MAELSTRYNLPANVTEKSINLDLNSTARWIKEPSVGGWTVKWGNFVFHIPNTGMALLHHL
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Lloviu_cuevavirus MARPSGRYNILQTDTFHENTVVKHDLCNFLVTTTITGWDVYWAGHLFHVPNKGIALLTRL
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** *** ** * * * * ** *
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Bundibugyo_virus KTADFAPAWSMTRNLFPHLFQNSNSTIESPLWALRVILAAGIQDQLIDQSLVEPLAGALS
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Reston_ebolavirus KTNDFAPAWAMTRNLFPHLFQNPNSVIQSPIWALRVILAAGLQDQLLDHSLVEPLTGALG
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Sudan_ebolavirus KVNDFAPAWAMTRNLFPHLFKNQQSEVQTPIWALRVILAAGILDQLMDHSLIEPLSGALN
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TaiForest_ebolavirus KTSDFAPAWSMTRNLFPHLFQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALG
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Zaire_ebolavirus KTNDFAPAWSMTRNLFPHLFQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALG
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LakeVictoria_marburgvirus KSNFVVPEWQQTRNLFSHLFKNPKSTIIEPFLALRILLGVALKDQELQQSLIPGFRSIVH
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Lloviu_cuevavirus KTSDFAPAWTLTKNLFPHLFHNPTSTLKDPVWGLRVILAAALYDQVMEQSLIKPLSETLT
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* * * * ** *** * * * ** * ** **
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Bundibugyo_virus LVSDWLLTTNTNHFQMRTQHAKEQLSLKMLSLVRSNILKFISQLDALHVVNYNGLLSSIE
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Reston_ebolavirus LISDWLLTTTSTHFNLRTRSVKDQLSLRMLSLIRSNILQFINKLDALHVVNYNGLLSSIE
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Sudan_ebolavirus LIADWLLTTSTNHFNMRTQRVKDQLSMRMLSLIRSNIINFINKLETLHVVNYKGLLSSVE
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TaiForest_ebolavirus LIADWLLTTGTNHFQMRTQQAKEQLSLKMLSLVRSNILKFINQLDALHVVNYNGLLSSIE
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Zaire_ebolavirus LISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKFINRLDALHVVNYNGLLSSIE
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LakeVictoria_marburgvirus MLSEWLLLEVTSAIHISPNLLGIYLTSDMFKILMAGVKNFFNKMFTLHVVNDHGKPSSIE
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Lloviu_cuevavirus LLGDWLLTTETQKFNLRTPRAQEQISLRMLSLVKKHVDNFILKLLELHVINNRGFTSSIE
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*** * * *** * * ** *
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Bundibugyo_virus IGTRNHTIIITRTNMGFLVELQEPDKSAMNQKK--PGPVKFSLLHESTFKALIKKPATKM
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Reston_ebolavirus IGTSTHTIIITRTNMGFLVEVQEPDKSAMNSKR--PGPVKFSLLHESAFKPFTRVPQSGM
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Sudan_ebolavirus IGTPSYAIIITRTNMGYLVEVQEPDKSAMDIRH--PGPVKFSLLHESTLKPVATPKPSSI
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TaiForest_ebolavirus IGTKSHTIIITRTNMGFLVELQEPDKSAMNTRK--PGPVKFSLLHESTLKTLAKKPATQM
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Zaire_ebolavirus IGTQNHTIIITRTNMGFLVELQEPDKSAMNRKK--PGPAKFSLLHESTLKAFTQGSSTRM
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LakeVictoria_marburgvirus IKLTGQQIIITRVNMGFLVEVRRIDIEPCCGETVLSESVVFGLVAEAVLREHSQMEKGQP
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Lloviu_cuevavirus IGNKCNTIIISRTNMGYLVEQQEPDKSALRKTK--PGPVKFTLVHEDAFRDF-KPERSSI
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* *** * *** *** * * * *
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Bundibugyo_virus QALILEFNSSLAI
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Reston_ebolavirus QSLIMEFNSLLAI
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Sudan_ebolavirus TSLIMEFNSSLAI
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TaiForest_ebolavirus QALILEFNSSLAI
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Zaire_ebolavirus QSLILEFNSSLAI
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LakeVictoria_marburgvirus LDLTQYMNSKIAI
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Lloviu_cuevavirus NLLIMEFNSSLAI
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* ** **
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‎snippets/data/VP24_Filoviridae/VP24_Filoviridae-alignment-tree.newick

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(
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(
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(
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LakeVictoria_marburgvirus:0.43470,
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Lloviu_cuevavirus:0.20930)
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:0.07985,
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Sudan_ebolavirus:0.12885)
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:0.02753,
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Reston_ebolavirus:0.09798,
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(
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Zaire_ebolavirus:0.05129,
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(
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Bundibugyo_virus:0.06300,
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TaiForest_ebolavirus:0.04855)
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:0.02640)
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:0.04644);

‎snippets/vp24_filovirida.js

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var opts = {
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el: yourDiv,
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importURL: "./data/VP24_Filoviridae/VP24_Filoviridae-alignment-clustal.aln",
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conf: {
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dropImport: true
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},
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vis: {
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conserv: false,
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overviewbox: true,
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seqlogo: true
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}
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};
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// init msa
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var m = msa(opts);
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m.render();
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// extend async
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m.u.file.importURL("./data/VP24_Filoviridae/VP24_Filoviridae-alignment-annotation.gff");
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m.u.file.importURL("./data/VP24_Filoviridae/VP24_Filoviridae-alignment-tree.newick");

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