Origin IGS: attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatgtataaaattatagtagtaaagatttttacttctgtacaggagataaattaagactccaagaaacagaggtaaaaatactaatgtaaatttaatctttttcattctattgcctcacttatttatttagtaataggttatagctttattaaaaaaatgtcaataaaaaatttacttctatataccaaatatattttttatgttataatataggatatttcaaatttagtgaacaaagttttctataaaggtggttaaaaaat Mask Tandem Repeat Region ================================================ attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Find is-nt database================================================ Query_seq: FN0533:FN0534|FN0533:FN0534:Hypothetical membrane-spanning protein:hypothetical protein:<-->:1188732..1188997 266 attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0533:FN0534|FN0533:FN0534:Hypothetical membrane-spanning protein:hypothetical protein:<-->:1188732..1188997 266 attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0533:FN0534|FN0533:FN0534:Hypothetical membrane-spanning protein:hypothetical protein:<-->:1188732..1188997 266 attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 159 End: 266 .............................................................................................................................................................. M K K I K F T L V F L P L F L G V L I Y L L Y R S K N L Y Y Y N F I H F Protein_Len: 34 Strand: - Start: 54 End: 155 ..................................................... I I V Y F I Y K T Y L L L N K I S M K K I F S Y G I V L Y I L S A M ............................................................................................................... attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 30 End: 59 .............................GTTCACTAAATTTGAAATATCCTATATTAT............................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 55 End: 84 ......................................................ATATACCAAATATATTTTTTATGTTATAAT...................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 100 End: 129 ...................................................................................................ATTGACATTTTTTTAATAAAGCTATAACCT......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0533:FN0534|FN0533:FN0534:Hypothetical membrane-spanning protein:hypothetical protein:<-->:1188732..1188997 266 attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: NC_003454_FN0533_FN0534|Hypothetical membrane-spanning protein:hypothetical protein|NEGATIVE:POSITIVE|[1188732,1188997]|266 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 266 Query Start:1 Query End:266 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacannnnnnnaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt attttttaaccacctttatagaaaactttgttcactaaatttgaaatatcctatattataacataaaaaatatatttggtatatagaagtaaattttttattgacatttttttaataaagctataacctattactaaataaataagtgaggcaatagaatgaaaaagattaaatttacattagtatttttacctctgtttcttggagtcttaatttatctcctgtacagaagtaaaaatctttactactataattttatacatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUUAACCACCUUUAUAGAAAACUUUGUUCACUAAAUUUGAAAUAUCCUAUAUUAUAACAUAAAAAAUAUAUUUGGUAUAUAGAAGUAAAUUUUUUAUUGACAUUUUUUUAAUAAAGCUAUAACCUAUUACUAAAUAAAUAAGUGAGGCAAUAGAAUGAAAAAGAUUAAAUUUACAUUAGUAUUUUUACCUCUGUUUCUUGGAGUCUUAAUUUAUCUCCUGUACAGAAGUAAAAAUCUUUACUACUAUAAUUUUAUACAUUUU ...............((((((....(((((((((((........(((((...)))))...............(((((((((.((((..((.....(((((((((.......))))))))).....)))))))))))))))....))))).)))).))......(((((((.....(((....)))..(((((.(((((.....((((...........))))...))))).))))))))))))....))))))............. (-38.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUAUAAAAUUAUAGUAGUAAAGAUUUUUACUUCUGUACAGGAGAUAAAUUAAGACUCCAAGAAACAGAGGUAAAAAUACUAAUGUAAAUUUAAUCUUUUUCAUUCUAUUGCCUCACUUAUUUAUUUAGUAAUAGGUUAUAGCUUUAUUAAAAAAAUGUCAAUAAAAAAUUUACUUCUAUAUACCAAAUAUAUUUUUUAUGUUAUAAUAUAGGAUAUUUCAAAUUUAGUGAACAAAGUUUUCUAUAAAGGUGGUUAAAAAAU .............(((((.(((((....(((((((((((((...((((...........)))).....)))))))))))))))))).))))).(((((((.........((((.((((...(((((.....))))).)))).))))((((((..((((..(((((.((((........((((((((....((((((.....))))))...)))))))).........)))).)).)))...))))..))))))..))))))).... (-47.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 669 60 11 151 102 NC_003454:FN0533|5end_Hypothetical_membrane-spanning_protein_1188641..1188871_NEGATIVE 231 226 181 125 76 NC_003454:FN2110|5end_Hypothetical_exported_24-amino_acid_repeat_protein_622330..622560_NEGATIVE 230 160 119 64 25 NC_003454:FN1800|5end_Peptidyl-prolyl_cis-trans_isomerase_281630..281860_POSITIVE 228 235 194 228 180 NC_003454:FN1621|5end_elongation_factor_Ts_128673..128903_POSITIVE 226 167 121 201 142 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 214 153 113 209 153 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 214 216 172 231 188 NC_003454:FN2013|5end_GTP-binding_protein_514652..514882_NEGATIVE 210 232 192 69 30 NC_003454:FN0385|5end_hypothetical_protein_1017920..1018150_POSITIVE 207 133 95 230 193 NC_003454:FN0340|5end_Hypothetical_membrane-spanning_Protein_973948..974178_NEGATIVE 206 226 184 123 82 NC_003454:FN1057|5end_Diamine_acetyltransferase_1704326..1704556_POSITIVE 206 159 117 80 41 NC_003454:FN0557|5end_hypothetical_protein_1210334..1210564_NEGATIVE 203 234 193 74 32 NC_003454:FN0040|5end_asparaginyl-tRNA_synthetase_680609..680839_NEGATIVE 200 208 175 224 181 NC_003454:FN1284|5end_30S_ribosomal_protein_S4_1943243..1943473_NEGATIVE 200 225 181 224 185 NC_003454:FN0974|5end_Lactoylglutathione_lyase_1627144..1627374_NEGATIVE 200 239 192 112 64 NC_003454:FN1939|5end_hypothetical_protein_439465..439695_NEGATIVE 195 37 13 210 187 NC_003454:FN0609|5end_SsrA-binding_protein_1264261..1264491_POSITIVE 194 208 174 116 81 NC_003454:FN1216|5end_RRF2_family_protein_1876602..1876832_NEGATIVE 193 129 83 109 48 NC_003454:FN1456|5end_UDP-N-acetylmuramate--alanine_ligase_2137922..2138152_NEGATIVE 193 224 187 78 43 NC_003454:FN1286|5end_30S_ribosomal_protein_S13_1944074..1944304_NEGATIVE 193 62 25 40 5 NC_003454:FN1176|5end_Hypothetical_cytosolic_protein_1837826..1838056_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 102 61 63 23 NC_003454:FN0542|3end_Beta_1,4_glucosyltransferase_1196094..1196244_POSITIVE 210 148 103 144 97 NC_003454:FN0341|3end_transport_protein_974053..974203_NEGATIVE 207 176 142 38 1 NC_003454:FN1435|3end_Export_ABC_transporter_2105347..2105497_POSITIVE 206 226 184 89 48 NC_003454:FN1056|3end_hypothetical_protein_1704372..1704522_POSITIVE 203 234 193 64 22 NC_003454:FN0041|3end_hypothetical_protein_680619..680769_NEGATIVE 194 208 174 119 84 NC_003454:FN1217|3end_Holliday_junction_DNA_helicase_ruvB_1876599..1876749_NEGATIVE 194 244 204 36 1 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 193 129 83 128 67 NC_003454:FN1457|3end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2137903..2138053_NEGATIVE 193 62 25 77 42 NC_003454:FN1177|3end_hypothetical_protein_1837789..1837939_NEGATIVE 192 228 185 60 17 NC_003454:FN0477|3end_Cell_wall_endopeptidase_family_M23/M37_1125917..1126067_POSITIVE 192 223 187 85 40 NC_003454:FN1640|3end_LSU_ribosomal_protein_L22P_138182..138332_NEGATIVE 191 244 219 31 3 NC_003454:FN0842|3end_hypothetical_protein_1502822..1502972_NEGATIVE 191 244 219 29 1 NC_003454:FN2053|3end_Serine/threonine_sodium_symporter_561228..561378_NEGATIVE 191 226 182 136 94 NC_003454:FN1978|3end_Cell_division_protein_ftsH_481703..481853_POSITIVE 191 244 219 31 3 NC_003454:FN1890|3end_hypothetical_protein_373045..373195_NEGATIVE 188 235 192 52 14 NC_003454:FN0237|3end_ABC_transporter_permease_protein_861403..861553_NEGATIVE 188 220 171 134 82 NC_003454:FN1846|3end_hypothetical_protein_336225..336375_POSITIVE 185 226 182 65 14 NC_003454:FN1492|3end_DNA_repair_protein_recO_2172769..2172919_NEGATIVE 183 243 204 58 24 NC_003454:FN1801|3end_Sodium/glutamate_symport_carrier_protein_282636..282786_NEGATIVE 183 259 211 131 78 NC_003454:FN1755|3end_thiamine_biosynthesis_protein_ThiF_251240..251390_NEGATIVE