Origin IGS: tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa .........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 tttttcattccccctttaattttttcgtttaaaaaacttgttatcagattcattataacataaaaaaattattttgtatcaatttttccctaaaaatataaatatatagttttaaagttaattgtaaataaaattttaaaaatgtttaaaaaaagtataaaaagattgatgattttaaagaaaatatgatataattagtttataataattttataaaaagggggataagtaaa Mask Tandem Repeat Region ================================================ tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Find is-nt database================================================ Query_seq: FN1547:FN1548|FN1547:FN1548:PTS permease for N-acetylglucosamine and glucose:hypothetical protein:<-->:63361..63593 233 tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1547:FN1548|FN1547:FN1548:PTS permease for N-acetylglucosamine and glucose:hypothetical protein:<-->:63361..63593 233 tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1547:FN1548|FN1547:FN1548:PTS permease for N-acetylglucosamine and glucose:hypothetical protein:<-->:63361..63593 233 tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 49 End: 141 ................................................ M F F K I I N L F I L F L N I F K I L F T I N F K T I Y L Y F ............................................................................................ tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa 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: 72 End: 101 .......................................................................TTTTATACTTTTTTTAAACATTTTTAAAAT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1547:FN1548|FN1547:FN1548:PTS permease for N-acetylglucosamine and glucose:hypothetical protein:<-->:63361..63593 233 tttacttatccccctttttataaaattattataaactaattatatcatattttctttaaaatcatcaatctttttatactttttttaaacatttttaaaattttatttacaattaactttaaaactatatatttatatttttagggaaaaattgatacaaaataatttttttatgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_003454_FN1547_FN1548|PTS permease for N-acetylglucosamine and glucose:hypothetical protein|NEGATIVE:POSITIVE|[63361,63593]|233 HSP 1 e-value: 1.0E-26 bit: 121.0 Len: 61 Query Start:173 Query End:233 Subject Strand: POSITIVE Subject Start: 173 Subject End: 233 ............................................................................................................................................................................atgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa ............................................................................................................................................................................atgttataatgaatctgataacaagttttttaaacgaaaaaattaaagggggaatgaaaaa HSP 2 e-value: 2.0E-19 bit: 97.6 Len: 49 Query Start:1 Query End:49 Subject Strand: POSITIVE Subject Start: 1 Subject End: 49 tttacttatccccctttttataaaattattataaactaattatatcata........................................................................................................................................................................................ tttacttatccccctttttataaaattattataaactaattatatcata........................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUUAUCCCCCUUUUUAUAAAAUUAUUAUAAACUAAUUAUAUCAUAUUUUCUUUAAAAUCAUCAAUCUUUUUAUACUUUUUUUAAACAUUUUUAAAAUUUUAUUUACAAUUAACUUUAAAACUAUAUAUUUAUAUUUUUAGGGAAAAAUUGAUACAAAAUAAUUUUUUUAUGUUAUAAUGAAUCUGAUAACAAGUUUUUUAAACGAAAAAAUUAAAGGGGGAAUGAAAAA ........(((((((((((((((.....))))))...............((((((((((((........(((.((((...(((.((((((((....((((..((((((.(((((..((((((((.((((....)))).))))))))...))))).....))))))..)))).))))).))).)))....)))).)))..))))))).)))))....)))))))))........ (-35.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCAUUCCCCCUUUAAUUUUUUCGUUUAAAAAACUUGUUAUCAGAUUCAUUAUAACAUAAAAAAAUUAUUUUGUAUCAAUUUUUCCCUAAAAAUAUAAAUAUAUAGUUUUAAAGUUAAUUGUAAAUAAAAUUUUAAAAAUGUUUAAAAAAAGUAUAAAAAGAUUGAUGAUUUUAAAGAAAAUAUGAUAUAAUUAGUUUAUAAUAAUUUUAUAAAAAGGGGGAUAAGUAAA ........(((((((((..(((((......)))))..(((((((.(((((.((((((.((((..............(((((((((((...........(((((((....((((((((((............)))))))))))))))))............))))))))))).............)))).)))))).))))))))))))........)))))))))........ (-38.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 613 50 1 141 92 NC_003454:FN1547|5end_PTS_permease_for_N-acetylglucosamine_and_glucose_63270..63500_NEGATIVE 287 110 65 129 88 NC_003454:FN0606|5end_Translation_initiation_inhibitor_1261014..1261244_POSITIVE 238 44 3 139 94 NC_003454:FN0832|5end_hypothetical_protein_1494305..1494535_POSITIVE 216 54 11 146 106 NC_003454:FN0348|5end_nicotinate_phosphoribosyltransferase_981723..981953_NEGATIVE 212 49 9 183 134 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 206 59 13 189 141 NC_003454:FN0256|5end_Hypothetical_cytosolic_protein_882208..882438_POSITIVE 198 56 11 144 100 NC_003454:FN1520|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_26073..26303_NEGATIVE 193 93 65 88 60 NC_003454:FN1063|5end_N-acyl-L-amino_acid_amidohydrolase_1709325..1709555_POSITIVE 191 98 51 126 69 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 190 55 11 166 126 NC_003454:FN1266|5end_UTP--glucose-1-phosphate_uridylyltransferase_1923063..1923293_NEGATIVE 188 52 13 109 65 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 188 67 23 227 179 NC_003454:FN0202|5end_Glutaconate_CoA-transferase_subunit_A_827780..828010_POSITIVE 187 109 61 90 32 NC_003454:FN1223|5end_Dihydropteridine_reductase_1882511..1882741_NEGATIVE 186 109 65 152 95 NC_003454:FN1316|5end_NGG1-interacting_factor_3_1970276..1970506_NEGATIVE 186 21 1 110 92 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 180 49 5 82 34 NC_003454:FN1039|5end_Branched-chain_amino_acid_transport_protein_azlC_1690997..1691227_POSITIVE 180 59 13 107 63 NC_003454:FN1884|5end_hypothetical_protein_370507..370737_NEGATIVE 179 98 55 171 121 NC_003454:FN1049|5end_hypothetical_protein_1699035..1699265_POSITIVE 179 84 42 62 18 NC_003454:FN1023|5end_5-Nitroimidazole_antibiotic_resistance_protein_1678030..1678260_NEGATIVE 173 204 165 66 24 NC_003454:FN0419|5end_aspartate_carbamoyltransferase_catalytic_subunit_1059713..1059943_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 110 65 132 91 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 223 56 11 105 59 NC_003454:FN0963|3end_hypothetical_protein_1617130..1617280_NEGATIVE 202 200 152 92 41 NC_003454:FN2071|3end_hypothetical_protein_582124..582274_NEGATIVE 188 67 23 116 68 NC_003454:FN0201|3end_Glutaconyl-COA_decarboxylase_beta_subunit_827749..827899_POSITIVE 187 109 61 61 3 NC_003454:FN1224|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1882540..1882690_NEGATIVE 186 21 1 91 73 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 180 49 5 71 23 NC_003454:FN1038|3end_Transporter_1691066..1691216_POSITIVE 179 98 55 150 100 NC_003454:FN1048|3end_Hypothetical_membrane-spanning_protein_1699094..1699244_POSITIVE 174 145 101 135 89 NC_003454:FN1973|3end_Translation_initiation_inhibitor_472230..472380_NEGATIVE 173 52 15 41 10 NC_003454:FN1102|3end_tRNA_2'phosphotransferase_1746571..1746721_POSITIVE 169 97 51 125 80 NC_003454:FN1486|3end_Integral_membrane_protein_with_CBS_domains_2168019..2168169_NEGATIVE 168 46 8 102 74 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 167 71 42 118 88 NC_003454:FN1183|3end_Hypothetical_cytosolic_protein_1845428..1845578_NEGATIVE 167 93 61 147 122 NC_003454:FN0255|3end_Hypothetical_cytosolic_protein_882117..882267_POSITIVE 167 224 190 57 21 NC_003454:FN0062|3end_Hypothetical_cytosolic_protein_698975..699125_POSITIVE 166 218 176 125 78 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 166 218 176 49 2 NC_003454:FN1496|3end_Rod_shape-determining_protein_mreC_-13..137_NEGATIVE 164 227 197 39 13 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 164 55 13 150 113 NC_003454:FN0966|3end_Precorrin-6Y_C5,15-methyltransferase_[decarboxylating]_1619280..1619430_NEGATIVE 163 89 42 126 80 NC_003454:FN0937|3end_Gamma-polyglutamic_acid_synthetase_1589097..1589247_NEGATIVE