Origin IGS: ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatataactaataaaatcattaataagaataactttttcataagaactcacctatatattatcttttttatatagaaataacttatattttttaaataagtttttcttaaaatttaatttttatatattttaaataaaactgctgcgatgtccattattgttgagagagcattttggagctcacgaaacactaatggctatcaagcagttgtgtataaaaataaaatttattatatacttattttaagaaaaactgttaattaatttggctagtaatgag Mask Tandem Repeat Region ================================================ ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Find is-nt database================================================ Query_seq: FN0222:FN0223|FN0222:FN0223:Melibiose carrier protein:COME operon protein 3:->->:848299..848579 281 ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0222:FN0223|FN0222:FN0223:Melibiose carrier protein:COME operon protein 3:->->:848299..848579 281 ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0222:FN0223|FN0222:FN0223:Melibiose carrier protein:COME operon protein 3:->->:848299..848579 281 ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 37 End: 147 .................................... F L Y I I F K I K I C L Q K I A M L T E H A G F H E R L L L P C R L L K M ...................................................................................................................................... Protein_Len: 45 Strand: - Start: 20 End: 154 ................... N V T K R L I L I Y Y I K N K Y V V A Q Y G N T N R S S W F A R E V I I S M A A T K N L M ............................................................................................................................... ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0222:FN0223|FN0222:FN0223:Melibiose carrier protein:COME operon protein 3:->->:848299..848579 281 ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcagttttatttaaaatatataaaaattaaattttaagaaaaacttatttaaaaaatataagttatttctatataaaaaagataatatataggtgagttcttatgaaaaagttattcttattaatgattttattagttatatta Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: NC_003454_FN0222_FN0223|Melibiose carrier protein:COME operon protein 3|POSITIVE:POSITIVE|[848299,848579]|281 HSP 1 e-value: 2.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcag............................................................................................................................................ ctcattactagccaaattaattaacagtttttcttaaaataagtatataataaattttatttttatacacaactgcttgatagccattagtgtttcgtgagctccaaaatgctctctcaacaataatggacatcgcagcag............................................................................................................................................ HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 34 Query Start:248 Query End:281 Subject Strand: POSITIVE Subject Start: 248 Subject End: 281 .......................................................................................................................................................................................................................................................gttattcttattaatgattttattagttatatta .......................................................................................................................................................................................................................................................gttattcttattaatgattttattagttatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUUACUAGCCAAAUUAAUUAACAGUUUUUCUUAAAAUAAGUAUAUAAUAAAUUUUAUUUUUAUACACAACUGCUUGAUAGCCAUUAGUGUUUCGUGAGCUCCAAAAUGCUCUCUCAACAAUAAUGGACAUCGCAGCAGUUUUAUUUAAAAUAUAUAAAAAUUAAAUUUUAAGAAAAACUUAUUUAAAAAAUAUAAGUUAUUUCUAUAUAAAAAAGAUAAUAUAUAGGUGAGUUCUUAUGAAAAAGUUAUUCUUAUUAAUGAUUUUAUUAGUUAUAUUA .((((.(((.(((...((((.((..(((((((((((((((..(((((.((((.....))))..)))))..(((((((((((..((((((.((((..(.((((........)))).)..)))).))))))..)))).)))))))........................))))))))))))))))).))))....((((.(((((((...........))))))).))))))).)))....)))).(((((((((......)))))))))............. (-59.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAACUAAUAAAAUCAUUAAUAAGAAUAACUUUUUCAUAAGAACUCACCUAUAUAUUAUCUUUUUUAUAUAGAAAUAACUUAUAUUUUUUAAAUAAGUUUUUCUUAAAAUUUAAUUUUUAUAUAUUUUAAAUAAAACUGCUGCGAUGUCCAUUAUUGUUGAGAGAGCAUUUUGGAGCUCACGAAACACUAAUGGCUAUCAAGCAGUUGUGUAUAAAAAUAAAAUUUAUUAUAUACUUAUUUUAAGAAAAACUGUUAAUUAAUUUGGCUAGUAAUGAG ...(((.((((.((((.......(((((.....(((......))).......(((((((..(....)..)))))))......))))).....((((...(((((((((((((((........................(((((((..((((.((((((.((((..(.((((........)))).)..)))).)))))).)))).)))))))((((((((.((......)).))))))))..))))))))))))))).))))....))))..)))).))).. (-61.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 634 130 81 172 122 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 488 138 91 214 167 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 361 99 55 119 74 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 303 143 103 65 32 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 276 106 74 223 192 NC_003454:FN0481|5end_hypothetical_protein_1127777..1128007_POSITIVE 254 129 84 221 176 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 251 102 72 206 176 NC_003454:FN0220|5end_Autolysin_sensor_kinase_844934..845164_NEGATIVE 245 115 72 187 146 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 245 115 72 83 42 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 235 115 72 186 142 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 233 111 75 73 39 NC_003454:FN1162|5end_Hydroxyacylglutathione_hydrolase_1820161..1820391_POSITIVE 233 120 74 122 77 NC_003454:FN1640|5end_LSU_ribosomal_protein_L22P_138517..138747_NEGATIVE 228 145 101 52 9 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 226 134 94 56 15 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 220 129 85 167 115 NC_003454:FN0703|5end_N-acyl-L-amino_acid_amidohydrolase_1361724..1361954_NEGATIVE 219 119 77 64 17 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 216 120 75 85 20 NC_003454:FN0503|5end_Transcriptional_regulatory_protein,_LYSR_family_1153572..1153802_NEGATIVE 214 123 81 65 31 NC_003454:FN1376|5end_oxaloacetate_decarboxylase_2023879..2024109_POSITIVE 213 27 2 154 129 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 213 160 116 191 155 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 634 130 81 70 20 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 585 150 101 58 8 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 517 138 91 64 17 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 488 138 91 81 34 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 321 120 74 48 2 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 270 143 108 32 2 NC_003454:FN1745|3end_Cystathionine_gamma-synthase_242953..243103_NEGATIVE 235 115 72 52 8 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 233 120 74 87 42 NC_003454:FN1641|3end_SSU_ribosomal_protein_S19P_138552..138702_NEGATIVE 210 125 84 142 113 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 209 120 84 58 26 NC_003454:FN0630|3end_PTS_system,_IIC_component_1289078..1289228_NEGATIVE 206 133 96 91 46 NC_003454:FN2108|3end_galactose-1-phosphate_uridylyltransferase_620928..621078_POSITIVE 204 149 106 89 36 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 202 98 73 149 117 NC_003454:FN0592|3end_ATP-dependent_DNA_helicase_pcrA_1247999..1248149_POSITIVE 198 103 81 151 126 NC_003454:FN1309|3end_hypothetical_protein_1965130..1965280_POSITIVE 198 100 55 146 99 NC_003454:FN1797|3end_Spermidine/putrescine_transport_ATP-binding_protein_potA_280031..280181_POSITIVE 196 117 77 78 38 NC_003454:FN0535|3end_hypothetical_protein_1190009..1190159_POSITIVE 196 116 71 40 2 NC_003454:FN0284|3end_16S_rRNA_processing_protein_rimM_913402..913552_NEGATIVE 195 138 91 65 12 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 195 156 111 79 18 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE 194 118 74 54 14 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE