Origin IGS: tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt .........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 aatacaccttccctatcaaccatttatatcacacattaaaatttcatctatttcaacattagcaagatgcccaaaaagataattaggttcacaatctaagtcactaagtcaaaatttttaatttcttttaaattcattttaaacttccaataaattagataattattagaattatagcatatataaaattttatttatagtaattaataaaaaaatctacttagtaataaactatttttctattagaaataaaaatttttactaagtaaagaaattatggttgacaataaaatataaaaagtttataataattaagttataattataaaaataataaaaaataagaaaggaggataaa Mask Tandem Repeat Region ================================================ tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Find is-nt database================================================ Query_seq: FN1558:FN1559|FN1558:FN1559:30S ribosomal protein S12:cell volume regulation protein CvrA:<-->:80609..80966 358 tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1558:FN1559|FN1558:FN1559:30S ribosomal protein S12:cell volume regulation protein CvrA:<-->:80609..80966 358 tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1558:FN1559|FN1558:FN1559:30S ribosomal protein S12:cell volume regulation protein CvrA:<-->:80609..80966 358 tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 165 End: 260 .................................................................................................................................................................... M K F Y I C Y N S N N Y L I Y W K F K M N L K E I K N F D L V T .................................................................................................. tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt 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: 91 Start: 50 End: 79 .................................................GTTGACAATAAAATATAAAAAGTTTATAAT....................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 159 End: 188 ..............................................................................................................................................................CTATAAATAAAATTTTATATATGCTATAAT.......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -4.9 Tail_Score: -5.87996 Start: 89 End: 143 Full_Region: GTCAACCATAATTTC TTTACTTAGTAAAAATTTTTATTTCT AAT AGAAAAATAGTTTATTACTAAGTAGA TTTTTTTATTAATTA ........................................................................................TTTACTTAGTAAAAATTTTTATTTCTAATAGAAAAATAGTTTATTACTAAGTAGA....................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN1558:FN1559|FN1558:FN1559:30S ribosomal protein S12:cell volume regulation protein CvrA:<-->:80609..80966 358 tttatcctcctttcttattttttattatttttataattataacttaattattataaactttttatattttattgtcaaccataatttctttacttagtaaaaatttttatttctaatagaaaaatagtttattactaagtagatttttttattaattactataaataaaattttatatatgctataattctaataattatctaatttattggaagtttaaaatgaatttaaaagaaattaaaaattttgacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt Intra-Species Hit: Count: 1 Min: 93 Max: 358 Len: 266 Subject: NC_003454_FN1558_FN1559|30S ribosomal protein S12:cell volume regulation protein CvrA|NEGATIVE:POSITIVE|[80609,80966]|358 HSP 1 e-value: 1.0E-55 bit: 218.0 Len: 110 Query Start:249 Query End:358 Subject Strand: POSITIVE Subject Start: 249 Subject End: 358 ........................................................................................................................................................................................................................................................gacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt ........................................................................................................................................................................................................................................................gacttagtgacttagattgtgaacctaattatctttttgggcatcttgctaatgttgaaatagatgaaattttaatgtgtgatataaatggttgatagggaaggtgtatt HSP 2 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:93 Query End:143 Subject Strand: POSITIVE Subject Start: 93 Subject End: 143 ............................................................................................cttagtaaaaatttttatttctaatagaaaaatagtttattactaagtaga....................................................................................................................................................................................................................... ............................................................................................cttagtaaaaatttttatttctaatagaaaaatagtttattactaagtaga....................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAGUAAAAAUUUUUAUUUCUAAUAGAAAAAUAGUUUAUUACUAAGUAGAUUUUUUUAUUAAUUACUAUAAAUAAAAUUUUAUAUAUGCUAUAAUUCUAAUAAUUAUCUAAUUUAUUGGAAGUUUAAAAUGAAUUUAAAAGAAAUUAAAAAUUUUGACUUAGUGACUUAGAUUGUGAACCUAAUUAUCUUUUUGGGCAUCUUGCUAAUGUUGAAAUAGAUGAAAUUUUAAUGUGUGAUAUAAAUGGUUGAUAGGGAAGGUGUAUU .((((((((((..(((((((.(((((((.......)))))))..)))))))..)))))))))).(((((....(((((((((.............(((((((((.........))))))))).((((((.....))))))........)))))))))...))))).(((...((((.((((....((((......(((.....))).((((((((((.......))))))))))..)))).....)))).))))..)))....... (-42.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACACCUUCCCUAUCAACCAUUUAUAUCACACAUUAAAAUUUCAUCUAUUUCAACAUUAGCAAGAUGCCCAAAAAGAUAAUUAGGUUCACAAUCUAAGUCACUAAGUCAAAAUUUUUAAUUUCUUUUAAAUUCAUUUUAAACUUCCAAUAAAUUAGAUAAUUAUUAGAAUUAUAGCAUAUAUAAAAUUUUAUUUAUAGUAAUUAAUAAAAAAAUCUACUUAGUAAUAAACUAUUUUUCUAUUAGAAAUAAAAAUUUUUACUAAG .....((((....((((.....((((..........))))....(((((...............)))))........))))...))))...............((.(((.((((((((((.(((((..((.........................(((((..(((((((.(((((((.(((..........))))))))))..)))))))....)))))..((((.....))))......))..))))))))))))))).))).)) (-24.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 551 48 1 231 184 NC_003454:FN1558|5end_30S_ribosomal_protein_S12_80518..80748_NEGATIVE 249 57 21 149 111 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 245 255 211 47 4 NC_003454:FN0572|5end_hypothetical_protein_1222555..1222785_NEGATIVE 234 215 179 204 166 NC_003454:FN1392|5end_SSU_ribosomal_protein_S16P_2049459..2049689_NEGATIVE 226 220 172 141 92 NC_003454:FN1145|5end_Oligoendopeptidase_F_1795931..1796161_NEGATIVE 225 220 173 55 2 NC_003454:FN0264|5end_hypothetical_protein_890862..891092_POSITIVE 201 57 26 155 123 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 191 221 196 68 48 NC_003454:FN0815|5end_Propionate_permease_1474390..1474620_POSITIVE 190 206 161 120 62 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 190 238 199 102 58 NC_003454:FN0665|5end_N-acetylmuramoyl-L-alanine_amidase_1321085..1321315_POSITIVE 186 219 192 78 48 NC_003454:FN1852|5end_hypothetical_protein_341616..341846_POSITIVE 185 240 191 162 115 NC_003454:FN0474|5end_Acriflavin_resistance_protein_B_1118939..1119169_POSITIVE 184 213 174 168 132 NC_003454:FN0138|5end_Transposase_771238..771468_POSITIVE 183 57 15 47 1 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 180 207 175 100 61 NC_003454:FN0332|5end_Magnesium_and_cobalt_transport_protein_corA_967230..967460_NEGATIVE 177 206 162 53 2 NC_003454:FN0704|5end_hypothetical_protein_1361855..1362085_NEGATIVE 177 206 162 184 133 NC_003454:FN0703|5end_N-acyl-L-amino_acid_amidohydrolase_1361724..1361954_NEGATIVE 177 218 180 230 178 NC_003454:FN0660|5end_ABC_transporter_ATP-binding_protein_1317388..1317618_NEGATIVE 176 57 11 142 90 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 174 213 174 42 6 NC_003454:FN1530|5end_Transposase_43625..43855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 57 28 30 1 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 205 212 179 150 115 NC_003454:FN1393|3end_Signal_recognition_particle,_subunit_FFH/SRP54_2049510..2049660_NEGATIVE 204 260 215 99 58 NC_003454:FN1705|3end_hypothetical_protein_201464..201614_NEGATIVE 189 179 139 59 5 NC_003454:FN1108|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1752878..1753028_POSITIVE 185 240 191 84 37 NC_003454:FN0473|3end_Regulatory_protein_betI_1118941..1119091_POSITIVE 184 213 174 130 94 NC_003454:FN0137|3end_Transposase_771280..771430_POSITIVE 180 207 175 83 44 NC_003454:FN0333|3end_Glycerol_uptake_operon_antiterminator_regulatory_protein_967247..967397_NEGATIVE 180 260 218 105 61 NC_003454:FN0115|3end_hypothetical_protein_748215..748365_NEGATIVE 173 103 66 101 60 NC_003454:FN1387|3end_Metal_dependent_hydrolase_2042890..2043040_NEGATIVE 170 200 173 72 46 NC_003454:FN0133|3end_hypothetical_protein_769653..769803_POSITIVE 169 199 151 68 20 NC_003454:FN0285|3end_RNA_binding_protein_913932..914082_NEGATIVE 168 107 72 50 17 NC_003454:FN1232|3end_Transcriptional_regulator,_MarR_family_1889000..1889150_NEGATIVE 167 207 161 149 92 NC_003454:FN0695|3end_ABC_transporter_ATP-binding_protein_1353691..1353841_POSITIVE 165 195 153 120 55 NC_003454:FN1448|3end_Hypothetical_cytosolic_protein_2117403..2117553_NEGATIVE 165 206 161 46 5 NC_003454:FN0077|3end_Ethanolamine_two-component_sensor_kinase_716172..716322_POSITIVE 164 219 185 64 30 NC_003454:FN0924|3end_hypothetical_protein_1579962..1580112_POSITIVE 163 258 232 24 2 NC_003454:FN1132|3end_Nicotinamide-nucleotide_adenylyltransferase_1780254..1780404_POSITIVE 162 194 157 91 51 NC_003454:FN0552|3end_Serine_racemase_1203606..1203756_NEGATIVE 159 137 100 60 22 NC_003454:FN1184|3end_hypothetical_protein_1846208..1846358_NEGATIVE 159 200 154 80 23 NC_003454:FN0360|3end_ATP_synthase_subunit_A_990854..991004_NEGATIVE