Origin IGS: caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg .........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 ccttattatagtagcgaggaggattatagtgaaagagctaataaaaaatgaaaaagctagagctttaataaaaaaagcagtagaagaagggattataacttatgaagaaattaatgaagaattaggtgatgattttccagctgaaaacatagaacaacttattaatgaaatgcttgaacaaggaattaaaatagttgatgaggaacaattagatgagttaggtgaagatgagttaagagaaaaagaattagaagatgattatacggataatgaagaacatgatgatttg Mask Tandem Repeat Region ================================================ caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Find is-nt database================================================ Query_seq: FN1318:FN1319|FN1318:FN1319:RNA polymerase sigma factor rpoD:DNA primase:<-<-:1972187..1972475 289 caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1318:FN1319|FN1318:FN1319:RNA polymerase sigma factor rpoD:DNA primase:<-<-:1972187..1972475 289 caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1318:FN1319|FN1318:FN1319:RNA polymerase sigma factor rpoD:DNA primase:<-<-:1972187..1972475 289 caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 98 End: 187 ................................................................................................. M L I P C S S I S L I S C S M F S A G K S S P N S S L I S S ...................................................................................................... Protein_Len: 32 Strand: + Start: 194 End: 289 ................................................................................................................................................................................................. M I P S S T A F F I K A L A F S F F I S S F T I I L L A T I I R Protein_Len: 60 Strand: - Start: 1 End: 285 G Q E L M E N I L Q E I N E A P F D D G L E E N I E E Y T I I G E E V A K K I L A R A K E N K I L E K V I I R R A V I M .... caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg 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: 85 Start: 256 End: 285 ...............................................................................................................................................................................................................................................................TTTCACTATAATCCTCCTCGCTACTATAAT.... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1318:FN1319|FN1318:FN1319:RNA polymerase sigma factor rpoD:DNA primase:<-<-:1972187..1972475 289 caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgctttttttattaaagctctagctttttcattttttattagctctttcactataatcctcctcgctactataataagg Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: NC_003454_FN1318_FN1319|RNA polymerase sigma factor rpoD:DNA primase|NEGATIVE:NEGATIVE|[1972187,1972475]|289 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgc............................................................................ caaatcatcatgttcttcattatccgtataatcatcttctaattctttttctcttaactcatcttcacctaactcatctaattgttcctcatcaactattttaattccttgttcaagcatttcattaataagttgttctatgttttcagctggaaaatcatcacctaattcttcattaatttcttcataagttataatcccttcttctactgc............................................................................ HSP 2 e-value: 3.0E-15 bit: 83.8 Len: 42 Query Start:248 Query End:289 Subject Strand: POSITIVE Subject Start: 248 Subject End: 289 .......................................................................................................................................................................................................................................................attagctctttcactataatcctcctcgctactataataagg .......................................................................................................................................................................................................................................................attagctctttcactataatcctcctcgctactataataagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUCAUCAUGUUCUUCAUUAUCCGUAUAAUCAUCUUCUAAUUCUUUUUCUCUUAACUCAUCUUCACCUAACUCAUCUAAUUGUUCCUCAUCAACUAUUUUAAUUCCUUGUUCAAGCAUUUCAUUAAUAAGUUGUUCUAUGUUUUCAGCUGGAAAAUCAUCACCUAAUUCUUCAUUAAUUUCUUCAUAAGUUAUAAUCCCUUCUUCUACUGCUUUUUUUAUUAAAGCUCUAGCUUUUUCAUUUUUUAUUAGCUCUUUCACUAUAAUCCUCCUCGCUACUAUAAUAAGG ...................................................................(((......((((.(((.....((((((((...(((((....(((....)))....)))))..)))))....)))....))).))))....................................((((((..........(((..(((((.......)))))..)))................((((.....................)))).)))))).))) (-19.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUAUUAUAGUAGCGAGGAGGAUUAUAGUGAAAGAGCUAAUAAAAAAUGAAAAAGCUAGAGCUUUAAUAAAAAAAGCAGUAGAAGAAGGGAUUAUAACUUAUGAAGAAAUUAAUGAAGAAUUAGGUGAUGAUUUUCCAGCUGAAAACAUAGAACAACUUAUUAAUGAAAUGCUUGAACAAGGAAUUAAAAUAGUUGAUGAGGAACAAUUAGAUGAGUUAGGUGAAGAUGAGUUAAGAGAAAAAGAAUUAGAAGAUGAUUAUACGGAUAAUGAAGAACAUGAUGAUUUG .((((((....((((..((((((((((........(.(((((..............(((..(((((.......)))))..)))...............(((...((....))....))).))))).).)))))))))).))))....(((..(((..(((((((((......(((.....)))..........)))))))))...((......)).)))..)))..))))))....................((((.(((((................))))).)))). (-36.68) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 811 100 51 191 142 NC_003454:FN1318|5end_RNA_polymerase_sigma_factor_rpoD_1972096..1972326_NEGATIVE 278 250 202 85 46 NC_003454:FN0902|5end_5-formyltetrahydrofolate_cyclo-ligase_1560549..1560779_POSITIVE 278 245 202 221 178 NC_003454:FN0805|5end_hypothetical_protein_1465587..1465817_NEGATIVE 277 257 213 195 143 NC_003454:FN1734|5end_V-type_ATP_synthase_subunit_B_234258..234488_NEGATIVE 274 90 44 195 147 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 269 109 73 112 70 NC_003454:FN1196|5end_hypothetical_protein_1857045..1857275_NEGATIVE 267 241 201 180 140 NC_003454:FN0504|5end_Arginine_permease_1155009..1155239_NEGATIVE 266 90 42 114 72 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 264 80 35 137 84 NC_003454:FN0163|5end_5-methyltetrahydrofolate--homocysteine_methyltransferase_791318..791548_POSITIVE 263 56 13 200 152 NC_003454:FN0701|5end_Methyltransferase_1359261..1359491_POSITIVE 260 246 206 168 118 NC_003454:FN1473|5end_N-acetylneuraminate_transporter_large_subunit_2155032..2155262_POSITIVE 257 268 221 73 30 NC_003454:FN0810|5end_Low-specificity_threonine_aldolase_1469038..1469268_POSITIVE 257 57 16 132 87 NC_003454:FN2124|5end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633712..633942_NEGATIVE 257 74 35 56 17 NC_003454:FN2032|5end_DNA-directed_RNA_polymerase_omega_chain_537315..537545_NEGATIVE 256 70 21 141 85 NC_003454:FN1607|5end_Cytidylate_kinase_117893..118123_NEGATIVE 252 260 211 103 53 NC_003454:FN1209|5end_Hypothetical_RNA_binding_protein_1868914..1869144_NEGATIVE 252 240 201 79 37 NC_003454:FN0480|5end_hypothetical_protein_1127454..1127684_POSITIVE 251 116 75 48 1 NC_003454:FN1373|5end_EBSC_protein_2021486..2021716_NEGATIVE 250 242 202 190 143 NC_003454:FN1908|5end_Glycerophosphoryl_diester_phosphodiesterase_401669..401899_NEGATIVE 246 248 201 97 43 NC_003454:FN0090|5end_Ethanolamine_utilization_protein_eutQ_726315..726545_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 250 202 95 56 NC_003454:FN0901|3end_DNA_polymerase,_bacteriophage-type_1560639..1560789_POSITIVE 269 109 73 122 80 NC_003454:FN1197|3end_hypothetical_protein_1857035..1857185_NEGATIVE 267 241 201 145 105 NC_003454:FN0505|3end_Anthranilate_synthase_component_II_1155044..1155194_NEGATIVE 266 90 42 102 60 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 264 80 35 83 30 NC_003454:FN0162|3end_Na+_driven_multidrug_efflux_pump_791344..791494_POSITIVE 260 246 206 144 94 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 257 268 221 62 19 NC_003454:FN0809|3end_23S_rRNA_methyltransferase_1469107..1469257_POSITIVE 257 57 16 119 74 NC_003454:FN2125|3end_DNA_gyrase_subunit_A_633725..633875_NEGATIVE 256 70 21 125 69 NC_003454:FN1608|3end_Ribosomal_protein_L11_methyltransferase_117909..118059_NEGATIVE 252 260 211 77 27 NC_003454:FN1210|3end_Metal_dependent_hydrolase_1868940..1869090_NEGATIVE 252 240 201 77 35 NC_003454:FN0479|3end_RNA_polymerase_sigma-E_factor_1127532..1127682_POSITIVE 250 80 34 146 109 NC_003454:FN1965|3end_Tetratricopeptide_repeat_family_protein_464060..464210_NEGATIVE 250 242 202 147 100 NC_003454:FN1909|3end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_401712..401862_NEGATIVE 247 265 229 79 44 NC_003454:FN0415|3end_hypothetical_protein_1053996..1054146_POSITIVE 246 248 201 86 32 NC_003454:FN0089|3end_Ethanolamine_permease_726384..726534_POSITIVE 245 259 233 135 104 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 241 277 235 140 95 NC_003454:FN0043|3end_Hypothetical_exported_24-amino_acid_repeat_protein_682818..682968_POSITIVE 240 217 173 109 59 NC_003454:FN0826|3end_periplasmic_component_of_efflux_system_1487591..1487741_POSITIVE 240 49 5 106 54 NC_003454:FN1562|3end_3-deoxy-7-phosphoheptulonate_synthase_83760..83910_NEGATIVE 239 247 201 130 82 NC_003454:FN0121|3end_hypothetical_protein_752908..753058_NEGATIVE