Origin IGS: gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctattatagatttacacaatagctttttttcttgtccaaaaaattaatatagtttttattaaatgctttacaaaaatagcacaatatactataattattaaatagagtattaactttaaaacgggaaagtatttagtttttataaggagatttatatatagatgaaaaaagaaagcaaaataaaaattcttttaccaatattagcagtaataattgttacagttttaatttttaatagacttttatttaaattaaaagctcaaattgataaagctgttctgccaattcaaagtaaagtatataatgtagccaatagagctattggaataaaagatataattttctcttatgaaaacttcataacagaaaatgaaaatttaaaaaaagaaaac Mask Tandem Repeat Region ================================================ gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Find is-nt database================================================ Query_seq: FN1496:FN1497|FN1496:FN1497:Rod shape-determining protein mreC:Multidrug resistance protein 2:<-<-:710..1103 394 gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1496:FN1497|FN1496:FN1497:Rod shape-determining protein mreC:Multidrug resistance protein 2:<-<-:710..1103 394 gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1496:FN1497|FN1496:FN1497:Rod shape-determining protein mreC:Multidrug resistance protein 2:<-<-:710..1103 394 gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 16 End: 138 ............... M F I F C Y E V F I R E N Y I F Y S N S S I G Y I I Y F T L N W Q N S F I N L S F ................................................................................................................................................................................................................................................................ Protein_Len: 47 Strand: + Start: 238 End: 378 ............................................................................................................................................................................................................................................. M N L L I K T K Y F P V L K L I L Y L I I I V Y C A I F V K H L I K T I L I F W T R K K A I V ................ Protein_Len: 42 Strand: + Start: 261 End: 386 .................................................................................................................................................................................................................................................................... M L S R F K V N T L F N N Y S I L C Y F C K A F N K N Y I N F L D K K K S Y C V N L ........ Protein_Len: 31 Strand: - Start: 291 End: 383 .................................................................................................................................................................................................................................................................................................. K I I I T Y Q A I K T F C K I F V I N I K Q V L F F A I T Y M ........... Protein_Len: 60 Strand: - Start: 1 End: 231 I I D K I G I A R N A V N Y V K S Q I P L V A K D I Q A K L K F L L R N F I L V T V I I V A L I P L L I K I K S E K K M ................................................................................................................................................................... gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct 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: 87 Start: 298 End: 327 .........................................................................................................................................................................................................................................................................................................CTTTACAAAAATAGCACAATATACTATAAT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1496:FN1497|FN1496:FN1497:Rod shape-determining protein mreC:Multidrug resistance protein 2:<-<-:710..1103 394 gttttctttttttaaattttcattttctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaatttttattttgctttcttttttcatctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Intra-Species Hit: Count: 1 Min: 27 Max: 394 Len: 368 Subject: NC_003454_FN1496_FN1497|Rod shape-determining protein mreC:Multidrug resistance protein 2|NEGATIVE:NEGATIVE|[710,1103]|394 HSP 1 e-value: 2.0E-97 bit: 357.0 Len: 180 Query Start:27 Query End:206 Subject Strand: POSITIVE Subject Start: 27 Subject End: 206 ..........................ctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaa............................................................................................................................................................................................ ..........................ctgttatgaagttttcataagagaaaattatatcttttattccaatagctctattggctacattatatactttactttgaattggcagaacagctttatcaatttgagcttttaatttaaataaaagtctattaaaaattaaaactgtaacaattattactgctaatattggtaaaagaa............................................................................................................................................................................................ HSP 2 e-value: 1.0E-76 bit: 287.0 Len: 166 Query Start:229 Query End:394 Subject Strand: POSITIVE Subject Start: 229 Subject End: 394 ....................................................................................................................................................................................................................................catctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagnnnnnnngctattgtgtaaatctataatagct ....................................................................................................................................................................................................................................catctatatataaatctccttataaaaactaaatactttcccgttttaaagttaatactctatttaataattatagtatattgtgctatttttgtaaagcatttaataaaaactatattaattttttggacaagaaaaaaagctattgtgtaaatctataatagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUAUGAAGUUUUCAUAAGAGAAAAUUAUAUCUUUUAUUCCAAUAGCUCUAUUGGCUACAUUAUAUACUUUACUUUGAAUUGGCAGAACAGCUUUAUCAAUUUGAGCUUUUAAUUUAAAUAAAAGUCUAUUAAAAAUUAAAACUGUAACAAUUAUUACUGCUAAUAUUGGUAAAAGAAUUUUUAUUUUGCUUUCUUUUUUCAUCUAUAUAUAAAUCUCCUUAUAAAAACUAAAUACUUUCCCGUUUUAAAGUUAAUACUCUAUUUAAUAAUUAUAGUAUAUUGUGCUAUUUUUGUAAAGCAUUUAAUAAAAACUAUAUUAAUUUUUUGGACAAGAAAAAAAGCUAUUGUGUAAAUCUAUAAUAGCU ....(((..((((((.((((((((.................((((((....)))))).....(((((((...........((((((((...(((((.........)))))((((((((.((((......))))..))))))))................))))))))..(((.(((((((.............))))))).)))....))))))).))).))))).))))))..))).((((..((((.((((((((((.........((((..(((((((...)))))))..))))......(((....)))....))))))))))..))))..))))...((((((((((......)))))))))) (-59.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAUUAUAGAUUUACACAAUAGCUUUUUUUCUUGUCCAAAAAAUUAAUAUAGUUUUUAUUAAAUGCUUUACAAAAAUAGCACAAUAUACUAUAAUUAUUAAAUAGAGUAUUAACUUUAAAACGGGAAAGUAUUUAGUUUUUAUAAGGAGAUUUAUAUAUAGAUGAAAAAAGAAAGCAAAAUAAAAAUUCUUUUACCAAUAUUAGCAGUAAUAAUUGUUACAGUUUUAAUUUUUAAUAGACUUUUAUUUAAAUUAAAAGCUCAAAUUGAUAAAGCUGUUCUGCCAAUUCAAAGUAAAGUAUAUAAUGUAGCCAAUAGAGCUAUUGGAAUAAAAGAUAUAAUUUUCUCUUAUGAAAACUUCAUAACAG (((((((............)))))))...((((((((............((((((...((((...((((..........)))).)))).)))))).........((((((....))))))..)))))))).(((..((((((((((((((((.((((((................................((((((....(((.((((...........(((((((((....(((((.((((((((.......)))))).))..)))))))))))))).)))).))).....))))))............((((((....))))))........)))))).)))).))))))))))))..))).... (-63.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 90 41 207 158 NC_003454:FN1496|5end_Rod_shape-determining_protein_mreC_619..849_NEGATIVE 256 90 47 59 11 NC_003454:FN1860|5end_NA+/H+_antiporter_NHAC_351477..351707_NEGATIVE 248 222 187 111 71 NC_003454:FN1513|5end_Phophatidylinositol-4-phosphate_5-kinase_17007..17237_POSITIVE 241 106 71 42 8 NC_003454:FN1378|5end_Citrate_lyase_acyl_carrier_protein_2026062..2026292_POSITIVE 237 76 40 88 46 NC_003454:FN0495|5end_Acetyl-CoA_acetyltransferase_1139567..1139797_POSITIVE 230 178 131 73 27 NC_003454:FN2003|5end_bioY_protein_503745..503975_POSITIVE 229 222 183 164 112 NC_003454:FN1784|5end_hypothetical_protein_266190..266420_NEGATIVE 226 109 70 180 138 NC_003454:FN2042|5end_Protein_translocase_subunit_SecE_549832..550062_NEGATIVE 224 77 46 35 1 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 224 207 161 120 68 NC_003454:FN1096|5end_hypothetical_protein_1740587..1740817_POSITIVE 222 70 28 86 46 NC_003454:FN1204|5end_Methyltransferase_1863868..1864098_NEGATIVE 220 198 151 102 61 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 220 73 32 101 59 NC_003454:FN0147|5end_fatty_acid/phospholipid_synthesis_protein_775462..775692_POSITIVE 213 80 33 135 84 NC_003454:FN1708|5end_Polyribonucleotide_nucleotidyltransferase_203288..203518_POSITIVE 212 222 186 102 67 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 210 197 152 162 117 NC_003454:FN0984|5end_Tetracenomycin_polyketide_synthesis_O-methyltransferase_tcmP_1637295..1637525_NEGATIVE 210 67 38 112 83 NC_003454:FN0922|5end_Homoserine_kinase_1577526..1577756_NEGATIVE 210 222 192 166 136 NC_003454:FN2109|5end_UDP-glucose_4-epimerase_620848..621078_POSITIVE 209 58 34 231 210 NC_003454:FN1561|5end_Hypothetical_cytosolic_protein_83760..83990_NEGATIVE 208 64 30 157 119 NC_003454:FN1524|5end_Dipeptide_transport_ATP-binding_protein_dppD_29799..30029_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 222 187 139 99 NC_003454:FN1512|3end_Phophatidylinositol-4-phosphate_5-kinase_17115..17265_POSITIVE 229 222 183 142 90 NC_003454:FN1785|3end_hypothetical_protein_266212..266362_NEGATIVE 226 109 70 55 13 NC_003454:FN2044|3end_LSU_ribosomal_protein_L33P_549957..550107_NEGATIVE 224 207 161 127 75 NC_003454:FN1095|3end_hypothetical_protein_1740674..1740824_POSITIVE 222 70 28 75 35 NC_003454:FN1205|3end_Protease_1863879..1864029_NEGATIVE 219 113 81 44 12 NC_003454:FN2065|3end_Transcriptional_repressor_576397..576547_POSITIVE 212 222 186 81 46 NC_003454:FN1786|3end_ADP-heptose_synthase_267821..267971_POSITIVE 210 197 152 142 97 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 210 67 38 100 71 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 210 297 252 114 67 NC_003454:FN1934|3end_hypothetical_protein_434266..434416_NEGATIVE 208 64 30 145 107 NC_003454:FN1523|3end_Dipeptide-binding_protein_29867..30017_POSITIVE 206 306 262 121 75 NC_003454:FN0766|3end_Large-conductance_mechanosensitive_channel_1422418..1422568_POSITIVE 206 200 159 85 45 NC_003454:FN0464|3end_hypothetical_protein_1110087..1110237_POSITIVE 205 296 258 62 23 NC_003454:FN1169|3end_L-lactate_dehydrogenase_1827580..1827730_NEGATIVE 202 79 31 122 66 NC_003454:FN0910|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_1567664..1567814_NEGATIVE 202 55 11 117 74 NC_003454:FN0156|3end_Phosphopantetheine_adenylyltransferase_784974..785124_POSITIVE 201 58 33 132 101 NC_003454:FN0583|3end_hypothetical_protein_1239518..1239668_POSITIVE 201 78 31 115 70 NC_003454:FN0075|3end_Ethanolamine_utilization_protein_eutP_714216..714366_POSITIVE 201 221 183 105 68 NC_003454:FN1633|3end_LSU_ribosomal_protein_L24P_135838..135988_NEGATIVE 200 106 75 31 1 NC_003454:FN1377|3end_CITG_protein_2026131..2026281_POSITIVE