Origin IGS: aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctatcaccaattttatataatgatatattttatcatttttttgctaaaatgaaaataaaaaaaagtccgtttttgaggtggactttttaatgggattaactatgtattaggctatctatattatgtcgttatcattatgggaaattaccctcctttt Mask Tandem Repeat Region ================================================ aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Find is-nt database================================================ Query_seq: FN0171:FN0172|FN0171:FN0172:Hypothetical cytosolic protein:RNA binding protein:->->:796982..797139 158 aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0171:FN0172|FN0171:FN0172:Hypothetical cytosolic protein:RNA binding protein:->->:796982..797139 158 aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0171:FN0172|FN0171:FN0172:Hypothetical cytosolic protein:RNA binding protein:->->:796982..797139 158 aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Predict ORF larger than 30AA ================================================ aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga 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: 84 Start: 102 End: 131 .....................................................................................................ATTTTCATTTTAGCAAAAAAATGATAAAAT........................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 34 End: 63 .................................ATTAACTATGTATTAGGCTATCTATATTAT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.9 Tail_Score: -3.52459 Start: 123 End: 137 Full_Region: ATTTTAGCAAAAAAA TGATA AAATA TATCA TTATATAAAATTGGT ..........................................................................................................................TGATAAAATATATCA..................... Find igs database================================================ Query_seq: FN0171:FN0172|FN0171:FN0172:Hypothetical cytosolic protein:RNA binding protein:->->:796982..797139 158 aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggacttttttttattttcattttagcaaaaaaatgataaaatatatcattatataaaattggtgataga Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_003454_FN0171_FN0172|Hypothetical cytosolic protein:RNA binding protein|POSITIVE:POSITIVE|[796982,797139]|158 HSP 1 e-value: 6.0E-46 bit: 184.0 Len: 93 Query Start:1 Query End:93 Subject Strand: POSITIVE Subject Start: 1 Subject End: 93 aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggac................................................................. aaaaggagggtaatttcccataatgataacgacataatatagatagcctaatacatagttaatcccattaaaaagtccacctcaaaaacggac................................................................. HSP 2 e-value: 6.0E-12 bit: 71.9 Len: 36 Query Start:123 Query End:158 Subject Strand: POSITIVE Subject Start: 123 Subject End: 158 ..........................................................................................................................tgataaaatatatcattatataaaattggtgataga ..........................................................................................................................tgataaaatatatcattatataaaattggtgataga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGGAGGGUAAUUUCCCAUAAUGAUAACGACAUAAUAUAGAUAGCCUAAUACAUAGUUAAUCCCAUUAAAAAGUCCACCUCAAAAACGGACUUUUUUUUAUUUUCAUUUUAGCAAAAAAAUGAUAAAAUAUAUCAUUAUAUAAAAUUGGUGAUAGA ....((.(((......))).......((((.........(((.....))).......))))...))...(((((((((...........))))))))).......(((((((......))))))).......((((((((........)))))))).. (-24.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUCACCAAUUUUAUAUAAUGAUAUAUUUUAUCAUUUUUUUGCUAAAAUGAAAAUAAAAAAAAGUCCGUUUUUGAGGUGGACUUUUUAAUGGGAUUAACUAUGUAUUAGGCUAUCUAUAUUAUGUCGUUAUCAUUAUGGGAAAUUACCCUCCUUUU .................(((((((((((.....(((((((......))))))).......((((((((((..(...)..))))))))))....((((...(((.....)))...))))....)))))))))))......(((......)))....... (-30.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 96 63 106 67 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 215 100 56 121 75 NC_003454:FN0241|5end_Dihydrofolate_reductase_864721..864951_POSITIVE 214 110 63 101 47 NC_003454:FN0862|5end_hypothetical_protein_1522371..1522601_NEGATIVE 212 116 78 145 98 NC_003454:FN0177|5end_Cell_division_inhibitor_MinE_801957..802187_POSITIVE 204 39 10 98 72 NC_003454:FN0121|5end_hypothetical_protein_753300..753530_NEGATIVE 199 89 42 183 133 NC_003454:FN0995|5end_hypothetical_protein_1649966..1650196_POSITIVE 198 139 94 171 121 NC_003454:FN0164|5end_Anhydro-N-acetylmuramyl-tripeptide_amidase_792345..792575_POSITIVE 197 117 76 166 127 NC_003454:FN0166|5end_hypothetical_protein_793732..793962_POSITIVE 196 81 45 177 145 NC_003454:FN1592|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103746..103976_NEGATIVE 195 83 63 219 199 NC_003454:FN1261|5end_Two-component_response_regulator_1917871..1918101_NEGATIVE 193 110 65 49 6 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 190 65 21 205 163 NC_003454:FN0649|5end_Exoenzyme_regulatory_protein_aepA_precursor_1307717..1307947_NEGATIVE 187 68 39 184 148 NC_003454:FN2041|5end_Transcription_antitermination_protein_nusG_549659..549889_NEGATIVE 186 118 73 179 129 NC_003454:FN1027|5end_Rod_shape-determining_protein_rodA_1681923..1682153_NEGATIVE 185 82 51 125 86 NC_003454:FN1410|5end_Transporter_2069934..2070164_POSITIVE 184 98 55 147 92 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 183 70 28 106 65 NC_003454:FN2033|5end_Guanylate_kinase_537904..538134_NEGATIVE 180 98 54 166 117 NC_003454:FN1087|5end_hypothetical_protein_1730958..1731188_POSITIVE 178 82 52 104 74 NC_003454:FN0978|5end_NA+/H+_antiporter_NHAC_1631965..1632195_NEGATIVE 176 66 23 189 154 NC_003454:FN1222|5end_hypothetical_protein_1881969..1882199_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 117 71 107 53 NC_003454:FN0512|3end_Flavoprotein_1161386..1161536_NEGATIVE 215 100 56 121 75 NC_003454:FN0240|3end_Thymidylate_synthase_864801..864951_POSITIVE 214 110 63 74 20 NC_003454:FN0863|3end_hypothetical_protein_1522398..1522548_NEGATIVE 212 116 78 139 92 NC_003454:FN0176|3end_Cell_division_inhibitor_MinD_802031..802181_POSITIVE 198 139 94 73 23 NC_003454:FN0163|3end_5-methyltetrahydrofolate--homocysteine_methyltransferase_792327..792477_POSITIVE 192 112 76 149 113 NC_003454:FN0165|3end_hypothetical_protein_793798..793948_POSITIVE 184 98 55 127 72 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 183 70 28 93 52 NC_003454:FN2034|3end_Protein_yicC_537917..538067_NEGATIVE 182 34 3 149 118 NC_003454:FN0186|3end_Cytochrome_c-type_biogenesis_protein_ccdA_811586..811736_POSITIVE 179 110 69 82 40 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 176 116 71 63 21 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 175 78 37 85 53 NC_003454:FN1237|3end_Choline_kinase_1893453..1893603_NEGATIVE 171 98 54 53 7 NC_003454:FN0187|3end_Thiol:disulfide_interchange_protein_tlpA_812299..812449_POSITIVE 171 66 35 64 36 NC_003454:FN2084|3end_Permease_596507..596657_POSITIVE 170 67 40 141 118 NC_003454:FN1797|3end_Spermidine/putrescine_transport_ATP-binding_protein_potA_280031..280181_POSITIVE 169 25 2 122 104 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 167 83 47 38 5 NC_003454:FN2100|3end_hypothetical_protein_610316..610466_POSITIVE 167 77 53 50 25 NC_003454:FN1862|3end_L-beta-lysine_5,6-aminomutase_beta_subunit_352331..352481_NEGATIVE 165 127 93 52 15 NC_003454:FN0758|3end_Rod_shape-determining_protein_mreB_1416214..1416364_NEGATIVE 165 115 72 67 19 NC_003454:FN1594|3end_Nitrogen_fixation_protein_RNFG_104360..104510_NEGATIVE