Origin IGS: gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatctctcctatttcccttagtttaatttcatctttttaataatgtgtatctgttaaaaataagtgagttacaaatgtagattttaaataaaaaatctactcagtaatgaactatttttaac Mask Tandem Repeat Region ================================================ gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Find is-nt database================================================ Query_seq: FN0422:FN0423|FN0422:FN0423:carbamoyl-phosphate synthase large subunit:Dihydroorotate dehydrogenase electron transfer subunit:->->:1066344..1066467 124 gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0422:FN0423|FN0422:FN0423:carbamoyl-phosphate synthase large subunit:Dihydroorotate dehydrogenase electron transfer subunit:->->:1066344..1066467 124 gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0422:FN0423|FN0422:FN0423:carbamoyl-phosphate synthase large subunit:Dihydroorotate dehydrogenase electron transfer subunit:->->:1066344..1066467 124 gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Predict ORF larger than 30AA ================================================ gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt 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================================================ gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0422:FN0423|FN0422:FN0423:carbamoyl-phosphate synthase large subunit:Dihydroorotate dehydrogenase electron transfer subunit:->->:1066344..1066467 124 gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_003454_FN0422_FN0423|carbamoyl-phosphate synthase large subunit:Dihydroorotate dehydrogenase electron transfer subunit|POSITIVE:POSITIVE|[1066344,1066467]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt gttaaaaatagttcattactgagtagattttttatttaaaatctacatttgtaactcacttatttttaacagatacacattattaaaaagatgaaattaaactaagggaaataggagagatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAAAAAUAGUUCAUUACUGAGUAGAUUUUUUAUUUAAAAUCUACAUUUGUAACUCACUUAUUUUUAACAGAUACACAUUAUUAAAAAGAUGAAAUUAAACUAAGGGAAAUAGGAGAGAUUUU ((((((((((((...((((.(((((((((((......))))))))).)).))))...)).)))))))))).......((((........))))............................... (-20.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCUCCUAUUUCCCUUAGUUUAAUUUCAUCUUUUUAAUAAUGUGUAUCUGUUAAAAAUAAGUGAGUUACAAAUGUAGAUUUUAAAUAAAAAAUCUACUCAGUAAUGAACUAUUUUUAAC ......................................................((((((((((.((..(((((....(((((((((......)))))))))...)))))..)))))))))))) (-20.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 68 24 175 131 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 278 34 3 156 125 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 223 69 22 162 119 NC_003454:FN1440|5end_1-phosphofructokinase_2107238..2107468_POSITIVE 217 67 29 139 101 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 212 60 11 102 52 NC_003454:FN1121|5end_ATP-dependent_Zn_protease_1764640..1764870_NEGATIVE 203 60 11 222 174 NC_003454:FN1615|5end_Integral_membrane_protein_125125..125355_POSITIVE 200 34 4 150 120 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 198 60 11 169 122 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 196 91 51 99 52 NC_003454:FN0489|5end_Prolipoprotein_diacylglyceryl_transferase_1135425..1135655_NEGATIVE 195 87 43 98 55 NC_003454:FN2018|5end_Single-stranded-DNA-specific_exonuclease_recJ_521927..522157_NEGATIVE 192 60 13 92 45 NC_003454:FN1608|5end_Ribosomal_protein_L11_methyltransferase_118847..119077_NEGATIVE 190 56 17 106 66 NC_003454:FN1458|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2140341..2140571_NEGATIVE 184 68 50 157 139 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 183 73 49 204 181 NC_003454:FN0551|5end_Bacterial_regulatory_proteins,_crp_family_1203276..1203506_POSITIVE 174 46 4 189 141 NC_003454:FN2080|5end_ABC_transporter_integral_membrane_protein_591957..592187_NEGATIVE 171 120 102 19 1 NC_003454:FN0879|5end_ABC_transporter_integral_membrane_protein_1540946..1541176_NEGATIVE 167 60 11 210 151 NC_003454:FN0466|5end_Lysyl-tRNA_synthetase_1111301..1111531_POSITIVE 167 78 31 119 71 NC_003454:FN2015|5end_ATP-dependent_protease_ATP-binding_subunit_518255..518485_NEGATIVE 166 46 4 185 137 NC_003454:FN0921|5end_hypothetical_protein_1576482..1576712_NEGATIVE 166 34 4 195 165 NC_003454:FN0798|5end_Fructose-1,6-bisphosphatase_1455835..1456065_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 68 24 82 38 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 375 67 29 40 1 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 331 37 4 34 1 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 223 69 22 89 46 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 196 67 26 57 16 NC_003454:FN0796|3end_pyruvate_phosphate_dikinase_1455643..1455793_POSITIVE 196 91 51 72 25 NC_003454:FN0490|3end_Integral_membrane_protein_1135452..1135602_NEGATIVE 195 87 43 95 52 NC_003454:FN2019|3end_Ribosome-binding_factor_A_521930..522080_NEGATIVE 194 118 89 31 5 NC_003454:FN0219|3end_Autolysin_response_regulator_842594..842744_NEGATIVE 192 60 13 117 70 NC_003454:FN1609|3end_hypothetical_protein_118822..118972_NEGATIVE 185 46 1 71 37 NC_003454:FN1954|3end_Glycerophosphoryl_diester_phosphodiesterase_459777..459927_NEGATIVE 180 67 29 76 38 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 174 46 4 71 23 NC_003454:FN2081|3end_ABC_transporter_substrate-binding_protein_592075..592225_NEGATIVE 173 46 1 68 21 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 172 68 23 71 28 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 167 70 21 123 82 NC_003454:FN0894|3end_hypothetical_protein_1554893..1555043_POSITIVE 167 78 31 107 59 NC_003454:FN2016|3end_ATP-dependent_Clp_protease_proteolytic_subunit_518267..518417_NEGATIVE 166 119 102 56 37 NC_003454:FN1467|3end_hypothetical_protein_2149841..2149991_POSITIVE 166 46 4 79 31 NC_003454:FN0922|3end_Homoserine_kinase_1576588..1576738_NEGATIVE 166 49 1 97 48 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 163 58 12 68 23 NC_003454:FN0522|3end_Exonuclease_SBCC_1172965..1173115_NEGATIVE