Origin IGS: acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaatcctcctaacaataaaataaacaataaaatttgatttattatactatttatatatagttttgtaaagtgagagaaaatgtttaaattttaggattttatggtaaaataaagataatcaacataaatgaaacattatgtaaattttaaataaaaagaggt Mask Tandem Repeat Region ================================================ acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Find is-nt database================================================ Query_seq: FN1374:FN1375|FN1374:FN1375:Transcriptional regulator:Citrate-sodium symport:<-->:2022392..2022555 164 acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1374:FN1375|FN1374:FN1375:Transcriptional regulator:Citrate-sodium symport:<-->:2022392..2022555 164 acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1374:FN1375|FN1374:FN1375:Transcriptional regulator:Citrate-sodium symport:<-->:2022392..2022555 164 acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Predict ORF larger than 30AA ================================================ acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta 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: 93 End: 122 ............................................................................................CTTTACAAAACTATATATAAATAGTATAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1374:FN1375|FN1374:FN1375:Transcriptional regulator:Citrate-sodium symport:<-->:2022392..2022555 164 acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_003454_FN1374_FN1375|Transcriptional regulator:Citrate-sodium symport|NEGATIVE:POSITIVE|[2022392,2022555]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta acctctttttatttaaaatttacataatgtttcatttatgttgattatctttattttaccataaaatcctaaaatttaaacattttctctcactttacaaaactatatataaatagtataataaatcaaattttattgtttattttattgttaggaggatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCUUUUUAUUUAAAAUUUACAUAAUGUUUCAUUUAUGUUGAUUAUCUUUAUUUUACCAUAAAAUCCUAAAAUUUAAACAUUUUCUCUCACUUUACAAAACUAUAUAUAAAUAGUAUAAUAAAUCAAAUUUUAUUGUUUAUUUUAUUGUUAGGAGGAUUUUA .((((((..((..((((((..((((((.((((.((((((..........(((((......)))))....................................(((((......)))))...)))))).)))).))).)))..)))))).))..))))))...... (-20.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCCUCCUAACAAUAAAAUAAACAAUAAAAUUUGAUUUAUUAUACUAUUUAUAUAUAGUUUUGUAAAGUGAGAGAAAAUGUUUAAAUUUUAGGAUUUUAUGGUAAAAUAAAGAUAAUCAACAUAAAUGAAACAUUAUGUAAAUUUUAAAUAAAAAGAGGU ......((((..........(((((((((......))).)))))).((..(((((((((..((((..(...(((....(((((......)))))....((((((......))))))........)))..)..))))..)))))))))..))........)))). (-19.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 651 70 21 161 112 NC_003454:FN1374|5end_Transcriptional_regulator_2022301..2022531_NEGATIVE 254 84 44 117 71 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 238 130 81 211 153 NC_003454:FN0401|5end_hypothetical_protein_1040150..1040380_NEGATIVE 226 50 6 185 136 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 196 50 1 150 100 NC_003454:FN1398|5end_Amino_acid_carrier_protein_alsT_2052808..2053038_POSITIVE 190 65 23 230 190 NC_003454:FN0525|5end_Penicillin-binding_protein_1181840..1182070_NEGATIVE 188 73 32 225 179 NC_003454:FN0090|5end_Ethanolamine_utilization_protein_eutQ_726315..726545_POSITIVE 188 64 28 194 153 NC_003454:FN0059|5end_NifU_protein_695153..695383_POSITIVE 184 77 31 100 59 NC_003454:FN0909|5end_DNA_repair_protein_radC_1567654..1567884_NEGATIVE 184 92 59 51 13 NC_003454:FN1902|5end_Deoxycytidylate_deaminase_390551..390781_NEGATIVE 183 42 2 139 96 NC_003454:FN1977|5end_Cell_cycle_protein_MesJ_478136..478366_POSITIVE 182 70 24 139 95 NC_003454:FN2089|5end_hypothetical_protein_601549..601779_NEGATIVE 182 70 31 101 65 NC_003454:FN1978|5end_Cell_division_protein_ftsH_479479..479709_POSITIVE 179 68 23 140 104 NC_003454:FN1345|5end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998957..1999187_NEGATIVE 179 97 62 105 68 NC_003454:FN1325|5end_Phosphatidate_cytidylyltransferase_1981205..1981435_NEGATIVE 179 43 2 221 180 NC_003454:FN1913|5end_hydrolase_(HD_superfamily)_411580..411810_NEGATIVE 176 120 75 126 83 NC_003454:FN0886|5end_Hemin_receptor_1545768..1545998_POSITIVE 175 42 2 137 100 NC_003454:FN1056|5end_hypothetical_protein_1703693..1703923_POSITIVE 174 90 46 171 127 NC_003454:FN1669|5end_Choline_transport_protein_166486..166716_NEGATIVE 173 117 81 123 89 NC_003454:FN0291|5end_Hemolysin_924999..925229_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 50 6 92 43 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 196 50 1 92 42 NC_003454:FN1397|3end_glutaminase_2052830..2052980_POSITIVE 188 64 28 141 100 NC_003454:FN0058|3end_Cysteine_desulfhydrase_695180..695330_POSITIVE 184 77 31 90 49 NC_003454:FN0910|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_1567664..1567814_NEGATIVE 183 42 2 130 87 NC_003454:FN1976|3end_4-amino-4-deoxychorismate_lyase_478207..478357_POSITIVE 182 70 31 104 68 NC_003454:FN1977|3end_Cell_cycle_protein_MesJ_479562..479712_POSITIVE 180 57 24 140 108 NC_003454:FN2090|3end_hypothetical_protein_601536..601686_NEGATIVE 179 68 23 120 84 NC_003454:FN1346|3end_Hypothetical_cytosolic_protein_1998977..1999127_NEGATIVE 179 97 62 112 75 NC_003454:FN1326|3end_Undecaprenyl_pyrophosphate_synthetase_1981198..1981348_NEGATIVE 175 95 66 34 6 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 173 117 81 111 77 NC_003454:FN0292|3end_Hemolysin_activator_protein_precursor_925011..925161_NEGATIVE 173 60 11 150 102 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 172 50 6 62 19 NC_003454:FN0796|3end_pyruvate_phosphate_dikinase_1455643..1455793_POSITIVE 169 84 41 108 61 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 169 160 115 141 97 NC_003454:FN0036|3end_Hypothetical_membrane-spanning_Protein_676977..677127_NEGATIVE 167 44 2 123 84 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 165 90 41 148 97 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 165 97 52 146 98 NC_003454:FN0220|3end_Autolysin_sensor_kinase_843309..843459_NEGATIVE 165 97 54 93 40 NC_003454:FN2016|3end_ATP-dependent_Clp_protease_proteolytic_subunit_518267..518417_NEGATIVE 163 38 2 149 117 NC_003454:FN1914|3end_Anti-sigma_F_factor_antagonist_411643..411793_NEGATIVE