Origin IGS: ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt .........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 aaattttatttgttgacactacttgaaaagtgtgctaaaataacaaagtcttagaaagcagaatacaggaaaaactcgcataccatattaaattatgggaggatcattgaagataccgttaaagagtggacttgtttttgataaatagtttacactttgatgtagattgtgaagaatttaaatcaaaagatttcttcgtttagttgagtagaattgtatgagctatataagattagaaaatacaatttaataggaggaatgcag Mask Tandem Repeat Region ================================================ ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Find is-nt database================================================ Query_seq: FN2044:FN2045|FN2044:FN2045:LSU ribosomal protein L33P:Ferric uptake regulation protein:<-<-:550200..550463 264 ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2044:FN2045|FN2044:FN2045:LSU ribosomal protein L33P:Ferric uptake regulation protein:<-<-:550200..550463 264 ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2044:FN2045|FN2044:FN2045:LSU ribosomal protein L33P:Ferric uptake regulation protein:<-<-:550200..550463 264 ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Predict ORF larger than 30AA ================================================ ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt 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: 90 Start: 224 End: 253 ...............................................................................................................................................................................................................................GTTGACACTACTTGAAAAGTGTGCTAAAAT........... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2044:FN2045|FN2044:FN2045:LSU ribosomal protein L33P:Ferric uptake regulation protein:<-<-:550200..550463 264 ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: NC_003454_FN2044_FN2045|LSU ribosomal protein L33P:Ferric uptake regulation protein|NEGATIVE:NEGATIVE|[550200,550463]|264 HSP 1 e-value: 1.0E-148 bit: 523.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt ctgcattcctcctattaaattgtattttctaatcttatatagctcatacaattctactcaactaaacgaagaaatcttttgatttaaattcttcacaatctacatcaaagtgtaaactatttatcaaaaacaagtccactctttaacggtatcttcaatgatcctcccataatttaatatggtatgcgagtttttcctgtattctgctttctaagactttgttattttagcacacttttcaagtagtgtcaacaaataaaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCAUUCCUCCUAUUAAAUUGUAUUUUCUAAUCUUAUAUAGCUCAUACAAUUCUACUCAACUAAACGAAGAAAUCUUUUGAUUUAAAUUCUUCACAAUCUACAUCAAAGUGUAAACUAUUUAUCAAAAACAAGUCCACUCUUUAACGGUAUCUUCAAUGAUCCUCCCAUAAUUUAAUAUGGUAUGCGAGUUUUUCCUGUAUUCUGCUUUCUAAGACUUUGUUAUUUUAGCACACUUUUCAAGUAGUGUCAACAAAUAAAAUUU ...................((((.........(((((...(((..(((((.....((((........(((((.(((.((((((..........(((.............)))..........))))))...(((......)))....))).)))))..........(((((......))))).....))))......)))))...)))...))))).............(.(((((........)))))).))))......... (-34.87) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUAUUUGUUGACACUACUUGAAAAGUGUGCUAAAAUAACAAAGUCUUAGAAAGCAGAAUACAGGAAAAACUCGCAUACCAUAUUAAAUUAUGGGAGGAUCAUUGAAGAUACCGUUAAAGAGUGGACUUGUUUUUGAUAAAUAGUUUACACUUUGAUGUAGAUUGUGAAGAAUUUAAAUCAAAAGAUUUCUUCGUUUAGUUGAGUAGAAUUGUAUGAGCUAUAUAAGAUUAGAAAAUACAAUUUAAUAGGAGGAAUGCAG ..((((..((((((((..(((((((........((((((......(((((((......(((((.(((((....((((.....(((((......)))))..(((((......))).))......))))...))))))))))....((((((((((......))))))))))................))))))).....))))))))))))).(((((((...(((........)))...)))))))))))))))..)))).... (-52.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 50 1 141 92 NC_003454:FN2044|5end_LSU_ribosomal_protein_L33P_550109..550339_NEGATIVE 291 200 151 73 29 NC_003454:FN0853|5end_Glycogen_synthase_1512307..1512537_NEGATIVE 282 230 185 166 120 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 270 223 186 71 30 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 268 183 141 118 70 NC_003454:FN1433|5end_Short_chain_dehydrogenase_2102520..2102750_NEGATIVE 245 200 152 64 8 NC_003454:FN1062|5end_Hydrolase_1709186..1709416_NEGATIVE 239 157 129 170 143 NC_003454:FN0104|5end_Acetyltransferase_739896..740126_NEGATIVE 236 170 121 91 42 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 234 44 7 105 67 NC_003454:FN1220|5end_Cysteine_synthase_1879262..1879492_POSITIVE 225 196 151 178 142 NC_003454:FN1455|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2136519..2136749_NEGATIVE 225 209 162 51 11 NC_003454:FN1159|5end_fructose_1,6-bisphosphatase_II_1814731..1814961_POSITIVE 224 48 3 156 95 NC_003454:FN0823|5end_GTP-binding_protein_hflX_1482367..1482597_POSITIVE 224 176 145 126 96 NC_003454:FN0332|5end_Magnesium_and_cobalt_transport_protein_corA_967230..967460_NEGATIVE 222 224 184 173 127 NC_003454:FN1629|5end_50S_ribosomal_protein_L6_134508..134738_NEGATIVE 220 253 217 49 2 NC_003454:FN0796|5end_pyruvate_phosphate_dikinase_1453008..1453238_POSITIVE 218 178 152 111 85 NC_003454:FN0396|5end_Dipeptide-binding_protein_1034203..1034433_POSITIVE 218 50 1 69 18 NC_003454:FN1539|5end_Iron-sulfur_cluster-binding_protein_52461..52691_POSITIVE 217 226 188 49 5 NC_003454:FN0643|5end_hypothetical_protein_1299871..1300101_NEGATIVE 217 48 5 90 49 NC_003454:FN1944|5end_Sodium-dependent_tryptophan_transporter_446567..446797_POSITIVE 217 170 137 91 46 NC_003454:FN1863|5end_L-beta-lysine_5,6-aminomutase_alpha_subunit_354678..354908_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 200 151 56 12 NC_003454:FN0854|3end_Glucose-1-phosphate_adenylyltransferase_1512324..1512474_NEGATIVE 268 183 141 100 52 NC_003454:FN1434|3end_Tetratricopeptide_repeat_family_protein_2102538..2102688_NEGATIVE 236 170 121 89 40 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 225 209 162 54 14 NC_003454:FN1158|3end_hypothetical_protein_1814814..1814964_POSITIVE 224 48 3 135 74 NC_003454:FN0822|3end_Shikimate_kinase_1482426..1482576_POSITIVE 224 176 145 109 79 NC_003454:FN0333|3end_Glycerol_uptake_operon_antiterminator_regulatory_protein_967247..967397_NEGATIVE 222 224 184 148 102 NC_003454:FN1630|3end_SSU_ribosomal_protein_S8P_134533..134683_NEGATIVE 217 170 137 91 46 NC_003454:FN1864|3end_DNA_mismatch_repair_protein_mutS_354678..354828_NEGATIVE 217 210 163 125 75 NC_003454:FN1558|3end_30S_ribosomal_protein_S12_80150..80300_NEGATIVE 214 43 4 116 83 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 212 44 3 124 70 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 210 210 161 84 19 NC_003454:FN2084|3end_Permease_596507..596657_POSITIVE 205 170 132 66 16 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 205 218 180 148 118 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 205 228 181 59 7 NC_003454:FN0639|3end_hypothetical_protein_1297131..1297281_NEGATIVE 205 240 192 74 22 NC_003454:FN0302|3end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_937578..937728_POSITIVE 205 234 197 55 18 NC_003454:FN1762|3end_Protein_yaaA_255258..255408_NEGATIVE 204 178 131 100 42 NC_003454:FN1704|3end_Serine_protease_201497..201647_POSITIVE 199 67 25 127 84 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE 199 230 185 37 2 NC_003454:FN0750|3end_hypothetical_protein_1408974..1409124_NEGATIVE