Origin IGS: gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa .........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 ttctcctccttactaaatttactaaaattttaaaatctatatttaattcaattttattctatattgctaaaaatatcaataagatagttaagaattttcttgaataagactactgtgatgttcattattgttgagagagtatttaggagctctcgaaacactaatggctatcaagtagtcgctttaacaaacttatttatacttttagatttttagttatataaaaggggaaaagtgtaactaatccccttattatataaattgtatcctgtatctatccttaatttatattaagttgatc Mask Tandem Repeat Region ================================================ gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Find is-nt database================================================ Query_seq: FN1983:FN1984|FN1983:FN1984:Alkyl hydroperoxide reductase C22 protein:Glutaredoxin-like protein:->->:485326..485626 301 gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1983:FN1984|FN1983:FN1984:Alkyl hydroperoxide reductase C22 protein:Glutaredoxin-like protein:->->:485326..485626 301 gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1983:FN1984|FN1983:FN1984:Alkyl hydroperoxide reductase C22 protein:Glutaredoxin-like protein:->->:485326..485626 301 gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 141 End: 245 ............................................................................................................................................ M F R E L L N T L S T I M N I T V V L F K K I L N Y L I D I F S N I E ........................................................ Protein_Len: 40 Strand: - Start: 89 End: 208 ........................................................................................ F D L L I F L N T L A V V Q Y G N T N R S S R F V R E V I I F M V T T K N L F M ............................................................................................. gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa 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: 88 Start: 222 End: 251 .............................................................................................................................................................................................................................ATTGATATTTTTAGCAATATAGAATAAAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -9.2 Tail_Score: -2.74983 Start: 42 End: 85 Full_Region: cttttagatttttag ttatataaaaggggaaaagt gta actaatccccttattatataa attgtatcctgtatc .........................................ttatataaaaggggaaaagtgtaactaatccccttattatataa........................................................................................................................................................................................................................ TransTerm Strand: + Conf: 72 HP_score: -6.2 Tail_Score: -4.55287 Start: 53 End: 75 Full_Region: CAATTTATATAATAA GGGGATTAGT TAC ACTTTTCCCC TTTTATATAACTAAA ....................................................GGGGATTAGTTACACTTTTCCCC.................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: FN1983:FN1984|FN1983:FN1984:Alkyl hydroperoxide reductase C22 protein:Glutaredoxin-like protein:->->:485326..485626 301 gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattgatatttttagcaatatagaataaaattgaattaaatatagattttaaaattttagtaaatttagtaaggaggagaa Intra-Species Hit: Count: 1 Min: 1 Max: 225 Len: 225 Subject: NC_003454_FN1983_FN1984|Alkyl hydroperoxide reductase C22 protein:Glutaredoxin-like protein|POSITIVE:POSITIVE|[485326,485626]|301 HSP 1 e-value: 1.0E-124 bit: 446.0 Len: 225 Query Start:1 Query End:225 Subject Strand: POSITIVE Subject Start: 1 Subject End: 225 gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattg............................................................................ gatcaacttaatataaattaaggatagatacaggatacaatttatataataaggggattagttacacttttccccttttatataactaaaaatctaaaagtataaataagtttgttaaagcgactacttgatagccattagtgtttcgagagctcctaaatactctctcaacaataatgaacatcacagtagtcttattcaagaaaattcttaactatcttattg............................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCAACUUAAUAUAAAUUAAGGAUAGAUACAGGAUACAAUUUAUAUAAUAAGGGGAUUAGUUACACUUUUCCCCUUUUAUAUAACUAAAAAUCUAAAAGUAUAAAUAAGUUUGUUAAAGCGACUACUUGAUAGCCAUUAGUGUUUCGAGAGCUCCUAAAUACUCUCUCAACAAUAAUGAACAUCACAGUAGUCUUAUUCAAGAAAAUUCUUAACUAUCUUAUUG ......((((((....))))))..(((((...(....)...((((((((.(((((((..((.....))..)))))))))))))))......)))))........((((((...((((....(((((((((((...(((((.((((..(((((..........)))))..)))).)))))...)))).))))))).......(((....)))))))...)))))). (-52.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUAAGAUAGUUAAGAAUUUUCUUGAAUAAGACUACUGUGAUGUUCAUUAUUGUUGAGAGAGUAUUUAGGAGCUCUCGAAACACUAAUGGCUAUCAAGUAGUCGCUUUAACAAACUUAUUUAUACUUUUAGAUUUUUAGUUAUAUAAAAGGGGAAAAGUGUAACUAAUCCCCUUAUUAUAUAAAUUGUAUCCUGUAUCUAUCCUUAAUUUAUAUUAAGUUGAUC .((((((....((((((....))))))....(((((((.(((((..(((((.((((..((((((........))))))..)))).)))))..))))))))))))...........))))))........(((((...((((((((((((((((((..((.....))..))))))).))))))))........))).)))))..((((((....))))))...... (-59.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 532 179 132 170 122 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 267 80 51 41 5 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 266 199 151 224 176 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 266 171 135 231 195 NC_003454:FN1584|5end_Beta-lactamase_96158..96388_NEGATIVE 257 156 121 129 89 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 254 153 118 174 140 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 254 153 118 70 36 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 250 153 119 194 158 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 242 220 186 102 66 NC_003454:FN1917|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_413756..413986_NEGATIVE 239 170 124 64 13 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 239 204 166 74 40 NC_003454:FN1183|5end_Hypothetical_cytosolic_protein_1846180..1846410_NEGATIVE 232 157 118 147 115 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 228 166 124 165 128 NC_003454:FN1627|5end_SSU_ribosomal_protein_S5P_133556..133786_NEGATIVE 224 193 151 64 30 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 221 158 111 99 54 NC_003454:FN1621|5end_elongation_factor_Ts_128673..128903_POSITIVE 216 157 119 96 63 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 216 84 45 139 103 NC_003454:FN1793|5end_Phosphoenolpyruvate-protein_phosphotransferase_275273..275503_NEGATIVE 212 158 124 103 60 NC_003454:FN1164|5end_Glucokinase_1821754..1821984_POSITIVE 211 170 128 45 7 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 210 166 122 186 141 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 532 179 132 68 20 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 396 199 151 56 7 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 351 170 125 47 2 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 335 173 135 48 10 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 293 85 42 49 6 NC_003454:FN1983|3end_Alkyl_hydroperoxide_reductase_C22_protein_485265..485415_POSITIVE 291 80 49 39 1 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 266 199 151 91 43 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 242 220 186 118 82 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 239 204 166 46 12 NC_003454:FN1184|3end_hypothetical_protein_1846208..1846358_NEGATIVE 236 168 128 78 38 NC_003454:FN0535|3end_hypothetical_protein_1190009..1190159_POSITIVE 232 157 118 127 95 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 228 166 124 141 104 NC_003454:FN1628|3end_LSU_ribosomal_protein_L18P_133580..133730_NEGATIVE 222 176 135 142 113 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 221 158 111 65 20 NC_003454:FN1620|3end_30S_ribosomal_protein_S2_128719..128869_POSITIVE 216 84 45 84 48 NC_003454:FN1794|3end_Phosphocarrier_protein_HPr_275328..275478_NEGATIVE 212 158 124 79 36 NC_003454:FN1163|3end_Thioredoxin_reductase_1821810..1821960_POSITIVE 212 78 33 105 67 NC_003454:FN0218|3end_Anthranilate_synthase_component_II_842601..842751_POSITIVE 210 166 122 52 7 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 204 109 65 54 8 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE 203 115 74 120 76 NC_003454:FN1087|3end_hypothetical_protein_1731616..1731766_POSITIVE