Origin IGS: taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga .........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 tcaaatattaaataaaatggactatttactaaatagtgttgataaaaaagtttagaatatgacttgacatagttaagagaattttttgagagcaaaaacttaaaaattctcttttttcatattattaaattttatattgttaatatagaaaaaatatgttaatctatattataaaaataagaatggagtgagaaaatgaaaaaaatacttatattaatagtaatggtttttggctta Mask Tandem Repeat Region ================================================ taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Find is-nt database================================================ Query_seq: FN1871:FN1872|FN1871:FN1872:hypothetical protein:hypothetical protein:<-<-:362642..362878 237 taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1871:FN1872|FN1871:FN1872:hypothetical protein:hypothetical protein:<-<-:362642..362878 237 taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1871:FN1872|FN1871:FN1872:hypothetical protein:hypothetical protein:<-<-:362642..362878 237 taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 131 End: 235 .................................................................................................................................. M F K F L L S K N S L N Y V K S Y S K L F Y Q H Y L V N S P F Y L I F .. taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga 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: 41 End: 70 ........................................ATTTTCTCACTCCATTCTTATTTTTATAAT....................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1871:FN1872|FN1871:FN1872:hypothetical protein:hypothetical protein:<-<-:362642..362878 237 taagccaaaaaccattactattaatataagtatttttttcattttctcactccattcttatttttataatatagattaacatattttttctatattaacaatataaaatttaataatatgaaaaaagagaatttttaagtttttgctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga Intra-Species Hit: Count: 1 Min: 1 Max: 237 Len: 237 Subject: NC_003454_FN1871_FN1872|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[362642,362878]|237 HSP 1 e-value: 9.0E-46 bit: 184.0 Len: 93 Query Start:145 Query End:237 Subject Strand: POSITIVE Subject Start: 145 Subject End: 237 ................................................................................................................................................gctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga ................................................................................................................................................gctctcaaaaaattctcttaactatgtcaagtcatattctaaacttttttatcaacactatttagtaaatagtccattttatttaatatttga HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 taagccaaaaaccattactattaatataagta............................................................................................................................................................................................................. taagccaaaaaccattactattaatataagta............................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCAAAAACCAUUACUAUUAAUAUAAGUAUUUUUUUCAUUUUCUCACUCCAUUCUUAUUUUUAUAAUAUAGAUUAACAUAUUUUUUCUAUAUUAACAAUAUAAAAUUUAAUAAUAUGAAAAAAGAGAAUUUUUAAGUUUUUGCUCUCAAAAAAUUCUCUUAACUAUGUCAAGUCAUAUUCUAAACUUUUUUAUCAACACUAUUUAGUAAAUAGUCCAUUUUAUUUAAUAUUUGA ..........................((((((((................................(((((((((..((.....))..))))))))).....(((((((.....(((((((...((((((((((((.(((....)))....))))))))))))..((......)))))))))..................((((((.....))))))..)))))))..)))))))). (-26.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUAUUAAAUAAAAUGGACUAUUUACUAAAUAGUGUUGAUAAAAAAGUUUAGAAUAUGACUUGACAUAGUUAAGAGAAUUUUUUGAGAGCAAAAACUUAAAAAUUCUCUUUUUUCAUAUUAUUAAAUUUUAUAUUGUUAAUAUAGAAAAAAUAUGUUAAUCUAUAUUAUAAAAAUAAGAAUGGAGUGAGAAAAUGAAAAAAAUACUUAUAUUAAUAGUAAUGGUUUUUGGCUUA ..................((.(((...((((..((.((((((((...((((........(((((......))))).((((((((((.(((........))))))))))))).((((((((.(((((..(((((.((((..(((((((((.............)))))))))....)))))))))..)))))....))))))))...)))).)))))))).)).))))...))))).. (-38.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 674 60 11 151 102 NC_003454:FN1871|5end_hypothetical_protein_362551..362781_NEGATIVE 313 160 116 195 153 NC_003454:FN1075|5end_hypothetical_protein_1722042..1722272_POSITIVE 285 64 21 99 55 NC_003454:FN0668|5end_High-affinity_zinc_uptake_system_protein_znuA_precursor_1323969..1324199_POSITIVE 277 70 26 142 102 NC_003454:FN1009|5end_hypothetical_protein_1663950..1664180_NEGATIVE 245 180 131 180 135 NC_003454:FN2122|5end_Phenylalanyl-tRNA_synthetase_beta_chain_632194..632424_NEGATIVE 243 77 32 127 81 NC_003454:FN0236|5end_ABC_transporter_substrate-binding_protein_861416..861646_NEGATIVE 240 62 29 183 145 NC_003454:FN0577|5end_hypothetical_protein_1227237..1227467_POSITIVE 239 59 12 127 78 NC_003454:FN0465|5end_hypothetical_protein_1110046..1110276_POSITIVE 234 58 12 93 36 NC_003454:FN0410|5end_6-phosphofructokinase_1047230..1047460_POSITIVE 230 67 33 120 82 NC_003454:FN1181|5end_hypothetical_protein_1843872..1844102_NEGATIVE 228 159 116 231 186 NC_003454:FN0657|5end_Acetyltransferase_1314266..1314496_POSITIVE 227 65 26 118 75 NC_003454:FN1323|5end_Thymidylate_kinase_1979152..1979382_NEGATIVE 227 55 14 105 66 NC_003454:FN1980|5end_Transporter_482063..482293_POSITIVE 226 167 126 182 135 NC_003454:FN1634|5end_LSU_ribosomal_protein_L24P_136179..136409_NEGATIVE 223 70 29 116 74 NC_003454:FN1518|5end_RNA_polymerase_sigma-70_factor_24077..24307_NEGATIVE 221 56 15 103 63 NC_003454:FN0989|5end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641667..1641897_NEGATIVE 219 54 23 103 71 NC_003454:FN0974|5end_Lactoylglutathione_lyase_1627144..1627374_NEGATIVE 215 48 3 127 76 NC_003454:FN1809|5end_Iron/zinc/copper-binding_protein_291031..291261_NEGATIVE 211 59 25 107 74 NC_003454:FN0519|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1171669..1171899_NEGATIVE 210 167 128 195 158 NC_003454:FN0218|5end_Anthranilate_synthase_component_II_841652..841882_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 445 200 152 89 41 NC_003454:FN1815|3end_Transposase_295626..295776_NEGATIVE 313 160 116 81 39 NC_003454:FN1074|3end_Signal_recognition_particle_receptor_FtsY_1722008..1722158_POSITIVE 299 162 121 75 30 NC_003454:FN0792|3end_urocanate_hydratase_1450364..1450514_POSITIVE 295 162 122 79 38 NC_003454:FN1951|3end_ATPase_associated_with_chromosome_architecture/replication_458400..458550_NEGATIVE 294 224 182 73 32 NC_003454:FN0273|3end_Butyrate-acetoacetate_CoA-transferase_subunit_B_900162..900312_POSITIVE 285 48 1 82 33 NC_003454:FN1873|3end_Bis(5'-nucleosyl)-tetraphosphatase_363102..363252_NEGATIVE 282 162 121 73 29 NC_003454:FN0656|3end_hypothetical_protein_1314185..1314335_POSITIVE 281 162 121 63 19 NC_003454:FN0470|3end_Putative_efflux_pump_component_MtrF_1116359..1116509_POSITIVE 256 224 182 56 15 NC_003454:FN0813|3end_Transcriptional_regulator,_TetR_family_1471504..1471654_NEGATIVE 249 67 27 108 63 NC_003454:FN0825|3end_Hypothetical_cytosolic_protein_1486436..1486586_POSITIVE 243 77 32 140 94 NC_003454:FN0237|3end_ABC_transporter_permease_protein_861403..861553_NEGATIVE 239 59 12 88 39 NC_003454:FN0464|3end_hypothetical_protein_1110087..1110237_POSITIVE 234 58 12 81 24 NC_003454:FN0409|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_alpha_1047298..1047448_POSITIVE 230 67 33 107 69 NC_003454:FN1182|3end_hypothetical_protein_1843885..1844035_NEGATIVE 230 196 152 67 23 NC_003454:FN0451|3end_hypothetical_protein_1095427..1095577_POSITIVE 227 65 26 130 87 NC_003454:FN1324|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1979140..1979290_NEGATIVE 224 55 23 35 2 NC_003454:FN1979|3end_SSU_ribosomal_protein_S15P_482073..482223_POSITIVE 223 70 29 105 63 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 221 56 15 91 51 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 219 162 122 59 15 NC_003454:FN1161|3end_Glutamate_racemase_1820053..1820203_POSITIVE