Origin IGS: aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctatcattcctcccctaacatttatattttaaatacaggaaattttataatattgaaaggcttttgtcaatcatttttattagaaatttatattaaaaaaaatctataattttttaatacaaaaactt Mask Tandem Repeat Region ================================================ aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Find is-nt database================================================ Query_seq: FN0256:FN0257|FN0256:FN0257:Hypothetical cytosolic protein:Transporter:->->:882528..882655 128 aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0256:FN0257|FN0256:FN0257:Hypothetical cytosolic protein:Transporter:->->:882528..882655 128 aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0256:FN0257|FN0256:FN0257:Hypothetical cytosolic protein:Transporter:->->:882528..882655 128 aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Predict ORF larger than 30AA ================================================ aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag 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: 89 Start: 58 End: 87 .........................................................ATTGACAAAAGCCTTTCAATATTATAAAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0256:FN0257|FN0256:FN0257:Hypothetical cytosolic protein:Transporter:->->:882528..882655 128 aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_003454_FN0256_FN0257|Hypothetical cytosolic protein:Transporter|POSITIVE:POSITIVE|[882528, 882655]|128 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 aagtttttgtattaaaaaattatagannnnnnnnaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag aagtttttgtattaaaaaattatagattttttttaatataaatttctaataaaaatgattgacaaaagcctttcaatattataaaatttcctgtatttaaaatataaatgttaggggaggaatgatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUUUUUGUAUUAAAAAAUUAUAGAUUUUUUUUAAUAUAAAUUUCUAAUAAAAAUGAUUGACAAAAGCCUUUCAAUAUUAUAAAAUUUCCUGUAUUUAAAAUAUAAAUGUUAGGGGAGGAAUGAUAG .((..((((((((((((((.........))))))))))))))...))........(((..(........)..))).((((((....((((((.((((((.....))))))...))))))..)))))). (-18.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUCAUUCCUCCCCUAACAUUUAUAUUUUAAAUACAGGAAAUUUUAUAAUAUUGAAAGGCUUUUGUCAAUCAUUUUUAUUAGAAAUUUAUAUUAAAAAAAAUCUAUAAUUUUUUAAUACAAAAACUU .............(((...(((((.....)))))..)))(((((((.(((((.(((..(((....)))..)))....)))))))))))).((((((((((.........))))))))))......... (-11.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 97 56 227 179 NC_003454:FN1073|5end_hypothetical_protein_1720403..1720633_POSITIVE 205 98 66 56 26 NC_003454:FN0452|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1095699..1095929_POSITIVE 191 119 76 132 90 NC_003454:FN0261|5end_Pyruvate_formate-lyase_activating_enzyme_887510..887740_NEGATIVE 162 94 63 58 25 NC_003454:FN0029|5end_Flavodoxin_667027..667257_NEGATIVE 157 91 67 46 17 NC_003454:FN0720|5end_elongation_factor_P_1376976..1377206_POSITIVE 156 60 18 171 131 NC_003454:FN0991|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1645810..1646040_POSITIVE 156 105 62 191 154 NC_003454:FN0314|5end_Caffeoyl-CoA_O-methyltransferase_951204..951434_POSITIVE 155 117 79 115 88 NC_003454:FN0248|5end_hypothetical_protein_871562..871792_POSITIVE 154 75 62 140 127 NC_003454:FN1193|5end_hypothetical_protein_1855052..1855282_POSITIVE 153 94 53 107 68 NC_003454:FN0996|5end_Hypothetical_membrane-spanning_protein_1651371..1651601_NEGATIVE 152 120 78 221 184 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 151 95 62 80 45 NC_003454:FN1703|5end_ADP-L-glycero-D-manno-heptose-6-epimerase_198992..199222_NEGATIVE 149 92 63 65 28 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 149 78 35 155 107 NC_003454:FN2120|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628930..629160_NEGATIVE 148 102 67 66 26 NC_003454:FN0779|5end_Putative_GTPase_(G3E_family)_1436980..1437210_NEGATIVE 148 115 87 169 139 NC_003454:FN0315|5end_Transcriptional_regulator,_AraC_family_951934..952164_POSITIVE 148 94 66 168 133 NC_003454:FN2100|5end_hypothetical_protein_608986..609216_POSITIVE 147 85 42 100 43 NC_003454:FN0327|5end_Bacterial_Protein_Translation_Initiation_Factor_3_(IF-3)_962149..962379_NEGATIVE 147 108 67 213 168 NC_003454:FN1848|5end_Metal_dependent_hydrolase_337112..337342_POSITIVE 146 118 81 77 48 NC_003454:FN0416|5end_Type_III_restriction-modification_system_methylation_subunit_1054300..1054530_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 191 119 76 66 24 NC_003454:FN0262|3end_Formate_acetyltransferase_887576..887726_NEGATIVE 168 109 67 42 2 NC_003454:FN0564|3end_hypothetical_protein_1216466..1216616_NEGATIVE 157 91 67 46 17 NC_003454:FN0719|3end_Hypothetical_cytosolic_protein_1377056..1377206_POSITIVE 155 117 79 51 24 NC_003454:FN0247|3end_Hypothetical_cytosolic_protein_871578..871728_POSITIVE 155 99 69 66 35 NC_003454:FN1983|3end_Alkyl_hydroperoxide_reductase_C22_protein_485265..485415_POSITIVE 154 75 62 39 26 NC_003454:FN1192|3end_hypothetical_protein_1855031..1855181_POSITIVE 153 94 53 94 55 NC_003454:FN0997|3end_hypothetical_protein_1651384..1651534_NEGATIVE 149 78 35 49 1 NC_003454:FN2121|3end_Hypothetical_exported_24-amino_acid_repeat_protein_629036..629186_NEGATIVE 148 102 67 47 7 NC_003454:FN0780|3end_Hypothetical_membrane-spanning_protein_1436999..1437149_NEGATIVE 148 115 87 86 56 NC_003454:FN0314|3end_Caffeoyl-CoA_O-methyltransferase_951931..952081_POSITIVE 148 76 38 71 42 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 144 107 69 133 82 NC_003454:FN0309|3end_Iron(III)-transport_system_permease_protein_sfuB_945861..946011_POSITIVE 144 120 86 117 73 NC_003454:FN0266|3end_membrane_protein_related_to_metalloendopeptidase_893611..893761_POSITIVE 143 98 60 118 80 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 142 98 59 127 96 NC_003454:FN1809|3end_Iron/zinc/copper-binding_protein_290180..290330_NEGATIVE 141 106 70 122 81 NC_003454:FN0269|3end_Transposase_896846..896996_POSITIVE 140 82 55 122 98 NC_003454:FN1665|3end_Virulence-associated_protein_I_162894..163044_POSITIVE 138 59 27 118 85 NC_003454:FN1262|3end_Integral_membrane_protein_1919682..1919832_POSITIVE 138 106 90 26 10 NC_003454:FN0157|3end_DNA_repair_protein_RadA_786336..786486_POSITIVE 137 69 29 151 107 NC_003454:FN0623|3end_Malonate_transporter_1282988..1283138_POSITIVE