Origin IGS: gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaatatcctccttatagatatagcagaaatttcaagttagctagagggggggcttttgttttcagctaggattgccgacttgacgttttcctgctctgccccctcgctcctcttcatttc Mask Tandem Repeat Region ================================================ gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Find is-nt database================================================ Query_seq: SSA_0825:SSA_0826|SSA_0825:SSA_0826:DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32), putative:hypothetical protein:->->:805117..805237 121 gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0825:SSA_0826|SSA_0825:SSA_0826:DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32), putative:hypothetical protein:->->:805117..805237 121 gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0825:SSA_0826|SSA_0825:SSA_0826:DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32), putative:hypothetical protein:->->:805117..805237 121 gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Predict ORF larger than 30AA ================================================ gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0825:SSA_0826|SSA_0825:SSA_0826:DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32), putative:hypothetical protein:->->:805117..805237 121 gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: NC_009009_SSA_0825_SSA_0826|DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32), putative:hypothetical protein|POSITIVE:POSITIVE|[805117,805237]|121 HSP 1 e-value: 3.0E-50 bit: 198.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagnnnnnnntctagctaacttgaaatttctgctatatctataaggaggatattgc gaaatgaagaggagcgagggggcagagcaggaaaacgtcaagtcggcaatcctagctgaaaacaaaagccccccctctagctaacttgaaatttctgctatatctataaggaggatattgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUGAAGAGGAGCGAGGGGGCAGAGCAGGAAAACGUCAAGUCGGCAAUCCUAGCUGAAAACAAAAGCCCCCCCUCUAGCUAACUUGAAAUUUCUGCUAUAUCUAUAAGGAGGAUAUUGC (((((...(((.((((((((((..(.((..((.....))...(((((.......)))))........))))))))))..)))..)))...))))).((.((((((.......)))))).)) (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUAUCCUCCUUAUAGAUAUAGCAGAAAUUUCAAGUUAGCUAGAGGGGGGGCUUUUGUUUUCAGCUAGGAUUGCCGACUUGACGUUUUCCUGCUCUGCCCCCUCGCUCCUCUUCAUUUC ((.(((((.........))))).)).(((((...(((..(((....((((((((..........(((.((((..((.........))..)))))))..)))))))))))...))).))))) (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 38 1 66 19 NC_009009:SSA_1578|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1581803..1582033_POSITIVE 343 58 11 160 117 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 341 49 3 73 20 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 334 60 11 192 144 NC_009009:SSA_2059|5end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2061222..2061452_NEGATIVE 330 56 14 200 147 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 327 59 15 193 139 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 327 58 11 190 128 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 327 57 12 51 3 NC_009009:SSA_0635|5end_Indole-3-glycerol_phosphate_synthase,_putative_624388..624618_POSITIVE 326 45 4 190 141 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 322 60 13 76 23 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 317 58 11 205 162 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 315 60 12 196 152 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 313 49 4 202 135 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 312 117 71 150 101 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 311 57 14 224 168 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 310 79 36 48 4 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 310 53 11 93 34 NC_009009:SSA_0898|5end_hypothetical_protein_889863..890093_NEGATIVE 309 58 11 180 131 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 306 54 11 65 14 NC_009009:SSA_0731|5end_Integral_membrane_protein,_putative_715065..715295_POSITIVE 305 58 11 215 165 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 43 4 83 39 NC_009009:SSA_1325|3end_Ketoacyl_reductase_hetN,_putative_1341573..1341723_NEGATIVE 341 49 3 101 48 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 328 53 11 81 38 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 327 57 12 54 6 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 326 86 44 67 24 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 325 48 8 62 14 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 314 59 15 70 22 NC_009009:SSA_1019|3end_Collagen-binding_surface_protein,_putative_1035377..1035527_POSITIVE 313 57 14 80 28 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 312 117 71 147 98 NC_009009:SSA_1880|3end_Glycyl-tRNA_synthetase_alpha_chain,_putative_1874265..1874415_NEGATIVE 309 56 16 77 50 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 306 54 11 87 36 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 305 58 21 81 47 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 304 58 15 147 111 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 297 63 21 91 49 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 295 58 20 57 16 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 292 58 11 49 3 NC_009009:SSA_2190|3end_33_kDa_chaperonin,_putative_2192118..2192268_POSITIVE 290 48 5 52 12 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 288 47 8 132 93 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 288 59 11 73 15 NC_009009:SSA_0608|3end_Macrolide-efflux_protein,_putative_596901..597051_NEGATIVE 288 57 15 111 61 NC_009009:SSA_0414|3end_hypothetical_protein_410569..410719_POSITIVE