Origin IGS: atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catttttatcagaatcaaaactcagttggctttggctgactgagttgttttaacatcaaaaatccttgcctggtttgaagaagcaaggtagaaaataggtctat Mask Tandem Repeat Region ================================================ atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Find is-nt database================================================ Query_seq: SSA_1618:SSA_1619|SSA_1618:SSA_1619:hypothetical protein:Ribosome recycling factor, putative:<-<-:1621665..1621768 104 atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1618:SSA_1619|SSA_1618:SSA_1619:hypothetical protein:Ribosome recycling factor, putative:<-<-:1621665..1621768 104 atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1618:SSA_1619|SSA_1618:SSA_1619:hypothetical protein:Ribosome recycling factor, putative:<-<-:1621665..1621768 104 atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Predict ORF larger than 30AA ================================================ atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg 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================================================ atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1618:SSA_1619|SSA_1618:SSA_1619:hypothetical protein:Ribosome recycling factor, putative:<-<-:1621665..1621768 104 atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1618_SSA_1619|hypothetical protein:Ribosome recycling factor, putative|NEGATIVE:NEGATIVE|[1621665,1621768]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg atagacctattttctaccttgcttcttcaaaccaggcaaggatttttgatgttaaaacaactcagtcagccaaagccaactgagttttgattctgataaaaatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGACCUAUUUUCUACCUUGCUUCUUCAAACCAGGCAAGGAUUUUUGAUGUUAAAACAACUCAGUCAGCCAAAGCCAACUGAGUUUUGAUUCUGAUAAAAAUG .((((...........((((((((.........)))))))).........((((((...(((((((..((....))..)))))))))))))))))......... (-22.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUUUAUCAGAAUCAAAACUCAGUUGGCUUUGGCUGACUGAGUUGUUUUAACAUCAAAAAUCCUUGCCUGGUUUGAAGAAGCAAGGUAGAAAAUAGGUCUAU ..((((((((........((((((((..((....))..))))))))(((((....(((((...((......))))))).)))))..)))))))).......... (-27.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 886 80 31 171 122 NC_009009:SSA_1618|5end_hypothetical_protein_1621574..1621804_NEGATIVE 306 49 7 81 40 NC_009009:SSA_0827|5end_Conserved_uncharacterized_cytosolic_protein,_putative_806033..806263_POSITIVE 297 99 59 156 115 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 295 95 54 150 105 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 279 43 5 136 101 NC_009009:SSA_1888|5end_hypothetical_protein_1886025..1886255_NEGATIVE 272 70 22 217 161 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 271 100 63 73 26 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 271 76 32 175 125 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 267 46 3 142 93 NC_009009:SSA_1358|5end_hypothetical_protein_1374036..1374266_NEGATIVE 265 60 26 36 1 NC_009009:SSA_0795|5end_hypothetical_protein_776620..776850_POSITIVE 263 85 46 155 117 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 259 97 64 231 186 NC_009009:SSA_1528|5end_Phosphoglycerate_mutase,_putative_1535135..1535365_POSITIVE 259 96 64 47 16 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 254 79 33 198 144 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 253 99 60 75 32 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 252 79 34 150 118 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 251 38 7 143 110 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 248 82 50 164 134 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 245 48 6 136 78 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 244 92 55 52 10 NC_009009:SSA_2247|5end_hypothetical_protein_2242645..2242875_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 99 59 101 60 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 295 95 54 75 30 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 285 95 51 79 36 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 259 76 32 41 3 NC_009009:SSA_0794|3end_Zn-dependent_protease,_putative_776695..776845_POSITIVE 259 96 64 50 19 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 252 79 34 143 111 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 252 95 61 45 6 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 251 70 21 42 7 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE 247 37 7 132 96 NC_009009:SSA_1583|3end_6-O-methylguanine-DNA_methyltransferase,_putative_1585523..1585673_NEGATIVE 245 48 6 135 77 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 237 53 17 143 107 NC_009009:SSA_2067|3end_hypothetical_protein_2070876..2071026_POSITIVE 237 42 2 122 84 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 237 78 32 74 26 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 237 98 59 47 7 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 223 75 32 104 57 NC_009009:SSA_1709|3end_hypothetical_protein_1698313..1698463_NEGATIVE 223 77 33 117 69 NC_009009:SSA_1350|3end_hypothetical_protein_1366945..1367095_NEGATIVE 223 41 2 129 84 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 221 47 10 148 98 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 220 69 21 70 5 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 219 97 66 45 16 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE