Origin IGS: agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagacaagccctcgcctatctggaaaagtcttagtactggcttttcctagccttaaaattgtgatataataagacctaatactctttgggaatttaactgcgactttccttgagtaaacccttgtttcaggagtattct Mask Tandem Repeat Region ================================================ agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Find is-nt database================================================ Query_seq: SSA_1959:SSA_1960|SSA_1959:SSA_1960:Undecaprenyl-diphosphatase, putative:hypothetical protein:<-<-:1956522..1956660 139 agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1959:SSA_1960|SSA_1959:SSA_1960:Undecaprenyl-diphosphatase, putative:hypothetical protein:<-<-:1956522..1956660 139 agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1959:SSA_1960|SSA_1959:SSA_1960:Undecaprenyl-diphosphatase, putative:hypothetical protein:<-<-:1956522..1956660 139 agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Predict ORF larger than 30AA ================================================ agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta 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: 83 Start: 70 End: 99 .....................................................................CTTTTCCTAGCCTTAAAATTGTGATATAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1959:SSA_1960|SSA_1959:SSA_1960:Undecaprenyl-diphosphatase, putative:hypothetical protein:<-<-:1956522..1956660 139 agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: NC_009009_SSA_1959_SSA_1960|Undecaprenyl-diphosphatase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1956522,1956660]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta agaatactcctgaaacaagggtttactcaaggaaagtcgcagttaaattcccaaagagtattaggtcttattatatcacaattttaaggctaggaaaagccagtactaagacttttccagataggcgagggcttgtcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUACUCCUGAAACAAGGGUUUACUCAAGGAAAGUCGCAGUUAAAUUCCCAAAGAGUAUUAGGUCUUAUUAUAUCACAAUUUUAAGGCUAGGAAAAGCCAGUACUAAGACUUUUCCAGAUAGGCGAGGGCUUGUCUA ..(((((((.........(((....)))..((((.............))))....))))))).(((((((..((......))..))))))).(((((((.(........).))))))).(((((((....))))))).. (-31.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACAAGCCCUCGCCUAUCUGGAAAAGUCUUAGUACUGGCUUUUCCUAGCCUUAAAAUUGUGAUAUAAUAAGACCUAAUACUCUUUGGGAAUUUAACUGCGACUUUCCUUGAGUAAACCCUUGUUUCAGGAGUAUUCU .(((...((....))...)))(((((.(((.((((...((((......))))......................(((((......)))))......)))).))))))))..(((((...(((......)))..))))). (-27.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 903 130 81 221 172 NC_009009:SSA_1959|5end_Undecaprenyl-diphosphatase,_putative_1956431..1956661_NEGATIVE 294 53 11 140 105 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 289 130 98 32 3 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 289 44 1 156 109 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 278 130 82 177 122 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 272 130 88 196 148 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 268 130 92 134 93 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 266 39 1 68 23 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 264 45 9 42 9 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 264 69 27 42 7 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 261 110 77 61 36 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 259 70 21 65 26 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 259 101 61 109 72 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 255 130 87 74 25 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 253 130 81 68 26 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 252 110 65 133 85 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 251 129 86 65 13 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 250 79 31 164 117 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 249 127 88 210 172 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 248 120 71 134 93 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 130 87 115 77 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 294 53 11 41 6 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE 289 44 1 151 104 NC_009009:SSA_1129|3end_Periplasmic_iron_transport_lipoprotein,_putative_1155877..1156027_POSITIVE 268 130 92 141 100 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 266 127 84 49 1 NC_009009:SSA_2171|3end_hypothetical_protein_2170224..2170374_NEGATIVE 266 39 1 62 17 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 266 129 87 45 3 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 264 69 27 45 10 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 259 101 61 105 68 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 255 123 85 63 27 NC_009009:SSA_0385|3end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_378526..378676_NEGATIVE 251 39 5 123 92 NC_009009:SSA_1943|3end_Aspartate_kinase,_putative_1930159..1930309_POSITIVE 250 79 31 99 52 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 249 130 87 70 15 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 248 120 71 102 61 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 247 126 87 44 8 NC_009009:SSA_0715|3end_DNA_uptake_protein,_putative_701486..701636_POSITIVE 244 73 35 56 14 NC_009009:SSA_1561|3end_Ribonuclease_III,_putative_1565185..1565335_NEGATIVE 242 42 1 48 5 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 241 130 84 73 39 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 239 121 88 47 7 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 239 42 8 134 101 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE