Origin IGS: aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataattttcaggggatatatcaaacaagagcttgaaatcgcttgcaaaacttggagtaaaaggctatactgaatatagtatttcattttgtaattttttacaaaaaaacaaaggagatattttt Mask Tandem Repeat Region ================================================ aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Find is-nt database================================================ Query_seq: SSA_1591:SSA_1592|SSA_1591:SSA_1592:Dipeptidase, putative:hypothetical protein:<-<-:1595542..1595665 124 aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1591:SSA_1592|SSA_1591:SSA_1592:Dipeptidase, putative:hypothetical protein:<-<-:1595542..1595665 124 aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1591:SSA_1592|SSA_1591:SSA_1592:Dipeptidase, putative:hypothetical protein:<-<-:1595542..1595665 124 aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 F I D G K N K Q L F N C F S I S Y E T Y G K V G L K A L S K L S K N S M ................ aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat 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: 82 Start: 55 End: 84 ......................................................CTTGCAAAACTTGGAGTAAAAGGCTATACT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -2.9 Tail_Score: -3.7278 Start: 47 End: 61 Full_Region: acttggagtaaaagg ctata ctgaa tatag tatttcattttgtaa ..............................................ctatactgaatatag............................................................... Find igs database================================================ Query_seq: SSA_1591:SSA_1592|SSA_1591:SSA_1592:Dipeptidase, putative:hypothetical protein:<-<-:1595542..1595665 124 aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_009009_SSA_1591_SSA_1592|Dipeptidase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1595542,1595665]|124 HSP 1 e-value: 5.0E-52 bit: 204.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 aaaaatatctcctttgnnnnnnngtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat aaaaatatctcctttgtttttttgtaaaaaattacaaaatgaaatactatattcagtatagccttttactccaagttttgcaagcgatttcaagctcttgtttgatatatcccctgaaaattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAUCUCCUUUGUUUUUUUGUAAAAAAUUACAAAAUGAAAUACUAUAUUCAGUAUAGCCUUUUACUCCAAGUUUUGCAAGCGAUUUCAAGCUCUUGUUUGAUAUAUCCCCUGAAAAUUAU ............(((((..((((....))))..))))).(((((..((((((...))))))..))))).....((((((.((.(.(((.((((((....))))))...))).).)))))))).. (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUUUUCAGGGGAUAUAUCAAACAAGAGCUUGAAAUCGCUUGCAAAACUUGGAGUAAAAGGCUAUACUGAAUAUAGUAUUUCAUUUUGUAAUUUUUUACAAAAAAACAAAGGAGAUAUUUUU ...((((((..(..((((.........((((........))))...........((((........)))).......))))..).((((((((....)))))))).......))))))...... (-17.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 854 100 51 191 142 NC_009009:SSA_1591|5end_Dipeptidase,_putative_1595451..1595681_NEGATIVE 297 105 61 219 172 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 291 120 72 210 159 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 287 104 61 149 98 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 286 99 55 57 17 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 283 100 55 172 119 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 281 120 78 220 162 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 280 100 62 141 105 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 277 96 52 193 148 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 271 96 55 195 161 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 264 89 55 212 178 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 261 109 63 92 28 NC_009009:SSA_1008|5end_Galactokinase,_putative_1009856..1010086_POSITIVE 259 97 59 135 85 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 258 100 53 62 7 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 256 104 61 59 9 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 253 116 74 70 24 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 251 98 58 59 24 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 246 100 56 165 126 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 241 100 53 133 78 NC_009009:SSA_0120|5end_30S_ribosomal_protein_S8,_putative_114618..114848_POSITIVE 240 108 62 149 98 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 104 61 148 97 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 286 99 55 47 7 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 280 100 62 106 70 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 278 100 55 52 8 NC_009009:SSA_1060|3end_hypothetical_protein_1077447..1077597_POSITIVE 274 115 74 137 95 NC_009009:SSA_1259|3end_Purine_nucleoside_phosphorylase,_putative_1284910..1285060_NEGATIVE 259 97 59 132 82 NC_009009:SSA_0824|3end_DNA_primase_(bacterial_type),_putative_803941..804091_POSITIVE 256 104 61 66 16 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 253 116 74 85 39 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 243 108 62 87 41 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 242 115 72 141 86 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 241 109 61 71 16 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 240 108 62 149 98 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 239 86 53 114 73 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 239 106 75 82 45 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 237 100 55 138 94 NC_009009:SSA_0023|3end_Aspartate_aminotransferase,_putative_29781..29931_POSITIVE 235 101 62 131 84 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 233 117 71 45 3 NC_009009:SSA_2379|3end_Signal_transduction_protein_with_a_C-terminal_ATPase/histidine_kinase_domain,_putative_2383899..2384049_NEGATIVE 233 95 55 145 107 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 232 120 71 72 23 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 230 86 52 139 104 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE