Origin IGS: aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataatcctcatttcttttgataagactagtatgccataaaaagcagaaaaatgcttgatttggaaatgaaaaaccagagaatatgaaattcatcctctggttgattggttgatagtgttgtt Mask Tandem Repeat Region ================================================ aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Find is-nt database================================================ Query_seq: SSA_1204:SSA_1205|SSA_1204:SSA_1205:Phosphoglucomutase:Bta, putative:->->:1229646..1229769 124 aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1204:SSA_1205|SSA_1204:SSA_1205:Phosphoglucomutase:Bta, putative:->->:1229646..1229769 124 aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1204:SSA_1205|SSA_1204:SSA_1205:Phosphoglucomutase:Bta, putative:->->:1229646..1229769 124 aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 18 End: 122 ................. M N Q R M N F I F S G F S F P N Q A F F C F L W H T S L I K R N E D Y .. Protein_Len: 30 Strand: + Start: 34 End: 123 ................................. M S Y S L V F H F Q I K H F S A F Y G I L V L S K E M R I I . aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt 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================================================ aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.3 Tail_Score: -3.46824 Start: 23 End: 49 Full_Region: tttggaaatgaaaaa ccagagaat atgaaattc atcctctgg ttgattggttgatag ......................ccagagaatatgaaattcatcctctgg........................................................................... Find igs database================================================ Query_seq: SSA_1204:SSA_1205|SSA_1204:SSA_1205:Phosphoglucomutase:Bta, putative:->->:1229646..1229769 124 aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_009009_SSA_1204_SSA_1205|Phosphoglucomutase:Bta, putative|POSITIVE:POSITIVE|[1229646,1229769]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt aacaacactatcaaccaatcaaccagaggatgaatttcatattctctggtttttcatttccaaatcaagcatttttctgctttttatggcatactagtcttatcaaaagaaatgaggattattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAACACUAUCAACCAAUCAACCAGAGGAUGAAUUUCAUAUUCUCUGGUUUUUCAUUUCCAAAUCAAGCAUUUUUCUGCUUUUUAUGGCAUACUAGUCUUAUCAAAAGAAAUGAGGAUUAUUU ..............((....((((((((((((.......))))))))))))..(((((((......(((((......))))).....(((......))).........)))))))))....... (-26.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAUCCUCAUUUCUUUUGAUAAGACUAGUAUGCCAUAAAAAGCAGAAAAAUGCUUGAUUUGGAAAUGAAAAACCAGAGAAUAUGAAAUUCAUCCUCUGGUUGAUUGGUUGAUAGUGUUGUU ....................(((((.((((....((((....(((((......)))))...............((((((((...(((.....))).))))))))...))))...)))).))))) (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 90 41 223 175 NC_009009:SSA_0932|5end_hypothetical_protein_941453..941683_POSITIVE 285 70 22 108 61 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 264 110 64 167 112 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 261 80 37 124 88 NC_009009:SSA_0656|5end_Cell_division_protein_FtsZ,_putative_640159..640389_POSITIVE 258 90 46 48 9 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 257 99 59 208 161 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 250 90 45 230 193 NC_009009:SSA_1187|5end_Transcriptional_antiterminator,_BglG_family,_putative_1216037..1216267_NEGATIVE 247 89 43 110 52 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 246 108 67 131 85 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 245 57 12 79 44 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 243 98 52 183 132 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 243 101 63 53 4 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 243 89 45 223 171 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 243 90 45 224 186 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 243 87 41 140 98 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 241 118 72 207 155 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 241 50 6 81 32 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 241 96 53 134 101 NC_009009:SSA_1223|5end_30S_ribosomal_protein_S1,_putative_1246872..1247102_NEGATIVE 241 90 43 120 72 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 239 101 65 157 107 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 90 43 133 87 NC_009009:SSA_1111|3end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1137940..1138090_POSITIVE 277 51 21 70 40 NC_009009:SSA_1204|3end_Phosphoglucomutase_1229585..1229735_POSITIVE 261 80 37 107 71 NC_009009:SSA_0655|3end_Cell_division_protein_FtsA,_putative_640222..640372_POSITIVE 258 90 46 61 22 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 246 108 67 121 75 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 243 90 45 72 34 NC_009009:SSA_1144|3end_Beta-N-acetylhexosaminidase,_putative_1173649..1173799_NEGATIVE 241 118 72 53 1 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 241 90 43 114 66 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 238 90 46 59 24 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 237 89 41 96 51 NC_009009:SSA_2311|3end_Nitric_oxide_reductase_NorD_/_Von_Willebrand_factor_type_A_(vWA)_domain_protein,_putative_2313431..2313581_NEGATIVE 235 90 41 134 84 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 234 90 47 44 1 NC_009009:SSA_1924|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1912691..1912841_NEGATIVE 231 80 35 117 84 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 227 90 43 143 108 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 225 85 43 128 77 NC_009009:SSA_1655|3end_hypothetical_protein_1651391..1651541_NEGATIVE 222 90 43 54 1 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 221 99 51 81 36 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE 220 106 68 94 58 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 220 89 42 128 81 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 218 80 35 141 89 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE