Origin IGS: tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatggaaataggaacagttatgtgagaattaatgaagaagacaattagttttttatcaaggtaacagtactttattcttaaaaatcctcatatgataagataactagtcttcatagtttactcttacaaaaaacgactgatacaagatttgtctcagtcgctttttaata Mask Tandem Repeat Region ================================================ tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Find is-nt database================================================ Query_seq: SSA_1630:SSA_1631|SSA_1630:SSA_1631:hypothetical protein:Sortase-like protein, putative:-><-:1631569..1631740 172 tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1630:SSA_1631|SSA_1630:SSA_1631:hypothetical protein:Sortase-like protein, putative:-><-:1631569..1631740 172 tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1630:SSA_1631|SSA_1630:SSA_1631:hypothetical protein:Sortase-like protein, putative:-><-:1631569..1631740 172 tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Predict ORF larger than 30AA ================================================ tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa 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================================================ tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1630:SSA_1631|SSA_1630:SSA_1631:hypothetical protein:Sortase-like protein, putative:-><-:1631569..1631740 172 tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_009009_SSA_1630_SSA_1631|hypothetical protein:Sortase-like protein, putative|POSITIVE:NEGATIVE|[1631569,1631740]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa tattaaaaagcgactgagacaaatcttgtatcagtcgttttttgtaagagtaaactatgaagactagttatcttatcatatgaggatttttaagaataaagtactgttaccttgataaaaaactaattgtcttcttcattaattctcacataactgttcctatttccataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAAAAAGCGACUGAGACAAAUCUUGUAUCAGUCGUUUUUUGUAAGAGUAAACUAUGAAGACUAGUUAUCUUAUCAUAUGAGGAUUUUUAAGAAUAAAGUACUGUUACCUUGAUAAAAAACUAAUUGUCUUCUUCAUUAAUUCUCACAUAACUGUUCCUAUUUCCAUAAA ....(((((((((((((.(((.....))).)))))))))))))((.(((((.......(((((((((((...((((((.....(((((((.......))))).)).......))))))..)))))...)))))).......))))).))....................... (-36.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUGGAAAUAGGAACAGUUAUGUGAGAAUUAAUGAAGAAGACAAUUAGUUUUUUAUCAAGGUAACAGUACUUUAUUCUUAAAAAUCCUCAUAUGAUAAGAUAACUAGUCUUCAUAGUUUACUCUUACAAAAAACGACUGAUACAAGAUUUGUCUCAGUCGCUUUUUAAUA (((((....)))))........(((((((...(((...((((((...((((((((((((((((........................)))....)))))))).)))))))))))...)))...)))))))((((((((((((.(((.....))).))))))).))))).... (-37.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 50 7 174 125 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 252 46 5 224 182 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 252 67 31 45 1 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 235 40 7 230 195 NC_009009:SSA_1646|5end_hypothetical_protein_1646771..1647001_NEGATIVE 229 80 32 231 178 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 223 51 21 188 150 NC_009009:SSA_1827|5end_Alpha-glycerophosphate_oxidase,_putative_1816112..1816342_POSITIVE 222 60 12 154 110 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 219 78 31 155 91 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 218 50 9 229 192 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 217 60 11 123 71 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 212 60 11 123 71 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 212 79 31 91 48 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 210 45 10 41 5 NC_009009:SSA_2255|5end_Transcriptional_regulator,_XRE_family,_putative_2250144..2250374_POSITIVE 210 45 7 147 106 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 210 80 31 92 40 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 209 137 94 211 166 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 209 148 111 45 11 NC_009009:SSA_1829|5end_RNA_methyltransferase,_putative_1820329..1820559_NEGATIVE 209 48 13 209 167 NC_009009:SSA_1500|5end_Translation_initiation_factor_IF-3,_putative_1504921..1505151_NEGATIVE 209 138 102 176 135 NC_009009:SSA_0032|5end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_37938..38168_POSITIVE 208 49 9 149 112 NC_009009:SSA_1089|5end_hypothetical_protein_1107427..1107657_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 43 1 86 39 NC_009009:SSA_1630|3end_hypothetical_protein_1631508..1631658_POSITIVE 234 45 1 86 44 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 225 50 7 51 9 NC_009009:SSA_0266|3end_ORFB,_transposon_ISSsa1_260822..260972_POSITIVE 223 51 21 120 82 NC_009009:SSA_1826|3end_Glycerol_kinase,_putative_1816124..1816274_POSITIVE 219 42 7 92 58 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 218 50 9 46 9 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 217 40 1 77 29 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 212 79 31 104 61 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 210 45 7 94 53 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 210 80 31 80 28 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 209 50 10 145 110 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 209 138 102 116 75 NC_009009:SSA_0031|3end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_37958..38108_POSITIVE 206 167 123 135 91 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 204 42 5 92 60 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 202 41 6 88 55 NC_009009:SSA_0998|3end_hypothetical_protein_998758..998908_POSITIVE 197 46 6 60 21 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 197 49 9 85 48 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 196 67 39 38 11 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 196 110 61 91 46 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 196 67 24 48 5 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE