Origin IGS: tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggatgagtttggtaattgattgattccagaatctcaagaccagaaataagacggaaggaaggccttccgtcttattttcatttcctgtgcactaaatttaaaaatatgatataatcagatttacttatacatttcgaggagaaagaatca Mask Tandem Repeat Region ================================================ tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Find is-nt database================================================ Query_seq: SSA_1761:SSA_1762|SSA_1761:SSA_1762:Hemolysin (containing CBS domains), putative:Permease, putative:<-<-:1748868..1749017 150 tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1761:SSA_1762|SSA_1761:SSA_1762:Hemolysin (containing CBS domains), putative:Permease, putative:<-<-:1748868..1749017 150 tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1761:SSA_1762|SSA_1761:SSA_1762:Hemolysin (containing CBS domains), putative:Permease, putative:<-<-:1748868..1749017 150 tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 40 End: 135 ....................................... I M N K F K T C L F H F Y S P L G E K R R I E P R S I R S D I M ............... tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc 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================================================ tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -17.2 Tail_Score: -4.6038 Start: 77 End: 104 Full_Region: tctcaagaccagaaa taagacggaagg aagg ccttccgtctta ttttcatttcctgtg ............................................................................taagacggaaggaaggccttccgtctta.............................................. Find igs database================================================ Query_seq: SSA_1761:SSA_1762|SSA_1761:SSA_1762:Hemolysin (containing CBS domains), putative:Permease, putative:<-<-:1748868..1749017 150 tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_009009_SSA_1761_SSA_1762|Hemolysin (containing CBS domains), putative:Permease, putative|NEGATIVE:NEGATIVE|[1748868,1749017]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc tgattctttctcctcgaaatgtataagtaaatctgattatatcatatttttaaatttagtgcacaggaaatgaaaataagacggaaggccttccttccgtcttatttctggtcttgagattctggaatcaatcaattaccaaactcatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUCUUUCUCCUCGAAAUGUAUAAGUAAAUCUGAUUAUAUCAUAUUUUUAAAUUUAGUGCACAGGAAAUGAAAAUAAGACGGAAGGCCUUCCUUCCGUCUUAUUUCUGGUCUUGAGAUUCUGGAAUCAAUCAAUUACCAAACUCAUCC (((((((.((((.......(((((((((((((.((((...)))).))))....)))).))))).((((...((((.((((((((((((....))))))))))))))))...))))))))....))))))).................... (-37.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUGAGUUUGGUAAUUGAUUGAUUCCAGAAUCUCAAGACCAGAAAUAAGACGGAAGGAAGGCCUUCCGUCUUAUUUUCAUUUCCUGUGCACUAAAUUUAAAAAUAUGAUAUAAUCAGAUUUACUUAUACAUUUCGAGGAGAAAGAAUCA ((.(((((((((.((((....)))))))))..))))...)).((((((((((((((((....))))))))))))))))..((((((.((............((((.((((...)))).))))............))))))))........ (-37.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 130 81 221 172 NC_009009:SSA_1761|5end_Hemolysin_(containing_CBS_domains),_putative_1748777..1749007_NEGATIVE 308 130 81 211 154 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 294 139 93 73 12 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 294 96 55 160 113 NC_009009:SSA_0646|5end_hypothetical_protein_630778..631008_POSITIVE 282 129 82 181 135 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 280 117 80 225 188 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 277 98 59 219 180 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 274 124 85 52 15 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 273 130 84 190 152 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 271 129 85 226 182 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 268 110 79 229 194 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 267 129 82 197 126 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 266 129 86 211 159 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 265 130 82 178 130 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 265 118 72 124 67 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 264 124 85 63 30 NC_009009:SSA_1110|5end_hypothetical_protein_1135551..1135781_POSITIVE 263 125 82 76 19 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 260 122 82 187 140 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 260 128 82 206 163 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 259 127 86 183 141 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 120 75 110 63 NC_009009:SSA_1233|3end_Membrane_protein,_YqiH_family,_putative_1257626..1257776_POSITIVE 307 120 79 149 106 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 294 96 55 67 20 NC_009009:SSA_0644|3end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630765..630915_POSITIVE 274 124 85 50 13 NC_009009:SSA_0544|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_540930..541080_POSITIVE 272 119 71 60 12 NC_009009:SSA_0778|3end_Glycogen_synthase,_putative_762076..762226_POSITIVE 268 110 79 110 75 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 268 115 82 116 82 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 267 115 74 98 46 NC_009009:SSA_1234|3end_5'-nucleotidase,_putative_1257636..1257786_NEGATIVE 265 118 72 108 51 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 263 99 66 67 34 NC_009009:SSA_2024|3end_hypothetical_protein_2029105..2029255_NEGATIVE 263 125 82 68 11 NC_009009:SSA_1873|3end_S-adenosyl-methyltransferase_mraW,_putative_1869194..1869344_NEGATIVE 261 109 82 151 120 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 257 112 77 135 92 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 255 140 92 106 41 NC_009009:SSA_2299|3end_hypothetical_protein_2300655..2300805_NEGATIVE 254 115 80 108 72 NC_009009:SSA_1804|3end_NADPH-flavin_oxidoreductase,_putative_1787952..1788102_NEGATIVE 251 127 83 123 64 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 250 130 81 146 93 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 250 125 89 133 105 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 249 130 86 119 75 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 245 118 79 68 30 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE