Origin IGS: gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttactttgctattctagctcaagaagctgctcaatccaaatttgagcagtttcttttcttaacagcaatcttctgtgtacgttttcataaataaaaatttgatttttttaagacattttcagataaaaaacgtataatgagagataagaaatcattgaaattttaaaaggagattctttcgagc Mask Tandem Repeat Region ================================================ gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Find is-nt database================================================ Query_seq: SSA_1052:SSA_1053|SSA_1052:SSA_1053:hypothetical protein:Pyruvate phosphate dikinase, putative:<-<-:1067353..1067536 184 gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1052:SSA_1053|SSA_1052:SSA_1053:hypothetical protein:Pyruvate phosphate dikinase, putative:<-<-:1067353..1067536 184 gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1052:SSA_1053|SSA_1052:SSA_1053:hypothetical protein:Pyruvate phosphate dikinase, putative:<-<-:1067353..1067536 184 gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Predict ORF larger than 30AA ================================================ gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa 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================================================ gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -4.3 Tail_Score: -3.65224 Start: 135 End: 159 Full_Region: CTGTTAAGAAAAGAA ACTGCTCAA ATTTGGA TTGAGCAGC TTCTTGAGCTAGAAT ......................................................................................................................................ACTGCTCAAATTTGGATTGAGCAGC......................... TransTerm Strand: + Conf: 66 HP_score: -7.8 Tail_Score: -2.78813 Start: 136 End: 158 Full_Region: TGTTAAGAAAAGAAA CTGCTCAA ATTTGGA TTGAGCAG CTTCTTGAGCTAGAA .......................................................................................................................................CTGCTCAAATTTGGATTGAGCAG.......................... Find igs database================================================ Query_seq: SSA_1052:SSA_1053|SSA_1052:SSA_1053:hypothetical protein:Pyruvate phosphate dikinase, putative:<-<-:1067353..1067536 184 gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_009009_SSA_1052_SSA_1053|hypothetical protein:Pyruvate phosphate dikinase, putative|NEGATIVE:NEGATIVE|[1067353,1067536]|184 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttnnnnnnntcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa gctcgaaagaatctccttttaaaatttcaatgatttcttatctctcattatacgttttttatctgaaaatgtcttaaaaaaatcaaatttttatttatgaaaacgtacacagaagattgctgttaagaaaagaaactgctcaaatttggattgagcagcttcttgagctagaatagcaaagtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCGAAAGAAUCUCCUUUUAAAAUUUCAAUGAUUUCUUAUCUCUCAUUAUACGUUUUUUAUCUGAAAAUGUCUUAAAAAAAUCAAAUUUUUAUUUAUGAAAACGUACACAGAAGAUUGCUGUUAAGAAAAGAAACUGCUCAAAUUUGGAUUGAGCAGCUUCUUGAGCUAGAAUAGCAAAGUAA ..((....)).....(((((........(((((...........))))).(((((((((((..(((((((................)))))))..)).)))))))))...))))).((((((((.((..(((((.((((((((.......)))))))).)))))...))..))))))))..... (-39.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUUUGCUAUUCUAGCUCAAGAAGCUGCUCAAUCCAAAUUUGAGCAGUUUCUUUUCUUAACAGCAAUCUUCUGUGUACGUUUUCAUAAAUAAAAAUUUGAUUUUUUUAAGACAUUUUCAGAUAAAAAACGUAUAAUGAGAGAUAAGAAAUCAUUGAAAUUUUAAAAGGAGAUUCUUUCGAGC ................((((.(((((((((((((.......))))))))))))).........((.((((((((.((((((((((......((((((.......)))))).((.....))......))))))))))......(((.....)))..............))))))))))...)))) (-40.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 759 140 91 231 182 NC_009009:SSA_1052|5end_hypothetical_protein_1067262..1067492_NEGATIVE 287 164 128 45 12 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 277 177 137 59 20 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 276 179 135 215 163 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 271 179 136 57 1 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 271 171 136 141 109 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 268 170 125 81 29 NC_009009:SSA_0253|5end_CAAX_amino_terminal_protease_family_protein,_putative_246289..246519_POSITIVE 260 177 136 197 155 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 256 166 140 71 40 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 252 178 135 68 13 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 252 180 131 171 119 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 244 177 139 41 2 NC_009009:SSA_2181|5end_Conserved_uncharacterized_protein_2180083..2180313_NEGATIVE 244 172 136 43 13 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 244 179 136 228 184 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 242 168 121 155 108 NC_009009:SSA_0125|5end_50S_ribosomal_protein_L30,_putative_116930..117160_POSITIVE 241 43 3 174 130 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 241 50 3 107 52 NC_009009:SSA_0537|5end_Propanediol_utilization:dioldehydratase_reactivation,_putative_531957..532187_POSITIVE 241 177 136 155 100 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 241 173 139 202 171 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 240 178 138 156 122 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 169 136 34 9 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 293 160 114 133 80 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 271 179 136 60 4 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 253 168 127 71 29 NC_009009:SSA_2345|3end_hypothetical_protein_2347502..2347652_POSITIVE 252 180 131 120 68 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 251 169 131 137 97 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 250 168 137 139 110 NC_009009:SSA_1383|3end_Aspartate_aminotransferase,_putative_1400537..1400687_NEGATIVE 246 173 136 43 10 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 244 178 131 116 70 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 243 166 144 25 1 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 242 169 127 70 27 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 242 168 121 141 94 NC_009009:SSA_0124|3end_30S_ribosomal_protein_S5,_putative_116996..117146_POSITIVE 241 43 3 84 40 NC_009009:SSA_1635|3end_hypothetical_protein_1637152..1637302_NEGATIVE 241 172 138 147 113 NC_009009:SSA_0753|3end_Foldase_protein_prsA_precursor,_putative_736055..736205_POSITIVE 237 47 12 119 84 NC_009009:SSA_1004|3end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1006094..1006244_POSITIVE 236 65 25 106 71 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 235 175 137 59 21 NC_009009:SSA_0368|3end_hypothetical_protein_359722..359872_POSITIVE 234 180 136 123 81 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 232 162 136 144 124 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 231 173 131 140 98 NC_009009:SSA_0108|3end_50S_ribosomal_protein_L4,_putative_109519..109669_POSITIVE