Origin IGS: ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaattttatcgataatctaatatcaccgttattctttcacacgttttttataaagaaacttgaaatgaaggtataactcaaaatagtttactaatccatcgtcaaaggcttggtgcaacttaagatctagaaattccttaaaagtttaattgaataattacagatccagaacggacacaagctgtgtaattatattattaataaatcactctcattatcaggataaacaaagtatgcctagtgcacatacatttttcccttttattgaaatagtatgtcctaatctcaataa Mask Tandem Repeat Region ================================================ ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Find is-nt database================================================ Query_seq: SSA_0561:SSA_0562|SSA_0561:SSA_0562:RNA:NAD 2'-phosphotransferase, putative:hypothetical protein:->->:554316..554607 292 ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0561:SSA_0562|SSA_0561:SSA_0562:RNA:NAD 2'-phosphotransferase, putative:hypothetical protein:->->:554316..554607 292 ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0561:SSA_0562|SSA_0561:SSA_0562:RNA:NAD 2'-phosphotransferase, putative:hypothetical protein:->->:554316..554607 292 ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M E I R T Y Y F N K R E K C M C T R H T L F I L I M R V I Y ........................................................................................................................................................................................................ Protein_Len: 47 Strand: - Start: 3 End: 143 .. N L N P C V I E I F P F F T H A S P M S Q K D Q Y H S H N I L L I I V C S T D T R S R Y N N M ..................................................................................................................................................... ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc 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================================================ ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0561:SSA_0562|SSA_0561:SSA_0562:RNA:NAD 2'-phosphotransferase, putative:hypothetical protein:->->:554316..554607 292 ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: NC_009009_SSA_0561_SSA_0562|RNA:NAD 2'-phosphotransferase, putative:hypothetical protein|POSITIVE:POSITIVE|[554316,554607]|292 HSP 1 e-value: 1.0E-164 bit: 579.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc ttattgagattaggacatactatttcaataaaagggaaaaatgtatgtgcactaggcatactttgtttatcctgataatgagagtgatttattaataatataattacacagcttgtgtccgttctggatctgtaattattcaattaaacttttaaggaatttctagatcttaagttgcaccaagcctttgacgatggattagtaaactattttgagttataccttcatttcaagtttctttataaaaaacgtgtgaaagaataacggtgatattagattatcgataaaattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUGAGAUUAGGACAUACUAUUUCAAUAAAAGGGAAAAAUGUAUGUGCACUAGGCAUACUUUGUUUAUCCUGAUAAUGAGAGUGAUUUAUUAAUAAUAUAAUUACACAGCUUGUGUCCGUUCUGGAUCUGUAAUUAUUCAAUUAAACUUUUAAGGAAUUUCUAGAUCUUAAGUUGCACCAAGCCUUUGACGAUGGAUUAGUAAACUAUUUUGAGUUAUACCUUCAUUUCAAGUUUCUUUAUAAAAAACGUGUGAAAGAAUAACGGUGAUAUUAGAUUAUCGAUAAAAUUC ((((((((((.((......))))))))))))..((((.(((((..(((((.....)))))...))))).))))..(((((((.....))))))).........((((((.(((((.((.((....(((((((.....((((..((((....)))).))))...))))))).....)).))))))).(((((.((((((...(((((((......)))).))).)))))))))))................))))))........(((((((.....)))))))......... (-54.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUUUAUCGAUAAUCUAAUAUCACCGUUAUUCUUUCACACGUUUUUUAUAAAGAAACUUGAAAUGAAGGUAUAACUCAAAAUAGUUUACUAAUCCAUCGUCAAAGGCUUGGUGCAACUUAAGAUCUAGAAAUUCCUUAAAAGUUUAAUUGAAUAAUUACAGAUCCAGAACGGACACAAGCUGUGUAAUUAUAUUAUUAAUAAAUCACUCUCAUUAUCAGGAUAAACAAAGUAUGCCUAGUGCACAUACAUUUUUCCCUUUUAUUGAAAUAGUAUGUCCUAAUCUCAAUAA ....(((((..(((((.((((..(((.(((((.((((((((.((((((.....)))))).))...)))))).))))).............................((((((((.(.......(((((.(.((((..((((........))))..)))).))))))......).)).)))))))))..)))).)))))..)))))..............((((((.((...(((((.........)))))...((((.........))))..)).))))))........... (-45.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 132 108 39 12 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 272 134 102 42 14 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 257 138 105 84 55 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 250 135 108 150 118 NC_009009:SSA_0795|5end_hypothetical_protein_776620..776850_POSITIVE 249 210 168 173 133 NC_009009:SSA_1930|5end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1918547..1918777_NEGATIVE 247 209 161 53 1 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 247 200 173 221 194 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 245 200 153 201 158 NC_009009:SSA_2265|5end_Maltodextrin_phosphorylase,_putative_2264197..2264427_NEGATIVE 245 188 149 199 159 NC_009009:SSA_2253|5end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2249424..2249654_NEGATIVE 244 240 192 116 58 NC_009009:SSA_1081|5end_1-phosphofructokinase,_putative_1098278..1098508_POSITIVE 242 197 156 77 34 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 242 194 156 65 15 NC_009009:SSA_0756|5end_Alanyl-tRNA_synthetase,_putative_736736..736966_POSITIVE 242 88 41 52 6 NC_009009:SSA_0621|5end_SOS_responce_UmuC_protein,_putative_613737..613967_NEGATIVE 239 204 161 138 98 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 237 198 154 49 7 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 231 197 153 212 172 NC_009009:SSA_1060|5end_hypothetical_protein_1076765..1076995_POSITIVE 231 89 41 212 171 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 231 199 153 172 121 NC_009009:SSA_0408|5end_hypothetical_protein_404684..404914_NEGATIVE 230 142 110 93 60 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 230 141 110 75 36 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 230 182 50 1 NC_009009:SSA_1458|3end_hypothetical_protein_1464469..1464619_NEGATIVE 250 135 108 145 113 NC_009009:SSA_0794|3end_Zn-dependent_protease,_putative_776695..776845_POSITIVE 244 240 192 119 61 NC_009009:SSA_1080|3end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1098361..1098511_POSITIVE 242 197 156 90 47 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 242 88 41 47 1 NC_009009:SSA_0622|3end_Transcriptional_regulator_(XRE_family),_SOS-response_transcriptional_repressors_(RecA-mediated_autopeptidases),_putative_613742..613892_NEGATIVE 238 159 114 70 21 NC_009009:SSA_1063|3end_Peptidoglycan-binding_domain-containing_protein,_putative_1080260..1080410_POSITIVE 235 189 148 50 9 NC_009009:SSA_2175|3end_hypothetical_protein_2173146..2173296_NEGATIVE 231 197 153 121 81 NC_009009:SSA_1059|3end_hypothetical_protein_1076754..1076904_POSITIVE 231 89 41 87 46 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE 228 196 155 72 23 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 226 202 168 131 89 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 226 200 163 36 2 NC_009009:SSA_2117|3end_DNA_recombination_protein_RmuC,_putative_2118556..2118706_NEGATIVE 225 197 155 42 4 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 225 226 181 100 45 NC_009009:SSA_2296|3end_Transcriptional_regulator,_XRE_family,_putative_2298549..2298699_NEGATIVE 225 220 171 114 52 NC_009009:SSA_0371|3end_NADP-specific_glutamate_dehydrogenase,_putative_360413..360563_NEGATIVE 224 74 45 132 106 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 217 203 177 76 38 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 217 196 151 141 90 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 215 145 108 39 9 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE 215 199 160 144 107 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE