Origin IGS: accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct .........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 agggacctccaagtcatgagtttttacactgcttattataacaaatttctgtcaaaagtaaataattttctgataattctgaaatgtttttctaaattttaaaaaagagatttatactgttgcatattctgataaaaaatttttataaccagctttaaaaaaatctattggacggcttcgcagaggagtggtaagatatactatatcaaaataagggggaatcacggt Mask Tandem Repeat Region ================================================ accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Find is-nt database================================================ Query_seq: SSA_2164:SSA_2165|SSA_2164:SSA_2165:Glutamine amidotransferase, putative:ABC-type oligopeptide transporter, periplasmic component, putative:<-->:2161646..2161873 228 accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2164:SSA_2165|SSA_2164:SSA_2165:Glutamine amidotransferase, putative:ABC-type oligopeptide transporter, periplasmic component, putative:<-->:2161646..2161873 228 accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2164:SSA_2165|SSA_2164:SSA_2165:Glutamine amidotransferase, putative:ABC-type oligopeptide transporter, periplasmic component, putative:<-->:2161646..2161873 228 accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 4 End: 114 ... M I P P Y F D I V Y L T T P L R S R P I D F F K A G Y K N F L S E Y A T V .................................................................................................................. Protein_Len: 30 Strand: - Start: 1 End: 90 G H N G R I K I Y Y I K G S R Q S A T W Y I K K F S T I F M .......................................................................................................................................... accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct 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================================================ accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2164:SSA_2165|SSA_2164:SSA_2165:Glutamine amidotransferase, putative:ABC-type oligopeptide transporter, periplasmic component, putative:<-->:2161646..2161873 228 accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: NC_009009_SSA_2164_SSA_2165|Glutamine amidotransferase, putative:ABC-type oligopeptide transporter, periplasmic component, putative|NEGATIVE:POSITIVE|[2161646,2161873]|228 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagannnnnnnaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct accgtgattcccccttattttgatatagtatatcttaccactcctctgcgaagccgtccaatagatttttttaaagctggttataaaaattttttatcagaatatgcaacagtataaatctcttttttaaaatttagaaaaacatttcagaattatcagaaaattatttacttttgacagaaatttgttataataagcagtgtaaaaactcatgacttggaggtccct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGUGAUUCCCCCUUAUUUUGAUAUAGUAUAUCUUACCACUCCUCUGCGAAGCCGUCCAAUAGAUUUUUUUAAAGCUGGUUAUAAAAAUUUUUUAUCAGAAUAUGCAACAGUAUAAAUCUCUUUUUUAAAAUUUAGAAAAACAUUUCAGAAUUAUCAGAAAAUUAUUUACUUUUGACAGAAAUUUGUUAUAAUAAGCAGUGUAAAAACUCAUGACUUGGAGGUCCCU .....................(((((...)))))......((((...(((....)))......((.(((((((..(((.(((((((....(((((.(((((((((((....)))))......((((((..(((((.((((....)))).)))))...))))))........)))))).)))))....))))))).)))..)).))))).)).......))))...... (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGACCUCCAAGUCAUGAGUUUUUACACUGCUUAUUAUAACAAAUUUCUGUCAAAAGUAAAUAAUUUUCUGAUAAUUCUGAAAUGUUUUUCUAAAUUUUAAAAAAGAGAUUUAUACUGUUGCAUAUUCUGAUAAAAAAUUUUUAUAACCAGCUUUAAAAAAAUCUAUUGGACGGCUUCGCAGAGGAGUGGUAAGAUAUACUAUAUCAAAAUAAGGGGGAAUCACGGU .((..(((((..((..(((.((((((....(((..((((((.((((((.((((((((((.....))))).)))))..((.(((((((.....((((((((......)))))))).......)))).))).))....))))))))))))..)))..))))))....((((..((.(((((.....))))).))..)))).......)))..))..)))))..))..... (-38.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 931 60 11 151 102 NC_009009:SSA_2164|5end_Glutamine_amidotransferase,_putative_2161555..2161785_NEGATIVE 346 47 1 96 48 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 309 80 33 52 9 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 301 59 11 152 98 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 294 80 34 155 97 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 280 59 11 53 3 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 274 80 44 209 173 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 274 65 38 212 188 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 269 79 33 230 169 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 267 80 31 146 91 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 266 79 31 208 159 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 264 82 41 58 5 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 264 90 42 79 28 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 263 46 2 138 88 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 260 56 38 45 22 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 259 49 1 106 41 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 258 107 61 130 90 NC_009009:SSA_1741|5end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728007..1728237_POSITIVE 257 58 14 169 104 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 255 55 25 37 11 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 252 72 32 85 42 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 59 11 140 86 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 277 59 20 50 15 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 267 80 31 149 94 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 264 90 42 73 22 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 263 46 2 128 78 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 260 56 38 52 29 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 259 49 1 115 50 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 255 55 25 40 14 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 255 69 44 147 118 NC_009009:SSA_1477|3end_Truncated_transposase,_putative_1482914..1483064_POSITIVE 252 60 11 146 72 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 249 45 2 91 48 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 247 72 33 48 9 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 246 61 23 115 79 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 245 65 30 47 6 NC_009009:SSA_0604|3end_hypothetical_protein_592992..593142_POSITIVE 245 48 2 148 104 NC_009009:SSA_0310|3end_hypothetical_protein_305973..306123_POSITIVE 244 73 34 151 107 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 239 58 29 126 92 NC_009009:SSA_1358|3end_hypothetical_protein_1373104..1373254_NEGATIVE 237 83 41 148 103 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 236 83 42 125 75 NC_009009:SSA_1952|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1948212..1948362_NEGATIVE 235 60 14 136 90 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE