Origin IGS: cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaatatgctccttttttaagatgtttttattgtatatgaaaacgcttcaaaaatcaagaaaaaatcggagaggtttgctttcattagtgaattgtgctattctgttaagaaaaaataggaggccccg Mask Tandem Repeat Region ================================================ cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Find is-nt database================================================ Query_seq: SSA_1614:SSA_1615|SSA_1614:SSA_1615:Acetyltransferase, GNAT family, putative:Alanine dehydrogenase, putative:<-->:1618136..1618265 130 cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1614:SSA_1615|SSA_1614:SSA_1615:Acetyltransferase, GNAT family, putative:Alanine dehydrogenase, putative:<-->:1618136..1618265 130 cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1614:SSA_1615|SSA_1614:SSA_1615:Acetyltransferase, GNAT family, putative:Alanine dehydrogenase, putative:<-->:1618136..1618265 130 cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 3 End: 125 .. P R R N K R L L I A C N V L S L L G R R N K R S K Q L T K M Y L L F M K F F S C M ..... cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 70 End: 99 .....................................................................CTTGATTTTTGAAGCGTTTTCATATACAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 39 HP_score: -2.1 Tail_Score: -2.53905 Start: 46 End: 60 Full_Region: atcaagaaaaaatcg gagag gtttg ctttc attagtgaattgtgc .............................................gagaggtttgctttc...................................................................... Find igs database================================================ Query_seq: SSA_1614:SSA_1615|SSA_1614:SSA_1615:Acetyltransferase, GNAT family, putative:Alanine dehydrogenase, putative:<-->:1618136..1618265 130 cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_009009_SSA_1614_SSA_1615|Acetyltransferase, GNAT family, putative:Alanine dehydrogenase, putative|NEGATIVE:POSITIVE|[1618136,1618265]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt cggggcctcctattttttcttaacagaatagcacaattcactaatgaaagcaaacctctccgattttttcttgatttttgaagcgttttcatatacaataaaaacatcttaaaaaaggagcatatttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGGGCCUCCUAUUUUUUCUUAACAGAAUAGCACAAUUCACUAAUGAAAGCAAACCUCUCCGAUUUUUUCUUGAUUUUUGAAGCGUUUUCAUAUACAAUAAAAACAUCUUAAAAAAGGAGCAUAUUUUUU ....((.((((.((((.........((((......))))....((((((((...(.((...((((.......))))...)).).))))))))..................)))).))))))......... (-15.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUAUGCUCCUUUUUUAAGAUGUUUUUAUUGUAUAUGAAAACGCUUCAAAAAUCAAGAAAAAAUCGGAGAGGUUUGCUUUCAUUAGUGAAUUGUGCUAUUCUGUUAAGAAAAAAUAGGAGGCCCCG ..........(((((((((.(((.(((((((((.....)))))))))))).))))).............)))).((...((((((..((((.......))))((((....))))......)))))).)). (-22.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 844 50 1 141 92 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 277 70 24 56 10 NC_009009:SSA_1162|5end_Possible_fimbrial_assembly_protein_fimC,_putative_1189250..1189480_NEGATIVE 261 90 41 201 150 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 258 95 55 162 106 NC_009009:SSA_1846|5end_Phosphoprotein_phosphatase,_putative_1840918..1841148_NEGATIVE 256 89 53 140 102 NC_009009:SSA_2256|5end_hypothetical_protein_2250604..2250834_POSITIVE 253 47 1 144 96 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 246 68 22 174 126 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 238 87 42 225 190 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 236 89 42 140 79 NC_009009:SSA_0354|5end_Uncharacterized_membrane_protein_346241..346471_POSITIVE 233 58 24 78 47 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 233 49 1 178 133 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 230 32 2 132 101 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 228 84 44 171 133 NC_009009:SSA_1409|5end_DTDP-glucose-4,6-dehydratase,_putative_1422255..1422485_NEGATIVE 227 89 50 221 179 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 226 60 11 171 118 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 226 85 56 125 97 NC_009009:SSA_2392|5end_50S_ribosomal_protein_L36,_putative_120198..120428_POSITIVE 222 47 1 79 20 NC_009009:SSA_1422|5end_hypothetical_protein_1431555..1431785_NEGATIVE 221 89 44 147 90 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 220 62 24 226 186 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 218 85 43 69 8 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 95 55 143 87 NC_009009:SSA_1847|3end_RRNA_methyltransferase_RsmB,_putative_1840937..1841087_NEGATIVE 254 20 2 37 19 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 253 47 1 53 5 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 236 89 42 129 68 NC_009009:SSA_0353|3end_Conserved_uncharacterized_protein_346310..346460_POSITIVE 226 85 56 102 74 NC_009009:SSA_0129|3end_Translation_initiation_factor_IF-1,_putative_120255..120405_POSITIVE 225 78 31 55 1 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 223 92 52 58 15 NC_009009:SSA_1472|3end_hypothetical_protein_1478485..1478635_NEGATIVE 222 47 1 73 14 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 221 89 44 133 76 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 218 63 24 61 13 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 218 84 45 145 102 NC_009009:SSA_0629|3end_hypothetical_protein_619586..619736_POSITIVE 217 74 51 76 55 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 212 62 25 148 107 NC_009009:SSA_0225|3end_10_kDa_chaperonin_219003..219153_POSITIVE 211 70 38 62 36 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 209 85 44 61 1 NC_009009:SSA_1873|3end_S-adenosyl-methyltransferase_mraW,_putative_1869194..1869344_NEGATIVE 209 28 1 151 124 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 208 42 5 32 3 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 206 89 53 148 106 NC_009009:SSA_2328|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2332309..2332459_POSITIVE 206 90 51 58 5 NC_009009:SSA_2316|3end_General_secretory_pathway_protein_F,_putative_2317116..2317266_NEGATIVE 202 62 27 32 8 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE