Origin IGS: tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt .........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 aacagcctttctataccaaagaatgagagtttatactagtatctattatatagaaaaatccagctattaatgtttatgataaaaagagacatcttgctgcagcaaaaaagctgagacatcttgcctcaacctttagagaaaataattatacatctatttgaatctaacagcaagtgacaaca Mask Tandem Repeat Region ================================================ tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Find is-nt database================================================ Query_seq: SSA_0149:SSA_0150|SSA_0149:SSA_0150:hypothetical protein:hypothetical protein:->->:143894..144075 182 tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0149:SSA_0150|SSA_0149:SSA_0150:hypothetical protein:hypothetical protein:->->:143894..144075 182 tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0149:SSA_0150|SSA_0149:SSA_0150:hypothetical protein:hypothetical protein:->->:143894..144075 182 tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 25 End: 117 ........................ I S T Y N N E R F T S A L H R L K K A A A L H R K K D Y V N M ................................................................. tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt 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: 84 Start: 9 End: 38 ........CTTGCTGTTAGATTCAAATAGATGTATAAT................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -8.3 Tail_Score: -5.14563 Start: 53 End: 73 Full_Region: TTATTTTCTCTAAAG GTTGAGGCA AGA TGTCTCAGC TTTTTTGCTGCAGCA ....................................................GTTGAGGCAAGATGTCTCAGC............................................................................................................. Find igs database================================================ Query_seq: SSA_0149:SSA_0150|SSA_0149:SSA_0150:hypothetical protein:hypothetical protein:->->:143894..144075 182 tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_009009_SSA_0149_SSA_0150|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[143894,144075]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt tgttgtcacttgctgttagattcaaatagatgtataattattttctctaaaggttgaggcaagatgtctcagcttttttgctgcagcaagatgtctctttttatcataaacattaatagctggatttttctatataatagatactagtataaactctcattctttggtatagaaaggctgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUGUCACUUGCUGUUAGAUUCAAAUAGAUGUAUAAUUAUUUUCUCUAAAGGUUGAGGCAAGAUGUCUCAGCUUUUUUGCUGCAGCAAGAUGUCUCUUUUUAUCAUAAACAUUAAUAGCUGGAUUUUUCUAUAUAAUAGAUACUAGUAUAAACUCUCAUUCUUUGGUAUAGAAAGGCUGUU ....(.((((((((((.((........(((.(((....)))..)))..((((((((((((.....))))))))))))...)))))))))).)).)...................(((((((.....(((((((((...(((....(((....))).....)))...)))))))))))))))) (-43.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGCCUUUCUAUACCAAAGAAUGAGAGUUUAUACUAGUAUCUAUUAUAUAGAAAAAUCCAGCUAUUAAUGUUUAUGAUAAAAAGAGACAUCUUGCUGCAGCAAAAAAGCUGAGACAUCUUGCCUCAACCUUUAGAGAAAAUAAUUAUACAUCUAUUUGAAUCUAACAGCAAGUGACAACA ..((((.((((((((....(((.((..(((....)))..)))))....))))))))....((((.....((((((...........))))))...))))..........))))...((.(((((........(((((..(((((..........)))))...)))))..)))))))...... (-28.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 88 43 199 150 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 339 90 44 201 154 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 331 87 44 157 117 NC_009009:SSA_1653|5end_hypothetical_protein_1651371..1651601_NEGATIVE 329 76 50 176 151 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 327 95 51 188 146 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 324 90 41 65 25 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 320 100 60 53 13 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 318 87 41 96 49 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 314 79 38 140 99 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 307 99 64 201 157 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 303 99 52 198 149 NC_009009:SSA_1640|5end_hypothetical_protein_1642530..1642760_NEGATIVE 302 82 51 216 188 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 301 77 38 133 88 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 294 95 51 174 135 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 293 88 54 189 145 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 292 98 51 67 27 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 291 100 51 161 110 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 287 89 41 73 33 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 286 96 51 59 4 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 285 99 51 180 144 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 97 51 107 60 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 378 90 49 106 63 NC_009009:SSA_0743|3end_Transcriptional_repressor_(arginine_synthesis),_putative_725289..725439_NEGATIVE 336 92 51 101 58 NC_009009:SSA_0844|3end_hypothetical_protein_828491..828641_NEGATIVE 331 87 44 137 97 NC_009009:SSA_1655|3end_hypothetical_protein_1651391..1651541_NEGATIVE 329 76 50 86 61 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 324 90 41 55 15 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 321 90 41 141 81 NC_009009:SSA_1386|3end_NADPH-dependent_FMN_reductase,_putative_1403428..1403578_POSITIVE 318 87 41 75 28 NC_009009:SSA_2173|3end_Aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase,_putative_2170781..2170931_NEGATIVE 314 79 38 149 108 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 305 85 44 149 105 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 301 79 48 92 57 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 301 77 38 85 40 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 294 95 51 151 112 NC_009009:SSA_1879|3end_Glycyl-tRNA_synthetase_beta_chain,_putative_1872223..1872373_NEGATIVE 292 78 49 61 32 NC_009009:SSA_1110|3end_hypothetical_protein_1136185..1136335_POSITIVE 292 100 57 87 47 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 291 100 51 144 93 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 288 95 51 112 72 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 287 89 41 73 33 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 286 99 51 122 62 NC_009009:SSA_2080|3end_hypothetical_protein_2084598..2084748_NEGATIVE 286 96 51 62 7 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE