Origin IGS: gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaataatcaaattccttttctattttgtaaactaatttaagacggtctgtcctagtcaaatctaaatacgcttcgctctctgtctaaggtggttctatgtcctgaagatgagagagcagacgagtgaaaaacaagtgattgctcattatttgtcctccttctggcttggtatgtc Mask Tandem Repeat Region ================================================ gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Find is-nt database================================================ Query_seq: SSA_0492:SSA_0493|SSA_0492:SSA_0493:NADH-dependent flavin oxidoreductase, putative:ABC-type dipeptide/nickel transport system, periplasmic component, putative:->->:492832..493007 176 gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0492:SSA_0493|SSA_0492:SSA_0493:NADH-dependent flavin oxidoreductase, putative:ABC-type dipeptide/nickel transport system, periplasmic component, putative:->->:492832..493007 176 gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0492:SSA_0493|SSA_0492:SSA_0493:NADH-dependent flavin oxidoreductase, putative:ABC-type dipeptide/nickel transport system, periplasmic component, putative:->->:492832..493007 176 gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 3 End: 110 .. M G L W F S S L Y H A I V Q K E S T Q E R M K L V Y F W R L C L A F R M .................................................................. gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt 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================================================ gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0492:SSA_0493|SSA_0492:SSA_0493:NADH-dependent flavin oxidoreductase, putative:ABC-type dipeptide/nickel transport system, periplasmic component, putative:->->:492832..493007 176 gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_009009_SSA_0492_SSA_0493|NADH-dependent flavin oxidoreductase, putative:ABC-type dipeptide/nickel transport system, periplasmic component, putative|POSITIVE:POSITIVE|[492832,493007]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt gacataccaagccagaaggaggacaaataatgagcaatcacttgtttttcactcgtctgctctctcatcttcaggacatagaaccaccttagacagagagcgaagcgtatttagatttgactaggacagaccgtcttaaattagtttacaaaatagaaaaggaatttgattatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUACCAAGCCAGAAGGAGGACAAAUAAUGAGCAAUCACUUGUUUUUCACUCGUCUGCUCUCUCAUCUUCAGGACAUAGAACCACCUUAGACAGAGAGCGAAGCGUAUUUAGAUUUGACUAGGACAGACCGUCUUAAAUUAGUUUACAAAAUAGAAAAGGAAUUUGAUUAUUUU ......((..((.(((..(((((.(((((((((....))).)))))).)).))).)))(((((((..(((..(((...........))).))).)))))))...)).....((((((....((((((.....))))))....))))))............)).............. (-35.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAUCAAAUUCCUUUUCUAUUUUGUAAACUAAUUUAAGACGGUCUGUCCUAGUCAAAUCUAAAUACGCUUCGCUCUCUGUCUAAGGUGGUUCUAUGUCCUGAAGAUGAGAGAGCAGACGAGUGAAAAACAAGUGAUUGCUCAUUAUUUGUCCUCCUUCUGGCUUGGUAUGUC .........................................((((......((.(((((................(((((((((((.(((...........)))..)))).))))))).(((((((((....(((....)))....))))))))).......))))).))..)))) (-36.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 109 65 92 30 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 302 88 43 205 152 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 301 134 97 72 33 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 299 135 93 49 12 NC_009009:SSA_1221|5end_L-lactate_dehydrogenase,_putative_1243956..1244186_POSITIVE 296 87 41 55 13 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 290 98 51 180 138 NC_009009:SSA_1061|5end_50S_ribosomal_protein_L21,_putative_1077592..1077822_POSITIVE 287 76 32 228 190 NC_009009:SSA_2242|5end_hypothetical_protein_2238663..2238893_NEGATIVE 287 133 93 168 116 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 283 86 45 186 140 NC_009009:SSA_1069|5end_Lipoprotein_signal_peptidase,_putative_1088291..1088521_POSITIVE 281 83 45 187 140 NC_009009:SSA_1627|5end_hypothetical_protein_1629690..1629920_NEGATIVE 281 125 86 222 167 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 280 83 48 151 115 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 280 42 4 185 132 NC_009009:SSA_0357|5end_Thioredoxin,_putative_350763..350993_POSITIVE 278 120 86 134 98 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 278 69 34 171 138 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 278 43 4 172 128 NC_009009:SSA_0564|5end_Potential_aminotransferase,_putative_555694..555924_POSITIVE 277 103 70 206 173 NC_009009:SSA_1241|5end_Orotidine-5'-phosphate_decarboxylase,_putative_1266201..1266431_NEGATIVE 275 75 31 112 60 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 275 99 53 201 142 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 273 107 64 227 194 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 109 65 99 37 NC_009009:SSA_0023|3end_Aspartate_aminotransferase,_putative_29781..29931_POSITIVE 287 76 32 122 84 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 280 42 4 99 46 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE 275 75 31 115 63 NC_009009:SSA_1805|3end_Primosomal_protein_DnaI,_putative_1788665..1788815_NEGATIVE 275 79 37 149 101 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 266 98 54 75 28 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE 265 70 32 117 74 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 263 60 14 78 39 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 259 60 11 66 21 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 254 89 42 131 91 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 254 98 52 65 21 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 253 57 12 104 69 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 252 77 43 149 110 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 251 89 44 47 3 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 250 90 51 119 89 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 250 136 92 92 58 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 249 90 47 113 58 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 248 47 6 83 36 NC_009009:SSA_0383|3end_Beta-glucosidase,_putative_376053..376203_POSITIVE 248 140 91 117 62 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 247 89 52 53 16 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE