Origin IGS: gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa .........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 tttgtttctcctatttacttagttccctcttattttaccataaatagctgctgaaataccactaaaagccaattttttgtaatttttcaagaatttgttttcattctgctcggtctaagggaggattttgtagtaaattcttgcaaagttcgagaatactgatataatgaaactataaaactttgactatttttgacctttaatcatttctataaatagcttgcacactaaaagaaaagaggtatctgc Mask Tandem Repeat Region ================================================ gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Find is-nt database================================================ Query_seq: SSA_0669:SSA_0670|SSA_0669:SSA_0670:ATP dependent protease, putative:Conserved uncharacterized protein:<-->:653811..654059 249 gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0669:SSA_0670|SSA_0669:SSA_0670:ATP dependent protease, putative:Conserved uncharacterized protein:<-->:653811..654059 249 gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0669:SSA_0670|SSA_0669:SSA_0670:ATP dependent protease, putative:Conserved uncharacterized protein:<-->:653811..654059 249 gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 86 End: 178 ..................................................................................... I L I R S S Q L F K S C F G G K S R A S H F C I R S F N C F M ....................................................................... gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa 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================================================ gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0669:SSA_0670|SSA_0669:SSA_0670:ATP dependent protease, putative:Conserved uncharacterized protein:<-->:653811..654059 249 gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: NC_009009_SSA_0669_SSA_0670|ATP dependent protease, putative:Conserved uncharacterized protein|NEGATIVE:POSITIVE|[653811,654059]|249 HSP 1 e-value: 1.0E-139 bit: 494.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa gcagatacctcttttcttttagtgtgcaagctatttatagaaatgattaaaggtcaaaaatagtcaaagttttatagtttcattatatcagtattctcgaactttgcaagaatttactacaaaatcctcccttagaccgagcagaatgaaaacaaattcttgaaaaattacaaaaaattggcttttagtggtatttcagcagctatttatggtaaaataagagggaactaagtaaataggagaaacaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGAUACCUCUUUUCUUUUAGUGUGCAAGCUAUUUAUAGAAAUGAUUAAAGGUCAAAAAUAGUCAAAGUUUUAUAGUUUCAUUAUAUCAGUAUUCUCGAACUUUGCAAGAAUUUACUACAAAAUCCUCCCUUAGACCGAGCAGAAUGAAAACAAAUUCUUGAAAAAUUACAAAAAAUUGGCUUUUAGUGGUAUUUCAGCAGCUAUUUAUGGUAAAAUAAGAGGGAACUAAGUAAAUAGGAGAAACAAA (((((((((...(((((..((((......)))).....)))))..((((((((((((.......((((((((((((((...))))))...........))))))))(((((((((...........(((.........)))............)))))))))...............)))))))))))))))))))..))..((((((((...........((....))..)))))))).......... (-39.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUUCUCCUAUUUACUUAGUUCCCUCUUAUUUUACCAUAAAUAGCUGCUGAAAUACCACUAAAAGCCAAUUUUUUGUAAUUUUUCAAGAAUUUGUUUUCAUUCUGCUCGGUCUAAGGGAGGAUUUUGUAGUAAAUUCUUGCAAAGUUCGAGAAUACUGAUAUAAUGAAACUAUAAAACUUUGACUAUUUUUGACCUUUAAUCAUUUCUAUAAAUAGCUUGCACACUAAAAGAAAAGAGGUAUCUGC ...................(((...((((((.(((((........(((((..(((((............(((.((((((........)))))).))).(((((((.((.(((((........(((((((((((.......)))))))))))......))))))).))))))).................................)))))......))))).......)))))...))))))...))). (-36.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 140 91 231 182 NC_009009:SSA_0669|5end_ATP_dependent_protease,_putative_653720..653950_NEGATIVE 310 217 179 56 15 NC_009009:SSA_2374|5end_Inosine-5'-monophosphate_dehydrogenase,_putative_2377015..2377245_NEGATIVE 260 213 176 73 41 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 256 140 94 60 11 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 252 120 77 73 25 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 248 66 21 183 133 NC_009009:SSA_0042|5end_Amino_acid_recemase,_putative_47893..48123_POSITIVE 247 229 182 163 115 NC_009009:SSA_1542|5end_Peptidase,_U32_family,_putative_1547796..1548026_NEGATIVE 244 141 120 97 70 NC_009009:SSA_0499|5end_ABC-type_dipeptide_transport_system,_periplasmic_component,_putative_498915..499145_POSITIVE 244 165 125 75 32 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 238 155 121 189 157 NC_009009:SSA_1686|5end_hypothetical_protein_1679176..1679406_POSITIVE 236 217 179 62 31 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 232 160 119 47 3 NC_009009:SSA_1999|5end_hypothetical_protein_1996974..1997204_NEGATIVE 231 138 103 52 6 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 230 149 104 48 1 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 229 48 8 146 103 NC_009009:SSA_0120|5end_30S_ribosomal_protein_S8,_putative_114618..114848_POSITIVE 227 137 97 182 141 NC_009009:SSA_1754|5end_hypothetical_protein_1743478..1743708_NEGATIVE 225 140 96 116 73 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 224 149 124 213 187 NC_009009:SSA_1780|5end_Tyrosine_recombinase_xerD,_putative_1767147..1767377_NEGATIVE 222 149 118 39 3 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 222 164 125 98 51 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 213 176 83 51 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 254 149 102 50 3 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 252 120 77 61 13 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 246 214 177 120 80 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 244 165 125 62 19 NC_009009:SSA_0432|3end_Formate--tetrahydrofolate_ligase,_putative_433288..433438_NEGATIVE 230 145 102 138 98 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 227 142 103 146 106 NC_009009:SSA_1276|3end_Conserved_uncharacterized_protein_1298156..1298306_NEGATIVE 222 164 125 76 29 NC_009009:SSA_0476|3end_Precorrin-2_C20-methyltransferase,_putative_479281..479431_POSITIVE 218 33 9 130 110 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 218 145 105 131 101 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 217 225 182 61 11 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 217 67 21 67 20 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 216 212 178 44 7 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 215 40 21 44 26 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 215 144 103 141 99 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 214 198 177 113 90 NC_009009:SSA_0736|3end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_718414..718564_POSITIVE 213 119 89 53 18 NC_009009:SSA_2277|3end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2275983..2276133_NEGATIVE 211 164 122 54 1 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 210 204 177 143 115 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 207 145 122 133 101 NC_009009:SSA_1628|3end_MutT/nudix_family_protein,_putative_1630363..1630513_POSITIVE