Origin IGS: gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag .........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 cttaaaggaatgaaaaatttgaacaatcttgcttatctcttgaaaaaagttttggtgctcaggcttctacaaactttgaagatttagtcggtaaaaattggacaaaagctttcttgtttttcaaaaaataggtttgtgaattttttagatttgtgatagaatagtatggaattttgaattcaacaattaaatagatttggagtaaaaac Mask Tandem Repeat Region ================================================ gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Find is-nt database================================================ Query_seq: SSA_1852:SSA_1853|SSA_1852:SSA_1853:Metal dependent phosphohydrolase (HD motif), putative:S-ribosylhomocysteine lyase, putative:<-->:1848573..1848781 209 gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1852:SSA_1853|SSA_1852:SSA_1853:Metal dependent phosphohydrolase (HD motif), putative:S-ribosylhomocysteine lyase, putative:<-->:1848573..1848781 209 gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1852:SSA_1853|SSA_1852:SSA_1853:Metal dependent phosphohydrolase (HD motif), putative:S-ribosylhomocysteine lyase, putative:<-->:1848573..1848781 209 gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 31 End: 123 .............................. M Q N S I L F Y H K S K K F T N L F F E K Q E S F C P I F T D ...................................................................................... Protein_Len: 45 Strand: + Start: 14 End: 148 ............. M Y L I V E F K I P Y Y S I T N L K N S Q T Y F L K N K K A F V Q F L P T K S S K F V E A ............................................................. gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag 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: 85 Start: 48 End: 77 ...............................................TTTGTGAATTTTTTAGATTTGTGATAGAAT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1852:SSA_1853|SSA_1852:SSA_1853:Metal dependent phosphohydrolase (HD motif), putative:S-ribosylhomocysteine lyase, putative:<-->:1848573..1848781 209 gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_009009_SSA_1852_SSA_1853|Metal dependent phosphohydrolase (HD motif), putative:S-ribosylhomocysteine lyase, putative|NEGATIVE:POSITIVE|[1848573,1848781]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag gtttttactccaaatctatttaattgttgaattcaaaattccatactattctatcacaaatctaaaaaattcacaaacctattttttgaaaaacaagaaagcttttgtccaatttttaccgactaaatcttcaaagtttgtagaagcctgagcaccaaaacttttttcaagagataagcaagattgttcaaatttttcattcctttaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUACUCCAAAUCUAUUUAAUUGUUGAAUUCAAAAUUCCAUACUAUUCUAUCACAAAUCUAAAAAAUUCACAAACCUAUUUUUUGAAAAACAAGAAAGCUUUUGUCCAAUUUUUACCGACUAAAUCUUCAAAGUUUGUAGAAGCCUGAGCACCAAAACUUUUUUCAAGAGAUAAGCAAGAUUGUUCAAAUUUUUCAUUCCUUUAAG ............(((((......((((.(((((..................................)))))))))...((((((((((((((.......((((..((.....((((((.((((..........)))).))))))))..)))).........))))))))))))))....)))))........................ (-23.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAAGGAAUGAAAAAUUUGAACAAUCUUGCUUAUCUCUUGAAAAAAGUUUUGGUGCUCAGGCUUCUACAAACUUUGAAGAUUUAGUCGGUAAAAAUUGGACAAAAGCUUUCUUGUUUUUCAAAAAAUAGGUUUGUGAAUUUUUUAGAUUUGUGAUAGAAUAGUAUGGAAUUUUGAAUUCAACAAUUAAAUAGAUUUGGAGUAAAAAC .................((((..((((((...(((....(((((..(((.(((.(((((.(..((..((((((.((((((((....(((.(.......).)))....((...((((((((....))))))))...))....))))))))))))))..))..)))))).))).)))...)))))....)))..))).)))...))))... (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 739 140 91 231 182 NC_009009:SSA_1852|5end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1848482..1848712_NEGATIVE 272 159 111 200 154 NC_009009:SSA_0316|5end_hypothetical_protein_310576..310806_POSITIVE 265 167 125 60 11 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 260 189 142 86 40 NC_009009:SSA_1497|5end_DCMP_deaminase,_putative_1503535..1503765_NEGATIVE 255 157 113 166 108 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 252 148 101 129 75 NC_009009:SSA_0164|5end_hypothetical_protein_162478..162708_POSITIVE 242 168 125 85 30 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 237 158 130 71 44 NC_009009:SSA_1568|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571200..1571430_POSITIVE 236 189 142 170 118 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 235 147 107 139 101 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 234 79 38 154 106 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 233 168 136 83 55 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 231 118 79 169 119 NC_009009:SSA_1100|5end_Hemolysin_exporter,_ATPase_component,_putative_1119873..1120103_POSITIVE 226 179 133 201 156 NC_009009:SSA_1083|5end_Conserved_uncharacterized_protein_1101298..1101528_POSITIVE 226 188 142 197 157 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 224 157 112 195 142 NC_009009:SSA_2064|5end_hypothetical_protein_2065031..2065261_NEGATIVE 224 169 135 90 47 NC_009009:SSA_1943|5end_Aspartate_kinase,_putative_1928697..1928927_POSITIVE 224 135 97 74 37 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 222 180 131 227 178 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 222 186 141 172 125 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 167 125 50 1 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 255 168 129 138 99 NC_009009:SSA_0661|3end_Isoleucyl-tRNA_synthetase,_putative_647748..647898_POSITIVE 252 148 101 113 59 NC_009009:SSA_0163|3end_hypothetical_protein_162542..162692_POSITIVE 242 180 131 87 37 NC_009009:SSA_1317|3end_hypothetical_protein_1333398..1333548_NEGATIVE 237 158 130 58 31 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 235 147 107 137 99 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 233 163 126 79 34 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 233 168 136 90 62 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 231 118 79 90 40 NC_009009:SSA_1099|3end_Calcium_binding_hemolysin-like_protein,_putative_1119874..1120024_POSITIVE 228 180 131 133 84 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 226 179 133 74 29 NC_009009:SSA_1082|3end_PTS_system,_fructose_specific_II_ABC_components,_putative_1101251..1101401_POSITIVE 221 168 121 87 45 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 218 159 119 66 28 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 218 157 113 45 2 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 218 150 109 144 98 NC_009009:SSA_0135|3end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_131097..131247_POSITIVE 217 179 134 69 30 NC_009009:SSA_1979|3end_Alkaline-shock_protein,_putative_1973936..1974086_NEGATIVE 213 189 141 64 12 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 213 131 92 86 49 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 213 154 111 130 86 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 212 82 41 55 6 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE