Origin IGS: ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtactcctccttccactttgctagtataccataaaagactgattttgatacaagaaagctataaaatcttcaataaatcactcactttttcaagcaactagtcacaaggaa Mask Tandem Repeat Region ================================================ ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Find is-nt database================================================ Query_seq: SSA_0887:SSA_0888|SSA_0887:SSA_0888:hypothetical protein:Magnesium/cobalt transporter, putative:<-->:881357..881468 112 ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0887:SSA_0888|SSA_0887:SSA_0888:hypothetical protein:Magnesium/cobalt transporter, putative:<-->:881357..881468 112 ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0887:SSA_0888|SSA_0887:SSA_0888:hypothetical protein:Magnesium/cobalt transporter, putative:<-->:881357..881468 112 ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Predict ORF larger than 30AA ================================================ ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca 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================================================ ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0887:SSA_0888|SSA_0887:SSA_0888:hypothetical protein:Magnesium/cobalt transporter, putative:<-->:881357..881468 112 ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_0887_SSA_0888|hypothetical protein:Magnesium/cobalt transporter, putative|NEGATIVE:POSITIVE|[881357,881468]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca ttccttgtgactagttgcttgaaaaagtgagtgatttattgaagattttatagctttcttgtatcaaaatcagtcttttatggtatactagcaaagtggaaggaggagtaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUUGUGACUAGUUGCUUGAAAAAGUGAGUGAUUUAUUGAAGAUUUUAUAGCUUUCUUGUAUCAAAAUCAGUCUUUUAUGGUAUACUAGCAAAGUGGAAGGAGGAGUACA ((((...((.((((((((((((((.(.(((.((((.((..((((.........))))..)).))))...))).).))))).)))).)))))))....))))........... (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUACUCCUCCUUCCACUUUGCUAGUAUACCAUAAAAGACUGAUUUUGAUACAAGAAAGCUAUAAAAUCUUCAAUAAAUCACUCACUUUUUCAAGCAACUAGUCACAAGGAA ........(((((.......((((((.......(((((..((((((......((((...........))))....))))))....))))).......))))))...))))). (-13.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 110 61 201 152 NC_009009:SSA_0887|5end_hypothetical_protein_881266..881496_NEGATIVE 253 67 27 172 134 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 231 50 2 159 113 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 230 109 84 231 199 NC_009009:SSA_0381|5end_hypothetical_protein_372763..372993_POSITIVE 227 107 66 149 107 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 226 105 68 206 174 NC_009009:SSA_1916|5end_hypothetical_protein_1905487..1905717_POSITIVE 224 99 52 83 37 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 219 60 16 179 147 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 218 110 61 195 141 NC_009009:SSA_1858|5end_hypothetical_protein_1853686..1853916_NEGATIVE 218 100 54 42 1 NC_009009:SSA_0541|5end_Acetate_kinase,_putative_535803..536033_POSITIVE 217 92 51 64 19 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 217 103 62 173 135 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 217 110 66 157 114 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 217 49 1 143 97 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 216 109 61 129 83 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 215 88 45 223 169 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 214 107 64 230 182 NC_009009:SSA_1348|5end_hypothetical_protein_1365355..1365585_POSITIVE 213 100 53 181 113 NC_009009:SSA_1863|5end_NH(3)-dependent_NAD(+)_synthetase,_putative_1859413..1859643_NEGATIVE 212 43 1 141 101 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 211 107 71 63 16 NC_009009:SSA_0651|5end_hypothetical_protein_634548..634778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 92 53 132 85 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 262 100 51 141 96 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 232 98 53 128 74 NC_009009:SSA_2041|3end_Leucine-rich_protein,_putative_2045807..2045957_NEGATIVE 231 50 2 144 98 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 222 99 55 151 113 NC_009009:SSA_1732|3end_Uracil_phosphoribosyltransferase,_putative_1716916..1717066_NEGATIVE 217 109 64 77 31 NC_009009:SSA_2143|3end_Conserved_uncharacterized_protein_2143590..2143740_NEGATIVE 217 106 70 136 91 NC_009009:SSA_1644|3end_hypothetical_protein_1645471..1645621_NEGATIVE 217 49 1 67 21 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 215 88 45 116 62 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 214 109 64 91 54 NC_009009:SSA_1540|3end_hypothetical_protein_1544915..1545065_NEGATIVE 213 106 74 89 47 NC_009009:SSA_0573|3end_hypothetical_protein_568616..568766_NEGATIVE 212 43 1 125 85 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 211 39 5 150 109 NC_009009:SSA_1738|3end_Polysaccharide_biosynthesis_protein,_putative_1723875..1724025_NEGATIVE 208 109 74 91 66 NC_009009:SSA_1538|3end_hypothetical_protein_1544918..1545068_POSITIVE 207 99 52 122 58 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 203 99 53 59 11 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 202 83 43 137 100 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 202 100 52 67 22 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 201 110 72 64 13 NC_009009:SSA_1180|3end_hypothetical_protein_1207819..1207969_NEGATIVE 200 110 71 140 81 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE