Origin IGS: tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaacacctcatttctttgcacctattttctcataaaagaagttgaaattatagcaatttgattagaactttcttcaaattgatatgaaaagctgggtcttaatgacaatcaacccagccatgttcttcatttcaaatcactacaactcttgtatagaaga Mask Tandem Repeat Region ================================================ tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Find is-nt database================================================ Query_seq: SSA_0373:SSA_0374|SSA_0373:SSA_0374:Dihydroorotate dehydrogenase, putative:Peptide methionine sulfoxide reductase msrA/msrB, putative:->->:363141..363302 162 tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0373:SSA_0374|SSA_0373:SSA_0374:Dihydroorotate dehydrogenase, putative:Peptide methionine sulfoxide reductase msrA/msrB, putative:->->:363141..363302 162 tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0373:SSA_0374|SSA_0373:SSA_0374:Dihydroorotate dehydrogenase, putative:Peptide methionine sulfoxide reductase msrA/msrB, putative:->->:363141..363302 162 tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Predict ORF larger than 30AA ================================================ tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt 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================================================ tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0373:SSA_0374|SSA_0373:SSA_0374:Dihydroorotate dehydrogenase, putative:Peptide methionine sulfoxide reductase msrA/msrB, putative:->->:363141..363302 162 tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_009009_SSA_0373_SSA_0374|Dihydroorotate dehydrogenase, putative:Peptide methionine sulfoxide reductase msrA/msrB, putative|POSITIVE:POSITIVE|[363141,363302]|162 HSP 1 e-value: 4.0E-87 bit: 321.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt tcttctatacaagagttgtagtgatttgaaatgaagaacatggctgggttgattgtcattaagacccagcttttcatatcaatttgaagaaagttctaatcaaattgctataatttcaacttcttttatgagaaaataggtgcaaagaaatgaggtgttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUCUAUACAAGAGUUGUAGUGAUUUGAAAUGAAGAACAUGGCUGGGUUGAUUGUCAUUAAGACCCAGCUUUUCAUAUCAAUUUGAAGAAAGUUCUAAUCAAAUUGCUAUAAUUUCAACUUCUUUUAUGAGAAAAUAGGUGCAAAGAAAUGAGGUGUUUUU .((((.......(((((((((..((((((.....(((((..(((((((((............)))))))))(((((........)))))...)))))..))))))..)))))))))....(((((....))))).................))))....... (-41.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACACCUCAUUUCUUUGCACCUAUUUUCUCAUAAAAGAAGUUGAAAUUAUAGCAAUUUGAUUAGAACUUUCUUCAAAUUGAUAUGAAAAGCUGGGUCUUAAUGACAAUCAACCCAGCCAUGUUCUUCAUUUCAAAUCACUACAACUCUUGUAUAGAAGA ..........................((((((.(((.((((.((((...(((((.((((((((..(((....))))))))))).)))))...(((((((.....((.....)))))))))........................)))))))).))))))))) (-32.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 77 31 210 158 NC_009009:SSA_2332|5end_D-alanyl_carrier_protein,_putative_2335196..2335426_NEGATIVE 292 74 40 187 151 NC_009009:SSA_2169|5end_Glucose-1-phosphate_uridylyltransferase,_putative_2168446..2168676_POSITIVE 288 79 40 170 127 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 272 70 28 65 30 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 269 48 10 166 130 NC_009009:SSA_1360|5end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1376350..1376580_POSITIVE 261 75 32 193 149 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 257 81 42 142 113 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 254 60 15 117 73 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 251 80 36 218 176 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 251 72 31 161 117 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 251 84 41 74 34 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 246 70 27 191 145 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 245 152 117 133 97 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 242 85 41 177 130 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 241 143 105 123 76 NC_009009:SSA_1500|5end_Translation_initiation_factor_IF-3,_putative_1504921..1505151_NEGATIVE 241 76 31 63 9 NC_009009:SSA_0590|5end_hypothetical_protein_582144..582374_POSITIVE 241 109 65 201 157 NC_009009:SSA_0247|5end_hypothetical_protein_240032..240262_POSITIVE 239 85 41 225 173 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 237 73 36 230 191 NC_009009:SSA_0137|5end_ABC_transporter_(permease),_Zn_porter,_putative_131717..131947_POSITIVE 236 76 42 112 77 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 79 40 69 26 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 282 77 31 60 14 NC_009009:SSA_0373|3end_Dihydroorotate_dehydrogenase,_putative_363080..363230_POSITIVE 276 82 43 102 61 NC_009009:SSA_1703|3end_Methionyl-tRNA_synthetase,_putative_1693640..1693790_NEGATIVE 272 70 28 72 37 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 268 81 42 48 17 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 257 70 30 150 106 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 257 81 42 151 122 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 251 72 31 139 95 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 251 84 41 64 24 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 242 85 41 135 88 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 241 77 39 141 100 NC_009009:SSA_2346|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2347602..2347752_NEGATIVE 236 70 25 69 14 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 236 76 42 115 80 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 230 76 35 142 97 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 224 157 112 122 71 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 224 76 35 82 34 NC_009009:SSA_1259|3end_Purine_nucleoside_phosphorylase,_putative_1284910..1285060_NEGATIVE 223 110 63 71 7 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 219 80 33 102 58 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE 219 108 69 129 89 NC_009009:SSA_1260|3end_Phosphopentomutase,_putative_1285752..1285902_NEGATIVE 218 75 39 63 22 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE