Origin IGS: gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc .........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 gcttgttcctccatttcattttccgacatatttgcttttcatcataatacactatcgtcaaattatagtcaaaagcttataaaagataggagcctcactttttttactgcttttgtcattttcttgactctttatggacgggagtcttatagaatgtaggagaaagatattttacacttaactaaaaggaggatttttc Mask Tandem Repeat Region ================================================ gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Find is-nt database================================================ Query_seq: SSA_0435:SSA_0436|SSA_0435:SSA_0436:Urocanate hydratase, putative:Imidazolonepropionase, putative:<-->:438810..439008 199 gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0435:SSA_0436|SSA_0435:SSA_0436:Urocanate hydratase, putative:Imidazolonepropionase, putative:<-->:438810..439008 199 gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0435:SSA_0436|SSA_0435:SSA_0436:Urocanate hydratase, putative:Imidazolonepropionase, putative:<-->:438810..439008 199 gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 32 End: 139 ............................... M F L L H S I R L P S I K S Q E N D K S S K K S E A P I F Y K L L T I I ............................................................ Protein_Len: 48 Strand: - Start: 44 End: 187 ........................................... M R Y S E R G Y L T L F I V F A T F F T L S R D K I L K Q S Y N S S L T N H H F A F I D S F S M ............ gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc 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: 87 Start: 127 End: 156 ..............................................................................................................................TTTGACTATAATTTGACGATAGTGTATTAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0435:SSA_0436|SSA_0435:SSA_0436:Urocanate hydratase, putative:Imidazolonepropionase, putative:<-->:438810..439008 199 gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_009009_SSA_0435_SSA_0436|Urocanate hydratase, putative:Imidazolonepropionase, putative|NEGATIVE:POSITIVE|[438810,439008]|199 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtnnnnnnngtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc gaaaaatcctccttttagttaagtgtaaaatatctttctcctacattctataagactcccgtccataaagagtcaagaaaatgacaaaagcagtaaaaaaagtgaggctcctatcttttataagcttttgactataatttgacgatagtgtattatgatgaaaagcaaatatgtcggaaaatgaaatggaggaacaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAUCCUCCUUUUAGUUAAGUGUAAAAUAUCUUUCUCCUACAUUCUAUAAGACUCCCGUCCAUAAAGAGUCAAGAAAAUGACAAAAGCAGUAAAAAAAGUGAGGCUCCUAUCUUUUAUAAGCUUUUGACUAUAAUUUGACGAUAGUGUAUUAUGAUGAAAAGCAAAUAUGUCGGAAAAUGAAAUGGAGGAACAAGC ......(((((((((((....((((((..............))))))......(((((...........))))).......(((((...........(((((..((....))..)))))....((((((.(.((((((...((....))..)))))).).)))))).....))))).....))))).))))))...... (-36.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGUUCCUCCAUUUCAUUUUCCGACAUAUUUGCUUUUCAUCAUAAUACACUAUCGUCAAAUUAUAGUCAAAAGCUUAUAAAAGAUAGGAGCCUCACUUUUUUUACUGCUUUUGUCAUUUUCUUGACUCUUUAUGGACGGGAGUCUUAUAGAAUGUAGGAGAAAGAUAUUUUACACUUAACUAAAAGGAGGAUUUUUC ......((((((...((.((((((.((.(((..((((((.((.(((((..((....))...))))).)).))))))..)))...(((((((((...............)))))))))...((((.(((((((.......)))))))....)))).)).)))))).))..(((((........)))))))))))...... (-41.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 80 31 171 122 NC_009009:SSA_0435|5end_Urocanate_hydratase,_putative_438719..438949_NEGATIVE 259 49 8 128 98 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 258 93 57 64 24 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 251 79 34 81 23 NC_009009:SSA_0672|5end_hypothetical_protein_655191..655421_POSITIVE 245 141 102 141 97 NC_009009:SSA_1207|5end_Phosphate_acetyltransferase,_putative_1232274..1232504_NEGATIVE 244 63 30 206 173 NC_009009:SSA_1357|5end_hypothetical_protein_1373024..1373254_NEGATIVE 243 75 38 78 46 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 241 80 56 23 1 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 240 109 72 191 162 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 236 65 29 157 121 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 234 59 28 32 5 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 232 148 101 176 124 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 229 75 40 63 31 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 227 78 33 71 6 NC_009009:SSA_1380|5end_hypothetical_protein_1399131..1399361_NEGATIVE 226 150 105 70 30 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 225 129 81 176 108 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 223 80 37 152 97 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 221 77 33 144 94 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 221 62 33 174 144 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 221 132 103 73 40 NC_009009:SSA_1026|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1042794..1043024_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 93 57 67 27 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 251 79 34 84 26 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 250 86 48 124 87 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 248 104 68 145 116 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 245 141 102 117 73 NC_009009:SSA_1208|3end_23S_rRNA_pseudouridine_synthase,_putative_1232298..1232448_NEGATIVE 244 63 30 126 93 NC_009009:SSA_1358|3end_hypothetical_protein_1373104..1373254_NEGATIVE 238 131 91 113 69 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 230 147 123 150 121 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE 229 75 40 70 38 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 228 126 87 96 52 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 221 77 33 133 83 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE 221 85 45 129 88 NC_009009:SSA_2062|3end_hypothetical_protein_2063291..2063441_NEGATIVE 220 72 34 42 5 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 220 129 86 86 38 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 218 86 45 138 88 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 216 60 11 103 55 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 216 75 37 93 55 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 213 66 22 135 93 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 210 76 37 149 107 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 210 149 102 125 61 NC_009009:SSA_0455|3end_Sucrose-6-phosphate_hydrolase,_putative_456996..457146_NEGATIVE