Origin IGS: gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt .........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 aaacactcgcctccagaaatttcctatcactagtgtagcaaggataagaggctaagtcaataaaagatggactattcgaaaaactttagaaatattttagaattacttgaaggatatttgagaatcgaactttaaaatagaaagaaataagaaatgcatgtgctataaaaaggaggctcaatatgtttaaaattttttgcaaaatcgtttttaaaagtattactttcgcccttgagggctaaggaaaaaaggagaatcgc Mask Tandem Repeat Region ================================================ gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Find is-nt database================================================ Query_seq: SSA_0400:SSA_0401|SSA_0400:SSA_0401:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-->:398342..398601 260 gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0400:SSA_0401|SSA_0400:SSA_0401:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-->:398342..398601 260 gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0400:SSA_0401|SSA_0400:SSA_0401:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-->:398342..398601 260 gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 4 End: 126 ... M L L F S L A L K G E S N T F K N D F A K N F K H I E P P F Y S T C I S Y F F L F ...................................................................................................................................... Protein_Len: 44 Strand: + Start: 41 End: 172 ........................................ M L L K T I L Q K I L N I L S L L F I A H A F L I S F Y F K V R F S N I L Q V I L K Y F ........................................................................................ Protein_Len: 31 Strand: - Start: 22 End: 114 ..................... G E L A F T I S K F V I K C F I K F M N L R R K I A C A N R M .................................................................................................................................................. gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt 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: 84 Start: 200 End: 229 .......................................................................................................................................................................................................ATTGACTTAGCCTCTTATCCTTGCTACACT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0400:SSA_0401|SSA_0400:SSA_0401:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-->:398342..398601 260 gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Intra-Species Hit: Count: 1 Min: 1 Max: 260 Len: 260 Subject: NC_009009_SSA_0400_SSA_0401|hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative|NEGATIVE:POSITIVE|[398342,398601]|260 HSP 1 e-value: 1.0E-145 bit: 515.0 Len: 260 Query Start:1 Query End:260 Subject Strand: POSITIVE Subject Start: 1 Subject End: 260 gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt gcgattctccttttttccttagccctcaagggcgaaagtaatacttttaaaaacgattttgcaaaaaattttaaacatattgagcctcctttttatagcacatgcatttcttatttctttctattttaaagttcgattctcaaatatccttcaagtaattctaaaatatttctaaagtttttcgaatagtccatcttttattgacttagcctcttatccttgctacactagtgataggaaatttctggaggcgagtgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAUUCUCCUUUUUUCCUUAGCCCUCAAGGGCGAAAGUAAUACUUUUAAAAACGAUUUUGCAAAAAAUUUUAAACAUAUUGAGCCUCCUUUUUAUAGCACAUGCAUUUCUUAUUUCUUUCUAUUUUAAAGUUCGAUUCUCAAAUAUCCUUCAAGUAAUUCUAAAAUAUUUCUAAAGUUUUUCGAAUAGUCCAUCUUUUAUUGACUUAGCCUCUUAUCCUUGCUACACUAGUGAUAGGAAAUUUCUGGAGGCGAGUGUUU ((((...((.(((((......((((....)))).((((.....)))).))))).))..))))..........((((((.....((((((........((....)).(((((((((.((............((((((..((.((((((.....((....)).....))))))....))....))))))...................((((...........))))....)).))))))))).....))))))..)))))) (-41.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACACUCGCCUCCAGAAAUUUCCUAUCACUAGUGUAGCAAGGAUAAGAGGCUAAGUCAAUAAAAGAUGGACUAUUCGAAAAACUUUAGAAAUAUUUUAGAAUUACUUGAAGGAUAUUUGAGAAUCGAACUUUAAAAUAGAAAGAAAUAAGAAAUGCAUGUGCUAUAAAAAGGAGGCUCAAUAUGUUUAAAAUUUUUUGCAAAAUCGUUUUUAAAAGUAUUACUUUCGCCCUUGAGGGCUAAGGAAAAAAGGAGAAUCGC .....(((((((((.((.........))..(((..(((((.......(((....((((.((.....)).)))).)))......((((.....((((((((((((.((..((.....))..))))).....))))))))).))))..........))).))..)))......))))))..(((((.(((((((....((....))....))))))).))))).((((.((((....)))).)))).......)))...... (-44.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 868 50 1 141 92 NC_009009:SSA_0400|5end_hypothetical_protein_398251..398481_NEGATIVE 346 239 191 140 88 NC_009009:SSA_0248|5end_hypothetical_protein_241360..241590_POSITIVE 325 123 82 169 119 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 319 177 131 177 132 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 307 247 201 172 127 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 300 246 205 228 179 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 295 34 3 225 184 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 294 177 140 181 144 NC_009009:SSA_0407|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_403843..404073_NEGATIVE 290 140 96 127 85 NC_009009:SSA_1964|5end_conserved_uncharacterized_protein_1961211..1961441_NEGATIVE 289 125 84 118 73 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 288 260 211 152 97 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 282 259 213 148 93 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 272 224 181 196 150 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 271 46 1 182 131 NC_009009:SSA_2365|5end_Cobalt_transport_protein_cbiQ,_putative_2368037..2368267_NEGATIVE 269 41 5 104 71 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 266 44 23 66 45 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 262 225 181 136 75 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 262 260 212 228 192 NC_009009:SSA_0432|5end_Formate--tetrahydrofolate_ligase,_putative_434991..435221_NEGATIVE 261 250 205 187 138 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 260 247 208 121 84 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 232 191 148 103 NC_009009:SSA_0247|3end_hypothetical_protein_241455..241605_POSITIVE 297 193 151 50 6 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 294 256 211 126 88 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 283 44 1 146 102 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 282 259 213 145 90 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 269 41 5 131 98 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 266 44 23 73 52 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 262 225 181 139 78 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 261 250 205 147 98 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 260 247 208 124 87 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 260 260 213 77 23 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 256 46 2 96 60 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 256 35 1 48 16 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 255 260 227 145 115 NC_009009:SSA_0561|3end_RNA:NAD_2'-phosphotransferase,_putative_554255..554405_POSITIVE 252 234 200 97 55 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 252 36 4 150 117 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 249 249 204 143 90 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 247 246 201 68 24 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 247 43 2 142 95 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 247 249 203 67 18 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE