Origin IGS: gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttgtactgtttctattataccattttcaagggattttgaaagatggaatccagttttcactgacaaaaactataactcacttctaaagagttaatctctgattgacctctaaaattaaaagttgtataattctgaccggaggaataatc Mask Tandem Repeat Region ================================================ gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Find is-nt database================================================ Query_seq: SSA_0288:SSA_0289|SSA_0288:SSA_0289:hypothetical protein:Leucyl-tRNA synthetase, putative:<-->:281394..281545 152 gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0288:SSA_0289|SSA_0288:SSA_0289:hypothetical protein:Leucyl-tRNA synthetase, putative:<-->:281394..281545 152 gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0288:SSA_0289|SSA_0288:SSA_0289:hypothetical protein:Leucyl-tRNA synthetase, putative:<-->:281394..281545 152 gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Predict ORF larger than 30AA ================================================ gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa 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: 89 Start: 20 End: 49 ...................ATTGACCTCTAAAATTAAAAGTTGTATAAT....................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 107 End: 136 ..........................................................................................................TCTTTCAAAATCCCTTGAAAATGGTATAAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -3.2 Tail_Score: -2.78463 Start: 104 End: 130 Full_Region: AGTGAAAACTGGATT CCATCTTTCAA AATCCC TTGAAAATGG TATAATAGAAACAGT .......................................................................................................CCATCTTTCAAAATCCCTTGAAAATGG...................... Find igs database================================================ Query_seq: SSA_0288:SSA_0289|SSA_0288:SSA_0289:hypothetical protein:Leucyl-tRNA synthetase, putative:<-->:281394..281545 152 gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_009009_SSA_0288_SSA_0289|hypothetical protein:Leucyl-tRNA synthetase, putative|NEGATIVE:POSITIVE|[281394,281545]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa gattattcctccggtcagaattatacaacttttaattttagaggtcaatcagagattaactctttagaagtgagttatagtttttgtcagtgaaaactggattccatctttcaaaatcccttgaaaatggtataatagaaacagtacaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAUUCCUCCGGUCAGAAUUAUACAACUUUUAAUUUUAGAGGUCAAUCAGAGAUUAACUCUUUAGAAGUGAGUUAUAGUUUUUGUCAGUGAAAACUGGAUUCCAUCUUUCAAAAUCCCUUGAAAAUGGUAUAAUAGAAACAGUACAAAAA ((((...((((.....(((((((.........))))))).))))..))))......((((((.........))))))..((((((((((((....))))....((((.((((((......))))))))))....)))))))).......... (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUGUACUGUUUCUAUUAUACCAUUUUCAAGGGAUUUUGAAAGAUGGAAUCCAGUUUUCACUGACAAAAACUAUAACUCACUUCUAAAGAGUUAAUCUCUGAUUGACCUCUAAAAUUAAAAGUUGUAUAAUUCUGACCGGAGGAAUAAUC .........((((((.......(((((((((((....)))).)))))))..(((.(((......)))......(((((((.........((((((((((...)))))).)))).........)))))))...........)))))))))... (-24.67) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 798 90 41 181 132 NC_009009:SSA_0288|5end_hypothetical_protein_281303..281533_NEGATIVE 260 100 53 157 107 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 250 122 82 207 160 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 247 130 85 165 121 NC_009009:SSA_0738|5end_Ornithine_carbamoyltransferase,_catabolic,_putative_719904..720134_POSITIVE 246 42 3 88 46 NC_009009:SSA_2010|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_2012024..2012254_NEGATIVE 245 139 91 222 176 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 239 129 84 52 7 NC_009009:SSA_0408|5end_hypothetical_protein_404684..404914_NEGATIVE 238 148 102 115 70 NC_009009:SSA_1134|5end_Xanthine_phosphoribosyltransferase,_putative_1159628..1159858_POSITIVE 233 100 57 142 96 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 232 91 51 165 130 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 231 74 32 135 93 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 231 106 65 134 91 NC_009009:SSA_1397|5end_hypothetical_protein_1410589..1410819_POSITIVE 223 69 29 118 67 NC_009009:SSA_0443|5end_Possible_ABC-type_efflux_pump_permease_component,_putative_442877..443107_POSITIVE 223 106 69 53 16 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 221 135 102 133 92 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 220 92 51 184 141 NC_009009:SSA_1781|5end_hypothetical_protein_1767605..1767835_NEGATIVE 214 100 51 178 128 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 213 79 37 92 45 NC_009009:SSA_2367|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2369732..2369962_NEGATIVE 213 119 71 102 60 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 211 109 77 62 30 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 100 53 143 93 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 247 130 85 114 70 NC_009009:SSA_0737|3end_Arginine_deiminase,_putative_719933..720083_POSITIVE 246 42 3 95 53 NC_009009:SSA_2011|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012017..2012167_NEGATIVE 242 108 61 102 55 NC_009009:SSA_0252|3end_hypothetical_protein_245042..245192_NEGATIVE 238 148 102 72 27 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 236 106 67 66 30 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 231 106 61 89 45 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 228 89 45 57 1 NC_009009:SSA_0503|3end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503102..503252_POSITIVE 228 99 51 48 1 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 223 106 69 51 14 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 220 119 71 100 51 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 216 80 40 133 94 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 216 88 43 81 34 NC_009009:SSA_0998|3end_hypothetical_protein_998758..998908_POSITIVE 215 80 37 149 106 NC_009009:SSA_1853|3end_S-ribosylhomocysteine_lyase,_putative_1849360..1849510_POSITIVE 214 100 51 135 78 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 213 79 37 141 94 NC_009009:SSA_2368|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase,_putative_2369683..2369833_NEGATIVE 213 119 71 112 70 NC_009009:SSA_0692|3end_D-Ala-D-Ala_adding_enzyme,_putative_677820..677970_POSITIVE 212 91 54 147 115 NC_009009:SSA_1725|3end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1710993..1711143_NEGATIVE 211 109 77 69 37 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 209 120 77 57 14 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE