Origin IGS: aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttcctccggtatatatgtatcgcttgtgcttttcacaagatttttccatttaccattgtagcgctttttgcactatttttcaatcaaaaataaaagaagggcaccatatttgtacccttgcatcattcttttaaaaaatatt Mask Tandem Repeat Region ================================================ aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Find is-nt database================================================ Query_seq: SMT_106:SMT_107|SMT_106:SMT_107:hypothetical protein:ribose-phosphate pyrophosphokinase:->->:52397..52541 145 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_106:SMT_107|SMT_106:SMT_107:hypothetical protein:ribose-phosphate pyrophosphokinase:->->:52397..52541 145 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_106:SMT_107|SMT_106:SMT_107:hypothetical protein:ribose-phosphate pyrophosphokinase:->->:52397..52541 145 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 12 End: 128 ........... F F S A L T C I H H G E K I K S Q F I T C F A S C H Y I S F D Q S F C L R Y M ................. aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc 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: 88 Start: 59 End: 88 ..........................................................ATTGAAAAATAGTGCAAAAAGCGCTACAAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_106:SMT_107|SMT_106:SMT_107:hypothetical protein:ribose-phosphate pyrophosphokinase:->->:52397..52541 145 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: smit_SMT_106_SMT_107|hypothetical protein:ribose-phosphate pyrophosphokinase|POSITIVE:POSITIVE|[52397,52541]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Inter-species Hit: Count: 2 Min: 1 Max: 145 Len: 145 Subject: NC_008533_SPD_0032_SPD_0033|hypothetical protein:ribose-phosphate pyrophosphokinase|POSITIVE:POSITIVE|[28490,28633]|144 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc aatatttttcaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtagatgg-aaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc Subject: NC_003028_SP_0026_SP_0027|hypothetical protein:ribose-phosphate pyrophosphokinase|POSITIVE:POSITIVE|[28718,28861]|144 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 aatattttttaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtaaatggaaaaatcttgtgaaaagcacaagcgatacatatataccggaggaaatc aatatttttcaaaagaatgatgcaagggtacaaatatggtgcccttcttttatttttgattgaaaaatagtgcaaaaagcgctacaatggtagatgg-aaaatcttgtgaaaagcacaagttatacatatataccggaggaaatc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUUUUUUAAAAGAAUGAUGCAAGGGUACAAAUAUGGUGCCCUUCUUUUAUUUUUGAUUGAAAAAUAGUGCAAAAAGCGCUACAAUGGUAAAUGGAAAAAUCUUGUGAAAAGCACAAGCGAUACAUAUAUACCGGAGGAAAUC ..((((((((((((((((((...((((((((.......))))))))...))))))))..))))))))))((((.....))))..(..(((((.(((.......((((((.....)))))).......))).)))))..)...... (-37.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCCUCCGGUAUAUAUGUAUCGCUUGUGCUUUUCACAAGAUUUUUCCAUUUACCAUUGUAGCGCUUUUUGCACUAUUUUUCAAUCAAAAAUAAAAGAAGGGCACCAUAUUUGUACCCUUGCAUCAUUCUUUUAAAAAAUAUU ((((......((((...(((.....((((((.....)))))).......))).))))...((((.((.....)).)))).....)))).....(((((((((((.((.......)).))))........)))))))......... (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 108 67 231 191 smit:SMT_1588|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1577062..1577292_POSITIVE 242 52 22 197 161 smit:SMT_405|5end_zinc_metalloprotease_ZmpB,_truncated_333952..334182_POSITIVE 239 46 4 197 151 smit:SMT_2104|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_1995547..1995777_POSITIVE 226 57 11 159 108 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 226 126 81 48 3 smit:SMT_784|5end_hypothetical_protein_696298..696528_NEGATIVE 223 124 81 209 169 smit:SMT_1011|5end_xanthine_phosphoribosyltransferase_948831..949061_POSITIVE 220 50 18 82 54 smit:SMT_1977|5end_endopeptidase_O_1907832..1908062_POSITIVE 220 85 41 139 98 smit:SMT_694|5end_putative_ATP-binding_component_of_a_transport_system_604362..604592_POSITIVE 220 98 68 33 1 smit:SMT_238|5end_hypothetical_protein_predicted_by_Glimmer/Critica_177058..177288_NEGATIVE 220 109 67 180 129 smit:SMT_124|5end_hypothetical_protein_76654..76884_NEGATIVE 219 51 14 106 71 smit:SMT_1345|5end_K06198_competence_protein_CoiA_1323770..1324000_NEGATIVE 217 43 21 191 167 smit:SMT_2037|5end_lysine_decarboxylase_1948260..1948490_NEGATIVE 216 122 95 231 201 smit:SMT_1462|5end_phosphate_ABC_transporter,_ATP-binding_protein,_putative_1443140..1443370_POSITIVE 212 80 40 186 147 smit:SMT_1456|5end_pyrimidine-nucleoside_phosphorylase_1439832..1440062_NEGATIVE 209 111 72 57 18 smit:SMT_827|5end_hypothetical_protein_750389..750619_POSITIVE 208 47 13 65 29 smit:SMT_330|5end_membrane-associated_phospholipid_phosphatase_265793..266023_POSITIVE 207 60 13 188 142 smit:SMT_1676|5end_S4_domain_protein_1661764..1661994_NEGATIVE 207 60 13 188 142 smit:SMT_95|5end_S4_domain_protein_28177..28407_POSITIVE 206 69 22 131 75 smit:SMT_1760|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1735910..1736140_NEGATIVE 204 125 88 208 169 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 46 3 67 22 smit:SMT_106|3end_hypothetical_protein_52336..52486_POSITIVE 261 49 1 92 43 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 252 50 24 138 109 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 236 83 43 121 82 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE 227 60 13 129 57 smit:SMT_369|3end_hypothetical_cytosolic_protein_304487..304637_POSITIVE 226 57 11 88 37 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 223 124 81 59 19 smit:SMT_1010|3end_hypothetical_protein_948761..948911_POSITIVE 220 98 68 146 114 smit:SMT_238|3end_hypothetical_protein_predicted_by_Glimmer/Critica_176945..177095_NEGATIVE 220 109 67 117 66 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 217 67 30 52 11 smit:SMT_1346|3end_tellurite_resistance_protein_TehB_1323843..1323993_NEGATIVE 208 47 13 75 39 smit:SMT_329|3end_hypothetical_protein_265883..266033_POSITIVE 207 60 13 130 84 smit:SMT_2117|3end_transcription-repair_coupling_factor_2003907..2004057_NEGATIVE 207 60 13 130 84 smit:SMT_1969|3end_transcription-repair_coupling_factor_1900816..1900966_NEGATIVE 207 60 13 130 84 smit:SMT_1677|3end_transcription-repair_coupling_factor_1661822..1661972_NEGATIVE 207 60 13 130 84 smit:SMT_94|3end_transcription-repair_coupling_factor_28199..28349_POSITIVE 204 138 102 115 80 smit:SMT_1431|3end_K08986_putative_membrane_protein_1416654..1416804_POSITIVE 201 48 16 50 12 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 200 120 72 101 62 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 200 48 18 92 59 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 197 60 13 95 44 smit:SMT_1067|3end_alanine_racemase_1006952..1007102_POSITIVE