Origin IGS: agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga .........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 tcaaaactcctctaacctcttatatgataattcattataacacaaaacaagatttttaacatccttaaactctctaaacgttcgtaaatatctctatttttaagaattttagagccctttcttaaattttatatggctttatagtttgaaactatagtaaatcttcgtttttaccaaaaatttatcacttttattttacttaccgtttatttttgtgtacaatagtgct Mask Tandem Repeat Region ================================================ agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Find is-nt database================================================ Query_seq: SMT_1632:SMT_1633|SMT_1632:SMT_1633:hypothetical protein:formate--tetrahydrofolate ligase:<-->:1619151..1619379 229 agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1632:SMT_1633|SMT_1632:SMT_1633:hypothetical protein:formate--tetrahydrofolate ligase:<-->:1619151..1619379 229 agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1632:SMT_1633|SMT_1632:SMT_1633:hypothetical protein:formate--tetrahydrofolate ligase:<-->:1619151..1619379 229 agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 123 End: 215 .......................................................................................................................... M L K N R D I Y E R L E S L R M L K I L F C V I M N Y H I R G .............. agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga 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: 85 Start: 7 End: 36 ......TTTTACTTACCGTTTATTTTTGTGTACAAT................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 167 End: 196 ......................................................................................................................................................................GATGTTAAAAATCTTGTTTTGTGTTATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1632:SMT_1633|SMT_1632:SMT_1633:hypothetical protein:formate--tetrahydrofolate ligase:<-->:1619151..1619379 229 agcactattgtacacaaaaataaacggtaagtaaaataaaagtgataaatttttggtaaaaacgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Intra-Species Hit: Count: 1 Min: 63 Max: 229 Len: 167 Subject: smit_SMT_1632_SMT_1633|hypothetical protein:formate--tetrahydrofolate ligase|NEGATIVE:POSITIVE|[1619151,1619379]|229 HSP 1 e-value: 6.0E-90 bit: 331.0 Len: 167 Query Start:63 Query End:229 Subject Strand: POSITIVE Subject Start: 63 Subject End: 229 ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga Inter-species Hit: Count: 3 Min: 63 Max: 229 Len: 167 Subject: NC_003028_SP_1229_SP_1230|formate--tetrahydrofolate ligase:hypothetical protein|NEGATIVE:POSITIVE|[1163389,1163617]|229 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 167 Query Start:63 Query End:229 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 167 ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga ..............................................................cgaagatttattatagtttcaaactataaagccatataaaatttaagaaaggactctaaaagtcttaaaaacagagatatttacgaacgtttagagagttttaggatgttaaaaatcttgttttgtgatataatgaattatcatataagaggttagaggaattttga Subject: NC_008533_SPD_1087_SPD_1088|formate--tetrahydrofolate ligase:phosphopantothenate--cysteine ligase|NEGATIVE:POSITIVE|[1119069,1119297]|229 HSP 1 e-value: 2.0E-68 bit: 260.0 Len: 167 Query Start:63 Query End:229 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 167 ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaaggattctaaaagccttaaaaacagagatatttacgaacgtttagagggttttaggatgttaaaaatcttgttttgtgatataatgaattatcatataagaggttagaggaattttga Subject: NC_003098_spr1109_spr1110|Formate--tetrahydrofolate ligase:hypothetical protein|NEGATIVE:POSITIVE|[1111538,1111751]|214 HSP 1 e-value: 2.0E-68 bit: 260.0 Len: 167 Query Start:63 Query End:229 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 167 ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaagggctctaaaattcttaaaaatagagatatttacgaacgtttagagagtttaaggatgttaaaaatcttgttttgtgttataatgaattatcatataagaggttagaggagttttga ..............................................................cgaagatttactatagtttcaaactataaagccatataaaatttaagaaaggattctaaaagccttaaaaacagagatatttacgaacgtttagagggttttaggatgttaaaaatcttgttttgtgatataatgaattatcatataagaggttagaggaattttga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAGAUUUACUAUAGUUUCAAACUAUAAAGCCAUAUAAAAUUUAAGAAAGGGCUCUAAAAUUCUUAAAAAUAGAGAUAUUUACGAACGUUUAGAGAGUUUAAGGAUGUUAAAAAUCUUGUUUUGUGUUAUAAUGAAUUAUCAUAUAAGAGGUUAGAGGAGUUUUGA ...........((((((.....)))))).((((..................)))).((((((((((.........(((((((..((((.........))))..)))))))...((((((....((((.((........)).))))...))))))..)))))))))). (-23.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAACUCCUCUAACCUCUUAUAUGAUAAUUCAUUAUAACACAAAACAAGAUUUUUAACAUCCUUAAACUCUCUAAACGUUCGUAAAUAUCUCUAUUUUUAAGAAUUUUAGAGCCCUUUCUUAAAUUUUAUAUGGCUUUAUAGUUUGAAACUAUAGUAAAUCUUCG ...................((((((((....))).)))))........(((((((................(((((((.((((..(((((....)))))....))))))))))).................(((((.((((.....)))).)))))..))))))).. (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 718 60 11 213 164 smit:SMT_1632|5end_hypothetical_protein_1619060..1619290_NEGATIVE 217 127 82 52 4 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 215 130 81 185 136 smit:SMT_1989|5end_multimodular_transpeptidase-transglycosylase_1917607..1917837_NEGATIVE 213 137 91 190 146 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 211 125 89 172 140 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 205 58 20 69 38 smit:SMT_879|5end_hypothetical_protein_826989..827219_NEGATIVE 202 58 11 139 109 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 183 57 16 47 18 smit:SMT_551|5end_K07170_GAF_domain-containing_protein_468948..469178_POSITIVE 183 125 81 171 124 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 182 110 75 171 137 smit:SMT_2091|5end_hypothetical_protein_1986235..1986465_POSITIVE 182 87 41 230 181 smit:SMT_1822|5end_hypothetical_protein_1794452..1794682_POSITIVE 180 158 114 150 100 smit:SMT_1072|5end_Cof_family_protein_1011193..1011423_NEGATIVE 179 160 117 183 144 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 179 160 113 161 121 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 177 84 49 154 122 smit:SMT_1861|5end_sucrose_operon_repressor_(SCR_operon_regulatory_protein)_1823713..1823943_POSITIVE 176 96 69 87 52 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 176 130 87 218 173 smit:SMT_1283|5end_K02240_competence_protein_ComFA_1245667..1245897_POSITIVE 175 111 72 230 193 smit:SMT_710|5end_hypothetical_protein_predicted_by_Glimmer/Critica_619320..619550_NEGATIVE 171 155 120 90 58 smit:SMT_2105|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1996458..1996688_POSITIVE 171 55 13 101 72 smit:SMT_1482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1463111..1463341_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 99 51 108 56 smit:SMT_964|3end_cadmium_resistance_transporter,_putative_909891..910041_NEGATIVE 217 127 82 55 7 smit:SMT_1185|3end_beta-galactosidase_1142034..1142184_NEGATIVE 195 119 72 70 26 smit:SMT_711|3end_choline_kinase_619487..619637_NEGATIVE 184 127 82 95 32 smit:SMT_838|3end_cation_efflux_family_protein_784203..784353_POSITIVE 176 96 69 90 55 smit:SMT_2076|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1978482..1978632_NEGATIVE 171 55 13 72 43 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 171 55 13 151 122 smit:SMT_1482|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1463061..1463211_NEGATIVE 170 56 19 46 12 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 170 56 19 46 12 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 169 56 15 53 6 smit:SMT_1591|3end_DNA-entry_nuclease_1579468..1579618_POSITIVE 169 156 117 75 19 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 169 66 31 116 70 smit:SMT_556|3end_putative_aminotransferase_474850..475000_POSITIVE 169 108 61 79 37 smit:SMT_150|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_99400..99550_POSITIVE 165 119 73 91 36 smit:SMT_1237|3end_transposase,_TnpA_1198631..1198781_POSITIVE 164 77 31 61 17 smit:SMT_1016|3end_alcohol_dehydrogenase,_zinc-containing_953057..953207_NEGATIVE 164 79 45 105 69 smit:SMT_724|3end_hypothetical_protein_629770..629920_NEGATIVE 164 126 93 91 62 smit:SMT_595|3end_phosphoglycerate_mutase_511976..512126_NEGATIVE 163 129 91 54 23 smit:SMT_1810|3end_hypothetical_protein_1785598..1785748_POSITIVE 163 112 73 122 74 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 163 53 18 57 23 smit:SMT_515|3end_hypothetical_protein_442526..442676_POSITIVE