Origin IGS: tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag .........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 cttatttctccttttctttacttaactatttaatcatctttatgataaaaaatcaactgttgctacttttggctaatattctaactaccaaaacaaggtggacataaaaataaaaatgttcggtttttttcagtgtatccatgaaataaaaagtgatacatgttataataaagttagctctttaatggaggtgtttga Mask Tandem Repeat Region ================================================ tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Find is-nt database================================================ Query_seq: SMT_1510:SMT_1511|SMT_1510:SMT_1511:ribose 5-phosphate isomerase:hypothetical protein:<-->:1493579..1493776 198 tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1510:SMT_1511|SMT_1510:SMT_1511:ribose 5-phosphate isomerase:hypothetical protein:<-->:1493579..1493776 198 tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1510:SMT_1511|SMT_1510:SMT_1511:ribose 5-phosphate isomerase:hypothetical protein:<-->:1493579..1493776 198 tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 30 End: 143 ............................. M I T C I T F Y F M D T L K K T E H F Y F Y V H L V L V V R I L A K S S N S ....................................................... Protein_Len: 33 Strand: - Start: 3 End: 101 .. F V E M L S S V K N Y C T D S K I E H I C Q F F G F M K I K I D M ................................................................................................. tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag 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: 30 End: 59 .............................CATGAAATAAAAAGTGATACATGTTATAAT........................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1510:SMT_1511|SMT_1510:SMT_1511:ribose 5-phosphate isomerase:hypothetical protein:<-->:1493579..1493776 198 tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: smit_SMT_1510_SMT_1511|ribose 5-phosphate isomerase:hypothetical protein|NEGATIVE:POSITIVE|[1493579,1493776]|198 HSP 1 e-value: 6.0E-96 bit: 351.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgnnnnnnnccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag tcaaacacctccattaaagagctaactttattataacatgtatcactttttatttcatggatacactgaaaaaaaccgaacatttttatttttatgtccaccttgttttggtagttagaatattagccaaaagtagcaacagttgattttttatcataaagatgattaaatagttaagtaaagaaaaggagaaataag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAACACCUCCAUUAAAGAGCUAACUUUAUUAUAACAUGUAUCACUUUUUAUUUCAUGGAUACACUGAAAAAAACCGAACAUUUUUAUUUUUAUGUCCACCUUGUUUUGGUAGUUAGAAUAUUAGCCAAAAGUAGCAACAGUUGAUUUUUUAUCAUAAAGAUGAUUAAAUAGUUAAGUAAAGAAAAGGAGAAAUAAG ........((((..((......)).(((((((.((((.((((((.(............)))))))....................(((((((((((.........((((((((((......))).))))))).((((....)))).........))))))))))).......)))))))))))....))))....... (-28.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUUCUCCUUUUCUUUACUUAACUAUUUAAUCAUCUUUAUGAUAAAAAAUCAACUGUUGCUACUUUUGGCUAAUAUUCUAACUACCAAAACAAGGUGGACAUAAAAAUAAAAAUGUUCGGUUUUUUUCAGUGUAUCCAUGAAAUAAAAAGUGAUACAUGUUAUAAUAAAGUUAGCUCUUUAAUGGAGGUGUUUGA (..((.(((((......((((((...(((((...........(((.(((((((((((....((((....))))...........(((((.......)))))................))).)))))))))))...........)))))..))))))............(((((......)))))..))))).))..). (-29.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 800 140 91 231 182 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 291 121 81 128 89 smit:SMT_1466|5end_endopeptidase_O_1446962..1447192_POSITIVE 279 50 8 126 85 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 261 129 87 231 191 smit:SMT_1732|5end_transcriptional_repressor_protein,_putative_1716451..1716681_POSITIVE 245 144 103 163 121 smit:SMT_1002|5end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B_943627..943857_POSITIVE 240 139 91 161 103 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 235 130 94 91 54 smit:SMT_1969|5end_transcription-repair_coupling_factor_1901691..1901921_NEGATIVE 231 109 61 110 61 smit:SMT_1231|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1192622..1192852_POSITIVE 225 109 64 185 143 smit:SMT_1699|5end_purine_operon_repressor_1681138..1681368_POSITIVE 222 137 91 131 87 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 221 136 96 204 156 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 221 130 84 55 19 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 221 143 109 196 163 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 221 140 98 213 170 smit:SMT_242|5end_PTS_system,_mannose-specific_IID_component_180074..180304_NEGATIVE 221 139 91 136 87 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 220 116 76 115 65 smit:SMT_1878|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836577..1836807_NEGATIVE 218 129 82 130 84 smit:SMT_357|5end_tRNA_(guanine-N7-)-methyltransferase_293185..293415_POSITIVE 216 138 91 223 168 smit:SMT_983|5end_GTP_pyrophosphokinase_930304..930534_NEGATIVE 215 108 76 108 73 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 214 44 6 58 22 smit:SMT_2153|5end_putative_cell_division_protein_2026905..2027135_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 109 64 80 38 smit:SMT_1698|3end_CMP-binding_factor_1681113..1681263_POSITIVE 222 137 91 106 62 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 220 116 76 125 75 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 218 129 82 133 87 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 215 108 76 111 76 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 214 44 6 40 4 smit:SMT_2152|3end_cell_division_protein_2026967..2027117_POSITIVE 214 44 6 40 4 smit:SMT_2138|3end_cell_division_protein_FtsA_2017145..2017295_POSITIVE 214 44 6 40 4 smit:SMT_2136|3end_cell_division_protein_FtsA_2015859..2016009_POSITIVE 214 44 6 40 4 smit:SMT_2128|3end_cell_division_protein_FtsA_2010152..2010302_POSITIVE 214 44 6 40 4 smit:SMT_1547|3end_cell_division_protein_FtsA_1532446..1532596_POSITIVE 211 129 95 49 12 smit:SMT_216|3end_Holliday_junction_DNA_helicase_RuvB_149335..149485_POSITIVE 210 135 94 51 15 smit:SMT_1610|3end_tyrosine_recombinase_1599385..1599535_POSITIVE 210 155 125 90 52 smit:SMT_297|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_240606..240756_POSITIVE 205 144 102 78 33 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 205 137 95 150 100 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 203 137 95 41 2 smit:SMT_324|3end_K02029_polar_amino_acid_transport_system_permease_protein_261912..262062_NEGATIVE 200 128 92 96 57 smit:SMT_1681|3end_D-alanine-activating_enzyme_1665052..1665202_POSITIVE 199 149 101 82 22 smit:SMT_1024|3end_transcriptional_regulator,_MarR_family_958961..959111_NEGATIVE 199 146 106 41 8 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 198 144 110 59 16 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE