Origin IGS: taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata .........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 tattctaaacatctccttaattttattcagggatttccccagttatttcaattttatcacttttgaaaagctttgtcacggatatacatttcagttcttgatgtaaacgttttagtggttttagatgtctgaaatatagcggacattatggtataatatagttaattactaatagtgaaatgaggcatttatta Mask Tandem Repeat Region ================================================ taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Find is-nt database================================================ Query_seq: SMT_647:SMT_648|SMT_647:SMT_648:DNA gyrase, A subunit:L-lactate dehydrogenase:<-->:554261..554454 194 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_647:SMT_648|SMT_647:SMT_648:DNA gyrase, A subunit:L-lactate dehydrogenase:<-->:554261..554454 194 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_647:SMT_648|SMT_647:SMT_648:DNA gyrase, A subunit:L-lactate dehydrogenase:<-->:554261..554454 194 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 46 End: 135 ............................................. M M S A I F Q T S K T T K T F T S R T E M Y I R D K A F Q K ........................................................... Protein_Len: 34 Strand: - Start: 92 End: 193 ........................................................................................... M L F Q F T Y G H C L K E F T I F N F Y S P F D R F L I L S I N L M . taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata 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: 86 Start: 38 End: 67 .....................................TCTGAAATATAGCGGACATTATGGTATAAT............................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 115 End: 144 ..................................................................................................................CGTGACAAAGCTTTTCAAAAGTGATAAAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_647:SMT_648|SMT_647:SMT_648:DNA gyrase, A subunit:L-lactate dehydrogenase:<-->:554261..554454 194 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: smit_SMT_647_SMT_648|DNA gyrase, A subunit:L-lactate dehydrogenase|NEGATIVE:POSITIVE|[554261,554454]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataactggggaaatccctgaataaaattaaggagatgtttagaata Inter-species Hit: Count: 3 Min: 1 Max: 189 Len: 189 Subject: NC_008533_SPD_1077_SPD_1078|DNA gyrase, A subunit:L-lactate dehydrogenase|NEGATIVE:POSITIVE|[1105463,1105655]|193 HSP 1 e-value: 1.0E-22 bit: 107.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataact-ggggaaatccctgaataaaattaaggagatgttta..... taataaatgcctcatttcacaattagtaagtaacaacattataccataaattcccatctatttcag-cctct-aaaccactaaaacgtttacatcgagaactataaggcatattcgtgacaaagttttttaaaagtgatagaatgaagttgtctagggaaaatcccctaataaaattaaggagatgttta..... Subject: NC_003098_spr1099_spr1100|DNA gyrase subunit A:L-lactate dehydrogenase|NEGATIVE:POSITIVE|[1097932,1098124]|193 HSP 1 e-value: 1.0E-22 bit: 107.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataact-ggggaaatccctgaataaaattaaggagatgttta..... taataaatgcctcatttcacaattagtaagtaacaacattataccataaattcccatctatttcag-cctct-aaaccactaaaacgtttacatcgagaactataaggcatattcgtgacaaagttttttaaaagtgatagaatgaagttgtctagggaaaatcccctaataaaattaaggagatgttta..... Subject: NC_003028_SP_1219_SP_1220|DNA gyrase subunit A:L-lactate dehydrogenase|NEGATIVE:POSITIVE|[1149859,1150051]|193 HSP 1 e-value: 1.0E-22 bit: 107.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 taataaatgcctcatttcactattagtaattaactatattataccataatgtccgctatatttcagacatctaaaaccactaaaacgtttacatcaagaactgaaatgtatatccgtgacaaagcttttcaaaagtgataaaattgaaataact-ggggaaatccctgaataaaattaaggagatgttta..... taataaatgcctcatttcacaattagtaagtaacaacattataccataaattcccatctatttcag-cctct-aaaccactaaaacgtttacatcgagaactataaggcatattcgtgacaaagttttttaaaagtgatagaatgaagttgtctagggaaaatcccctaataaaattaaggagatgttta..... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAUGCCUCAUUUCACUAUUAGUAAUUAACUAUAUUAUACCAUAAUGUCCGCUAUAUUUCAGACAUCUAAAACCACUAAAACGUUUACAUCAAGAACUGAAAUGUAUAUCCGUGACAAAGCUUUUCAAAAGUGAUAAAAUUGAAAUAACUGGGGAAAUCCCUGAAUAAAAUUAAGGAGAUGUUUA ...(((((..(((...(((((..((((.....)))).............((((((.((((((((((...(((........................))).))))))))))....)).))))............)))))................((((....)))).............)))..))))) (-29.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAUCUCCUUAAUUUUAUUCAGGGAUUUCCCCAGUUAUUUCAAUUUUAUCACUUUUGAAAAGCUUUGUCACGGAUAUACAUUUCAGUUCUUGAUGUAAACGUUUUAGUGGUUUUAGAUGUCUGAAAUAUAGCGGACAUUAUGGUAUAAUAUAGUUAAUUACUAAUAGUGAAAUGAGGCAUUUAUUA ........................(((.....))).....((((((...........)))))).(((((.((((...(((((...(((.(....((((....))))..).))).....((((((((........))))))))...)))))...((((.....))))...))))...)))))........ (-32.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 100 51 191 142 smit:SMT_647|5end_DNA_gyrase,_A_subunit_554170..554400_NEGATIVE 220 146 119 57 30 smit:SMT_566|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_483498..483728_POSITIVE 219 48 11 131 94 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 219 89 41 231 177 smit:SMT_220|5end_Hypothetical_zinc_metalloprotease_151747..151977_POSITIVE 212 130 92 83 52 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 212 138 91 171 126 smit:SMT_1422|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1407467..1407697_NEGATIVE 208 158 118 50 16 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 205 120 74 54 12 smit:SMT_1324|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1293801..1294031_POSITIVE 201 90 49 182 144 smit:SMT_320|5end_alcohol_dehydrogenase,_zinc-containing_259492..259722_NEGATIVE 200 130 87 42 7 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 200 65 37 196 173 smit:SMT_666|5end_GTP_pyrophosphokinase-like_protein_577400..577630_NEGATIVE 198 90 41 67 9 smit:SMT_1876|5end_transcriptional_regulator,_MarR_family_1833594..1833824_POSITIVE 198 172 139 64 23 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 197 84 41 87 38 smit:SMT_1150|5end_hypothetical_protein_1094803..1095033_NEGATIVE 197 138 112 30 4 smit:SMT_1097|5end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1041369..1041599_NEGATIVE 196 90 41 209 156 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 195 96 54 141 85 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 195 131 92 208 170 smit:SMT_1278|5end_30S_ribosomal_protein_S2_1241473..1241703_POSITIVE 194 87 43 61 12 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 193 180 149 38 3 smit:SMT_789|5end_hypothetical_protein_701072..701302_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 48 11 114 77 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 212 130 92 45 14 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 201 90 42 71 3 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 198 172 139 55 14 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 197 126 85 72 42 smit:SMT_151|3end_K02073_D-methionine_transport_system_substrate-binding_protein_100393..100543_POSITIVE 190 58 11 61 8 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 189 104 61 77 35 smit:SMT_1302|3end_hypothetical_protein_1264649..1264799_POSITIVE 188 85 44 54 1 smit:SMT_2135|3end_dipeptidase_2014754..2014904_NEGATIVE 188 85 44 54 1 smit:SMT_874|3end_dipeptidase_821365..821515_NEGATIVE 184 110 65 130 83 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 183 138 94 99 57 smit:SMT_889|3end_K02029_polar_amino_acid_transport_system_permease_protein_837023..837173_POSITIVE 181 159 113 142 98 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 181 166 134 83 55 smit:SMT_135|3end_hypothetical_protein_86178..86328_NEGATIVE 180 56 14 132 81 smit:SMT_1992|3end_carboxynorspermidine_decarboxylase_1918557..1918707_NEGATIVE 180 165 121 72 30 smit:SMT_1081|3end_K06901_putative_MFS_transporter,_AGZA_family,_xanthine/uracil_permease_1018595..1018745_NEGATIVE 178 125 85 44 6 smit:SMT_1827|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1797722..1797872_POSITIVE 178 121 83 63 26 smit:SMT_609|3end_laminin-binding_surface_protein_521731..521881_POSITIVE 175 126 87 97 65 smit:SMT_733|3end_hypothetical_protein_639412..639562_NEGATIVE 173 159 112 151 106 smit:SMT_859|3end_K02086_DNA_replication_protein_803381..803531_NEGATIVE 173 89 46 120 75 smit:SMT_786|3end_hypothetical_protein_697239..697389_NEGATIVE