Origin IGS: ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgagaaccgtgtgtgaagatgatgatgaccttactacttataaatcgcattgaaagaaaaatattgttttctgacttaatttttgttcgaaaatcggattgctacaaatttatttatatatttgtcccgtgtttttaatcttaactgttttgtatactgagag Mask Tandem Repeat Region ================================================ ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Find is-nt database================================================ Query_seq: TF1953:TF1954|TF1953:TF1954:methlytransferase, possible UbiE/COQ5 family:long-chain-fatty-acid--CoA ligase:->->:2104933..2105095 163 ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1953:TF1954|TF1953:TF1954:methlytransferase, possible UbiE/COQ5 family:long-chain-fatty-acid--CoA ligase:->->:2104933..2105095 163 ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1953:TF1954|TF1953:TF1954:methlytransferase, possible UbiE/COQ5 family:long-chain-fatty-acid--CoA ligase:->->:2104933..2105095 163 ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 29 End: 151 ............................ F C P V F I Y I F K Y C D S K R V F I L D S F L I K R E I R N I L L L T M M M K M ............ ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1953:TF1954|TF1953:TF1954:methlytransferase, possible UbiE/COQ5 family:long-chain-fatty-acid--CoA ligase:->->:2104933..2105095 163 ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: tfor_TF1953_TF1954|methlytransferase, possible UbiE/COQ5 family:long-chain-fatty-acid--CoA ligase|POSITIVE:POSITIVE|[2104933,2105095]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg ctctcagtatacaaaacagttaagattaaaaacacgggacaaatatataaataaatttgtagcaatccgattttcgaacaaaaattaagtcagaaaacaatatttttctttcaatgcgatttataagtagtaaggtcatcatcatcttcacacacggttctcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCAGUAUACAAAACAGUUAAGAUUAAAAACACGGGACAAAUAUAUAAAUAAAUUUGUAGCAAUCCGAUUUUCGAACAAAAAUUAAGUCAGAAAACAAUAUUUUUCUUUCAAUGCGAUUUAUAAGUAGUAAGGUCAUCAUCAUCUUCACACACGGUUCUCG ..................................((((((((((.((....)).)))))).....))))......((((......((((((((((((......))))))........))))))...((.(((((((.......))))).))))...))))... (-15.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAGAACCGUGUGUGAAGAUGAUGAUGACCUUACUACUUAUAAAUCGCAUUGAAAGAAAAAUAUUGUUUUCUGACUUAAUUUUUGUUCGAAAAUCGGAUUGCUACAAAUUUAUUUAUAUAUUUGUCCCGUGUUUUUAAUCUUAACUGUUUUGUAUACUGAGAG ........(((((..((((((.((((.................))))))))..(((((((((((.((..(((((.....(((((....))))))))))..)).((((((.((....)).))))))...)))))))...))))......))..)))))...... (-18.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 79 33 135 89 tfor:TF3018|5end_polyphosphate_kinase_3240122..3240352_POSITIVE 242 160 116 216 172 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 238 135 97 228 187 tfor:TF2242|5end_hypothetical_protein_2416947..2417177_POSITIVE 235 159 111 231 184 tfor:TF1291|5end_response_regulator_(fimR__protein)_1371959..1372189_POSITIVE 234 100 52 207 159 tfor:TF2542|5end_DNA_topoisomerase_III_2725544..2725774_POSITIVE 231 76 31 195 155 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 222 159 113 181 125 tfor:TF0054|5end_possible_flavodoxin_57817..58047_POSITIVE 220 157 117 34 2 tfor:TF2281|5end_hypothetical_protein_2439574..2439804_POSITIVE 216 80 33 220 171 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 214 160 111 156 108 tfor:TF0308|5end_hypothetical_protein_333745..333975_POSITIVE 211 102 61 65 18 tfor:TF1692|5end_conserved_hypothetical_protein;_possible_mobilizable_transposon,_TnpC_1810687..1810917_POSITIVE 210 157 111 203 152 tfor:TF2583|5end_possible_ABC_transporter,__permease_component_2750206..2750436_POSITIVE 209 149 106 99 56 tfor:TF2154|5end_conserved_hypothetical_protein_2329153..2329383_POSITIVE 208 80 36 143 96 tfor:TF1771|5end_prolipoprotein_diacylglyceryl_transferase_1909562..1909792_POSITIVE 206 158 133 31 8 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 206 149 101 153 113 tfor:TF1758|5end_conserved_hypothetical_protein_1894769..1894999_POSITIVE 206 75 33 89 34 tfor:TF1140|5end_transcriptional_regulator,_AraC_family_1216855..1217085_POSITIVE 205 146 114 41 12 tfor:TF1246|5end_protease,_with_chaperone_function_1329390..1329620_POSITIVE 204 77 31 206 166 tfor:TF0676|5end_methyltransferase_719027..719257_POSITIVE 202 160 113 158 104 tfor:TF2758|5end_hypothetical_protein_2942392..2942622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 97 55 74 25 tfor:TF2923|3end_hypothetical_protein_3122403..3122553_POSITIVE 222 159 113 136 80 tfor:TF0052|3end_hypothetical_protein_57852..58002_POSITIVE 222 159 113 70 14 tfor:TF0053|3end_hypothetical_protein_57786..57936_POSITIVE 214 160 111 81 33 tfor:TF0307|3end_conserved_hypothetical_protein_333750..333900_POSITIVE 213 160 113 96 48 tfor:TF0258|3end_hypothetical_protein_289534..289684_POSITIVE 211 102 61 65 18 tfor:TF1691|3end_integrase_1810767..1810917_POSITIVE 208 80 36 140 93 tfor:TF2973|3end_transposase_3180181..3180331_POSITIVE 206 149 101 129 89 tfor:TF1757|3end_chromosome_partitioning_protein_1894825..1894975_POSITIVE 205 146 114 33 4 tfor:TF1245|3end_LemA_protein_1329462..1329612_POSITIVE 204 77 31 118 78 tfor:TF0675|3end_conserved_hypothetical_protein_719019..719169_POSITIVE 194 160 134 29 4 tfor:TF2842|3end_methyltransferase_3032872..3033022_POSITIVE 194 157 111 150 98 tfor:TF0120|3end_hexouronate_transporter_132811..132961_POSITIVE 193 57 11 74 22 tfor:TF0371|3end_beta-mannosidase_precursor_390469..390619_POSITIVE 192 150 104 124 75 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 189 160 126 120 74 tfor:TF1545|3end_conserved_hypothetical_protein_1651546..1651696_POSITIVE 189 145 103 92 41 tfor:TF0233|3end_DNA_polymerase_III_gamma/tau_subunit_260556..260706_POSITIVE 187 145 112 57 20 tfor:TF2618|3end_integral_membrane_protein,_possible_zinc_transporter_2796113..2796263_POSITIVE 187 160 116 107 56 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 187 160 116 97 46 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 187 145 105 107 63 tfor:TF1723|3end_alpha-rhamnosidase_1851332..1851482_POSITIVE