Origin IGS: atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatgtaactcctatttgttaatcttaaagttttatgattttatcacatagcaagtatagggtcaagatattttataaaatcttgtcaatccattttaaaaggcttgcttgacagaatcggaatttaccatataatatatctat Mask Tandem Repeat Region ================================================ atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Find is-nt database================================================ Query_seq: TDE0980:TDE0981|TDE0980:TDE0981:asparaginyl-tRNA synthetase:hypothetical protein:<-->:1005491..1005635 145 atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0980:TDE0981|TDE0980:TDE0981:asparaginyl-tRNA synthetase:hypothetical protein:<-->:1005491..1005635 145 atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0980:TDE0981|TDE0980:TDE0981:asparaginyl-tRNA synthetase:hypothetical protein:<-->:1005491..1005635 145 atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . L Y I I H Y I G I R D L L G K L I S Q C S K I F Y R S G I S A M ................................................ atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt 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: 78 End: 107 .............................................................................CTTGACCCTATACTTGCTATGTGATAAAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0980:TDE0981|TDE0980:TDE0981:asparaginyl-tRNA synthetase:hypothetical protein:<-->:1005491..1005635 145 atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE0980_TDE0981|asparaginyl-tRNA synthetase:hypothetical protein|NEGATIVE:POSITIVE|[1005491,1005635]|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 atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt atagatatattatatggtaaattccgattctgtcaagcaagccttttaaaatggattgacaagattttataaaatatcttgaccctatacttgctatgtgataaaatcataaaactttaagattaacaaataggagttacatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAUAUAUUAUAUGGUAAAUUCCGAUUCUGUCAAGCAAGCCUUUUAAAAUGGAUUGACAAGAUUUUAUAAAAUAUCUUGACCCUAUACUUGCUAUGUGAUAAAAUCAUAAAACUUUAAGAUUAACAAAUAGGAGUUACAUUUU ..((((((.(((((.((......))...((((((((.....((.........)).))))).)))...))))).))))))(((((((((........((((((...))))))...(.....)........))))).))))...... (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUAACUCCUAUUUGUUAAUCUUAAAGUUUUAUGAUUUUAUCACAUAGCAAGUAUAGGGUCAAGAUAUUUUAUAAAAUCUUGUCAAUCCAUUUUAAAAGGCUUGCUUGACAGAAUCGGAAUUUACCAUAUAAUAUAUCUAU ..........((((((((((((....(((((((....))))))).....))))))..))))))...((((((.(((((...(((.(((((..((............)).))))))))...((......)).))))).)))))).. (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 803 60 11 151 102 NC_002967:TDE0980|5end_asparaginyl-tRNA_synthetase_1005400..1005630_NEGATIVE 240 66 25 45 1 NC_002967:TDE0163|5end_flavodoxin_193383..193613_NEGATIVE 225 64 24 111 79 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 218 64 24 41 1 NC_002967:TDE0985|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1011037..1011267_POSITIVE 217 58 12 162 116 NC_002967:TDE0844|5end_pyruvate_phosphate_dikinase,_putative_864886..865116_POSITIVE 217 61 21 67 24 NC_002967:TDE0479|5end_hydroxylamine_reductase_536660..536890_NEGATIVE 216 40 2 169 131 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 215 68 30 117 63 NC_002967:TDE1192|5end_hypothetical_protein_1219332..1219562_POSITIVE 214 66 27 88 54 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 213 64 24 169 128 NC_002967:TDE0889|5end_hypothetical_protein_905090..905320_POSITIVE 211 58 16 185 140 NC_002967:TDE1844|5end_DNA_integrase_1874204..1874434_NEGATIVE 209 118 71 216 163 NC_002967:TDE2647|5end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_2686997..2687227_NEGATIVE 208 60 16 85 48 NC_002967:TDE2065|5end_FeoA_family_protein_2091779..2092009_NEGATIVE 208 58 22 60 32 NC_002967:TDE1900|5end_hypothetical_protein_1921124..1921354_POSITIVE 207 59 36 177 154 NC_002967:TDE0347|5end_methyl-accepting_chemotaxis_protein_DmcA_390239..390469_NEGATIVE 206 68 24 207 168 NC_002967:TDE1999|5end_DNA_polymerase_III_domain_protein_2017063..2017293_POSITIVE 205 45 12 169 131 NC_002967:TDE2113|5end_hypothetical_protein_2139412..2139642_NEGATIVE 205 43 11 89 53 NC_002967:TDE0305|5end_GTP-binding_protein_YchF_336751..336981_NEGATIVE 203 51 15 41 1 NC_002967:TDE1744|5end_chromate_transport_protein_1799090..1799320_NEGATIVE 203 64 23 71 37 NC_002967:TDE1719|5end_transcriptional_regulator,_MarR_family_1774029..1774259_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 59 14 116 65 NC_002967:TDE2319|3end_hypothetical_protein_2355835..2355985_NEGATIVE 242 108 70 136 92 NC_002967:TDE2709|3end_BNR_domain_protein_2761694..2761844_NEGATIVE 225 64 24 127 95 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 217 58 12 151 105 NC_002967:TDE0843|3end_hypothetical_protein_864955..865105_POSITIVE 216 40 2 134 96 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 213 50 10 73 38 NC_002967:TDE1194|3end_hypothetical_protein_1227623..1227773_POSITIVE 209 118 71 131 78 NC_002967:TDE2648|3end_hypothetical_protein_2687082..2687232_NEGATIVE 205 43 11 50 14 NC_002967:TDE0306|3end_signal_peptide_peptidase_SppA_336790..336940_NEGATIVE 202 38 4 140 104 NC_002967:TDE1128|3end_hypothetical_protein_1161785..1161935_POSITIVE 202 57 13 99 57 NC_002967:TDE0192|3end_hypothetical_protein_227817..227967_NEGATIVE 201 68 24 48 1 NC_002967:TDE2507|3end_hypothetical_protein_2531643..2531793_NEGATIVE 201 64 24 75 30 NC_002967:TDE0946|3end_hypothetical_protein_968735..968885_POSITIVE 199 50 19 54 25 NC_002967:TDE2401|3end_hypothetical_protein_2427722..2427872_POSITIVE 198 47 16 136 106 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 197 44 14 74 44 NC_002967:TDE1791|3end_hypothetical_protein_1828308..1828458_NEGATIVE 196 123 85 97 65 NC_002967:TDE2189|3end_M23/M37_peptidase_domain_protein_2223198..2223348_NEGATIVE 196 94 59 59 16 NC_002967:TDE0153|3end_coenzyme_A_disulfide_reductase,_putative_174488..174638_NEGATIVE 194 54 26 149 124 NC_002967:TDE2659|3end_GAF_domain/HD_domain_protein_2697183..2697333_POSITIVE 194 67 21 87 21 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 192 58 24 137 101 NC_002967:TDE2342|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2379238..2379388_NEGATIVE