Origin IGS: taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taataaaaggaattaaagcgtaaagggcagtttcaagaggttgtttttatcctcctgattccctttgcgctttaactccttgtttagcttttatctctta Mask Tandem Repeat Region ================================================ taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Find is-nt database================================================ Query_seq: PI2139:PI2140|PI2139:PI2140:cysteinyl-tRNA synthetase:conserved hypothetical protein:->->:2086813..2086912 100 taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2139:PI2140|PI2139:PI2140:cysteinyl-tRNA synthetase:conserved hypothetical protein:->->:2086813..2086912 100 taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2139:PI2140|PI2139:PI2140:cysteinyl-tRNA synthetase:conserved hypothetical protein:->->:2086813..2086912 100 taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Predict ORF larger than 30AA ================================================ taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta 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================================================ taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2139:PI2140|PI2139:PI2140:cysteinyl-tRNA synthetase:conserved hypothetical protein:->->:2086813..2086912 100 taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: pint_PI2139_PI2140|cysteinyl-tRNA synthetase:conserved hypothetical protein|POSITIVE:POSITIVE|[2086813,2086912]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta taagagataaaagctaaacaaggagttaaagcgcaaagggaatcaggaggataaaaacaacctcttgaaactgccctttacgctttaattccttttatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAGAUAAAAGCUAAACAAGGAGUUAAAGCGCAAAGGGAAUCAGGAGGAUAAAAACAACCUCUUGAAACUGCCCUUUACGCUUUAAUUCCUUUUAUUA ...................((((((((((((((.((((((..((((((((..........)))))))).....)))))).))))))))))))))...... (-38.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAAGGAAUUAAAGCGUAAAGGGCAGUUUCAAGAGGUUGUUUUUAUCCUCCUGAUUCCCUUUGCGCUUUAACUCCUUGUUUAGCUUUUAUCUCUUA (((...(((((.(((((((((((((((.....(((.((((.((....)).)))).)))..))))))))))))))).)))))..))).............. (-36.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 50 2 64 18 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 316 49 2 195 160 pint:PI0982|5end_hypothetical_protein_909432..909662_POSITIVE 310 75 31 49 6 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 301 48 3 216 183 pint:PI1244|5end_hypothetical_protein_1168803..1169033_POSITIVE 281 79 31 102 43 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 281 68 22 56 5 pint:PI1373|5end_purine_nucleoside_phosphorylase_(PNP)_1294031..1294261_POSITIVE 273 83 45 209 171 pint:PI0323|5end_hypothetical_protein_305349..305579_POSITIVE 259 60 11 78 23 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 253 78 31 158 113 pint:PI2168|5end_hypothetical_protein_2111286..2111516_POSITIVE 253 59 12 210 162 pint:PI1038|5end_hypothetical_protein_958685..958915_POSITIVE 243 50 4 62 17 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 242 51 12 224 187 pint:PI1135|5end_hypothetical_protein_1061935..1062165_POSITIVE 238 51 12 187 144 pint:PI1856|5end_nicotinate-nucleotide_adenylyltransferase_1803203..1803433_POSITIVE 238 85 58 206 183 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 238 85 58 39 16 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 236 50 13 63 36 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 235 46 1 188 144 pint:PI0440|5end_transcription_antiterminator_410582..410812_POSITIVE 235 94 59 128 88 pint:PI0027|5end_aminopeptidase_C_30468..30698_POSITIVE 234 59 11 86 41 pint:PI0918|5end_Fe-S_oxidoreductase,_family_2_847078..847308_POSITIVE 233 43 9 37 1 pint:PI2048|5end_possible_two-component_system_sensor_histidine_kinase_2000705..2000935_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 94 61 71 41 pint:PI2139|3end_cysteinyl-tRNA_synthetase_2086752..2086902_POSITIVE 316 49 2 73 38 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 301 48 3 93 60 pint:PI1243|3end_conserved_hypothetical_protein_1168760..1168910_POSITIVE 294 60 13 91 44 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 273 52 11 96 54 pint:PI0058|3end_conserved_hypothetical_protein_57044..57194_POSITIVE 259 91 62 66 34 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE 247 52 22 48 22 pint:PI0970|3end_hypothetical_protein_897654..897804_POSITIVE 245 53 21 70 35 pint:PI0189|3end_integrase_180437..180587_POSITIVE 240 52 21 81 53 pint:PI1909|3end_DNA_gyrase,_B_subunit_1855270..1855420_POSITIVE 238 51 12 72 29 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 235 94 59 117 77 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 233 68 25 68 18 pint:PI1361|3end_CTP_synthase_(UTP-ammonia_lyase)_1279893..1280043_POSITIVE 230 52 12 52 2 pint:PI1540|3end_hypothetical_protein_1461771..1461921_POSITIVE 229 58 13 138 87 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 226 57 18 47 14 pint:PI2019|3end_elongation_factor_P_1976774..1976924_POSITIVE 226 79 32 99 55 pint:PI1017|3end_ISPg3-related_transposase,_C-terminal_region_937661..937811_POSITIVE 226 76 31 118 73 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 225 50 19 118 76 pint:PI2076|3end_hypothetical_protein_2035758..2035908_POSITIVE 225 85 58 147 124 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 225 60 11 53 5 pint:PI0883|3end_para-aminobenzoate_synthase_component_I_817251..817401_POSITIVE