Origin IGS: aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaatgtcaggcaggtaaaaaagtcggggtagaaacttctgtgtctgcctgccgatatcgattgaacaaacaataaacaaacaaataaggaacagacttt Mask Tandem Repeat Region ================================================ aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Find is-nt database================================================ Query_seq: TF3027:TF3028|TF3027:TF3028:zinc metalloprotease:1-deoxy-d-xylulose-5-phosphate reductoisomerase:->->:3251680..3251781 102 aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3027:TF3028|TF3027:TF3028:zinc metalloprotease:1-deoxy-d-xylulose-5-phosphate reductoisomerase:->->:3251680..3251781 102 aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3027:TF3028|TF3027:TF3028:zinc metalloprotease:1-deoxy-d-xylulose-5-phosphate reductoisomerase:->->:3251680..3251781 102 aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 6 End: 101 ..... M F L I C L F I V C S I D I G R Q T Q K F L P R L F Y L P D I F . aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta 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================================================ aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3027:TF3028|TF3027:TF3028:zinc metalloprotease:1-deoxy-d-xylulose-5-phosphate reductoisomerase:->->:3251680..3251781 102 aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: tfor_TF3027_TF3028|zinc metalloprotease:1-deoxy-d-xylulose-5-phosphate reductoisomerase|POSITIVE:POSITIVE|[3251680,3251781]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta aaagtctgttccttatttgtttgtttattgtttgttcaatcgatatcggcaggcagacacagaagtttctaccccgacttttttacctgcctgacattttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCUGUUCCUUAUUUGUUUGUUUAUUGUUUGUUCAAUCGAUAUCGGCAGGCAGACACAGAAGUUUCUACCCCGACUUUUUUACCUGCCUGACAUUUUUA ...(((...............((((.((((......)))).))))..((((((.(((....((((((........))))))))).)))))).)))....... (-19.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUGUCAGGCAGGUAAAAAAGUCGGGGUAGAAACUUCUGUGUCUGCCUGCCGAUAUCGAUUGAACAAACAAUAAACAAACAAAUAAGGAACAGACUUU .......(((.((((((((.(...(..(((((....)))))..).).)))))))).......((((......))))....................)))... (-19.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 66 22 219 170 tfor:TF2340|5end_hypothetical_protein_2500665..2500895_POSITIVE 330 49 1 209 161 tfor:TF0298|5end_dipeptidase_323127..323357_POSITIVE 324 90 41 89 20 tfor:TF2515|5end_outer_membrane_protein,_TonB_dependent_receptor_2692854..2693084_POSITIVE 320 90 41 50 1 tfor:TF3096|5end_conserved_hypothetical_protein_3327963..3328193_POSITIVE 318 58 16 221 166 tfor:TF0221|5end_aminoacyl-histidine_dipeptidase_247782..248012_POSITIVE 317 56 11 186 135 tfor:TF1161|5end_large_conductance_mechanosensitive_channel_protein_1240931..1241161_POSITIVE 315 79 34 74 25 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 314 78 41 64 22 tfor:TF0141|5end_exodeoxyribonuclease_VII,_large_subunit_148422..148652_POSITIVE 309 89 41 125 68 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 305 78 31 165 111 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 302 94 52 210 173 tfor:TF2565|5end_50S_ribosomal_protein_L24_2739986..2740216_POSITIVE 301 89 41 147 83 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 299 63 25 182 131 tfor:TF0558|5end_conserved_hypothetical_protein_590116..590346_POSITIVE 298 89 46 230 184 tfor:TF0528|5end_two-component_system_sensor_histidine_kinase_552357..552587_POSITIVE 296 78 37 70 18 tfor:TF2281|5end_hypothetical_protein_2439574..2439804_POSITIVE 294 67 24 74 35 tfor:TF2189|5end_conserved_hypothetical_protein_2363455..2363685_POSITIVE 293 90 47 189 139 tfor:TF2402|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2574582..2574812_POSITIVE 289 59 11 219 169 tfor:TF2377|5end_orotidine_5'_phosphate_decarboxylase_2541799..2542029_POSITIVE 289 89 47 88 41 tfor:TF1436|5end_phosphoglycolate_phosphatase_1521128..1521358_POSITIVE 288 50 2 167 114 tfor:TF2255|5end_transfer_region-related_protein,_TraH_2427504..2427734_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 78 41 45 3 tfor:TF0140|3end_exodeoxyribonuclease_VII,_small_subunit_148483..148633_POSITIVE 305 78 31 150 96 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 301 89 41 99 35 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 294 90 41 103 55 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 294 67 24 74 35 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 294 50 3 105 48 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 292 76 38 146 108 tfor:TF3158|3end_inner_membrane_protein_3395206..3395356_POSITIVE 290 56 12 134 87 tfor:TF1607|3end_conserved_hypothetical_protein_1725838..1725988_POSITIVE 289 66 39 85 53 tfor:TF1322|3end_conserved_hypothetical_protein;_possible_surface_protein_1402567..1402717_POSITIVE 288 50 2 114 61 tfor:TF2253|3end_conjugative_transposon_protein,_TraG_2427531..2427681_POSITIVE 284 62 32 128 91 tfor:TF2154|3end_conserved_hypothetical_protein_2329529..2329679_POSITIVE 282 90 46 128 82 tfor:TF2189|3end_conserved_hypothetical_protein_2364884..2365034_POSITIVE 282 76 32 137 92 tfor:TF0210|3end_DNA_polymerase_III,_beta_subunit_236970..237120_POSITIVE 281 90 41 117 69 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 270 65 26 151 118 tfor:TF2530|3end_conserved_hypothetical_protein_2712926..2713076_POSITIVE 269 95 60 103 65 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 268 90 41 139 97 tfor:TF2676|3end_conserved_hypothetical_protein_2850831..2850981_POSITIVE 266 77 37 49 6 tfor:TF1009|3end_conserved_hypothetical_protein;_posible_rod-shape_determining_protein,_MreD_1064885..1065035_POSITIVE 264 90 47 40 6 tfor:TF3095|3end_ABC_transporter,_ATP-binding_protein_3328033..3328183_POSITIVE 263 74 32 107 53 tfor:TF1660|3end_hypothetical_protein_1775600..1775750_POSITIVE