Origin IGS: gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatattccaactgtttttcactacttttgcagatacctcgtaaagagagacatcgtgaaaaacggtctcgaacagaaaacaatcagaccttttcacttggaatgtaataagaataacaaacgattaaactgac Mask Tandem Repeat Region ================================================ gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Find is-nt database================================================ Query_seq: TF1460:TF1461|TF1460:TF1461:6-phosphogluconate dehydrogenase:DNA-damage-inducible protein F:->->:1550851..1550984 134 gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1460:TF1461|TF1460:TF1461:6-phosphogluconate dehydrogenase:DNA-damage-inducible protein F:->->:1550851..1550984 134 gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1460:TF1461|TF1460:TF1461:6-phosphogluconate dehydrogenase:DNA-damage-inducible protein F:->->:1550851..1550984 134 gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 20 End: 133 ................... M L I T F Q V K R S D C F L F E T V F H D V S L Y E V S A K V V K N S W N I . Protein_Len: 43 Strand: - Start: 5 End: 130 .... * N L R K N N K N C E L H F P R I T K Q E L G N K V I D R K V L Y R C F Y H F V T P M .... gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca 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================================================ gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1460:TF1461|TF1460:TF1461:6-phosphogluconate dehydrogenase:DNA-damage-inducible protein F:->->:1550851..1550984 134 gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: tfor_TF1460_TF1461|6-phosphogluconate dehydrogenase:DNA-damage-inducible protein F|POSITIVE:POSITIVE|[1550851,1550984]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca gtcagtttaatcgtttgttattcttattacattccaagtgaaaaggtctgattgttttctgttcgagaccgtttttcacgatgtctctctttacgaggtatctgcaaaagtagtgaaaaacagttggaatatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAGUUUAAUCGUUUGUUAUUCUUAUUACAUUCCAAGUGAAAAGGUCUGAUUGUUUUCUGUUCGAGACCGUUUUUCACGAUGUCUCUCUUUACGAGGUAUCUGCAAAAGUAGUGAAAAACAGUUGGAAUAUCA ..............................(((((((.((....(((((((...........)).)))))..((((((((((..(((.......)))..))).((....)).))))))).)).))))))).... (-28.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUUCCAACUGUUUUUCACUACUUUUGCAGAUACCUCGUAAAGAGAGACAUCGUGAAAAACGGUCUCGAACAGAAAACAAUCAGACCUUUUCACUUGGAAUGUAAUAAGAAUAACAAACGAUUAAACUGAC ..((((((((..((((((((......(((((((....)).)))))))))))))..(((((((..(((((.((...........)))))))))))))).))))))))............................ (-27.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 93 52 121 72 tfor:TF1737|5end_outer_membrane_protein,_TonB_dependent_receptor_1861834..1862064_POSITIVE 317 105 64 219 171 tfor:TF2513|5end_conserved_hypothetical_protein_2691146..2691376_POSITIVE 315 90 41 217 164 tfor:TF0976|5end_outer_membrane_receptor,_Ton-linked_1024482..1024712_POSITIVE 314 80 31 229 176 tfor:TF0714|5end_endonuclease;_resolvase_764009..764239_POSITIVE 305 80 37 145 90 tfor:TF3156|5end_conserved_hypothetical_protein_3391364..3391594_POSITIVE 302 99 54 147 84 tfor:TF2469|5end_oxidoreductase,_possible_Gfo/Idh/MocA_family_2646505..2646735_POSITIVE 302 90 44 151 100 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 300 90 43 220 174 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 299 92 52 79 36 tfor:TF2889|5end_50S_ribosomal_protein_L27_3078333..3078563_POSITIVE 290 87 45 183 151 tfor:TF1785|5end_histidine_ammonia-lyase_1924494..1924724_POSITIVE 277 104 65 59 17 tfor:TF2842|5end_methyltransferase_3032094..3032324_POSITIVE 277 105 69 215 173 tfor:TF2419|5end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2598358..2598588_POSITIVE 277 106 61 68 13 tfor:TF1018|5end_50S_ribosomal_protein_L9_1074815..1075045_POSITIVE 276 89 45 64 8 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 275 87 42 169 122 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 271 102 64 176 140 tfor:TF2847|5end_hypothetical_protein_3034744..3034974_POSITIVE 271 110 64 51 10 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 271 87 49 206 168 tfor:TF1403|5end_hypothetical_protein_1477775..1478005_POSITIVE 270 99 59 54 19 tfor:TF0324|5end_conserved_hypothetical_protein_351228..351458_POSITIVE 266 103 62 173 138 tfor:TF3121|5end_nicotinate_phosphoribosyltransferase_3354815..3355045_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 93 52 119 70 tfor:TF1736|3end_hypothetical_protein_1861912..1862062_POSITIVE 305 80 37 145 90 tfor:TF3155|3end_glycosyltransferase,_group_2_family_protein_3391444..3391594_POSITIVE 302 99 54 144 81 tfor:TF2468|3end_hypothetical_protein_2646582..2646732_POSITIVE 302 90 44 145 94 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE 299 92 52 55 12 tfor:TF2888|3end_50S_ribosomal_protein_L21_3078389..3078539_POSITIVE 284 69 40 83 53 tfor:TF0112|3end_outer_membrane_protein_123027..123177_POSITIVE 276 89 45 65 9 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE 275 87 42 146 99 tfor:TF0954|3end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_999272..999422_POSITIVE 273 106 67 144 92 tfor:TF1771|3end_prolipoprotein_diacylglyceryl_transferase_1910607..1910757_POSITIVE 271 102 64 109 73 tfor:TF2845|3end_hypothetical_protein_3034757..3034907_POSITIVE 266 103 62 53 18 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 264 87 46 149 102 tfor:TF1803|3end_conserved_hypothetical_protein_1947120..1947270_POSITIVE 264 88 48 72 30 tfor:TF1262|3end_PDZ_domain_protein_1348831..1348981_POSITIVE 263 106 61 75 30 tfor:TF1655|3end_long-chain-fatty-acid-CoA_ligase_1771068..1771218_POSITIVE 262 104 61 41 1 tfor:TF2841|3end_conserved_hypothetical_protein_3032156..3032306_POSITIVE 260 105 61 150 107 tfor:TF1213|3end_D-3-phosphoglycerate_dehydrogenase_1301196..1301346_POSITIVE 259 110 61 60 6 tfor:TF0028|3end_hypothetical_protein_24763..24913_POSITIVE 258 90 44 135 83 tfor:TF0378|3end_aspartyl-tRNA_synthetase_399520..399670_POSITIVE 257 78 34 128 95 tfor:TF3144|3end_phosphomannomutase/phosphoglucomutase_3381184..3381334_POSITIVE 257 100 54 150 116 tfor:TF2721|3end_conserved_hypothetical_protein_2896956..2897106_POSITIVE