Origin IGS: tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgcttctaatggctaatggcttacatttatctccgcaaagatagccatcctttccggaaaacgggattaatttccttttattttatgtccgtaaactctttgccttataaaacaaagatca Mask Tandem Repeat Region ================================================ tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Find is-nt database================================================ Query_seq: TF2121:TF2123|TF2121:TF2123:phosphoenolpyruvate synthase:conserved hypothetical protein; TPR-repeat protein:->->:2297286..2297407 122 tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2121:TF2123|TF2121:TF2123:phosphoenolpyruvate synthase:conserved hypothetical protein; TPR-repeat protein:->->:2297286..2297407 122 tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2121:TF2123|TF2121:TF2123:phosphoenolpyruvate synthase:conserved hypothetical protein; TPR-repeat protein:->->:2297286..2297407 122 tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 2 End: 106 . I K T K Y P L S N V S M F Y F S I L G T K R F P H S D K R L Y I Y A M ................ tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt 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================================================ tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2121:TF2123|TF2121:TF2123:phosphoenolpyruvate synthase:conserved hypothetical protein; TPR-repeat protein:->->:2297286..2297407 122 tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: tfor_TF2121_TF2123|phosphoenolpyruvate synthase:conserved hypothetical protein; TPR-repeat protein|POSITIVE:POSITIVE|[2297286,2297407]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt tgatctttgttttataaggcaaagagtttacggacataaaataaaaggaaattaatcccgttttccggaaaggatggctatctttgcggagataaatgtaagccattagccattagaagcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCUUUGUUUUAUAAGGCAAAGAGUUUACGGACAUAAAAUAAAAGGAAAUUAAUCCCGUUUUCCGGAAAGGAUGGCUAUCUUUGCGGAGAUAAAUGUAAGCCAUUAGCCAUUAGAAGCGU ........(((((.((((((.((..(((((((..............(((......)))...((((((.(((((.......))))).))))))....)))))))..)).))).)))))))).. (-27.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUUCUAAUGGCUAAUGGCUUACAUUUAUCUCCGCAAAGAUAGCCAUCCUUUCCGGAAAACGGGAUUAAUUUCCUUUUAUUUUAUGUCCGUAAACUCUUUGCCUUAUAAAACAAAGAUCA ..(((......)))..((((((.......((((......))))))))))...(((((.....)))))........((((..(((((((...((((.....))))..))))))).)))).... (-18.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 119 72 175 130 tfor:TF0073|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_80946..81176_POSITIVE 330 88 46 176 134 tfor:TF1488|5end_conserved_hypothetical_protein_1588464..1588694_POSITIVE 325 98 52 85 34 tfor:TF1994|5end_acyl-CoA_synthetase_2144980..2145210_POSITIVE 320 89 46 84 37 tfor:TF0812|5end_conserved_hypothetical_protein_872087..872317_POSITIVE 309 97 51 155 107 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 308 77 31 118 81 tfor:TF2169|5end_hypothetical_protein_2344927..2345157_POSITIVE 307 89 46 68 18 tfor:TF0029|5end_hypothetical_protein_24824..25054_POSITIVE 305 89 41 131 91 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 300 114 71 153 105 tfor:TF0175|5end_hypothetical_protein_185585..185815_POSITIVE 299 99 51 199 157 tfor:TF0499|5end_hypothetical_protein_526257..526487_POSITIVE 298 90 46 218 172 tfor:TF2683|5end_translation_initiation_factor_IF-2_2857722..2857952_POSITIVE 297 93 52 194 160 tfor:TF0713|5end_polypeptide_deformylase;_formylmethionine_deformylase;_763440..763670_POSITIVE 293 99 58 210 163 tfor:TF2877|5end_regulatory_protein_3065601..3065831_POSITIVE 291 93 58 202 151 tfor:TF3082|5end_conserved_hypothetical_protein_3316431..3316661_POSITIVE 291 93 58 81 30 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 291 88 59 231 199 tfor:TF0312|5end_outer_membrane_protein_336473..336703_POSITIVE 289 114 71 99 55 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 287 89 45 187 144 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 286 93 60 195 150 tfor:TF1275|5end_transcription-repair_coupling_factor_1357866..1358096_POSITIVE 284 90 59 57 21 tfor:TF1471|5end_conserved_hypothetical_protein_1564608..1564838_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 89 46 98 51 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 319 93 60 45 4 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 319 86 46 149 112 tfor:TF1487|3end_orotate_phosphoribosyltransferase_1588522..1588672_POSITIVE 300 114 71 88 40 tfor:TF0174|3end_hypothetical_protein_185600..185750_POSITIVE 293 98 59 72 29 tfor:TF0311|3end_conserved_hypothetical_protein_336383..336533_POSITIVE 286 93 60 144 99 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 284 90 59 41 5 tfor:TF1470|3end_phosphohydrolase,_Icc_family_1564672..1564822_POSITIVE 282 89 47 35 1 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 276 98 64 32 1 tfor:TF2121|3end_phosphoenolpyruvate_synthase_2297225..2297375_POSITIVE 272 89 47 66 23 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 272 120 71 59 8 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 272 99 59 47 10 tfor:TF1738|3end_outer_membrane_protein_1866946..1867096_POSITIVE 271 103 65 72 24 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 269 104 67 151 114 tfor:TF2025|3end_hypothetical_protein_2182180..2182330_POSITIVE 269 104 67 78 45 tfor:TF0344|3end_hypothetical_protein_366963..367113_POSITIVE 269 104 67 38 5 tfor:TF0343|3end_hypothetical_protein_366923..367073_POSITIVE 269 92 66 36 10 tfor:TF0279|3end_conserved_hypothetical_protein_308679..308829_POSITIVE 269 87 46 141 105 tfor:TF0017|3end_hypothetical_protein_11231..11381_POSITIVE 266 110 64 94 51 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 266 93 57 64 27 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE