Origin IGS: ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcggataaacatgttataaaacataaccgtcttgtttaaaaaaaatccgaaaaatttggggtactcaattttagtggctacattagtgcgcgaattatcaaataatattattaacccataaaaacagacatgaacc Mask Tandem Repeat Region ================================================ ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Find is-nt database================================================ Query_seq: TF0550:TF0551|TF0550:TF0551:stationary-phase-upregulated protein, UstA:possible membrane-associated phospholipid phosphatase:->->:582985..583123 139 ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0550:TF0551|TF0550:TF0551:stationary-phase-upregulated protein, UstA:possible membrane-associated phospholipid phosphatase:->->:582985..583123 139 ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0550:TF0551|TF0550:TF0551:stationary-phase-upregulated protein, UstA:possible membrane-associated phospholipid phosphatase:->->:582985..583123 139 ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 26 End: 139 ......................... M I L F D N S R T N V A T K I E Y P K F F G F F L N K T V M F Y N M F I R L Protein_Len: 32 Strand: - Start: 19 End: 114 .................. P N I I N N S L E R V L T A V L I S Y G L N K P N K K F L V T M ......................... ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta 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================================================ ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0550:TF0551|TF0550:TF0551:stationary-phase-upregulated protein, UstA:possible membrane-associated phospholipid phosphatase:->->:582985..583123 139 ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: tfor_TF0550_TF0551|stationary-phase-upregulated protein, UstA:possible membrane-associated phospholipid phosphatase|POSITIVE:POSITIVE|[582985,583123]|139 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggannnnnnnnaaacaagacggttatgttttataacatgtttatccgctta ggttcatgtctgtttttatgggttaataatattatttgataattcgcgcactaatgtagccactaaaattgagtaccccaaatttttcggattttttttaaacaagacggttatgttttataacatgtttatccgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUCAUGUCUGUUUUUAUGGGUUAAUAAUAUUAUUUGAUAAUUCGCGCACUAAUGUAGCCACUAAAAUUGAGUACCCCAAAUUUUUCGGAUUUUUUUUAAACAAGACGGUUAUGUUUUAUAACAUGUUUAUCCGCUUA (((((((...(((.....(((((((.(((......))).))))))).)))...))).))))..(((((..((((.((...........)))))).)))))...(((.(((.((((((....)))))).....)))))). (-18.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCGGAUAAACAUGUUAUAAAACAUAACCGUCUUGUUUAAAAAAAAUCCGAAAAAUUUGGGGUACUCAAUUUUAGUGGCUACAUUAGUGCGCGAAUUAUCAAAUAAUAUUAUUAACCCAUAAAAACAGACAUGAACC ............((((((...(((((.........)))))...................(((((((((.......((((....)))))))))..((....))...............))))........)))))).... (-16.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 79 35 217 164 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 266 90 43 104 54 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 265 90 43 163 117 tfor:TF2823|5end_TPR-containing_protein_3012398..3012628_POSITIVE 254 120 73 87 36 tfor:TF0758|5end_peptidyl-tRNA_hydrolase_805307..805537_POSITIVE 248 77 34 198 160 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 243 89 45 217 174 tfor:TF2673|5end_conserved_hypothetical_protein_2846987..2847217_POSITIVE 243 64 43 223 199 tfor:TF1545|5end_conserved_hypothetical_protein_1651134..1651364_POSITIVE 237 90 45 231 188 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 234 76 33 119 70 tfor:TF1734|5end_conserved_hypothetical_protein_1856556..1856786_POSITIVE 232 110 68 47 3 tfor:TF2600|5end_ribose-phosphate_pyrophosphokinase_2773688..2773918_POSITIVE 229 88 41 201 162 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 227 90 41 84 23 tfor:TF2367|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_2532002..2532232_POSITIVE 226 90 43 224 176 tfor:TF0119|5end_gluconate_aldolase_130577..130807_POSITIVE 224 89 44 66 13 tfor:TF0693|5end_sigma-54_dependent_transcriptional_regulator_736902..737132_POSITIVE 223 129 87 222 177 tfor:TF2946|5end_conserved_hypothetical_protein;_possible_ATPase_3151750..3151980_POSITIVE 220 49 2 139 86 tfor:TF1889|5end_hypothetical_protein_2041479..2041709_POSITIVE 213 49 1 205 151 tfor:TF1950|5end_conserved_hypothetical_protein;_possible_transporter_2099828..2100058_POSITIVE 212 47 1 130 85 tfor:TF2551|5end_30S_ribosomal_protein_S10_2734433..2734663_POSITIVE 211 46 1 49 9 tfor:TF2225|5end_CTn_excision_protein_2394935..2395165_POSITIVE 210 110 68 89 44 tfor:TF2781|5end_hypothetical_protein_2965822..2966052_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 90 43 64 18 tfor:TF2822|3end_arginine_repressor_3012379..3012529_POSITIVE 224 89 44 76 23 tfor:TF0692|3end_conserved_hypothetical_protein_736992..737142_POSITIVE 220 49 2 139 86 tfor:TF1888|3end_RNA_polymerase_ECF-type_sigma_factor_2041559..2041709_POSITIVE 218 96 55 80 35 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 218 96 55 76 31 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 215 76 42 45 3 tfor:TF1733|3end_conserved_hypothetical_protein_1856562..1856712_POSITIVE 212 47 1 109 64 tfor:TF2550|3end_translation_elongation_factor_G_2734492..2734642_POSITIVE 211 50 2 133 93 tfor:TF1716|3end_hypothetical_protein_1837710..1837860_POSITIVE 210 110 68 119 74 tfor:TF2779|3end_fucose_permease_2965932..2966082_POSITIVE 208 49 4 109 51 tfor:TF1799|3end_quinolinate_synthetase_1941294..1941444_POSITIVE 205 58 16 124 89 tfor:TF0310|3end_conserved_hypothetical_protein_335997..336147_POSITIVE 204 73 37 151 113 tfor:TF2672|3end_lipoic_acid_synthetase_2847014..2847164_POSITIVE 198 90 42 107 69 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 197 48 5 115 69 tfor:TF2249|3end_transfer_region-related_protein,_TraC_2423418..2423568_POSITIVE 194 78 44 73 39 tfor:TF1940|3end_TPR-repeat-containing_protein_2088814..2088964_POSITIVE 194 105 70 58 23 tfor:TF0017|3end_hypothetical_protein_11231..11381_POSITIVE 194 105 70 66 31 tfor:TF0016|3end_hypothetical_protein_10581..10731_POSITIVE 193 90 42 81 27 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 193 80 31 65 12 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 192 68 21 114 57 tfor:TF2395|3end_conserved_hypothetical_protein_2567664..2567814_POSITIVE