Origin IGS: tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgacgttggtcaataaaataactcaacaacacaataatagaacattttttcgttatctatttgcgtagttagacaaaaaatatctatttttgcaaacgaaataataaatacaagata Mask Tandem Repeat Region ================================================ tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Find is-nt database================================================ Query_seq: TF3058:TF3059|TF3058:TF3059:conserved hypothetical protein:conserved hypothetical protein:->->:3282102..3282218 117 tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3058:TF3059|TF3058:TF3059:conserved hypothetical protein:conserved hypothetical protein:->->:3282102..3282218 117 tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3058:TF3059|TF3058:TF3059:conserved hypothetical protein:conserved hypothetical protein:->->:3282102..3282218 117 tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 13 End: 105 ............ M I S F A K I D I F C L T T Q I D N E K M F Y Y C V V E L F Y ............ tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca 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================================================ tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3058:TF3059|TF3058:TF3059:conserved hypothetical protein:conserved hypothetical protein:->->:3282102..3282218 117 tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: tfor_TF3058_TF3059|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3282102,3282218]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca tatcttgtatttattatttcgtttgcaaaaatagatattttttgtctaactacgcaaatagataacgaaaaaatgttctattattgtgttgttgagttattttattgaccaacgtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUGUAUUUAUUAUUUCGUUUGCAAAAAUAGAUAUUUUUUGUCUAACUACGCAAAUAGAUAACGAAAAAAUGUUCUAUUAUUGUGUUGUUGAGUUAUUUUAUUGACCAACGUCA .........((..((((((.((((((.....((((((.....)))))).....))))))))))))..)).................((.(((((.((((......))))))))).)) (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACGUUGGUCAAUAAAAUAACUCAACAACACAAUAAUAGAACAUUUUUUCGUUAUCUAUUUGCGUAGUUAGACAAAAAAUAUCUAUUUUUGCAAACGAAAUAAUAAAUACAAGAUA ((((....))))...................(((.((((((..(((((((.(((..((((....))))...)))))))))).)))))).)))......................... (-13.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 110 61 131 92 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 250 98 64 46 7 tfor:TF0177|5end_hypothetical_protein_186925..187155_POSITIVE 233 35 3 129 98 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 215 90 42 106 57 tfor:TF0861|5end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_913377..913607_POSITIVE 203 90 41 186 129 tfor:TF2377|5end_orotidine_5'_phosphate_decarboxylase_2541799..2542029_POSITIVE 194 48 3 90 41 tfor:TF3006|5end_response_regulator,_transcriptional_regulator_RprY_3226360..3226590_POSITIVE 192 103 69 167 130 tfor:TF1472|5end_acyl-ACP_thioesterase_1565475..1565705_POSITIVE 191 94 65 144 115 tfor:TF2738|5end_30S_ribosomal_protein_S16_2919303..2919533_POSITIVE 181 96 53 138 87 tfor:TF2917|5end_conserved_hypothetical_protein_3112255..3112485_POSITIVE 181 90 66 133 109 tfor:TF0226|5end_hypothetical_protein_253585..253815_POSITIVE 180 96 55 111 63 tfor:TF0836|5end_possible_transposase_889335..889565_POSITIVE 179 47 5 226 184 tfor:TF2564|5end_50S_ribosomal_protein_L14_2739604..2739834_POSITIVE 179 88 42 77 35 tfor:TF2095|5end_5'-nucleotidase_precursor_2263591..2263821_POSITIVE 179 46 1 155 97 tfor:TF0948|5end_50S_ribosomal_protein_L34_993686..993916_POSITIVE 178 90 41 82 26 tfor:TF2385|5end_conserved_hypothetical_protein;_possible_MazG_family_protein_2550676..2550906_POSITIVE 178 90 66 44 15 tfor:TF1727|5end_hypothetical_protein_1852311..1852541_POSITIVE 178 58 13 211 177 tfor:TF1670|5end_ATP_synthase,_alpha_subunit_1784455..1784685_POSITIVE 178 43 1 133 96 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 173 55 19 134 104 tfor:TF1553|5end_copper_homeostasis_protein_1658873..1659103_POSITIVE 172 94 53 102 41 tfor:TF3051|5end_conserved_hypothetical_protein_3277649..3277879_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 48 3 67 18 tfor:TF3005|3end_histidine_kinase_sensor_protein_3226417..3226567_POSITIVE 194 89 41 151 95 tfor:TF2375|3end_conserved_hypothetical_protein_2541845..2541995_POSITIVE 192 103 69 133 96 tfor:TF1471|3end_conserved_hypothetical_protein_1565521..1565671_POSITIVE 191 94 65 65 36 tfor:TF2737|3end_conserved_hypothetical_protein;_TPR-repeat-containing_protein_2919304..2919454_POSITIVE 184 97 53 103 61 tfor:TF2658|3end_transposase_2832473..2832623_POSITIVE 183 100 56 119 71 tfor:TF2916|3end_conserved_hypothetical_protein_3112178..3112328_POSITIVE 181 90 66 108 84 tfor:TF0227|3end_transcriptional_regulator,_Crp/Fnr_family_253640..253790_POSITIVE 180 96 55 62 14 tfor:TF0835|3end_conserved_hypothetical_protein_889366..889516_POSITIVE 179 100 65 151 110 tfor:TF2634|3end_conserved_hypothetical_protein_2804286..2804436_POSITIVE 178 90 41 82 26 tfor:TF2384|3end_thiol:disulfide_interchange_protein_2550756..2550906_POSITIVE 178 43 1 49 12 tfor:TF0226|3end_hypothetical_protein_253847..253997_POSITIVE 175 96 54 83 36 tfor:TF2229.1|3end_rteR_regulatory_ortholog_(with_internal_stop)_2399727..2399877_POSITIVE 175 96 54 59 12 tfor:TF2229|3end_CTn_excision_protein;_DNA_topoisomerase_IA_2399703..2399853_POSITIVE 175 110 74 82 50 tfor:TF0108|3end_thiamine_biosynthesis_protein,_ThiF_family_116000..116150_POSITIVE 172 94 53 81 20 tfor:TF3050|3end_conserved_hypothetical_protein_3277708..3277858_POSITIVE 170 110 73 101 62 tfor:TF0442|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_4_465928..466078_POSITIVE 168 89 41 111 57 tfor:TF0123|3end_conserved_hypothetical_protein_134947..135097_POSITIVE 167 110 81 144 111 tfor:TF2859|3end_possibly_related_to_Rhs_family_proteins_and_to_SAP_protein_3051033..3051183_POSITIVE 167 54 12 65 18 tfor:TF0265|3end_conserved_hypothetical_protein,_Rhs_family_295170..295320_POSITIVE 166 67 25 89 48 tfor:TF0471|3end_conserved_hypothetical_protein_487886..488036_POSITIVE