Origin IGS: taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagaaaatctgcattttcatgaaaagagggtgtatcaaaaatcattctttatggtacatcctcttcttctttttatatctctttacctttgcttcatgcggctatttta Mask Tandem Repeat Region ================================================ taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Find is-nt database================================================ Query_seq: TF0135:TF0137|TF0135:TF0137:hypothetical protein:conserved hypothetical protein:->->:146615..146724 110 taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0135:TF0137|TF0135:TF0137:hypothetical protein:conserved hypothetical protein:->->:146615..146724 110 taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0135:TF0137|TF0135:TF0137:hypothetical protein:conserved hypothetical protein:->->:146615..146724 110 taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. F L R M F C L Y L S I F L L L P H V M F F S K Q Y V R K E H F H M ......... Protein_Len: 34 Strand: - Start: 2 End: 103 . F Y G C S A F T F L Y L F F F L I Y W L S H N K I C G R K M F I C M ....... taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca 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================================================ taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.5 Tail_Score: -5.1104 Start: 41 End: 89 Full_Region: aatctgcattttcat gaaaagagggtgtatcaaaaa tcattc tttatggtacatcctcttcttc tttttatatctcttt ........................................gaaaagagggtgtatcaaaaatcattctttatggtacatcctcttcttc..................... TransTerm Strand: - Conf: 88 HP_score: -8.6 Tail_Score: -4.37863 Start: 47 End: 84 Full_Region: gcattttcatgaaaa gagggtgtatcaaaaa tcattc tttatggtacatcctc ttcttctttttatat ..............................................gagggtgtatcaaaaatcattctttatggtacatcctc.......................... Find igs database================================================ Query_seq: TF0135:TF0137|TF0135:TF0137:hypothetical protein:conserved hypothetical protein:->->:146615..146724 110 taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: tfor_TF0135_TF0137|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[146615,146724]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca taaaatagccgcatgaagcaaaggtaaagagatataaaaagaagaagaggatgtaccataaagaatgatttttgatacaccctcttttcatgaaaatgcagattttctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAGCCGCAUGAAGCAAAGGUAAAGAGAUAUAAAAAGAAGAAGAGGAUGUACCAUAAAGAAUGAUUUUUGAUACACCCUCUUUUCAUGAAAAUGCAGAUUUUCUCA .......(((((.....))...)))...((((..........((((((((.((((.((.(((......))).)).)))).))))))))(((....))).......)))). (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAAAUCUGCAUUUUCAUGAAAAGAGGGUGUAUCAAAAAUCAUUCUUUAUGGUACAUCCUCUUCUUCUUUUUAUAUCUCUUUACCUUUGCUUCAUGCGGCUAUUUUA ...((((((....))))))..(((((((((((((((((.(((......))).)))))))))))))).)))...................((((.....))))........ (-25.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 87 43 228 185 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 334 89 42 202 157 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 318 110 70 211 176 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 309 87 45 149 108 tfor:TF0107|5end_ion_channel_protein_113913..114143_POSITIVE 303 88 46 163 120 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 302 56 11 208 162 tfor:TF2045|5end_aminoacyl-histidine_dipeptidase_2206114..2206344_POSITIVE 279 89 44 216 172 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 262 83 42 167 127 tfor:TF0216|5end_50S_ribosomal_protein_L20_242476..242706_POSITIVE 259 90 41 207 160 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 258 88 43 151 108 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 256 88 41 228 184 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 254 89 41 166 120 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 250 87 46 166 122 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 246 74 40 68 36 tfor:TF0024|5end_conserved_hypothetical_protein;_possible_ATPase_20191..20421_POSITIVE 245 49 10 126 85 tfor:TF3140|5end_Na+-translocating_NADH-quinone_reductase,_subunit_B_3373309..3373539_POSITIVE 238 45 7 63 22 tfor:TF0489|5end_D-xylose-proton_symporter_511493..511723_POSITIVE 233 88 41 78 34 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 233 50 3 160 93 tfor:TF0433|5end_60_kDa_inner_membrane_protein_453357..453587_POSITIVE 231 33 7 142 116 tfor:TF2518|5end_ATP-dependent_DNA_helicase_2695541..2695771_POSITIVE 230 87 49 109 80 tfor:TF1733|5end_conserved_hypothetical_protein_1856015..1856245_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 87 43 47 4 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 334 89 42 63 18 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 318 110 70 37 2 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 309 87 45 63 22 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 288 89 43 58 9 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 281 109 70 47 9 tfor:TF1504|3end_conserved_hypothetical_protein_1610665..1610815_POSITIVE 259 90 41 52 5 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 256 88 41 65 21 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 245 49 10 126 85 tfor:TF3139|3end_Na+-translocating_NADH-quinone_reductase,_subunit_C_3373389..3373539_POSITIVE 239 88 43 58 15 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 233 87 47 113 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 233 88 41 65 21 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 233 50 3 89 22 tfor:TF0432|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_453366..453516_POSITIVE 224 102 64 47 11 tfor:TF1935|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2083881..2084031_POSITIVE 223 84 42 39 2 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE 221 87 41 56 19 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE 216 90 41 77 20 tfor:TF0675|3end_conserved_hypothetical_protein_719019..719169_POSITIVE 215 110 78 98 60 tfor:TF2240|3end__tetracycline_resistance_element_mobilization_regulatory_protein_2415417..2415567_POSITIVE 215 90 47 58 14 tfor:TF1620|3end_TPR_domain_protein_1735223..1735373_POSITIVE 215 53 17 102 53 tfor:TF1580|3end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1689258..1689408_POSITIVE