Origin IGS: gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagatagagtgaggaggttgtattttggggtttgtgtatccatagactggttttttttgtctgtttttattaaattttatacggacgataacataacaagaacaac Mask Tandem Repeat Region ================================================ gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Find is-nt database================================================ Query_seq: TF1030:TF1031|TF1030:TF1031:3-oxoacyl-[acyl-carrier-protein] synthase:conserved hypothetical protein:->->:1089593..1089699 107 gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1030:TF1031|TF1030:TF1031:3-oxoacyl-[acyl-carrier-protein] synthase:conserved hypothetical protein:->->:1089593..1089699 107 gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1030:TF1031|TF1030:TF1031:3-oxoacyl-[acyl-carrier-protein] synthase:conserved hypothetical protein:->->:1089593..1089699 107 gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 18 End: 107 ................. M V R I K F N K N R Q K K P V Y G Y T N P K I Q P P H S I L Protein_Len: 32 Strand: - Start: 3 End: 98 .. T R T I N D D T Y F K I F V S L F F W D I S V C V G F Y L R R M ......... gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta 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================================================ gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1030:TF1031|TF1030:TF1031:3-oxoacyl-[acyl-carrier-protein] synthase:conserved hypothetical protein:->->:1089593..1089699 107 gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: tfor_TF1030_TF1031|3-oxoacyl-[acyl-carrier-protein] synthase:conserved hypothetical protein|POSITIVE:POSITIVE|[1089593,1089699]|107 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacnnnnnnnnccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta gttgttcttgttatgttatcgtccgtataaaatttaataaaaacagacaaaaaaaaccagtctatggatacacaaaccccaaaatacaacctcctcactctatctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUCUUGUUAUGUUAUCGUCCGUAUAAAAUUUAAUAAAAACAGACAAAAAAAACCAGUCUAUGGAUACACAAACCCCAAAAUACAACCUCCUCACUCUAUCUUA (((((..(((..........((((((..................((((...........))))))))))..........)))...)))))................. ( -9.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUAGAGUGAGGAGGUUGUAUUUUGGGGUUUGUGUAUCCAUAGACUGGUUUUUUUUGUCUGUUUUUAUUAAAUUUUAUACGGACGAUAACAUAACAAGAACAAC .................(((((.(((((.((((((((....)))))))).(((....((((((((...((........)).)))))))).)))....)))))))))) (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 100 57 72 24 tfor:TF3088|5end_conserved_hypothetical_protein_3322512..3322742_POSITIVE 246 98 57 80 38 tfor:TF1758|5end_conserved_hypothetical_protein_1894769..1894999_POSITIVE 242 90 43 68 27 tfor:TF0791|5end_transposase_845166..845396_POSITIVE 231 98 59 48 6 tfor:TF2290|5end_ABC_transporter,_ATP-binding/permease_component_2443942..2444172_POSITIVE 226 25 7 228 210 tfor:TF2153|5end_6-phosphofructokinase_2328112..2328342_POSITIVE 214 100 58 132 98 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 206 90 43 79 36 tfor:TF0485|5end_transposase_fragment_507353..507583_POSITIVE 205 100 77 63 38 tfor:TF2312|5end_conserved_hypothetical_protein;_possible_glycosyl_transferase_2471537..2471767_POSITIVE 203 27 3 50 28 tfor:TF0478|5end_conserved_hypothetical_protein_498233..498463_POSITIVE 202 99 77 208 188 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 202 99 77 29 9 tfor:TF2293|5end_hypothetical_protein_2447833..2448063_POSITIVE 197 99 60 80 25 tfor:TF2701|5end_conserved_hypothetical_protein_2874174..2874404_POSITIVE 196 24 1 178 154 tfor:TF1224|5end_hypothetical_protein_1311203..1311433_POSITIVE 195 37 1 103 65 tfor:TF0950|5end_ribosomal_large_subunit_pseudouridine_synthase_D_(pseudouridylate_synthase)_(uracil_hydrolyase)_994630..994860_POSITIVE 189 31 1 117 93 tfor:TF1789|5end_conserved_hypothetical_protein_1930219..1930449_POSITIVE 189 29 5 193 162 tfor:TF0399|5end_hypothetical_protein_419775..420005_POSITIVE 188 95 55 124 84 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 187 100 88 203 191 tfor:TF2275|5end_conserved_hypothetical_protein_2436934..2437164_POSITIVE 186 100 60 71 27 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 185 83 53 69 37 tfor:TF2525|5end_conserved_hypothetical_protein_2704027..2704257_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 100 57 62 14 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 246 98 57 56 14 tfor:TF1757|3end_chromosome_partitioning_protein_1894825..1894975_POSITIVE 226 25 7 97 79 tfor:TF2152|3end_uronate_isomerase_2328061..2328211_POSITIVE 214 100 58 55 21 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 205 100 77 58 33 tfor:TF2311|3end_conserved_hypothetical_protein_2471612..2471762_POSITIVE 203 100 56 72 14 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 203 27 3 142 120 tfor:TF0479|3end_transcriptional_regulator_498405..498555_POSITIVE 197 100 57 64 14 tfor:TF2985|3end_glycosyltransferase_protein_3201646..3201796_POSITIVE 195 37 1 91 53 tfor:TF0949|3end_conserved_hypothetical_protein_994698..994848_POSITIVE 189 29 5 142 111 tfor:TF0398|3end_Fe-S_oxidoreductase_419804..419954_POSITIVE 188 100 51 60 4 tfor:TF0498|3end_hypothetical_protein_525955..526105_POSITIVE 186 100 60 75 31 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 185 83 53 52 20 tfor:TF2524|3end_conserved_hypothetical_protein;_possible_endonuclease/exonuclease/phosphatase_family_protein_2704090..2704240_POSITIVE 183 96 70 38 15 tfor:TF2744|3end_methionyl-tRNA_formyltransferase_2927378..2927528_POSITIVE 179 25 3 114 94 tfor:TF1789|3end_conserved_hypothetical_protein_1931204..1931354_POSITIVE 179 96 58 132 89 tfor:TF0207|3end_conserved_hypothetical_protein_233505..233655_POSITIVE 174 96 57 59 21 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 173 28 4 104 84 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 173 47 16 85 42 tfor:TF3071|3end_integral_membrane_protein,_possible_MotA/TolQ/ExbB_proton_channel_family_3295382..3295532_POSITIVE 173 97 58 63 23 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE