Origin IGS: taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttttatccatataaaaaatgatgtgacaaaattgtcatttgcaaatttctatggctttttttatatggccaaataataaatgttaatatatgcaatgggttttgttttttcatta Mask Tandem Repeat Region ================================================ taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Find is-nt database================================================ Query_seq: TF3084:TF3085|TF3084:TF3085:conserved hypothetical protein:hypothetical protein:->->:3318703..3318820 118 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3084:TF3085|TF3084:TF3085:conserved hypothetical protein:hypothetical protein:->->:3318703..3318820 118 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3084:TF3085|TF3084:TF3085:conserved hypothetical protein:hypothetical protein:->->:3318703..3318820 118 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 3 End: 110 .. M K K Q N P L H I L T F I I W P Y K K S H R N L Q M T I L S H H F L Y G ........ taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt 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================================================ taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3084:TF3085|TF3084:TF3085:conserved hypothetical protein:hypothetical protein:->->:3318703..3318820 118 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Intra-Species Hit: Count: 2 Min: 1 Max: 118 Len: 118 Subject: tfor_TF3084_TF3085|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3318703,3318820]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatatnnnnnnngccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Subject: tfor_TF3082_TF3083|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3317399,3317516]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatatnnnnnnngccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt taatgaaaaaacaaaacccattgcatatattaacatttattatttggccatataaaaaaagccatagaaatttgcaaatgacaattttgtcacatcattttttatatggataaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAAAAAACAAAACCCAUUGCAUAUAUUAACAUUUAUUAUUUGGCCAUAUAAAAAAAGCCAUAGAAAUUUGCAAAUGACAAUUUUGUCACAUCAUUUUUUAUAUGGAUAAAAAUU ..........................................((((.((((((((((((.((...(....)..))...(((((....))))).....)))))))))))).)))).... (-17.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUAUCCAUAUAAAAAAUGAUGUGACAAAAUUGUCAUUUGCAAAUUUCUAUGGCUUUUUUUAUAUGGCCAAAUAAUAAAUGUUAAUAUAUGCAAUGGGUUUUGUUUUUUCAUUA ...................(((((...((((((((..(((((.(((........(((((..........)))))..((((....)))).....))))))))))))))))...))))). (-21.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 102 61 99 45 tfor:TF3015|5end_hypothetical_protein_3238430..3238660_POSITIVE 212 84 41 159 125 tfor:TF2012|5end_conserved_hypothetical_protein_2165380..2165610_POSITIVE 203 81 61 231 212 tfor:TF0381|5end_cell_cycle_protein_401632..401862_POSITIVE 195 90 45 60 18 tfor:TF0928|5end_conserved_hypothetical_protein_964722..964952_POSITIVE 185 101 63 160 123 tfor:TF2286|5end_hypothetical_protein_2440901..2441131_POSITIVE 185 101 63 42 5 tfor:TF2285|5end_hypothetical_protein_2440783..2441013_POSITIVE 183 90 44 206 160 tfor:TF2104|5end_transposase_2275286..2275516_POSITIVE 183 75 32 141 94 tfor:TF0574|5end_AMP_nucleosidase_604787..605017_POSITIVE 181 75 43 170 132 tfor:TF0446|5end_hypothetical_protein_466473..466703_POSITIVE 179 109 66 102 57 tfor:TF2991|5end_conserved_hypothetical_protein_3206316..3206546_POSITIVE 179 51 17 73 36 tfor:TF1445|5end_RNA_polymerase_sigma_factor_1530048..1530278_POSITIVE 178 104 61 45 9 tfor:TF0717|5end_signal_recognition_particle_767654..767884_POSITIVE 177 58 17 113 60 tfor:TF2097|5end_glucose_inhibited_division_protein_A_2269137..2269367_POSITIVE 176 49 16 195 150 tfor:TF2387|5end_transposase_2554464..2554694_POSITIVE 175 103 71 148 120 tfor:TF2857|5end_conserved_hypothetical_protein_3043082..3043312_POSITIVE 174 55 20 118 85 tfor:TF1091|5end_conserved_hypothetical_protein_1159429..1159659_POSITIVE 173 90 46 97 60 tfor:TF3123|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_3357775..3358005_POSITIVE 173 103 63 126 71 tfor:TF2284|5end_hypothetical_protein_2440557..2440787_POSITIVE 171 97 63 217 181 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 171 97 63 113 77 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 189 80 39 136 97 tfor:TF1280|3end_electron_transfer_flavoprotein,_beta_subunit_1365257..1365407_POSITIVE 188 88 41 76 30 tfor:TF2027|3end_conserved_hypothetical_protein_2184176..2184326_POSITIVE 187 80 61 151 133 tfor:TF0380|3end_conserved_hypothetical_protein_401633..401783_POSITIVE 184 90 60 41 11 tfor:TF0927|3end_conserved_hypothetical_protein;_possible_ATPase_of_the_AAA_superfamily_964783..964933_POSITIVE 183 75 32 126 79 tfor:TF0573|3end_DNA_polymerase_III,_delta_subunit_604852..605002_POSITIVE 181 75 43 135 97 tfor:TF0444|3end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_466518..466668_POSITIVE 179 109 66 95 50 tfor:TF2990|3end_nicotinate-nucleotide_pyrophosphorylase_3206389..3206539_POSITIVE 176 49 16 100 55 tfor:TF2386|3end_beta-galactosidase_2554449..2554599_POSITIVE 172 103 70 101 71 tfor:TF2758|3end_hypothetical_protein_2943470..2943620_POSITIVE 171 51 15 63 34 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 171 65 21 126 83 tfor:TF2618|3end_integral_membrane_protein,_possible_zinc_transporter_2796113..2796263_POSITIVE 165 96 60 108 67 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 163 89 46 59 15 tfor:TF0459|3end_sulfatase_476836..476986_POSITIVE 162 95 55 115 75 tfor:TF0519|3end_thiamine_monophosphate_kinase_544814..544964_POSITIVE 159 75 44 95 60 tfor:TF2369|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2536103..2536253_POSITIVE 158 82 47 125 95 tfor:TF0392|3end_hypothetical_protein_412945..413095_POSITIVE 157 110 76 141 110 tfor:TF2074|3end_pyridoxal-phosphate-dependent_aminotransferase_2240950..2241100_POSITIVE 157 86 62 52 27 tfor:TF0936|3end_subtilisin-like_serine_protease_978461..978611_POSITIVE 156 102 63 53 1 tfor:TF3014|3end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3238464..3238614_POSITIVE 156 76 34 141 106 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE