Origin IGS: taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttccttcaattttggggtacaaagatacaaagtaaaacaaaggcgtttatctgttaacggataaaatgaacataaaacattcctttctgaatctttttta Mask Tandem Repeat Region ================================================ taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Find is-nt database================================================ Query_seq: TF0772:TF0773|TF0772:TF0773:conserved hypothetical protein:outer membrane efflux protein:->->:821258..821357 100 taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0772:TF0773|TF0772:TF0773:conserved hypothetical protein:outer membrane efflux protein:->->:821258..821357 100 taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0772:TF0773|TF0772:TF0773:conserved hypothetical protein:outer membrane efflux protein:->->:821258..821357 100 taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Predict ORF larger than 30AA ================================================ taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa 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================================================ taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0772:TF0773|TF0772:TF0773:conserved hypothetical protein:outer membrane efflux protein:->->:821258..821357 100 taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: tfor_TF0772_TF0773|conserved hypothetical protein:outer membrane efflux protein|POSITIVE:POSITIVE|[821258,821357]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa taaaaaagattcagaaaggaatgttttatgttcattttatccgttaacagataaacgcctttgttttactttgtatctttgtaccccaaaattgaaggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGAUUCAGAAAGGAAUGUUUUAUGUUCAUUUUAUCCGUUAACAGAUAAACGCCUUUGUUUUACUUUGUAUCUUUGUACCCCAAAAUUGAAGGAA ...((((.((((......)))).))))........((((((.(....).))))))..(((((..(((.....((((....))))....)))..))))).. (-11.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUUCAAUUUUGGGGUACAAAGAUACAAAGUAAAACAAAGGCGUUUAUCUGUUAACGGAUAAAAUGAACAUAAAACAUUCCUUUCUGAAUCUUUUUUA .((((........))))...((((((.((..((.........)).((((((((....))))))))......................)).)))))).... (-11.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 59 17 40 3 tfor:TF1789|5end_conserved_hypothetical_protein_1930219..1930449_POSITIVE 277 67 36 210 173 tfor:TF1803|5end_conserved_hypothetical_protein_1946327..1946557_POSITIVE 275 98 56 71 35 tfor:TF1888|5end_RNA_polymerase_ECF-type_sigma_factor_2040940..2041170_POSITIVE 265 99 63 191 157 tfor:TF2656|5end_valyl-tRNA_synthetase_2827076..2827306_POSITIVE 265 95 62 110 71 tfor:TF0055|5end_integrase_fragment,_N-terminal_58706..58936_POSITIVE 252 82 42 195 160 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 235 100 54 78 32 tfor:TF2533|5end_adenylosuccinate_synthetase_2715666..2715896_POSITIVE 233 90 50 216 166 tfor:TF3048|5end_conserved_hypothetical_protein_3276747..3276977_POSITIVE 227 63 27 49 7 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 226 58 11 137 89 tfor:TF2887|5end_phosphomannomutase/phosphoglucomutase_3076327..3076557_POSITIVE 226 90 42 135 89 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 224 98 58 132 102 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 223 87 41 198 149 tfor:TF3143|5end_conserved_hypothetical_protein;_possible_membrane_protein_3377465..3377695_POSITIVE 221 99 53 219 175 tfor:TF1045|5end_conserved_hypothetical_protein_1107665..1107895_POSITIVE 220 58 11 99 55 tfor:TF0783|5end_periplasmic_TonB_membrane-linking_protein_836552..836782_POSITIVE 218 88 42 86 46 tfor:TF3135|5end_hypothetical_protein_3369821..3370051_POSITIVE 217 60 12 208 155 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 216 90 41 65 19 tfor:TF2581|5end_50S_ribosomal_protein_L17_2748814..2749044_POSITIVE 215 91 56 187 150 tfor:TF3123|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_3357775..3358005_POSITIVE 214 98 58 230 200 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 44 6 138 101 tfor:TF0638|3end_GTP-binding_protein_LepA_677283..677433_POSITIVE 252 82 42 58 23 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 226 90 42 102 56 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 224 86 44 53 8 tfor:TF2934|3end_acetyltransferase/carbonic_anhydrase_3137245..3137395_POSITIVE 222 87 41 52 6 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 220 58 11 59 15 tfor:TF0782|3end_ThiJ/PfpI_family_protein_836592..836742_POSITIVE 219 80 33 88 48 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 218 88 42 98 58 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 216 90 41 55 9 tfor:TF2580|3end_RNA_polymerase,_alpha_subunit_2748884..2749034_POSITIVE 215 91 56 75 38 tfor:TF3122|3end_ABC_transporter,_ATP-binding_protein_3357743..3357893_POSITIVE 215 98 57 56 10 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 215 98 57 52 6 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 214 98 58 71 41 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 213 75 39 69 30 tfor:TF3092|3end_30S_ribosomal_protein_S9_3325179..3325329_POSITIVE 212 98 58 55 23 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 210 66 22 59 21 tfor:TF2647|3end_transcriptional_regulator,_possible_arylsulfatase_regulator_2818135..2818285_POSITIVE 209 98 58 78 49 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 209 98 58 97 68 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 207 78 31 113 66 tfor:TF2683|3end_translation_initiation_factor_IF-2_2860756..2860906_POSITIVE 205 61 41 146 119 tfor:TF0244|3end_DNA_recombination_protein_275776..275926_POSITIVE