Origin IGS: tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctattttattattttcacgtcaggtcgcaaaagtaatgaattcggtgtgcaaaaccttgtcatctccggtaaacatttctttataatttatttttcaatcatttgcagatca Mask Tandem Repeat Region ================================================ tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Find is-nt database================================================ Query_seq: TF0522:TF0524|TF0522:TF0524:hypothetical protein:possible cation efflux pump (multidrug resistance protein):->->:547934..548045 112 tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0522:TF0524|TF0522:TF0524:hypothetical protein:possible cation efflux pump (multidrug resistance protein):->->:547934..548045 112 tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0522:TF0524|TF0522:TF0524:hypothetical protein:possible cation efflux pump (multidrug resistance protein):->->:547934..548045 112 tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 1 End: 105 S R C I I S F Y I I F F H K G S I V L N Q V G F E N S K R G S T F I M ....... tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag 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================================================ tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0522:TF0524|TF0522:TF0524:hypothetical protein:possible cation efflux pump (multidrug resistance protein):->->:547934..548045 112 tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: tfor_TF0522_TF0524|hypothetical protein:possible cation efflux pump (multidrug resistance protein)|POSITIVE:POSITIVE|[547934,548045]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag tgatctgcaaatgattgaaaaataaattataaagaaatgtttaccggagatgacaaggttttgcacaccgaattcattacttttgcgacctgacgtgaaaataataaaatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCUGCAAAUGAUUGAAAAAUAAAUUAUAAAGAAAUGUUUACCGGAGAUGACAAGGUUUUGCACACCGAAUUCAUUACUUUUGCGACCUGACGUGAAAAUAAUAAAAUAG ...(((....((((((........))))))..)))..(((((..(((.(.((.(((....)))))).))).....((((.(((..((......))..))).)))).))))). (-13.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUUAUUAUUUUCACGUCAGGUCGCAAAAGUAAUGAAUUCGGUGUGCAAAACCUUGUCAUCUCCGGUAAACAUUUCUUUAUAAUUUAUUUUUCAAUCAUUUGCAGAUCA ....(((((((((((..((......))..)))))))))))...(((.((((((...(((.........(((((......)))))...........)))...)))))).))). (-18.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 89 41 76 25 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 313 89 41 64 13 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 311 87 44 177 130 tfor:TF0214|5end_DNA_recombination_and_repair_protein,_RecN_239830..240060_POSITIVE 309 90 41 154 97 tfor:TF2434|5end_conserved_hypothetical_protein_2613969..2614199_POSITIVE 296 86 42 89 23 tfor:TF2515|5end_outer_membrane_protein,_TonB_dependent_receptor_2692854..2693084_POSITIVE 287 89 43 207 165 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 279 89 44 228 188 tfor:TF1660|5end_hypothetical_protein_1775269..1775499_POSITIVE 274 71 34 157 118 tfor:TF3068|5end_flavodoxin_A_3292812..3293042_POSITIVE 271 87 42 56 14 tfor:TF2606|5end_conserved_hypothetical_protein_2782260..2782490_POSITIVE 267 90 45 222 170 tfor:TF1438|5end_hypothetical_protein_1522244..1522474_POSITIVE 266 97 55 224 180 tfor:TF2441|5end_10_kDa_chaperonin_2618239..2618469_POSITIVE 265 96 51 60 3 tfor:TF2556|5end_conserved_hypothetical_protein_2736131..2736361_POSITIVE 258 97 54 62 22 tfor:TF2099|5end_D-tyrosyl-tRNA(Tyr)_deacylase_2272896..2273126_POSITIVE 258 100 56 185 143 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 257 70 36 170 128 tfor:TF2330|5end_conserved_hypothetical_protein_2489920..2490150_POSITIVE 257 100 55 204 159 tfor:TF1555|5end_hypothetical_protein_1661061..1661291_POSITIVE 256 90 44 50 16 tfor:TF2562|5end_50S_ribosomal_protein_L29_2739133..2739363_POSITIVE 256 89 43 227 185 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 256 89 43 121 79 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 256 70 32 41 10 tfor:TF1472|5end_acyl-ACP_thioesterase_1565475..1565705_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 90 41 148 91 tfor:TF2433|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_2614043..2614193_POSITIVE 287 89 43 114 72 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 279 89 44 88 48 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 274 71 34 142 103 tfor:TF3067|3end_conserved_hypothetical_protein_3292877..3293027_POSITIVE 258 87 45 116 83 tfor:TF2954|3end_outer_membrane_protein,_TonB_dependent_receptor_3162121..3162271_POSITIVE 258 100 56 151 109 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 257 70 36 136 94 tfor:TF2329|3end_conserved_hypothetical_protein_2489966..2490116_POSITIVE 257 100 55 76 31 tfor:TF1554|3end_UDP-glucose_dehydrogenase_1661013..1661163_POSITIVE 256 90 44 41 7 tfor:TF2561|3end_50S_ribosomal_protein_L16_2739204..2739354_POSITIVE 256 89 43 114 72 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 255 97 67 28 2 tfor:TF2098|3end_excinuclease_ABC,_subunit_C_2272942..2273092_POSITIVE 253 88 44 103 64 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 252 89 43 114 72 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 252 89 43 104 62 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 250 100 54 110 56 tfor:TF1271|3end_hypothetical_protein_1355462..1355612_POSITIVE 246 90 45 99 55 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 246 102 66 53 3 tfor:TF2473|3end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2652010..2652160_POSITIVE 244 90 46 59 23 tfor:TF1206|3end_conserved_hypothetical_protein_1290136..1290286_POSITIVE 241 90 45 69 22 tfor:TF2126|3end_S-adenosylhomocysteine_hydrolase_2303996..2304146_POSITIVE 241 88 44 82 34 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE