Origin IGS: cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggaaaacggcaattgtaacgcaaaactcccacaagtggggtattgcgtttcggacgagggacataattttgcaaaacattaaacatcaaattccctgcaag Mask Tandem Repeat Region ================================================ cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Find is-nt database================================================ Query_seq: TF1292:TF1293|TF1292:TF1293:sensor histidine protein kinase:ATPase, possible AAA superfamily:->->:1374615..1374718 104 cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1292:TF1293|TF1292:TF1293:sensor histidine protein kinase:ATPase, possible AAA superfamily:->->:1374615..1374718 104 cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1292:TF1293|TF1292:TF1293:sensor histidine protein kinase:ATPase, possible AAA superfamily:->->:1374615..1374718 104 cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 13 End: 102 ............ M M F N V L Q N Y V P R P K R N T P L V G V L R Y N C R F P .. Protein_Len: 30 Strand: - Start: 1 End: 90 K C P I Q H K I N Q L I I D R T R F A I G W K H S N Q T V M .............. cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta 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================================================ cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1292:TF1293|TF1292:TF1293:sensor histidine protein kinase:ATPase, possible AAA superfamily:->->:1374615..1374718 104 cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF1292_TF1293|sensor histidine protein kinase:ATPase, possible AAA superfamily|POSITIVE:POSITIVE|[1374615,1374718]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta cttgcagggaatttgatgtttaatgttttgcaaaattatgtccctcgtccgaaacgcaataccccacttgtgggagttttgcgttacaattgccgttttcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGCAGGGAAUUUGAUGUUUAAUGUUUUGCAAAAUUAUGUCCCUCGUCCGAAACGCAAUACCCCACUUGUGGGAGUUUUGCGUUACAAUUGCCGUUUUCCUUA ...(((((((...((((...(((....)))....))))..))))).))..(.(((((((.((((((....)))).)).))))))).)................. (-25.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAAACGGCAAUUGUAACGCAAAACUCCCACAAGUGGGGUAUUGCGUUUCGGACGAGGGACAUAAUUUUGCAAAACAUUAAACAUCAAAUUCCCUGCAAG ...........((..(((.(((((((.((.((((....)))))).))))))).)))...(((((..............................)))))))... (-23.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 80 31 185 136 tfor:TF1294|5end_conserved_hypothetical_protein_1377142..1377372_POSITIVE 364 82 45 168 125 tfor:TF1928|5end_conserved_hypothetical_protein_2075529..2075759_POSITIVE 351 88 41 187 131 tfor:TF1398|5end_conserved_hypothetical_protein_1471474..1471704_POSITIVE 334 75 42 201 158 tfor:TF3082|5end_conserved_hypothetical_protein_3316431..3316661_POSITIVE 334 75 42 80 37 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 334 75 42 221 176 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 317 88 42 228 172 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 315 85 41 201 140 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 315 85 41 62 6 tfor:TF2423|5end_papain_family_cysteine_protease_2601608..2601838_POSITIVE 311 84 44 222 186 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 310 60 12 226 165 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 310 80 32 142 98 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 309 100 53 171 111 tfor:TF1507|5end_outer_membrane_receptor,_TonB-dependent_1614536..1614766_POSITIVE 303 77 31 66 25 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 300 78 38 80 28 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 295 96 55 49 9 tfor:TF2671|5end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2843918..2844148_POSITIVE 295 82 47 42 5 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 288 87 44 182 135 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 282 95 54 45 8 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 282 88 43 198 151 tfor:TF0456|5end_conserved_hypothetical_protein_473403..473633_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 86 41 65 16 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 327 95 53 45 6 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 311 84 44 131 95 tfor:TF0099|3end_glycosyltransferase_of_PMT_family_111124..111274_POSITIVE 310 80 32 46 2 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 309 58 11 74 22 tfor:TF0833|3end_conserved_hypothetical_protein_889052..889202_POSITIVE 303 77 31 66 25 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 300 78 38 84 32 tfor:TF0288|3end_conserved_hypothetical_protein_318099..318249_POSITIVE 299 76 36 150 104 tfor:TF1273|3end_hypothetical_protein_1357462..1357612_POSITIVE 297 83 41 35 1 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 294 94 55 130 81 tfor:TF1046|3end_hypothetical_protein_1108446..1108596_POSITIVE 292 82 42 40 1 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 289 58 12 137 96 tfor:TF2831|3end_ABC_transporter,_permease_component_3022671..3022821_POSITIVE 282 95 54 45 8 tfor:TF0809|3end_cation_efflux_protein_868518..868668_POSITIVE 281 98 52 146 90 tfor:TF2473|3end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2652010..2652160_POSITIVE 281 83 42 145 111 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 281 75 42 143 100 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 281 83 42 145 111 tfor:TF0346|3end_hypothetical_protein_367316..367466_POSITIVE 278 83 42 145 111 tfor:TF0366|3end_hypothetical_protein_383811..383961_POSITIVE 278 83 42 145 111 tfor:TF0362|3end_hypothetical_protein_380199..380349_POSITIVE 277 76 36 84 38 tfor:TF2852|3end_conserved_hypothetical_protein_3040221..3040371_POSITIVE