Origin IGS: tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggatgttatacgtattatgcccttaaatttcgcctgtttttatacaatcgggagccgtctcatctggggacggctctttttaaatcgggcctgtcgaaaagtatataaattctgatttttcaataaaataattaacactatccctgcaaaagtacaagatttctattcattttgcatcaaattctttatctttgcatttatgttcaaatatcgctcacaaaaacagttgttagtttatgattttcacctatgaataaaaacggactattgaaagacttgtaatctatcta Mask Tandem Repeat Region ================================================ tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Find is-nt database================================================ Query_seq: TF0089:TF0090|TF0089:TF0090:conserved hypothetical protein:conserved hypothetical protein:->->:96132..96424 293 tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0089:TF0090|TF0089:TF0090:conserved hypothetical protein:conserved hypothetical protein:->->:96132..96424 293 tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0089:TF0090|TF0089:TF0090:conserved hypothetical protein:conserved hypothetical protein:->->:96132..96424 293 tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 150 End: 248 ..................................................................................................................................................... M V L I I L L K N Q N L Y T F R Q A R F K K S R P Q M R R L P I V ............................................. Protein_Len: 35 Strand: - Start: 179 End: 283 .................................................................................................................................................................................. F K Y V K R C A R N L F L R G W I L R S G I T Y F C A F N L P M I R M .......... Protein_Len: 41 Strand: - Start: 41 End: 163 ........................................ L H F D Y V L L Q K Q S R Y K F M F A F I F F K I C F S Y F D Q V K A P I T N I M .................................................................................................................................. tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta 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================================================ tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -4.65895 Start: 215 End: 239 Full_Region: tttttatacaatcgg gagccgtctc atctg gggacggctc tttttaaatcgggcc ......................................................................................................................................................................................................................gagccgtctcatctggggacggctc...................................................... Find igs database================================================ Query_seq: TF0089:TF0090|TF0089:TF0090:conserved hypothetical protein:conserved hypothetical protein:->->:96132..96424 293 tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Intra-Species Hit: Count: 1 Min: 1 Max: 293 Len: 293 Subject: tfor_TF0089_TF0090|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[96132,96424]|293 HSP 1 e-value: 1.0E-165 bit: 581.0 Len: 293 Query Start:1 Query End:293 Subject Strand: POSITIVE Subject Start: 1 Subject End: 293 tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta tagatagattacaagtctttcaatagtccgtttttattcataggtgaaaatcataaactaacaactgtttttgtgagcgatatttgaacataaatgcaaagataaagaatttgatgcaaaatgaatagaaatcttgtacttttgcagggatagtgttaattattttattgaaaaatcagaatttatatacttttcgacaggcccgatttaaaaagagccgtccccagatgagacggctcccgattgtataaaaacaggcgaaatttaagggcataatacgtataacatcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUAGAUUACAAGUCUUUCAAUAGUCCGUUUUUAUUCAUAGGUGAAAAUCAUAAACUAACAACUGUUUUUGUGAGCGAUAUUUGAACAUAAAUGCAAAGAUAAAGAAUUUGAUGCAAAAUGAAUAGAAAUCUUGUACUUUUGCAGGGAUAGUGUUAAUUAUUUUAUUGAAAAAUCAGAAUUUAUAUACUUUUCGACAGGCCCGAUUUAAAAAGAGCCGUCCCCAGAUGAGACGGCUCCCGAUUGUAUAAAAACAGGCGAAAUUUAAGGGCAUAAUACGUAUAACAUCCUUA ..((.((((.....)))).))........((((((((((((...((...((((............(((.((((((..(((...)))..)))))).))).............)))).))..)))))))))))).((((((...((..(..(.(((((.....((((((((....))).)))))....))))))..)..)).((((..........(((((((((......).)))))))).((.((((......)))).))........)))).......))))))........ (-59.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAUGUUAUACGUAUUAUGCCCUUAAAUUUCGCCUGUUUUUAUACAAUCGGGAGCCGUCUCAUCUGGGGACGGCUCUUUUUAAAUCGGGCCUGUCGAAAAGUAUAUAAAUUCUGAUUUUUCAAUAAAAUAAUUAACACUAUCCCUGCAAAAGUACAAGAUUUCUAUUCAUUUUGCAUCAAAUUCUUUAUCUUUGCAUUUAUGUUCAAAUAUCGCUCACAAAAACAGUUGUUAGUUUAUGAUUUUCACCUAUGAAUAAAAACGGACUAUUGAAAGACUUGUAAUCUAUCUA ..(((((..(((((....((.((((........((..(((......)))..)).((((((((((.....))))))))))..........)))).)).......)))))...)))))..((((((((((...................((((((..((.((((.((..((.(.....).))..)).))))))..))))))....((((((......(((.((((......)))).)))...((.....))....)))))).........))))))))))............... (-55.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 240 196 67 12 tfor:TF2646|5end_conserved_hypothetical_protein_2814998..2815228_POSITIVE 378 240 200 131 78 tfor:TF0570|5end_possible_transcriptional_regulator_602483..602713_POSITIVE 354 240 197 108 50 tfor:TF1257|5end_hypothetical_protein_1338118..1338348_POSITIVE 354 240 197 73 15 tfor:TF1256|5end_hypothetical_protein_1338083..1338313_POSITIVE 350 239 194 187 152 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 345 239 195 183 136 tfor:TF0549|5end_universal_stress_protein,_UspA_581454..581684_POSITIVE 337 259 218 49 7 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 337 236 191 79 24 tfor:TF0317|5end_conserved_hypothetical_protein_341586..341816_POSITIVE 336 237 191 165 110 tfor:TF1343|5end_hypothetical_protein_1424630..1424860_POSITIVE 335 240 192 185 131 tfor:TF2739|5end_thioredoxin_2920126..2920356_POSITIVE 332 260 215 193 142 tfor:TF2752|5end_endonuclease_III_2936781..2937011_POSITIVE 330 260 215 214 153 tfor:TF0779|5end_possible_outer_membrane_protein_830346..830576_POSITIVE 327 240 196 130 81 tfor:TF1986|5end_hypothetical_protein_2137021..2137251_POSITIVE 318 260 217 231 174 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 318 240 191 183 143 tfor:TF1232|5end_hypothetical_protein_1317331..1317561_POSITIVE 317 248 211 69 33 tfor:TF2447|5end_lipoprotein_2623549..2623779_POSITIVE 313 237 191 186 129 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 311 238 196 201 150 tfor:TF1398|5end_conserved_hypothetical_protein_1471474..1471704_POSITIVE 311 260 212 87 29 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 310 237 200 46 8 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 240 197 61 3 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 350 239 194 110 75 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 345 239 204 59 27 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 345 239 195 66 19 tfor:TF0548|3end_TPR-repeat-containing_protein_581417..581567_POSITIVE 337 259 218 49 7 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 336 237 191 75 20 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 335 240 192 63 9 tfor:TF2738|3end_30S_ribosomal_protein_S16_2920084..2920234_POSITIVE 332 243 201 41 9 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE 332 260 215 147 96 tfor:TF2751|3end_phenylalanyl-tRNA_synthetase,_alpha_subunit_2936815..2936965_POSITIVE 321 240 191 59 3 tfor:TF1527|3end_hypothetical_protein_1633056..1633206_POSITIVE 311 260 212 73 15 tfor:TF1314|3end_conserved_hypothetical_protein_1390302..1390452_POSITIVE 310 237 200 46 8 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 310 242 215 134 98 tfor:TF2406|3end_anti-sigma_factor_2581659..2581809_POSITIVE 308 280 231 54 7 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 304 247 202 149 95 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 302 236 199 96 60 tfor:TF2815|3end_meso-diaminopimelate_D-dehydrogenase_3006420..3006570_POSITIVE 300 235 195 92 47 tfor:TF0529|3end_transposase_556193..556343_POSITIVE 296 242 217 128 94 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 296 236 191 60 19 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 293 247 201 57 10 tfor:TF1899|3end_anti-sigma_factor_2053815..2053965_POSITIVE