Origin IGS: tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggttcatgcggtaggtgtctaaaacagctttccgtaccggtatggcaagtcggtacgacaggactcgccaaaatcaacaacgtatcctgatcatcgcagtccggactcatatccaccacgttcaagaaatttcccgaggtttgctttgcgcccatgaaaagaatgtcactctcttcctcactaaggtttttcaaagtttctctccgggaaattaatatttcacagattatgaaattttgtctgagaacagggaggagattattgcttttttgtatgaattttttcaaagaaaaaatccgttcatta .........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 taatgaacggattttttctttgaaaaaattcatacaaaaaagcaataatctcctccctgttctcagacaaaatttcataatctgtgaaatattaatttcccggagagaaactttgaaaaaccttagtgaggaagagagtgacattcttttcatgggcgcaaagcaaacctcgggaaatttcttgaacgtggtggatatgagtccggactgcgatgatcaggatacgttgttgattttggcgagtcctgtcgtaccgacttgccataccggtacggaaagctgttttagacacctaccgcatgaaccgaattagattttttcagtaaactggaaaaaattttaaattggagctaaa Mask Tandem Repeat Region ================================================ tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggttcatgcggtaggtgtctaaaacagctttccgtaccggtatggcaagtcggtacgacaggactcgccaaaatcaacaacgtatcctgatcatcgcagtccggactcatatccaccacgttcaagaaatttcccgaggtttgctttgcgcccatgaaaagaatgtcactctcttcctcactaaggtttttcaaagtttctctccgggaaattaatatttcacagattatgaaattttgtctgagaacagggaggagattattgcttttttgtatgaattttttcaaagaaaaaatccgttcatta Find is-nt database================================================ Query_seq: AA01222:AA01223|AA01222:AA01223:hypothetical protein:branched-chain amino acid carrier protein:->->:834447..834801 355 tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggttcatgcggtaggtgtctaaaacagctttccgtaccggtatggcaagtcggtacgacaggactcgccaaaatcaacaacgtatcctgatcatcgcagtccggactcatatccaccacgttcaagaaatttcccgaggtttgctttgcgcccatgaaaagaatgtcactctcttcctcactaaggtttttcaaagtttctctccgggaaattaatatttcacagattatgaaattttgtctgagaacagggaggagattattgcttttttgtatgaattttttcaaagaaaaaatccgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01222:AA01223|AA01222:AA01223:hypothetical protein:branched-chain amino acid carrier protein:->->:834447..834801 355 tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggttcatgcggtaggtgtctaaaacagctttccgtaccggtatggcaagtcggtacgacaggactcgccaaaatcaacaacgtatcctgatcatcgcagtccggactcatatccaccacgttcaagaaatttcccgaggtttgctttgcgcccatgaaaagaatgtcactctcttcctcactaaggtttttcaaagtttctctccgggaaattaatatttcacagattatgaaattttgtctgagaacagggaggagattattgcttttttgtatgaattttttcaaagaaaaaatccgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 52 Max: 321 Len: 270 Subject: gi|89108847|ref|AP_002627.1| fused phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase [Escherichia coli W3110] HSP 1 e-value: 4.0E-15 bit: 76.6 Len: 270 Query Start:52 Query End:321 Subject Strand: null Subject Start: 13 Subject End: 111 ................................................... Q K S N N L L P V L R Q N F I I C E I L I - - - S R R E T L K N L S E E E S D I L F M G A K Q - - - - - - - T S G N F L N V V D M S P D C D D Q D T L L I L A S P V V P T C H T G T E S C F R H L P H E .................................. ................................................... E K T D G L M P V I V Q H A V S G E V L M L G Y M N P E A L D K T L E S G K V T F F S R T K Q R L W T K G E T S G N F L N V V S I A P D C D N - D T L L V L A N P I G P T C H K G T S S C F G D T A H Q .................................. Find nr database================================================ Query_seq: AA01222:AA01223|AA01222:AA01223:hypothetical protein:branched-chain amino acid carrier protein:->->:834447..834801 355 tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatgaattttttcaaagaaaaaatccgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatgaattttttcaaagaaaaaatccgttcatta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 64 End: 261 ............................................................... M S K T A F R T G M A S R Y D R T R Q N Q Q R I L I I A V R T H I H H V Q E I S R G L L C A H E K N V T L F L T K V F Q .............................................................................................. Protein_Len: 60 Strand: + Start: 158 End: 355 ............................................................................................................................................................. M S T T F K K F P E V C F A P M K R M S L S S S L R F F K V S L R E I N I S Q I M K F C L R T G R R L L L F C M N F F K Protein_Len: 60 Strand: - Start: 46 End: 345 ............................................. V N L F N G S T Q K A G M F L I D S E E E S L N K L T E R R S I L I E C I I F N Q R L V P L L N N S K Q I F K K L S F M .......... tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatgaattttttcaaagaaaaaatccgttcatta 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================================================ tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatgaattttttcaaagaaaaaatccgttcatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01222:AA01223|AA01222:AA01223:hypothetical protein:branched-chain amino acid carrier protein:->->:834447..834801 355 tttagctccaatttaaaattttttccagtttactgaaaaaatctaattcggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatgaattttttcaaagaaaaaatccgttcatta Intra-Species Hit: Count: 1 Min: 1 Max: 355 Len: 355 Subject: aact_AA01222_AA01223|hypothetical protein:branched-chain amino acid carrier protein|POSITIVE:POSITIVE|[834447,834801]|355 HSP 1 e-value: 3.0E-19 bit: 97.6 Len: 49 Query Start:1 Query End:49 Subject Strand: POSITIVE Subject Start: 1 Subject End: 49 tttagctccaatttaaaattttttccagtttactgaaaaaatctaattc.................................................................................................................................................................................................................................................................................................................. tttagctccaatttaaaattttttccagtttactgaaaaaatctaattc.................................................................................................................................................................................................................................................................................................................. HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 34 Query Start:322 Query End:355 Subject Strand: POSITIVE Subject Start: 322 Subject End: 355 .................................................................................................................................................................................................................................................................................................................................tatgaattttttcaaagaaaaaatccgttcatta .................................................................................................................................................................................................................................................................................................................................tatgaattttttcaaagaaaaaatccgttcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCUCCAAUUUAAAAUUUUUUCCAGUUUACUGAAAAAAUCUAAUUCGGUUCAUGCGGUAGGUGUCUAAAACAGCUUUCCGUACCGGUAUGGCAAGUCGGUACGACAGGACUCGCCAAAAUCAACAACGUAUCCUGAUCAUCGCAGUCCGGACUCAUAUCCACCACGUUCAAGAAAUUUCCCGAGGUUUGCUUUGCGCCCAUGAAAAGAAUGUCACUCUCUUCCUCACUAAGGUUUUUCAAAGUUUCUCUCCGGGAAAUUAAUAUUUCACAGAUUAUGAAAUUUUGUCUGAGAACAGGGAGGAGAUUAUUGCUUUUUUGUAUGAAUUUUUUCAAAGAAAAAAUCCGUUCAUUA .....((((........((((((((.((....))))))))))....(((((....((((((.(.(((.....))).)....((((((((.........)))))))).(((((..((.............))..)))))...))))))..)))))..........((..((((....(((((((((..(...((((((.(((..(((.((((.........))))..)))....)))....))))))....)..))))))))).........(((((...........))))).))))..)).)))).............((.(((.((((((((...)))))))).))).))... (-80.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAACGGAUUUUUUCUUUGAAAAAAUUCAUACAAAAAAGCAAUAAUCUCCUCCCUGUUCUCAGACAAAAUUUCAUAAUCUGUGAAAUAUUAAUUUCCCGGAGAGAAACUUUGAAAAACCUUAGUGAGGAAGAGAGUGACAUUCUUUUCAUGGGCGCAAAGCAAACCUCGGGAAAUUUCUUGAACGUGGUGGAUAUGAGUCCGGACUGCGAUGAUCAGGAUACGUUGUUGAUUUUGGCGAGUCCUGUCGUACCGACUUGCCAUACCGGUACGGAAAGCUGUUUUAGACACCUACCGCAUGAACCGAAUUAGAUUUUUUCAGUAAACUGGAAAAAAUUUUAAAUUGGAGCUAAA ........((((((((((...))))))))))..........((.......(((.((.(((((..(((....(((((((.....)))))))...(((((((((..(.....(((((.....(((.......(((((((((...)))))))))..)))..)))))....)..)))))))))))).))))).)).))).....(((.(((((((.(.((((((.(.....).)))))).).)).)))))..((((((((...........))))))))............))).......)).....((((.((((((((((((((....)))))))))..))))).))))....... (-93.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 117 79 215 160 aact:AA01419|5end_D-ribulose-phosphate-3_epimerase_954378..954608_POSITIVE 385 130 82 178 127 aact:AA00163|5end_type_IV_prepilin_peptidase;_type_II_secretion_pathway_related_protein_116006..116236_POSITIVE 376 118 76 46 1 aact:AA01519.1|5end_conserved_hypothetical_protein_1022466..1022696_POSITIVE 368 150 101 218 152 aact:AA01054|5end_conserved_hypothetical_protein_733678..733908_POSITIVE 367 118 75 224 179 aact:AA00123|5end_hypothetical_protein_90221..90451_POSITIVE 367 118 75 215 170 aact:AA00122|5end_hypothetical_protein_90212..90442_POSITIVE 359 160 114 86 40 aact:AA00574|5end_regulatory_protein_392113..392343_POSITIVE 355 200 151 207 148 aact:AA01730|5end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1168725..1168955_POSITIVE 355 200 151 67 8 aact:AA01729|5end_hypothetical_protein_1168585..1168815_POSITIVE 347 129 81 207 147 aact:AA00528|5end_conserved_hypothetical_protein_361396..361626_POSITIVE 344 107 63 162 120 aact:AA00409|5end_methionyl-tRNA_formyltransferase_273611..273841_POSITIVE 342 230 181 109 60 aact:AA01724|5end_valyl-tRNA_synthetase_1164446..1164676_POSITIVE 342 119 75 56 16 aact:AA01547|5end_deoxyribose-phosphate_aldolase_1036271..1036501_POSITIVE 341 110 64 61 19 aact:AA00479|5end_mannose-specific_phosphotransferase_system_IIC_333475..333705_POSITIVE 340 116 77 146 99 aact:AA01950|5end_ABC_transporter,_membrane_spanning_protein_1318116..1318346_POSITIVE 339 117 74 186 127 aact:AA02199|5end_hypothetical_protein_1497627..1497857_POSITIVE 337 206 167 135 95 aact:AA01996|5end_prephenate_dehydrogenase_1355314..1355544_POSITIVE 337 129 82 231 177 aact:AA01383|5end_DNA_processing_chain_A_934171..934401_POSITIVE 325 129 81 174 131 aact:AA01418|5end_conserved_hypothetical_protein_953951..954181_POSITIVE 324 124 81 195 152 aact:AA02439|5end_integral_membrane_protein;_possible_ABC_transporter_permease_1683902..1684132_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 117 79 63 8 aact:AA01418|3end_conserved_hypothetical_protein_954306..954456_POSITIVE 355 200 151 67 8 aact:AA01728|3end_conserved_hypothetical_protein(related_to_HipA_protein)_1168665..1168815_POSITIVE 345 119 76 146 115 aact:AA00377|3end_acetyl-CoA_acetyltransferase_(Beta-ketothiolase,3-ketoacyl-CoA_thiolase)_254300..254450_POSITIVE 344 118 74 113 70 aact:AA01291|3end_excinuclease_ABC_subunit_A_876001..876151_POSITIVE 340 116 77 146 99 aact:AA01948|3end_ABC_transporter_permease,_membrane_spanning_protein_1318196..1318346_POSITIVE 337 110 62 53 1 aact:AA02552|3end_iron_(chelated)_ABC_transporter,_permease_protein_1779420..1779570_POSITIVE 337 206 167 135 95 aact:AA01995|3end_conserved_hypothetical_protein_(possible_chorismate_mutase)_1355394..1355544_POSITIVE 332 66 24 143 102 aact:AA01305|3end_conserved_hypothetical_protein_886520..886670_POSITIVE 328 114 73 47 9 aact:AA00478|3end_mannose-specific_phosphotransferase_element_333534..333684_POSITIVE 319 130 81 127 68 aact:AA01046|3end_conserved_hypothetical_protein_729280..729430_POSITIVE 318 119 74 50 2 aact:AA01422|3end_cell_division_protein_E,_ABC_system_ATP-binding_protein_956736..956886_POSITIVE 315 188 141 59 5 aact:AA01976|3end_colicin_V_production_protein_1337132..1337282_POSITIVE 314 117 74 90 39 aact:AA01183|3end_conserved_hypothetical_protein_810902..811052_POSITIVE 313 126 81 89 48 aact:AA01829|3end_hypothetical_protein_1231662..1231812_POSITIVE 312 133 94 55 22 aact:AA01692|3end_hexulose-6-phosphate_synthase_1149929..1150079_POSITIVE 306 119 75 76 19 aact:AA00740|3end_citrate_lyase_related_biosynthesis_protein_(2-(5'-triphosphoribosyl)-3'-dephosphocoenzyme-A_synthase)_506749..506899_POSITIVE 299 189 141 53 4 aact:AA02205|3end_short_chain_dehydrogenase/reductase_1501984..1502134_POSITIVE 299 104 62 78 35 aact:AA02019|3end_hypothetical_protein_1373925..1374075_POSITIVE 298 110 64 111 61 aact:AA01875|3end_PTS_system,_glucose-specific_enzyme_II,_A_component_1263506..1263656_POSITIVE 298 116 75 52 7 aact:AA01184|3end_hypothetical_protein_811133..811283_POSITIVE