Origin IGS: aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag .........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 ctcccatgatgcaatttccgatagaaacgttgcacggtcgtcttcttttttccggcaaaaataatataaatcgtgaaactcagctaagtggatgatacgatcatttatgactccttatttgacgatttgttgaaaaatgtgttgtctttgtttcggaatgtgccggagcggagagttgtctgtcggtctatattctataattctattctatacgattctatcattctattctatacgttcgatgttgaaatattaggtaagagaaattcgtattctaaaaaaatgactacttttgtcgcaataaaatgctcataaaattcaaacagtt Mask Tandem Repeat Region ================================================ aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Find is-nt database================================================ Query_seq: TF0658:TF0659|TF0658:TF0659:2-amino-3-ketobutyrate coenzyme A ligase:RNA polymerase, ECF-type sigma factor:->->:705240..705567 328 aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0658:TF0659|TF0658:TF0659:2-amino-3-ketobutyrate coenzyme A ligase:RNA polymerase, ECF-type sigma factor:->->:705240..705567 328 aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0658:TF0659|TF0658:TF0659:2-amino-3-ketobutyrate coenzyme A ligase:RNA polymerase, ECF-type sigma factor:->->:705240..705567 328 aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 3 End: 95 .. M F E F Y E H F I A T K V V I F L E Y E F L L P N I S T S N V ......................................................................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 221 End: 328 ............................................................................................................................................................................................................................ M N D R I I H L A E F H D L Y Y F C R K K E D D R A T F L S E I A S W E Protein_Len: 39 Strand: - Start: 76 End: 192 ........................................................................... Y K L M S R I S Y F S L I T Y F L I I S Y L G V S L E G S R C M G F C L C C M ........................................................................................................................................ Protein_Len: 60 Strand: - Start: 17 End: 241 ................ N R K G L I E V D F T Y F L I I S D Y L I S N Y F I S R C V V R R E P V N R F L S L V N K L L D D F L S D Y I I T D D M ....................................................................................... aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag 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================================================ aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0658:TF0659|TF0658:TF0659:2-amino-3-ketobutyrate coenzyme A ligase:RNA polymerase, ECF-type sigma factor:->->:705240..705567 328 aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacgtatagaatagaatgatagaatcgtatagaatagaattatagaatatagaccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag Intra-Species Hit: Count: 1 Min: 1 Max: 328 Len: 328 Subject: tfor_TF0658_TF0659|2-amino-3-ketobutyrate coenzyme A ligase:RNA polymerase, ECF-type sigma factor|POSITIVE:POSITIVE|[705240,705567]|328 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:143 Query End:328 Subject Strand: POSITIVE Subject Start: 143 Subject End: 328 ..............................................................................................................................................ccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag ..............................................................................................................................................ccgacagacaactctccgctccggcacattccgaaacaaagacaacacatttttcaacaaatcgtcaaataaggagtcataaatgatcgtatcatccacttagctgagtttcacgatttatattatttttgccggaaaaaagaagacgaccgtgcaacgtttctatcggaaattgcatcatgggag HSP 2 e-value: 4.0E-33 bit: 143.0 Len: 93 Query Start:1 Query End:93 Subject Strand: POSITIVE Subject Start: 1 Subject End: 93 aactgtttgaattttatgagcattttattgcgacaaaagtagtcannnnnnnagaatacgaatttctcttacctaatatttcaacatcgaacg........................................................................................................................................................................................................................................... aactgtttgaattttatgagcattttattgcgacaaaagtagtcatttttttagaatacgaatttctcttacctaatatttcaacatcgaacg........................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGUUUGAAUUUUAUGAGCAUUUUAUUGCGACAAAAGUAGUCAUUUUUUUAGAAUACGAAUUUCUCUUACCUAAUAUUUCAACAUCGAACGUAUAGAAUAGAAUGAUAGAAUCGUAUAGAAUAGAAUUAUAGAAUAUAGACCGACAGACAACUCUCCGCUCCGGCACAUUCCGAAACAAAGACAACACAUUUUUCAACAAAUCGUCAAAUAAGGAGUCAUAAAUGAUCGUAUCAUCCACUUAGCUGAGUUUCACGAUUUAUAUUAUUUUUGCCGGAAAAAAGAAGACGACCGUGCAACGUUUCUAUCGGAAAUUGCAUCAUGGGAG ..(.(((((.(((((((((..(((((((.((((........((((((((.((...(((((...(((......................))))))))..)).))))))))....)))))))))))....))))))))).))))).)..........((((..(((((((......((((...............))))...(((((((.((((..((........(((((...)))))........))..)))).)))))))..........)))))))...............(((((..(((((.....))))))))))....)))) (-56.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCCAUGAUGCAAUUUCCGAUAGAAACGUUGCACGGUCGUCUUCUUUUUUCCGGCAAAAAUAAUAUAAAUCGUGAAACUCAGCUAAGUGGAUGAUACGAUCAUUUAUGACUCCUUAUUUGACGAUUUGUUGAAAAAUGUGUUGUCUUUGUUUCGGAAUGUGCCGGAGCGGAGAGUUGUCUGUCGGUCUAUAUUCUAUAAUUCUAUUCUAUACGAUUCUAUCAUUCUAUUCUAUACGUUCGAUGUUGAAAUAUUAGGUAAGAGAAAUUCGUAUUCUAAAAAAAUGACUACUUUUGUCGCAAUAAAAUGCUCAUAAAAUUCAAACAGUU .....((((.(((....(((((((((((.((((.(((..............))))))).......(((((((((.(((.........(((((((((...))))))))).........))).)))))))))..............((((((((((((......))))))))))))))).)))))))).......................((((((((((.....(((((((...((((...)))).)))....))))....))))..))))))...........(((.......))).........)))))))............... (-66.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 318 271 55 8 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 356 176 143 53 21 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 355 185 158 174 152 tfor:TF1990|5end_outer_membrane_protein_2141320..2141550_POSITIVE 349 313 271 230 185 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 346 187 143 59 3 tfor:TF2898|5end_conserved_hypothetical_protein_3087061..3087291_POSITIVE 336 185 141 228 181 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 336 185 141 54 7 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 333 173 142 147 105 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 330 177 137 156 104 tfor:TF1898|5end_RNA_polymerase_ECF-type_sigma_factor_2052115..2052345_POSITIVE 314 190 142 73 24 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 310 318 272 124 69 tfor:TF2918|5end_hypothetical_protein_3114084..3114314_POSITIVE 310 183 141 136 93 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 303 185 143 213 173 tfor:TF2992|5end_hexapeptide_transferase_family_protein_3209042..3209272_POSITIVE 300 175 143 160 122 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 297 310 266 47 3 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 296 180 140 224 176 tfor:TF0175|5end_hypothetical_protein_185585..185815_POSITIVE 293 175 131 54 8 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 292 175 143 167 138 tfor:TF0819|5end_phosphoglycerate_mutase_878447..878677_POSITIVE 292 176 143 201 161 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 291 189 144 174 110 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 176 143 53 21 tfor:TF1067|3end_conserved_hypothetical_protein_1138116..1138266_POSITIVE 333 173 142 132 90 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 330 177 137 68 16 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 310 318 272 121 66 tfor:TF2917|3end_conserved_hypothetical_protein_3114161..3114311_POSITIVE 310 183 141 103 60 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 293 175 131 49 3 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 293 190 144 137 96 tfor:TF0128|3end_hypothetical_protein_140556..140706_POSITIVE 290 180 134 78 25 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 289 313 284 120 93 tfor:TF2368|3end_uridine_phosphorylase_2534618..2534768_POSITIVE 289 170 123 149 90 tfor:TF0174|3end_hypothetical_protein_185600..185750_POSITIVE 286 176 141 66 29 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 285 189 143 125 85 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 285 318 279 65 34 tfor:TF1603|3end_RNA_polymerase_ECF-type_sigma_factor_1717846..1717996_POSITIVE 284 172 139 68 28 tfor:TF0188|3end_membrane-associated_porT_protein_203249..203399_POSITIVE 283 178 140 82 34 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 276 166 138 34 10 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 276 302 264 125 84 tfor:TF1472|3end_acyl-ACP_thioesterase_1566337..1566487_POSITIVE 275 317 272 102 50 tfor:TF1035|3end_iron(III)_ABC_transporter,_periplasmic-binding_protein_1097240..1097390_POSITIVE 273 311 284 137 106 tfor:TF2329|3end_conserved_hypothetical_protein_2489966..2490116_POSITIVE 272 181 148 85 54 tfor:TF0472|3end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_491057..491207_POSITIVE