Origin IGS: tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct .........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 aggcggtgttctattgttgaatattattcacaaggctatccgattttttcctactaatcaaatgaatcaaagttttttataatgcacaaatcaaaacgaaacgcggaataatcctctcgcccgcttgagggagagagagacggaaattgcgtcaggcaattttcgtcagagagagggggaacgatattgattttcccctctccctccgagaattctgcgaattttctccacccaatactcgcttcgctcgccccttcggggtcgttggcagagccaacgctcaaatgcaagcatttgtcctgcaagcgagagaggggataaggtagccccaaaattcaataaaacaaggaaaaacaaa Mask Tandem Repeat Region ================================================ tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Find is-nt database================================================ Query_seq: AA00983:AA00985|AA00983:AA00985:aldo-keto reductase:transcriptional regulator (LysR family):->->:688553..688910 358 tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00983:AA00985|AA00983:AA00985:aldo-keto reductase:transcriptional regulator (LysR family):->->:688553..688910 358 tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00983:AA00985|AA00983:AA00985:aldo-keto reductase:transcriptional regulator (LysR family):->->:688553..688910 358 tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 2 End: 190 . M F F L V L L N F G A T L S P L S L A G Q M L A F E R W L C Q R P R R G E R S E Y W V E K I R R I L G G R G E N Q Y R S ........................................................................................................................................................................ Protein_Len: 41 Strand: + Start: 82 End: 204 ................................................................................. M A L P T T P K G R A K R V L G G E N S Q N S R R E R G K S I S F P L S L T K I A .......................................................................................................................................................... Protein_Len: 60 Strand: + Start: 24 End: 302 ....................... M L G L P Y P L S R L Q D K C L H L S V G S A N D P E G A S E A S I G W R K F A E F S E G E G K I N I V P P L S D E N C ........................................................ Protein_Len: 45 Strand: - Start: 41 End: 175 ........................................ G R E R K C S L H K C K L T P E A L S G S P A L S A L I P H L F N A S N E S P S P F I L M ....................................................................................................................................................................................... Protein_Len: 59 Strand: - Start: 36 End: 212 ................................... R I G E R A Q L V F A Q M Q A N A R G V V G F P R A F R T N P P S F E C F E R L S L P F D I D N G R E R V F I A Q R M .................................................................................................................................................. Protein_Len: 49 Strand: - Start: 1 End: 147 K N K R T K N F K P A V K D G R E S A P C I S A N S R Q S Q W R G R L P S R L S Y Q T S F I R L M ................................................................................................................................................................................................................... tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 276 End: 305 ...................................................................................................................................................................................................................................................................................CTAATCAAATGAATCAAAGTTTTTTATAAT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.4 Tail_Score: -3.61268 Start: 55 End: 73 Full_Region: ATCCCCTCTCTCGCT TGCAGG ACAAATG CTTGCA TTTGAGCGTTGGCTC ......................................................TGCAGGACAAATGCTTGCA............................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 42 HP_score: -2.1 Tail_Score: -3.05715 Start: 147 End: 199 Full_Region: AGAAAATTCGCAGAA TTCTCGGAGGGAGAGGGGAAA ATCAATATCG TTCCCCCTCTCTCTGACGAAAA TTGCCTGACGCAATT ..................................................................................................................................................TTCTCGGAGGGAGAGGGGAAAATCAATATCGTTCCCCCTCTCTCTGACGAAAA............................................................................................................................................................... TransTerm Strand: - Conf: 51 HP_score: -4.3 Tail_Score: -3.36919 Start: 147 End: 199 Full_Region: aattgcgtcaggcaa ttttcgtcagagagagggggaa cgatattgat tttcccctctccctccgagaa ttctgcgaattttct ..................................................................................................................................................ttttcgtcagagagagggggaacgatattgattttcccctctccctccgagaa............................................................................................................................................................... TransTerm Strand: + Conf: 42 HP_score: -2.7 Tail_Score: -2.87463 Start: 159 End: 186 Full_Region: GAATTCTCGGAGGGA GAGGGGAAA ATCAATATCG TTCCCCCTC TCTCTGACGAAAATT ..............................................................................................................................................................GAGGGGAAAATCAATATCGTTCCCCCTC............................................................................................................................................................................ TransTerm Strand: + Conf: 73 HP_score: -10.4 Tail_Score: -3.0094 Start: 192 End: 220 Full_Region: GTTCCCCCTCTCTCT GACGAAAATTGC CTGAC GCAATTTCCGTC TCTCTCTCCCTCAAG ...............................................................................................................................................................................................GACGAAAATTGCCTGACGCAATTTCCGTC.......................................................................................................................................... TransTerm Strand: + Conf: 57 HP_score: -7.2 Tail_Score: -3.05993 Start: 194 End: 218 Full_Region: TCCCCCTCTCTCTGA CGAAAATTGC CTGAC GCAATTTCCG TCTCTCTCTCCCTCA .................................................................................................................................................................................................CGAAAATTGCCTGACGCAATTTCCG............................................................................................................................................ Find igs database================================================ Query_seq: AA00983:AA00985|AA00983:AA00985:aldo-keto reductase:transcriptional regulator (LysR family):->->:688553..688910 358 tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Intra-Species Hit: Count: 2 Min: 1 Max: 358 Len: 358 Subject: aact_AA00983_AA00985|aldo-keto reductase:transcriptional regulator (LysR family)|POSITIVE:POSITIVE|[688553,688910]|358 HSP 1 e-value: 0.0 bit: 710.0 Len: 358 Query Start:1 Query End:358 Subject Strand: POSITIVE Subject Start: 1 Subject End: 358 tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct tttgtttttccttgttttattgaattttggggctaccttatcccctctctcgcttgcaggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagaggggaaaatcaatatcgttccccctctctctgacgaaaattgcctgacgcaatttccgtctctctctccctcaagcgggcgagaggattattccgcgtttcgttttgatttgtgcattataaaaaactttgattcatttgattagtaggaaaaaatcggatagccttgtgaataatattcaacaatagaacaccgcct Subject: aact_AA00199_AA00200|hypothetical protein:thymidylate synthase|POSITIVE:POSITIVE|[138805,139031]|227 HSP 1 e-value: 5.0E-39 bit: 163.0 Len: 106 Query Start:59 Query End:164 Subject Strand: NEGATIVE Subject Start: 41 Subject End: 146 ..........................................................ggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagcgaagcgagtattgggtggagaaaattcgcagaattctcggagggagagggg.................................................................................................................................................................................................. ..........................................................ggacaaatgcttgcatttgagcgttggctctgccaacgaccccgaaggggcgagtgaagcgagtattgggtggagaaaatccgagggattttcggagggagagggg.................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUUUUCCUUGUUUUAUUGAAUUUUGGGGCUACCUUAUCCCCUCUCUCGCUUGCAGGACAAAUGCUUGCAUUUGAGCGUUGGCUCUGCCAACGACCCCGAAGGGGCGAGCGAAGCGAGUAUUGGGUGGAGAAAAUUCGCAGAAUUCUCGGAGGGAGAGGGGAAAAUCAAUAUCGUUCCCCCUCUCUCUGACGAAAAUUGCCUGACGCAAUUUCCGUCUCUCUCUCCCUCAAGCGGGCGAGAGGAUUAUUCCGCGUUUCGUUUUGAUUUGUGCAUUAUAAAAAACUUUGAUUCAUUUGAUUAGUAGGAAAAAAUCGGAUAGCCUUGUGAAUAAUAUUCAACAAUAGAACACCGCCU ............((((((((((......(((((((..........((((((((((((......(((((((((.((((..(((((((...)))))))..(((....)))....)))))))))))))(((.(((((......((((..(((((((((((((.((((((...........)))))))))))))))).)))..))))..((((.......))))....))))))))..)))))))))))).....((((..((((.(.((((((.(((.((((..........)))).)))..)))))).).))))....))))))))))).(((((...))))).))))))))))...... (-123.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCGGUGUUCUAUUGUUGAAUAUUAUUCACAAGGCUAUCCGAUUUUUUCCUACUAAUCAAAUGAAUCAAAGUUUUUUAUAAUGCACAAAUCAAAACGAAACGCGGAAUAAUCCUCUCGCCCGCUUGAGGGAGAGAGAGACGGAAAUUGCGUCAGGCAAUUUUCGUCAGAGAGAGGGGGAACGAUAUUGAUUUUCCCCUCUCCCUCCGAGAAUUCUGCGAAUUUUCUCCACCCAAUACUCGCUUCGCUCGCCCCUUCGGGGUCGUUGGCAGAGCCAACGCUCAAAUGCAAGCAUUUGUCCUGCAAGCGAGAGAGGGGAUAAGGUAGCCCCAAAAUUCAAUAAAACAAGGAAAAACAAA ...(..((((.(((((.(((((...)))))...(((((((.(((((.................))))).............................((((((((((((..(((((((.(((......))).))))).((((((((((((.....))))))))))))...(((((((((((..........))))))))))).....))..))))))))...))))....(((....(((((((.((....(((....))).(((((((...)))))))..((((((....))))))....)))))))))....)))....)))))))........))))).))))..)......... (-115.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1079 110 61 224 175 aact:AA00200|5end_thymidylate_synthase_138892..139122_POSITIVE 633 120 74 203 153 aact:AA02108|5end_2-acylglycerophosphoethanolamine_acyltransferase;_acyl-acyl_carrier_protein_synthetase_1433393..1433623_POSITIVE 633 120 74 51 1 aact:AA02106|5end_hypothetical_protein_1433241..1433471_POSITIVE 620 247 205 48 3 aact:AA00199|5end_hypothetical_protein_138575..138805_POSITIVE 586 110 64 156 113 aact:AA01633|5end_probable_ferredoxin-like_protein_1104008..1104238_POSITIVE 578 120 71 136 86 aact:AA01098|5end_bis(5'-nucleosyl)-tetraphosphatase_757699..757929_POSITIVE 535 119 74 208 154 aact:AA01090|5end_leucyl-tRNA_synthetase,_leucyl-tRNA_ligase_753548..753778_POSITIVE 500 119 77 52 1 aact:AA01089|5end_hypothetical_protein_753392..753622_POSITIVE 467 111 74 224 187 aact:AA00988|5end_conserved_hypothetical_protein_690898..691128_POSITIVE 463 257 214 145 95 aact:AA00976|5end_conserved_hypothetical_protein_681206..681436_POSITIVE 452 94 51 231 183 aact:AA01174|5end_hypothetical_protein_804700..804930_POSITIVE 449 130 81 190 125 aact:AA00413|5end_conserved_hypothetical_protein_280142..280372_POSITIVE 445 110 66 226 170 aact:AA00404|5end_conserved_hypothetical_protein_269822..270052_POSITIVE 437 248 215 131 103 aact:AA00982|5end_aldo-keto_reductase_686526..686756_POSITIVE 416 130 81 189 125 aact:AA02422|5end_conserved_hypothetical_protein_1668014..1668244_POSITIVE 416 130 81 189 125 aact:AA02298|5end_conserved_hypothetical_protein_1570588..1570818_POSITIVE 416 130 81 189 125 aact:AA00622|5end_conserved_hypothetical_protein_429692..429922_POSITIVE 414 132 93 204 163 aact:AA01354|5end_conserved_hypothetical_protein_916489..916719_POSITIVE 413 120 72 68 5 aact:AA02466|5end_N-acetylneuraminate_lyase_1704963..1705193_POSITIVE 387 142 101 231 189 aact:AA01416|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_952780..953010_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 669 160 115 46 1 aact:AA00199|3end_hypothetical_protein_138744..138894_POSITIVE 550 130 81 49 3 aact:AA01097|3end_conserved_hypothetical_protein_757685..757835_POSITIVE 538 247 217 36 4 aact:AA00198|3end_conserved_hypothetical_protein_(Cytosine_deaminase-related_enzyme)_138643..138793_POSITIVE 535 119 74 63 9 aact:AA01088|3end_rare_lipoprotein_B_precursor_753483..753633_POSITIVE 529 118 71 64 16 aact:AA01342|3end_conserved_hypotheticl_protein_(possible_ribosomal_RNA_adenine_dimethylase)_911085..911235_POSITIVE 500 120 74 143 90 aact:AA02167|3end_hypothetical_protein_1483474..1483624_POSITIVE 391 259 217 51 8 aact:AA01421|3end_phosphoglycolate_phosphatase_955806..955956_POSITIVE 387 109 63 83 34 aact:AA01289|3end_hypothetical_protein_872848..872998_POSITIVE 369 240 191 147 92 aact:AA02270|3end_endopeptidase_La;_lon_protease;_protease_La_homolog;_ATP-dependent_protease_LA_(lon-1)_1548668..1548818_POSITIVE 362 119 71 150 108 aact:AA00723|3end_peptidase_B_(leucyl_aminopeptidase)_497841..497991_POSITIVE 354 119 77 151 100 aact:AA02922|3end_gamma-glutamylphosphate_reductase_2047441..2047591_POSITIVE 354 240 194 144 100 aact:AA01561|3end_conserved_hypothetical_protein_1046971..1047121_POSITIVE 349 90 44 150 106 aact:AA01024|3end_thiamine_biosynthesis_lipoprotein_precursor_717602..717752_POSITIVE 346 127 83 143 107 aact:AA03010|3end_thiophene_and_furan_oxidation_protein_2102534..2102684_POSITIVE 346 58 11 60 4 aact:AA02150|3end_conserved_hypothetical_protein_1470985..1471135_POSITIVE 341 118 74 65 24 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE 340 132 91 54 15 aact:AA01325|3end_formamidopyrimidine-DNA_glycosylase_895639..895789_POSITIVE 336 119 71 61 16 aact:AA02932|3end_lytic_murein_transglycosylase_A_2053544..2053694_POSITIVE 336 96 66 151 116 aact:AA00402|3end_conserved_hypothetical_protein_(possible_periplasmic_protein)_269848..269998_POSITIVE 335 240 201 39 3 aact:AA02705|3end_hypothetical_protein_1886928..1887078_POSITIVE