Origin IGS: taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct .........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 agcatttacctcttattgttgtgaatgggtcgaagacccggttaaaatccttagttacaacatagttatgttgattggacttttcaaggtttttttgatggttggaggagaaaatccgaaaaatatgatctgggtctgataattgaaaaaagaaaccttttttgtgaaccaaaattgttatgataaagcggatattgttttttaatatccgcttttacaccatcacatta Mask Tandem Repeat Region ================================================ taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Find is-nt database================================================ Query_seq: AA00167:AA00168|AA00167:AA00168:possible amino-acid transporter (sodium-alanine symporters):possible sigma 54 modulation protein:->->:119750..119979 230 taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00167:AA00168|AA00167:AA00168:possible amino-acid transporter (sodium-alanine symporters):possible sigma 54 modulation protein:->->:119750..119979 230 taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00167:AA00168|AA00167:AA00168:possible amino-acid transporter (sodium-alanine symporters):possible sigma 54 modulation protein:->->:119750..119979 230 taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 25 End: 144 ........................ M K K Q Y P L Y H N N F G S Q K R F L F S I I R P R S Y F S D F L L Q P S K K P ...................................................................................... Protein_Len: 60 Strand: + Start: 23 End: 229 ...................... M L K N N I R F I I T I L V H K K G F F F Q L S D P D H I F R I F S S N H Q K N L E K S N Q H N Y V V T K D F N R V F D . Protein_Len: 30 Strand: - Start: 95 End: 184 .............................................................................................. V W I M N K P N E G G V M L F V K F L G I L M V I N Y S L M .............................................. taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct 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================================================ taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -9.4 Tail_Score: -4.09685 Start: 19 End: 43 Full_Region: aattgttatgataaa gcggatattg ttttt taatatccgc ttttacaccatcaca ..................gcggatattgttttttaatatccgc........................................................................................................................................................................................... Find igs database================================================ Query_seq: AA00167:AA00168|AA00167:AA00168:possible amino-acid transporter (sodium-alanine symporters):possible sigma 54 modulation protein:->->:119750..119979 230 taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: aact_AA00167_AA00168|possible amino-acid transporter (sodium-alanine symporters):possible sigma 54 modulation protein|POSITIVE:POSITIVE|[119750,119979]|230 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcnnnnnnnccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct taatgtgatggtgtaaaagcggatattaaaaaacaatatccgctttatcataacaattttggttcacaaaaaaggtttcttttttcaattatcagacccagatcatatttttcggattttctcctccaaccatcaaaaaaaccttgaaaagtccaatcaacataactatgttgtaactaaggattttaaccgggtcttcgacccattcacaacaataagaggtaaatgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGUGAUGGUGUAAAAGCGGAUAUUAAAAAACAAUAUCCGCUUUAUCAUAACAAUUUUGGUUCACAAAAAAGGUUUCUUUUUUCAAUUAUCAGACCCAGAUCAUAUUUUUCGGAUUUUCUCCUCCAACCAUCAAAAAAACCUUGAAAAGUCCAAUCAACAUAACUAUGUUGUAACUAAGGAUUUUAACCGGGUCUUCGACCCAUUCACAACAAUAAGAGGUAAAUGCU .....(((((((...((((((((((((.......))))))))))))...........((((((....(((((((....))))))).....)))))).................(((........))).))))))).....(((((..(((((((...((((((....)))))).......)))))))....(((((...)))))..............)))))....... (-54.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAUUUACCUCUUAUUGUUGUGAAUGGGUCGAAGACCCGGUUAAAAUCCUUAGUUACAACAUAGUUAUGUUGAUUGGACUUUUCAAGGUUUUUUUGAUGGUUGGAGGAGAAAAUCCGAAAAAUAUGAUCUGGGUCUGAUAAUUGAAAAAAGAAACCUUUUUUGUGAACCAAAAUUGUUAUGAUAAAGCGGAUAUUGUUUUUUAAUAUCCGCUUUUACACCAUCACAUUA ..(((((((..(.....)..)))))))((((..((((((((((((((.((((((((.((((((....))))))....))))....))))...))))))...(((((........)))))..........))))))))........(((((((....)))))))..).))).....(((.(((..(((((((((((((.....))))))))))))).....))).)))... (-57.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 206 161 151 105 aact:AA01674|5end_hypothetical_protein_1132017..1132247_POSITIVE 249 110 61 188 141 aact:AA02399|5end_30S_ribosomal_protein_S21_1650900..1651130_POSITIVE 243 49 4 187 147 aact:AA00753|5end_galactoside_ABC_transporter,_permease_protein_517528..517758_POSITIVE 242 224 188 114 74 aact:AA02521|5end_conserved_hypothetical_protein_1752603..1752833_POSITIVE 241 203 170 197 172 aact:AA00665|5end_plasmid_protein_457195..457425_POSITIVE 239 199 169 227 196 aact:AA00117|5end_hypothetical_protein_88246..88476_POSITIVE 237 131 93 188 146 aact:AA02538|5end_conserved_hypothetical_protein_1765187..1765417_POSITIVE 237 165 122 154 99 aact:AA00876|5end_tight_adherence_protein_C_607761..607991_POSITIVE 237 126 95 178 144 aact:AA00658|5end_hypothetical_protein_451618..451848_POSITIVE 235 46 4 231 189 aact:AA01854|5end_conserved_hypothetical_protein_1246662..1246892_POSITIVE 232 210 169 112 57 aact:AA00265|5end_transcription_termination_factor_185307..185537_POSITIVE 230 134 95 109 73 aact:AA01241|5end_30S_ribosomal_protein_S4_845294..845524_POSITIVE 228 80 32 199 152 aact:AA00983|5end_aldo-keto_reductase_687570..687800_POSITIVE 226 135 94 108 59 aact:AA02936|5end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2055610..2055840_POSITIVE 226 209 165 192 154 aact:AA02738|5end_phosphate_permease_1919372..1919602_POSITIVE 224 50 3 54 2 aact:AA01451|5end_D-xylulokinase_971935..972165_POSITIVE 223 228 181 82 38 aact:AA01845|5end_gamma-glutamyltranspeptidase_precursor_1239841..1240071_POSITIVE 223 137 92 108 69 aact:AA00825|5end_P-protein_(chorismate_mutase/prephenate_dehydratase)_567020..567250_POSITIVE 221 204 168 43 12 aact:AA00452|5end_phosphomannomutase;_phosphoglucomutase_315288..315518_POSITIVE 220 132 100 35 7 aact:AA00768|5end_conserved_hypothetical_protein_528100..528330_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 50 4 139 92 aact:AA01853|3end_hypothetical_protein_1246645..1246795_POSITIVE 253 206 161 147 101 aact:AA01673|3end_riboflavin_synthase,_alpha_chain_1132093..1132243_POSITIVE 251 219 179 124 78 aact:AA02465|3end_glucosamine-6-phosphate_isomerase_1704885..1705035_POSITIVE 249 110 61 63 16 aact:AA02398|3end_DNA_primase_1650855..1651005_POSITIVE 248 50 4 82 36 aact:AA00167|3end_possible_amino-acid_transporter_(sodium-alanine_symporters)_119689..119839_POSITIVE 242 224 188 43 3 aact:AA02519|3end_DNA_gyrase_A_1752612..1752762_POSITIVE 241 209 169 113 77 aact:AA00116|3end_conserved_hypothetical_protein_88207..88357_POSITIVE 230 134 95 76 40 aact:AA01240|3end_30S_ribosomal_protein_S11_845341..845491_POSITIVE 230 160 115 146 95 aact:AA00875|3end_tight_adherence_protein_B_607841..607991_POSITIVE 228 80 32 132 85 aact:AA00982|3end_aldo-keto_reductase_687583..687733_POSITIVE 224 50 3 71 19 aact:AA01450|3end_hypothetical_protein_972032..972182_POSITIVE 223 137 92 133 94 aact:AA00824|3end_hypothetical_protein_567125..567275_POSITIVE 220 144 103 49 13 aact:AA02003|3end_purine_nucleotide_synthesis_repressor_protein_1361708..1361858_POSITIVE 219 131 93 139 96 aact:AA02762|3end_ribonuclease_H_1933708..1933858_POSITIVE 219 220 181 81 38 aact:AA00043|3end_formate_dependent_nitrite_reductase,_transmembrane_protein_35420..35570_POSITIVE 218 134 92 60 18 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE 215 135 94 133 79 aact:AA02103|3end_D-alanyl-D-alanine-endopeptidase;_penicillin-binding_protein_7_1431784..1431934_POSITIVE 214 154 123 135 102 aact:AA00977|3end_transcriptional_regulator_(LysR_family)_683334..683484_POSITIVE 214 135 94 68 28 aact:AA00899|3end_possible_quaternary_ammonium_compound_resistance_protein_623479..623629_POSITIVE 214 43 5 138 107 aact:AA00111|3end_hypothetical_protein_79986..80136_POSITIVE