Origin IGS: tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag .........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 ctgtattgtctattaattaataattcaattatatttatgtttggtattgggttttgggggttaggtgttggggtgtaaaaaacacaattttaccctaaccatttgctcttgctcggcaattacgtctctacaacacacccaagaccgaataccaaacgcccaatacctattaaagaacattgttctaattcgttcaaaaaaaatattttgttca Mask Tandem Repeat Region ================================================ tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Find is-nt database================================================ Query_seq: TF2603:TF2604|TF2603:TF2604:transcriptional regulator, AraC family:possible membrane transport protein:->->:2777333..2777546 214 tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2603:TF2604|TF2603:TF2604:transcriptional regulator, AraC family:possible membrane transport protein:->->:2777333..2777546 214 tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2603:TF2604|TF2603:TF2604:transcriptional regulator, AraC family:possible membrane transport protein:->->:2777333..2777546 214 tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 11 End: 151 .......... M F F E R I R T M F F N R Y W A F G I R S W V C C R D V I A E Q E Q M V R V K L C F L H P N T ............................................................... Protein_Len: 37 Strand: - Start: 2 End: 112 . F L I N K K F S N S C H E K I P I P R K T N P R P H T T S V Y N G L L L M ...................................................................................................... Protein_Len: 50 Strand: - Start: 1 End: 150 S C F I K K S R I L V I N K L L Y Q A N P I R D Q T H Q L S T I A S C S C I T L T F N H K K C G L M ................................................................ tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag 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================================================ tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2603:TF2604|TF2603:TF2604:transcriptional regulator, AraC family:possible membrane transport protein:->->:2777333..2777546 214 tgaacaaaatattttttttgaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Intra-Species Hit: Count: 1 Min: 20 Max: 214 Len: 195 Subject: tfor_TF2603_TF2604|transcriptional regulator, AraC family:possible membrane transport protein|POSITIVE:POSITIVE|[2777333,2777546]|214 HSP 1 e-value: 1.0E-106 bit: 387.0 Len: 195 Query Start:20 Query End:214 Subject Strand: POSITIVE Subject Start: 20 Subject End: 214 ...................gaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag ...................gaacgaattagaacaatgttctttaataggtattgggcgtttggtattcggtcttgggtgtgttgtagagacgtaattgccgagcaagagcaaatggttagggtaaaattgtgttttttacaccccaacacctaacccccaaaacccaataccaaacataaatataattgaattattaattaatagacaatacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACGAAUUAGAACAAUGUUCUUUAAUAGGUAUUGGGCGUUUGGUAUUCGGUCUUGGGUGUGUUGUAGAGACGUAAUUGCCGAGCAAGAGCAAAUGGUUAGGGUAAAAUUGUGUUUUUUACACCCCAACACCUAACCCCCAAAACCCAAUACCAAACAUAAAUAUAAUUGAAUUAUUAAUUAAUAGACAAUACAG .........(((((...))))).......((((((...((((((((((.(((.(((((..............((..((((...))))..))....(((((((........((((.....)))).......)))))))))))).))).)))))))))).......(((((((....))))))).....)))))).. (-51.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUAUUGUCUAUUAAUUAAUAAUUCAAUUAUAUUUAUGUUUGGUAUUGGGUUUUGGGGGUUAGGUGUUGGGGUGUAAAAAACACAAUUUUACCCUAACCAUUUGCUCUUGCUCGGCAAUUACGUCUCUACAACACACCCAAGACCGAAUACCAAACGCCCAAUACCUAUUAAAGAACAUUGUUCUAAUUCGUUC ..((((((.....(((((........))))).......((((((((((.((((((((((((((((.((....((((.....))))......)))))))))..(((((.......)))))..................))))))))).))))))))))...)))))).......(((((...)))))......... (-55.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 60 17 166 116 tfor:TF0835|5end_conserved_hypothetical_protein_888933..889163_POSITIVE 345 99 51 225 177 tfor:TF1889|5end_hypothetical_protein_2041479..2041709_POSITIVE 333 70 24 219 166 tfor:TF1047|5end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1108483..1108713_POSITIVE 331 66 29 190 151 tfor:TF2410|5end_possible_endo-1,4-beta-xylanase_2584000..2584230_POSITIVE 330 73 36 229 188 tfor:TF2214|5end_peptidyl-prolyl_cis-trans_isomerase_2386897..2387127_POSITIVE 330 86 47 189 145 tfor:TF1041|5end_dihydroorotate_dehydrogenase,_catalytic_subunit_1102029..1102259_POSITIVE 329 67 33 185 151 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 327 86 46 128 79 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 325 67 28 178 133 tfor:TF1551|5end_hypothetical_protein_1656864..1657094_POSITIVE 324 74 33 58 11 tfor:TF2922|5end_surface_antigen_BspA_3119122..3119352_POSITIVE 322 63 34 212 181 tfor:TF0185|5end_4-alpha-glucanotransferase_(amylomaltase)_196486..196716_POSITIVE 320 68 28 195 154 tfor:TF1528|5end_malate_dehydrogenase_1633287..1633517_POSITIVE 319 73 36 138 106 tfor:TF2664|5end_hypothetical_protein_2841399..2841629_POSITIVE 319 80 34 49 1 tfor:TF1296|5end_possible_DNA-binding_protein,_histone-like_family_1378432..1378662_POSITIVE 318 90 49 204 173 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 316 90 41 189 136 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 316 97 51 74 14 tfor:TF1162|5end_Na+/H+_antiporter_1241408..1241638_POSITIVE 314 63 21 183 132 tfor:TF2251|5end_conjugative_transposon_protein,_TraE_2424272..2424502_POSITIVE 308 80 34 197 145 tfor:TF1243|5end_periplasmic_protease_1327243..1327473_POSITIVE 305 75 32 185 121 tfor:TF2674|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2848176..2848406_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 81 43 52 1 tfor:TF2406|3end_anti-sigma_factor_2581659..2581809_POSITIVE 333 70 24 102 49 tfor:TF1046|3end_hypothetical_protein_1108446..1108596_POSITIVE 327 86 46 125 76 tfor:TF1048|3end_permease_1110217..1110367_POSITIVE 326 80 36 108 66 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 326 80 36 108 66 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 325 80 36 108 65 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 319 73 36 149 117 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 319 153 111 87 42 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 318 70 25 104 50 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 316 90 41 74 21 tfor:TF1475|3end_glucose-6-phosphate_1-dehydrogenase_1569688..1569838_POSITIVE 303 99 58 38 1 tfor:TF2068|3end_N-acetylneuraminic_acid_synthetase_2235273..2235423_POSITIVE 303 105 61 95 54 tfor:TF1848|3end_conserved_hypothetical_protein_1997944..1998094_POSITIVE 303 79 32 105 42 tfor:TF0549|3end_universal_stress_protein,_UspA_582658..582808_POSITIVE 297 96 58 44 5 tfor:TF0609|3end_conserved_hypothetical_protein_642813..642963_POSITIVE 293 96 60 140 107 tfor:TF2352|3end_phosphotransacetylase_2517784..2517934_POSITIVE 291 103 68 46 6 tfor:TF2067|3end_UDP-N-acetylglucosamine_2-epimerase_2234104..2234254_POSITIVE 291 70 29 61 11 tfor:TF1032|3end_possible_internalin-related_protein_1092842..1092992_POSITIVE 289 58 26 142 107 tfor:TF1979|3end_conserved_hypothetical_protein_2129923..2130073_POSITIVE 289 80 33 135 64 tfor:TF1663|3end_ABC_transporter,_permease_component_1778755..1778905_POSITIVE 287 85 43 143 104 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE