Origin IGS: gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagcgattaatcgcacatcaaatgatgaaaaacctgatggtgcgagcctcctttccgcaaacatttttttagaccggacaaacacagcatattgaaatgaaaattacacgaaacgaacatataacaaattataatcaaaataaatc Mask Tandem Repeat Region ================================================ gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Find is-nt database================================================ Query_seq: TF0371:TF0372|TF0371:TF0372:beta-mannosidase precursor:transcriptional regulator:->->:390530..390677 148 gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0371:TF0372|TF0371:TF0372:beta-mannosidase precursor:transcriptional regulator:->->:390530..390677 148 gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0371:TF0372|TF0371:TF0372:beta-mannosidase precursor:transcriptional regulator:->->:390530..390677 148 gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 6 End: 137 ..... M L I I I C Y M F V S C N F H F N M L C L S G L K K C L R K G G S H H Q V F H H L M C D ........... gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta 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================================================ gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0371:TF0372|TF0371:TF0372:beta-mannosidase precursor:transcriptional regulator:->->:390530..390677 148 gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: tfor_TF0371_TF0372|beta-mannosidase precursor:transcriptional regulator|POSITIVE:POSITIVE|[390530,390677]|148 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctnnnnnnntgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta gatttattttgattataatttgttatatgttcgtttcgtgtaattttcatttcaatatgctgtgtttgtccggtctaaaaaaatgtttgcggaaaggaggctcgcaccatcaggtttttcatcatttgatgtgcgattaatcgcttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUAUUUUGAUUAUAAUUUGUUAUAUGUUCGUUUCGUGUAAUUUUCAUUUCAAUAUGCUGUGUUUGUCCGGUCUAAAAAAAUGUUUGCGGAAAGGAGGCUCGCACCAUCAGGUUUUUCAUCAUUUGAUGUGCGAUUAAUCGCUUUA ..........(((((..............(((.((((.(((((....(((((...((.((((........)))).))...))))).))))))))).)))..((((((.(((((((........))))))))))))).)))))...... (-29.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCGAUUAAUCGCACAUCAAAUGAUGAAAAACCUGAUGGUGCGAGCCUCCUUUCCGCAAACAUUUUUUUAGACCGGACAAACACAGCAUAUUGAAAUGAAAAUUACACGAAACGAACAUAUAACAAAUUAUAAUCAAAAUAAAUC ......(((((.((((((((((..............)))).))))))................((((((..((..(.(........).)..))..))))))................................))))).......... (-18.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 120 89 176 146 tfor:TF1350|5end_possible_transcriptional_regulator_1429639..1429869_POSITIVE 341 134 99 210 171 tfor:TF3006|5end_response_regulator,_transcriptional_regulator_RprY_3226360..3226590_POSITIVE 339 126 83 147 74 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 329 113 71 76 31 tfor:TF0832|5end_conserved_hypothetical_protein_888466..888696_POSITIVE 300 130 84 104 58 tfor:TF3032|5end_thiamin_biosynthesis_protein_3255220..3255450_POSITIVE 300 76 34 168 122 tfor:TF1714|5end_hypothetical_protein_1834125..1834355_POSITIVE 299 117 83 51 17 tfor:TF2152|5end_uronate_isomerase_2326575..2326805_POSITIVE 298 104 68 107 66 tfor:TF0720|5end_ABC_transporter,_permease_component_770046..770276_POSITIVE 294 115 87 62 25 tfor:TF2526|5end_outer_membrane_protein,_TonB_dependent_receptor_2705547..2705777_POSITIVE 292 108 70 219 175 tfor:TF3155|5end_glycosyltransferase,_group_2_family_protein_3390417..3390647_POSITIVE 292 114 71 192 136 tfor:TF1304|5end_conserved_hypothetical_protein_1385008..1385238_POSITIVE 291 135 91 203 169 tfor:TF3013|5end_conserved_hypothetical_protein_3236158..3236388_POSITIVE 291 106 62 188 143 tfor:TF1891|5end_hypothetical_protein_2043389..2043619_POSITIVE 284 108 63 166 120 tfor:TF2454|5end_D-alanyl-D-alanine_dipeptidase_2631259..2631489_POSITIVE 284 126 89 76 41 tfor:TF0907|5end_conserved_hypothetical_protein_950160..950390_POSITIVE 283 137 91 211 160 tfor:TF2158|5end_conserved_hypothetical_protein_2333857..2334087_POSITIVE 283 125 90 155 117 tfor:TF0515|5end_conserved_hypothetical_protein_538944..539174_POSITIVE 282 138 95 197 155 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 281 109 61 197 145 tfor:TF2794|5end_possible_transcriptional_regulator_2979938..2980168_POSITIVE 281 100 59 88 26 tfor:TF0043|5end_conserved_hypothetical_protein_46857..47087_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 120 89 142 112 tfor:TF1349|3end_conserved_hypothetical_protein;_possible_prophage_maintanence_or_virulance_related_1429685..1429835_POSITIVE 301 135 91 123 80 tfor:TF3045|3end_two-component_system_response_regulator_3274633..3274783_POSITIVE 299 117 83 51 17 tfor:TF2150|3end_Na+/phosphate_symporter_2326655..2326805_POSITIVE 294 115 87 47 10 tfor:TF2525|3end_conserved_hypothetical_protein_2705612..2705762_POSITIVE 294 123 83 82 30 tfor:TF0399|3end_hypothetical_protein_421207..421357_POSITIVE 284 126 89 46 11 tfor:TF0906|3end_conserved_hypothetical_protein_950210..950360_POSITIVE 283 125 90 148 110 tfor:TF0514|3end_conserved_hypothetical_protein_539017..539167_POSITIVE 281 109 61 67 15 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 278 105 61 144 92 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 277 125 84 70 32 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 277 116 84 120 89 tfor:TF0717|3end_signal_recognition_particle_769059..769209_POSITIVE 272 112 71 64 10 tfor:TF2818|3end_acetylornithine_aminotransferase_3008949..3009099_POSITIVE 271 123 84 45 5 tfor:TF2809|3end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_3000511..3000661_POSITIVE 268 130 86 111 65 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 268 115 78 143 100 tfor:TF0701|3end_Fe-S-cluster_redox_enzyme_744922..745072_POSITIVE 267 73 32 99 41 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 266 136 95 72 8 tfor:TF2475|3end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2654221..2654371_POSITIVE 265 73 39 147 105 tfor:TF0950|3end_ribosomal_large_subunit_pseudouridine_synthase_D_(pseudouridylate_synthase)_(uracil_hydrolyase)_995777..995927_POSITIVE 263 108 63 143 92 tfor:TF3102|3end_hypothetical_protein_3332969..3333119_POSITIVE 262 105 64 135 86 tfor:TF2112|3end_glycine_cleavage_H_protein_2282573..2282723_POSITIVE