Origin IGS: taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcattgctcctttctgatatttagcggataaagactgttttattccgaaagacaattgttgagggtgtgtcaaacattgtgttttgacacaccctcctttcaaatgaggcagcctcaataaaacatgcattttattataagacagcctctgccttgctccgattctttta Mask Tandem Repeat Region ================================================ taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Find is-nt database================================================ Query_seq: TF3006:TF3007|TF3006:TF3007:response regulator, transcriptional regulator RprY:conserved hypothetical protein:->->:3227223..3227395 173 taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3006:TF3007|TF3006:TF3007:response regulator, transcriptional regulator RprY:conserved hypothetical protein:->->:3227223..3227395 173 taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3006:TF3007|TF3006:TF3007:response regulator, transcriptional regulator RprY:conserved hypothetical protein:->->:3227223..3227395 173 taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 52 End: 147 ................................................... M E A A S F E R R V C Q N T M F D T P S T I V F R N K T V F I R .......................... Protein_Len: 55 Strand: + Start: 8 End: 172 ....... M G A R Q R L S Y N K M H V L L R L P H L K G G C V K T Q C L T H P Q Q L S F G I K Q S L S A K Y Q K G A M I . taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta 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================================================ taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.1 Tail_Score: -3.59979 Start: 74 End: 111 Full_Region: ccgaaagacaattgt tgagggtgtgtcaaaca ttg tgttttgacacaccctcc tttcaaatgaggcag .........................................................................tgagggtgtgtcaaacattgtgttttgacacaccctcc.............................................................. TransTerm Strand: - Conf: 100 HP_score: -18.6 Tail_Score: -2.75844 Start: 75 End: 110 Full_Region: cgaaagacaattgtt gagggtgtgtcaaaca ttg tgttttgacacaccctc ctttcaaatgaggca ..........................................................................gagggtgtgtcaaacattgtgttttgacacaccctc............................................................... TransTerm Strand: - Conf: 100 HP_score: -15.4 Tail_Score: -2.92613 Start: 77 End: 108 Full_Region: aaagacaattgttga gggtgtgtcaaaca ttg tgttttgacacaccc tcctttcaaatgagg ............................................................................gggtgtgtcaaacattgtgttttgacacaccc................................................................. Find igs database================================================ Query_seq: TF3006:TF3007|TF3006:TF3007:response regulator, transcriptional regulator RprY:conserved hypothetical protein:->->:3227223..3227395 173 taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: tfor_TF3006_TF3007|response regulator, transcriptional regulator RprY:conserved hypothetical protein|POSITIVE:POSITIVE|[3227223,3227395]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta taaaagaatcggagcaaggcagaggctgtcttataataaaatgcatgttttattgaggctgcctcatttgaaaggagggtgtgtcaaaacacaatgtttgacacaccctcaacaattgtctttcggaataaaacagtctttatccgctaaatatcagaaaggagcaatgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAAUCGGAGCAAGGCAGAGGCUGUCUUAUAAUAAAAUGCAUGUUUUAUUGAGGCUGCCUCAUUUGAAAGGAGGGUGUGUCAAAACACAAUGUUUGACACACCCUCAACAAUUGUCUUUCGGAAUAAAACAGUCUUUAUCCGCUAAAUAUCAGAAAGGAGCAAUGAUUA ......(((((..((.((((.(((((.((((((..(((((((....))))))))))))).))))).((((((((((((((((((((((........)))))))))))))).........))))))))........))))...(((.((.......))...)))))..))))). (-57.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAUUGCUCCUUUCUGAUAUUUAGCGGAUAAAGACUGUUUUAUUCCGAAAGACAAUUGUUGAGGGUGUGUCAAACAUUGUGUUUUGACACACCCUCCUUUCAAAUGAGGCAGCCUCAAUAAAACAUGCAUUUUAUUAUAAGACAGCCUCUGCCUUGCUCCGAUUCUUUUA .((((...((..(.....).......(((((....(.(((((((((...((((..((..((((((((((((((((((........))))))))))))))........(((((...)))))....))))))..))))...)))))))))).)))))...))...))))...... (-45.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 517 110 64 225 178 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 509 110 73 160 122 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 507 110 65 197 152 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 466 110 75 168 132 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 443 110 68 163 114 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 427 107 64 159 116 tfor:TF0702|5end_possible_peptidyl-prolyl_isomerase_744977..745207_POSITIVE 417 110 65 211 167 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 415 107 71 151 114 tfor:TF1024|5end_50S_ribosomal_protein_L19_1081948..1082178_POSITIVE 401 110 62 74 27 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 400 109 75 170 136 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 388 109 73 167 130 tfor:TF0216|5end_50S_ribosomal_protein_L20_242476..242706_POSITIVE 369 110 72 147 108 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 362 110 64 199 152 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 361 110 72 201 161 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 359 109 70 229 182 tfor:TF1454|5end_sugar_phosphate_epimerase/isomerase_1539696..1539926_POSITIVE 355 110 73 154 116 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 346 109 69 147 100 tfor:TF0107|5end_ion_channel_protein_113913..114143_POSITIVE 338 110 62 158 105 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 336 82 41 138 86 tfor:TF3033|5end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3256786..3257016_POSITIVE 331 110 71 226 187 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 507 110 65 58 13 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 500 120 71 58 4 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 490 110 65 49 4 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 408 110 75 110 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 401 110 62 61 14 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 362 110 64 53 6 tfor:TF2319|3end_acyl_carrier_protein_2476588..2476738_POSITIVE 361 110 72 46 6 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 359 109 70 110 63 tfor:TF1452|3end_conserved_hypothetical_protein;_possible_transglutaminase-like_enzyme_1539657..1539807_POSITIVE 346 109 69 61 14 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 336 82 41 110 58 tfor:TF3032|3end_thiamin_biosynthesis_protein_3256838..3256988_POSITIVE 331 110 71 63 24 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 326 65 22 69 26 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 316 109 63 57 12 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 311 120 73 78 30 tfor:TF1532|3end_potassium_uptake_system_protein_1639415..1639565_POSITIVE 307 110 67 53 16 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE 304 110 69 54 9 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 302 120 74 73 27 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 299 110 69 44 1 tfor:TF0135|3end_hypothetical_protein_146554..146704_POSITIVE 286 92 57 143 105 tfor:TF1848|3end_conserved_hypothetical_protein_1997944..1998094_POSITIVE 282 30 5 39 12 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE