Origin IGS: tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat .........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 attagttcctcctataataaatgtttaatacataatgcattatgtattttattaaattaagtataactctttttaatttatttgtcaaattattttgatagtgttttaaattagtaaattaagttataaatcttacatataaataaatttatatagatatatttagaatattttttatgaactagattttttagttttataagtggaagaaatttcatttttttattatgtttgaagttttttgttaaatatgttatatttgctatatagtttaagattgggggataaagaaaatgaaa Mask Tandem Repeat Region ================================================ tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Find is-nt database================================================ Query_seq: FN1987:FN1988|FN1987:FN1988:Transcriptional regulator, GntR family:Tyrosine phenol-lyase:<-->:490759..491057 299 tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1987:FN1988|FN1987:FN1988:Transcriptional regulator, GntR family:Tyrosine phenol-lyase:<-->:490759..491057 299 tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1987:FN1988|FN1987:FN1988:Transcriptional regulator, GntR family:Tyrosine phenol-lyase:<-->:490759..491057 299 tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 22 End: 186 ..................... M L N Y I A N I T Y L T K N F K H N K K M K F L P L I K L K N L V H K K Y S K Y I Y I N L F I C K I Y N L I Y ................................................................................................................. tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat 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: 90 Start: 211 End: 240 ..................................................................................................................................................................................................................TTTGACAAATAAATTAAAAAGAGTTATACT........................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 40 End: 69 .......................................TTTGAAGTTTTTTGTTAAATATGTTATATT...................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 190 End: 219 .............................................................................................................................................................................................TTTGTCAAATTATTTTGATAGTGTTTTAAA................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1987:FN1988|FN1987:FN1988:Transcriptional regulator, GntR family:Tyrosine phenol-lyase:<-->:490759..491057 299 tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaacaaaaaacttcaaacataataaaaaaatgaaatttcttccacttataaaactaaaaaatctagttcataaaaaatattctaaatatatctatataaatttatttatatgtaagatttataacttaatttactaatttaaaacactatcaaaataatttgacaaataaattaaaaagagttatacttaatttaataaaatacataatgcattatgtattaaacatttattataggaggaactaat Intra-Species Hit: Count: 1 Min: 1 Max: 299 Len: 299 Subject: NC_003454_FN1987_FN1988|Transcriptional regulator, GntR family:Tyrosine phenol-lyase|NEGATIVE:POSITIVE|[490759,491057]|299 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 56 Query Start:1 Query End:56 Subject Strand: POSITIVE Subject Start: 1 Subject End: 56 tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaac................................................................................................................................................................................................................................................... tttcattttctttatcccccaatcttaaactatatagcaaatataacatatttaac................................................................................................................................................................................................................................................... HSP 2 e-value: 8.0E-13 bit: 75.8 Len: 38 Query Start:262 Query End:299 Subject Strand: POSITIVE Subject Start: 262 Subject End: 299 .....................................................................................................................................................................................................................................................................gcattatgtattaaacatttattataggaggaactaat .....................................................................................................................................................................................................................................................................gcattatgtattaaacatttattataggaggaactaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAUUUUCUUUAUCCCCCAAUCUUAAACUAUAUAGCAAAUAUAACAUAUUUAACAAAAAACUUCAAACAUAAUAAAAAAAUGAAAUUUCUUCCACUUAUAAAACUAAAAAAUCUAGUUCAUAAAAAAUAUUCUAAAUAUAUCUAUAUAAAUUUAUUUAUAUGUAAGAUUUAUAACUUAAUUUACUAAUUUAAAACACUAUCAAAAUAAUUUGACAAAUAAAUUAAAAAGAGUUAUACUUAAUUUAAUAAAAUACAUAAUGCAUUAUGUAUUAAACAUUUAUUAUAGGAGGAACUAAU (((((((((.(((((...............(((((.....))))).....(((....))).............)))))))))))))).(((((((........(((((.......))))).((((.((((....(((((.....((((((((....)))))))).......((((((((.......(((((((........(((((....)))))....)))))))....))))))))....)))))....(((((((((....)))))))))....)))).)))).)))))))..... (-30.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAGUUCCUCCUAUAAUAAAUGUUUAAUACAUAAUGCAUUAUGUAUUUUAUUAAAUUAAGUAUAACUCUUUUUAAUUUAUUUGUCAAAUUAUUUUGAUAGUGUUUUAAAUUAGUAAAUUAAGUUAUAAAUCUUACAUAUAAAUAAAUUUAUAUAGAUAUAUUUAGAAUAUUUUUUAUGAACUAGAUUUUUUAGUUUUAUAAGUGGAAGAAAUUUCAUUUUUUUAUUAUGUUUGAAGUUUUUUGUUAAAUAUGUUAUAUUUGCUAUAUAGUUUAAGAUUGGGGGAUAAAGAAAAUGAAA ......((((((..............(((((((((....)))))))))...((((((((............(((((..((((.((((((....))))))))))..))))).((((((((.................(((((((....))))))).(((((((((((.......(((((((((((((...))))).))))))))...(((((((((((...............))))))))))).)))))))))))..))))))))..))))))))....)))))).............. (-51.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 702 50 1 141 92 NC_003454:FN1987|5end_Transcriptional_regulator,_GntR_family_490668..490898_NEGATIVE 240 35 1 127 86 NC_003454:FN1797|5end_Spermidine/putrescine_transport_ATP-binding_protein_potA_278821..279051_POSITIVE 207 38 1 136 86 NC_003454:FN1754|5end_thiazole_synthase_251117..251347_NEGATIVE 205 123 89 91 58 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 199 290 242 147 94 NC_003454:FN1008|5end_hypothetical_protein_1663067..1663297_NEGATIVE 189 45 2 125 87 NC_003454:FN0788|5end_hypothetical_protein_1444359..1444589_NEGATIVE 186 20 1 104 86 NC_003454:FN0819|5end_Tetratricopeptide_repeat_family_protein_1477248..1477478_POSITIVE 181 39 2 130 93 NC_003454:FN0592|5end_ATP-dependent_DNA_helicase_pcrA_1245712..1245942_POSITIVE 179 57 18 184 146 NC_003454:FN1710|5end_Integral_membrane_protein,_YGGT_family_205992..206222_POSITIVE 176 24 5 156 139 NC_003454:FN0551|5end_Bacterial_regulatory_proteins,_crp_family_1203276..1203506_POSITIVE 170 122 81 196 155 NC_003454:FN1026|5end_tRNA_pseudouridine_synthase_A_1680823..1681053_NEGATIVE 169 54 11 105 50 NC_003454:FN0850|5end_Hypothetical_cytosolic_protein_1508913..1509143_POSITIVE 165 46 15 113 83 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 163 37 1 133 94 NC_003454:FN2108|5end_galactose-1-phosphate_uridylyltransferase_619319..619549_POSITIVE 162 54 15 183 138 NC_003454:FN0930|5end_Glycerol-3-phosphate_cytidylyltransferase_1583964..1584194_NEGATIVE 162 26 5 94 74 NC_003454:FN0623|5end_Malonate_transporter_1281952..1282182_POSITIVE 160 132 91 44 8 NC_003454:FN0696|5end_hypothetical_protein_1353694..1353924_POSITIVE 160 204 161 202 168 NC_003454:FN1838|5end_Glycerol_uptake_facilitator_protein_327489..327719_POSITIVE 159 35 1 119 86 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 159 26 11 110 94 NC_003454:FN0919|5end_DNA-dependent_DNA_polymerase_III_alpha_chain_1574535..1574765_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 189 45 2 48 10 NC_003454:FN0789|3end_Transporter_1444436..1444586_NEGATIVE 170 111 71 77 29 NC_003454:FN0377|3end_Iron(III)-transport_system_permease_protein_sfuB_1009196..1009346_POSITIVE 169 54 11 104 49 NC_003454:FN0849|3end_8-amino-7-oxononanoate_synthase_1508992..1509142_POSITIVE 163 37 1 133 94 NC_003454:FN2107|3end_galactokinase_619399..619549_POSITIVE 162 39 2 112 75 NC_003454:FN1444|3end_GMP_synthase_[glutamine-hydrolyzing]_2113203..2113353_POSITIVE 162 26 5 73 53 NC_003454:FN0622|3end_N-glycosylase/DNA_lyase_1282011..1282161_POSITIVE 159 35 1 100 67 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 159 26 11 27 11 NC_003454:FN0920|3end_Protease_HTPX_1574618..1574768_NEGATIVE 159 35 2 125 94 NC_003454:FN0426|3end_Orotidine_5'-phosphate_decarboxylase_1069513..1069663_POSITIVE 159 26 2 119 94 NC_003454:FN0399|3end_Dipeptide_transport_ATP-binding_protein_dppD_1038733..1038883_POSITIVE 158 131 91 69 36 NC_003454:FN0712|3end_Chromate_transport_protein_1371416..1371566_POSITIVE 157 35 1 103 74 NC_003454:FN0292|3end_Hemolysin_activator_protein_precursor_925011..925161_NEGATIVE 155 48 2 119 68 NC_003454:FN0446|3end_hypothetical_protein_1089404..1089554_POSITIVE 154 104 71 67 32 NC_003454:FN1065|3end_hypothetical_protein_1711817..1711967_POSITIVE 154 31 1 114 86 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE 154 212 177 76 40 NC_003454:FN0410|3end_6-phosphofructokinase_1048299..1048449_POSITIVE 154 47 6 74 34 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 153 48 1 139 89 NC_003454:FN1290|3end_hypothetical_protein_1946444..1946594_NEGATIVE 153 31 1 96 67 NC_003454:FN0661|3end_hypothetical_protein_1318213..1318363_POSITIVE 152 50 1 53 5 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE