Origin IGS: atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt .........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 aaatataaattttactaactgattataaaattttttatagtcagttttttattgtaaaatgaagaaacggttcccaaatagttacttcatcaatttttcgataagtatctgtatacttatatttactataaaaaatgattatagtagcaagcattaagcacatattaatttatattcatactacattaattatgcttgtactgttagcataatagaaaaaataatttatttaatatgataatat Mask Tandem Repeat Region ================================================ atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Find is-nt database================================================ Query_seq: FN1249:FN1250|FN1249:FN1250:Transcriptional regulator, DeoR family:Guanine-hypoxanthine permease:<-<-:1906332..1906575 244 atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1249:FN1250|FN1249:FN1250:Transcriptional regulator, DeoR family:Guanine-hypoxanthine permease:<-<-:1906332..1906575 244 atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1249:FN1250|FN1249:FN1250:Transcriptional regulator, DeoR family:Guanine-hypoxanthine permease:<-<-:1906332..1906575 244 atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 76 End: 201 ........................................................................... M N M C L M L A T I I I F Y S K Y K Y T D T Y R K I D E V T I W E P F L H F T I K N ........................................... Protein_Len: 32 Strand: - Start: 91 End: 186 .......................................................................................... H K S S Y D N K I T F I L I C I S I S F N I F Y S N P F R K K M .......................................................... atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt 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: 81 Start: 185 End: 214 ........................................................................................................................................................................................TTTTTTATAGTCAGTTTTTTATTGTAAAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1249:FN1250|FN1249:FN1250:Transcriptional regulator, DeoR family:Guanine-hypoxanthine permease:<-<-:1906332..1906575 244 atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: NC_003454_FN1249_FN1250|Transcriptional regulator, DeoR family:Guanine-hypoxanthine permease|NEGATIVE:NEGATIVE|[1906332,1906575]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt atattatcatattaaataaattattttttctattatgctaacagtacaagcataattaatgtagtatgaatataaattaatatgtgcttaatgcttgctactataatcattttttatagtaaatataagtatacagatacttatcgaaaaattgatgaagtaactatttgggaaccgtttcttcattttacaataaaaaactgactataaaaaattttataatcagttagtaaaatttatattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUAUCAUAUUAAAUAAAUUAUUUUUUCUAUUAUGCUAACAGUACAAGCAUAAUUAAUGUAGUAUGAAUAUAAAUUAAUAUGUGCUUAAUGCUUGCUACUAUAAUCAUUUUUUAUAGUAAAUAUAAGUAUACAGAUACUUAUCGAAAAAUUGAUGAAGUAACUAUUUGGGAACCGUUUCUUCAUUUUACAAUAAAAAACUGACUAUAAAAAAUUUUAUAAUCAGUUAGUAAAAUUUAUAUUU ......((((((((.....((((........((((((((.........)))))))))))).)))))))).((((((((....((((............((((((((.......))))))))...((((((((....)))))))).........(((((((.(((............))).))))))).))))......((((((.((((((....)))))).)))))).....))))))))... (-41.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUAAAUUUUACUAACUGAUUAUAAAAUUUUUUAUAGUCAGUUUUUUAUUGUAAAAUGAAGAAACGGUUCCCAAAUAGUUACUUCAUCAAUUUUUCGAUAAGUAUCUGUAUACUUAUAUUUACUAUAAAAAAUGAUUAUAGUAGCAAGCAUUAAGCACAUAUUAAUUUAUAUUCAUACUACAUUAAUUAUGCUUGUACUGUUAGCAUAAUAGAAAAAAUAAUUUAUUUAAUAUGAUAAUAU ................(((((((((((((....)))))))))))))..((((..((..((((((.(((.(((....))).))).))))))...((((((.((((((((....))))))))...((((((((.......))))))))((.((((.((((((...((((((.((.........)).))))))..))))))...)))).))......)))))).............))..))))... (-44.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 714 110 61 201 152 NC_003454:FN1249|5end_Transcriptional_regulator,_DeoR_family_1906241..1906471_NEGATIVE 212 118 85 199 166 NC_003454:FN0102|5end_Ribonucleoside-diphosphate_reductase_alpha_chain_736233..736463_POSITIVE 203 50 3 52 9 NC_003454:FN1940|5end_Na+_driven_multidrug_efflux_pump_440955..441185_NEGATIVE 196 191 156 110 68 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 194 115 82 88 49 NC_003454:FN1910|5end_hypothetical_protein_403208..403438_NEGATIVE 190 72 38 160 125 NC_003454:FN2012|5end_hypothetical_protein_513899..514129_NEGATIVE 188 186 166 54 34 NC_003454:FN1632|5end_LSU_ribosomal_protein_L5P_135819..136049_NEGATIVE 185 53 22 170 146 NC_003454:FN1168|5end_Macrolide-efflux_protein_1827559..1827789_NEGATIVE 184 49 26 229 206 NC_003454:FN2108|5end_galactose-1-phosphate_uridylyltransferase_619319..619549_POSITIVE 183 118 90 171 142 NC_003454:FN2019|5end_Ribosome-binding_factor_A_522292..522522_NEGATIVE 182 189 152 189 139 NC_003454:FN0387|5end_Fusobacterium_outer_membrane_protein_family_1021342..1021572_POSITIVE 182 47 2 150 107 NC_003454:FN1526|5end_Fusobacterium_outer_membrane_protein_family_38183..38413_NEGATIVE 178 48 20 173 138 NC_003454:FN1849|5end_Coenzyme_F390_synthetase_337934..338164_POSITIVE 174 129 85 168 127 NC_003454:FN1202|5end_NAD(+)_synthetase_1862298..1862528_NEGATIVE 174 240 202 115 82 NC_003454:FN0237|5end_ABC_transporter_permease_protein_862128..862358_NEGATIVE 172 180 131 204 153 NC_003454:FN0553|5end_D-serine_dehydratase_1206060..1206290_NEGATIVE 172 138 91 107 65 NC_003454:FN2058|5end_Fusobacterium_outer_membrane_protein_family_571095..571325_NEGATIVE 171 209 167 41 2 NC_003454:FN1017|5end_hypothetical_protein_1671266..1671496_POSITIVE 168 138 98 82 49 NC_003454:FN0946|5end_Zinc_metalloprotease_1599634..1599864_POSITIVE 168 187 155 88 56 NC_003454:FN0232|5end_hypothetical_protein_858018..858248_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 203 139 100 122 90 NC_003454:FN0674|3end_Transporter_1330401..1330551_POSITIVE 194 115 82 47 8 NC_003454:FN1911|3end_Outer_membrane_protein_403249..403399_NEGATIVE 188 186 166 35 15 NC_003454:FN1633|3end_LSU_ribosomal_protein_L24P_135838..135988_NEGATIVE 185 53 22 149 125 NC_003454:FN1169|3end_L-lactate_dehydrogenase_1827580..1827730_NEGATIVE 178 48 20 142 107 NC_003454:FN1848|3end_Metal_dependent_hydrolase_337983..338133_POSITIVE 171 209 167 44 5 NC_003454:FN1016|3end_Lipid_A_biosynthesis_lauroyl_acyltransferase_1671349..1671499_POSITIVE 170 179 136 57 16 NC_003454:FN0501|3end_Arginase_1149587..1149737_NEGATIVE 170 133 92 47 1 NC_003454:FN0328|3end_Na(+)-linked_D-alanine_glycine_permease_962335..962485_NEGATIVE 168 187 155 42 10 NC_003454:FN0233|3end_hypothetical_protein_858064..858214_NEGATIVE 168 199 156 99 55 NC_003454:FN0167|3end_hypothetical_protein_794416..794566_POSITIVE 168 197 156 120 68 NC_003454:FN1920|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_415879..416029_NEGATIVE 164 162 137 65 41 NC_003454:FN0313|3end_16S_rRNA_m(5)C_967_methyltransferase_951290..951440_POSITIVE 162 192 164 47 9 NC_003454:FN0090|3end_Ethanolamine_utilization_protein_eutQ_726844..726994_POSITIVE 162 57 19 128 89 NC_003454:FN2037|3end_LSU_ribosomal_protein_L12P_(L7/L12)_546769..546919_NEGATIVE 160 134 94 107 62 NC_003454:FN1330|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1983903..1984053_NEGATIVE 160 53 36 131 112 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 158 137 92 65 20 NC_003454:FN0870|3end_Rhodanese-related_sulfurtransferase_1528913..1529063_NEGATIVE 158 120 93 31 7 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 158 69 44 43 13 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 157 192 152 95 55 NC_003454:FN0790|3end_Xylose_repressor_1445294..1445444_NEGATIVE