Origin IGS: tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa .........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 tttttatgcactgcaaaccttttgcagtgcattttttattccagcttaattcccttgccttttaaattctcgacacactcaagataatagttattcatcgtgttcgacatagatgggtttccctactttaacagccttcaaattatcatagccgatagcttattgacatgaaaagtaaattatgttatatttatactataaatcatacaaatcatactttatgtttggaggtgagaaa Mask Tandem Repeat Region ================================================ tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Find is-nt database================================================ Query_seq: TDE0703:TDE0704|TDE0703:TDE0704:transcriptional regulator, AbrB family:SPFH domain/Band 7 family protein:<-<-:738281..738518 238 tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0703:TDE0704|TDE0703:TDE0704:transcriptional regulator, AbrB family:SPFH domain/Band 7 family protein:<-<-:738281..738518 238 tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0703:TDE0704|TDE0703:TDE0704:transcriptional regulator, AbrB family:SPFH domain/Band 7 family protein:<-<-:738281..738518 238 tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Predict ORF larger than 30AA ================================================ tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa 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: 89 Start: 48 End: 77 ...............................................ATTGACATGAAAAGTAAATTATGTTATATT................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0703:TDE0704|TDE0703:TDE0704:transcriptional regulator, AbrB family:SPFH domain/Band 7 family protein:<-<-:738281..738518 238 tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: NC_002967_TDE0703_TDE0704|transcriptional regulator, AbrB family:SPFH domain/Band 7 family protein|NEGATIVE:NEGATIVE|[738281,738518]|238 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 238 Query Start:1 Query End:238 Subject Strand: POSITIVE Subject Start: 1 Subject End: 238 tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa tttctcacctccaaacataaagtatgatttgtatgatttatagtataaatataacataatttacttttcatgtcaataagctatcggctatgataatttgaaggctgttaaagtagggaaacccatctatgtcgaacacgatgaataactattatcttgagtgtgtcgagaatttaaaaggcaagggaattaagctggaataaaaaatgcactgcaaaaggtttgcagtgcataaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCACCUCCAAACAUAAAGUAUGAUUUGUAUGAUUUAUAGUAUAAAUAUAACAUAAUUUACUUUUCAUGUCAAUAAGCUAUCGGCUAUGAUAAUUUGAAGGCUGUUAAAGUAGGGAAACCCAUCUAUGUCGAACACGAUGAAUAACUAUUAUCUUGAGUGUGUCGAGAAUUUAAAAGGCAAGGGAAUUAAGCUGGAAUAAAAAAUGCACUGCAAAAGGUUUGCAGUGCAUAAAAA .........((((........((...((((((((........))))))))...))....((((.((..(.((((.........(((((...(((.........(((.....))).((....)).)))...)))))...................((((((.....))))))........)))).)..)).)))).)))).......(((((((((((.....)))))))))))..... (-51.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUGCACUGCAAACCUUUUGCAGUGCAUUUUUUAUUCCAGCUUAAUUCCCUUGCCUUUUAAAUUCUCGACACACUCAAGAUAAUAGUUAUUCAUCGUGUUCGACAUAGAUGGGUUUCCCUACUUUAACAGCCUUCAAAUUAUCAUAGCCGAUAGCUUAUUGACAUGAAAAGUAAAUUAUGUUAUAUUUAUACUAUAAAUCAUACAAAUCAUACUUUAUGUUUGGAGGUGAGAAA .....(((((((((((.....)))))))))))..................................(((((..................(..((((((((((.....))).)))))))..)............((((((((((..(((.(((.....)))...))).....((((((.....(((...((((((...))))))...))).....))))))..))))))))))))))). (-47.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 870 140 91 231 182 NC_002967:TDE0703|5end_transcriptional_regulator,_AbrB_family_738190..738420_NEGATIVE 355 84 41 183 140 NC_002967:TDE0700|5end_hypothetical_protein_736398..736628_NEGATIVE 260 106 65 230 176 NC_002967:TDE0865|5end_hypothetical_protein_887127..887357_POSITIVE 259 142 104 163 121 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 258 220 177 129 80 NC_002967:TDE2524|5end_ABC_transporter,_ATP-binding_protein_2550456..2550686_POSITIVE 258 198 162 63 17 NC_002967:TDE0683|5end_hypothetical_protein_721303..721533_NEGATIVE 254 130 84 197 139 NC_002967:TDE2261|5end_hypothetical_protein_2298013..2298243_NEGATIVE 251 108 63 55 11 NC_002967:TDE0181|5end_methyl-accepting_chemotaxis_protein_215077..215307_NEGATIVE 241 195 158 147 100 NC_002967:TDE0903|5end_ATP-dependent_DNA_helicase_PcrA_920228..920458_POSITIVE 240 196 157 171 128 NC_002967:TDE1267|5end_phosphoribosylamine--glycine_ligase_1302940..1303170_NEGATIVE 239 140 91 148 91 NC_002967:TDE0388|5end_hypothetical_protein_439173..439403_POSITIVE 238 140 103 74 29 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 235 142 104 139 105 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 235 230 202 144 114 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 233 97 60 110 80 NC_002967:TDE2756|5end_bacterial_extracellular_solute-binding_protein,_family_5_2813517..2813747_NEGATIVE 233 199 157 214 171 NC_002967:TDE2106|5end_hypothetical_protein_2131740..2131970_NEGATIVE 233 118 81 195 164 NC_002967:TDE0916|5end_ABC_transporter,_ATP-binding/permease_protein_933359..933589_POSITIVE 233 139 97 169 121 NC_002967:TDE0863|5end_MgtC_family_protein_884526..884756_POSITIVE 233 213 178 31 3 NC_002967:TDE0045|5end_ABC_transporter,_ATP-binding_protein_55113..55343_NEGATIVE 231 125 82 182 127 NC_002967:TDE1862|5end_hypothetical_protein_1886928..1887158_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 84 41 62 19 NC_002967:TDE0701|3end_hypothetical_protein_736519..736669_NEGATIVE 299 198 155 143 95 NC_002967:TDE2292|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_2329383..2329533_POSITIVE 283 119 73 39 1 NC_002967:TDE2199|3end_racemase,_Asp/Glu/Hydantoin_family_2236476..2236626_NEGATIVE 279 192 157 139 107 NC_002967:TDE0404|3end_hypothetical_protein_455359..455509_NEGATIVE 275 118 71 122 68 NC_002967:TDE0035|3end_acetyltransferase,_GNAT_family_41580..41730_NEGATIVE 274 200 167 44 6 NC_002967:TDE1967|3end_hypothetical_protein_1982533..1982683_POSITIVE 270 200 154 66 13 NC_002967:TDE1500|3end_hypothetical_protein_1546763..1546913_NEGATIVE 269 143 103 58 5 NC_002967:TDE0894|3end_hypothetical_protein_911239..911389_POSITIVE 259 142 104 89 47 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 258 220 177 108 59 NC_002967:TDE2523|3end_hypothetical_protein_2550515..2550665_POSITIVE 245 129 82 140 85 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 240 196 157 91 48 NC_002967:TDE1268|3end_type_II_restriction_endonuclease_TdeI_1303020..1303170_NEGATIVE 239 140 91 151 94 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE 238 140 103 77 32 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 238 119 78 86 41 NC_002967:TDE2339|3end_leucyl-tRNA_synthetase_2377501..2377651_POSITIVE 238 229 182 149 92 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 233 227 181 128 79 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 231 120 80 33 1 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 231 118 84 141 113 NC_002967:TDE0574|3end_surface_protein,_putative_605862..606012_POSITIVE 227 89 42 72 17 NC_002967:TDE0683|3end_hypothetical_protein_721187..721337_NEGATIVE