Origin IGS: aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag .........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 ctttacctccaatatatctacgataatataagtataccctattcaaaactaaagtgcaagacaacgcttggatttaaaaagctctcatggatacctcttttattaaaaaaatattacaaaattgatttccgtgttgaggcaatgcgcagacttgacaacttacaaagtgattgctagaataataagtaggaactaaaaacttcagtttttagaaatgcccatatattaatataggaggtgttttt Mask Tandem Repeat Region ================================================ aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Find is-nt database================================================ Query_seq: TDE0462:TDE0463|TDE0462:TDE0463:metallo-beta-lactamase family protein:purine nucleoside phosphorylase:<-->:517078..517322 245 aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0462:TDE0463|TDE0462:TDE0463:metallo-beta-lactamase family protein:purine nucleoside phosphorylase:<-->:517078..517322 245 aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0462:TDE0463|TDE0462:TDE0463:metallo-beta-lactamase family protein:purine nucleoside phosphorylase:<-->:517078..517322 245 aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 41 End: 169 ........................................ M K F L V P T Y Y S S N H F V S C Q V C A L P Q H G N Q F C N I F L I K E V S M R A F ............................................................................ Protein_Len: 53 Strand: - Start: 72 End: 230 ....................................................................... C D S Q L N D L R R M A E V R F D I K Y Y K K L L L P I W S L K K F G L T T K C K L K S Y P I S I N D Y M ............... aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag 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: 91 Start: 66 End: 95 .................................................................CTTGACAACTTACAAAGTGATTGCTAGAAT...................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 186 End: 215 .........................................................................................................................................................................................CTTGCACTTTAGTTTTGAATAGGGTATACT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0462:TDE0463|TDE0462:TDE0463:metallo-beta-lactamase family protein:purine nucleoside phosphorylase:<-->:517078..517322 245 aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_002967_TDE0462_TDE0463|metallo-beta-lactamase family protein:purine nucleoside phosphorylase|NEGATIVE:POSITIVE|[517078,517322]|245 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatannnnnnnaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag aaaaacacctcctatattaatatatgggcatttctaaaaactgaagtttttagttcctacttattattctagcaatcactttgtaagttgtcaagtctgcgcattgcctcaacacggaaatcaattttgtaatatttttttaataaaagaggtatccatgagagctttttaaatccaagcgttgtcttgcactttagttttgaatagggtatacttatattatcgtagatatattggaggtaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACACCUCCUAUAUUAAUAUAUGGGCAUUUCUAAAAACUGAAGUUUUUAGUUCCUACUUAUUAUUCUAGCAAUCACUUUGUAAGUUGUCAAGUCUGCGCAUUGCCUCAACACGGAAAUCAAUUUUGUAAUAUUUUUUUAAUAAAAGAGGUAUCCAUGAGAGCUUUUUAAAUCCAAGCGUUGUCUUGCACUUUAGUUUUGAAUAGGGUAUACUUAUAUUAUCGUAGAUAUAUUGGAGGUAAAG ......((((((.(((((((((..((((.....((((((((....))))))))..))))..))))).((((.(((..(((....((((.(.((((.(.((((..((((((...((((((.....))))))..((((.....))))...))))))....((.((..........)))).)))).).))))))))).))).))).(((((.....))))).......)))).)))).)))))).... (-50.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUACCUCCAAUAUAUCUACGAUAAUAUAAGUAUACCCUAUUCAAAACUAAAGUGCAAGACAACGCUUGGAUUUAAAAAGCUCUCAUGGAUACCUCUUUUAUUAAAAAAAUAUUACAAAAUUGAUUUCCGUGUUGAGGCAAUGCGCAGACUUGACAACUUACAAAGUGAUUGCUAGAAUAAUAAGUAGGAACUAAAAACUUCAGUUUUUAGAAAUGCCCAUAUAUUAAUAUAGGAGGUGUUUUU ...(((((((.((((........(((((((.((((..((((((........((((.((((......)))).))))......(((.((((((....................................))))))..)))(((((.(((....(((........))).))))))))..........))))))..((((((((....))))))))..))))...))))))))))).)))))))..... (-45.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 921 120 71 211 162 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 624 159 113 220 174 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 495 166 121 207 161 NC_002967:TDE1955|5end_hypothetical_protein_1970900..1971130_NEGATIVE 366 62 23 48 8 NC_002967:TDE2377|5end_hypothetical_protein_2407667..2407897_NEGATIVE 366 62 23 188 148 NC_002967:TDE2376|5end_hypothetical_protein_2407527..2407757_NEGATIVE 361 58 22 202 162 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 321 119 75 201 140 NC_002967:TDE1493|5end_chemotaxis_protein_CheX_1538590..1538820_POSITIVE 312 117 77 185 149 NC_002967:TDE1350|5end_rod_shape-determining_protein_MreC_1390327..1390557_POSITIVE 307 129 81 183 140 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 301 50 1 172 120 NC_002967:TDE2199|5end_racemase,_Asp/Glu/Hydantoin_family_2237150..2237380_NEGATIVE 290 210 164 74 25 NC_002967:TDE0412|5end_hypothetical_protein_464936..465166_POSITIVE 288 118 80 194 143 NC_002967:TDE0898|5end_hypothetical_protein_915878..916108_POSITIVE 270 112 82 164 142 NC_002967:TDE0968|5end_translation_elongation_factor_P_993126..993356_NEGATIVE 265 212 174 167 121 NC_002967:TDE0748|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_784288..784518_NEGATIVE 263 122 89 185 154 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 261 202 163 53 8 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 258 108 68 197 153 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 258 165 126 75 33 NC_002967:TDE1617|5end_hypothetical_protein_1664859..1665089_NEGATIVE 258 165 126 211 169 NC_002967:TDE1616|5end_glycerate_dehydrogenase_1664723..1664953_NEGATIVE 257 190 148 177 124 NC_002967:TDE1769|5end_hypothetical_protein_1814377..1814607_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 430 173 131 42 2 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 361 58 22 78 38 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 316 59 26 85 48 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 314 64 26 70 30 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 306 65 21 95 44 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 301 50 1 72 20 NC_002967:TDE2200|3end_methionine_gamma-lyase_2237250..2237400_NEGATIVE 285 209 164 151 104 NC_002967:TDE0411|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_465095..465245_POSITIVE 273 130 87 45 3 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 263 122 89 60 29 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 262 58 16 85 38 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 255 207 161 109 55 NC_002967:TDE1943|3end_30S_ribosomal_protein_S4_1959436..1959586_NEGATIVE 251 196 151 83 37 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 248 208 161 144 93 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 241 62 25 55 10 NC_002967:TDE1072|3end_lipoprotein,_putative_1103436..1103586_POSITIVE 239 110 61 138 91 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 237 210 161 69 20 NC_002967:TDE2564|3end_PemK_family_protein_2590393..2590543_POSITIVE 237 200 151 113 38 NC_002967:TDE2500|3end_DJ-1_family_protein_2523952..2524102_NEGATIVE 236 107 77 147 111 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 235 192 154 61 27 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 235 117 72 49 6 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE