Origin IGS: gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt .........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 aaaaaaataaaaatccccatcggaggggcgaagtcttccgatggggtaaggcttgttttaattttgattaaggttactatagttattcagcgttcgctatttggtcagcagtataatctgaagattttgttcccactaaataaaaatcatcaccgtctttaccaatagtcagcgtatttccttctattttgaaggttgtagtttcatcttcattatcgtcaaatgttatcttgttgcctgatattgtgtatttcgctttctacaacttatataattcaccttctaccgctaaaagaaggatagctaaaaatattttatttttcattaaaatctccttaaggttac Mask Tandem Repeat Region ================================================ gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Find is-nt database================================================ Query_seq: TDE2557:TDE2558|TDE2557:TDE2558:hypothetical protein:ABC transporter, ATP-binding/permease protein:<-<-:2583474..2583818 345 gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2557:TDE2558|TDE2557:TDE2558:hypothetical protein:ABC transporter, ATP-binding/permease protein:<-<-:2583474..2583818 345 gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2557:TDE2558|TDE2557:TDE2558:hypothetical protein:ABC transporter, ATP-binding/permease protein:<-<-:2583474..2583818 345 gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 102 End: 260 ..................................................................................................... M S G N K I T F D D N E D E T T T F K I E G N T L T I G K D G D D F Y L V G T K S S D Y T A D Q I A N A E ..................................................................................... Protein_Len: 53 Strand: - Start: 181 End: 339 .................................................................................................................................................................................... Q Y L R H H N K N L P F L I K L N Y Q Q G F L S R Q I V I T V K I L I L V L R V G D S S K A G G I P I K M ...... Protein_Len: 33 Strand: - Start: 108 End: 206 ........................................................................................................... A V L Y C K V I I F I F S C G E F Y F S I R Q S N T F V T I I K M ........................................................................................................................................... Protein_Len: 60 Strand: - Start: 2 End: 181 . L R L S I K I F F L I N K A I R R K A T S P S N Y L N Y F A F Y V I D P L L I V N S S L S S S V V V K L I S P F V S V M .................................................................................................................................................................... gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt 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================================================ gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2557:TDE2558|TDE2557:TDE2558:hypothetical protein:ABC transporter, ATP-binding/permease protein:<-<-:2583474..2583818 345 gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatggggatttttattttttt Intra-Species Hit: Count: 1 Min: 1 Max: 332 Len: 332 Subject: NC_002967_TDE2557_TDE2558|hypothetical protein:ABC transporter, ATP-binding/permease protein|NEGATIVE:NEGATIVE|[2583474,2583818]|345 HSP 1 e-value: 0.0 bit: 658.0 Len: 332 Query Start:1 Query End:332 Subject Strand: POSITIVE Subject Start: 1 Subject End: 332 gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatgggga............. gtaaccttaaggagattttaatgaaaaataaaatatttttagctatccttcttttagcggtagaaggtgaattatataagttgtagaaagcgaaatacacaatatcaggcaacaagataacatttgacgataatgaagatgaaactacaaccttcaaaatagaaggaaatacgctgactattggtaaagacggtgatgatttttatttagtgggaacaaaatcttcagattatactgctgaccaaatagcgaacgctgaataactatagtaaccttaatcaaaattaaaacaagccttaccccatcggaagacttcgcccctccgatgggga............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAACCUUAAGGAGAUUUUAAUGAAAAAUAAAAUAUUUUUAGCUAUCCUUCUUUUAGCGGUAGAAGGUGAAUUAUAUAAGUUGUAGAAAGCGAAAUACACAAUAUCAGGCAACAAGAUAACAUUUGACGAUAAUGAAGAUGAAACUACAACCUUCAAAAUAGAAGGAAAUACGCUGACUAUUGGUAAAGACGGUGAUGAUUUUUAUUUAGUGGGAACAAAAUCUUCAGAUUAUACUGCUGACCAAAUAGCGAACGCUGAAUAACUAUAGUAACCUUAAUCAAAAUUAAAACAAGCCUUACCCCAUCGGAAGACUUCGCCCCUCCGAUGGGGA .......(((((...(((((((...................((((.........)))).(...(((((..(((((...((((((....((((..........((((.(....).......((((.......))))..)))).........(((((......))))).....(((((....(((((..((.(((((.((((((........((....))........))))))))))))).))))).)))))..))))..))))))))))).)))))...)...)))))))....)))))((((((((((.(........).)))))))))). (-75.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCCAUCGGAGGGGCGAAGUCUUCCGAUGGGGUAAGGCUUGUUUUAAUUUUGAUUAAGGUUACUAUAGUUAUUCAGCGUUCGCUAUUUGGUCAGCAGUAUAAUCUGAAGAUUUUGUUCCCACUAAAUAAAAAUCAUCACCGUCUUUACCAAUAGUCAGCGUAUUUCCUUCUAUUUUGAAGGUUGUAGUUUCAUCUUCAUUAUCGUCAAAUGUUAUCUUGUUGCCUGAUAUUGUGUAUUUCGCUUUCUACAACUUAUAUAAUUCACCUUCUACCGCUAAAAGAAGGAUAGCUAAAAAUAUUUUAUUUUUCAUUAAAAUCUCCUUAAGGUUAC .(((((((((((((......)))))))))))))(((((...((((((((..((((.(((((.((((((........(((((.((((((.(((...(((......)))..((((((..............))))))............))))))))).)))))....(((((......))))).))))))...))))).)))).....(((((((.....((((...((....(((.....)))..))..))))............((((((.........)))))).........)))))))........))))))))..)))))....... (-75.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 815 90 41 181 132 NC_002967:TDE2557|5end_hypothetical_protein_2583383..2583613_NEGATIVE 310 327 292 146 95 NC_002967:TDE2181|5end_PAP2_family_protein_2213035..2213265_NEGATIVE 294 330 295 116 79 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 294 330 295 95 58 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 294 330 295 217 180 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 291 330 284 108 56 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 280 329 295 210 173 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 276 330 304 30 3 NC_002967:TDE2317|5end_hemolysin_III_2354771..2355001_NEGATIVE 276 327 282 214 161 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 275 325 282 47 3 NC_002967:TDE1427|5end_glycosyl_transferase,_group_1_family_protein_1469713..1469943_POSITIVE 274 330 287 200 150 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 274 329 292 141 95 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 272 330 293 58 13 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 269 329 293 160 119 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 269 240 191 187 128 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 267 91 55 155 115 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 264 320 271 106 48 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 262 329 292 154 110 NC_002967:TDE1649|5end_hypothetical_protein_1697437..1697667_NEGATIVE 261 324 288 70 28 NC_002967:TDE1440|5end_glucose-1-phosphate_thymidylyltransferase_1485353..1485583_POSITIVE 260 269 222 197 150 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 329 292 84 47 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE 317 329 293 149 111 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 310 327 292 146 95 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 298 330 293 142 87 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 291 330 284 95 43 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 288 326 293 122 96 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 276 327 282 103 50 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 275 325 282 59 15 NC_002967:TDE1426|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1469805..1469955_POSITIVE 270 140 101 91 57 NC_002967:TDE2336|3end_sodium/dicarboxylate_symporter_family_protein_2371925..2372075_NEGATIVE 267 91 55 151 111 NC_002967:TDE1910|3end_1-deoxy-D-xylulose-5-phosphate_synthase_1926876..1927026_NEGATIVE 266 69 45 74 51 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 264 320 271 106 48 NC_002967:TDE1744|3end_chromate_transport_protein_1798503..1798653_NEGATIVE 262 330 302 49 22 NC_002967:TDE0108|3end_hypothetical_protein_128787..128937_POSITIVE 260 269 222 142 95 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 258 207 164 95 43 NC_002967:TDE2296|3end_hypothetical_protein_2334283..2334433_NEGATIVE 258 68 36 149 120 NC_002967:TDE1963|3end_selenocysteine-specific_translation_elongation_factor_1977141..1977291_POSITIVE 258 73 36 141 104 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 257 330 287 68 38 NC_002967:TDE2061|3end_hypothetical_protein_2086779..2086929_NEGATIVE 254 194 153 59 9 NC_002967:TDE0451|3end_arginine_deiminase_509965..510115_POSITIVE 253 326 290 84 51 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE