Origin IGS: aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt .........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 actaagtttgtaattaaacttttgtttttaaaatactcaatgtactaaaatacattgggtatcttttataatttttattattaaaaatctttgcgtagctcaagccttggcttgagctctttgcgctccttgcggttaaaaaaacttgtccggattaaaattctaaagtgttgacaaaagatcgggggtatactatagtcaaagttaagaggagaatctttaaatgcaaagtttaaaaaaaataatttctatgtataagttaaaaaagcatatatttattcttgtgctcttatatcgtttattttttcactt Mask Tandem Repeat Region ================================================ aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Find is-nt database================================================ Query_seq: TDE2440:TDE2441|TDE2440:TDE2441:ABC transporter, ATP-binding/permease protein, putative:hypothetical protein:<-<-:2472134..2472445 312 aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2440:TDE2441|TDE2440:TDE2441:ABC transporter, ATP-binding/permease protein, putative:hypothetical protein:<-<-:2472134..2472445 312 aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2440:TDE2441|TDE2440:TDE2441:ABC transporter, ATP-binding/permease protein, putative:hypothetical protein:<-<-:2472134..2472445 312 aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 122 End: 229 ......................................................................................................................... M P P I F C Q H F R I L I R T S F F N R K E R K E L K P R L E L R K D F ................................................................................... aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt 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: 87 Start: 114 End: 143 .................................................................................................................GTTGACAAAAGATCGGGGGTATACTATAGT......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -9.6 Tail_Score: -3.63895 Start: 194 End: 217 Full_Region: ttaaaaatctttgcg tagctcaagc cttg gcttgagctc tttgcgctccttgcg .................................................................................................................................................................................................tagctcaagccttggcttgagctc............................................................................................... TransTerm Strand: - Conf: 95 HP_score: -12.2 Tail_Score: -3.39732 Start: 196 End: 215 Full_Region: aaaaatctttgcgta gctcaagc cttg gcttgagc tctttgcgctccttg ...................................................................................................................................................................................................gctcaagccttggcttgagc................................................................................................. TransTerm Strand: - Conf: 73 HP_score: -5.3 Tail_Score: -4.73912 Start: 250 End: 281 Full_Region: aacttttgtttttaa aatactcaatgta ctaaaa tacattgggtatc ttttataatttttat .........................................................................................................................................................................................................................................................aatactcaatgtactaaaatacattgggtatc............................... TransTerm Strand: + Conf: 70 HP_score: -6.4 Tail_Score: -4.07568 Start: 252 End: 279 Full_Region: AAAAATTATAAAAGA TACCCAATGTAT TTTA GTACATTGAGTA TTTTAAAAACAAAAG ...........................................................................................................................................................................................................................................................TACCCAATGTATTTTAGTACATTGAGTA................................. TransTerm Strand: - Conf: 75 HP_score: -7.9 Tail_Score: -3.95276 Start: 252 End: 279 Full_Region: cttttgtttttaaaa tactcaatgta ctaaaa tacattgggta tcttttataattttt ...........................................................................................................................................................................................................................................................tactcaatgtactaaaatacattgggta................................. Find igs database================================================ Query_seq: TDE2440:TDE2441|TDE2440:TDE2441:ABC transporter, ATP-binding/permease protein, putative:hypothetical protein:<-<-:2472134..2472445 312 aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: NC_002967_TDE2440_TDE2441|ABC transporter, ATP-binding/permease protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2472134,2472445]|312 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattannnnnnnnaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagnnnnnnnaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt aagtgaaaaaataaacgatataagagcacaagaataaatatatgcttttttaacttatacatagaaattattttttttaaactttgcatttaaagattctcctcttaactttgactatagtatacccccgatcttttgtcaacactttagaattttaatccggacaagtttttttaaccgcaaggagcgcaaagagctcaagccaaggcttgagctacgcaaagatttttaataataaaaattataaaagatacccaatgtattttagtacattgagtattttaaaaacaaaagtttaattacaaacttagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUGAAAAAAUAAACGAUAUAAGAGCACAAGAAUAAAUAUAUGCUUUUUUAACUUAUACAUAGAAAUUAUUUUUUUUAAACUUUGCAUUUAAAGAUUCUCCUCUUAACUUUGACUAUAGUAUACCCCCGAUCUUUUGUCAACACUUUAGAAUUUUAAUCCGGACAAGUUUUUUUAACCGCAAGGAGCGCAAAGAGCUCAAGCCAAGGCUUGAGCUACGCAAAGAUUUUUAAUAAUAAAAAUUAUAAAAGAUACCCAAUGUAUUUUAGUACAUUGAGUAUUUUAAAAACAAAAGUUUAAUUACAAACUUAGU ...(((((((((...((...((((((....(((((......((((...(((((.........(((((....))))))))))....))))......))))).))))))...(((((...((............))...)))))..................)).....))))))))).((....)).(((.....(((((((((....))))))))).)))...((((((((....))))))))....(((((((.((((((((....)))))))).)))))))........((((((......))))))... (-61.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAAGUUUGUAAUUAAACUUUUGUUUUUAAAAUACUCAAUGUACUAAAAUACAUUGGGUAUCUUUUAUAAUUUUUAUUAUUAAAAAUCUUUGCGUAGCUCAAGCCUUGGCUUGAGCUCUUUGCGCUCCUUGCGGUUAAAAAAACUUGUCCGGAUUAAAAUUCUAAAGUGUUGACAAAAGAUCGGGGGUAUACUAUAGUCAAAGUUAAGAGGAGAAUCUUUAAAUGCAAAGUUUAAAAAAAAUAAUUUCUAUGUAUAAGUUAAAAAAGCAUAUAUUUAUUCUUGUGCUCUUAUAUCGUUUAUUUUUUCACUU ...((((......(((((((((.((.((((((.(((((((((((......)))))))))))((((((.(((((((.(((((.....(((((((((((((((((((....)))))))))....))))..(((...(((((....((((....(((.......))).)))).)))))..)))...)))))).....))))).))))))))))))).....)))))).)))))))))))(((((((((.....(((((((((.......((((((..........)))))))))))).)))))))))))).)))) (-70.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 831 130 81 221 172 NC_002967:TDE2440|5end_ABC_transporter,_ATP-binding/permease_protein,_putative_2472043..2472273_NEGATIVE 427 220 173 117 72 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 427 220 173 193 148 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 386 208 176 135 108 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 364 198 159 72 37 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 358 209 161 212 158 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 352 211 176 111 75 NC_002967:TDE2168|5end_hypothetical_protein_2201003..2201233_NEGATIVE 339 220 177 87 42 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 333 210 162 224 175 NC_002967:TDE0786|5end_ribosomal_protein_L15_814602..814832_POSITIVE 331 219 176 59 7 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 331 210 161 162 108 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 330 208 173 221 191 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 328 208 161 123 74 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 306 220 177 164 122 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 304 210 161 208 150 NC_002967:TDE1864|5end_crossover_junction_endodeoxyribonuclease_RuvC_1889108..1889338_NEGATIVE 301 220 176 180 128 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 300 208 173 195 165 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 300 130 87 143 89 NC_002967:TDE1511|5end_pathogen-specific_surface_antigen,_putative_1558488..1558718_POSITIVE 299 198 161 226 192 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 299 198 161 99 65 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 484 220 174 80 29 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 386 208 176 71 44 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 364 198 159 79 44 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE 340 220 178 122 67 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 337 220 178 90 34 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 321 202 176 128 102 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 307 220 171 146 80 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 305 219 177 151 109 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 303 220 171 60 6 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 301 220 176 118 66 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 300 130 87 103 49 NC_002967:TDE1510|3end_hypothetical_protein_1558528..1558678_POSITIVE 299 220 178 133 96 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 297 210 182 50 19 NC_002967:TDE1077|3end_hypothetical_protein_1109680..1109830_POSITIVE 286 204 161 151 99 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 285 199 152 149 93 NC_002967:TDE0024|3end_glycosyl_hydrolase,_family_3_29419..29569_NEGATIVE 283 220 173 135 90 NC_002967:TDE2733|3end_hypothetical_protein_2789126..2789276_POSITIVE 283 221 184 44 6 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 282 221 183 151 111 NC_002967:TDE2728|3end_hypothetical_protein_2785815..2785965_POSITIVE 281 208 163 86 45 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 278 218 171 147 95 NC_002967:TDE1944|3end_hypothetical_protein_1961071..1961221_POSITIVE