Origin IGS: gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtaactgtaacttaccctatagggtaagtcaagcttactgcataaggtaagccgcacttaccctgtaaggtaacaccggcttaccgcacagggtaagcaaaataaatctttaaggaggtttgac Mask Tandem Repeat Region ================================================ gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Find is-nt database================================================ Query_seq: TDE2258:TDE2259|TDE2258:TDE2259:surface antigen BspA, putative:hypothetical protein:<-<-:2296492..2296616 125 gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2258:TDE2259|TDE2258:TDE2259:surface antigen BspA, putative:hypothetical protein:<-<-:2296492..2296616 125 gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2258:TDE2259|TDE2258:TDE2259:surface antigen BspA, putative:hypothetical protein:<-<-:2296492..2296616 125 gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Predict ORF larger than 30AA ================================================ gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc 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: 82 Start: 92 End: 121 ...........................................................................................CTTGACTTACCCTATAGGGTAAGTTACAGT.... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -10.0 Tail_Score: -3.3334 Start: 40 End: 79 Full_Region: TTGCTTACCCTGTGC GGTAAGCCGGTGTTACCT TACA GGGTAAGTGCGGCTTACC TTATGCAGTAAGCTT .......................................GGTAAGCCGGTGTTACCTTACAGGGTAAGTGCGGCTTACC.............................................. Find igs database================================================ Query_seq: TDE2258:TDE2259|TDE2258:TDE2259:surface antigen BspA, putative:hypothetical protein:<-<-:2296492..2296616 125 gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002967_TDE2258_TDE2259|surface antigen BspA, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2296492,2296616]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc gtcaaacctccttaaagatttattttgcttaccctgtgcggtaagccggtgttaccttacagggtaagtgcggcttaccttatgcagtaagcttgacttaccctatagggtaagttacagttacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAAACCUCCUUAAAGAUUUAUUUUGCUUACCCUGUGCGGUAAGCCGGUGUUACCUUACAGGGUAAGUGCGGCUUACCUUAUGCAGUAAGCUUGACUUACCCUAUAGGGUAAGUUACAGUUACC ..........................((((((((((((.(((((.......))))).))))))))))))..(((((((........)))))))((((((((((....))))))))))........ (-45.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAACUGUAACUUACCCUAUAGGGUAAGUCAAGCUUACUGCAUAAGGUAAGCCGCACUUACCCUGUAAGGUAACACCGGCUUACCGCACAGGGUAAGCAAAAUAAAUCUUUAAGGAGGUUUGAC (((.........(((((.((((((((((((...(((((((......)))))))...)))))))))))).))))).))).(((((((......)))))))....((((((((....)))))))).. (-48.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1064 80 31 171 122 NC_002967:TDE2258|5end_surface_antigen_BspA,_putative_2296401..2296631_NEGATIVE 376 80 34 208 161 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 371 80 33 206 155 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 357 90 45 44 2 NC_002967:TDE0104|5end_3-dehydroquinate_synthase_124714..124944_NEGATIVE 340 79 33 89 36 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 335 73 31 141 94 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 330 74 31 231 179 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 324 89 45 159 103 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 322 79 32 69 21 NC_002967:TDE0748|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_784288..784518_NEGATIVE 319 70 24 183 129 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 318 72 33 188 139 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 315 79 32 61 23 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 312 70 31 53 8 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 311 73 31 141 94 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 310 90 41 202 153 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 310 79 31 227 165 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 310 79 31 196 134 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 308 80 32 201 158 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 308 74 33 59 15 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 307 78 32 209 154 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 78 31 66 14 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 345 76 31 73 14 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 336 76 38 143 103 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE 335 73 31 71 24 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 332 62 21 146 92 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 327 58 11 135 90 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 326 79 31 63 2 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 324 89 45 131 75 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 318 79 31 61 8 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 318 72 33 144 95 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 314 70 24 86 39 NC_002967:TDE0098|3end_hypothetical_protein_114842..114992_NEGATIVE 311 73 31 71 24 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 308 64 27 138 96 NC_002967:TDE2495|3end_hypothetical_protein_2518735..2518885_NEGATIVE 307 88 44 49 2 NC_002967:TDE1469|3end_conserved_hypothetical_protein_TIGR00150_1517333..1517483_NEGATIVE 306 79 39 83 31 NC_002967:TDE2152|3end_hypothetical_protein_2188804..2188954_NEGATIVE 306 80 32 82 34 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 303 80 35 48 10 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 302 64 26 68 22 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 300 75 32 69 12 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 300 89 47 146 96 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE