Origin IGS: aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatattataggcctcagtttgaaaattgtcaaagggttatctttaaaaatagggggtagttattattgacataagagtgcttatattatacaattatgtcagcttttatagctaaaccggagaatgactt Mask Tandem Repeat Region ================================================ aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Find is-nt database================================================ Query_seq: TDE2002:TDE2003|TDE2002:TDE2003:hypothetical protein:internalin-related protein:<-->:2022286..2022416 131 aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2002:TDE2003|TDE2002:TDE2003:hypothetical protein:internalin-related protein:<-->:2022286..2022416 131 aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2002:TDE2003|TDE2002:TDE2003:hypothetical protein:internalin-related protein:<-->:2022286..2022416 131 aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Predict ORF larger than 30AA ================================================ aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa 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: 93 Start: 98 End: 127 .................................................................................................TTTGACAATTTTCAAACTGAGGCCTATAAT.... PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 37 End: 66 ....................................ATTGACATAAGAGTGCTTATATTATACAAT................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2002:TDE2003|TDE2002:TDE2003:hypothetical protein:internalin-related protein:<-->:2022286..2022416 131 aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_002967_TDE2002_TDE2003|hypothetical protein:internalin-related protein|NEGATIVE:POSITIVE|[2022286,2022416]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa aagtcattctccggtttagctataaaagctgacataattgtataatataagcactcttatgtcaataataactaccccctatttttaaagataaccctttgacaattttcaaactgaggcctataatataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCAUUCUCCGGUUUAGCUAUAAAAGCUGACAUAAUUGUAUAAUAUAAGCACUCUUAUGUCAAUAAUAACUACCCCCUAUUUUUAAAGAUAACCCUUUGACAAUUUUCAAACUGAGGCCUAUAAUAUAA .......((((.(((((.(((.....))).(((((((..((...........))..))))))).....................((((((......))))))........)))))))))............ (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAUUAUAGGCCUCAGUUUGAAAAUUGUCAAAGGGUUAUCUUUAAAAAUAGGGGGUAGUUAUUAUUGACAUAAGAGUGCUUAUAUUAUACAAUUAUGUCAGCUUUUAUAGCUAAACCGGAGAAUGACUU ..........(((((...(((((......))))))))))..............((..(((((((..(((((((((..(((.........)))..))))))))).....)))))))..))............ (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 817 120 71 211 162 NC_002967:TDE2002|5end_hypothetical_protein_2022195..2022425_NEGATIVE 321 109 73 173 138 NC_002967:TDE2457|5end_hypothetical_protein_2485570..2485800_NEGATIVE 257 45 4 166 136 NC_002967:TDE1872|5end_hypothetical_protein_1894691..1894921_NEGATIVE 237 116 76 152 99 NC_002967:TDE2187|5end_ParB-like_nuclease_domain_protein_2221548..2221778_NEGATIVE 235 92 51 138 95 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 233 89 42 110 68 NC_002967:TDE0315|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_346938..347168_POSITIVE 228 55 11 198 157 NC_002967:TDE2340|5end_FMN-binding_domain_protein_2377855..2378085_NEGATIVE 224 104 69 121 85 NC_002967:TDE2682|5end_hypothetical_protein_2723358..2723588_NEGATIVE 216 121 96 60 28 NC_002967:TDE2586|5end_DNA_polymerase_III_subunits_gamma_and_tau_2622089..2622319_NEGATIVE 216 120 95 138 103 NC_002967:TDE0486|5end_hypothetical_protein_543612..543842_NEGATIVE 209 38 10 43 8 NC_002967:TDE2217|5end_galactose/glucose-binding_lipoprotein_2257975..2258205_NEGATIVE 207 54 12 56 14 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 205 68 24 156 110 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 205 42 1 53 9 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 205 55 11 59 19 NC_002967:TDE0186|5end_hypothetical_protein_223698..223928_NEGATIVE 203 120 75 127 98 NC_002967:TDE2352|5end_flagellar_hook-associated_protein_2387235..2387465_POSITIVE 201 125 103 80 57 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 201 31 3 151 119 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 197 31 2 171 146 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 194 121 87 231 196 NC_002967:TDE2345|5end_ribosome_recycling_factor_2382503..2382733_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 45 4 128 98 NC_002967:TDE1873|3end_hypothetical_protein_1894729..1894879_NEGATIVE 248 32 2 47 21 NC_002967:TDE2309|3end_sigma-54_dependent_transcriptional_regulator,_putative_2346558..2346708_NEGATIVE 237 116 76 126 73 NC_002967:TDE2188|3end_hypothetical_protein_2221574..2221724_NEGATIVE 224 104 69 112 76 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 224 41 1 150 93 NC_002967:TDE0697|3end_hypothetical_protein_734220..734370_NEGATIVE 218 120 75 122 80 NC_002967:TDE1691|3end_hypothetical_protein_1747407..1747557_NEGATIVE 216 120 95 122 87 NC_002967:TDE0487|3end_ABC_transporter,_ATP-binding_protein_543628..543778_NEGATIVE 211 80 31 99 57 NC_002967:TDE1291|3end_HD_domain_protein_1328638..1328788_NEGATIVE 207 54 12 59 17 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 207 120 73 150 92 NC_002967:TDE2346|3end_elongation_factor_Ts_2382587..2382737_NEGATIVE 205 42 1 56 12 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 203 120 75 116 87 NC_002967:TDE2351|3end_hypothetical_protein_2387304..2387454_POSITIVE 193 99 54 115 69 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE 192 31 10 28 6 NC_002967:TDE0812|3end_ABC_transporter,_ATP-binding/permease_protein_834137..834287_POSITIVE 192 102 75 53 33 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 192 123 89 87 50 NC_002967:TDE0361|3end_transporter,_putative_407442..407592_POSITIVE 190 21 9 96 84 NC_002967:TDE2615|3end_signal_peptidase_II_2657146..2657296_NEGATIVE 182 82 51 94 58 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 178 32 2 119 87 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 176 110 71 128 93 NC_002967:TDE1464|3end_SsrA-binding_protein_1513076..1513226_NEGATIVE