Origin IGS: ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtacggcaaatagaaaatacaaaggttccgtttttgtagaccgtcagtgataagacacttaaactctcagccgcttttatagaacaaaatgagtattctcatcttgag Mask Tandem Repeat Region ================================================ ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Find is-nt database================================================ Query_seq: TDE1904:TDE1905|TDE1904:TDE1905:hypothetical protein:hypothetical protein:<-<-:1923704..1923811 108 ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1904:TDE1905|TDE1904:TDE1905:hypothetical protein:hypothetical protein:<-<-:1923704..1923811 108 ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1904:TDE1905|TDE1904:TDE1905:hypothetical protein:hypothetical protein:<-<-:1923704..1923811 108 ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Predict ORF larger than 30AA ================================================ ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac 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================================================ ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1904:TDE1905|TDE1904:TDE1905:hypothetical protein:hypothetical protein:<-<-:1923704..1923811 108 ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002967_TDE1904_TDE1905|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1923704,1923811]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac ctcaagatgagaatactcattttgttctataaaagcggctgagagtttaagtgtcttatcactgacggtctacaaaaacggaacctttgtattttctatttgccgtac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAGAUGAGAAUACUCAUUUUGUUCUAUAAAAGCGGCUGAGAGUUUAAGUGUCUUAUCACUGACGGUCUACAAAAACGGAACCUUUGUAUUUUCUAUUUGCCGUAC ..(((((((((....)))))))))..........(((((.((((((...((((......))))...(((((........)).))).....)))))).....))))).. (-25.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUACGGCAAAUAGAAAAUACAAAGGUUCCGUUUUUGUAGACCGUCAGUGAUAAGACACUUAAACUCUCAGCCGCUUUUAUAGAACAAAAUGAGUAUUCUCAUCUUGAG ...((((..........((((((((.....))))))))....(((........))).............))))...........(((.(((((....))))).))).. (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 890 80 31 171 122 NC_002967:TDE1904|5end_hypothetical_protein_1923613..1923843_NEGATIVE 326 97 52 76 30 NC_002967:TDE0948|5end_hypothetical_protein_971837..972067_NEGATIVE 320 97 51 75 32 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 318 97 52 76 30 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 281 60 16 59 11 NC_002967:TDE1050|5end_hypothetical_protein_1077387..1077617_POSITIVE 262 61 29 227 193 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 251 71 35 191 151 NC_002967:TDE0032|5end_histidine_kinase-related_ATPase,_putative_39977..40207_NEGATIVE 250 69 22 229 185 NC_002967:TDE1339|5end_stage_V_sporulation_protein_G_1375807..1376037_POSITIVE 246 97 52 76 30 NC_002967:TDE0975|5end_hypothetical_protein_998921..999151_POSITIVE 246 48 7 40 1 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 239 59 17 169 124 NC_002967:TDE2206|5end_hypothetical_protein_2245364..2245594_NEGATIVE 238 90 41 208 166 NC_002967:TDE1366|5end_CDP-alcohol_phosphatidyltransferase_family_protein_1408358..1408588_POSITIVE 237 97 61 192 155 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 236 71 36 231 196 NC_002967:TDE0890|5end_hypothetical_protein_905890..906120_POSITIVE 235 68 25 217 180 NC_002967:TDE0003|5end_hypothetical_protein_3483..3713_POSITIVE 233 46 1 140 87 NC_002967:TDE2079|5end_sigma-54_dependent_transcriptional_regulator,_putative_2109035..2109265_NEGATIVE 230 75 33 172 131 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 230 67 25 206 166 NC_002967:TDE0767|5end_ribosomal_protein_L3_806355..806585_POSITIVE 227 78 37 179 144 NC_002967:TDE0589|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_629044..629274_NEGATIVE 226 68 21 183 143 NC_002967:TDE0905|5end_hypothetical_protein_922432..922662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 97 51 82 39 NC_002967:TDE0611|3end_hypothetical_protein_647279..647429_NEGATIVE 288 70 33 74 32 NC_002967:TDE2712|3end_hypothetical_protein_2769615..2769765_POSITIVE 280 53 13 46 1 NC_002967:TDE0123|3end_hypothetical_protein_141543..141693_NEGATIVE 262 61 29 79 45 NC_002967:TDE1712|3end_flagellar_filament_outer_layer_protein_1766866..1767016_NEGATIVE 250 73 35 74 37 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 247 68 28 84 37 NC_002967:TDE1316|3end_hypothetical_protein_1355024..1355174_POSITIVE 238 71 31 105 75 NC_002967:TDE0575|3end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_606252..606402_NEGATIVE 236 71 36 75 40 NC_002967:TDE0889|3end_hypothetical_protein_905814..905964_POSITIVE 233 46 1 126 73 NC_002967:TDE2080|3end_cytidylate_kinase/ribosomal_protein_S1_2109049..2109199_NEGATIVE 230 67 25 143 103 NC_002967:TDE0766|3end_30S_ribosomal_protein_S10_806372..806522_POSITIVE 226 71 33 51 11 NC_002967:TDE1049|3end_elongation_factor_EF-2_1077454..1077604_POSITIVE 224 70 29 146 108 NC_002967:TDE1473|3end_flagellin_FlaG,_putative_1520760..1520910_NEGATIVE 223 69 30 91 58 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 222 42 4 111 72 NC_002967:TDE0934|3end_chaperonin,_10_kDa_959395..959545_NEGATIVE 221 68 25 151 115 NC_002967:TDE0590|3end_acetyl-CoA_carboxylase,_carboxyl_transferase,_beta_subunit_629065..629215_NEGATIVE 219 49 2 74 26 NC_002967:TDE1453|3end_alpha-galactosidase_1501516..1501666_POSITIVE 218 57 16 142 105 NC_002967:TDE1068|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095694..1095844_NEGATIVE 216 68 23 134 95 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 216 97 61 75 39 NC_002967:TDE0410|3end_peptidase,_M48_family_462999..463149_POSITIVE 216 70 35 77 47 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE