Origin IGS: gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctctctcatcctttatctgtagttcgctttattataccaaaatttatcagaaaattctcgctttttcacagagaatataagaaaaagcccatttctgggcttgttttcatc Mask Tandem Repeat Region ================================================ gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Find is-nt database================================================ Query_seq: SSA_0094:SSA_0095|SSA_0094:SSA_0095:Cell wall metabolism, LysM type protein, putative:Threonine synthase, putative:->->:96583..96694 112 gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0094:SSA_0095|SSA_0094:SSA_0095:Cell wall metabolism, LysM type protein, putative:Threonine synthase, putative:->->:96583..96694 112 gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0094:SSA_0095|SSA_0094:SSA_0095:Cell wall metabolism, LysM type protein, putative:Threonine synthase, putative:->->:96583..96694 112 gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Predict ORF larger than 30AA ================================================ gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga 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================================================ gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0094:SSA_0095|SSA_0094:SSA_0095:Cell wall metabolism, LysM type protein, putative:Threonine synthase, putative:->->:96583..96694 112 gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_0094_SSA_0095|Cell wall metabolism, LysM type protein, putative:Threonine synthase, putative|POSITIVE:POSITIVE|[96583,96694]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga gatgaaaacaagcccagaaatgggctttttcttatattctctgtgaaaaagcgagaattttctgataaattttggtataataaagcgaactacagataaaggatgagagaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAAACAAGCCCAGAAAUGGGCUUUUUCUUAUAUUCUCUGUGAAAAAGCGAGAAUUUUCUGAUAAAUUUUGGUAUAAUAAAGCGAACUACAGAUAAAGGAUGAGAGAGA .........(((((((....)))))))((((((((.((.((((((.....((.........(..(......)..).........))....)))))).))...)))))))).. (-27.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUCUCAUCCUUUAUCUGUAGUUCGCUUUAUUAUACCAAAAUUUAUCAGAAAAUUCUCGCUUUUUCACAGAGAAUAUAAGAAAAAGCCCAUUUCUGGGCUUGUUUUCAUC ..(((((...........((((((.......)))))).............(((((........)))))..)))))......(((((((((((....))))))..)))))... (-20.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 60 12 224 158 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 286 59 11 80 20 NC_009009:SSA_0688|5end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_671360..671590_POSITIVE 254 53 14 127 82 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 238 57 13 168 130 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 235 52 14 42 1 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 234 55 12 54 11 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 230 52 14 52 9 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 228 57 13 207 158 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 228 67 21 145 92 NC_009009:SSA_0295|5end_Transcriptional_regulator,_LysR_family,_putative_288901..289131_NEGATIVE 227 52 14 62 26 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 225 62 23 104 56 NC_009009:SSA_2138|5end_RNA-binding_protein,_Jag_family,_putative_2139487..2139717_NEGATIVE 224 43 1 51 5 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 224 56 11 121 59 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 222 87 43 226 181 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 221 69 21 189 139 NC_009009:SSA_1700|5end_hypothetical_protein_1691288..1691518_NEGATIVE 221 41 1 196 149 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 220 44 1 212 173 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 219 43 9 169 141 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 219 59 11 132 85 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 218 45 10 209 177 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 46 1 107 60 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 249 52 11 114 64 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 246 45 5 83 40 NC_009009:SSA_1064|3end_hypothetical_protein_1080325..1080475_NEGATIVE 238 57 13 85 47 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 235 47 1 105 52 NC_009009:SSA_2235|3end_Conserved_uncharacterized_protein_2234971..2235121_NEGATIVE 234 55 12 51 8 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 228 57 13 53 4 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 225 62 23 82 34 NC_009009:SSA_2139|3end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2139509..2139659_NEGATIVE 224 43 1 58 12 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 224 56 11 131 69 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 221 41 1 98 51 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 217 53 11 109 72 NC_009009:SSA_0629|3end_hypothetical_protein_619586..619736_POSITIVE 215 64 21 76 23 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 215 35 4 79 44 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 213 47 4 113 60 NC_009009:SSA_0094|3end_Cell_wall_metabolism,_LysM_type_protein,_putative_96522..96672_POSITIVE 211 52 17 41 9 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 211 60 11 72 17 NC_009009:SSA_0328|3end_Xaa-Pro_dipeptidyl-peptidase,_putative_320487..320637_NEGATIVE 211 59 15 125 70 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 210 44 9 144 106 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 210 53 12 146 101 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE