Origin IGS: gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgaccatcctnnnnnttaattaattaannnnnattcgtcctcagggaacgattcttatgatgggagttagtgacttttaagtcaatctcaatacacgcgatgccttagaaaaaggcttgctc Mask Tandem Repeat Region ================================================ gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Find is-nt database================================================ Query_seq: SMT_712:SMT_713|SMT_712:SMT_713:alcohol dehydrogenase, zinc-containing:heat shock protein HtpX:<-<-:620472..620594 123 gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_712:SMT_713|SMT_712:SMT_713:alcohol dehydrogenase, zinc-containing:heat shock protein HtpX:<-<-:620472..620594 123 gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_712:SMT_713|SMT_712:SMT_713:alcohol dehydrogenase, zinc-containing:heat shock protein HtpX:<-<-:620472..620594 123 gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Predict ORF larger than 30AA ================================================ gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac 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: 83 Start: 37 End: 66 ....................................ATTGACTTAAAAGTCACTAACTCCCATCAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_712:SMT_713|SMT_712:SMT_713:alcohol dehydrogenase, zinc-containing:heat shock protein HtpX:<-<-:620472..620594 123 gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: smit_SMT_712_SMT_713|alcohol dehydrogenase, zinc-containing:heat shock protein HtpX|NEGATIVE:NEGATIVE|[620472,620594]|123 HSP 1 e-value: 4.0E-46 bit: 184.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac gagcaagcctttttctaaggcatcgcgtgtattgagattgacttaaaagtcactaactcccatcataagaatcgttccctgaggacgaatnnnnnttaattaattaannnnnaggatggtcac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCAAGCCUUUUUCUAAGGCAUCGCGUGUAUUGAGAUUGACUUAAAAGUCACUAACUCCCAUCAUAAGAAUCGUUCCCUGAGGACGAAUNNNNNUUAAUUAAUUAANNNNNAGGAUGGUCAC ((.((.(((((.....))))).((..(((....(((..(((((....)))))....)))....)))..)).((((((.....))))))............................)).)).. (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGACCAUCCUNNNNNUUAAUUAAUUAANNNNNAUUCGUCCUCAGGGAACGAUUCUUAUGAUGGGAGUUAGUGACUUUUAAGUCAAUCUCAAUACACGCGAUGCCUUAGAAAAAGGCUUGCUC (((.(((((........(((....)))........((((((....)).)))).......)))))(((....(((((....)))))..)))....)))((((.(((((.....))))))))).. (-27.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 878 90 41 181 132 smit:SMT_712|5end_alcohol_dehydrogenase,_zinc-containing_620381..620611_NEGATIVE 307 89 49 58 17 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 276 62 23 168 121 smit:SMT_1426|5end_K03095_SprT-like_protein_1411313..1411543_NEGATIVE 270 44 1 116 71 smit:SMT_499|5end_hypothetical_protein_432572..432802_POSITIVE 259 35 1 207 171 smit:SMT_1140|5end_glycogen_phosphorylase_1083574..1083804_NEGATIVE 259 88 60 159 124 smit:SMT_1109|5end_hypothetical_protein_1050315..1050545_NEGATIVE 254 84 42 195 139 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 251 44 7 42 6 smit:SMT_909|5end_type_I_restriction_enzyme_M_protein_858827..859057_NEGATIVE 250 70 23 211 158 smit:SMT_447|5end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386257..386487_POSITIVE 246 59 19 96 59 smit:SMT_1131|5end_threonine_synthase_1066755..1066985_NEGATIVE 246 50 1 209 155 smit:SMT_340|5end_chaperone_protein_278663..278893_POSITIVE 245 42 6 40 5 smit:SMT_2174|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2043987..2044217_POSITIVE 245 42 6 40 5 smit:SMT_2173|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2043289..2043519_POSITIVE 245 42 6 61 26 smit:SMT_2155|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2028863..2029093_POSITIVE 245 42 6 40 5 smit:SMT_2154|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2027454..2027684_POSITIVE 245 42 6 40 5 smit:SMT_2149|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2023671..2023901_POSITIVE 245 42 6 40 5 smit:SMT_2140|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2017620..2017850_POSITIVE 245 42 6 142 107 smit:SMT_2131|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2011665..2011895_POSITIVE 245 70 21 111 56 smit:SMT_1779|5end_hypothetical_protein_1755908..1756138_NEGATIVE 245 42 6 40 5 smit:SMT_1705|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_1688558..1688788_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 88 60 98 63 smit:SMT_1110|3end_hypothetical_protein_1050376..1050526_NEGATIVE 251 44 7 42 6 smit:SMT_910|3end_type_I_restriction_enzyme_R_protein_858827..858977_NEGATIVE 245 70 21 59 4 smit:SMT_1780|3end_PTS_system,_glucose-specific_IIABC_component_1755960..1756110_NEGATIVE 235 65 25 74 33 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 231 85 45 36 3 smit:SMT_119|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_72021..72171_POSITIVE 228 85 41 143 88 smit:SMT_923|3end_methionyl-tRNA_formyltransferase_876559..876709_NEGATIVE 222 41 6 79 42 smit:SMT_2123|3end_hypothetical_protein_2008541..2008691_POSITIVE 222 44 5 98 56 smit:SMT_1280|3end_cysteine_synthase_1243543..1243693_NEGATIVE 222 41 6 49 12 smit:SMT_752|3end_prephenate_dehydrogenase_655688..655838_NEGATIVE 216 60 15 114 62 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 215 64 24 129 79 smit:SMT_1285|3end_ribosomal_subunit_interface_protein_1248332..1248482_POSITIVE 211 22 4 84 63 smit:SMT_933|3end_ATP-dependent_RNA_helicase_885365..885515_NEGATIVE 208 68 22 64 12 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 206 26 3 150 126 smit:SMT_2142|3end_hypothetical_protein_predicted_by_Glimmer/Critica_2020252..2020402_POSITIVE 206 59 17 92 42 smit:SMT_727|3end_phage_transcriptional_repressor_631830..631980_NEGATIVE 204 44 2 80 36 smit:SMT_1918|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1861816..1861966_NEGATIVE 204 50 3 54 1 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 203 90 42 77 20 smit:SMT_899|3end_5,10-methylenetetrahydrofolate_reductase_847397..847547_NEGATIVE 201 42 1 83 40 smit:SMT_692|3end_hypothetical_protein_603008..603158_NEGATIVE 199 29 2 84 42 smit:SMT_1858|3end_K03497_chromosome_partitioning_protein,_ParB_family_1821687..1821837_NEGATIVE