Origin IGS: atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaattactatattgacaagaaaagatttatatcttaccatatactataggaggattaagtatgaaagaaaattcaaacataaaaaaatcaggaatcagaatattaaccattgaagagctgtat Mask Tandem Repeat Region ================================================ atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Find is-nt database================================================ Query_seq: TDE0431:TDE0432|TDE0431:TDE0432:LysM domain protein:TPR domain protein, truncation:<-<-:487685..487809 125 atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0431:TDE0432|TDE0431:TDE0432:LysM domain protein:TPR domain protein, truncation:<-<-:487685..487809 125 atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0431:TDE0432|TDE0431:TDE0432:LysM domain protein:TPR domain protein, truncation:<-<-:487685..487809 125 atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 14 End: 121 ............. H N I N Q N R I K K H K F K R E Y K I R R Y Y I T L Y L D K R T L I T M .... Protein_Len: 33 Strand: - Start: 1 End: 99 Y L E E I T L I R I G S K K I N S N E K M S L G G I T Y P L I Y M .......................... atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt 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: 86 Start: 84 End: 113 ...................................................................................ATTGACAAGAAAAGATTTATATCTTACCAT............ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0431:TDE0432|TDE0431:TDE0432:LysM domain protein:TPR domain protein, truncation:<-<-:487685..487809 125 atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002967_TDE0431_TDE0432|LysM domain protein:TPR domain protein, truncation|NEGATIVE:NEGATIVE|[487685,487809]|125 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 atacagctcttcaatggttaatattctgattcctgannnnnnnatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt atacagctcttcaatggttaatattctgattcctgatttttttatgtttgaattttctttcatacttaatcctcctatagtatatggtaagatataaatcttttcttgtcaatatagtaattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAGCUCUUCAAUGGUUAAUAUUCUGAUUCCUGAUUUUUUUAUGUUUGAAUUUUCUUUCAUACUUAAUCCUCCUAUAGUAUAUGGUAAGAUAUAAAUCUUUUCUUGUCAAUAUAGUAAUUUUU ..........(((..(((((......)))))..))).....(((.((.((((......)))).)).)))........((.((((((..((((...........))))..).))))).))...... (-12.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUACUAUAUUGACAAGAAAAGAUUUAUAUCUUACCAUAUACUAUAGGAGGAUUAAGUAUGAAAGAAAAUUCAAACAUAAAAAAAUCAGGAAUCAGAAUAUUAACCAUUGAAGAGCUGUAU .........................(((((..(((((.((..........)))))))...((.((((......)))).)).............)))))........................... ( -9.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 745 110 61 201 152 NC_002967:TDE0431|5end_LysM_domain_protein_487594..487824_NEGATIVE 298 87 54 118 81 NC_002967:TDE2783|5end_methyl-accepting_chemotaxis_protein_2834410..2834640_POSITIVE 298 80 31 143 87 NC_002967:TDE0079|5end_DNA-binding_protein_90670..90900_NEGATIVE 278 74 31 103 52 NC_002967:TDE2305|5end_hypothetical_protein_2343652..2343882_POSITIVE 247 118 71 149 97 NC_002967:TDE1663|5end_OmpA_family_protein_1717319..1717549_POSITIVE 246 89 48 86 40 NC_002967:TDE0967|5end_hypothetical_protein_992201..992431_POSITIVE 243 76 31 102 56 NC_002967:TDE2749|5end_hypothetical_protein_2805626..2805856_POSITIVE 241 75 33 100 61 NC_002967:TDE2073|5end_TPR_domain_protein_2099171..2099401_POSITIVE 237 76 31 160 115 NC_002967:TDE2613|5end_hypothetical_protein_2655372..2655602_POSITIVE 235 110 61 139 89 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 235 60 16 61 2 NC_002967:TDE2593|5end_sigma-54-binding_protein_2627747..2627977_POSITIVE 234 79 31 109 60 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 230 75 31 104 60 NC_002967:TDE2472|5end_ISTde1,_transposase_2494962..2495192_POSITIVE 230 75 31 104 60 NC_002967:TDE2033|5end_ISTde1,_transposase_2061476..2061706_NEGATIVE 230 75 31 104 60 NC_002967:TDE0039|5end_ISTde1,_transposase_45673..45903_NEGATIVE 229 100 54 135 76 NC_002967:TDE2602|5end_outer_membrane_protein,_putative_2640956..2641186_POSITIVE 226 84 51 155 123 NC_002967:TDE1843|5end_hypothetical_protein_1873005..1873235_NEGATIVE 226 90 58 121 86 NC_002967:TDE1339|5end_stage_V_sporulation_protein_G_1375807..1376037_POSITIVE 225 89 45 117 71 NC_002967:TDE1147|5end_hypothetical_protein_1185960..1186190_NEGATIVE 224 115 71 114 60 NC_002967:TDE2035|5end_glucose-1-phosphate_adenylyltransferase_2062801..2063031_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 50 2 135 85 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 298 80 31 85 29 NC_002967:TDE0080|3end_betaine_aldehyde_dehydrogenase_90728..90878_NEGATIVE 278 74 31 106 55 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE 247 118 71 65 13 NC_002967:TDE1662|3end_replicative_DNA_helicase_1717315..1717465_POSITIVE 241 75 33 44 5 NC_002967:TDE2072|3end_hypothetical_protein_2099195..2099345_POSITIVE 234 79 31 89 40 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 233 50 8 122 74 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE 230 52 12 36 2 NC_002967:TDE2193|3end_deoxycytidylate_deaminase,_putative_2229263..2229413_NEGATIVE 229 100 54 125 66 NC_002967:TDE2601|3end_surface_antigen,_putative_2641026..2641176_POSITIVE 226 90 58 57 22 NC_002967:TDE1338|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_1375823..1375973_POSITIVE 225 89 45 103 57 NC_002967:TDE1148|3end_hypothetical_protein_1185974..1186124_NEGATIVE 224 115 71 56 2 NC_002967:TDE2034|3end_glycosyl_transferase,_group_1_family_protein_2062823..2062973_POSITIVE 222 81 45 113 77 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 209 49 15 80 41 NC_002967:TDE1723|3end_hypothetical_protein_1777779..1777929_POSITIVE 206 83 51 126 96 NC_002967:TDE0421|3end_lipoprotein,_putative_474782..474932_POSITIVE 204 45 1 47 7 NC_002967:TDE2243|3end_CutC_family_protein_2282214..2282364_NEGATIVE 204 39 5 114 75 NC_002967:TDE0842|3end_cytoplasmic_filament_protein_A_863843..863993_POSITIVE 204 85 49 100 70 NC_002967:TDE0036|3end_hypothetical_protein_42135..42285_NEGATIVE 202 107 70 81 41 NC_002967:TDE2467|3end_hypothetical_protein_2489881..2490031_NEGATIVE 202 77 31 93 46 NC_002967:TDE0775|3end_ribosomal_protein_L29_810886..811036_POSITIVE