Origin IGS: tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagttgattaacttatattttatttctaaggaggctttaagattatcatagaatattttataggtatattttcaaaatctataattataaatcttttgataaatattgtttttcagttcatattggtgataaattgtgtttagaaagatctatttttatgttagagaaacctaaaaatataattttatttaatgaaaacgcaatttttaatttaatttcaaaaattgatttatagaaaaggtaaaaactgttccatttttatccgaataacttattaagggaggctaaata Mask Tandem Repeat Region ================================================ tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Find is-nt database================================================ Query_seq: TDE2015:TDE2016|TDE2015:TDE2016:lipoprotein, putative:hypothetical protein:<-<-:2037623..2037913 291 tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2015:TDE2016|TDE2015:TDE2016:lipoprotein, putative:hypothetical protein:<-<-:2037623..2037913 291 tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2015:TDE2016|TDE2015:TDE2016:lipoprotein, putative:hypothetical protein:<-<-:2037623..2037913 291 tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 67 End: 171 .................................................................. M F E I K L K I A F S L N K I I F L G F S N I K I D L S K H N L S P I ........................................................................................................................ Protein_Len: 33 Strand: - Start: 152 End: 250 ....................................................................................................................................................... V C N I V L I F Q F V I N I L L N I I I S K S F I G I F Y E I I M ......................................... Protein_Len: 60 Strand: - Start: 60 End: 239 ........................................................... L D I K S I L N F I A N E N F L I I N K P K E L M F I S R E L C L K D G I H V S F C Y K D F S K Y N Y I K F I Y R Y F M .................................................... tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg 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: 168 End: 197 .......................................................................................................................................................................TTTGATAAATATTGTTTTTCAGTTCATATT.............................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 207 End: 236 ..............................................................................................................................................................................................................TTTTATAGGTATATTTTCAAAATCTATAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -3.2 Tail_Score: -2.54881 Start: 65 End: 91 Full_Region: ACCTTTTCTATAAAT CAATTTTTGA AATTAAA TTAAAAATTG CGTTTTCATTAAATA ................................................................CAATTTTTGAAATTAAATTAAAAATTG........................................................................................................................................................................................................ TransTerm Strand: - Conf: 42 HP_score: -2.2 Tail_Score: -3.55603 Start: 111 End: 143 Full_Region: ttgtgtttagaaaga tctatttttatgtt agaga aacctaaaaatata attttatttaatgaa ..............................................................................................................tctatttttatgttagagaaacctaaaaatata.................................................................................................................................................... TransTerm Strand: - Conf: 52 HP_score: -4.8 Tail_Score: -3.34291 Start: 113 End: 141 Full_Region: gtgtttagaaagatc tatttttatgtt agaga aacctaaaaata taattttatttaatg ................................................................................................................tatttttatgttagagaaacctaaaaata...................................................................................................................................................... Find igs database================================================ Query_seq: TDE2015:TDE2016|TDE2015:TDE2016:lipoprotein, putative:hypothetical protein:<-<-:2037623..2037913 291 tatttagcctcccttaataagttattcggataaaaatggaacagtttttaccttttctataaatcaatttttgaaattaaattaaaaattgcgttttcattaaataaaattatatttttaggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg Intra-Species Hit: Count: 1 Min: 1 Max: 291 Len: 291 Subject: NC_002967_TDE2015_TDE2016|lipoprotein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2037623,2037913]|291 HSP 1 e-value: 3.0E-92 bit: 339.0 Len: 171 Query Start:121 Query End:291 Subject Strand: POSITIVE Subject Start: 121 Subject End: 291 ........................................................................................................................ggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg ........................................................................................................................ggtttctctaacataaaaatagatctttctaaacacaatttatcaccaatatgaactgaaaaacaatatttatcaaaagatttataattatagattttgaaaatatacctataaaatattctatgataatcttaaagcctccttagaaataaaatataagttaatcaactg HSP 2 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:1 Query End:52 Subject Strand: POSITIVE Subject Start: 1 Subject End: 52 tatttagcctcccttaataagttattcggataaaaatggaacagtttttacc............................................................................................................................................................................................................................................... tatttagcctcccttaataagttattcggataaaaatggaacagtttttacc............................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUAGCCUCCCUUAAUAAGUUAUUCGGAUAAAAAUGGAACAGUUUUUACCUUUUCUAUAAAUCAAUUUUUGAAAUUAAAUUAAAAAUUGCGUUUUCAUUAAAUAAAAUUAUAUUUUUAGGUUUCUCUAACAUAAAAAUAGAUCUUUCUAAACACAAUUUAUCACCAAUAUGAACUGAAAAACAAUAUUUAUCAAAAGAUUUAUAAUUAUAGAUUUUGAAAAUAUACCUAUAAAAUAUUCUAUGAUAAUCUUAAAGCCUCCUUAGAAAUAAAAUAUAAGUUAAUCAACUG ...(((((...................((.(((((((......))))))))).((((((.....((((((((((.......)))))))))).(((.((((..((((........(((((((..................((((....))))...........(((......))).)))))))...((((((.((((..(((((((....)))))))))))))))))..........))))..)))).))).............))))))..........)))))....... (-31.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUUGAUUAACUUAUAUUUUAUUUCUAAGGAGGCUUUAAGAUUAUCAUAGAAUAUUUUAUAGGUAUAUUUUCAAAAUCUAUAAUUAUAAAUCUUUUGAUAAAUAUUGUUUUUCAGUUCAUAUUGGUGAUAAAUUGUGUUUAGAAAGAUCUAUUUUUAUGUUAGAGAAACCUAAAAAUAUAAUUUUAUUUAAUGAAAACGCAAUUUUUAAUUUAAUUUCAAAAAUUGAUUUAUAGAAAAGGUAAAAACUGUUCCAUUUUUAUCCGAAUAACUUAUUAAGGGAGGCUAAAUA ................................((((((..............(((((((.(((((...(((((.((...(((((..(((.(((((((..(((((((.((((.(((.(.......).))).)))).)))))))))))))).)))..))))))).))))))))))))))))).......((((((((.....((((((((((......)).))))))))............((((((((........))))))))........)))))))).))))))..... (-40.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 738 50 1 141 92 NC_002967:TDE2015|5end_lipoprotein,_putative_2037532..2037762_NEGATIVE 640 60 12 144 96 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 258 44 6 47 8 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 228 31 6 123 98 NC_002967:TDE1578|5end_phosphoesterase,_putative_1625370..1625600_POSITIVE 220 54 18 228 196 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 219 59 11 231 182 NC_002967:TDE0683|5end_hypothetical_protein_721303..721533_NEGATIVE 216 58 23 183 153 NC_002967:TDE0714|5end_capsular_polysaccharide_biosynthesis_protein_747633..747863_POSITIVE 216 44 7 144 95 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 208 58 12 71 34 NC_002967:TDE1440|5end_glucose-1-phosphate_thymidylyltransferase_1485353..1485583_POSITIVE 206 49 5 80 24 NC_002967:TDE1162|5end_ParB-like_nuclease_domain_protein_1197684..1197914_NEGATIVE 204 153 120 129 93 NC_002967:TDE0928|5end_phosphonate_ABC_transporter,_ATP-binding_protein,_putative_951640..951870_NEGATIVE 204 49 6 164 123 NC_002967:TDE0388|5end_hypothetical_protein_439173..439403_POSITIVE 203 174 131 93 52 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 200 58 21 150 109 NC_002967:TDE0193|5end_hypothetical_protein_230589..230819_NEGATIVE 199 29 6 119 97 NC_002967:TDE0868|5end_oxidoreductase,_FAD/FMN-binding_890385..890615_POSITIVE 196 58 12 50 1 NC_002967:TDE2677|5end_hypothetical_protein_2715604..2715834_POSITIVE 196 177 143 189 151 NC_002967:TDE2109|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2135287..2135517_NEGATIVE 196 52 25 143 115 NC_002967:TDE1447|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1492612..1492842_POSITIVE 195 58 11 221 174 NC_002967:TDE0771|5end_ribosomal_protein_S19_808795..809025_POSITIVE 193 56 19 231 198 NC_002967:TDE0992|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1019010..1019240_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 640 60 12 129 81 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 228 31 6 119 94 NC_002967:TDE1577|3end_lipoprotein,_putative_1625446..1625596_POSITIVE 216 44 7 131 82 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 206 49 5 64 8 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 204 153 120 50 14 NC_002967:TDE0929|3end_ornithine_carbamoyltransferase_951719..951869_NEGATIVE 199 29 6 54 32 NC_002967:TDE0867|3end_hypothetical_protein_890400..890550_POSITIVE 196 52 25 130 102 NC_002967:TDE1446|3end_hypothetical_protein_1492679..1492829_POSITIVE 195 45 6 46 13 NC_002967:TDE2678|3end_alpha-amylase_family_protein_2715785..2715935_NEGATIVE 192 44 6 56 15 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 188 70 27 79 37 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 186 46 5 104 62 NC_002967:TDE2737|3end_hypothetical_protein_2792690..2792840_POSITIVE 183 271 249 59 39 NC_002967:TDE1216|3end_flagellar_motor_protein_1249570..1249720_POSITIVE 181 60 11 147 88 NC_002967:TDE0961|3end_DnaJ_domain_protein_984012..984162_POSITIVE 181 54 34 92 72 NC_002967:TDE0658|3end_ABC_transporter,_permease_protein_695679..695829_POSITIVE 179 55 14 86 45 NC_002967:TDE2228|3end_aminoacyl-histidine_dipeptidase,_putative_2267287..2267437_NEGATIVE 179 57 14 87 47 NC_002967:TDE0954|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978840..978990_POSITIVE 178 49 5 118 80 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 178 267 228 125 98 NC_002967:TDE2341|3end_membrane-associated_zinc_metalloprotease,_putative_2377866..2378016_NEGATIVE 178 45 7 68 27 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 178 30 6 45 11 NC_002967:TDE0100|3end_hypothetical_protein_116974..117124_NEGATIVE