Origin IGS: ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttacaaaaaaacgtgtaatcggtaccaggcaaaaacaccgattacacggtatctaaacccttgaattcctatcaaaatataattagaatatttacaaaatcttttatgggagaaacaaaa Mask Tandem Repeat Region ================================================ ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Find is-nt database================================================ Query_seq: TDE1101:TDE1102|TDE1101:TDE1102:acetyltransferase, GNAT family:hypothetical protein:<-<-:1135233..1135353 121 ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1101:TDE1102|TDE1101:TDE1102:acetyltransferase, GNAT family:hypothetical protein:<-<-:1135233..1135353 121 ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1101:TDE1102|TDE1101:TDE1102:acetyltransferase, GNAT family:hypothetical protein:<-<-:1135233..1135353 121 ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Predict ORF larger than 30AA ================================================ ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa 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: 82 Start: 32 End: 61 ...............................CTTGAATTCCTATCAAAATATAATTAGAAT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1101:TDE1102|TDE1101:TDE1102:acetyltransferase, GNAT family:hypothetical protein:<-<-:1135233..1135353 121 ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacgtttttttgtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE1101_TDE1102|acetyltransferase, GNAT family:hypothetical protein|NEGATIVE:NEGATIVE|[1135233,1135353]|121 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacg............ ttttgtttctcccataaaagattttgtaaatattctaattatattttgataggaattcaagggtttagataccgtgtaatcggtgtttttgcctggtaccgattacacg............ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUUUCUCCCAUAAAAGAUUUUGUAAAUAUUCUAAUUAUAUUUUGAUAGGAAUUCAAGGGUUUAGAUACCGUGUAAUCGGUGUUUUUGCCUGGUACCGAUUACACG ...(((((..(((.((((....)))).....(((((.((((.....)))).)))))....)))...))))).(((((((((((((((.......))))))))))))))) (-24.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGUAAUCGGUACCAGGCAAAAACACCGAUUACACGGUAUCUAAACCCUUGAAUUCCUAUCAAAAUAUAAUUAGAAUAUUUACAAAAUCUUUUAUGGGAGAAACAAAA ((((((((((((.............))))))))))))((.(((...(((.((((.........((((((.......)))))).........)))).)))))).)).... (-23.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 910 100 51 191 142 NC_002967:TDE1101|5end_acetyltransferase,_GNAT_family_1135142..1135372_NEGATIVE 319 99 56 205 148 NC_002967:TDE0744|5end_thioredoxin_779844..780074_POSITIVE 297 96 61 111 77 NC_002967:TDE2333|5end_sanA_protein,_putative_2368551..2368781_NEGATIVE 293 100 56 77 17 NC_002967:TDE0958|5end_patatin_family_protein_981040..981270_POSITIVE 284 100 61 227 190 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 278 99 58 52 7 NC_002967:TDE2206|5end_hypothetical_protein_2245364..2245594_NEGATIVE 274 99 56 91 36 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 274 99 56 202 147 NC_002967:TDE1324|5end_hypothetical_protein_1361610..1361840_NEGATIVE 272 94 68 33 6 NC_002967:TDE2301|5end_FlhB_domain_protein_2341509..2341739_POSITIVE 262 99 51 193 142 NC_002967:TDE0451|5end_arginine_deiminase_508653..508883_POSITIVE 259 100 58 217 168 NC_002967:TDE1721|5end_radical_SAM_domain_protein_1775140..1775370_POSITIVE 259 95 56 46 10 NC_002967:TDE1007|5end_flagellar_basal-body_rod_protein_FlgG_1031261..1031491_POSITIVE 255 94 55 190 141 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 255 100 60 65 15 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 253 99 56 196 158 NC_002967:TDE1091|5end_hypothetical_protein_1123775..1124005_NEGATIVE 251 98 56 219 164 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 250 99 56 206 147 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 246 93 51 220 175 NC_002967:TDE2126|5end_hypothetical_protein_2159533..2159763_POSITIVE 243 100 56 64 18 NC_002967:TDE2080|5end_cytidylate_kinase/ribosomal_protein_S1_2111484..2111714_NEGATIVE 243 98 56 200 146 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 99 58 50 5 NC_002967:TDE2207|3end_hypothetical_protein_2245366..2245516_NEGATIVE 257 85 43 59 8 NC_002967:TDE0010|3end_MutT/nudix_family_protein_15226..15376_POSITIVE 255 100 60 72 22 NC_002967:TDE0611|3end_hypothetical_protein_647279..647429_NEGATIVE 252 95 71 24 5 NC_002967:TDE1006|3end_flagellar_basal-body_rod_protein_FlgG_1031319..1031469_POSITIVE 251 98 56 145 90 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 246 93 51 138 93 NC_002967:TDE2125|3end_leucyl/phenylalanyl-tRNA--protein_transferase_2159531..2159681_POSITIVE 241 90 45 84 44 NC_002967:TDE1238|3end_translocase_1271245..1271395_POSITIVE 239 100 56 90 47 NC_002967:TDE0990|3end_hypothetical_protein_1017828..1017978_POSITIVE 237 95 61 74 43 NC_002967:TDE2581|3end_hypothetical_protein_2611632..2611782_POSITIVE 236 93 51 82 44 NC_002967:TDE0889|3end_hypothetical_protein_905814..905964_POSITIVE 235 100 51 150 101 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 230 72 31 81 39 NC_002967:TDE2026|3end_hypothetical_protein_2051492..2051642_NEGATIVE 224 93 62 120 82 NC_002967:TDE2051|3end_hypothetical_protein_2079990..2080140_NEGATIVE 224 45 7 66 23 NC_002967:TDE1479|3end_DHH_superfamily_protein,_subfamily_1_1524091..1524241_NEGATIVE 222 93 51 147 104 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE 221 95 52 137 77 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 221 99 51 94 49 NC_002967:TDE1011|3end_hypothetical_protein_1041402..1041552_POSITIVE 220 100 60 118 81 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 220 100 56 62 12 NC_002967:TDE2656|3end_cobalt_chelatase_2693900..2694050_POSITIVE 220 85 44 56 1 NC_002967:TDE1856|3end_radical_SAM_domain_protein_1883956..1884106_POSITIVE