Origin IGS: atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa .........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 ttgagaatataaacttataaaaatagttctttgaggcggcaaaatgagagggaaacctcatacaagtattttttgttctcttataaataagcaataggaaaagatggaataagccgtattatcttattgaaaaacaagagaaagaaaacaactttgatgcgaacataaaaggagaatgtat Mask Tandem Repeat Region ================================================ atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Find is-nt database================================================ Query_seq: TDE0501:TDE0502|TDE0501:TDE0502:hypothetical protein:ankyrin repeat protein:<-<-:555403..555583 181 atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0501:TDE0502|TDE0501:TDE0502:hypothetical protein:ankyrin repeat protein:<-<-:555403..555583 181 atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0501:TDE0502|TDE0501:TDE0502:hypothetical protein:ankyrin repeat protein:<-<-:555403..555583 181 atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 88 End: 180 ....................................................................................... M L I Y K R T K N T C M R F P S H F A A S K N Y F Y K F I F S . Protein_Len: 31 Strand: - Start: 3 End: 95 .. C E G K I N A D F N N E K E Q K E I L Y Y P K N W R K R N S M ...................................................................................... atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa 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: 139 End: 168 ..........................................................................................................................................TTTGCCGCCTCAAAGAACTATTTTTATAAG............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0501:TDE0502|TDE0501:TDE0502:hypothetical protein:ankyrin repeat protein:<-<-:555403..555583 181 atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002967_TDE0501_TDE0502|hypothetical protein:ankyrin repeat protein|NEGATIVE:NEGATIVE|[555403,555583]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa atacattctccttttatgttcgcatcaaagttgttttctttctcttgtttttcaataagataatacggcttattccatcttttcctattgcttatttataagagaacaaaaaatacttgtatgaggtttccctctcattttgccgcctcaaagaactatttttataagtttatattctcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAUUCUCCUUUUAUGUUCGCAUCAAAGUUGUUUUCUUUCUCUUGUUUUUCAAUAAGAUAAUACGGCUUAUUCCAUCUUUUCCUAUUGCUUAUUUAUAAGAGAACAAAAAAUACUUGUAUGAGGUUUCCCUCUCAUUUUGCCGCCUCAAAGAACUAUUUUUAUAAGUUUAUAUUCUCAA .................((((......((((..((((..(((((((((.....((((((.(((((.((...............))))))))))))).)))))))))..))))..))))...((((((.................))))))..))))......................... (-26.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGAAUAUAAACUUAUAAAAAUAGUUCUUUGAGGCGGCAAAAUGAGAGGGAAACCUCAUACAAGUAUUUUUUGUUCUCUUAUAAAUAAGCAAUAGGAAAAGAUGGAAUAAGCCGUAUUAUCUUAUUGAAAAACAAGAGAAAGAAAACAACUUUGAUGCGAACAUAAAAGGAGAAUGUAU .((((........))))........(((((((......(((......((((....))))....((((..(((((.(((((((.........((((((((.((.((((......)))).)).))))))))......))))))).)))))..))))...)))..........))))))).... (-36.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 775 70 21 161 112 NC_002967:TDE0501|5end_hypothetical_protein_555312..555542_NEGATIVE 279 150 115 74 47 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 269 154 112 112 71 NC_002967:TDE0397|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446777..447007_POSITIVE 267 145 101 60 16 NC_002967:TDE1465|5end_signal_peptidase_I,_putative_1513564..1513794_POSITIVE 256 156 117 107 72 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 256 170 129 191 150 NC_002967:TDE1172|5end_hypothetical_protein_1201006..1201236_POSITIVE 252 70 27 88 50 NC_002967:TDE1523|5end_citXG_protein,_putative_1568826..1569056_POSITIVE 247 77 45 42 3 NC_002967:TDE0378|5end_hypothetical_protein_432164..432394_POSITIVE 246 180 139 90 39 NC_002967:TDE1077|5end_hypothetical_protein_1108395..1108625_POSITIVE 244 153 120 225 201 NC_002967:TDE1615|5end_hypothetical_protein_1663708..1663938_NEGATIVE 244 50 6 157 97 NC_002967:TDE0555|5end_hypothetical_protein_591522..591752_NEGATIVE 244 45 2 59 17 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 243 169 130 95 53 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 240 165 125 91 49 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 240 163 130 208 171 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 240 53 14 99 54 NC_002967:TDE1041|5end_polyribonucleotide_nucleotidyltransferase_1068324..1068554_POSITIVE 239 166 132 115 81 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 239 166 125 227 186 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 239 46 7 187 141 NC_002967:TDE1463|5end_hypothetical_protein_1513072..1513302_NEGATIVE 239 85 44 197 155 NC_002967:TDE1282|5end_hypothetical_protein_1316801..1317031_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 170 123 104 53 NC_002967:TDE0460|3end_transporter,_putative_515274..515424_NEGATIVE 279 150 115 74 47 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 276 92 66 98 68 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 269 154 112 115 74 NC_002967:TDE0396|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446860..447010_POSITIVE 256 156 117 106 71 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 254 157 121 126 85 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 254 149 114 131 92 NC_002967:TDE0938|3end_hypothetical_protein_960963..961113_NEGATIVE 253 166 125 105 54 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 252 70 27 70 32 NC_002967:TDE1522|3end_citrate_lyase_ligase_1568888..1569038_POSITIVE 251 135 116 151 129 NC_002967:TDE1989|3end_acyltransferase_family_protein_2005585..2005735_NEGATIVE 247 152 119 33 1 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 244 50 6 141 81 NC_002967:TDE0556|3end_hypothetical_protein_591538..591688_NEGATIVE 243 52 11 103 60 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 243 52 11 103 60 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 243 52 11 103 60 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 240 165 125 74 32 NC_002967:TDE1137|3end_hypothetical_protein_1166066..1166216_NEGATIVE 240 163 130 76 39 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 239 166 132 118 84 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE 237 155 111 130 85 NC_002967:TDE0879|3end_hypothetical_protein_900057..900207_POSITIVE 234 49 2 138 92 NC_002967:TDE0819|3end_ABC_transporter,_ATP-binding/permease_protein_841649..841799_NEGATIVE