Origin IGS: ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaccataaggtttaggtttttgcctatgattatgtgaaaattcatagtgaaataaaaaagtatttactataggcataaaggtatcattatggtataatgatacctttaggag Mask Tandem Repeat Region ================================================ ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Find is-nt database================================================ Query_seq: TDE0291:TDE0292|TDE0291:TDE0292:hypothetical protein:hypothetical protein:<-<-:321151..321264 114 ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0291:TDE0292|TDE0291:TDE0292:hypothetical protein:hypothetical protein:<-<-:321151..321264 114 ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0291:TDE0292|TDE0291:TDE0292:hypothetical protein:hypothetical protein:<-<-:321151..321264 114 ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Predict ORF larger than 30AA ================================================ ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct 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: 84 Start: 15 End: 44 ..............ATAGGCATAAAGGTATCATTATGGTATAAT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0291:TDE0292|TDE0291:TDE0292:hypothetical protein:hypothetical protein:<-<-:321151..321264 114 ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE0291_TDE0292|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[321151,321264]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct ctcctaaaggtatcattataccataatgatacctttatgcctatagtaaatacttttttatttcactatgaattttcacataatcataggcaaaaacctaaaccttatggttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUAAAGGUAUCAUUAUACCAUAAUGAUACCUUUAUGCCUAUAGUAAAUACUUUUUUAUUUCACUAUGAAUUUUCACAUAAUCAUAGGCAAAAACCUAAACCUUAUGGUUCU ....(((((((((((((((...)))))))))))))))(((((((.(((((......))))).....((((........))))...)))))))........((((....)))).. (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAACCAUAAGGUUUAGGUUUUUGCCUAUGAUUAUGUGAAAAUUCAUAGUGAAAUAAAAAAGUAUUUACUAUAGGCAUAAAGGUAUCAUUAUGGUAUAAUGAUACCUUUAGGAG .(((((....))))).......((((((((....(((((....)))))...(((((......)))))..))))))))(((((((((((((((...))))))))))))))).... (-31.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 777 50 1 141 92 NC_002967:TDE0291|5end_hypothetical_protein_321060..321290_NEGATIVE 247 80 32 148 98 NC_002967:TDE2649|5end_ABC_transporter,_ATP-binding_protein_2688648..2688878_NEGATIVE 225 90 47 169 121 NC_002967:TDE0275|5end_CAAX_amino_terminal_protease_family_protein_306633..306863_POSITIVE 225 49 1 148 98 NC_002967:TDE0241|5end_hypothetical_protein_275303..275533_NEGATIVE 224 90 41 196 145 NC_002967:TDE1558|5end_YD_repeat_protein_1600757..1600987_POSITIVE 214 46 19 174 145 NC_002967:TDE2603|5end_DNA_mismatch_repair_protein_2641476..2641706_POSITIVE 206 59 26 147 109 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 200 105 83 119 95 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 197 49 7 72 31 NC_002967:TDE0052|5end_flagellar_biosynthetic_protein_FliQ_61305..61535_POSITIVE 194 46 1 113 66 NC_002967:TDE1049|5end_elongation_factor_EF-2_1075287..1075517_POSITIVE 193 42 1 137 105 NC_002967:TDE2363|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398409_NEGATIVE 186 46 4 189 137 NC_002967:TDE2032|5end_hypothetical_protein_2060169..2060399_NEGATIVE 185 106 61 78 34 NC_002967:TDE0568|5end_hypothetical_protein_598849..599079_POSITIVE 184 71 32 111 63 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 182 80 38 46 14 NC_002967:TDE1502|5end_chorismate_mutase_1550920..1551150_POSITIVE 180 59 13 231 179 NC_002967:TDE2473|5end_30S_ribosomal_protein_S21_2496298..2496528_POSITIVE 180 110 61 169 118 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 178 49 1 115 63 NC_002967:TDE0967|5end_hypothetical_protein_992201..992431_POSITIVE 177 45 10 131 88 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 174 55 26 47 18 NC_002967:TDE2250|5end_hypothetical_protein_2288568..2288798_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 80 32 130 80 NC_002967:TDE2650|3end_transcriptional_regulator,_putative_2688666..2688816_NEGATIVE 225 49 1 137 87 NC_002967:TDE0242|3end_hypothetical_protein_275314..275464_NEGATIVE 224 90 41 129 78 NC_002967:TDE1557|3end_hypothetical_protein_1600770..1600920_POSITIVE 206 59 26 87 49 NC_002967:TDE1053|3end_lipoprotein,_putative_1078930..1079080_NEGATIVE 200 105 83 114 90 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 195 73 31 141 101 NC_002967:TDE1280|3end_hypothetical_protein_1315750..1315900_NEGATIVE 193 42 1 137 105 NC_002967:TDE2364|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398329_NEGATIVE 186 46 4 66 14 NC_002967:TDE2033|3end_ISTde1,_transposase_2060292..2060442_NEGATIVE 185 106 61 65 21 NC_002967:TDE0567|3end_hypothetical_protein_598916..599066_POSITIVE 180 59 13 79 27 NC_002967:TDE2472|3end_ISTde1,_transposase_2496226..2496376_POSITIVE 180 59 13 79 27 NC_002967:TDE0039|3end_ISTde1,_transposase_44489..44639_NEGATIVE 177 45 10 78 35 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 169 76 31 133 87 NC_002967:TDE0494|3end_hypothetical_protein_549559..549709_NEGATIVE 168 49 9 89 41 NC_002967:TDE0889|3end_hypothetical_protein_905814..905964_POSITIVE 167 46 1 70 17 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 167 66 38 111 88 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 165 48 19 33 5 NC_002967:TDE1225|3end_zinc_ABC_transporter,_ATP-binding_protein_1258751..1258901_NEGATIVE 164 42 3 123 79 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 163 43 3 146 100 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 163 99 54 113 60 NC_002967:TDE2377|3end_hypothetical_protein_2407530..2407680_NEGATIVE