Origin IGS: cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagttaaaagcatgttgcaaggcttatgagaaaatcggccggaattaagtttcggccgattttttttcttttactaaatctaaggtagacctctaaagttttttaag Mask Tandem Repeat Region ================================================ cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Find is-nt database================================================ Query_seq: TDE0008:TDE0009|TDE0008:TDE0009:copper-translocating P-type ATPase:hypothetical protein:-><-:13707..13813 107 cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0008:TDE0009|TDE0008:TDE0009:copper-translocating P-type ATPase:hypothetical protein:-><-:13707..13813 107 cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0008:TDE0009|TDE0008:TDE0009:copper-translocating P-type ATPase:hypothetical protein:-><-:13707..13813 107 cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Predict ORF larger than 30AA ================================================ cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -10.0 Tail_Score: -4.4648 Start: 49 End: 73 Full_Region: GTAAAAGAAAAAAAA TCGGCCGAAA CTTAA TTCCGGCCGA TTTTCTCATAAGCCT ................................................TCGGCCGAAACTTAATTCCGGCCGA.................................. Find igs database================================================ Query_seq: TDE0008:TDE0009|TDE0008:TDE0009:copper-translocating P-type ATPase:hypothetical protein:-><-:13707..13813 107 cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002967_TDE0008_TDE0009|copper-translocating P-type ATPase:hypothetical protein|POSITIVE:NEGATIVE|[13707,13813]|107 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 cttaaaaaactttagaggtctaccttagatttagtaaaagnnnnnnnntcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg cttaaaaaactttagaggtctaccttagatttagtaaaagaaaaaaaatcggccgaaacttaattccggccgattttctcataagccttgcaacatgcttttaactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAAAAACUUUAGAGGUCUACCUUAGAUUUAGUAAAAGAAAAAAAAUCGGCCGAAACUUAAUUCCGGCCGAUUUUCUCAUAAGCCUUGCAACAUGCUUUUAACUG ..............((((....)))).....(((((((((....(((((((((((...........))))))))))).......((...))......))))).)))) (-22.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUUAAAAGCAUGUUGCAAGGCUUAUGAGAAAAUCGGCCGGAAUUAAGUUUCGGCCGAUUUUUUUUCUUUUACUAAAUCUAAGGUAGACCUCUAAAGUUUUUUAAG ..............(((.(((((((..((((((((((((((((((...))))))))))))))))))...((((((........))))))......))))))).))). (-29.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 89 49 69 31 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 332 87 48 52 8 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 321 100 51 208 146 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 288 99 51 177 128 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 274 87 49 79 43 NC_002967:TDE2303|5end_hypothetical_protein_2343055..2343285_POSITIVE 270 90 48 219 180 NC_002967:TDE1734|5end_exodeoxyribonuclease_III_1788613..1788843_POSITIVE 264 86 58 152 120 NC_002967:TDE0537|5end_hypothetical_protein_579024..579254_POSITIVE 262 99 51 88 44 NC_002967:TDE0096|5end_NADH_oxidase_112723..112953_POSITIVE 261 83 50 92 58 NC_002967:TDE0069|5end_conserved_hypothetical_protein_TIGR00238_76551..76781_POSITIVE 257 90 48 187 147 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 254 88 53 39 1 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 252 88 48 189 150 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 252 98 51 89 28 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 250 90 49 224 170 NC_002967:TDE1640|5end_3-dehydroquinate_dehydratase,_type_1,_putative/shikimate_5-dehydrogenase,_putative_1690396..1690626_POSITIVE 248 91 67 64 43 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 245 95 53 142 100 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 243 95 66 56 27 NC_002967:TDE1468|5end_glycoprotease_family_protein_1517336..1517566_NEGATIVE 243 93 51 190 118 NC_002967:TDE0447|5end_TPR_domain_protein_502758..502988_POSITIVE 241 90 50 156 112 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 240 100 66 230 197 NC_002967:TDE0352|5end_ribose_5-phosphate_isomerase_B_396207..396437_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 89 49 85 47 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 324 77 43 49 11 NC_002967:TDE2446|3end_malate_dehydrogenase_2474774..2474924_NEGATIVE 314 89 48 144 103 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 313 77 45 46 14 NC_002967:TDE0008|3end_copper-translocating_P-type_ATPase_13646..13796_POSITIVE 306 88 42 55 9 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 291 88 42 69 20 NC_002967:TDE0680|3end_protein-export_membrane_protein_SecF_717613..717763_NEGATIVE 287 87 42 151 106 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 280 87 43 75 24 NC_002967:TDE2729|3end_hypothetical_protein_2785756..2785906_NEGATIVE 280 90 47 138 103 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 274 87 49 79 43 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 271 97 51 72 17 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 264 77 39 78 35 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 262 88 48 145 110 NC_002967:TDE1312|3end_hypothetical_protein_1350715..1350865_POSITIVE 261 83 50 73 39 NC_002967:TDE0068|3end_succinyl-diaminopimelate_desuccinylase_76612..76762_POSITIVE 252 98 51 85 24 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 245 90 50 48 1 NC_002967:TDE2445|3end_DNA-binding_protein_2474667..2474817_POSITIVE 245 95 53 145 103 NC_002967:TDE0273|3end_ABC_transporter,_ATP-binding/permease_protein_302867..303017_NEGATIVE 243 95 66 59 30 NC_002967:TDE1469|3end_conserved_hypothetical_protein_TIGR00150_1517333..1517483_NEGATIVE 242 87 47 129 81 NC_002967:TDE1665|3end_hypothetical_protein_1718908..1719058_NEGATIVE 237 99 52 150 99 NC_002967:TDE0016|3end_ATPase,_AAA_family_21862..22012_POSITIVE