Origin IGS: aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtatataagaaaatgaagaccgttatgatgtttaacataacggtctttttttatattcttgtaaaatcataaaaattaccttgctatttttttaaatatatattacaatgctttt Mask Tandem Repeat Region ================================================ aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Find is-nt database================================================ Query_seq: TDE1174:TDE1175|TDE1174:TDE1175:hypothetical protein:chaperonin GroEL:<-<-:1203491..1203606 116 aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1174:TDE1175|TDE1174:TDE1175:hypothetical protein:chaperonin GroEL:<-<-:1203491..1203606 116 aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1174:TDE1175|TDE1174:TDE1175:hypothetical protein:chaperonin GroEL:<-<-:1203491..1203606 116 aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Predict ORF larger than 30AA ================================================ aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact 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: 86 Start: 7 End: 36 ......CTTGCTATTTTTTTAAATATATATTACAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -11.4 Tail_Score: -3.86445 Start: 71 End: 98 Full_Region: AAGAATATAAAAAAA GACCGTTATGTT AAAC ATCATAACGGTC TTCATTTTCTTATAT ......................................................................GACCGTTATGTTAAACATCATAACGGTC.................. Find igs database================================================ Query_seq: TDE1174:TDE1175|TDE1174:TDE1175:hypothetical protein:chaperonin GroEL:<-<-:1203491..1203606 116 aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_002967_TDE1174_TDE1175|hypothetical protein:chaperonin GroEL|NEGATIVE:NEGATIVE|[1203491,1203606]|116 HSP 1 e-value: 9.0E-35 bit: 147.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 aaaagcattgtaatatatatttnnnnnnntagcaaggtaatttttatgattttacaagaatatnnnnnnngaccgttatgttaaacatcataacggtcttcattttcttatatact aaaagcattgtaatatatatttaaaaaaatagcaaggtaatttttatgattttacaagaatataaaaaaagaccgttatgttaaacatcataacggtcttcattttcttatatact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGCAUUGUAAUAUAUAUUUAAAAAAAUAGCAAGGUAAUUUUUAUGAUUUUACAAGAAUAUAAAAAAAGACCGUUAUGUUAAACAUCAUAACGGUCUUCAUUUUCUUAUAUACU .......((((((.......(((.((((((.((...)).)))))).)))..))))))..(((((((((((((((((((((........)))))))))))...)))).))))))... (-21.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUAUAAGAAAAUGAAGACCGUUAUGAUGUUUAACAUAACGGUCUUUUUUUAUAUUCUUGUAAAAUCAUAAAAAUUACCUUGCUAUUUUUUUAAAUAUAUAUUACAAUGCUUUU .((((.((((((((((((((((((((((........)))))))))))))(((((((....)))))))...................))))))))).))))................ (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 708 100 51 191 142 NC_002967:TDE1174|5end_hypothetical_protein_1203400..1203630_NEGATIVE 215 109 66 88 45 NC_002967:TDE0411|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_462931..463161_POSITIVE 190 106 72 180 149 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 188 77 31 63 12 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 186 106 69 76 35 NC_002967:TDE2655|5end_hypothetical_protein_2693070..2693300_NEGATIVE 185 103 68 105 75 NC_002967:TDE0611|5end_hypothetical_protein_647389..647619_NEGATIVE 185 103 68 208 178 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 184 109 69 97 51 NC_002967:TDE0398|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_447773..448003_POSITIVE 183 109 73 114 78 NC_002967:TDE1183|5end_ABC_transporter,_ATP-binding_protein_1210612..1210842_POSITIVE 183 84 43 177 143 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 181 108 66 96 56 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 175 107 69 199 157 NC_002967:TDE2656|5end_cobalt_chelatase_2693065..2693295_POSITIVE 175 109 71 97 59 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 174 97 53 59 22 NC_002967:TDE2390|5end_hypothetical_protein_2420558..2420788_NEGATIVE 173 100 52 152 107 NC_002967:TDE0814|5end_transcriptional_regulator,_putative_835879..836109_NEGATIVE 172 105 72 230 193 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 171 109 65 167 114 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 171 108 69 58 15 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 171 47 4 78 30 NC_002967:TDE1187|5end_hypothetical_protein_1213588..1213818_POSITIVE 171 77 31 164 125 NC_002967:TDE1099|5end_acetyltransferase,_GNAT_family_1134251..1134481_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 215 109 66 76 33 NC_002967:TDE0410|3end_peptidase,_M48_family_462999..463149_POSITIVE 213 92 53 66 18 NC_002967:TDE0494|3end_hypothetical_protein_549559..549709_NEGATIVE 194 99 54 84 29 NC_002967:TDE1986|3end_adenylate_cyclase,_putative_2000283..2000433_NEGATIVE 188 77 31 75 24 NC_002967:TDE1313|3end_signal_peptidase_I_1351266..1351416_POSITIVE 185 103 68 127 97 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 184 109 69 78 32 NC_002967:TDE0397|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_447834..447984_POSITIVE 183 109 73 100 64 NC_002967:TDE1182|3end_hypothetical_protein_1210678..1210828_POSITIVE 181 100 55 133 97 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 181 108 66 115 75 NC_002967:TDE1496|3end_chromosome_partition_protein_SmC,_putative_1543307..1543457_POSITIVE 180 101 73 55 33 NC_002967:TDE0570|3end_hypothetical_protein_600956..601106_POSITIVE 177 102 73 151 123 NC_002967:TDE1565|3end_hypothetical_protein_1617422..1617572_POSITIVE 175 107 69 53 11 NC_002967:TDE2654|3end_macrolide_efflux_protein,_putative_2692999..2693149_POSITIVE 175 109 71 81 43 NC_002967:TDE0829|3end_putative_aminopeptidase_2_850185..850335_NEGATIVE 174 100 59 36 4 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 173 100 52 54 9 NC_002967:TDE0815|3end_hypothetical_protein_835977..836127_NEGATIVE 171 77 31 147 108 NC_002967:TDE1100|3end_acetyltransferase,_GNAT_family_1134268..1134418_NEGATIVE 167 101 73 50 21 NC_002967:TDE0039|3end_ISTde1,_transposase_44489..44639_NEGATIVE 166 100 57 120 74 NC_002967:TDE0929|3end_ornithine_carbamoyltransferase_951719..951869_NEGATIVE 165 101 69 138 110 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE 164 82 49 128 93 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE