Origin IGS: tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggagagttgataaacagttcggcagaaattcagcctcactgtttatctgacgagttttgtgctttgcacaaaacatcgcattattgattgccgtttctcacaggtgttgcgaaacggcgtaaaaagtcaaatcgaaaattgatattttttcattgactttttataggagacttaaa Mask Tandem Repeat Region ================================================ tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Find is-nt database================================================ Query_seq: TDE0590:TDE0591|TDE0590:TDE0591:acetyl-CoA carboxylase, carboxyl transferase, beta subunit:acetyl-CoA carboxylase, biotin carboxylase:<-<-:629947..630122 176 tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0590:TDE0591|TDE0590:TDE0591:acetyl-CoA carboxylase, carboxyl transferase, beta subunit:acetyl-CoA carboxylase, biotin carboxylase:<-<-:629947..630122 176 tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0590:TDE0591|TDE0590:TDE0591:acetyl-CoA carboxylase, carboxyl transferase, beta subunit:acetyl-CoA carboxylase, biotin carboxylase:<-<-:629947..630122 176 tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 38 End: 130 ..................................... N E I Q S K V G N R L V Q S F R C D I I R H K T C L V F S T M .............................................. tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc 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================================================ tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -9.4 Tail_Score: -3.82262 Start: 97 End: 129 Full_Region: gcctcactgtttatc tgacgagttttgtgc ttt gcacaaaacatcgca ttattgattgccgtt ................................................................................................tgacgagttttgtgctttgcacaaaacatcgca............................................... Find igs database================================================ Query_seq: TDE0590:TDE0591|TDE0590:TDE0591:acetyl-CoA carboxylase, carboxyl transferase, beta subunit:acetyl-CoA carboxylase, biotin carboxylase:<-<-:629947..630122 176 tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_002967_TDE0590_TDE0591|acetyl-CoA carboxylase, carboxyl transferase, beta subunit:acetyl-CoA carboxylase, biotin carboxylase|NEGATIVE:NEGATIVE|[629947,630122]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc tttaagtctcctataaaaagtcaatgaaaaaatatcaattttcgatttgactttttacgccgtttcgcaacacctgtgagaaacggcaatcaataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtgaggctgaatttctgccgaactgtttatcaactctcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGUCUCCUAUAAAAAGUCAAUGAAAAAAUAUCAAUUUUCGAUUUGACUUUUUACGCCGUUUCGCAACACCUGUGAGAAACGGCAAUCAAUAAUGCGAUGUUUUGUGCAAAGCACAAAACUCGUCAGAUAAACAGUGAGGCUGAAUUUCUGCCGAACUGUUUAUCAACUCUCC .............(((((((((((((((((........))))))..))))))))))).((((((((...((....))..))))))))..........((((.(((((((((...)))))))))))))..((((((((((..(((.(.....).)))..))))))))))........ (-61.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGAGUUGAUAAACAGUUCGGCAGAAAUUCAGCCUCACUGUUUAUCUGACGAGUUUUGUGCUUUGCACAAAACAUCGCAUUAUUGAUUGCCGUUUCUCACAGGUGUUGCGAAACGGCGUAAAAAGUCAAAUCGAAAAUUGAUAUUUUUUCAUUGACUUUUUAUAGGAGACUUAAA ...(((((((((((((((..(((.(.....).)))..)))))))))).(.((((((((((((...))))))))).))))..........((((((((.(((....).)).)))))))).(((((((((((...(((((........))))).))))))))))).....)))))... (-57.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 928 100 51 191 142 NC_002967:TDE0590|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_beta_subunit_629856..630086_NEGATIVE 813 169 121 190 142 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 813 169 121 191 143 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 813 169 121 90 42 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 813 169 121 66 18 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 812 140 92 227 179 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 796 168 121 167 120 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 794 160 111 169 120 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 773 160 113 170 124 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 773 160 113 60 14 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 761 160 111 173 125 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 749 160 111 172 124 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 747 149 101 231 184 NC_002967:TDE0064|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_72651..72881_NEGATIVE 704 169 121 90 42 NC_002967:TDE1131|5end_hypothetical_protein_1163182..1163412_POSITIVE 703 169 121 147 96 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 699 169 121 90 42 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 687 168 123 151 100 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 676 169 130 152 113 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 657 140 91 61 13 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 657 140 91 227 179 NC_002967:TDE2396|5end_putative_inner_membrane_protein_translocase_component_YidC_2425398..2425628_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 813 169 121 79 31 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 813 169 121 70 22 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 813 169 121 51 3 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 813 169 121 73 25 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 812 160 111 71 23 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 794 160 111 65 16 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 778 168 121 73 26 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 761 160 111 71 23 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 752 168 121 82 35 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 704 150 101 151 103 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 704 169 121 68 20 NC_002967:TDE1130|3end_methyltransferase,_putative_1163240..1163390_POSITIVE 703 169 121 80 29 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 702 168 121 75 29 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 690 168 121 61 15 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 676 169 130 140 101 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 660 169 121 73 25 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 646 170 123 78 25 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 604 169 121 73 26 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 600 168 134 35 1 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 586 169 121 79 24 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE