Origin IGS: atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgggagtatcgataaacagttcggcagaaatacagcctcactgtttatcttcgagttttgtgctttgcacaaaacatcgtattattttatgggagtagat Mask Tandem Repeat Region ================================================ atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Find is-nt database================================================ Query_seq: TDE1298:TDE1299|TDE1298:TDE1299:cyclic nucleotide binding domain protein:hypothetical protein:<-<-:1335406..1335506 101 atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1298:TDE1299|TDE1298:TDE1299:cyclic nucleotide binding domain protein:hypothetical protein:<-<-:1335406..1335506 101 atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1298:TDE1299|TDE1298:TDE1299:cyclic nucleotide binding domain protein:hypothetical protein:<-<-:1335406..1335506 101 atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 6 End: 101 ..... * E W L I I R H K T C L V F S S S L C H P Q I E A S S N I S V G M Protein_Len: 31 Strand: - Start: 1 End: 93 D V G M F Y Y S T K H L A C F E F I F L S A T N R G F Q K D M ........ atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa 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================================================ atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -9.6 Tail_Score: -4.31397 Start: 20 End: 51 Full_Region: gcctcactgtttatc ttcgagttttgtgc ttt gcacaaaacatcgta ttattttatgggagt ...................ttcgagttttgtgctttgcacaaaacatcgta.................................................. TransTerm Strand: - Conf: 93 HP_score: -12.2 Tail_Score: -3.75581 Start: 22 End: 49 Full_Region: ctcactgtttatctt cgagttttgtgc ttt gcacaaaacatcg tattattttatggga .....................cgagttttgtgctttgcacaaaacatcg.................................................... TransTerm Strand: + Conf: 51 HP_score: -2.1 Tail_Score: -3.93695 Start: 58 End: 84 Full_Region: AAACTCGAAGATAAA CAGTGAGGCTG TATTT CTGCCGAACTG TTTATCGATACTCCC .........................................................CAGTGAGGCTGTATTTCTGCCGAACTG................. Find igs database================================================ Query_seq: TDE1298:TDE1299|TDE1298:TDE1299:cyclic nucleotide binding domain protein:hypothetical protein:<-<-:1335406..1335506 101 atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002967_TDE1298_TDE1299|cyclic nucleotide binding domain protein:hypothetical protein|NEGATIVE:NEGATIVE|[1335406,1335506]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa atctactcccataaaataatacgatgttttgtgcaaagcacaaaactcgaagataaacagtgaggctgtatttctgccgaactgtttatcgatactcccaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUACUCCCAUAAAAUAAUACGAUGUUUUGUGCAAAGCACAAAACUCGAAGAUAAACAGUGAGGCUGUAUUUCUGCCGAACUGUUUAUCGAUACUCCCAA .....................(((.(((((((((...))))))))))))..((((((((((..(((.........)))..))))))))))........... (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGGAGUAUCGAUAAACAGUUCGGCAGAAAUACAGCCUCACUGUUUAUCUUCGAGUUUUGUGCUUUGCACAAAACAUCGUAUUAUUUUAUGGGAGUAGAU ...((((((..((((((((((..(((.........)))..))))))))))..((((((((((((...))))))))).)))...))))))............ (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 80 31 171 122 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 830 68 22 228 182 NC_002967:TDE0064|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_72651..72881_NEGATIVE 809 80 31 168 119 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 809 80 31 58 9 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 804 80 31 170 121 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 803 80 31 167 117 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 753 99 51 175 128 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 753 99 51 73 26 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 714 90 43 189 141 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 714 90 43 190 142 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 714 90 43 89 41 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 704 80 31 79 30 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 694 90 41 89 39 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 676 98 52 154 108 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 672 98 51 157 110 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 665 66 22 231 186 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 663 65 22 230 187 NC_002967:TDE2396|5end_putative_inner_membrane_protein_translocase_component_YidC_2425398..2425628_NEGATIVE 662 80 31 130 81 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 655 98 52 159 113 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 649 66 21 227 182 NC_002967:TDE1582|5end_glycogen_synthase_1631759..1631989_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 864 80 31 69 20 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 803 80 31 63 13 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 803 80 31 72 22 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 770 68 21 147 100 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 764 90 41 82 32 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 753 99 51 58 11 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 721 90 43 75 28 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 714 90 43 78 30 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 714 90 43 69 21 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 714 90 43 72 24 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 712 90 43 61 14 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 704 80 31 57 8 NC_002967:TDE2398|3end_conserved_hypothetical_protein_TIGR00278_2425586..2425736_NEGATIVE 677 90 41 73 23 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 676 98 52 87 41 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 675 99 56 43 1 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 672 98 51 84 37 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 662 80 31 62 13 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 641 90 41 67 17 NC_002967:TDE1130|3end_methyltransferase,_putative_1163240..1163390_POSITIVE 635 97 52 146 101 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 607 98 51 80 33 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE