Origin IGS: agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggtgaagtatagaatagaaagcctctcttgtcaaggaagttttcaccatgcttgaaacaattaaaaaaattctatataatcggcggattaaggagataattctatttaaggagagaattct Mask Tandem Repeat Region ================================================ agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Find is-nt database================================================ Query_seq: TDE2476:TDE2477|TDE2476:TDE2477:carbamate kinase:selenocysteine synthase:<-->:2499541..2499662 122 agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2476:TDE2477|TDE2476:TDE2477:carbamate kinase:selenocysteine synthase:<-->:2499541..2499662 122 agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2476:TDE2477|TDE2476:TDE2477:carbamate kinase:selenocysteine synthase:<-->:2499541..2499662 122 agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 4 End: 120 ... M L S L N R I I S L I R R L Y R I F L I V S S M V K T S L T R E A F Y S I L H .. agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc 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: 88 Start: 42 End: 71 .........................................CTTGAAACAATTAAAAAAATTCTATATAAT................................................... PromScan Matrix: RpoD-17 Strand: + Score: 88 Start: 87 End: 116 ......................................................................................CTTGACAAGAGAGGCTTTCTATTCTATACT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2476:TDE2477|TDE2476:TDE2477:carbamate kinase:selenocysteine synthase:<-->:2499541..2499662 122 agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002967_TDE2476_TDE2477|carbamate kinase:selenocysteine synthase|NEGATIVE:POSITIVE|[2499541,2499662]|122 HSP 1 e-value: 7.0E-51 bit: 200.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 agaattctctccttaaatagaattatctccttaatccgccgattatatagaannnnnnnaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc agaattctctccttaaatagaattatctccttaatccgccgattatatagaatttttttaattgtttcaagcatggtgaaaacttccttgacaagagaggctttctattctatacttcaccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUUCUCUCCUUAAAUAGAAUUAUCUCCUUAAUCCGCCGAUUAUAUAGAAUUUUUUUAAUUGUUUCAAGCAUGGUGAAAACUUCCUUGACAAGAGAGGCUUUCUAUUCUAUACUUCACCC ((((.((((((......(((((...(((...(((((....)))))...)))....)))))......(((((...(((....)))..)))))...))))))..))))................ (-20.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUGAAGUAUAGAAUAGAAAGCCUCUCUUGUCAAGGAAGUUUUCACCAUGCUUGAAACAAUUAAAAAAAUUCUAUAUAAUCGGCGGAUUAAGGAGAUAAUUCUAUUUAAGGAGAGAAUUCU .(.(((.(((((((((.((((((.(((........))).))))))..((....))..............)))))))))..))).)......((((.....((((.....)))).....)))) (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 868 120 71 211 162 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 261 106 65 41 1 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 246 60 16 101 53 NC_002967:TDE0304|5end_hypothetical_protein_333883..334113_POSITIVE 245 119 79 200 148 NC_002967:TDE1930|5end_hypothetical_protein_1948556..1948786_NEGATIVE 242 104 69 52 14 NC_002967:TDE0045|5end_ABC_transporter,_ATP-binding_protein_55113..55343_NEGATIVE 237 120 84 98 62 NC_002967:TDE2048|5end_hypothetical_protein_2076411..2076641_POSITIVE 236 78 36 81 36 NC_002967:TDE2229|5end_hypothetical_protein_2269077..2269307_NEGATIVE 232 118 71 144 88 NC_002967:TDE0366|5end_type_I_restriction-modification_system,_R_subunit_415541..415771_NEGATIVE 228 106 61 52 2 NC_002967:TDE0823|5end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_844741..844971_POSITIVE 224 106 66 51 6 NC_002967:TDE0667|5end_FeS_assembly_protein_SufB_704290..704520_POSITIVE 223 113 73 168 129 NC_002967:TDE1162|5end_ParB-like_nuclease_domain_protein_1197684..1197914_NEGATIVE 221 109 63 169 115 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 220 106 63 210 144 NC_002967:TDE0844|5end_pyruvate_phosphate_dikinase,_putative_864886..865116_POSITIVE 219 94 64 77 48 NC_002967:TDE1654|5end_ATP-dependent_helicase_HrpA,_putative_1702219..1702449_POSITIVE 218 106 67 184 147 NC_002967:TDE1941|5end_hypothetical_protein_1959285..1959515_NEGATIVE 217 109 79 205 174 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 216 41 17 42 12 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 216 65 27 153 97 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 214 42 4 97 58 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 213 51 17 159 120 NC_002967:TDE1857|5end_hypothetical_protein_1884450..1884680_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 106 72 37 3 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 232 118 71 151 95 NC_002967:TDE0367|3end_hypothetical_protein_415534..415684_NEGATIVE 227 104 61 55 1 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 224 106 66 54 9 NC_002967:TDE0666|3end_FeS_assembly_ATPase_SufC_704373..704523_POSITIVE 217 109 79 148 117 NC_002967:TDE0999|3end_formate/nitrite_transporter_1026786..1026936_POSITIVE 216 102 62 67 21 NC_002967:TDE2402|3end_radical_SAM_domain_protein_2428664..2428814_POSITIVE 216 118 76 108 58 NC_002967:TDE2186|3end_AMP-binding_enzyme_family_protein_2221083..2221233_POSITIVE 216 60 11 109 60 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 210 112 73 151 113 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 206 104 62 53 12 NC_002967:TDE0057|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_67001..67151_POSITIVE 205 68 29 100 58 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 205 38 11 34 5 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 205 68 27 111 77 NC_002967:TDE1449|3end_GTPase_YjeQ_1495379..1495529_POSITIVE 205 118 72 82 31 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 205 110 64 148 94 NC_002967:TDE0093|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_112308..112458_POSITIVE 204 30 3 112 85 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 204 104 61 59 3 NC_002967:TDE2624|3end_hypothetical_protein_2664321..2664471_NEGATIVE 204 39 5 113 72 NC_002967:TDE1142|3end_phage_minor_structural_protein,_putative_1171468..1171618_NEGATIVE 204 79 34 54 1 NC_002967:TDE0791|3end_DNA-directed_RNA_polymerase_alpha_subunit_818477..818627_POSITIVE 203 100 52 57 17 NC_002967:TDE0857|3end_lipoprotein,_putative_879598..879748_POSITIVE