Origin IGS: agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattcctccaaatgagtaaaattgtattataaaatacttatattgtacttgagtatccgataattctcaaaaattgtcaagctgtccgttaaatgtatcgttaaattttagtcttgacagaattcaaaataaaaagtacaattttgct Mask Tandem Repeat Region ================================================ agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Find is-nt database================================================ Query_seq: TDE2307:TDE2308|TDE2307:TDE2308:seryl-tRNA synthetase:hypothetical protein:<-->:2345594..2345743 150 agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2307:TDE2308|TDE2307:TDE2308:seryl-tRNA synthetase:hypothetical protein:<-->:2345594..2345743 150 agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2307:TDE2308|TDE2307:TDE2308:seryl-tRNA synthetase:hypothetical protein:<-->:2345594..2345743 150 agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Predict ORF larger than 30AA ================================================ agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt 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: 7 End: 36 ......CTTGACAGAATTCAAAATAAAAAGTACAAT.................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 78 End: 107 .............................................................................TTTGAGAATTATCGGATACTCAAGTACAAT........................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 68 End: 97 ...................................................................CTTGACAATTTTTGAGAATTATCGGATACT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2307:TDE2308|TDE2307:TDE2308:seryl-tRNA synthetase:hypothetical protein:<-->:2345594..2345743 150 agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_002967_TDE2307_TDE2308|seryl-tRNA synthetase:hypothetical protein|NEGATIVE:POSITIVE|[2345594,2345743]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt agcaaaattgtactttttattttgaattctgtcaagactaaaatttaacgatacatttaacggacagcttgacaatttttgagaattatcggatactcaagtacaatataagtattttataatacaattttactcatttggaggaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAAAUUGUACUUUUUAUUUUGAAUUCUGUCAAGACUAAAAUUUAACGAUACAUUUAACGGACAGCUUGACAAUUUUUGAGAAUUAUCGGAUACUCAAGUACAAUAUAAGUAUUUUAUAAUACAAUUUUACUCAUUUGGAGGAAUUUU ......(((((((((..(((((..((((((((((((.((.....((((........)))).....))))))))........))))))...)))))...)))))))))....(((((....))))).......(((.....)))....... (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCCUCCAAAUGAGUAAAAUUGUAUUAUAAAAUACUUAUAUUGUACUUGAGUAUCCGAUAAUUCUCAAAAAUUGUCAAGCUGUCCGUUAAAUGUAUCGUUAAAUUUUAGUCUUGACAGAAUUCAAAAUAAAAAGUACAAUUUUGCU ................((((((((((((((.....(((((((.........))))))).................(((((((((((....((((........))))....))).))))))))..............)))))))))))))) (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 808 110 61 201 152 NC_002967:TDE2307|5end_seryl-tRNA_synthetase_2345503..2345733_NEGATIVE 248 103 61 66 25 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 236 91 55 54 14 NC_002967:TDE1728|5end_hypothetical_protein_1783234..1783464_NEGATIVE 226 93 64 229 198 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 223 80 31 88 39 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 222 99 55 163 105 NC_002967:TDE1850|5end_ABC_transporter,_permease_protein,_putative_1879561..1879791_NEGATIVE 220 94 60 66 26 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 216 99 55 188 139 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 213 78 46 51 22 NC_002967:TDE1965|5end_sodium/hydrogen_exchanger_family_protein_1980151..1980381_NEGATIVE 207 97 57 62 21 NC_002967:TDE0632|5end_anti-anti-sigma_factor_667431..667661_POSITIVE 201 38 7 230 183 NC_002967:TDE0552|5end_ankyrin_repeat_protein_589393..589623_NEGATIVE 199 82 42 159 116 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 199 106 63 72 35 NC_002967:TDE1023|5end_methylaspartate_mutase_subunit_S_1055123..1055353_POSITIVE 196 45 8 151 116 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 194 101 62 167 130 NC_002967:TDE1085|5end_UDP-N-acetylmuramate--L-alanine_ligase_1116328..1116558_POSITIVE 193 78 49 230 204 NC_002967:TDE0701|5end_hypothetical_protein_737247..737477_NEGATIVE 190 103 66 225 190 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 190 93 55 115 65 NC_002967:TDE1770|5end_hypothetical_protein_1814236..1814466_POSITIVE 189 93 61 214 181 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 189 112 74 136 96 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 106 61 75 29 NC_002967:TDE0950|3end_hypothetical_protein_974166..974316_NEGATIVE 248 103 61 60 19 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 222 99 55 147 89 NC_002967:TDE1851|3end_ABC_transporter,_permease_protein,_putative_1879577..1879727_NEGATIVE 220 94 60 66 26 NC_002967:TDE1935|3end_hypothetical_protein_1953166..1953316_POSITIVE 207 97 57 52 11 NC_002967:TDE0631|3end_sigma_factor_regulatory_protein,_putative_667501..667651_POSITIVE 205 92 54 75 44 NC_002967:TDE0407|3end_glutamate_synthase_(NADPH),_homotetrameric_459011..459161_NEGATIVE 191 67 27 65 24 NC_002967:TDE1038|3end_hypothetical_protein_1065405..1065555_NEGATIVE 190 98 71 111 86 NC_002967:TDE2655|3end_hypothetical_protein_2692963..2693113_NEGATIVE 188 69 28 92 42 NC_002967:TDE0891|3end_transcriptional_regulator,_putative_908592..908742_POSITIVE 187 96 61 139 99 NC_002967:TDE1723|3end_hypothetical_protein_1777779..1777929_POSITIVE 183 68 21 123 75 NC_002967:TDE1489|3end_hypothetical_protein_1532730..1532880_NEGATIVE 182 89 49 147 103 NC_002967:TDE0080|3end_betaine_aldehyde_dehydrogenase_90728..90878_NEGATIVE 181 68 29 74 40 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 180 82 49 66 29 NC_002967:TDE1600|3end_ABC_transporter,_ATP-binding/permease_protein_1650645..1650795_NEGATIVE 179 85 56 119 90 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 178 70 27 92 52 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 178 97 60 141 100 NC_002967:TDE0455|3end_kinase,_GHMP_family_512477..512627_POSITIVE 176 98 58 107 66 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE 176 87 48 55 6 NC_002967:TDE2496|3end_methyl-accepting_chemotaxis_protein_2521170..2521320_NEGATIVE 175 103 64 127 93 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE