Origin IGS: aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cataaaataaaccgcaaaggttaagaagatcgcaaagatttttttaggatgttttttaatcaattattattctttgcgctcttgtggggtaattttataatataattattataaagtgtatctt Mask Tandem Repeat Region ================================================ aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Find is-nt database================================================ Query_seq: TDE1641:TDE1642|TDE1641:TDE1642:ribose 5-phosphate isomerase A:hypothetical protein:-><-:1692737..1692860 124 aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1641:TDE1642|TDE1641:TDE1642:ribose 5-phosphate isomerase A:hypothetical protein:-><-:1692737..1692860 124 aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1641:TDE1642|TDE1641:TDE1642:ribose 5-phosphate isomerase A:hypothetical protein:-><-:1692737..1692860 124 aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Predict ORF larger than 30AA ================================================ aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg 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: 82 Start: 24 End: 53 .......................CTTTGCGCTCTTGTGGGGTAATTTTATAAT....................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1641:TDE1642|TDE1641:TDE1642:ribose 5-phosphate isomerase A:hypothetical protein:-><-:1692737..1692860 124 aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_002967_TDE1641_TDE1642|ribose 5-phosphate isomerase A:hypothetical protein|POSITIVE:NEGATIVE|[1692737,1692860]|124 HSP 1 e-value: 5.0E-52 bit: 204.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctnnnnnnntctttgcgatcttcttaacctttgcggtttattttatg aagatacactttataataattatattataaaattaccccacaagagcgcaaagaataataattgattaaaaaacatcctaaaaaaatctttgcgatcttcttaacctttgcggtttattttatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUACACUUUAUAAUAAUUAUAUUAUAAAAUUACCCCACAAGAGCGCAAAGAAUAAUAAUUGAUUAAAAAACAUCCUAAAAAAAUCUUUGCGAUCUUCUUAACCUUUGCGGUUUAUUUUAUG ((((((...(((((((((....)))))))))..........((((.((((((((.........(((........))).........)))))))).))))...((((.....))))))))))... (-18.77) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAAAUAAACCGCAAAGGUUAAGAAGAUCGCAAAGAUUUUUUUAGGAUGUUUUUUAAUCAAUUAUUAUUCUUUGCGCUCUUGUGGGGUAAUUUUAUAAUAUAAUUAUUAUAAAGUGUAUCUU .........((((.....))))...((((.((((((((.........(((........))).........)))))))).))))..(((((((((((((((((....))))))))))).)))))) (-29.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 115 71 135 86 NC_002967:TDE0161|5end_hypothetical_protein_187829..188059_NEGATIVE 270 115 81 204 169 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 268 115 80 71 36 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 258 120 85 196 170 NC_002967:TDE2169|5end_hypothetical_protein_2201037..2201267_POSITIVE 258 120 91 127 96 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 247 116 73 219 166 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 241 116 74 154 120 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 239 115 76 143 101 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 235 113 92 42 21 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 232 53 35 180 155 NC_002967:TDE2733|5end_hypothetical_protein_2788573..2788803_POSITIVE 232 53 35 55 30 NC_002967:TDE2732|5end_hypothetical_protein_2788448..2788678_POSITIVE 227 117 78 170 120 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 223 120 87 200 167 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 222 113 88 48 25 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 220 116 89 214 190 NC_002967:TDE2424|5end_50S_ribosomal_protein_L1_2454717..2454947_NEGATIVE 220 116 91 162 138 NC_002967:TDE0262|5end_hypothetical_protein_296300..296530_NEGATIVE 216 120 73 200 163 NC_002967:TDE0418|5end_lipoprotein,_putative_469602..469832_POSITIVE 216 70 24 56 5 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 208 114 88 116 91 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 202 113 89 32 9 NC_002967:TDE0051|5end_alcohol_dehydrogenase,_iron-containing_61224..61454_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 116 74 110 76 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 237 120 75 56 11 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 235 119 79 78 29 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 232 53 35 147 122 NC_002967:TDE2732|3end_hypothetical_protein_2788620..2788770_POSITIVE 227 117 78 125 75 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 223 120 87 88 55 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 222 113 88 76 53 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 220 116 91 62 38 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE 216 120 73 40 3 NC_002967:TDE0416|3end_bacteriocin-type_signal_domain_protein_469522..469672_POSITIVE 216 70 24 56 5 NC_002967:TDE0409|3end_hypothetical_protein_462133..462283_POSITIVE 214 113 94 20 2 NC_002967:TDE0981|3end_hypothetical_protein_1006535..1006685_POSITIVE 208 114 88 119 94 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 205 110 88 137 116 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 202 116 94 50 27 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 201 115 92 136 107 NC_002967:TDE0789|3end_30S_ribosomal_protein_S13_817007..817157_POSITIVE 201 116 77 67 28 NC_002967:TDE0682|3end_preprotein_translocase,_YajC_subunit_720665..720815_NEGATIVE 193 115 76 112 61 NC_002967:TDE1674|3end_hypothetical_protein_1728232..1728382_NEGATIVE 191 114 89 81 56 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 191 114 75 137 87 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 190 115 78 41 1 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE