Origin IGS: atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggattcctccaaaacttctgatattatgatactataaatcgcaaaaaaattcaaatacctaagataaaacaaattgttttaagcggaggagttaagctgaatgaaactcggcat Mask Tandem Repeat Region ================================================ atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Find is-nt database================================================ Query_seq: TDE2534:TDE2535|TDE2534:TDE2535:endonuclease III:pyruvate kinase:->->:2560917..2561031 115 atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2534:TDE2535|TDE2534:TDE2535:endonuclease III:pyruvate kinase:->->:2560917..2561031 115 atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2534:TDE2535|TDE2534:TDE2535:endonuclease III:pyruvate kinase:->->:2560917..2561031 115 atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Predict ORF larger than 30AA ================================================ atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc 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: 86 Start: 60 End: 89 ...........................................................TTTGAATTTTTTTGCGATTTATAGTATCAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2534:TDE2535|TDE2534:TDE2535:endonuclease III:pyruvate kinase:->->:2560917..2561031 115 atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE2534_TDE2535|endonuclease III:pyruvate kinase|POSITIVE:POSITIVE|[2560917,2561031]|115 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaannnnnnngcgatttatagtatcataatatcagaagttttggaggaatccc atgccgagtttcattcagcttaactcctccgcttaaaacaatttgttttatcttaggtatttgaatttttttgcgatttatagtatcataatatcagaagttttggaggaatccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCCGAGUUUCAUUCAGCUUAACUCCUCCGCUUAAAACAAUUUGUUUUAUCUUAGGUAUUUGAAUUUUUUUGCGAUUUAUAGUAUCAUAAUAUCAGAAGUUUUGGAGGAAUCCC ..((.((((...)))).)).....((((((...((((((.....)))))).....((((((((((((.......)))))).)))))).................))))))..... (-21.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAUUCCUCCAAAACUUCUGAUAUUAUGAUACUAUAAAUCGCAAAAAAAUUCAAAUACCUAAGAUAAAACAAAUUGUUUUAAGCGGAGGAGUUAAGCUGAAUGAAACUCGGCAU ..(((((((((.........(((.(((((....))))))))........................((((((.....))))))...)))))))))..(((((.......))))).. (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 41 2 81 41 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 288 69 30 199 166 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 282 35 16 30 9 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 275 48 2 63 16 NC_002967:TDE1727|5end_hypothetical_protein_1781190..1781420_NEGATIVE 262 49 1 131 72 NC_002967:TDE1322|5end_hypothetical_protein_1360736..1360966_NEGATIVE 256 36 2 133 103 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 251 31 2 104 79 NC_002967:TDE2296|5end_hypothetical_protein_2336337..2336567_NEGATIVE 244 32 3 159 135 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 238 99 51 214 157 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 233 32 2 42 2 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 230 39 3 55 15 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 228 68 24 208 160 NC_002967:TDE1714|5end_N-acetylmuramoyl-L-alanine_amidase,_family_3_1769496..1769726_NEGATIVE 227 47 3 190 137 NC_002967:TDE2777|5end_hypothetical_protein_2828312..2828542_POSITIVE 227 34 3 185 154 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 226 50 3 122 75 NC_002967:TDE0952|5end_ABC_transporter,_ATP-binding_protein_975322..975552_POSITIVE 225 43 3 80 42 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 221 50 3 65 15 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 220 34 2 36 5 NC_002967:TDE0589|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_629044..629274_NEGATIVE 220 56 15 154 104 NC_002967:TDE0284|5end_hypothetical_protein_313428..313658_NEGATIVE 218 37 1 144 115 NC_002967:TDE1913|5end_hypothetical_protein_1929810..1930040_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 41 2 75 35 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 280 45 2 46 6 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 272 31 3 128 98 NC_002967:TDE2174|3end_hypothetical_protein_2203099..2203249_NEGATIVE 255 55 13 140 97 NC_002967:TDE0650|3end_hypothetical_protein_685811..685961_POSITIVE 251 31 2 102 77 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE 246 46 3 48 14 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 245 36 2 36 6 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 230 39 3 58 18 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 228 45 4 52 11 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 227 46 2 126 78 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 226 50 3 98 51 NC_002967:TDE0951|3end_lipoprotein,_putative_975378..975528_POSITIVE 221 50 3 72 22 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 218 37 1 142 113 NC_002967:TDE1912|3end_redox-sensing_transcriptional_repressor_Rex_1929888..1930038_POSITIVE 217 31 10 30 7 NC_002967:TDE0950|3end_hypothetical_protein_974166..974316_NEGATIVE 216 34 3 28 1 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 215 34 4 108 73 NC_002967:TDE1369|3end_excinuclease_ABC_subunit_B_1409804..1409954_NEGATIVE 214 32 3 117 78 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 209 35 4 143 99 NC_002967:TDE1502|3end_chorismate_mutase_1551377..1551527_POSITIVE 207 34 4 148 113 NC_002967:TDE1077|3end_hypothetical_protein_1109680..1109830_POSITIVE 205 60 14 149 109 NC_002967:TDE1600|3end_ABC_transporter,_ATP-binding/permease_protein_1650645..1650795_NEGATIVE