Origin IGS: tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accttatagagcattataatctgcccttttagggtttacttataaggaataaagaaaggcatcgcaaccggccccgtaagtgggaggttgcgatgcctttcttgtaagcgaatagacgtttttaagta Mask Tandem Repeat Region ================================================ tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Find is-nt database================================================ Query_seq: PG1290:PG1291|PG1290:PG1291:branched-chain amino acid aminotransferase:hypothetical protein:-><-:1369413..1369540 128 tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1290:PG1291|PG1290:PG1291:branched-chain amino acid aminotransferase:hypothetical protein:-><-:1369413..1369540 128 tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1290:PG1291|PG1290:PG1291:branched-chain amino acid aminotransferase:hypothetical protein:-><-:1369413..1369540 128 tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Predict ORF larger than 30AA ================================================ tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt 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================================================ tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -21.4 Tail_Score: -4.36596 Start: 28 End: 75 Full_Region: TCTATTCGCTTACAA GAAAGGCATCGCAACCTCCCAC TTAC GGGGCCGGTTGCGATGCCTTTC TTTATTCCTTATAAG ...........................GAAAGGCATCGCAACCTCCCACTTACGGGGCCGGTTGCGATGCCTTTC..................................................... TransTerm Strand: - Conf: 100 HP_score: -21.4 Tail_Score: -3.29511 Start: 28 End: 75 Full_Region: cttataaggaataaa gaaaggcatcgcaaccggcccc gtaa gtgggaggttgcgatgcctttc ttgtaagcgaataga ...........................gaaaggcatcgcaaccggccccgtaagtgggaggttgcgatgcctttc..................................................... TransTerm Strand: + Conf: 100 HP_score: -16.4 Tail_Score: -4.73297 Start: 32 End: 71 Full_Region: TTCGCTTACAAGAAA GGCATCGCAACCTCCCAC TTAC GGGGCCGGTTGCGATGCC TTTCTTTATTCCTTA ...............................GGCATCGCAACCTCCCACTTACGGGGCCGGTTGCGATGCC......................................................... TransTerm Strand: - Conf: 100 HP_score: -16.4 Tail_Score: -4.30719 Start: 32 End: 71 Full_Region: taaggaataaagaaa ggcatcgcaaccggcccc gtaa gtgggaggttgcgatgcc tttcttgtaagcgaa ...............................ggcatcgcaaccggccccgtaagtgggaggttgcgatgcc......................................................... Find igs database================================================ Query_seq: PG1290:PG1291|PG1290:PG1291:branched-chain amino acid aminotransferase:hypothetical protein:-><-:1369413..1369540 128 tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_002950_PG1290_PG1291|branched-chain amino acid aminotransferase:hypothetical protein|POSITIVE:NEGATIVE|[1369413,1369540]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt tacttaaaaacgtctattcgcttacaagaaaggcatcgcaacctcccacttacggggccggttgcgatgcctttctttattccttataagtaaaccctaaaagggcagattataatgctctataaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUAAAAACGUCUAUUCGCUUACAAGAAAGGCAUCGCAACCUCCCACUUACGGGGCCGGUUGCGAUGCCUUUCUUUAUUCCUUAUAAGUAAACCCUAAAAGGGCAGAUUAUAAUGCUCUAUAAGGU ((((((....((......)).....((((((((((((((((((((((......))))..)))))))))))))))))).........))))))...(((.(.((((((........)))))).).))). (-49.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUAUAGAGCAUUAUAAUCUGCCCUUUUAGGGUUUACUUAUAAGGAAUAAAGAAAGGCAUCGCAACCGGCCCCGUAAGUGGGAGGUUGCGAUGCCUUUCUUGUAAGCGAAUAGACGUUUUUAAGUA ((((((.((.(((........))).))..)))))).((((((.........((((((((((((((((((..((((....).))).))))))))))))))))))..(((((......))))).)))))) (-54.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 77 32 139 65 NC_002950:PG1721|5end_ribonuclease_R_1810284..1810514_POSITIVE 405 60 11 54 10 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 392 78 31 65 6 NC_002950:PG0062|5end_TPR_domain_protein_73688..73918_POSITIVE 389 85 42 59 7 NC_002950:PG1879|5end_hypothetical_protein_1974451..1974681_POSITIVE 384 77 31 134 83 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 384 78 31 83 15 NC_002950:PG0633|5end_hypothetical_protein_685301..685531_POSITIVE 378 75 32 142 95 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 372 71 31 211 168 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 372 71 32 167 121 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 363 85 42 57 8 NC_002950:PG0484|5end_hypothetical_protein_524858..525088_NEGATIVE 357 70 26 214 162 NC_002950:PG2189|5end_aspartate_kinase_2297151..2297381_NEGATIVE 355 71 31 159 122 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 352 69 32 169 126 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 351 75 32 52 2 NC_002950:PG2188|5end_diaminopimelate_decarboxylase_2295781..2296011_NEGATIVE 347 85 44 97 45 NC_002950:PG1143|5end_sugar_dehydrogenase,_UDP-glucose/GDP-mannose_dehydrogenase_family_1227198..1227428_NEGATIVE 346 84 45 220 184 NC_002950:PG1286|5end_ferritin_1365501..1365731_NEGATIVE 346 75 31 215 162 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 341 71 37 66 21 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 341 69 35 74 38 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 339 92 53 72 34 NC_002950:PG1203|5end_transcriptional_regulator,_putative_1283446..1283676_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 634 77 31 65 19 NC_002950:PG1290|3end_branched-chain_amino_acid_aminotransferase_1369352..1369502_POSITIVE 394 70 22 141 91 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 392 78 31 60 1 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 384 78 31 78 10 NC_002950:PG0632|3end_biopolymer_transport_protein_ExbD,_putative_685376..685526_POSITIVE 356 75 31 151 102 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 354 76 31 60 16 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 352 78 31 102 47 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 348 73 31 64 30 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 345 72 32 83 44 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 334 74 31 55 14 NC_002950:PG2208|3end_hypothetical_protein_2320332..2320482_NEGATIVE 332 59 13 106 48 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 330 75 36 76 30 NC_002950:PG0906|3end_lipoprotein,_putative_971148..971298_POSITIVE 329 87 41 75 15 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 325 84 51 98 57 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 324 59 11 57 3 NC_002950:PG2147|3end_xanthine_phosphoribosyltransferase_2254819..2254969_NEGATIVE 324 77 32 138 78 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 319 71 31 119 76 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 312 84 53 148 109 NC_002950:PG0028|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_34431..34581_POSITIVE 311 78 33 122 73 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 311 80 31 73 16 NC_002950:PG0710|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_765447..765597_NEGATIVE