Origin IGS: ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacgaataaatcttctcgcagcttcaatgaagctgacttatatagcaatagcggccacggctatcaccctgctgtccgcctcatgctctgacaaaggaaaatccggatacaagatcgttggcacc Mask Tandem Repeat Region ================================================ ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Find is-nt database================================================ Query_seq: PG1638:PG1639|PG1638:PG1639:thioredoxin family protein:hypothetical protein:<-<-:1719741..1719865 125 ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1638:PG1639|PG1638:PG1639:thioredoxin family protein:hypothetical protein:<-<-:1719741..1719865 125 ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1638:PG1639|PG1638:PG1639:thioredoxin family protein:hypothetical protein:<-<-:1719741..1719865 125 ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 1 End: 120 T G V I K Y G S K G K D S C S A S L L T I A T A A I A I Y T L K M S A A L L N M ..... ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt 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================================================ ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1638:PG1639|PG1638:PG1639:thioredoxin family protein:hypothetical protein:<-<-:1719741..1719865 125 ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002950_PG1638_PG1639|thioredoxin family protein:hypothetical protein|NEGATIVE:NEGATIVE|[1719741,1719865]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt ggtgccaacgatcttgtatccggattttcctttgtcagagcatgaggcggacagcagggtgatagccgtggccgctattgctatataagtcagcttcattgaagctgcgagaagatttattcgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGCCAACGAUCUUGUAUCCGGAUUUUCCUUUGUCAGAGCAUGAGGCGGACAGCAGGGUGAUAGCCGUGGCCGCUAUUGCUAUAUAAGUCAGCUUCAUUGAAGCUGCGAGAAGAUUUAUUCGUU ......(((((.((((((...((.....))........((((...(((((....((.(((....))).)).)))))..)))).)))))).(((((((...))))))).............))))) (-33.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGAAUAAAUCUUCUCGCAGCUUCAAUGAAGCUGACUUAUAUAGCAAUAGCGGCCACGGCUAUCACCCUGCUGUCCGCCUCAUGCUCUGACAAAGGAAAAUCCGGAUACAAGAUCGUUGGCACC (((((.............(((((((...))))))).(((.(((.(((...((((..(((((.........)))))))))....))).........((.....))..))).))).)))))...... (-28.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1093 80 31 171 122 NC_002950:PG1638|5end_thioredoxin_family_protein_1719650..1719880_NEGATIVE 425 76 31 177 122 NC_002950:PG1067|5end_hypothetical_protein_1134219..1134449_POSITIVE 407 50 8 57 12 NC_002950:PG0376|5end_30S_ribosomal_protein_S9_406399..406629_POSITIVE 405 66 22 61 5 NC_002950:PG1620|5end_carboxyl-terminal_protease-related_protein_1700491..1700721_NEGATIVE 402 75 38 190 148 NC_002950:PG1043|5end_ferrous_iron_transport_protein_B_1112852..1113082_NEGATIVE 399 75 33 46 11 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 396 70 21 92 25 NC_002950:PG1551|5end_hmuY_protein_1628438..1628668_POSITIVE 390 77 37 50 4 NC_002950:PG2000|5end_signal_peptidase-related_protein_2089468..2089698_NEGATIVE 388 78 34 91 45 NC_002950:PG1145|5end_long-chain-fatty-acid--CoA_ligase,_putative_1230305..1230535_NEGATIVE 387 59 13 39 1 NC_002950:PG0320|5end_hypothetical_protein_353409..353639_POSITIVE 386 80 31 203 160 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 381 75 31 70 19 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 381 81 47 42 7 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 377 80 40 41 3 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 373 70 23 63 5 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 371 76 31 229 176 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 371 80 32 66 21 NC_002950:PG2054|5end_lipoprotein_PG3_2152014..2152244_NEGATIVE 371 74 34 81 34 NC_002950:PG0489|5end_polysaccharide_biosynthesis-related_protein_529247..529477_POSITIVE 370 78 33 98 46 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 369 69 22 76 28 NC_002950:PG0059|5end_hypothetical_protein_71526..71756_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 74 31 131 86 NC_002950:PG0897|3end_alpha-amylase_family_protein_960868..961018_NEGATIVE 453 81 41 125 92 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 425 76 31 123 68 NC_002950:PG1066|3end_butyrate-acetoacetate_CoA-transferase,_subunit_A_1134245..1134395_POSITIVE 407 50 8 47 2 NC_002950:PG0375|3end_50S_ribosomal_protein_L13_406469..406619_POSITIVE 405 66 22 68 12 NC_002950:PG1621|3end_hypothetical_protein_1700484..1700634_NEGATIVE 399 75 33 59 24 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 397 70 21 66 1 NC_002950:PG0977|3end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1040116..1040266_POSITIVE 390 77 37 60 14 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 381 75 31 63 12 NC_002950:PG2028|3end_ebsC_protein_2126616..2126766_POSITIVE 380 58 12 83 35 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 377 60 15 34 1 NC_002950:PG0072|3end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_86098..86248_NEGATIVE 370 78 33 80 28 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 369 69 22 62 14 NC_002950:PG0058|3end_nicotinic_acid_mononucleotide_adenyltransferase_71592..71742_POSITIVE 367 69 21 51 2 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 365 76 33 62 8 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 364 68 21 119 72 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 362 80 31 142 87 NC_002950:PG0935|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_994297..994447_NEGATIVE 362 85 46 108 60 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 362 76 31 91 44 NC_002950:PG0083|3end_hypothetical_protein_97817..97967_POSITIVE 361 69 21 73 19 NC_002950:PG1666|3end_efflux_transporter,_MFP_component,_RND_family_1749628..1749778_POSITIVE