Origin IGS: tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtgccttttaatgcttttcatctacttttttcgttaaaaatttgtcagaaaagataaaagtaattatatttgcacacgcataaacaataaaatgaattaaagatacaagcctataggaacaccattacttaaatataaatcattttaaaga Mask Tandem Repeat Region ================================================ tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Find is-nt database================================================ Query_seq: PI1279:PI1280|PI1279:PI1280:RNA polymerase sigma factor/ECF subfamily (sigma-70):conserved hypothetical protein:->->:1195952..1196104 153 tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1279:PI1280|PI1279:PI1280:RNA polymerase sigma factor/ECF subfamily (sigma-70):conserved hypothetical protein:->->:1195952..1196104 153 tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1279:PI1280|PI1279:PI1280:RNA polymerase sigma factor/ECF subfamily (sigma-70):conserved hypothetical protein:->->:1195952..1196104 153 tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Predict ORF larger than 30AA ================================================ tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta 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: 83 Start: 82 End: 111 .................................................................................TTTGTCAGAAAAGATAAAAGTAATTATATT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1279:PI1280|PI1279:PI1280:RNA polymerase sigma factor/ECF subfamily (sigma-70):conserved hypothetical protein:->->:1195952..1196104 153 tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: pint_PI1279_PI1280|RNA polymerase sigma factor/ECF subfamily (sigma-70):conserved hypothetical protein|POSITIVE:POSITIVE|[1195952,1196104]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta tctttaaaatgatttatatttaagtaatggtgttcctataggcttgtatctttaattcattttattgtttatgcgtgtgcaaatataattacttttatcttttctgacaaatttttaacgaaaaaagtagatgaaaagcattaaaaggcacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUAAAAUGAUUUAUAUUUAAGUAAUGGUGUUCCUAUAGGCUUGUAUCUUUAAUUCAUUUUAUUGUUUAUGCGUGUGCAAAUAUAAUUACUUUUAUCUUUUCUGACAAAUUUUUAACGAAAAAAGUAGAUGAAAAGCAUUAAAAGGCACUA .(..((((((((.(((....(((((...((....)).....)))))......))).))))))))..).........((((...........((((((.((((((.......(((((.....)))))......))))))...)))))))))).. (-22.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGCCUUUUAAUGCUUUUCAUCUACUUUUUUCGUUAAAAAUUUGUCAGAAAAGAUAAAAGUAAUUAUAUUUGCACACGCAUAAACAAUAAAAUGAAUUAAAGAUACAAGCCUAUAGGAACACCAUUACUUAAAUAUAAAUCAUUUUAAAGA ..((((....((((((((((.((((.....((((..(((....)))...)))))))))))))).)))).....))))............((((((((.(((.((........))...((....))............))).)))))))).... (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 67 21 167 119 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 244 80 41 205 147 pint:PI1598|5end_phosphate_ABC_transporter,_phosphate-binding_component_1526646..1526876_POSITIVE 242 110 63 129 91 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 241 104 61 89 50 pint:PI1839|5end_hypothetical_protein_1782178..1782408_POSITIVE 232 109 64 165 120 pint:PI1812|5end_possible_alpha-amylase_1750759..1750989_POSITIVE 232 87 44 189 154 pint:PI0050|5end_conserved_hypothetical_protein_51539..51769_POSITIVE 228 79 33 84 32 pint:PI1770|5end_4-alpha-glucanotransferase_1697336..1697566_POSITIVE 226 80 34 193 134 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 225 69 27 77 30 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 221 52 13 153 120 pint:PI1112|5end_glycosyltransferase_1036443..1036673_POSITIVE 221 78 31 83 38 pint:PI0335|5end_hypothetical_protein_313708..313938_POSITIVE 220 52 24 210 182 pint:PI1607|5end_ABC-related_lipoprotein_releasing_system,_ATP-binding_protein_1535125..1535355_POSITIVE 220 52 24 184 156 pint:PI1606|5end_conserved_hypothetical_protein_1535099..1535329_POSITIVE 218 48 1 197 151 pint:PI2108|5end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2059661..2059891_POSITIVE 211 121 88 203 171 pint:PI0472|5end_50S_ribosomal_protein_L5_438155..438385_POSITIVE 210 88 42 66 27 pint:PI1461|5end_conserved_hypothetical_protein_1384364..1384594_POSITIVE 205 80 31 130 84 pint:PI1095|5end_conserved_hypothetical_protein_1019759..1019989_POSITIVE 205 64 24 80 42 pint:PI0744|5end_DNA_primase/mobilizable_transposon,_excision_protein_674171..674401_POSITIVE 204 52 21 83 57 pint:PI2045|5end_hypothetical_protein_1998494..1998724_POSITIVE 204 80 37 143 111 pint:PI1285|5end_ATP_synthase,_B_subunit_1200348..1200578_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 68 24 137 103 pint:PI1003|3end_conserved_hypothetical_protein_925718..925868_POSITIVE 225 69 27 71 24 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE 221 52 13 34 1 pint:PI1111|3end_ISPg3-related_transposase_1036404..1036554_POSITIVE 221 78 31 83 38 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE 211 121 88 119 87 pint:PI0471|3end_50S_ribosomal_protein_L24_438151..438301_POSITIVE 210 88 42 58 19 pint:PI1460|3end_ribonucleotide_reductase,_alpha_subunit,_N-terminal_region_1384436..1384586_POSITIVE 205 80 31 119 73 pint:PI1094|3end_recombination_protein_1019828..1019978_POSITIVE 204 80 37 38 6 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 202 80 31 113 63 pint:PI1498|3end_probable_membrane_associated_lipoprotein_1419988..1420138_POSITIVE 201 68 28 94 46 pint:PI0744|3end_DNA_primase/mobilizable_transposon,_excision_protein_675186..675336_POSITIVE 201 60 22 141 106 pint:PI0370|3end_conserved_hypothetical_protein_341309..341459_POSITIVE 200 81 47 132 97 pint:PI2099|3end_D-alanyl-D-alanine_dipeptidase_2053277..2053427_POSITIVE 200 105 65 115 79 pint:PI0968|3end_hypothetical_protein_896646..896796_POSITIVE 195 79 38 100 45 pint:PI1684|3end_dimethyladenosine_transferase_1601773..1601923_POSITIVE 194 79 33 146 103 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE 192 80 40 119 78 pint:PI1773|3end_alpha-amylase_(neopullulanase)_1706107..1706257_POSITIVE 191 87 44 62 21 pint:PI1400|3end_hypothetical_protein_1321908..1322058_POSITIVE 191 50 8 83 40 pint:PI1389|3end_transcriptional_regulator,_LuxR_family_1310832..1310982_POSITIVE 191 70 22 111 59 pint:PI0231|3end_transcriptional_regulator_230510..230660_POSITIVE 190 105 73 96 60 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE