Origin IGS: cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaatagataatcatgttaccttatttcgttttatttggtttccttgcggtaatgttccttgcagataaatatgatgatcgtttcaaacccttcgtcttttggatatcaggacttgctcttgtaattttctccggtacaaggatcggg Mask Tandem Repeat Region ================================================ cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Find is-nt database================================================ Query_seq: PG1142:PG1143|PG1142:PG1143:exopolysaccharide synthesis-related protein:sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family:<-<-:1225570..1225719 150 cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1142:PG1143|PG1142:PG1143:exopolysaccharide synthesis-related protein:sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family:<-<-:1225570..1225719 150 cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1142:PG1143|PG1142:PG1143:exopolysaccharide synthesis-related protein:sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family:<-<-:1225570..1225719 150 cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 5 End: 124 .... M L V P E K I T R A S P D I Q K T K G L K R S S Y L S A R N I T A R K P N K T K .......................... Protein_Len: 47 Strand: - Start: 1 End: 141 G I R T G S F I V L A L G S I W F V F P K F R D D Y K D A L F M V A L F G F L V F Y P L M I M ......... cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt 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================================================ cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.1 Tail_Score: -3.18044 Start: 27 End: 41 Full_Region: tcgtcttttggatat cagga cttgc tcttg taattttctccggta ..........................caggacttgctcttg............................................................................................................. Find igs database================================================ Query_seq: PG1142:PG1143|PG1142:PG1143:exopolysaccharide synthesis-related protein:sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family:<-<-:1225570..1225719 150 cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_002950_PG1142_PG1143|exopolysaccharide synthesis-related protein:sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family|NEGATIVE:NEGATIVE|[1225570,1225719]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt cccgatccttgtaccggagaaaattacaagagcaagtcctgatatccaaaagacgaagggtttgaaacgatcatcatatttatctgcaaggaacattaccgcaaggaaaccaaataaaacgaaataaggtaacatgattatctatttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGAUCCUUGUACCGGAGAAAAUUACAAGAGCAAGUCCUGAUAUCCAAAAGACGAAGGGUUUGAAACGAUCAUCAUAUUUAUCUGCAAGGAACAUUACCGCAAGGAAACCAAAUAAAACGAAAUAAGGUAACAUGAUUAUCUAUUUUUU ...(.(((((((...(((..((((.....((.(((..(((....((.....))...)))..)))......)).....)))).)))))))))).)....((....))..............((((((.(((((.....))))))))))).. (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUAGAUAAUCAUGUUACCUUAUUUCGUUUUAUUUGGUUUCCUUGCGGUAAUGUUCCUUGCAGAUAAAUAUGAUGAUCGUUUCAAACCCUUCGUCUUUUGGAUAUCAGGACUUGCUCUUGUAAUUUUCUCCGGUACAAGGAUCGGG ........(((.(((((((((((..((........))..)))....((((((.......))..))))...)))))))).)))........(((...(((((.........)))))....(((((((...........)))))))...))) (-23.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 918 50 1 141 92 NC_002950:PG1142|5end_exopolysaccharide_synthesis-related_protein_1225479..1225709_NEGATIVE 417 45 1 49 3 NC_002950:PG1819|5end_hypothetical_protein_1914322..1914552_NEGATIVE 312 48 6 208 153 NC_002950:PG1030|5end_hypothetical_protein_1091400..1091630_POSITIVE 268 138 91 127 86 NC_002950:PG1662|5end_hypothetical_protein_1744736..1744966_POSITIVE 264 59 11 228 173 NC_002950:PG2144|5end_hypothetical_protein_2249911..2250141_POSITIVE 264 60 14 229 184 NC_002950:PG1501|5end_transcriptional_regulator,_tetR_family_1579099..1579329_NEGATIVE 262 59 14 203 158 NC_002950:PG1818|5end_hypothetical_protein_1913744..1913974_NEGATIVE 258 43 4 120 81 NC_002950:PG1159|5end_cobalamin_biosynthesis_protein_CbiB_1238967..1239197_NEGATIVE 257 50 2 230 179 NC_002950:PG2082|5end_POT_family_protein_2183384..2183614_NEGATIVE 257 63 29 194 155 NC_002950:PG1979|5end_hypothetical_protein_2067272..2067502_POSITIVE 257 48 1 189 152 NC_002950:PG1779|5end_hypothetical_protein_1867924..1868154_POSITIVE 253 50 2 178 119 NC_002950:PG0510|5end_hypothetical_protein_550060..550290_NEGATIVE 253 33 2 67 34 NC_002950:PG0350|5end_internalin-related_protein_386810..387040_NEGATIVE 252 73 35 63 26 NC_002950:PG0509|5end_hypothetical_protein_549588..549818_NEGATIVE 251 124 83 171 128 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 250 60 11 160 102 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 247 57 11 83 33 NC_002950:PG0373|5end_hypothetical_protein_404705..404935_POSITIVE 246 106 62 72 25 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 246 54 15 213 169 NC_002950:PG0119|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_142300..142530_POSITIVE 244 60 11 56 13 NC_002950:PG1881|5end_hypothetical_protein_1976524..1976754_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 48 6 64 9 NC_002950:PG1029|3end_hypothetical_protein_1091336..1091486_POSITIVE 277 59 13 59 2 NC_002950:PG1684|3end_hypothetical_protein_1771483..1771633_POSITIVE 272 49 6 111 67 NC_002950:PG1323|3end_PhoH_family_protein_1402844..1402994_POSITIVE 268 138 91 146 105 NC_002950:PG1661|3end_hypothetical_protein_1744835..1744985_POSITIVE 258 43 4 106 67 NC_002950:PG1160|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_1238981..1239131_NEGATIVE 257 60 14 111 60 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 257 48 1 107 70 NC_002950:PG1778|3end_hypothetical_protein_1867922..1868072_POSITIVE 253 50 2 142 83 NC_002950:PG0511|3end_spore_maturation_protein_A/spore_maturation_protein_B_550096..550246_NEGATIVE 252 73 35 46 9 NC_002950:PG0510|3end_hypothetical_protein_549605..549755_NEGATIVE 250 60 11 135 77 NC_002950:PG0449|3end_TPR_domain_protein_490867..491017_POSITIVE 241 47 14 34 5 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 241 36 1 108 68 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 239 43 3 46 4 NC_002950:PG1791|3end_hypothetical_protein_1880951..1881101_NEGATIVE 237 39 1 70 34 NC_002950:PG1333|3end_hypothetical_protein_1414226..1414376_NEGATIVE 236 61 28 86 52 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 233 49 1 52 5 NC_002950:PG1038|3end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1105121..1105271_POSITIVE 231 62 26 34 5 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 230 47 4 115 75 NC_002950:PG1537|3end_hypothetical_protein_1617603..1617753_POSITIVE 228 114 73 133 85 NC_002950:PG2187|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2293756..2293906_NEGATIVE 228 41 3 144 113 NC_002950:PG2080|3end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2179378..2179528_NEGATIVE