Origin IGS: aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtccttaacatacctacaataattaatcacaagtaggtatagtttgtattacaaatttattttatcgcagatagcatcgtagttttttattcgtttttatctttgagaatcaggtaaatgcagcgtttctatcttaatttgctaggataaggaaacgctcatttcccctatatttacttggtttcctctgcattggcatttgtttttgcaaatgaaaaactattgtttgaaaagacgaactcaaaccaatacctactctaaggttttaccaatacctactataagattggcaaaatactaattacaaggtattgtaaaacaatttcttattgagtaattttgcacccgatacatttaattcaactattttaaacgctattattt Mask Tandem Repeat Region ================================================ aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Find is-nt database================================================ Query_seq: PI0164:PI0165|PI0164:PI0165:conserved hypothetical protein:AAA family ATPase:->->:159356..159741 386 aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0164:PI0165|PI0164:PI0165:conserved hypothetical protein:AAA family ATPase:->->:159356..159741 386 aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0164:PI0165|PI0164:PI0165:conserved hypothetical protein:AAA family ATPase:->->:159356..159741 386 aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 135 End: 248 ...................................................................................................................................... M G L S S S F Q T I V F H L Q K Q M P M Q R K P S K Y R G N E R F L I L A N .......................................................................................................................................... Protein_Len: 46 Strand: - Start: 87 End: 224 ...................................................................................... Y K A L R I T P I P L V K S Y T N T Q T R R K L C Y N K M Q L F L H W H L P F W T F I P S M .................................................................................................................................................................. aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta 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: 70 End: 99 .....................................................................ATTGGCAAAATACTAATTACAAGGTATTGT............................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0164:PI0165|PI0164:PI0165:conserved hypothetical protein:AAA family ATPase:->->:159356..159741 386 aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Intra-Species Hit: Count: 1 Min: 1 Max: 386 Len: 386 Subject: pint_PI0164_PI0165|conserved hypothetical protein:AAA family ATPase|POSITIVE:POSITIVE|[159356,159741]|386 HSP 1 e-value: 0.0 bit: 765.0 Len: 386 Query Start:1 Query End:386 Subject Strand: POSITIVE Subject Start: 1 Subject End: 386 aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta aaataatagcgtttaaaatagttgaattaaatgtatcgggtgcaaaattactcaataagaaattgttttacaataccttgtaattagtattttgccaatcttatagtaggtattggtaaaaccttagagtaggtattggtttgagttcgtcttttcaaacaatagtttttcatttgcaaaaacaaatgccaatgcagaggaaaccaagtaaatataggggaaatgagcgtttccttatcctagcaaattaagatagaaacgctgcatttacctgattctcaaagataaaaacgaataaaaaactacgatgctatctgcgataaaataaatttgtaatacaaactatacctacttgtgattaattattgtaggtatgttaaggacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAUAGCGUUUAAAAUAGUUGAAUUAAAUGUAUCGGGUGCAAAAUUACUCAAUAAGAAAUUGUUUUACAAUACCUUGUAAUUAGUAUUUUGCCAAUCUUAUAGUAGGUAUUGGUAAAACCUUAGAGUAGGUAUUGGUUUGAGUUCGUCUUUUCAAACAAUAGUUUUUCAUUUGCAAAAACAAAUGCCAAUGCAGAGGAAACCAAGUAAAUAUAGGGGAAAUGAGCGUUUCCUUAUCCUAGCAAAUUAAGAUAGAAACGCUGCAUUUACCUGAUUCUCAAAGAUAAAAACGAAUAAAAAACUACGAUGCUAUCUGCGAUAAAAUAAAUUUGUAAUACAAACUAUACCUACUUGUGAUUAAUUAUUGUAGGUAUGUUAAGGACUA ........((((((((..........))))))))...(((((......)))))...........(((((...((((((.(((((((((.((((((((((((((...)))).)))))))))).....((((((((((.((((((.((((((.(((((........(.(((((.((((((..............))))))))))).)..(..(((.((((..(((((((((((((..((((.(((....))).)))))))))))).))))).)))))))..)...)).))).))))))............(((.....)))...................))))))))))))))))...)))))))))...))))))....))))).. (-87.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUCCUUAACAUACCUACAAUAAUUAAUCACAAGUAGGUAUAGUUUGUAUUACAAAUUUAUUUUAUCGCAGAUAGCAUCGUAGUUUUUUAUUCGUUUUUAUCUUUGAGAAUCAGGUAAAUGCAGCGUUUCUAUCUUAAUUUGCUAGGAUAAGGAAACGCUCAUUUCCCCUAUAUUUACUUGGUUUCCUCUGCAUUGGCAUUUGUUUUUGCAAAUGAAAAACUAUUGUUUGAAAAGACGAACUCAAACCAAUACCUACUCUAAGGUUUUACCAAUACCUACUAUAAGAUUGGCAAAAUACUAAUUACAAGGUAUUGUAAAACAAUUUCUUAUUGAGUAAUUUUGCACCCGAUACAUUUAAUUCAACUAUUUUAAACGCUAUUAUUU ((((..((((.(((....((((((.........((((((((((((((((....(((((..........((.....))...(((((((((((((.............((((((((((((((((.(((((((((((((((......))))))..)))))))))...........)))))))))))))..))).(((..(((....)))..))).))))))))))))).))))).....))))))).......))))))))).....(((((((.(((((((.......((((((.......))))))...))))))))))))))......)))))).(((....))).....................))).))))..))))...... (-82.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 229 182 217 165 pint:PI0982|5end_hypothetical_protein_909432..909662_POSITIVE 280 138 91 168 125 pint:PI0077|5end_hypothetical_protein_76244..76474_POSITIVE 278 235 194 127 82 pint:PI1422|5end_hypothetical_protein_1340690..1340920_POSITIVE 276 220 172 133 84 pint:PI1511|5end_hypothetical_protein_1429580..1429810_POSITIVE 276 220 172 82 33 pint:PI1512|5end_hypothetical_protein_1429529..1429759_POSITIVE 274 239 195 100 54 pint:PI0673|5end_hypothetical_protein_612206..612436_POSITIVE 272 265 223 211 156 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 262 140 92 116 60 pint:PI2139|5end_cysteinyl-tRNA_synthetase_2085266..2085496_POSITIVE 259 280 239 146 102 pint:PI1309|5end_excinuclease_ABC,_A_subunit_1223751..1223981_POSITIVE 258 228 182 68 27 pint:PI1766|5end_sugar_transporter,_possible_glucose/galactose_transporter_1693119..1693349_POSITIVE 256 200 153 181 144 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 255 244 202 130 86 pint:PI2154|5end_leucyl-tRNA_synthetase_2099861..2100091_POSITIVE 255 226 187 213 177 pint:PI0375|5end_hypothetical_protein_345634..345864_POSITIVE 254 205 163 124 80 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 254 266 225 82 46 pint:PI0062|5end_endopeptidase_60963..61193_POSITIVE 253 219 174 171 122 pint:PI1754|5end_conserved_hypothetical_protein_1681202..1681432_POSITIVE 253 228 187 100 45 pint:PI0021|5end_orotate_phosphoribosyltransferase_24939..25169_POSITIVE 251 240 194 110 59 pint:PI1867|5end_helicase_related_protein_1812390..1812620_POSITIVE 249 140 94 83 42 pint:PI1082|5end_polypeptide_deformylase_1001282..1001512_POSITIVE 249 350 301 180 134 pint:PI1001|5end_hypothetical_protein_923510..923740_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 229 182 95 43 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 272 265 223 109 54 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 258 228 182 47 6 pint:PI1765|3end_fructanase,_glycoside_hydrolase_family_1693178..1693328_POSITIVE 256 200 153 65 28 pint:PI1587|3end_conserved_hypothetical_protein;_possible_permease_1516266..1516416_POSITIVE 256 180 131 117 66 pint:PI0215|3end_hypothetical_protein_209004..209154_POSITIVE 254 205 163 124 80 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 251 266 221 77 34 pint:PI1990|3end_hypothetical_protein_1944766..1944916_POSITIVE 248 240 193 111 40 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 243 150 105 104 68 pint:PI1921|3end_conserved_hypothetical_protein_1865100..1865250_POSITIVE 242 72 31 56 8 pint:PI0865|3end_possible_phosphoglycerol_transferase_803684..803834_POSITIVE 239 229 185 151 113 pint:PI0273|3end_hypothetical_protein_263284..263434_POSITIVE 239 229 185 54 16 pint:PI0274|3end_conserved_hypothetical_protein_263187..263337_POSITIVE 236 229 190 142 102 pint:PI2111|3end_conserved_hypothetical_protein_2063258..2063408_POSITIVE 235 209 171 77 33 pint:PI0156|3end_conserved_hypothetical_protein_150913..151063_POSITIVE 232 157 115 144 102 pint:PI1999|3end_hypothetical_protein_1956668..1956818_POSITIVE 232 230 185 88 42 pint:PI1758|3end_hypothetical_protein_1684057..1684207_POSITIVE 232 140 92 142 98 pint:PI1611|3end_aspartate-semialdehyde_dehydrogenase_1539189..1539339_POSITIVE 231 115 73 126 84 pint:PI0512|3end_conserved_hypothetical_protein_471440..471590_POSITIVE 228 295 259 47 11 pint:PI1308|3end_hypothetical_protein_1223717..1223867_POSITIVE 228 139 94 118 67 pint:PI0904|3end_conserved_hypothetical_protein_834295..834445_POSITIVE