Origin IGS: agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt .........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 acagcagcttatttcgtctcattcctcttacctgatctcgtgccaattttatgtagggatgattgccgacaacaagcatatatatagctctctataggtattcattcgcgtttaagtcgcacctcgagactacttttctcgaatgcttattactcataatctcttcaaaaacctcgtaaaatcggagaaaatcaataagttaactctattcaatagaaatgcagtagaaaattcgcatacctacatgttggtatattcggttttctttctacctttgtttcacaaaagtgatacgataaacaaaatttgtcttaccataaaactattacaaaact Mask Tandem Repeat Region ================================================ agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Find is-nt database================================================ Query_seq: PG1421:PG1422|PG1421:PG1422:ferredoxin, 4Fe-4S:D-alanyl-D-alanine carboxypeptidase:<-<-:1507135..1507469 335 agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1421:PG1422|PG1421:PG1422:ferredoxin, 4Fe-4S:D-alanyl-D-alanine carboxypeptidase:<-<-:1507135..1507469 335 agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1421:PG1422|PG1421:PG1422:ferredoxin, 4Fe-4S:D-alanyl-D-alanine carboxypeptidase:<-<-:1507135..1507469 335 agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 140 End: 241 ........................................................................................................................................... M D F L R F Y E V F E E I M S N K H S R K V V S R C D L N A N E Y L .............................................................................................. Protein_Len: 30 Strand: + Start: 235 End: 324 .......................................................................................................................................................................................................................................... M P I E S Y I Y A C C R Q S S L H K I G T R S G K R N E T K ........... Protein_Len: 38 Strand: - Start: 160 End: 273 ............................................................................................................................................................... S T K S S I I L L L C E L F T T E L H S K F A F S Y R Y L A I Y I S T T P M .............................................................. Protein_Len: 60 Strand: - Start: 2 End: 193 . K I T L C I K N I T D S K H F L P L F F V S Y V L M Y T H S N E V A N R N F L T L K N I K E S K V L N K F L N H T I L M .............................................................................................................................................. agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt 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================================================ agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1421:PG1422|PG1421:PG1422:ferredoxin, 4Fe-4S:D-alanyl-D-alanine carboxypeptidase:<-<-:1507135..1507469 335 agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Intra-Species Hit: Count: 1 Min: 1 Max: 335 Len: 335 Subject: NC_002950_PG1421_PG1422|ferredoxin, 4Fe-4S:D-alanyl-D-alanine carboxypeptidase|NEGATIVE:NEGATIVE|[1507135,1507469]|335 HSP 1 e-value: 0.0 bit: 664.0 Len: 335 Query Start:1 Query End:335 Subject Strand: POSITIVE Subject Start: 1 Subject End: 335 agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt agttttgtaatagttttatggtaagacaaattttgtttatcgtatcacttttgtgaaacaaaggtagaaagaaaaccgaatataccaacatgtaggtatgcgaattttctactgcatttctattgaatagagttaacttattgattttctccgattttacgaggtttttgaagagattatgagtaataagcattcgagaaaagtagtctcgaggtgcgacttaaacgcgaatgaatacctatagagagctatatatatgcttgttgtcggcaatcatccctacataaaattggcacgagatcaggtaagaggaatgagacgaaataagctgctgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUGUAAUAGUUUUAUGGUAAGACAAAUUUUGUUUAUCGUAUCACUUUUGUGAAACAAAGGUAGAAAGAAAACCGAAUAUACCAACAUGUAGGUAUGCGAAUUUUCUACUGCAUUUCUAUUGAAUAGAGUUAACUUAUUGAUUUUCUCCGAUUUUACGAGGUUUUUGAAGAGAUUAUGAGUAAUAAGCAUUCGAGAAAAGUAGUCUCGAGGUGCGACUUAAACGCGAAUGAAUACCUAUAGAGAGCUAUAUAUAUGCUUGUUGUCGGCAAUCAUCCCUACAUAAAAUUGGCACGAGAUCAGGUAAGAGGAAUGAGACGAAAUAAGCUGCUGU .((((..(((.(((..(((((((.((((.....)))))))))))..))).)))..))))...(((((..((((((.((..((((((........))))))))..)))))).((.(((((((........(((....))).((((((((..(((((((((.((((........((((((.(((.((((((((((.........((((((((.(((((((.......)))........))))...)))).))))....)))))))))))))..)))).))))).).)))))))))...)))))))).....)))))))))..........))))).. (-77.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGCAGCUUAUUUCGUCUCAUUCCUCUUACCUGAUCUCGUGCCAAUUUUAUGUAGGGAUGAUUGCCGACAACAAGCAUAUAUAUAGCUCUCUAUAGGUAUUCAUUCGCGUUUAAGUCGCACCUCGAGACUACUUUUCUCGAAUGCUUAUUACUCAUAAUCUCUUCAAAAACCUCGUAAAAUCGGAGAAAAUCAAUAAGUUAACUCUAUUCAAUAGAAAUGCAGUAGAAAAUUCGCAUACCUACAUGUUGGUAUAUUCGGUUUUCUUUCUACCUUUGUUUCACAAAAGUGAUACGAUAAACAAAAUUUGUCUUACCAUAAAACUAUUACAAAACU ......((..((((.((..............((((....((((((((...(((((((.((((.((((.......(((.........))).......)))).))))..(((........(((..((((((.......)))))).)))...((((((((..(((((...................)))))................(((((...))))).))).)))))......)))...)))))))))))))))..))))..............((((.((((....)))).))))...)).))))..))......................... (-58.95) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 820 120 71 211 162 NC_002950:PG1421|5end_ferredoxin,_4Fe-4S_1507044..1507274_NEGATIVE 318 290 241 56 5 NC_002950:PG0442|5end_hypothetical_protein_481882..482112_NEGATIVE 310 280 239 126 78 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 302 271 231 61 23 NC_002950:PG1928|5end_50S_ribosomal_protein_L14_2019945..2020175_NEGATIVE 302 211 171 156 105 NC_002950:PG0060|5end_hypothetical_protein_71916..72146_POSITIVE 287 281 246 35 2 NC_002950:PG0491|5end_hypothetical_protein_532184..532414_POSITIVE 283 228 188 174 141 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 281 249 202 97 52 NC_002950:PG1952|5end_DedA_family_protein_2042870..2043100_POSITIVE 281 219 176 195 137 NC_002950:PG0573|5end_S-adenosyl-methyltransferase_MraW_628083..628313_POSITIVE 279 249 202 216 180 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 276 238 196 49 1 NC_002950:PG0602|5end_hypothetical_protein_658500..658730_POSITIVE 273 307 262 63 16 NC_002950:PG0777|5end_electron_transfer_flavoprotein,_beta_subunit_831059..831289_NEGATIVE 271 78 31 153 115 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 268 250 202 115 63 NC_002950:PG0320|5end_hypothetical_protein_353409..353639_POSITIVE 266 299 259 206 159 NC_002950:PG1081|5end_acetate_kinase_1149627..1149857_NEGATIVE 265 220 172 77 27 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 264 286 241 68 30 NC_002950:PG1335|5end_hypothetical_protein_1416894..1417124_NEGATIVE 263 285 241 108 55 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 262 322 292 54 29 NC_002950:PG0751|5end_porT_protein_797578..797808_NEGATIVE 261 230 190 211 166 NC_002950:PG1360|5end_phosphoribosylamine--glycine_ligase_1439913..1440143_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 271 231 59 21 NC_002950:PG1929|3end_ribosomal_protein_S17_2019947..2020097_NEGATIVE 302 211 171 149 98 NC_002950:PG0059|3end_hypothetical_protein_71989..72139_POSITIVE 289 310 262 79 21 NC_002950:PG1684|3end_hypothetical_protein_1771483..1771633_POSITIVE 283 228 188 64 31 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 281 249 202 69 24 NC_002950:PG1951|3end_glutaminyl-tRNA_synthetase_2042922..2043072_POSITIVE 278 175 132 47 8 NC_002950:PG0592|3end_50S_ribosomal_protein_L31_650225..650375_POSITIVE 271 319 273 82 32 NC_002950:PG0412|3end_DNA_mismatch_repair_protein_MutL_449584..449734_NEGATIVE 270 280 241 47 1 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 268 250 202 83 31 NC_002950:PG0319|3end_hypothetical_protein_353457..353607_POSITIVE 265 220 172 77 27 NC_002950:PG0927|3end_conserved_hypothetical_protein_TIGR00150_984634..984784_NEGATIVE 265 299 260 105 69 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 259 219 171 87 41 NC_002950:PG1603|3end_HAM1_protein_1682829..1682979_POSITIVE 259 229 192 113 79 NC_002950:PG0652|3end_hypothetical_protein_703899..704049_NEGATIVE 255 240 194 131 72 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 254 138 95 78 26 NC_002950:PG1697|3end_type_II_restriction_endonuclease,_putative_1785074..1785224_POSITIVE 253 115 89 145 118 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 251 330 289 39 6 NC_002950:PG0877|3end_hypothetical_protein_940838..940988_NEGATIVE 249 220 171 61 15 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 248 310 264 101 47 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 247 305 262 142 95 NC_002950:PG1648|3end_RelA/SpoT_family_protein_1730082..1730232_POSITIVE