Origin IGS: gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc .........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 ggtgaagtcgttgttattagtgtttttaacaatccggattagaatcgccgcttcgagaggctgtacaaacctcaggaagcggtgcgaatcatctttgcccgcaatgtagaaataatatccgaaaaaagcaatatacgccttgaacggatgtgaaaaagcgacaaaaatacagtgaaatggtgatgcaatcagggcgcgctccctctatgtacaagccgtataaagggggaaagacagggttgc Mask Tandem Repeat Region ================================================ gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Find is-nt database================================================ Query_seq: PG0932:PG0933|PG0932:PG0933:DNA polymerase III, delta prime subunit, putative:translation elongation factor G, putative:->->:989894..990136 243 gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0932:PG0933|PG0932:PG0933:DNA polymerase III, delta prime subunit, putative:translation elongation factor G, putative:->->:989894..990136 243 gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0932:PG0933|PG0932:PG0933:DNA polymerase III, delta prime subunit, putative:translation elongation factor G, putative:->->:989894..990136 243 gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 30 End: 152 ............................. M Y I E G A R P D C I T I S L Y F C R F F T S V Q G V Y C F F R I L F L H C G Q R ........................................................................................... Protein_Len: 38 Strand: + Start: 56 End: 169 ....................................................... M H H H F T V F L S L F H I R S R R I L L F S D I I S T L R A K M I R T A S .......................................................................... Protein_Len: 60 Strand: + Start: 52 End: 243 ................................................... M I A S P F H C I F V A F S H P F K A Y I A F F G Y Y F Y I A G K D D S H R F L R F V Q P L E A A I L I R I V K N T N N Protein_Len: 35 Strand: - Start: 138 End: 242 ......................................................................................................................................... M A P L S S E C R K R L N T C G R S A A I R I R I T L F V L L L S K M . Protein_Len: 30 Strand: - Start: 94 End: 183 ............................................................................................. M R E L R I N S K E S I I E V N R A F I I R V A E Q P K Y M ............................................................ Protein_Len: 31 Strand: - Start: 2 End: 94 . L G T K G G K Y P K Y M S P A R G S Q M V M E S Y K Q R K K M ..................................................................................................................................................... gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc 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================================================ gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.1 Tail_Score: -3.21194 Start: 142 End: 165 Full_Region: TATTATTTCTACATT GCGGGCAAA GATGA TTCGCACCGC TTCCTGAGGTTTGTA .............................................................................................................................................GCGGGCAAAGATGATTCGCACCGC.............................................................................. TransTerm Strand: + Conf: 56 HP_score: -6.0 Tail_Score: -3.41527 Start: 159 End: 199 Full_Region: GGGCAAAGATGATTC GCACCGCTTCCTGAGGTT TGTAC AGCCTCTCGAAGCGGCGA TTCTAATCCGGATTG ..............................................................................................................................................................GCACCGCTTCCTGAGGTTTGTACAGCCTCTCGAAGCGGCGA............................................ TransTerm Strand: + Conf: 68 HP_score: -9.5 Tail_Score: -2.64595 Start: 160 End: 198 Full_Region: GGCAAAGATGATTCG CACCGCTTCCTGAGGTT TGTAC AGCCTCTCGAAGCGGCG ATTCTAATCCGGATT ...............................................................................................................................................................CACCGCTTCCTGAGGTTTGTACAGCCTCTCGAAGCGGCG............................................. Find igs database================================================ Query_seq: PG0932:PG0933|PG0932:PG0933:DNA polymerase III, delta prime subunit, putative:translation elongation factor G, putative:->->:989894..990136 243 gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Intra-Species Hit: Count: 1 Min: 1 Max: 243 Len: 243 Subject: NC_002950_PG0932_PG0933|DNA polymerase III, delta prime subunit, putative:translation elongation factor G, putative|POSITIVE:POSITIVE|[989894,990136]|243 HSP 1 e-value: 1.0E-135 bit: 482.0 Len: 243 Query Start:1 Query End:243 Subject Strand: POSITIVE Subject Start: 1 Subject End: 243 gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc gcaaccctgtctttccccctttatacggcttgtacatagagggagcgcgccctgattgcatcaccatttcactgtatttttgtcgctttttcacatccgttcaaggcgtatattgcttttttcggatattatttctacattgcgggcaaagatgattcgcaccgcttcctgaggtttgtacagcctctcgaagcggcgattctaatccggattgttaaaaacactaataacaacgacttcacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAACCCUGUCUUUCCCCCUUUAUACGGCUUGUACAUAGAGGGAGCGCGCCCUGAUUGCAUCACCAUUUCACUGUAUUUUUGUCGCUUUUUCACAUCCGUUCAAGGCGUAUAUUGCUUUUUUCGGAUAUUAUUUCUACAUUGCGGGCAAAGAUGAUUCGCACCGCUUCCUGAGGUUUGUACAGCCUCUCGAAGCGGCGAUUCUAAUCCGGAUUGUUAAAAACACUAAUAACAACGACUUCACC ((((.((.((((((.(((.........((.((((....(((((((((.((...((.((((............)))).))..)))))))))))..(((((...((((((.....))))))...)))))........))))..))))).))))))((.((((..((((((..((((((.....))))))..)))))))))).))......)).))))............................ (-62.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGAAGUCGUUGUUAUUAGUGUUUUUAACAAUCCGGAUUAGAAUCGCCGCUUCGAGAGGCUGUACAAACCUCAGGAAGCGGUGCGAAUCAUCUUUGCCCGCAAUGUAGAAAUAAUAUCCGAAAAAAGCAAUAUACGCCUUGAACGGAUGUGAAAAAGCGACAAAAAUACAGUGAAAUGGUGAUGCAAUCAGGGCGCGCUCCCUCUAUGUACAAGCCGUAUAAAGGGGGAAAGACAGGGUUGC ((..(((..(((((((..........)))))))...((((.....(((((((((..((((.........))))..)))))))))..))))..)))..))...............(((((((...((.((.......)).))...)))))))......(((((.........(((...((((......))))...)))..(((((((.(((((.....))))).)))))))........))))) (-69.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 415 200 153 170 115 NC_002950:PG0203|5end_hypothetical_protein_240211..240441_NEGATIVE 391 68 26 139 95 NC_002950:PG1028|5end_TPR_domain_protein_1089670..1089900_POSITIVE 388 190 141 105 46 NC_002950:PG2071|5end_hypothetical_protein_2166437..2166667_POSITIVE 385 198 156 218 159 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 379 209 161 186 147 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 374 210 163 190 126 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 374 190 141 216 162 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 373 200 151 168 112 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 369 198 153 176 122 NC_002950:PG0998|5end_hypothetical_protein_1056929..1057159_POSITIVE 360 210 164 207 149 NC_002950:PG0581|5end_UDP-N-acetylmuramate--L-alanine_ligase_638236..638466_POSITIVE 358 210 162 87 28 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 357 210 163 136 73 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 354 208 161 227 176 NC_002950:PG2031|5end_hypothetical_protein_2130339..2130569_POSITIVE 352 190 141 93 24 NC_002950:PG1477|5end_hypothetical_protein_1553496..1553726_NEGATIVE 349 49 5 218 177 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 349 49 5 218 177 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 349 210 162 213 165 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 349 49 5 218 177 NC_002950:PG0101|5end_hypothetical_protein_119198..119428_POSITIVE 348 210 167 80 37 NC_002950:PG0054|5end_single-stranded-DNA-specific_exonuclease_RecJ_65065..65295_POSITIVE 347 186 141 162 119 NC_002950:PG1571|5end_metallo-beta-lactamase_superfamily_protein_1650353..1650583_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 415 200 153 119 64 NC_002950:PG0204|3end_hypothetical_protein_240262..240412_NEGATIVE 404 196 151 97 43 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 392 190 143 66 10 NC_002950:PG0317|3end_peptidase,_M49_family_349771..349921_NEGATIVE 388 190 141 135 76 NC_002950:PG2070|3end_hypothetical_protein_2166547..2166697_POSITIVE 382 190 142 53 2 NC_002950:PG0592|3end_50S_ribosomal_protein_L31_650225..650375_POSITIVE 377 54 11 131 77 NC_002950:PG0674|3end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724209..724359_NEGATIVE 374 190 141 137 83 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 373 58 18 76 41 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 358 210 162 67 8 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 357 210 163 107 44 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 352 190 141 96 27 NC_002950:PG1478|3end_conjugative_transposon_protein_TraK_1553493..1553643_NEGATIVE 349 68 27 60 15 NC_002950:PG1015|3end_hypothetical_protein_1075877..1076027_NEGATIVE 348 64 27 38 1 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 347 186 141 69 26 NC_002950:PG1572|3end_hypothetical_protein_1650446..1650596_NEGATIVE 345 50 4 114 51 NC_002950:PG0544|3end_type_I_restriction-modification_system,_M_subunit,_putative_598078..598228_POSITIVE 340 198 152 82 25 NC_002950:PG0240|3end_hydrolase,_haloacid_dehalogenase-like_family_276395..276545_NEGATIVE 339 106 64 83 50 NC_002950:PG0398|3end_recF_protein_434616..434766_NEGATIVE 338 176 132 77 31 NC_002950:PG2009|3end_DNA_repair_protein_RecO,_putative_2099131..2099281_POSITIVE 338 58 13 135 73 NC_002950:PG1314|3end_chorismate_synthase_1394362..1394512_NEGATIVE 337 86 43 77 21 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE