Origin IGS: cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaccttataaaagagaaacaccccttcccagggctgtaaaaagggtcgaaaaagaattcggacatcgtttacaccgtataaatcgaatcaaaaacggattttgagcctgagcagtcggccaaagctttatccgtggggtgtctctgcgaggacaaatgaatacctttgcccccg Mask Tandem Repeat Region ================================================ cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Find is-nt database================================================ Query_seq: PG0713:PG0714|PG0713:PG0714:anthranilate synthase component II:copper homeostasis protein CutC:<-<-:767840..768014 175 cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0713:PG0714|PG0713:PG0714:anthranilate synthase component II:copper homeostasis protein CutC:<-<-:767840..768014 175 cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0713:PG0714|PG0713:PG0714:anthranilate synthase component II:copper homeostasis protein CutC:<-<-:767840..768014 175 cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 14 End: 103 ............. M H L S S Q R H P T D K A L A D C S G S K S V F D S I Y T V ........................................................................ Protein_Len: 50 Strand: + Start: 18 End: 167 ................. M C P R R D T P R I K L W P T A Q A Q N P F L I R F I R C K R C P N S F S T L F T A L G R G V S L L ........ Protein_Len: 39 Strand: - Start: 3 End: 119 .. P C L Y E N T R A S V G W P Y L K P R S S L S L I R K Q N S K Y P T F S T R M ........................................................ cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt 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================================================ cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -3.8 Tail_Score: -3.33265 Start: 71 End: 87 Full_Region: GCCGACTGCTCAGGC TCAAAA TCCGT TTTTGA TTCGATTTATACGGT ......................................................................TCAAAATCCGTTTTTGA........................................................................................ TransTerm Strand: + Conf: 73 HP_score: -5.5 Tail_Score: -4.51238 Start: 139 End: 156 Full_Region: TTTCGACCCTTTTTA CAGCCCT GGGA AGGGGTG TTTCTCTTTTATAAG ..........................................................................................................................................CAGCCCTGGGAAGGGGTG................... Find igs database================================================ Query_seq: PG0713:PG0714|PG0713:PG0714:anthranilate synthase component II:copper homeostasis protein CutC:<-<-:767840..768014 175 cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: NC_002950_PG0713_PG0714|anthranilate synthase component II:copper homeostasis protein CutC|NEGATIVE:NEGATIVE|[767840,768014]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt cgggggcaaaggtattcatttgtcctcgcagagacaccccacggataaagctttggccgactgctcaggctcaaaatccgtttttgattcgatttatacggtgtaaacgatgtccgaattctttttcgaccctttttacagccctgggaaggggtgtttctcttttataaggtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGGGGCAAAGGUAUUCAUUUGUCCUCGCAGAGACACCCCACGGAUAAAGCUUUGGCCGACUGCUCAGGCUCAAAAUCCGUUUUUGAUUCGAUUUAUACGGUGUAAACGAUGUCCGAAUUCUUUUUCGACCCUUUUUACAGCCCUGGGAAGGGGUGUUUCUCUUUUAUAAGGUGU ((((((((((........)))))))))).(((((((((((.(((((..(((((.(((.....))).)))))....)))))...................((((((((....(((.(((......))))))....)))))).)).......))))))))))).............. (-54.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACCUUAUAAAAGAGAAACACCCCUUCCCAGGGCUGUAAAAAGGGUCGAAAAAGAAUUCGGACAUCGUUUACACCGUAUAAAUCGAAUCAAAAACGGAUUUUGAGCCUGAGCAGUCGGCCAAAGCUUUAUCCGUGGGGUGUCUCUGCGAGGACAAAUGAAUACCUUUGCCCCCG ...((((.....(((((..((((((.......((.((((((...(..((((......))))..)....))))))))..................((((((...((((.((.((.....))))..)))).)))))))))))))))))..))))....................... (-45.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1107 70 21 161 112 NC_002950:PG0713|5end_anthranilate_synthase_component_II_767749..767979_NEGATIVE 371 70 22 173 122 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 363 100 55 94 45 NC_002950:PG0361|5end_hypothetical_protein_394094..394324_POSITIVE 354 50 1 209 158 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 354 70 23 82 37 NC_002950:PG1143|5end_sugar_dehydrogenase,_UDP-glucose/GDP-mannose_dehydrogenase_family_1227198..1227428_NEGATIVE 353 45 1 183 135 NC_002950:PG0962|5end_prolyl-tRNA_synthetase_1023808..1024038_NEGATIVE 353 80 33 212 167 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 337 65 25 83 37 NC_002950:PG0571|5end_aspartate-semialdehyde_dehydrogenase_626399..626629_POSITIVE 333 34 1 68 32 NC_002950:PG1089|5end_DNA-binding_response_regulator_RprY_1156260..1156490_NEGATIVE 333 160 113 173 136 NC_002950:PG0046|5end_phosphatidate_cytidylyltransferase_57200..57430_NEGATIVE 332 80 36 58 3 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 331 68 21 223 169 NC_002950:PG1968|5end_hypothetical_protein_2058564..2058794_NEGATIVE 331 69 21 56 9 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 328 100 51 98 34 NC_002950:PG1358|5end_acetyltransferase,_GNAT_family_1437333..1437563_NEGATIVE 327 60 15 71 19 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 325 85 42 165 120 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 324 70 27 189 133 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 322 70 21 215 171 NC_002950:PG0729|5end_D-alanylalanine_synthetase_780818..781048_NEGATIVE 318 70 23 82 24 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 317 70 21 198 137 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 100 55 72 23 NC_002950:PG0360|3end_lemA_protein_394152..394302_POSITIVE 350 70 30 71 23 NC_002950:PG1152|3end_hypothetical_protein_1234674..1234824_NEGATIVE 344 86 42 151 105 NC_002950:PG2199|3end_ABC_transporter,_ATP-binding_protein,_putative_2304786..2304936_NEGATIVE 338 70 21 85 37 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 333 160 113 144 107 NC_002950:PG0047|3end_cell_division_protein_FtsH,_putative_57229..57379_NEGATIVE 323 160 118 92 38 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 318 70 23 77 19 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 309 69 22 78 10 NC_002950:PG2073|3end_hypothetical_protein_2174219..2174369_NEGATIVE 309 69 22 78 10 NC_002950:PG1669|3end_hypothetical_protein_1755411..1755561_NEGATIVE 309 69 22 78 10 NC_002950:PG1264|3end_hypothetical_protein_1344740..1344890_NEGATIVE 309 69 22 78 10 NC_002950:PG0103|3end_hypothetical_protein_121525..121675_POSITIVE 308 70 26 113 65 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE 304 70 25 50 8 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 302 80 34 76 28 NC_002950:PG0229|3end_hypothetical_protein_265350..265500_POSITIVE 301 70 22 115 66 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 300 156 111 109 66 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE 299 70 24 48 2 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 299 73 37 71 31 NC_002950:PG0049|3end_hypothetical_protein_60576..60726_NEGATIVE 298 70 22 149 98 NC_002950:PG2112|3end_hypothetical_protein_2222663..2222813_POSITIVE 298 55 11 78 36 NC_002950:PG1784|3end_hypothetical_protein_1873440..1873590_POSITIVE