Origin IGS: atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacgtctgatttttattgtaattaagtcttttaataatttgtatcggagcagtgtaaaaccgacaccgacaattttttaatcattataagaacatgatgaacggaaaaaggttcgaatcttggtcgtaaaaaccgat Mask Tandem Repeat Region ================================================ atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Find is-nt database================================================ Query_seq: PG1544:PG1545|PG1544:PG1545:hypothetical protein:superoxide dismutase, Fe-Mn:->->:1623503..1623639 137 atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1544:PG1545|PG1544:PG1545:hypothetical protein:superoxide dismutase, Fe-Mn:->->:1623503..1623639 137 atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1544:PG1545|PG1544:PG1545:hypothetical protein:superoxide dismutase, Fe-Mn:->->:1623503..1623639 137 atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Predict ORF larger than 30AA ================================================ atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt 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================================================ atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1544:PG1545|PG1544:PG1545:hypothetical protein:superoxide dismutase, Fe-Mn:->->:1623503..1623639 137 atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_002950_PG1544_PG1545|hypothetical protein:superoxide dismutase, Fe-Mn|POSITIVE:POSITIVE|[1623503,1623639]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt atcggtttttacgaccaagattcgaacctttttccgttcatcatgttcttataatgattaaaaaattgtcggtgtcggttttacactgctccgatacaaattattaaaagacttaattacaataaaaatcagacgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGGUUUUUACGACCAAGAUUCGAACCUUUUUCCGUUCAUCAUGUUCUUAUAAUGAUUAAAAAAUUGUCGGUGUCGGUUUUACACUGCUCCGAUACAAAUUAUUAAAAGACUUAAUUACAAUAAAAAUCAGACGUU ...((((((((.......(((..((((........)))))))....((((.((((((((.......((((((.(.((((.....))))).))))))..)))))))).))))...........))))))))....... (-24.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGUCUGAUUUUUAUUGUAAUUAAGUCUUUUAAUAAUUUGUAUCGGAGCAGUGUAAAACCGACACCGACAAUUUUUUAAUCAUUAUAAGAACAUGAUGAACGGAAAAAGGUUCGAAUCUUGGUCGUAAAAACCGAU ....((((((..((((((.............)))))).....))))))...((.((..(((((...(((...((((((..(((((((......)))))))...))))))...)))....)))))..))...)).... (-20.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 50 4 167 115 NC_002950:PG1778|5end_hypothetical_protein_1867054..1867284_POSITIVE 322 28 3 101 76 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 321 45 1 97 56 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 278 50 2 119 75 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 278 81 61 224 204 NC_002950:PG0568|5end_elongation_factor_P_624565..624795_NEGATIVE 276 42 2 201 155 NC_002950:PG0803|5end_glucosamine-6-phosphate_deaminase_860518..860748_NEGATIVE 275 95 66 212 180 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 267 50 1 192 134 NC_002950:PG0481|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_522622..522852_NEGATIVE 263 101 65 99 53 NC_002950:PG2085|5end_tryptophanyl-tRNA_synthetase_2185532..2185762_POSITIVE 262 93 65 179 148 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 259 100 66 147 107 NC_002950:PG1145|5end_long-chain-fatty-acid--CoA_ligase,_putative_1230305..1230535_NEGATIVE 250 78 35 81 40 NC_002950:PG1512|5end_hypothetical_protein_1588430..1588660_NEGATIVE 250 90 67 48 21 NC_002950:PG1118|5end_clpB_protein_1194674..1194904_NEGATIVE 248 53 12 205 162 NC_002950:PG1074|5end_D-lysine_5,6-aminomutase,_beta_subunit_1141963..1142193_POSITIVE 248 95 64 171 133 NC_002950:PG0368|5end_DNA_topoisomerase_IV_subunit_B_401245..401475_POSITIVE 247 49 2 96 54 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 244 48 7 151 100 NC_002950:PG1389|5end_DNA-binding_protein,_histone-like_family_1471328..1471558_NEGATIVE 244 39 1 56 6 NC_002950:PG0785|5end_tonB_protein,_putative_837592..837822_NEGATIVE 244 94 54 65 24 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 242 45 2 146 115 NC_002950:PG0871|5end_hypothetical_protein_934836..935066_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 98 61 108 72 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 327 50 4 138 86 NC_002950:PG1777|3end_hypothetical_protein_1867105..1867255_POSITIVE 277 48 1 88 30 NC_002950:PG2212|3end_hypothetical_protein_2324483..2324633_NEGATIVE 267 50 1 116 58 NC_002950:PG0482|3end_hypothetical_protein_522698..522848_NEGATIVE 252 59 15 106 42 NC_002950:PG2100|3end_immunoreactive_63_kDa_antigen_PG102_2208527..2208677_NEGATIVE 247 49 2 67 25 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 244 39 1 78 28 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 242 45 2 136 105 NC_002950:PG0872|3end_mobilizable_transposon,_xis_protein_934846..934996_NEGATIVE 242 98 65 113 75 NC_002950:PG0629|3end_inorganic_polyphosphate/ATP-NAD_kinase_682498..682648_NEGATIVE 236 74 35 145 108 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 235 50 1 88 31 NC_002950:PG1154|3end_hypothetical_protein_1235697..1235847_NEGATIVE 233 60 11 58 7 NC_002950:PG1933|3end_ribosomal_protein_L22_2021617..2021767_NEGATIVE 233 42 1 135 90 NC_002950:PG1487|3end_hypothetical_protein_1561799..1561949_POSITIVE 230 98 66 148 110 NC_002950:PG1589|3end_dihydropteroate_synthase_1666593..1666743_NEGATIVE 229 48 6 127 82 NC_002950:PG0538|3end_outer_membrane_efflux_protein_590610..590760_POSITIVE 228 97 69 70 42 NC_002950:PG1260|3end_anaerobic_ribonucleoside_triphosphate_reductase_1335498..1335648_NEGATIVE 226 50 2 70 29 NC_002950:PG1457|3end_hypothetical_protein_1539197..1539347_POSITIVE 225 92 66 126 99 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 225 45 1 72 31 NC_002950:PG0479|3end_hypothetical_protein_520545..520695_POSITIVE 224 95 66 149 110 NC_002950:PG1560|3end_dTDP-glucose_4,6-dehydratase_1639067..1639217_NEGATIVE