Origin IGS: aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttgttgtctttttggggtacccccccaatgatgtagctctgtgctaccgtggaaaattattcctgcaatagcgtagtcaggtgcattttcattattatttttgtgcctttcttgctcccaacgaggaataaggattatccgactaacactgactttatt Mask Tandem Repeat Region ================================================ aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Find is-nt database================================================ Query_seq: PG2148:PG2149|PG2148:PG2149:xanthine/uracil permease family protein:hypothetical protein:<-<-:2256865..2257025 161 aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2148:PG2149|PG2148:PG2149:xanthine/uracil permease family protein:hypothetical protein:<-<-:2256865..2257025 161 aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2148:PG2149|PG2148:PG2149:xanthine/uracil permease family protein:hypothetical protein:<-<-:2256865..2257025 161 aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 22 End: 159 ..................... M I L I P R W E Q E R H K N N N E N A P D Y A I A G I I F H G S T E L H H W G G T P K R Q Q .. Protein_Len: 37 Strand: - Start: 1 End: 111 I F D T N T P Y D K N R T P L L F P V F I I I F I C R V V S N C S Y N E M .................................................. aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac 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================================================ aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2148:PG2149|PG2148:PG2149:xanthine/uracil permease family protein:hypothetical protein:<-<-:2256865..2257025 161 aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: NC_002950_PG2148_PG2149|xanthine/uracil permease family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2256865,2257025]|161 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattnnnnnnntaccccaaaaagacaacaaac aataaagtcagtgttagtcggataatccttattcctcgttgggagcaagaaaggcacaaaaataataatgaaaatgcacctgactacgctattgcaggaataattttccacggtagcacagagctacatcattgggggggtaccccaaaaagacaacaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAGUCAGUGUUAGUCGGAUAAUCCUUAUUCCUCGUUGGGAGCAAGAAAGGCACAAAAAUAAUAAUGAAAAUGCACCUGACUACGCUAUUGCAGGAAUAAUUUUCCACGGUAGCACAGAGCUACAUCAUUGGGGGGGUACCCCAAAAAGACAACAAAC ......(((.((((.((((((......(((.(((((....))))).)))....(((.....((....)).....)))..)))))))))).......((((.....))))...(((((.....)))))....((((((.....))))))...)))....... (-41.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUGUUGUCUUUUUGGGGUACCCCCCCAAUGAUGUAGCUCUGUGCUACCGUGGAAAAUUAUUCCUGCAAUAGCGUAGUCAGGUGCAUUUUCAUUAUUAUUUUUGUGCCUUUCUUGCUCCCAACGAGGAAUAAGGAUUAUCCGACUAACACUGACUUUAUU ((((((((((...((((((.....))))))....(((((.....)))))...(((...((((((((.....((((.((..(((..((................))..)))..)))))).......))))))))......)))))).))))..)))...... (-40.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 971 140 91 231 182 NC_002950:PG2148|5end_xanthine/uracil_permease_family_protein_2256774..2257004_NEGATIVE 345 50 17 132 97 NC_002950:PG1125|5end_hypothetical_protein_1201727..1201957_NEGATIVE 321 147 103 66 8 NC_002950:PG1324|5end_Holliday_junction_resolvase_1403431..1403661_NEGATIVE 312 146 111 205 165 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 310 139 94 100 51 NC_002950:PG0306|5end_electron_transport_complex,_RnfABCDGE_type,_G_subunit_341916..342146_POSITIVE 309 146 111 133 96 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 303 58 11 72 22 NC_002950:PG1762|5end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1847988..1848218_POSITIVE 301 150 108 72 25 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 298 147 111 207 158 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 297 145 108 51 13 NC_002950:PG2096|5end_hypothetical_protein_2205415..2205645_NEGATIVE 297 134 92 52 11 NC_002950:PG1771|5end_phenylalanyl-tRNA_synthetase_alpha_subunit_1858038..1858268_POSITIVE 292 142 103 84 41 NC_002950:PG0296|5end_phosphoribosylformylglycinamidine_synthase_334997..335227_NEGATIVE 291 46 6 222 178 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 289 137 95 208 171 NC_002950:PG2178|5end_NADH:ubiquinone_oxidoreductase,_Na_translocating,_E_subunit_2287137..2287367_NEGATIVE 289 147 109 73 37 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 284 146 109 191 154 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 284 137 94 52 6 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 282 99 75 170 144 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 280 118 75 225 174 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 279 147 110 178 137 NC_002950:PG2189|5end_aspartate_kinase_2297151..2297381_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 50 17 113 78 NC_002950:PG1126|3end_uracil_permease_1201746..1201896_NEGATIVE 310 139 94 73 24 NC_002950:PG0305|3end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_341969..342119_POSITIVE 308 149 103 148 101 NC_002950:PG0989|3end_50S_ribosomal_protein_L20_1050699..1050849_NEGATIVE 296 150 110 55 3 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 294 146 104 44 3 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 286 141 102 84 40 NC_002950:PG1244|3end_ISPg1,_transposase_1320699..1320849_POSITIVE 286 141 102 84 40 NC_002950:PG0549|3end_ISPg1,_transposase_605987..606137_NEGATIVE 286 141 102 84 40 NC_002950:PG0460|3end_ISPg1,_transposase_503102..503252_POSITIVE 284 146 109 136 99 NC_002950:PG0962|3end_prolyl-tRNA_synthetase_1022327..1022477_NEGATIVE 282 99 75 121 95 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 281 146 111 65 30 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 277 48 6 126 93 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 276 45 5 133 88 NC_002950:PG0749|3end_hypothetical_protein_795538..795688_NEGATIVE 274 146 105 139 89 NC_002950:PG0028|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_34431..34581_POSITIVE 272 140 93 78 14 NC_002950:PG1774|3end_transcription-repair_coupling_factor_1861179..1861329_NEGATIVE 271 146 118 135 93 NC_002950:PG1375|3end_hypothetical_protein_1456743..1456893_POSITIVE 267 113 74 40 2 NC_002950:PG1809|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1905491..1905641_NEGATIVE 267 144 103 85 35 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 266 57 18 147 110 NC_002950:PG1487|3end_hypothetical_protein_1561799..1561949_POSITIVE 264 59 11 122 55 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE