Origin IGS: ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggcggatttcaaaaaaataagggctatctcccgacagcccttacttccttattaaccttaaaatctaataccatgaaaaacactgtacaaaaataaggcgatgtatttctcgtgcaactatattaggccaaaaaggcgcatattagtccaatcaatatttgttttcggcc Mask Tandem Repeat Region ================================================ ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Find is-nt database================================================ Query_seq: PG1221:PG1222|PG1221:PG1222:oxidoreductase, short chain dehydrogenase/reductase family:hypothetical protein:-><-:1298995..1299164 170 ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1221:PG1222|PG1221:PG1222:oxidoreductase, short chain dehydrogenase/reductase family:hypothetical protein:-><-:1298995..1299164 170 ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1221:PG1222|PG1221:PG1222:oxidoreductase, short chain dehydrogenase/reductase family:hypothetical protein:-><-:1298995..1299164 170 ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Predict ORF larger than 30AA ================================================ ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc 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================================================ ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.7 Tail_Score: -5.44119 Start: 128 End: 153 Full_Region: AGGTTAATAAGGAAG TAAGGGCTGTC GGGA GATAGCCCTTA TTTTTTTGAAATCCG ...............................................................................................................................TAAGGGCTGTCGGGAGATAGCCCTTA................. Find igs database================================================ Query_seq: PG1221:PG1222|PG1221:PG1222:oxidoreductase, short chain dehydrogenase/reductase family:hypothetical protein:-><-:1298995..1299164 170 ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagcccttatttttttgaaatccgcc Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_002950_PG1221_PG1222|oxidoreductase, short chain dehydrogenase/reductase family:hypothetical protein|POSITIVE:NEGATIVE|[1298995,1299164]|170 HSP 1 e-value: 1.0E-81 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagccctta................. ggccgaaaacaaatattgattggactaatatgcgcctttttggcctaatatagttgcacgagaaatacatcgccttatttttgtacagtgtttttcatggtattagattttaaggttaataaggaagtaagggctgtcgggagatagccctta................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCCGAAAACAAAUAUUGAUUGGACUAAUAUGCGCCUUUUUGGCCUAAUAUAGUUGCACGAGAAAUACAUCGCCUUAUUUUUGUACAGUGUUUUUCAUGGUAUUAGAUUUUAAGGUUAAUAAGGAAGUAAGGGCUGUCGGGAGAUAGCCCUUA (((((((((...((((((.......)))))).....)))))))))..........................((((((.(((.((((.(((.....))).)))).)))...))))))...........(((((((((((....))))))))))) (-42.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGGCUAUCUCCCGACAGCCCUUACUUCCUUAUUAACCUUAAAAUCUAAUACCAUGAAAAACACUGUACAAAAAUAAGGCGAUGUAUUUCUCGUGCAACUAUAUUAGGCCAAAAAGGCGCAUAUUAGUCCAAUCAAUAUUUGUUUUCGGCC ((((((((.((....)).)))))))).........................(((...((((.(((.(((...........))).))).))))..)))...........((((...((((((.(((((.(......)))))).)))))).)))) (-27.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 74 31 162 111 NC_002950:PG1761|5end_acetyltransferase,_GNAT_family_1847084..1847314_POSITIVE 338 150 112 106 70 NC_002950:PG1130|5end_TPR_domain_protein_1208053..1208283_POSITIVE 312 74 33 64 32 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 288 46 2 196 160 NC_002950:PG2109|5end_thiamine-phosphate_pyrophosphorylase_2219452..2219682_NEGATIVE 281 150 121 55 29 NC_002950:PG1035|5end_hypothetical_protein_1096875..1097105_POSITIVE 280 74 31 191 143 NC_002950:PG0204|5end_hypothetical_protein_240507..240737_NEGATIVE 279 100 51 188 121 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 277 69 21 151 93 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 275 149 122 28 1 NC_002950:PG0518|5end_abortive_infection_protein_family_562939..563169_NEGATIVE 275 150 134 219 203 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 269 149 125 132 108 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 266 75 33 229 184 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 265 148 112 133 100 NC_002950:PG1712|5end_alpha-1,2-mannosidase_family_protein_1801325..1801555_NEGATIVE 265 76 32 71 12 NC_002950:PG0476|5end_yngK_protein_518762..518992_NEGATIVE 264 150 114 136 92 NC_002950:PG0290|5end_hypothetical_protein_323904..324134_POSITIVE 261 150 123 49 5 NC_002950:PG0517|5end_hypothetical_protein_562097..562327_NEGATIVE 261 48 2 205 160 NC_002950:PG0472|5end_iron-sulfur_cluster_binding_protein,_putative_513339..513569_POSITIVE 259 73 33 180 138 NC_002950:PG1571|5end_metallo-beta-lactamase_superfamily_protein_1650353..1650583_NEGATIVE 259 68 24 215 171 NC_002950:PG0529|5end_carbamoyl-phosphate_synthase_small_subunit_574637..574867_POSITIVE 257 60 14 52 6 NC_002950:PG0465|5end_ferric_uptake_transcriptional_regulator_509403..509633_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 150 119 43 1 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 281 43 1 79 31 NC_002950:PG1104|3end_hypothetical_protein_1175782..1175932_POSITIVE 281 150 121 77 51 NC_002950:PG1034|3end_ABC_transporter,_ATP-binding_protein_1096977..1097127_POSITIVE 279 100 51 102 35 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 276 67 21 151 96 NC_002950:PG0661|3end_hypothetical_protein_709692..709842_NEGATIVE 269 140 110 128 91 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 269 149 125 35 11 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 266 150 118 110 74 NC_002950:PG2006|3end_hypothetical_protein_2095026..2095176_POSITIVE 265 148 112 51 18 NC_002950:PG1713|3end_lipoprotein,_putative_1801407..1801557_NEGATIVE 265 150 114 53 16 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 265 76 32 81 22 NC_002950:PG0477|3end_pantoate--beta-alanine_ligase_518752..518902_NEGATIVE 264 150 114 132 88 NC_002950:PG0289|3end_hypothetical_protein_323980..324130_POSITIVE 263 150 106 60 6 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 260 150 113 67 16 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 259 73 33 87 45 NC_002950:PG1572|3end_hypothetical_protein_1650446..1650596_NEGATIVE 257 142 122 151 131 NC_002950:PG1374|3end_immunoreactive_47_kDa_antigen_PG97_1455254..1455404_NEGATIVE 255 147 112 64 29 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 254 150 105 99 50 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 254 148 113 88 46 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 253 59 15 135 85 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE