Origin IGS: ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcctgaacggcttttcgagaggagtcgtcatattctgttccgagccaaattcgagctttggcacgtacttgatccaataatttgtctgtttccataagtattttgtgtttctgcaatacgcacaaagataagttttccgcaccgttttccggttagaaataaaacag Mask Tandem Repeat Region ================================================ ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Find is-nt database================================================ Query_seq: PG2009:PG2010|PG2009:PG2010:DNA repair protein RecO, putative:phosphomannomutase, putative:->->:2099192..2099359 168 ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2009:PG2010|PG2009:PG2010:DNA repair protein RecO, putative:phosphomannomutase, putative:->->:2099192..2099359 168 ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2009:PG2010|PG2009:PG2010:DNA repair protein RecO, putative:phosphomannomutase, putative:->->:2099192..2099359 168 ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 39 End: 137 ...................................... M F V R I A E T Q N T Y G N R Q I I G S S T C Q S S N L A R N R I ............................... Protein_Len: 53 Strand: + Start: 8 End: 166 ....... M S N R K T V R K T Y L C A Y C R N T K Y L W K Q T N Y W I K Y V P K L E F G S E Q N M T T P L E K P F R .. Protein_Len: 42 Strand: + Start: 43 End: 168 .......................................... M C V L Q K H K I L M E T D K L L D Q V R A K A R I W L G T E Y D D S S R K A V Q A ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct 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================================================ ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -5.7 Tail_Score: -2.78547 Start: 103 End: 127 Full_Region: cgtcatattctgttc cgagccaaa ttcgagc tttggcacg tacttgatccaataa ......................................................................................................cgagccaaattcgagctttggcacg......................................... Find igs database================================================ Query_seq: PG2009:PG2010|PG2009:PG2010:DNA repair protein RecO, putative:phosphomannomutase, putative:->->:2099192..2099359 168 ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_002950_PG2009_PG2010|DNA repair protein RecO, putative:phosphomannomutase, putative|POSITIVE:POSITIVE|[2099192,2099359]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct ctgttttatttctaaccggaaaacggtgcggaaaacttatctttgtgcgtattgcagaaacacaaaatacttatggaaacagacaaattattggatcaagtacgtgccaaagctcgaatttggctcggaacagaatatgacgactcctctcgaaaagccgttcaggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUUUAUUUCUAACCGGAAAACGGUGCGGAAAACUUAUCUUUGUGCGUAUUGCAGAAACACAAAAUACUUAUGGAAACAGACAAAUUAUUGGAUCAAGUACGUGCCAAAGCUCGAAUUUGGCUCGGAACAGAAUAUGACGACUCCUCUCGAAAAGCCGUUCAGGCU (((((((.(((((.((((.....))))..)))))............(((((((...((..((...........((....))..........))..)).)))))))((((((.......))))))..))))))).......(((......)))...((((.....)))) (-38.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUGAACGGCUUUUCGAGAGGAGUCGUCAUAUUCUGUUCCGAGCCAAAUUCGAGCUUUGGCACGUACUUGAUCCAAUAAUUUGUCUGUUUCCAUAAGUAUUUUGUGUUUCUGCAAUACGCACAAAGAUAAGUUUUCCGCACCGUUUUCCGGUUAGAAAUAAAACAG ((((.((((((....(((((.((((..(.......)..))))..((((((.......)))))).....)))))......(((((((((.....((((((...))))))....(((.....)))...))))))))).......))))))...))))............. (-33.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 60 14 203 159 NC_002950:PG0933|5end_translation_elongation_factor_G,_putative_989997..990227_POSITIVE 334 139 91 68 15 NC_002950:PG0211|5end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_247810..248040_NEGATIVE 326 149 103 213 153 NC_002950:PG0678|5end_pyrazinamidase/nicotinamidase,_putative_728879..729109_POSITIVE 318 59 12 49 1 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 313 160 111 71 30 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 312 160 111 103 49 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 311 153 111 55 15 NC_002950:PG1911|5end_DNA-directed_RNA_polymerase_alpha_subunit_2011762..2011992_NEGATIVE 310 133 91 42 2 NC_002950:PG2023|5end_methionyl-tRNA_formyltransferase_2118536..2118766_NEGATIVE 306 159 115 213 170 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 304 160 111 208 155 NC_002950:PG0672|5end_iron_compound_ABC_transporter,_ATP-binding_protein_723002..723232_POSITIVE 303 150 103 137 89 NC_002950:PG0085|5end_alpha-galactosidase_99172..99402_POSITIVE 302 147 103 75 29 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 301 56 11 57 12 NC_002950:PG0796|5end_leucyl-tRNA_synthetase_852450..852680_NEGATIVE 301 136 92 203 156 NC_002950:PG0648|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_701285..701515_NEGATIVE 300 150 103 184 143 NC_002950:PG0156|5end_modification_methylase,_HemK_family_178828..179058_POSITIVE 296 144 103 58 9 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 289 148 103 72 25 NC_002950:PG0985|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1046930..1047160_POSITIVE 287 49 1 215 167 NC_002950:PG0623|5end_triosephosphate_isomerase_677261..677491_POSITIVE 287 50 15 162 126 NC_002950:PG0620|5end_ATP-dependent_protease_La_672963..673193_POSITIVE 287 150 103 216 163 NC_002950:PG0448|5end_hypothetical_protein_488089..488319_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 139 91 54 1 NC_002950:PG0212|3end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_247824..247974_NEGATIVE 312 160 111 122 68 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 311 153 111 42 2 NC_002950:PG1912|3end_30S_ribosomal_protein_S4_2011775..2011925_NEGATIVE 306 159 115 66 23 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 302 147 103 55 9 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 298 160 111 140 84 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 284 160 114 143 98 NC_002950:PG1826|3end_hypothetical_protein_1919646..1919796_NEGATIVE 283 143 103 112 58 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 282 158 111 87 20 NC_002950:PG1755|3end_fructose-bisphosphate_aldolase_1842397..1842547_NEGATIVE 281 147 101 151 114 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 278 160 111 121 68 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 273 150 102 128 74 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE 269 129 94 130 89 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 268 160 112 151 106 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE 268 57 16 150 107 NC_002950:PG1824|3end_phosphopyruvate_hydratase_1918153..1918303_NEGATIVE 267 128 90 134 85 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 266 140 92 77 33 NC_002950:PG0476|3end_yngK_protein_517215..517365_NEGATIVE 264 160 112 96 47 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 263 49 13 67 32 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 263 128 105 144 118 NC_002950:PG1347|3end_hypothetical_protein_1428660..1428810_POSITIVE