Origin IGS: gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctgcggcatacaaaacgatcggtctgagaaatcattaggcccatatctttacagactaatactgctctggaaatagatctgatcaagtatcagatctc Mask Tandem Repeat Region ================================================ gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Find is-nt database================================================ Query_seq: PG1730:PG1731|PG1730:PG1731:O-methyltransferase family protein:3-dehydroquinate dehydratase:<-<-:1819668..1819767 100 gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1730:PG1731|PG1730:PG1731:O-methyltransferase family protein:3-dehydroquinate dehydratase:<-<-:1819668..1819767 100 gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1730:PG1731|PG1730:PG1731:O-methyltransferase family protein:3-dehydroquinate dehydratase:<-<-:1819668..1819767 100 gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Predict ORF larger than 30AA ================================================ gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct 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================================================ gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1730:PG1731|PG1730:PG1731:O-methyltransferase family protein:3-dehydroquinate dehydratase:<-<-:1819668..1819767 100 gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002950_PG1730_PG1731|O-methyltransferase family protein:3-dehydroquinate dehydratase|NEGATIVE:NEGATIVE|[1819668,1819767]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct gagatctgatacttgatcagatctatttccagagcagtattagtctgtaaagatatgggcctaatgatttctcagaccgatcgttttgtatgccgcagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUCUGAUACUUGAUCAGAUCUAUUUCCAGAGCAGUAUUAGUCUGUAAAGAUAUGGGCCUAAUGAUUUCUCAGACCGAUCGUUUUGUAUGCCGCAGCU .(((((((((.....))))))))).....((((((.(.((..(((((..(((.(((.......))).)))..)))))..)))))))))............ (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGCGGCAUACAAAACGAUCGGUCUGAGAAAUCAUUAGGCCCAUAUCUUUACAGACUAAUACUGCUCUGGAAAUAGAUCUGAUCAAGUAUCAGAUCUC .((....)).........(((.(((((((.......)))))))...)))....(((((.......).)))).....(((((((((.....))))))))). (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 962 100 51 191 142 NC_002950:PG1730|5end_O-methyltransferase_family_protein_1819577..1819807_NEGATIVE 323 98 51 70 23 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 310 98 56 71 6 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 305 95 55 163 123 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 303 100 55 38 1 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 303 100 55 96 53 NC_002950:PG1703|5end_MazG_family_protein_1790753..1790983_NEGATIVE 303 79 32 208 156 NC_002950:PG1110|5end_hypothetical_protein_1182741..1182971_POSITIVE 301 99 52 200 132 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 301 64 21 142 99 NC_002950:PG1026|5end_hypothetical_protein_1088177..1088407_POSITIVE 297 99 57 165 110 NC_002950:PG1152|5end_hypothetical_protein_1234946..1235176_NEGATIVE 290 48 6 46 3 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 288 100 51 161 117 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 287 97 57 90 29 NC_002950:PG1407|5end_nitroimidazole_resistance_protein,_putative_1491648..1491878_NEGATIVE 284 98 57 59 18 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 282 99 58 227 180 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 276 97 54 55 1 NC_002950:PG0417|5end_ATP-dependent_protease_ATP-binding_subunit_458624..458854_NEGATIVE 275 99 51 48 7 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 267 99 51 227 167 NC_002950:PG2001|5end_signal_peptidase_I_2090855..2091085_NEGATIVE 267 99 52 217 172 NC_002950:PG1480|5end_conjugative_transposon_protein_TraI_1555895..1556125_NEGATIVE 265 50 6 79 29 NC_002950:PG1795|5end_hypothetical_protein_1889776..1890006_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 100 58 108 58 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 323 98 51 83 36 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 304 99 54 47 1 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 303 100 55 78 35 NC_002950:PG1704|3end_thiol:disulfide_interchange_protein_dsbD,_putative_1790771..1790921_NEGATIVE 297 99 57 135 80 NC_002950:PG1153|3end_hypothetical_protein_1234976..1235126_NEGATIVE 288 100 51 127 83 NC_002950:PG2033|3end_glutamate_synthase,_small_subunit_2133415..2133565_NEGATIVE 279 97 51 130 81 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 277 99 59 147 87 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 276 64 28 58 19 NC_002950:PG2221|3end_MiaB-like_tRNA_modifying_enzyme_2336840..2336990_POSITIVE 271 38 1 148 114 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 271 99 57 109 68 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 267 60 12 146 100 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE 262 79 32 124 72 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 261 100 52 134 79 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE 258 100 58 125 65 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 256 100 58 92 50 NC_002950:PG1012|3end_tRNA-i(6)A37_modification_enzyme_MiaB_1070089..1070239_NEGATIVE 256 98 56 53 13 NC_002950:PG0156|3end_modification_methylase,_HemK_family_179789..179939_POSITIVE 254 99 55 81 43 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 253 100 51 123 70 NC_002950:PG2073|3end_hypothetical_protein_2174219..2174369_NEGATIVE 253 100 51 123 70 NC_002950:PG1669|3end_hypothetical_protein_1755411..1755561_NEGATIVE