Origin IGS: tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattattacctcgttagttactacaaatggatcgaaacaacacgcgcaatcaaaagcgcatgccaatttccattttcacctaaaaattttcttgattagtatctttttaagtctcttccacaatatcaaacaagacctaaaaaata Mask Tandem Repeat Region ================================================ tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Find is-nt database================================================ Query_seq: PG0181:PG0182|PG0181:PG0182:immunoreactive 32 kDa antigen PG49:von Willebrand factor type A domain protein:->->:205546..205691 146 tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0181:PG0182|PG0181:PG0182:immunoreactive 32 kDa antigen PG49:von Willebrand factor type A domain protein:->->:205546..205691 146 tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0181:PG0182|PG0181:PG0182:immunoreactive 32 kDa antigen PG49:von Willebrand factor type A domain protein:->->:205546..205691 146 tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 2 End: 145 . N K L D Q K I N H F L S L F I S I L F I K L H F H F N A H A K S Q A H Q K S G N T T V L S T I M . tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata 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================================================ tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0181:PG0182|PG0181:PG0182:immunoreactive 32 kDa antigen PG49:von Willebrand factor type A domain protein:->->:205546..205691 146 tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002950_PG0181_PG0182|immunoreactive 32 kDa antigen PG49:von Willebrand factor type A domain protein|POSITIVE:POSITIVE|[205546,205691]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata tattttttaggtcttgtttgatattgtggaagagacttaaaaagatactaatcaagaaaatttttaggtgaaaatggaaattggcatgcgcttttgattgcgcgtgttgtttcgatccatttgtagtaactaacgaggtaataata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUUUAGGUCUUGUUUGAUAUUGUGGAAGAGACUUAAAAAGAUACUAAUCAAGAAAAUUUUUAGGUGAAAAUGGAAAUUGGCAUGCGCUUUUGAUUGCGCGUGUUGUUUCGAUCCAUUUGUAGUAACUAACGAGGUAAUAAUA ...........(((((((.(.(((((..((....(((((((((....((.....))....)))))))))....((.(((((.(((((((((........)))))))))))))).))...))..))))).).)))))))........ (-34.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAUUACCUCGUUAGUUACUACAAAUGGAUCGAAACAACACGCGCAAUCAAAAGCGCAUGCCAAUUUCCAUUUUCACCUAAAAAUUUUCUUGAUUAGUAUCUUUUUAAGUCUCUUCCACAAUAUCAAACAAGACCUAAAAAAUA ..................(((((.(((((((.........((.((((........)))).))......)))))))(((..............))).)))))..((((((.((((..................)))).))))))... (-16.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 115 80 84 41 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 334 109 66 48 1 NC_002950:PG0927|5end_conserved_hypothetical_protein_TIGR00150_985050..985280_NEGATIVE 323 123 84 55 5 NC_002950:PG0302|5end_hypothetical_protein_338219..338449_POSITIVE 319 106 71 226 183 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 308 124 81 194 138 NC_002950:PG1868|5end_hypothetical_protein_1965619..1965849_NEGATIVE 300 121 81 231 186 NC_002950:PG2086|5end_hypothetical_protein_2186571..2186801_POSITIVE 300 120 75 134 80 NC_002950:PG2033|5end_glutamate_synthase,_small_subunit_2134803..2135033_NEGATIVE 300 127 81 68 14 NC_002950:PG0472|5end_iron-sulfur_cluster_binding_protein,_putative_513339..513569_POSITIVE 292 129 81 223 164 NC_002950:PG1532|5end_hypothetical_protein_1611716..1611946_NEGATIVE 291 119 76 164 118 NC_002950:PG2180|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_C_2288546..2288776_NEGATIVE 291 109 66 228 170 NC_002950:PG0646|5end_iron_compound_ABC_transporter,_ATP-binding_protein_699071..699301_NEGATIVE 290 119 74 78 26 NC_002950:PG1878|5end_cysteinyl-tRNA_synthetase_1972928..1973158_POSITIVE 290 140 96 164 122 NC_002950:PG1742|5end_hypothetical_protein_1827250..1827480_POSITIVE 289 123 85 70 29 NC_002950:PG1316|5end_hypothetical_protein_1396771..1397001_NEGATIVE 286 114 83 202 166 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 284 102 67 68 24 NC_002950:PG0398|5end_recF_protein_435710..435940_NEGATIVE 283 126 81 46 3 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 283 118 71 231 181 NC_002950:PG0462|5end_transporter,_putative_506279..506509_NEGATIVE 282 127 81 129 75 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 282 130 87 45 4 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 127 81 81 27 NC_002950:PG0471|3end_hypothetical_protein_513432..513582_POSITIVE 293 127 86 81 33 NC_002950:PG0155|3end_riboflavin_biosynthesis_protein_RibD_177861..178011_NEGATIVE 292 128 82 86 50 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 291 119 76 140 94 NC_002950:PG2181|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_2288570..2288720_NEGATIVE 289 123 85 97 56 NC_002950:PG1317|3end_hypothetical_protein_1396744..1396894_NEGATIVE 284 102 67 71 27 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE 283 126 81 49 6 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE 282 127 81 132 78 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 280 135 98 83 49 NC_002950:PG0495|3end_hypothetical_protein_536936..537086_POSITIVE 279 124 84 62 21 NC_002950:PG0205|3end_peptide_chain_release_factor_3_240513..240663_NEGATIVE 278 109 67 124 79 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 278 129 84 77 28 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 276 103 66 145 105 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 274 117 74 130 87 NC_002950:PG2206|3end_ABC_transporter,_ATP-binding_protein_2317250..2317400_NEGATIVE 274 117 74 68 21 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE 270 118 87 147 114 NC_002950:PG0162|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_184505..184655_NEGATIVE 269 110 67 111 64 NC_002950:PG0412|3end_DNA_mismatch_repair_protein_MutL_449584..449734_NEGATIVE 268 130 83 150 106 NC_002950:PG0965|3end_phosphatidylserine_decarboxylase_1025111..1025261_NEGATIVE 268 104 64 141 107 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 266 127 81 103 49 NC_002950:PG0841|3end_mobilizable_transposon,_excision_protein,_putative_902781..902931_NEGATIVE