Origin IGS: agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccatgggtgaacgataatacaatcagtaaaaagtaaaaacaaggaacgaaaacggtgaagagagaatcatgagccatcgtgctctcgtgaaaatcaagataacaaactaatcgctaatcaacaattcaagagactggagggctcctgtccgattgagtctcaaaaaaaagacaaaaact Mask Tandem Repeat Region ================================================ agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Find is-nt database================================================ Query_seq: PG2102:PG2103|PG2102:PG2103:immunoreactive 61 kDa antigen PG91:hypothetical protein:<-<-:2213137..2213315 179 agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2102:PG2103|PG2102:PG2103:immunoreactive 61 kDa antigen PG91:hypothetical protein:<-<-:2213137..2213315 179 agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2102:PG2103|PG2102:PG2103:immunoreactive 61 kDa antigen PG91:hypothetical protein:<-<-:2213137..2213315 179 agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Predict ORF larger than 30AA ================================================ agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg 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================================================ agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2102:PG2103|PG2102:PG2103:immunoreactive 61 kDa antigen PG91:hypothetical protein:<-<-:2213137..2213315 179 agtttttgtcttttttttgagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Intra-Species Hit: Count: 1 Min: 19 Max: 179 Len: 161 Subject: NC_002950_PG2102_PG2103|immunoreactive 61 kDa antigen PG91:hypothetical protein|NEGATIVE:NEGATIVE|[2213137,2213315]|179 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:19 Query End:179 Subject Strand: POSITIVE Subject Start: 19 Subject End: 179 ..................gagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg ..................gagactcaatcggacaggagccctccagtctcttgaattgttgattagcgattagtttgttatcttgattttcacgagagcacgatggctcatgattctctcttcaccgttttcgttccttgtttttactttttactgattgtattatcgttcacccatgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGACUCAAUCGGACAGGAGCCCUCCAGUCUCUUGAAUUGUUGAUUAGCGAUUAGUUUGUUAUCUUGAUUUUCACGAGAGCACGAUGGCUCAUGAUUCUCUCUUCACCGUUUUCGUUCCUUGUUUUUACUUUUUACUGAUUGUAUUAUCGUUCACCCAUGG ((....(((((((....(((((.((...((((.((((..((..(.((((((.....))))))..)..)).)))).))))....)).))))).(((........))).............................))))))).....))............ (-32.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAUGGGUGAACGAUAAUACAAUCAGUAAAAAGUAAAAACAAGGAACGAAAACGGUGAAGAGAGAAUCAUGAGCCAUCGUGCUCUCGUGAAAAUCAAGAUAACAAACUAAUCGCUAAUCAACAAUUCAAGAGACUGGAGGGCUCCUGUCCGAUUGAGUCUC ((.((..(..((.....(((.....)))....))..)..)).)).........(((((.(((((...(((((....)))))))))).((.....))..............)))))..............((((((.((((((....))))..)).)))))) (-31.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 986 50 1 159 110 NC_002950:PG2102|5end_immunoreactive_61_kDa_antigen_PG91_2213046..2213276_NEGATIVE 351 115 71 56 15 NC_002950:PG1678|5end_hypothetical_protein_1763862..1764092_NEGATIVE 338 120 72 55 1 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 337 51 11 83 49 NC_002950:PG0062|5end_TPR_domain_protein_73688..73918_POSITIVE 336 120 77 186 135 NC_002950:PG1170|5end_SerB_family_protein_1249163..1249393_POSITIVE 326 115 75 225 177 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 324 125 85 109 69 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 320 90 45 88 40 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 311 115 75 97 56 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 311 120 71 176 126 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 307 50 2 203 149 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 307 118 74 99 56 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 304 115 75 136 104 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 304 120 76 222 166 NC_002950:PG1718|5end_hypothetical_protein_1806807..1807037_NEGATIVE 304 109 62 217 160 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 302 120 76 207 155 NC_002950:PG1803|5end_V-type_ATP_synthase_subunit_A_1896488..1896718_POSITIVE 301 43 1 81 35 NC_002950:PG1620|5end_carboxyl-terminal_protease-related_protein_1700491..1700721_NEGATIVE 296 89 45 158 116 NC_002950:PG1926|5end_50S_ribosomal_protein_L5_2019237..2019467_NEGATIVE 294 119 75 204 153 NC_002950:PG0264|5end_glycosyl_transferase,_group_2_family_protein_296975..297205_POSITIVE 293 49 1 199 150 NC_002950:PG2092|5end_hypothetical_protein_2192910..2193140_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 90 45 114 63 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 344 115 74 69 38 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 344 59 11 106 37 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 337 51 11 78 44 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 324 125 85 96 56 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 321 118 75 85 33 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 314 110 63 101 38 NC_002950:PG2114|3end_hypothetical_protein_2223982..2224132_NEGATIVE 311 117 74 58 4 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 311 59 11 135 87 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 311 59 11 135 87 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 307 50 2 123 69 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE 304 115 75 127 95 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 302 60 14 147 93 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 301 43 1 88 42 NC_002950:PG1621|3end_hypothetical_protein_1700484..1700634_NEGATIVE 301 120 75 148 102 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 292 51 11 97 57 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE 290 67 25 138 100 NC_002950:PG0186|3end_lipoprotein_RagB_222997..223147_POSITIVE 285 49 17 124 81 NC_002950:PG2175|3end_hypothetical_protein_2282634..2282784_NEGATIVE 285 109 64 145 95 NC_002950:PG1566|3end_glutamyl-tRNA_synthetase_1645884..1646034_NEGATIVE 283 50 3 113 64 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE