Origin IGS: cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatcgtttgcttcgataaaagtagtaaataattttgttgtggatagaaaaccgatagaattatatatttcttgtcttaagctttatccgaaagcagtcatacgattattgtaatttagtggatgaaactattttcctgccaatcatatatattggaataaagattaaggggaatacatatcaacttcg Mask Tandem Repeat Region ================================================ cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Find is-nt database================================================ Query_seq: PG0442:PG0443|PG0442:PG0443:hypothetical protein:hemagglutinin-related protein:<-->:481973..482160 188 cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0442:PG0443|PG0442:PG0443:hypothetical protein:hemagglutinin-related protein:<-->:481973..482160 188 cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0442:PG0443|PG0442:PG0443:hypothetical protein:hemagglutinin-related protein:<-->:481973..482160 188 cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 79 End: 174 .............................................................................. L L R I V A K P Y L K L C S I Y L E I P K R D V V F N N V V K M .............. Protein_Len: 41 Strand: - Start: 3 End: 125 .. L Q Y T N G K I K I G I Y I I P L F I T E D V L N C Y D Y S Q K R I F S L V L F M ............................................................... cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata 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================================================ cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0442:PG0443|PG0442:PG0443:hypothetical protein:hemagglutinin-related protein:<-->:481973..482160 188 cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_002950_PG0442_PG0443|hypothetical protein:hemagglutinin-related protein|NEGATIVE:POSITIVE|[481973,482160]|188 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata cgaagttgatatgtattccccttaatctttattccaatatatatgattggcaggaaaatagtttcatccactaaattacaataatcgtatgactgctttcggataaagcttaagacaagaaatatataattctatcggttttctatccacaacaaaattatttactacttttatcgaagcaaacgata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAGUUGAUAUGUAUUCCCCUUAAUCUUUAUUCCAAUAUAUAUGAUUGGCAGGAAAAUAGUUUCAUCCACUAAAUUACAAUAAUCGUAUGACUGCUUUCGGAUAAAGCUUAAGACAAGAAAUAUAUAAUUCUAUCGGUUUUCUAUCCACAACAAAAUUAUUUACUACUUUUAUCGAAGCAAACGAUA ....((((.(((((((((..(((((.((((((((.((..((((((((((.........((((.......))))........))))))))))......)).)))))))).)))))....).))))))))........((........)).))))..................(((((.......))))) (-26.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCGUUUGCUUCGAUAAAAGUAGUAAAUAAUUUUGUUGUGGAUAGAAAACCGAUAGAAUUAUAUAUUUCUUGUCUUAAGCUUUAUCCGAAAGCAGUCAUACGAUUAUUGUAAUUUAGUGGAUGAAACUAUUUUCCUGCCAAUCAUAUAUAUUGGAAUAAAGAUUAAGGGGAAUACAUAUCAACUUCG ..(((((..((.((((((..(((....((((((((((((.(.........)))))))))))))................(((((.....))))).....)))..))))))......))..)))))...((((..(((.(((((.......)))))...........)))..))))............. (-35.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 808 110 61 201 152 NC_002950:PG0442|5end_hypothetical_protein_481882..482112_NEGATIVE 262 116 81 210 168 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 250 70 35 75 47 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 250 42 1 75 31 NC_002950:PG0257|5end_hypothetical_protein_290034..290264_POSITIVE 241 124 83 171 123 NC_002950:PG1433|5end_hydrolase_1518831..1519061_POSITIVE 241 74 44 54 19 NC_002950:PG0742|5end_antigen_PgaA_790637..790867_NEGATIVE 237 121 82 220 172 NC_002950:PG1723|5end_ribosomal_protein_S20_1813069..1813299_POSITIVE 230 58 15 105 69 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 227 50 1 199 152 NC_002950:PG0665|5end_beta-galactosidase_711827..712057_POSITIVE 225 120 85 170 135 NC_002950:PG1199|5end_hypothetical_protein_1276893..1277123_POSITIVE 225 49 1 169 117 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 223 180 131 131 69 NC_002950:PG1720|5end_hypothetical_protein_1808615..1808845_POSITIVE 221 122 89 193 156 NC_002950:PG0589|5end_bifunctional_GMP_synthase/glutamine_amidotransferase_protein_647708..647938_NEGATIVE 218 110 84 96 63 NC_002950:PG1259|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_1335465..1335695_NEGATIVE 213 50 1 107 51 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 212 148 101 46 5 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 208 76 48 104 76 NC_002950:PG1333|5end_hypothetical_protein_1415425..1415655_NEGATIVE 206 121 83 65 20 NC_002950:PG2197|5end_hypothetical_protein_2302605..2302835_POSITIVE 206 37 1 179 139 NC_002950:PG0951|5end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010242..1010472_POSITIVE 206 116 75 70 17 NC_002950:PG0004|5end_NAD-dependent_deacetylase_2968..3198_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 109 84 150 125 NC_002950:PG0387|3end_elongation_factor_Tu_421910..422060_POSITIVE 233 180 132 140 98 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 230 58 15 101 65 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 223 180 131 115 53 NC_002950:PG1719|3end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1808679..1808829_POSITIVE 221 137 93 76 24 NC_002950:PG0452|3end_hypothetical_protein_495106..495256_POSITIVE 218 110 84 63 30 NC_002950:PG1260|3end_anaerobic_ribonucleoside_triphosphate_reductase_1335498..1335648_NEGATIVE 212 148 101 59 18 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 208 76 48 107 79 NC_002950:PG1334|3end_band_7/Mec-2_family_protein_1415422..1415572_NEGATIVE 207 45 1 148 102 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 203 109 67 123 72 NC_002950:PG0063|3end_outer_membrane_efflux_protein_75878..76028_NEGATIVE 200 38 1 134 105 NC_002950:PG0664|3end_oxidoreductase,_Gfo/Idh/MocA_family_711860..712010_POSITIVE 199 49 5 70 32 NC_002950:PG1919|3end_ribosomal_protein_L15_2015835..2015985_NEGATIVE 198 70 47 143 113 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 196 110 66 115 67 NC_002950:PG1333|3end_hypothetical_protein_1414226..1414376_NEGATIVE 196 109 69 148 115 NC_002950:PG0357|3end_aspartate_carbamoyltransferase_catalytic_subunit_392434..392584_POSITIVE 195 179 137 99 62 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 189 140 91 146 97 NC_002950:PG1426|3end_hypothetical_protein_1511152..1511302_NEGATIVE 189 66 47 115 95 NC_002950:PG1421|3end_ferredoxin,_4Fe-4S_1506874..1507024_NEGATIVE 188 117 86 142 105 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 187 74 32 70 11 NC_002950:PG1164|3end_hypothetical_protein_1244107..1244257_NEGATIVE