Origin IGS: atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt .........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 aagaataaagccagagcggaaaacaacgagataaaattgaaatgtttcataccatgattttttatgattaaacaattacggtagataccgcataccactatatttgctgcactgcctgcaaattacttctttttttcaaatcaaaagtcaaattatctcaatttcttattttgattgcattatagcttctaacgttccacatat Mask Tandem Repeat Region ================================================ atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Find is-nt database================================================ Query_seq: PG1325:PG1326|PG1325:PG1326:hypothetical protein:hemagglutinin, putative:<-->:1403969..1404172 204 atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1325:PG1326|PG1325:PG1326:hypothetical protein:hemagglutinin, putative:<-->:1403969..1404172 204 atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1325:PG1326|PG1325:PG1326:hypothetical protein:hemagglutinin, putative:<-->:1403969..1404172 204 atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 104 End: 202 ....................................................................................................... M V V C G I Y R N C L I I K N H G M K H F N F I S L F S A L A L F .. Protein_Len: 36 Strand: - Start: 23 End: 130 ...................... L A I L I L F Q S L K V K S K F F L L L K C A T C C I Y H Y A T D V T M .......................................................................... Protein_Len: 37 Strand: - Start: 3 End: 113 .. H P V N S A I I C D F Y S I S I I Q S K I Q F F S T I Q L C H L L Y L P M ........................................................................................... atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt 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================================================ atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1325:PG1326|PG1325:PG1326:hypothetical protein:hemagglutinin, putative:<-->:1403969..1404172 204 atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Intra-Species Hit: Count: 1 Min: 1 Max: 204 Len: 204 Subject: NC_002950_PG1325_PG1326|hypothetical protein:hemagglutinin, putative|NEGATIVE:POSITIVE|[1403969,1404172]|204 HSP 1 e-value: 2.0E-99 bit: 363.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgnnnnnnngaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt atatgtggaacgttagaagctataatgcaatcaaaataagaaattgagataatttgacttttgatttgaaaaaaagaagtaatttgcaggcagtgcagcaaatatagtggtatgcggtatctaccgtaattgtttaatcataaaaaatcatggtatgaaacatttcaattttatctcgttgttttccgctctggctttattctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGUGGAACGUUAGAAGCUAUAAUGCAAUCAAAAUAAGAAAUUGAGAUAAUUUGACUUUUGAUUUGAAAAAAAGAAGUAAUUUGCAGGCAGUGCAGCAAAUAUAGUGGUAUGCGGUAUCUACCGUAAUUGUUUAAUCAUAAAAAAUCAUGGUAUGAAACAUUUCAAUUUUAUCUCGUUGUUUUCCGCUCUGGCUUUAUUCUU ....((((((((..(((.((......))...........(((((((((((..(((((((..((((((..............((((((..((...)).))))))..((..((.((((((....))))))))..))..........)))))).))).))))..))))))))))).)))...)))..)))))............... (-36.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUAAAGCCAGAGCGGAAAACAACGAGAUAAAAUUGAAAUGUUUCAUACCAUGAUUUUUUAUGAUUAAACAAUUACGGUAGAUACCGCAUACCACUAUAUUUGCUGCACUGCCUGCAAAUUACUUCUUUUUUUCAAAUCAAAAGUCAAAUUAUCUCAAUUUCUUAUUUUGAUUGCAUUAUAGCUUCUAACGUUCCACAUAU ..((((.........((((........((((((.........)))))).((((.(((((.((((....)))).))))).))))....))))......(((((..(((.(((.....)))...................((((((((...(((((.....)))))....))))))))))).)))))........))))....... (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 919 130 81 221 172 NC_002950:PG1325|5end_hypothetical_protein_1403878..1404108_NEGATIVE 314 124 89 190 156 NC_002950:PG0240|5end_hydrolase,_haloacid_dehalogenase-like_family_277093..277323_NEGATIVE 297 125 82 66 22 NC_002950:PG1484|5end_hypothetical_protein_1559979..1560209_NEGATIVE 287 126 85 228 194 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 286 127 86 48 7 NC_002950:PG0534|5end_hypothetical_protein_583242..583472_POSITIVE 284 119 78 71 22 NC_002950:PG0082|5end_hypothetical_protein_96044..96274_POSITIVE 283 99 55 97 51 NC_002950:PG1084|5end_thioredoxin_family_protein_1152958..1153188_NEGATIVE 281 128 88 188 137 NC_002950:PG1155|5end_ADP-heptose--LPS_heptosyltransferase,_putative_1235861..1236091_POSITIVE 275 125 83 180 133 NC_002950:PG2061|5end_dihydrofolate_reductase_2158422..2158652_POSITIVE 272 200 151 190 136 NC_002950:PG1104|5end_hypothetical_protein_1174935..1175165_POSITIVE 269 128 87 51 3 NC_002950:PG1664|5end_ABC_transporter,_permease_protein,_putative_1745813..1746043_POSITIVE 266 126 86 55 13 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 266 119 79 227 172 NC_002950:PG0946|5end_ABC_transporter,_ATP-binding_protein_1007396..1007626_NEGATIVE 262 130 95 47 3 NC_002950:PG1782|5end_hypothetical_protein_1870694..1870924_POSITIVE 262 98 61 112 69 NC_002950:PG1337|5end_umuD_protein_1417813..1418043_POSITIVE 261 126 85 52 7 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 261 128 88 182 128 NC_002950:PG0515|5end_hypothetical_protein_557958..558188_NEGATIVE 260 126 86 78 28 NC_002950:PG0598|5end_hypothetical_protein_654477..654707_POSITIVE 259 128 81 82 36 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 257 194 175 230 211 NC_002950:PG0319|5end_hypothetical_protein_352949..353179_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 129 85 67 25 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 297 125 82 61 17 NC_002950:PG1485|3end_conjugative_transposon_protein_TraC_1559984..1560134_NEGATIVE 281 127 85 67 22 NC_002950:PG2063|3end_hypothetical_protein_2160390..2160540_NEGATIVE 275 125 83 134 87 NC_002950:PG2060|3end_thymidylate_synthase_2158456..2158606_POSITIVE 270 139 92 100 60 NC_002950:PG1620|3end_carboxyl-terminal_protease-related_protein_1699415..1699565_NEGATIVE 269 127 86 97 48 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 268 196 152 151 95 NC_002950:PG1441|3end_lysozyme-related_protein_1527358..1527508_NEGATIVE 262 125 83 50 17 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 259 128 81 85 39 NC_002950:PG0977|3end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1040116..1040266_POSITIVE 253 126 85 128 89 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 253 117 85 52 14 NC_002950:PG1696|3end_type_II_DNA_modification_methyltransferase,_putative_1781090..1781240_POSITIVE 249 112 86 38 13 NC_002950:PG1317|3end_hypothetical_protein_1396744..1396894_NEGATIVE 248 126 89 57 16 NC_002950:PG1099|3end_hypothetical_protein_1167344..1167494_NEGATIVE 246 122 86 77 34 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 245 125 82 135 93 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 244 118 79 59 21 NC_002950:PG0217|3end_hypothetical_protein_253463..253613_POSITIVE 243 197 151 110 52 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 242 128 82 86 42 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 241 127 85 135 98 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 241 124 82 81 37 NC_002950:PG0320|3end_hypothetical_protein_354577..354727_POSITIVE