Origin IGS: cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggcttttacagggctattacctttcgtcctttcataaaattgcccgactttcccttttcggagagtcgggcaaactgtatttctgcaaagaaagtacctgatgaacttctctgctaagagagaaagg Mask Tandem Repeat Region ================================================ cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Find is-nt database================================================ Query_seq: PG1326:PG1327|PG1326:PG1327:hemagglutinin, putative:aminotransferase, putative:-><-:1405232..1405359 128 cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1326:PG1327|PG1326:PG1327:hemagglutinin, putative:aminotransferase, putative:-><-:1405232..1405359 128 cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1326:PG1327|PG1326:PG1327:hemagglutinin, putative:aminotransferase, putative:-><-:1405232..1405359 128 cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 26 End: 127 ......................... M R Y F L C R N T V C P T L R K G K V G Q F Y E R T K G N S P V K A . Protein_Len: 33 Strand: - Start: 14 End: 112 ............. C L L E D P V K K A S I C N A R S E S F P F D P L K I F P R F T M ................ cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct 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================================================ cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.4 Tail_Score: -4.36914 Start: 55 End: 88 Full_Region: TTGCAGAAATACAGT TTGCCCGACTCTCC GAAAAG GGAAAGTCGGGCAA TTTTATGAAAGGACG ......................................................TTGCCCGACTCTCCGAAAAGGGAAAGTCGGGCAA........................................ Find igs database================================================ Query_seq: PG1326:PG1327|PG1326:PG1327:hemagglutinin, putative:aminotransferase, putative:-><-:1405232..1405359 128 cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_002950_PG1326_PG1327|hemagglutinin, putative:aminotransferase, putative|POSITIVE:NEGATIVE|[1405232,1405359]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct cctttctctcttagcagagaagttcatcaggtactttctttgcagaaatacagtttgcccgactctccgaaaagggaaagtcgggcaattttatgaaaggacgaaaggtaatagccctgtaaaagcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUCUCUCUUAGCAGAGAAGUUCAUCAGGUACUUUCUUUGCAGAAAUACAGUUUGCCCGACUCUCCGAAAAGGGAAAGUCGGGCAAUUUUAUGAAAGGACGAAAGGUAAUAGCCCUGUAAAAGCCU ((((((((.(((.((((((((((((....)).)).))))))))...........((((((((((.(((......))).))))))))))........))))).)))))).................... (-41.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUUUACAGGGCUAUUACCUUUCGUCCUUUCAUAAAAUUGCCCGACUUUCCCUUUUCGGAGAGUCGGGCAAACUGUAUUUCUGCAAAGAAAGUACCUGAUGAACUUCUCUGCUAAGAGAGAAAGG .(((((.....)))))....((((((.....(((((....((((((((((((((......))))))))))))))...((((((((....)).))))))...)))))..(((((....))))))))))) (-47.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 87 46 162 111 NC_002950:PG1747|5end_ribose_5-phosphate_isomerase_B,_putative_1832815..1833045_NEGATIVE 302 70 22 125 77 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 301 88 53 84 44 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 294 77 35 108 70 NC_002950:PG0031|5end_hypothetical_protein_37579..37809_NEGATIVE 286 46 6 170 125 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 284 84 44 62 22 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 283 87 54 155 116 NC_002950:PG2120|5end_metallo-beta-lactamase_superfamily_protein_2228492..2228722_NEGATIVE 283 89 41 54 11 NC_002950:PG0789|5end_hypothetical_protein_841418..841648_NEGATIVE 283 85 49 181 141 NC_002950:PG0329|5end_formiminotransferase-cyclodeaminase-related_protein_364429..364659_NEGATIVE 281 77 34 52 8 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 279 102 67 45 4 NC_002950:PG0769|5end_fibronectin_type_III_domain_protein_824177..824407_NEGATIVE 278 83 41 57 20 NC_002950:PG2221|5end_MiaB-like_tRNA_modifying_enzyme_2335426..2335656_POSITIVE 275 108 67 68 34 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 273 86 41 95 44 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 273 88 54 44 1 NC_002950:PG0751|5end_porT_protein_797578..797808_NEGATIVE 272 86 50 170 135 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 271 77 36 220 170 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 271 59 14 174 136 NC_002950:PG0739|5end_ribonuclease_Z_786947..787177_POSITIVE 270 83 41 124 84 NC_002950:PG2219|5end_potassium_uptake_protein_TrkH_2332947..2333177_POSITIVE 270 83 51 120 89 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 88 55 36 3 NC_002950:PG1326|3end_hemagglutinin,_putative_1405171..1405321_POSITIVE 369 87 58 33 3 NC_002950:PG1458|3end_hypothetical_protein_1539682..1539832_POSITIVE 365 87 46 75 24 NC_002950:PG1748|3end_transketolase_1832902..1833052_NEGATIVE 353 90 41 77 16 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 342 100 53 61 3 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 332 102 63 77 30 NC_002950:PG0674|3end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724209..724359_NEGATIVE 316 86 42 46 13 NC_002950:PG0452|3end_hypothetical_protein_495106..495256_POSITIVE 315 93 52 72 31 NC_002950:PG2054|3end_lipoprotein_PG3_2151343..2151493_NEGATIVE 311 86 52 36 5 NC_002950:PG1837|3end_hemagglutinin_protein_HagA_1936734..1936884_POSITIVE 302 86 52 44 9 NC_002950:PG2053|3end_dithiobiotin_synthetase_2151267..2151417_POSITIVE 296 43 1 79 22 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 294 77 35 60 22 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 292 85 43 85 32 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 283 87 54 102 63 NC_002950:PG2121|3end_L-asparaginase_2228545..2228695_NEGATIVE 283 89 41 73 30 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 283 85 49 132 92 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 281 77 34 150 106 NC_002950:PG1024|3end_hypothetical_protein_1086876..1087026_POSITIVE 275 44 1 151 94 NC_002950:PG1516|3end_hypothetical_protein_1593197..1593347_POSITIVE 275 68 27 43 2 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 273 86 41 80 29 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE