Origin IGS: cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc .........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 gccgtagaaaggcaaaatttccttattgtcctgctaagccggattgcaaagataaacattctaccctgttatatcctaatccgtttttgccggatttcttgaaaagaaaaagtccggaacaagggggcaacctcctgatccggactttcatgtgaaacacagcttaataatccgttttccttatgttccgatctgctg Mask Tandem Repeat Region ================================================ cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Find is-nt database================================================ Query_seq: PG1382:PG1383|PG1382:PG1383:hypothetical protein:amino acid exporter, putative:->->:1462611..1462808 198 cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1382:PG1383|PG1382:PG1383:hypothetical protein:amino acid exporter, putative:->->:1462611..1462808 198 cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1382:PG1383|PG1382:PG1383:hypothetical protein:amino acid exporter, putative:->->:1462611..1462808 198 cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 39 End: 173 ...................................... M F H M K V R I R R L P P C S G L F L F K K S G K N G L G Y N R V E C L S L Q S G L A G Q ......................... cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc 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================================================ cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.1 Tail_Score: -5.45802 Start: 54 End: 87 Full_Region: GTGTTTCACATGAAA GTCCGGATCAGGAGG TTGC CCCCTTGTTCCGGAC TTTTTCTTTTCAAGA .....................................................GTCCGGATCAGGAGGTTGCCCCCTTGTTCCGGAC............................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.9 Tail_Score: -3.83026 Start: 54 End: 87 Full_Region: tcttgaaaagaaaaa gtccggaacaaggggg caa cctcctgatccggac tttcatgtgaaacac .....................................................gtccggaacaagggggcaacctcctgatccggac............................................................................................................... Find igs database================================================ Query_seq: PG1382:PG1383|PG1382:PG1383:hypothetical protein:amino acid exporter, putative:->->:1462611..1462808 198 cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: NC_002950_PG1382_PG1383|hypothetical protein:amino acid exporter, putative|POSITIVE:POSITIVE|[1462611,1462808]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc cagcagatcggaacataaggaaaacggattattaagctgtgtttcacatgaaagtccggatcaggaggttgcccccttgttccggactttttcttttcaagaaatccggcaaaaacggattaggatataacagggtagaatgtttatctttgcaatccggcttagcaggacaataaggaaattttgcctttctacggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCAGAUCGGAACAUAAGGAAAACGGAUUAUUAAGCUGUGUUUCACAUGAAAGUCCGGAUCAGGAGGUUGCCCCCUUGUUCCGGACUUUUUCUUUUCAAGAAAUCCGGCAAAAACGGAUUAGGAUAUAACAGGGUAGAAUGUUUAUCUUUGCAAUCCGGCUUAGCAGGACAAUAAGGAAAUUUUGCCUUUCUACGGC ..((((..((((...(((((((((((..(((((...((((..(((....(((((((((((.((((.((....)).)))).)))))))))))...........((((((.......)))))).)))....)))))))))..))))).))))))...))))..)).))...................(((.......))) (-54.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGUAGAAAGGCAAAAUUUCCUUAUUGUCCUGCUAAGCCGGAUUGCAAAGAUAAACAUUCUACCCUGUUAUAUCCUAAUCCGUUUUUGCCGGAUUUCUUGAAAAGAAAAAGUCCGGAACAAGGGGGCAACCUCCUGAUCCGGACUUUCAUGUGAAACACAGCUUAAUAAUCCGUUUUCCUUAUGUUCCGAUCUGCUG ...(((((..((...............((((.((.(((.(((((((....((((((((........)))).)))).))))))).))).)).)))).....(((((...((((((((((.((.((((....)))).)).))))))))))..((((...)))).............)))))........))..))))).. (-54.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 83 41 50 1 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 395 99 57 229 170 NC_002950:PG0264|5end_glycosyl_transferase,_group_2_family_protein_296975..297205_POSITIVE 375 80 35 83 38 NC_002950:PG0608|5end_hypothetical_protein_662945..663175_POSITIVE 369 93 54 218 186 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 365 114 71 180 136 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 353 98 52 168 123 NC_002950:PG2072|5end_UvrD/REP_helicase_domain_protein_2167369..2167599_POSITIVE 348 85 48 152 112 NC_002950:PG0486|5end_methylated-DNA--protein-cysteine_S-methyltransferase_525934..526164_NEGATIVE 337 110 63 172 111 NC_002950:PG0351|5end_hypothetical_protein_386774..387004_POSITIVE 335 108 63 96 60 NC_002950:PG1083|5end_hypothetical_protein_1151834..1152064_NEGATIVE 329 188 144 79 36 NC_002950:PG1711|5end_alpha-1,2-mannosidase_family_protein_1798913..1799143_NEGATIVE 327 96 55 137 94 NC_002950:PG0563|5end_hypothetical_protein_621438..621668_NEGATIVE 325 92 53 120 77 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 320 86 41 208 155 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 319 88 42 74 20 NC_002950:PG2162|5end_lipid_A_disaccharide_synthase_2268764..2268994_NEGATIVE 316 110 63 64 12 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 313 86 45 190 138 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 311 77 35 229 176 NC_002950:PG1604|5end_immunoreactive_84_kDa_antigen_PG93_1682737..1682967_POSITIVE 311 58 19 39 1 NC_002950:PG1326|5end_hemagglutinin,_putative_1404033..1404263_POSITIVE 311 120 71 63 13 NC_002950:PG0960|5end_tRNA_(guanine-N(7)-)-methyltransferase_1021895..1022125_NEGATIVE 311 93 57 64 19 NC_002950:PG0599|5end_3,4-dihydroxy-2-butanone_4-phosphate_synthase/GTP_cyclohydrolase_II_656435..656665_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 414 90 51 40 1 NC_002950:PG1382|3end_hypothetical_protein_1462550..1462700_POSITIVE 375 80 35 52 7 NC_002950:PG0607|3end_hypothetical_protein_662994..663144_POSITIVE 337 83 57 37 12 NC_002950:PG2108|3end_thiazole_synthase_2216671..2216821_NEGATIVE 337 87 51 49 2 NC_002950:PG1277|3end_UDP-glucose-6_dehydrogenase,_putative_1355099..1355249_POSITIVE 335 108 63 48 12 NC_002950:PG1084|3end_thioredoxin_family_protein_1151882..1152032_NEGATIVE 330 98 56 49 6 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 325 92 53 56 13 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 325 85 55 147 116 NC_002950:PG0564|3end_hypothetical_protein_621416..621566_NEGATIVE 311 93 57 61 16 NC_002950:PG0598|3end_hypothetical_protein_656512..656662_POSITIVE 309 84 46 124 69 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 308 110 62 118 69 NC_002950:PG1537|3end_hypothetical_protein_1617603..1617753_POSITIVE 304 83 48 39 3 NC_002950:PG1418|3end_DNA_polymerase_III,_gamma_and_tau_subunits_1504952..1505102_POSITIVE 303 92 55 43 4 NC_002950:PG1860|3end_hypothetical_protein_1958574..1958724_NEGATIVE 303 90 48 116 66 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 301 109 70 65 30 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 298 96 57 145 110 NC_002950:PG0628|3end_ABC_transporter,_ATP-binding_protein_681684..681834_NEGATIVE 288 86 46 136 85 NC_002950:PG0781|3end_hypothetical_protein_833239..833389_NEGATIVE 287 89 53 45 3 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 286 93 56 33 2 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 284 110 61 132 69 NC_002950:PG0380|3end_excinuclease_ABC_subunit_B_411218..411368_POSITIVE