Origin IGS: ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggctattcctcaattacggaaaacaaaaatagtctttttccccgacgcctatgtcatagggcaatcgcatttgaactgttaactcacttataaacctaacgattgctacgttcggttatcaaacaagtacgaa Mask Tandem Repeat Region ================================================ ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Find is-nt database================================================ Query_seq: PG0499:PG0500|PG0499:PG0500:hypothetical protein:queuine tRNA-ribosyltransferase:->->:539203..539336 134 ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0499:PG0500|PG0499:PG0500:hypothetical protein:queuine tRNA-ribosyltransferase:->->:539203..539336 134 ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0499:PG0500|PG0499:PG0500:hypothetical protein:queuine tRNA-ribosyltransferase:->->:539203..539336 134 ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Predict ORF larger than 30AA ================================================ ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc 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================================================ ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.5 Tail_Score: -3.29144 Start: 19 End: 39 Full_Region: taactcacttataaa cctaacg attgcta cgttcgg ttatcaaacaagtac ..................cctaacgattgctacgttcgg............................................................................................... Find igs database================================================ Query_seq: PG0499:PG0500|PG0499:PG0500:hypothetical protein:queuine tRNA-ribosyltransferase:->->:539203..539336 134 ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_002950_PG0499_PG0500|hypothetical protein:queuine tRNA-ribosyltransferase|POSITIVE:POSITIVE|[539203, 539336]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc ttcgtacttgtttgataaccgaacgtagcaatcgttaggtttataagtgagttaacagttcaaatgcgattgccctatgacataggcgtcggggaaaaagactatttttgttttccgtaattgaggaatagccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGUACUUGUUUGAUAACCGAACGUAGCAAUCGUUAGGUUUAUAAGUGAGUUAACAGUUCAAAUGCGAUUGCCCUAUGACAUAGGCGUCGGGGAAAAAGACUAUUUUUGUUUUCCGUAAUUGAGGAAUAGCCC ...(((((..((((..((((.((((.......)))).))))..))))..)))..))..(((((.((((....((((..(((......)))))))...(((((.......))))).)))).)))))......... (-29.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCUAUUCCUCAAUUACGGAAAACAAAAAUAGUCUUUUUCCCCGACGCCUAUGUCAUAGGGCAAUCGCAUUUGAACUGUUAACUCACUUAUAAACCUAACGAUUGCUACGUUCGGUUAUCAAACAAGUACGAA ((((((((((........)))........)))))))...........((((........))))..(((.(((((...((......))......((((.((((.......)))).))))......))))).))). (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 556 76 31 181 136 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 506 43 1 229 187 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 468 40 1 229 185 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 374 43 1 229 187 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 358 117 75 212 170 NC_002950:PG1049|5end_hypothetical_protein_1116387..1116617_POSITIVE 315 119 77 128 83 NC_002950:PG2073|5end_hypothetical_protein_2174374..2174604_NEGATIVE 315 119 77 128 83 NC_002950:PG1669|5end_hypothetical_protein_1755566..1755796_NEGATIVE 315 119 77 128 83 NC_002950:PG1264|5end_hypothetical_protein_1344895..1345125_NEGATIVE 315 119 77 128 83 NC_002950:PG0103|5end_hypothetical_protein_121290..121520_POSITIVE 306 110 63 215 166 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 306 110 63 70 21 NC_002950:PG0979|5end_hypothetical_protein_1040752..1040982_POSITIVE 300 94 71 166 143 NC_002950:PG0955|5end_hypothetical_protein_1014832..1015062_POSITIVE 295 93 66 40 15 NC_002950:PG1071|5end_hypothetical_protein_1138008..1138238_POSITIVE 294 89 45 158 116 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 293 107 65 93 47 NC_002950:PG1598|5end_lipoprotein_signal_peptidase,_putative_1678410..1678640_POSITIVE 293 95 70 156 131 NC_002950:PG0869|5end_mobilization_protein_932203..932433_NEGATIVE 285 100 63 78 50 NC_002950:PG2145|5end_polysaccharide_deacetylase_2253253..2253483_POSITIVE 284 96 58 226 183 NC_002950:PG2108|5end_thiazole_synthase_2217450..2217680_NEGATIVE 283 95 65 51 16 NC_002950:PG1343|5end_lipoate-protein_ligase_B_1423628..1423858_POSITIVE 281 43 1 230 187 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 80 47 36 2 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 312 119 71 81 26 NC_002950:PG0378|3end_elongation_factor_Ts_408808..408958_POSITIVE 306 110 63 100 51 NC_002950:PG0978|3end_shikimate_5-dehydrogenase_1040862..1041012_POSITIVE 302 91 56 150 104 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 301 76 31 72 28 NC_002950:PG0078|3end_hypothetical_protein_91566..91716_NEGATIVE 293 107 65 89 43 NC_002950:PG1597|3end_DnaK_suppressor_protein,_putative_1678486..1678636_POSITIVE 293 95 70 55 30 NC_002950:PG0870|3end_hypothetical_protein_932304..932454_NEGATIVE 292 117 72 108 62 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 288 94 51 46 5 NC_002950:PG1005|3end_lipoprotein,_putative_1063023..1063173_NEGATIVE 285 100 63 35 7 NC_002950:PG2144|3end_hypothetical_protein_2253290..2253440_POSITIVE 282 97 64 151 107 NC_002950:PG1048|3end_N-acetylmuramoyl-L-alanine_amidase,_family_3_1116426..1116576_POSITIVE 281 95 56 125 92 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 277 129 81 151 108 NC_002950:PG0108|3end_UDP-N-acetyl-D-mannosaminuronic_acid_dehydrogenase_131389..131539_POSITIVE 276 93 66 108 82 NC_002950:PG1589|3end_dihydropteroate_synthase_1666593..1666743_NEGATIVE 268 104 68 49 16 NC_002950:PG0142|3end_SpoOJ_regulator_protein_164755..164905_NEGATIVE 264 88 46 130 93 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 264 93 55 80 40 NC_002950:PG0742|3end_antigen_PgaA_789300..789450_NEGATIVE 261 116 71 64 17 NC_002950:PG0637|3end_thiamine_monophosphate_kinase_689064..689214_NEGATIVE 260 95 66 100 56 NC_002950:PG0498|3end_S-ribosylhomocysteinase_538527..538677_POSITIVE 257 98 55 137 86 NC_002950:PG0987|3end_hypothetical_protein_1048858..1049008_POSITIVE