Origin IGS: cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atataaacaaaatagtcaaaaacaatatcttttagatagctctctctcatatttgccaaaccttatgtcatttttctatcgaaatggtatgtttttgactttacggaagccg Mask Tandem Repeat Region ================================================ cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Find is-nt database================================================ Query_seq: PG0504:PG0505|PG0504:PG0505:lipoyl synthase:hypothetical protein:->->:545223..545334 112 cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0504:PG0505|PG0504:PG0505:lipoyl synthase:hypothetical protein:->->:545223..545334 112 cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0504:PG0505|PG0504:PG0505:lipoyl synthase:hypothetical protein:->->:545223..545334 112 cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Predict ORF larger than 30AA ================================================ cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat 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================================================ cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0504:PG0505|PG0504:PG0505:lipoyl synthase:hypothetical protein:->->:545223..545334 112 cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002950_PG0504_PG0505|lipoyl synthase:hypothetical protein|POSITIVE:POSITIVE|[545223,545334]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat cggcttccgtaaagtcaaaaacataccatttcgatagaaaaatgacataaggtttggcaaatatgagagagagctatctaaaagatattgtttttgactattttgtttatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGCUUCCGUAAAGUCAAAAACAUACCAUUUCGAUAGAAAAAUGACAUAAGGUUUGGCAAAUAUGAGAGAGAGCUAUCUAAAAGAUAUUGUUUUUGACUAUUUUGUUUAUAU (((...)))...(((((((((((((.(.(((.(((((........((((..(.....)...))))........))))).))).).)).)))))))))))............. (-19.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAAACAAAAUAGUCAAAAACAAUAUCUUUUAGAUAGCUCUCUCUCAUAUUUGCCAAACCUUAUGUCAUUUUUCUAUCGAAAUGGUAUGUUUUUGACUUUACGGAAGCCG .............(((((((((((.((((.(((.(((((........((((............))))........))))).))).)))))))))))))))...(....)... (-21.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 73 42 36 1 NC_002950:PG0910|5end_FHA_domain_protein_973666..973896_NEGATIVE 264 76 43 48 6 NC_002950:PG1600|5end_hypothetical_protein_1680984..1681214_NEGATIVE 246 34 1 54 19 NC_002950:PG2111|5end_thiS_protein_2221482..2221712_NEGATIVE 243 77 51 40 5 NC_002950:PG1652|5end_hypothetical_protein_1733340..1733570_POSITIVE 239 88 50 148 102 NC_002950:PG0345|5end_hypothetical_protein_380608..380838_NEGATIVE 237 79 50 193 163 NC_002950:PG0413|5end_hypothetical_protein_451781..452011_NEGATIVE 234 97 54 116 66 NC_002950:PG1849|5end_DNA_repair_protein_RecN_1949034..1949264_NEGATIVE 232 79 37 50 9 NC_002950:PG1373|5end_hypothetical_protein_1454750..1454980_POSITIVE 229 96 60 166 121 NC_002950:PG0269|5end_exodeoxyribonuclease_III_302028..302258_POSITIVE 226 97 52 211 167 NC_002950:PG2042|5end_thioredoxin_family_protein_2141109..2141339_NEGATIVE 225 75 37 72 33 NC_002950:PG0622|5end_hypothetical_protein_675937..676167_POSITIVE 224 79 31 136 77 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 218 70 21 209 156 NC_002950:PG1463|5end_hypothetical_protein_1541110..1541340_POSITIVE 217 34 1 146 110 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 216 99 51 157 111 NC_002950:PG2123|5end_hypothetical_protein_2229891..2230121_POSITIVE 214 79 42 48 5 NC_002950:PG0656|5end_50S_ribosomal_protein_L34_707097..707327_NEGATIVE 213 108 62 106 52 NC_002950:PG1175|5end_ABC_transporter,_ATP-binding_protein,_putative_1255876..1256106_NEGATIVE 211 50 1 171 119 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 210 87 51 62 26 NC_002950:PG1798|5end_immunoreactive_46_kDa_antigen_PG99_1894245..1894475_NEGATIVE 209 75 32 84 40 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 79 52 128 99 NC_002950:PG0906|3end_lipoprotein,_putative_971148..971298_POSITIVE 242 78 49 81 53 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 241 67 24 84 37 NC_002950:PG0309|3end_thiamine_biosynthesis_lipoprotein_ApbE_344010..344160_NEGATIVE 234 97 54 101 51 NC_002950:PG1850|3end_hypothetical_protein_1949049..1949199_NEGATIVE 229 96 60 121 76 NC_002950:PG0268|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_302063..302213_POSITIVE 225 75 37 75 36 NC_002950:PG0621|3end_hypothetical_protein_676020..676170_POSITIVE 213 108 62 59 5 NC_002950:PG1176|3end_ABC_transporter,_ATP-binding_protein,_putative_1255923..1256073_NEGATIVE 212 80 31 63 15 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 209 75 32 64 20 NC_002950:PG2174|3end_hypothetical_protein_2280833..2280983_NEGATIVE 209 108 65 47 13 NC_002950:PG2156|3end_conserved_hypothetical_protein_TIGR00046_2261899..2262049_NEGATIVE 208 85 51 98 58 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 205 79 51 41 9 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 205 89 44 71 20 NC_002950:PG0638|3end_tetraacyldisaccharide_4'-kinase_690110..690260_NEGATIVE 204 68 21 136 87 NC_002950:PG1169|3end_hypothetical_protein_1249083..1249233_NEGATIVE 204 78 44 95 59 NC_002950:PG0978|3end_shikimate_5-dehydrogenase_1040862..1041012_POSITIVE 202 38 1 95 55 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 202 74 34 71 31 NC_002950:PG1173|3end_YkgG_family_protein_1253129..1253279_POSITIVE 201 40 1 66 28 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 200 87 48 127 92 NC_002950:PG1599|3end_hypothetical_protein_1679955..1680105_POSITIVE 199 77 31 105 60 NC_002950:PG0397|3end_hypothetical_protein_434312..434462_NEGATIVE