Origin IGS: agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctctaaaaagaaaattgttttaattttaaaattatatcatgagtactggtaataaacaacaaaaagaaaaatagtacctgcctagcaagtactactttact Mask Tandem Repeat Region ================================================ agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Find is-nt database================================================ Query_seq: FN0054:FN0055|FN0054:FN0055:tyrosyl-tRNA synthetase:Ribosomal-protein-alanine acetyltransferase:->->:692197..692297 101 agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0054:FN0055|FN0054:FN0055:tyrosyl-tRNA synthetase:Ribosomal-protein-alanine acetyltransferase:->->:692197..692297 101 agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0054:FN0055|FN0054:FN0055:tyrosyl-tRNA synthetase:Ribosomal-protein-alanine acetyltransferase:->->:692197..692297 101 agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Predict ORF larger than 30AA ================================================ agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 42 End: 71 .........................................GTTGTTTATTACCAGTACTCATGATATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0054:FN0055|FN0054:FN0055:tyrosyl-tRNA synthetase:Ribosomal-protein-alanine acetyltransferase:->->:692197..692297 101 agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_003454_FN0054_FN0055|tyrosyl-tRNA synthetase:Ribosomal-protein-alanine acetyltransferase|POSITIVE:POSITIVE|[692197,692297]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag agtaaagtagtacttgctaggcaggtactatttttctttttgttgtttattaccagtactcatgatataattttaaaattaaaacaattttctttttagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAAGUAGUACUUGCUAGGCAGGUACUAUUUUUCUUUUUGUUGUUUAUUACCAGUACUCAUGAUAUAAUUUUAAAAUUAAAACAAUUUUCUUUUUAGAG ((.((((((((((((((...)))))))))))))).))..................................(((((((..(((.....)))..))))))). (-17.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUAAAAAGAAAAUUGUUUUAAUUUUAAAAUUAUAUCAUGAGUACUGGUAAUAAACAACAAAAAGAAAAAUAGUACCUGCCUAGCAAGUACUACUUUACU ..............(((((((((((....)))))(((((.......)))))..)))))).....((.(((.((((((.(((...))).)))))).))).)) (-10.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 34 4 202 171 NC_003454:FN0032|5end_hypothetical_protein_669778..670008_NEGATIVE 234 50 1 225 174 NC_003454:FN1452|5end_Cell_division_protein_ftsA_2134076..2134306_NEGATIVE 222 69 23 193 153 NC_003454:FN0552|5end_Serine_racemase_1204715..1204945_NEGATIVE 209 58 11 71 27 NC_003454:FN0913|5end_Cobinamide_kinase_1570735..1570965_NEGATIVE 200 40 6 32 1 NC_003454:FN2037|5end_LSU_ribosomal_protein_L12P_(L7/L12)_547137..547367_NEGATIVE 198 52 22 29 1 NC_003454:FN1005|5end_hypothetical_protein_1660422..1660652_POSITIVE 195 60 13 58 15 NC_003454:FN0164|5end_Anhydro-N-acetylmuramyl-tripeptide_amidase_792345..792575_POSITIVE 192 67 21 124 75 NC_003454:FN1518|5end_RNA_polymerase_sigma-70_factor_24077..24307_NEGATIVE 190 58 21 50 15 NC_003454:FN1456|5end_UDP-N-acetylmuramate--alanine_ligase_2137922..2138152_NEGATIVE 190 57 19 64 31 NC_003454:FN1790|5end_Cob(I)alamin_adenosyltransferase_271511..271741_POSITIVE 190 88 55 116 82 NC_003454:FN1707|5end_Aldose_1-epimerase_202181..202411_POSITIVE 188 57 11 130 94 NC_003454:FN0925|5end_hypothetical_protein_1579921..1580151_POSITIVE 188 64 21 219 174 NC_003454:FN0174|5end_Enoyl-[acyl-carrier-protein]_reductase_799427..799657_POSITIVE 187 45 14 39 11 NC_003454:FN2116|5end_Hypothetical_exported_24-amino_acid_repeat_protein_625504..625734_NEGATIVE 186 66 21 94 48 NC_003454:FN0082|5end_Ethanolamine_utilization_protein_eutM_720699..720929_POSITIVE 185 59 13 51 4 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 184 58 14 225 175 NC_003454:FN1739|5end_V-type_sodium_ATP_synthase_subunit_E_237902..238132_NEGATIVE 179 56 18 216 163 NC_003454:FN1535|5end_Acyl-CoA_dehydrogenase,_short-chain_specific_48260..48490_NEGATIVE 177 58 17 221 174 NC_003454:FN1229|5end_hypothetical_protein_1886700..1886930_NEGATIVE 177 64 23 153 111 NC_003454:FN0828|5end_ABC_transporter_permease_protein_1488199..1488429_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 39 1 92 54 NC_003454:FN0054|3end_tyrosyl-tRNA_synthetase_692136..692286_POSITIVE 223 48 4 84 36 NC_003454:FN2066|3end_hypothetical_protein_576773..576923_POSITIVE 195 44 4 95 50 NC_003454:FN2099|3end_hypothetical_protein_608702..608852_POSITIVE 192 67 21 113 64 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 190 58 21 69 34 NC_003454:FN1457|3end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2137903..2138053_NEGATIVE 190 57 19 52 19 NC_003454:FN1789|3end_Na+_driven_multidrug_efflux_pump_271579..271729_POSITIVE 190 88 55 132 98 NC_003454:FN1706|3end_Transporter_202277..202427_POSITIVE 189 49 4 93 52 NC_003454:FN0103|3end_Ribonucleoside-diphosphate_reductase_beta_chain_739607..739757_POSITIVE 188 57 11 91 55 NC_003454:FN0924|3end_hypothetical_protein_1579962..1580112_POSITIVE 186 66 21 83 37 NC_003454:FN0081|3end_Ethanolamine_utilization_protein_eutL_720768..720918_POSITIVE 185 59 13 49 2 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 185 50 1 94 38 NC_003454:FN0033|3end_hypothetical_protein_670146..670296_NEGATIVE 182 49 16 93 54 NC_003454:FN1382|3end_ATPase_2034437..2034587_POSITIVE 177 55 17 150 120 NC_003454:FN1170|3end_Pyruvate-flavodoxin_oxidoreductase_1828707..1828857_NEGATIVE 176 41 4 91 53 NC_003454:FN2079|3end_ABC_transporter_ATP-binding_protein_590342..590492_NEGATIVE 174 55 18 142 98 NC_003454:FN1194|3end_hypothetical_protein_1855668..1855818_POSITIVE 173 57 13 141 98 NC_003454:FN0470|3end_Putative_efflux_pump_component_MtrF_1116359..1116509_POSITIVE 173 57 14 99 53 NC_003454:FN2076|3end_MunI_regulatory_protein_587536..587686_NEGATIVE 173 50 6 101 56 NC_003454:FN1949|3end_Xaa-Pro_dipeptidase_453534..453684_NEGATIVE 173 63 26 110 70 NC_003454:FN1899|3end_Hypothetical_lipoprotein_386714..386864_NEGATIVE