Origin IGS: aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattaatgatagtgttatataaattatgttctttatttaaacaaattttatcaagaaattatttgtttatataagtaagagtagttcattagaaaatagtactctctttctaaaaaaatataaaaatgatataatattaattatagaatatagaaatggtgaggtgaagtt Mask Tandem Repeat Region ================================================ aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Find is-nt database================================================ Query_seq: FN1395:FN1396|FN1395:FN1396:hypothetical protein:hypothetical protein:<-->:2051621..2051791 171 aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1395:FN1396|FN1395:FN1396:hypothetical protein:hypothetical protein:<-->:2051621..2051791 171 aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1395:FN1396|FN1395:FN1396:hypothetical protein:hypothetical protein:<-->:2051621..2051791 171 aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 3 End: 122 .. K V E G N R Y E I I L I I D N K Y K K L F L T S N E L S S S K S I Y V F L K K M ................................................. aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata 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: 3 End: 32 ..CTTCACCTCACCATTTCTATATTCTATAAT........................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 37 End: 66 ....................................CTTTCTAAAAAAATATAAAAATGATATAAT......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1395:FN1396|FN1395:FN1396:hypothetical protein:hypothetical protein:<-->:2051621..2051791 171 aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_003454_FN1395_FN1396|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2051621,2051791]|171 HSP 1 e-value: 6.0E-80 bit: 297.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 aacttcacctcaccatttctatattctataattaatattatatcatttttatannnnnnnagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata aacttcacctcaccatttctatattctataattaatattatatcatttttatatttttttagaaagagagtactattttctaatgaactactcttacttatataaacaaataatttcttgataaaatttgtttaaataaagaacataatttatataacactatcattaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUCACCUCACCAUUUCUAUAUUCUAUAAUUAAUAUUAUAUCAUUUUUAUAUUUUUUUAGAAAGAGAGUACUAUUUUCUAAUGAACUACUCUUACUUAUAUAAACAAAUAAUUUCUUGAUAAAAUUUGUUUAAAUAAAGAACAUAAUUUAUAUAACACUAUCAUUAAUA ...................(((.((((.((.((((.(((.(((((......(((((.((((..(((((((((.....(((....))).))))))..)))...)))).)))))......))))).)))....)))).)).)))).)))........................ (-15.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAAUGAUAGUGUUAUAUAAAUUAUGUUCUUUAUUUAAACAAAUUUUAUCAAGAAAUUAUUUGUUUAUAUAAGUAAGAGUAGUUCAUUAGAAAAUAGUACUCUCUUUCUAAAAAAAUAUAAAAAUGAUAUAAUAUUAAUUAUAGAAUAUAGAAAUGGUGAGGUGAAGUU .....(((((((((((((((...(((((((.(((...(((((((((..(........)..)))))))))....((.(((((.(((..((((.....)))))))))))).)).))).))))))).....)))))))))).)))))........................... (-22.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 701 110 61 201 152 NC_003454:FN1395|5end_hypothetical_protein_2051530..2051760_NEGATIVE 245 38 3 137 98 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 216 31 3 39 8 NC_003454:FN0476|5end_transcription_termination_factor_Rho_1123450..1123680_POSITIVE 216 99 54 165 115 NC_003454:FN1709|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_205415..205645_POSITIVE 208 47 5 129 95 NC_003454:FN1617|5end_Prolipoprotein_diacylglyceryltransferase_126666..126896_NEGATIVE 206 90 60 98 67 NC_003454:FN1749|5end_Pyruvate-flavodoxin_oxidoreductase_247461..247691_POSITIVE 203 48 2 135 94 NC_003454:FN2005|5end_Cobalt_transport_ATP-binding_protein_cbiO_505081..505311_POSITIVE 202 86 42 189 140 NC_003454:FN1648|5end_Oligopeptide_transport_ATP-binding_protein_oppF_143317..143547_NEGATIVE 198 49 3 225 161 NC_003454:FN1826|5end_Protease_315886..316116_NEGATIVE 195 33 7 40 12 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 190 70 22 179 128 NC_003454:FN1717|5end_NAD-dependent_DNA_ligase_213150..213380_POSITIVE 189 48 7 214 172 NC_003454:FN0854|5end_Glucose-1-phosphate_adenylyltransferase_1513487..1513717_NEGATIVE 187 45 4 145 87 NC_003454:FN0183|5end_Glycerol-3-phosphate_dehydrogenase_808574..808804_NEGATIVE 185 28 1 77 45 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 185 28 2 118 85 NC_003454:FN1182|5end_hypothetical_protein_1845438..1845668_NEGATIVE 182 37 3 39 4 NC_003454:FN0594|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1248785..1249015_POSITIVE 177 43 1 112 73 NC_003454:FN0614|5end_Export_ABC_transporter_1271447..1271677_POSITIVE 177 48 4 98 59 NC_003454:FN0303|5end_Nitrogenase_iron_protein_937526..937756_POSITIVE 175 57 11 146 89 NC_003454:FN0269|5end_Transposase_896041..896271_POSITIVE 174 50 1 105 56 NC_003454:FN1884|5end_hypothetical_protein_370507..370737_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 30 3 150 122 NC_003454:FN1581|3end_DNA_mismatch_repair_protein_mutS_90895..91045_NEGATIVE 216 99 54 149 99 NC_003454:FN1708|3end_Polyribonucleotide_nucleotidyltransferase_205479..205629_POSITIVE 212 67 21 151 102 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 208 47 5 129 95 NC_003454:FN1618|3end_hypothetical_protein_126666..126816_NEGATIVE 206 90 60 116 85 NC_003454:FN1748|3end_Pyruvate-flavodoxin_oxidoreductase_247559..247709_POSITIVE 203 48 2 151 110 NC_003454:FN2004|3end_Cobalt_transport_ATP-binding_protein_cbiO_505177..505327_POSITIVE 190 70 22 74 23 NC_003454:FN1716|3end_hypothetical_protein_213125..213275_POSITIVE 187 90 41 80 18 NC_003454:FN0598|3end_Phospholipid-lipopolysaccharide_ABC_transporter_1253712..1253862_POSITIVE 187 45 4 63 5 NC_003454:FN0184|3end_hypothetical_protein_808656..808806_NEGATIVE 185 28 2 128 95 NC_003454:FN1183|3end_Hypothetical_cytosolic_protein_1845428..1845578_NEGATIVE 177 48 4 70 31 NC_003454:FN0302|3end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_937578..937728_POSITIVE 175 57 11 111 54 NC_003454:FN0268|3end_DNA_repair_protein_recN_896086..896236_POSITIVE 174 63 24 81 31 NC_003454:FN0571|3end_DNA_processing_chain_A_1222390..1222540_POSITIVE 174 33 2 150 114 NC_003454:FN2056|3end_hypothetical_protein_564763..564913_NEGATIVE 173 39 3 68 28 NC_003454:FN0869|3end_Hydrolase_(HAD_superfamily)_1528108..1528258_NEGATIVE 172 76 35 141 88 NC_003454:FN1542|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_57192..57342_POSITIVE 171 50 3 147 96 NC_003454:FN0716|3end_Phophatidylinositol-4-phosphate_5-kinase_1374993..1375143_POSITIVE 170 105 72 124 90 NC_003454:FN0110|3end_seryl-tRNA_synthetase_744793..744943_NEGATIVE 169 59 15 68 18 NC_003454:FN0886|3end_Hemin_receptor_1547830..1547980_POSITIVE 169 129 84 141 101 NC_003454:FN0044|3end_Shikimate_5-dehydrogenase_683041..683191_POSITIVE