Origin IGS: atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataacctcgtcaactttctttacccattgtagcataagagtttttatttttaaaataaaaaagatatgatataatgagagcagattagaatttggaggaagat Mask Tandem Repeat Region ================================================ atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Find is-nt database================================================ Query_seq: SSA_1270:SSA_1271|SSA_1270:SSA_1271:Flavodoxin:Conserved uncharacterized protein:<-->:1294007..1294111 105 atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1270:SSA_1271|SSA_1270:SSA_1271:Flavodoxin:Conserved uncharacterized protein:<-->:1294007..1294111 105 atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1270:SSA_1271|SSA_1270:SSA_1271:Flavodoxin:Conserved uncharacterized protein:<-->:1294007..1294111 105 atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Predict ORF larger than 30AA ================================================ atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt 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: 83 Start: 49 End: 78 ................................................TTTTAAAAATAAAAACTCTTATGCTACAAT........................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 29 End: 58 ............................ATTTTTAAAATAAAAAAGATATGATATAAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1270:SSA_1271|SSA_1270:SSA_1271:Flavodoxin:Conserved uncharacterized protein:<-->:1294007..1294111 105 atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_1270_SSA_1271|Flavodoxin:Conserved uncharacterized protein|NEGATIVE:POSITIVE|[1294007,1294111]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt atcttcctccaaattctaatctgctctcattatatcatatcttttttattttaaaaataaaaactcttatgctacaatgggtaaagaaagttgacgaggttattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUCCUCCAAAUUCUAAUCUGCUCUCAUUAUAUCAUAUCUUUUUUAUUUUAAAAAUAAAAACUCUUAUGCUACAAUGGGUAAAGAAAGUUGACGAGGUUAUUU .....((((..((((....(((...((((((.((.((((...((((((((.....))))))))....)))).)).))))))...))).))))...))))...... (-17.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAACCUCGUCAACUUUCUUUACCCAUUGUAGCAUAAGAGUUUUUAUUUUUAAAAUAAAAAAGAUAUGAUAUAAUGAGAGCAGAUUAGAAUUUGGAGGAAGAU ......((((................(((((((.((((....((((((((.....))))))))...)))).)))))))....(((((....)))))))))..... (-17.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 755 100 51 191 142 NC_009009:SSA_1270|5end_Flavodoxin_1293916..1294146_NEGATIVE 292 47 5 122 69 NC_009009:SSA_2083|5end_hypothetical_protein_2087969..2088199_NEGATIVE 269 100 63 135 98 NC_009009:SSA_1554|5end_hypothetical_protein_1555949..1556179_POSITIVE 235 50 2 156 93 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 230 50 3 138 96 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 226 39 2 137 93 NC_009009:SSA_0070|5end_Acetylxylan_esterase,_putative_73833..74063_POSITIVE 223 28 3 129 101 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 220 68 22 169 119 NC_009009:SSA_1421|5end_Adenine_phosphoribosyltransferase,_putative_1431285..1431515_NEGATIVE 218 27 2 183 151 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 218 45 5 146 98 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 214 35 2 30 3 NC_009009:SSA_1328|5end_hypothetical_protein_1344896..1345126_NEGATIVE 214 37 2 228 192 NC_009009:SSA_0932|5end_hypothetical_protein_941453..941683_POSITIVE 213 47 1 193 152 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 211 97 65 144 107 NC_009009:SSA_0668|5end_hypothetical_protein_650737..650967_POSITIVE 210 52 21 112 78 NC_009009:SSA_0655|5end_Cell_division_protein_FtsA,_putative_638784..639014_POSITIVE 209 49 13 40 1 NC_009009:SSA_1335|5end_Ankyrin_repeat_protein,_putative_1349663..1349893_NEGATIVE 206 43 2 202 151 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 203 100 51 174 113 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 202 27 2 29 1 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 202 58 22 161 123 NC_009009:SSA_1786|5end_Conserved_uncharacterized_protein_1770244..1770474_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 47 5 118 65 NC_009009:SSA_2084|3end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2087973..2088123_NEGATIVE 269 100 63 138 101 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 223 28 3 142 114 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 220 68 22 72 22 NC_009009:SSA_1422|3end_hypothetical_protein_1431382..1431532_NEGATIVE 211 97 65 84 47 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 210 99 66 149 103 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 209 49 13 122 83 NC_009009:SSA_1336|3end_Conserved_ankyrin_repeat_protein,_putative_1349581..1349731_NEGATIVE 202 27 2 36 8 NC_009009:SSA_1924|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1912691..1912841_NEGATIVE 202 58 22 104 66 NC_009009:SSA_1787|3end_Diaminopimelate_decarboxylase,_putative_1770301..1770451_NEGATIVE 194 46 2 58 15 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 194 28 1 114 84 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 194 41 3 120 83 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 193 42 3 144 101 NC_009009:SSA_1296|3end_hypothetical_protein_1312582..1312732_NEGATIVE 193 39 1 136 86 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 186 28 1 55 29 NC_009009:SSA_1292|3end_hypothetical_protein_1311099..1311249_NEGATIVE 185 46 2 146 104 NC_009009:SSA_1717|3end_Modification_methylase_DpnIIB,_putative_1704155..1704305_NEGATIVE 185 41 9 105 78 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 185 32 1 142 101 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 183 42 2 74 39 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 182 43 7 104 62 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE