Origin IGS: ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatctacctctttcattttattaataagtttaaaatttaccatatcctatattttaaagaattaatttatgtacttgtcaagtggttgctgtaatgagtttacaacaaccctaaacaagtaaggaattaagacaaatgagtaaag Mask Tandem Repeat Region ================================================ ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Find is-nt database================================================ Query_seq: FN1419:FN1420|FN1419:FN1420:methionine gamma-lyase:NA+/H+ antiporter NHAC:->->:2081893..2082038 146 ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1419:FN1420|FN1419:FN1420:methionine gamma-lyase:NA+/H+ antiporter NHAC:->->:2081893..2082038 146 ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1419:FN1420|FN1419:FN1420:methionine gamma-lyase:NA+/H+ antiporter NHAC:->->:2081893..2082038 146 ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 55 End: 144 ...................................................... L L W K V L V Y I L E K F Y L I H Y I K F K N I F H F L Y M .. ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat 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================================================ ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 60 HP_score: -6.7 Tail_Score: -2.64572 Start: 24 End: 76 Full_Region: ATTTGTCTTAATTCC TTACTTGTTTAGGGTTGTTGTAA ACTCA TTACAGCAACCACTTGACAAGTACA TAAATTAATTCTTTA .......................TTACTTGTTTAGGGTTGTTGTAAACTCATTACAGCAACCACTTGACAAGTACA...................................................................... Find igs database================================================ Query_seq: FN1419:FN1420|FN1419:FN1420:methionine gamma-lyase:NA+/H+ antiporter NHAC:->->:2081893..2082038 146 ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_003454_FN1419_FN1420|methionine gamma-lyase:NA+/H+ antiporter NHAC|POSITIVE:POSITIVE|[2081893,2082038]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat ctttactcatttgtcttaattccttacttgtttagggttgttgtaaactcattacagcaaccacttgacaagtacataaattaattctttaaaatataggatatggtaaattttaaacttattaataaaatgaaagaggtagatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUACUCAUUUGUCUUAAUUCCUUACUUGUUUAGGGUUGUUGUAAACUCAUUACAGCAACCACUUGACAAGUACAUAAAUUAAUUCUUUAAAAUAUAGGAUAUGGUAAAUUUUAAACUUAUUAAUAAAAUGAAAGAGGUAGAUAU ((((..((((((............((((((((.(((((((((((((.....))))))))))).)).)))))))).....((((((..((((((((.((........)).))))))))...)))))).))))))..))))....... (-33.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCUACCUCUUUCAUUUUAUUAAUAAGUUUAAAAUUUACCAUAUCCUAUAUUUUAAAGAAUUAAUUUAUGUACUUGUCAAGUGGUUGCUGUAAUGAGUUUACAACAACCCUAAACAAGUAAGGAAUUAAGACAAAUGAGUAAAG ............(((((((..........((((((((.((........)).))))))))...(((((((...(((((((..((.(((((.(((((.....))))).)))))))..)))))))..)))))))...)))))))..... (-30.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 67 26 167 128 NC_003454:FN1428|5end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2097573..2097803_NEGATIVE 235 76 34 95 57 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 234 49 2 130 83 NC_003454:FN1349|5end_ABC_transporter_permease_protein_2002355..2002585_NEGATIVE 234 70 24 50 6 NC_003454:FN0524|5end_DNA_helicase_II_1179643..1179873_NEGATIVE 225 69 34 216 185 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 221 65 22 187 143 NC_003454:FN0780|5end_Hypothetical_membrane-spanning_protein_1437490..1437720_NEGATIVE 211 69 21 218 170 NC_003454:FN1226|5end_uracil-DNA_glycosylase_1885503..1885733_NEGATIVE 208 44 5 125 86 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 202 62 26 213 172 NC_003454:FN1488|5end_Methenyltetrahydrofolate_cyclohydrolase_2170886..2171116_NEGATIVE 201 59 12 90 49 NC_003454:FN1204|5end_Methyltransferase_1863868..1864098_NEGATIVE 200 49 1 135 82 NC_003454:FN1477|5end_Hypothetical_membrane-spanning_protein_2159504..2159734_POSITIVE 198 46 2 182 137 NC_003454:FN0284|5end_16S_rRNA_processing_protein_rimM_913923..914153_NEGATIVE 195 68 27 199 157 NC_003454:FN1046|5end_hypothetical_protein_1696371..1696601_POSITIVE 194 74 35 145 121 NC_003454:FN1711|5end_Methyltransferase_206325..206555_POSITIVE 192 67 21 108 52 NC_003454:FN1361|5end_Dipeptide_transport_system_permease_protein_dppC_2013051..2013281_POSITIVE 191 59 11 127 85 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 191 107 62 122 71 NC_003454:FN0428|5end_hypothetical_protein_1070037..1070267_POSITIVE 189 77 35 153 106 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 188 73 31 192 145 NC_003454:FN1861|5end_L-lysine_permease_352308..352538_NEGATIVE 186 60 12 45 4 NC_003454:FN0401|5end_hypothetical_protein_1040150..1040380_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 70 25 62 17 NC_003454:FN1419|3end_methionine_gamma-lyase_2081832..2081982_POSITIVE 242 62 34 82 52 NC_003454:FN1080|3end_Export_ABC_transporter_1727308..1727458_POSITIVE 234 49 2 126 79 NC_003454:FN1350|3end_Integral_membrane_protein_2002359..2002509_NEGATIVE 234 70 24 48 4 NC_003454:FN0525|3end_Penicillin-binding_protein_1179645..1179795_NEGATIVE 225 69 34 85 54 NC_003454:FN2011|3end_Valyl-tRNA_synthetase_510433..510583_NEGATIVE 213 71 34 65 35 NC_003454:FN0557|3end_hypothetical_protein_1209600..1209750_NEGATIVE 208 44 5 138 99 NC_003454:FN1215|3end_Hypothetical_cytosolic_protein_1875460..1875610_NEGATIVE 201 59 12 79 38 NC_003454:FN1205|3end_Protease_1863879..1864029_NEGATIVE 194 74 35 87 63 NC_003454:FN1710|3end_Integral_membrane_protein,_YGGT_family_206347..206497_POSITIVE 192 67 21 108 52 NC_003454:FN1360|3end_Dipeptide_transport_system_permease_protein_dppB_2013131..2013281_POSITIVE 191 59 11 118 76 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 191 107 62 125 74 NC_003454:FN0427|3end_Orotate_phosphoribosyltransferase_1070120..1070270_POSITIVE 189 77 35 69 22 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 189 51 34 59 42 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 184 79 38 136 101 NC_003454:FN1287|3end_Bacterial_Protein_Translation_Initiation_Factor_1_(IF-1)_1944415..1944565_NEGATIVE 181 59 14 151 106 NC_003454:FN1862|3end_L-beta-lysine_5,6-aminomutase_beta_subunit_352331..352481_NEGATIVE 180 68 32 86 48 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE 180 44 6 126 77 NC_003454:FN0253|3end_Outer_membrane_protein_875063..875213_POSITIVE 179 47 5 72 25 NC_003454:FN1661|3end_Hypothetical_cytosolic_protein_157963..158113_NEGATIVE 178 50 7 140 95 NC_003454:FN1448|3end_Hypothetical_cytosolic_protein_2117403..2117553_NEGATIVE