Origin IGS: aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaataaaaaattgaatttagtctgctaaaaaggattgacttctgtaagaagcaggagttaatccttttaattgtaaaataaaaaagaagttgctacaaatttaattgtaacaacttctgtataatttt Mask Tandem Repeat Region ================================================ aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Find is-nt database================================================ Query_seq: FN1800:FN1801|FN1800:FN1801:Peptidyl-prolyl cis-trans isomerase:Sodium/glutamate symport carrier protein:-><-:282595..282725 131 aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1800:FN1801|FN1800:FN1801:Peptidyl-prolyl cis-trans isomerase:Sodium/glutamate symport carrier protein:-><-:282595..282725 131 aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1800:FN1801|FN1800:FN1801:Peptidyl-prolyl cis-trans isomerase:Sodium/glutamate symport carrier protein:-><-:282595..282725 131 aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Predict ORF larger than 30AA ================================================ aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt 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: 30 End: 59 .............................TTTGTAGCAACTTCTTTTTTATTTTACAAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -11.0 Tail_Score: -3.32844 Start: 59 End: 103 Full_Region: ttgaatttagtctgc taaaaaggattgacttctgt aagaa gcaggagttaatccttttaa ttgtaaaataaaaaa ..........................................................taaaaaggattgacttctgtaagaagcaggagttaatccttttaa............................ TransTerm Strand: + Conf: 68 HP_score: -4.9 Tail_Score: -4.57569 Start: 65 End: 97 Full_Region: ATTTTACAATTAAAA GGATTAACTCCTG CTTCTTA CAGAAGTCAATCC TTTTTAGCAGACTAA ................................................................GGATTAACTCCTGCTTCTTACAGAAGTCAATCC.................................. TransTerm Strand: - Conf: 91 HP_score: -10.0 Tail_Score: -4.49389 Start: 65 End: 97 Full_Region: ttagtctgctaaaaa ggattgacttctgt aagaa gcaggagttaatcc ttttaattgtaaaat ................................................................ggattgacttctgtaagaagcaggagttaatcc.................................. Find igs database================================================ Query_seq: FN1800:FN1801|FN1800:FN1801:Peptidyl-prolyl cis-trans isomerase:Sodium/glutamate symport carrier protein:-><-:282595..282725 131 aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaattttttatttttt Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_003454_FN1800_FN1801|Peptidyl-prolyl cis-trans isomerase:Sodium/glutamate symport carrier protein|POSITIVE:NEGATIVE|[282595,282725]|131 HSP 1 e-value: 6.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaa............. aaaattatacagaagttgttacaattaaatttgtagcaacttcttttttattttacaattaaaaggattaactcctgcttcttacagaagtcaatcctttttagcagactaaattcaa............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUAUACAGAAGUUGUUACAAUUAAAUUUGUAGCAACUUCUUUUUUAUUUUACAAUUAAAAGGAUUAACUCCUGCUUCUUACAGAAGUCAAUCCUUUUUAGCAGACUAAAUUCAA (((((.....((((((((((((((......)))))))))))))).....)))))......(((((((((.(((.(((.......))).))).)))))))))................. (-32.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAUUUAGUCUGCUAAAAAGGAUUGACUUCUGUAAGAAGCAGGAGUUAAUCCUUUUAAUUGUAAAAUAAAAAAGAAGUUGCUACAAAUUUAAUUGUAACAACUUCUGUAUAAUUUU .....((((...(((..((((((((((((((((((.....))))))))))))))))))....)))...))))..((((((((.(((((......))))).)))))))).......... (-38.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 108 61 172 119 NC_003454:FN1997|5end_Transcriptional_regulator_499758..499988_POSITIVE 410 104 61 209 166 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 295 51 11 226 185 NC_003454:FN1221|5end_hypothetical_protein_1880344..1880574_POSITIVE 268 110 61 206 164 NC_003454:FN0496|5end_hypothetical_protein_1140910..1141140_POSITIVE 245 80 33 80 39 NC_003454:FN1332|5end_Bacterial_Peptide_Chain_Release_Factor_1_(RF-1)_1987163..1987393_NEGATIVE 244 99 58 159 118 NC_003454:FN1343|5end_seC-independent_protein_TATD_1997232..1997462_NEGATIVE 238 105 64 61 14 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 232 110 70 166 130 NC_003454:FN0082|5end_Ethanolamine_utilization_protein_eutM_720699..720929_POSITIVE 229 91 61 227 197 NC_003454:FN1844|5end_Ketoacyl_reductase_hetN_333593..333823_POSITIVE 225 45 11 200 165 NC_003454:FN0052|5end_Arsenate_reductase_688849..689079_POSITIVE 224 101 65 104 64 NC_003454:FN1286|5end_30S_ribosomal_protein_S13_1944074..1944304_NEGATIVE 219 108 63 220 178 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 215 106 71 172 140 NC_003454:FN0284|5end_16S_rRNA_processing_protein_rimM_913923..914153_NEGATIVE 214 94 63 181 149 NC_003454:FN1616|5end_transcription_antitermination_protein_NusB_126437..126667_NEGATIVE 210 99 51 62 8 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 208 97 51 166 110 NC_003454:FN0623|5end_Malonate_transporter_1281952..1282182_POSITIVE 203 106 64 53 14 NC_003454:FN0883|5end_hypothetical_protein_1544357..1544587_POSITIVE 203 105 63 164 116 NC_003454:FN2031|5end_Thiamine_biosynthesis_lipoprotein_apbE_537083..537313_NEGATIVE 202 105 73 82 44 NC_003454:FN0977|5end_Cobyric_acid_synthase_1630580..1630810_NEGATIVE 199 95 72 31 13 NC_003454:FN1463|5end_pyridoxine_biosynthesis_protein_2145002..2145232_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 600 104 65 40 1 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 508 104 70 35 1 NC_003454:FN0842|3end_hypothetical_protein_1502822..1502972_NEGATIVE 508 104 70 35 1 NC_003454:FN1890|3end_hypothetical_protein_373045..373195_NEGATIVE 456 108 61 76 23 NC_003454:FN1996|3end_Transporter_499742..499892_POSITIVE 416 103 61 79 41 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE 410 104 61 69 26 NC_003454:FN0865|3end_hypothetical_protein_1523040..1523190_NEGATIVE 396 100 57 78 35 NC_003454:FN1235|3end_Ankyrin_repeat_proteins_1892428..1892578_POSITIVE 327 49 3 67 24 NC_003454:FN1881|3end_Esterase_368250..368400_NEGATIVE 318 58 11 103 53 NC_003454:FN1220|3end_Cysteine_synthase_1880292..1880442_POSITIVE 309 44 11 80 47 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE 308 98 72 27 1 NC_003454:FN2053|3end_Serine/threonine_sodium_symporter_561228..561378_NEGATIVE 290 52 11 92 48 NC_003454:FN1880|3end_Dihydropteridine_reductase_368211..368361_POSITIVE 268 110 61 71 29 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 262 49 1 86 38 NC_003454:FN0501|3end_Arginase_1149587..1149737_NEGATIVE 245 80 33 79 38 NC_003454:FN1333|3end_hypothetical_protein_1987164..1987314_NEGATIVE 242 53 11 90 43 NC_003454:FN0738|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1396981..1397131_POSITIVE 240 54 11 104 46 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 238 105 64 59 12 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 231 56 15 104 48 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 228 60 11 85 35 NC_003454:FN0739|3end_Formiminotetrahydrofolate_cyclodeaminase_1397017..1397167_NEGATIVE