Origin IGS: acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gccttgataaattaaaaaatatatgttagatttatagtaattactaactatttgtaaaaaataaatggagggattaatatgaaaaaaattttatgtgctttatttttaactttgtttttaagttcctgt Mask Tandem Repeat Region ================================================ acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Find is-nt database================================================ Query_seq: FN0316:FN0317|FN0316:FN0317:hypothetical protein:tryptophan synthase subunit beta:<-<-:953780..953908 129 acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0316:FN0317|FN0316:FN0317:hypothetical protein:tryptophan synthase subunit beta:<-<-:953780..953908 129 acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0316:FN0317|FN0316:FN0317:hypothetical protein:tryptophan synthase subunit beta:<-<-:953780..953908 129 acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Predict ORF larger than 30AA ================================================ acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc 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: 98 End: 127 .................................................................................................CTTGATAAATTAAAAAATATATGTTAGATT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0316:FN0317|FN0316:FN0317:hypothetical protein:tryptophan synthase subunit beta:<-<-:953780..953908 129 acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_003454_FN0316_FN0317|hypothetical protein:tryptophan synthase subunit beta|NEGATIVE:NEGATIVE|[953780,953908]|129 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 acaggaacttaaaaacaaagttaaaaataaagcacataaaannnnnnncatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc acaggaacttaaaaacaaagttaaaaataaagcacataaaatttttttcatattaatccctccatttattttttacaaatagttagtaattactataaatctaacatatattttttaatttatcaaggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGGAACUUAAAAACAAAGUUAAAAAUAAAGCACAUAAAAUUUUUUUCAUAUUAAUCCCUCCAUUUAUUUUUUACAAAUAGUUAGUAAUUACUAUAAAUCUAACAUAUAUUUUUUAAUUUAUCAAGGC ........(((((((....((.(((((((((.................................))))))))).)).....(((((..............)))))......)))))))........... ( -8.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUUGAUAAAUUAAAAAAUAUAUGUUAGAUUUAUAGUAAUUACUAACUAUUUGUAAAAAAUAAAUGGAGGGAUUAAUAUGAAAAAAAUUUUAUGUGCUUUAUUUUUAACUUUGUUUUUAAGUUCCUGU .........((((.(((((((...((((((..((.(((.....((..((((((((.....))))))))..))....((((((((....))))))))))).))..))))))..))))))).))))..... (-19.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 643 80 31 171 122 NC_003454:FN0316|5end_hypothetical_protein_953689..953919_NEGATIVE 302 68 24 111 64 NC_003454:FN0481|5end_hypothetical_protein_1127777..1128007_POSITIVE 270 63 27 79 44 NC_003454:FN1177|5end_hypothetical_protein_1838805..1839035_NEGATIVE 239 77 33 123 68 NC_003454:FN0575|5end_hypothetical_protein_1225331..1225561_POSITIVE 234 72 36 113 75 NC_003454:FN0941|5end_Gamma-glutamyltranspeptidase_1595266..1595496_NEGATIVE 233 75 32 152 111 NC_003454:FN0247|5end_Hypothetical_cytosolic_protein_870707..870937_POSITIVE 233 73 31 121 75 NC_003454:FN1692|5end_Glycosyl_transferase_188589..188819_NEGATIVE 232 66 29 178 136 NC_003454:FN0774|5end_Hypothetical_cytosolic_protein_1429692..1429922_POSITIVE 232 90 41 141 102 NC_003454:FN0579|5end_Hypothetical_cytosolic_protein_1229803..1230033_POSITIVE 230 84 46 137 92 NC_003454:FN0064|5end_Hypothetical_cytosolic_protein_699489..699719_POSITIVE 227 89 45 131 85 NC_003454:FN1035|5end_Iron-sulfur_flavoprotein_1688280..1688510_POSITIVE 227 67 32 106 73 NC_003454:FN0023|5end_Short-chain_fatty_acids_transporter_661201..661431_POSITIVE 227 74 31 149 103 NC_003454:FN2052|5end_hypothetical_protein_560943..561173_NEGATIVE 224 74 46 115 86 NC_003454:FN1869|5end_hypothetical_protein_360839..361069_NEGATIVE 223 77 39 118 77 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 219 64 29 101 63 NC_003454:FN0738|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1395846..1396076_POSITIVE 217 75 37 114 77 NC_003454:FN0929|5end_ATP/GTP_hydrolase_1583468..1583698_NEGATIVE 217 60 12 102 48 NC_003454:FN2119|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628052..628282_NEGATIVE 215 67 46 106 86 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 215 76 32 120 72 NC_003454:FN0854|5end_Glucose-1-phosphate_adenylyltransferase_1513487..1513717_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 68 24 93 46 NC_003454:FN0480|3end_hypothetical_protein_1127839..1127989_POSITIVE 270 63 27 91 56 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 233 75 32 45 4 NC_003454:FN0245|3end_Copper-exporting_ATPase_870680..870830_POSITIVE 233 73 31 124 78 NC_003454:FN1693|3end_hypothetical_protein_188586..188736_NEGATIVE 232 90 41 123 84 NC_003454:FN0578|3end_ATP-dependent_DNA_helicase_recQ_1229865..1230015_POSITIVE 227 89 45 116 70 NC_003454:FN1034|3end_Transcriptional_regulator,_TetR_family_1688345..1688495_POSITIVE 223 77 39 116 75 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 217 75 37 100 63 NC_003454:FN0930|3end_Glycerol-3-phosphate_cytidylyltransferase_1583482..1583632_NEGATIVE 215 67 46 91 71 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 215 76 32 99 51 NC_003454:FN0855|3end_glucose-1-phosphate_adenylyltransferase_1513508..1513658_NEGATIVE 214 66 31 41 1 NC_003454:FN0773|3end_hypothetical_protein_1429635..1429785_POSITIVE 209 80 32 72 29 NC_003454:FN0336|3end_hypothetical_protein_969748..969898_NEGATIVE 206 68 45 93 73 NC_003454:FN1928|3end_Transcriptional_regulator,_MerR_family_427964..428114_NEGATIVE 198 69 31 94 56 NC_003454:FN1434|3end_Tetratricopeptide_repeat_family_protein_2102538..2102688_NEGATIVE 197 86 42 122 79 NC_003454:FN1198|3end_Transporter_1857679..1857829_NEGATIVE 195 71 40 96 65 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 193 74 40 99 61 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 193 74 37 99 63 NC_003454:FN1686|3end_Spore_coat_polysaccharide_biosynthesis_protein_spsF_181027..181177_NEGATIVE 193 73 36 98 60 NC_003454:FN1528|3end_hypothetical_protein_42588..42738_NEGATIVE 191 67 34 41 10 NC_003454:FN0534|3end_hypothetical_protein_1189366..1189516_POSITIVE