Origin IGS: atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatagaatagctattgcatttttttataaatgtgatagctatattttttaaatagttttcttaaatttgcaataactattatttagaggtataatataaaattattagaaatcaagggggaaaaat Mask Tandem Repeat Region ================================================ atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Find is-nt database================================================ Query_seq: FN1926:FN1927|FN1926:FN1927:Nitrogen regulatory IIA protein:DEGV protein:<-<-:425378..425504 127 atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1926:FN1927|FN1926:FN1927:Nitrogen regulatory IIA protein:DEGV protein:<-<-:425378..425504 127 atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1926:FN1927|FN1926:FN1927:Nitrogen regulatory IIA protein:DEGV protein:<-<-:425378..425504 127 atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Predict ORF larger than 30AA ================================================ atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca 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: 89 Start: 32 End: 61 ...............................TTTGCAATAACTATTATTTAGAGGTATAAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1926:FN1927|FN1926:FN1927:Nitrogen regulatory IIA protein:DEGV protein:<-<-:425378..425504 127 atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_003454_FN1926_FN1927|Nitrogen regulatory IIA protein:DEGV protein|NEGATIVE:NEGATIVE|[425378,425504]|127 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttatnnnnnnntgcaatagctattctatca atttttcccccttgatttctaataattttatattatacctctaaataatagttattgcaaatttaagaaaactatttaaaaaatatagctatcacatttataaaaaaatgcaatagctattctatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCCCCCUUGAUUUCUAAUAAUUUUAUAUUAUACCUCUAAAUAAUAGUUAUUGCAAAUUUAAGAAAACUAUUUAAAAAAUAUAGCUAUCACAUUUAUAAAAAAAUGCAAUAGCUAUUCUAUCA ..........((((((((.(((((((....((((((........))))))))))))).))).))))).................((((((((..(((((......)))))..))))))))....... (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAGAAUAGCUAUUGCAUUUUUUUAUAAAUGUGAUAGCUAUAUUUUUUAAAUAGUUUUCUUAAAUUUGCAAUAACUAUUAUUUAGAGGUAUAAUAUAAAAUUAUUAGAAAUCAAGGGGGAAAAAU .......((((((((..(((((......)))))..)))))))).............(((((((...((((......(((.....))).....(((((......))))).....)))).))))))).. (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 656 50 1 141 92 NC_003454:FN1926|5end_Nitrogen_regulatory_IIA_protein_425287..425517_NEGATIVE 230 42 4 98 67 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 219 46 12 106 72 NC_003454:FN1501|5end_Nickel_transport_ATP-binding_protein_nikD_6710..6940_NEGATIVE 202 58 17 118 77 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 200 40 2 135 94 NC_003454:FN1540|5end_Iron-sulfur_cluster-binding_protein_53055..53285_POSITIVE 196 27 1 176 143 NC_003454:FN0611|5end_Threonyl-tRNA_synthetase_1268359..1268589_POSITIVE 193 58 16 152 109 NC_003454:FN0269|5end_Transposase_896041..896271_POSITIVE 190 30 1 118 90 NC_003454:FN0037|5end_hypothetical_protein_678061..678291_NEGATIVE 186 42 2 106 59 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 186 20 1 114 95 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 177 45 1 141 90 NC_003454:FN1942|5end_Hypothetical_cytosolic_protein_444689..444919_NEGATIVE 177 43 7 141 100 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 175 43 2 205 168 NC_003454:FN0419|5end_aspartate_carbamoyltransferase_catalytic_subunit_1059713..1059943_POSITIVE 174 40 1 133 90 NC_003454:FN0606|5end_Translation_initiation_inhibitor_1261014..1261244_POSITIVE 174 43 4 156 120 NC_003454:FN0459|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1104609..1104839_POSITIVE 173 43 3 99 66 NC_003454:FN0950|5end_Precorrin-6X_reductase_1607775..1608005_NEGATIVE 173 65 26 213 174 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 173 35 1 127 93 NC_003454:FN1851|5end_Ribonuclease_PH_340179..340409_POSITIVE 172 36 1 155 117 NC_003454:FN2061|5end_Hypothetical_membrane-spanning_protein_574046..574276_NEGATIVE 172 36 1 155 117 NC_003454:FN2050|5end_Hypothetical_membrane-spanning_protein_559970..560200_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 46 12 109 75 NC_003454:FN1502|3end_Nickel_transport_system_permease_protein_nikC_6707..6857_NEGATIVE 202 58 17 103 62 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 200 40 2 92 51 NC_003454:FN1539|3end_Iron-sulfur_cluster-binding_protein_53092..53242_POSITIVE 196 27 1 99 66 NC_003454:FN0610|3end_hypothetical_protein_1268362..1268512_POSITIVE 193 58 16 117 74 NC_003454:FN0268|3end_DNA_repair_protein_recN_896086..896236_POSITIVE 191 120 72 79 33 NC_003454:FN0059|3end_NifU_protein_695619..695769_POSITIVE 186 20 1 112 93 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 177 43 7 140 99 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE 175 43 2 143 106 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 174 58 12 111 52 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 174 40 1 136 93 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 174 43 4 112 76 NC_003454:FN0458|3end_hypothetical_protein_1104645..1104795_POSITIVE 173 43 3 127 94 NC_003454:FN0951|3end_Precorrin-3B_C17-methyltransferase_1607747..1607897_NEGATIVE 173 35 1 82 48 NC_003454:FN1850|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_340214..340364_POSITIVE 172 36 1 94 56 NC_003454:FN2062|3end_hypothetical_protein_574107..574257_NEGATIVE 172 36 1 94 56 NC_003454:FN2051|3end_hypothetical_protein_560031..560181_NEGATIVE 170 40 8 63 29 NC_003454:FN0619|3end_Small-conductance_mechanosensitive_channel_1278810..1278960_NEGATIVE 169 46 1 64 20 NC_003454:FN0767|3end_Hemin-binding_periplasmic_protein_hmuT_precursor_1423537..1423687_POSITIVE 169 47 10 90 44 NC_003454:FN1838|3end_Glycerol_uptake_facilitator_protein_328333..328483_POSITIVE 168 59 12 101 52 NC_003454:FN1483|3end_adenine_phosphoribosyltransferase_2166011..2166161_NEGATIVE