Origin IGS: taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatcctccaattatcttattctaaaaaaataggttgttacatatctataatattaataaaaaatctggctagtaacgaactattttttatatatttatatgtaacaaccctttttta Mask Tandem Repeat Region ================================================ taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Find is-nt database================================================ Query_seq: FN1069:FN1070|FN1069:FN1070:DNA topoisomerase I:glucose-inhibited division protein A:->->:1717143..1717260 118 taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1069:FN1070|FN1069:FN1070:DNA topoisomerase I:glucose-inhibited division protein A:->->:1717143..1717260 118 taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1069:FN1070|FN1069:FN1070:DNA topoisomerase I:glucose-inhibited division protein A:->->:1717143..1717260 118 taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 3 End: 116 .. F L T T V Y L Y I F F L E N S A L N K I L I I S I Y C G I K K S Y S L Q L M .. taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat 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================================================ taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1069:FN1070|FN1069:FN1070:DNA topoisomerase I:glucose-inhibited division protein A:->->:1717143..1717260 118 taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_003454_FN1069_FN1070|DNA topoisomerase I:glucose-inhibited division protein A|POSITIVE:POSITIVE|[1717143,1717260]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctannnnnnnagaataagataattggaggatat taaaaaagggttgttacatataaatatataaaaaatagttcgttactagccagattttttattaatattatagatatgtaacaacctatttttttagaataagataattggaggatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGGGUUGUUACAUAUAAAUAUAUAAAAAAUAGUUCGUUACUAGCCAGAUUUUUUAUUAAUAUUAUAGAUAUGUAACAACCUAUUUUUUUAGAAUAAGAUAAUUGGAGGAUAU (((((((((((((((((((((.((((((((((((((.(((.......)))...)))))))))..)))))....))))))))))))))..)))))))...................... (-25.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCCUCCAAUUAUCUUAUUCUAAAAAAAUAGGUUGUUACAUAUCUAUAAUAUUAAUAAAAAAUCUGGCUAGUAACGAACUAUUUUUUAUAUAUUUAUAUGUAACAACCCUUUUUUA .........................(((((..(((((((((((((....(((((..((((((((......((((.....))))))))))))))))).)))))))))))))..))))). (-22.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 59 18 159 116 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 400 61 21 132 95 NC_003454:FN1440|5end_1-phosphofructokinase_2107238..2107468_POSITIVE 366 61 27 150 115 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 265 60 11 202 149 NC_003454:FN1603|5end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_113661..113891_NEGATIVE 252 59 20 195 155 NC_003454:FN1615|5end_Integral_membrane_protein_125125..125355_POSITIVE 244 61 25 42 5 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 230 61 30 143 112 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 216 61 31 48 18 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 209 108 61 184 138 NC_003454:FN1403|5end_Histidine_permease_2061743..2061973_POSITIVE 208 61 29 195 163 NC_003454:FN0798|5end_Fructose-1,6-bisphosphatase_1455835..1456065_POSITIVE 208 41 1 146 110 NC_003454:FN0340|5end_Hypothetical_membrane-spanning_Protein_973948..974178_NEGATIVE 201 58 16 172 134 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 188 87 43 133 85 NC_003454:FN0269|5end_Transposase_896041..896271_POSITIVE 186 58 16 197 153 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 181 106 77 195 162 NC_003454:FN0346|5end_hypothetical_protein_979267..979497_NEGATIVE 173 61 34 83 56 NC_003454:FN1922|5end_hypothetical_protein_419435..419665_NEGATIVE 172 86 46 67 39 NC_003454:FN0465|5end_hypothetical_protein_1110046..1110276_POSITIVE 170 87 41 134 89 NC_003454:FN1278|5end_Acetyltransferase_1937174..1937404_NEGATIVE 169 70 23 78 45 NC_003454:FN0985|5end_Phosphoribosylglycinamide_formyltransferase_1637857..1638087_NEGATIVE 166 61 31 156 126 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 61 21 59 22 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 276 59 38 22 1 NC_003454:FN0368|3end_adenylosuccinate_lyase_997038..997188_NEGATIVE 246 88 42 109 64 NC_003454:FN1815|3end_Transposase_295626..295776_NEGATIVE 244 50 1 59 7 NC_003454:FN1989|3end_Sodium-dependent_tyrosine_transporter_493827..493977_POSITIVE 230 61 30 36 5 NC_003454:FN0080|3end_ethanolamine_ammonia-lyase_small_subunit_720008..720158_POSITIVE 227 63 31 33 1 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 209 108 61 61 15 NC_003454:FN1402|3end_Hypothetical_membrane-spanning_protein_2061700..2061850_POSITIVE 208 41 1 41 5 NC_003454:FN0341|3end_transport_protein_974053..974203_NEGATIVE 207 94 52 75 36 NC_003454:FN0273|3end_Butyrate-acetoacetate_CoA-transferase_subunit_B_900162..900312_POSITIVE 192 41 1 83 36 NC_003454:FN0590|3end_N-acyl-L-amino_acid_amidohydrolase_1242856..1243006_NEGATIVE 188 87 43 98 50 NC_003454:FN0268|3end_DNA_repair_protein_recN_896086..896236_POSITIVE 183 69 23 46 4 NC_003454:FN0454|3end_Aldehyde_dehydrogenase_B_1101022..1101172_POSITIVE 177 19 3 53 37 NC_003454:FN1784|3end_hypothetical_protein_265735..265885_NEGATIVE 175 97 55 104 60 NC_003454:FN0120|3end_hypothetical_protein_752718..752868_NEGATIVE 173 41 1 68 29 NC_003454:FN0739|3end_Formiminotetrahydrofolate_cyclodeaminase_1397017..1397167_NEGATIVE 172 41 1 84 41 NC_003454:FN0017|3end_hypothetical_protein_655957..656107_POSITIVE 170 94 70 99 70 NC_003454:FN0874|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1534372..1534522_NEGATIVE 169 90 46 83 36 NC_003454:FN1428|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2096860..2097010_NEGATIVE 169 70 23 90 57 NC_003454:FN0986|3end_phosphoribosylaminoimidazole_synthetase_1637845..1637995_NEGATIVE 164 96 54 90 55 NC_003454:FN1069|3end_DNA_topoisomerase_I_1717082..1717232_POSITIVE