Origin IGS: tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaatctcttatccgaaattttatttcggataagtattaaagcacttaagatacattagggattttaagtgttttggtacttatgtaatgagggagggataaa Mask Tandem Repeat Region ================================================ tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Find is-nt database================================================ Query_seq: FN2016:FN2017|FN2016:FN2017:ATP-dependent Clp protease proteolytic subunit:Trigger factor, ppiase:<-<-:518939..519041 103 tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2016:FN2017|FN2016:FN2017:ATP-dependent Clp protease proteolytic subunit:Trigger factor, ppiase:<-<-:518939..519041 103 tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2016:FN2017|FN2016:FN2017:ATP-dependent Clp protease proteolytic subunit:Trigger factor, ppiase:<-<-:518939..519041 103 tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Predict ORF larger than 30AA ================================================ tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa 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================================================ tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -11.0 Tail_Score: -2.78384 Start: 21 End: 73 Full_Region: aaattttatttcgga taagtattaaagcacttaagatac attag ggattttaagtgttttggtactta tgtaatgagggaggg ....................taagtattaaagcacttaagatacattagggattttaagtgttttggtactta.............................. TransTerm Strand: - Conf: 73 HP_score: -8.3 Tail_Score: -3.54475 Start: 24 End: 70 Full_Region: ttttatttcggataa gtattaaagcacttaagatac attag ggattttaagtgttttggtac ttatgtaatgaggga .......................gtattaaagcacttaagatacattagggattttaagtgttttggtac................................. TransTerm Strand: - Conf: 69 HP_score: -5.4 Tail_Score: -4.38129 Start: 33 End: 61 Full_Region: ggataagtattaaag cacttaagatac attag ggattttaagtg ttttggtacttatgt ................................cacttaagatacattagggattttaagtg.......................................... Find igs database================================================ Query_seq: FN2016:FN2017|FN2016:FN2017:ATP-dependent Clp protease proteolytic subunit:Trigger factor, ppiase:<-<-:518939..519041 103 tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_003454_FN2016_FN2017|ATP-dependent Clp protease proteolytic subunit:Trigger factor, ppiase|NEGATIVE:NEGATIVE|[518939,519041]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa tttatccctccctcattacataagtaccaaaacacttaaaatccctaatgtatcttaagtgctttaatacttatccgaaataaaatttcggataagagattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCCCUCCCUCAUUACAUAAGUACCAAAACACUUAAAAUCCCUAAUGUAUCUUAAGUGCUUUAAUACUUAUCCGAAAUAAAAUUUCGGAUAAGAGAUUAA ...........(((........((((..(((.(((((((...............))))))).)))..))))((((((((((...)))))))))).)))..... (-19.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUCUCUUAUCCGAAAUUUUAUUUCGGAUAAGUAUUAAAGCACUUAAGAUACAUUAGGGAUUUUAAGUGUUUUGGUACUUAUGUAAUGAGGGAGGGAUAAA ...(((((((.((((((((...))))))))((((((((((((((((((((((.(.....).))))))))))))))))))))))..........)))))))... (-36.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 802 50 1 141 92 NC_003454:FN2016|5end_ATP-dependent_Clp_protease_proteolytic_subunit_518848..519078_NEGATIVE 265 49 1 68 11 NC_003454:FN0859|5end_hypothetical_protein_1521229..1521459_NEGATIVE 262 46 5 71 31 NC_003454:FN0470|5end_Putative_efflux_pump_component_MtrF_1114741..1114971_POSITIVE 218 99 57 224 180 NC_003454:FN0830|5end_hypothetical_protein_1490254..1490484_POSITIVE 205 54 11 61 25 NC_003454:FN1495|5end_hypothetical_protein_2174410..2174640_NEGATIVE 205 54 11 85 49 NC_003454:FN1494|5end_Rod_shape-determining_protein_mreC_2174386..2174616_NEGATIVE 204 37 1 133 93 NC_003454:FN0657|5end_Acetyltransferase_1314266..1314496_POSITIVE 196 66 35 128 97 NC_003454:FN0058|5end_Cysteine_desulfhydrase_693907..694137_POSITIVE 194 36 8 137 104 NC_003454:FN0943|5end_Sensory_Transduction_Protein_Kinase_1596800..1597030_POSITIVE 179 100 52 80 35 NC_003454:FN1116|5end_Peptidase_E_1759521..1759751_POSITIVE 178 14 1 73 60 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 175 69 27 66 16 NC_003454:FN2101|5end_Transporter_610246..610476_POSITIVE 175 99 62 135 98 NC_003454:FN1951|5end_ATPase_associated_with_chromosome_architecture/replication_458927..459157_NEGATIVE 173 45 12 39 8 NC_003454:FN1466|5end_hypothetical_protein_2148862..2149092_POSITIVE 173 15 1 109 94 NC_003454:FN0273|5end_Butyrate-acetoacetate_CoA-transferase_subunit_B_899423..899653_POSITIVE 172 48 1 185 141 NC_003454:FN0764|5end_Transporter,_LysE_family_1420327..1420557_POSITIVE 170 52 33 109 89 NC_003454:FN0192|5end_Dipeptide-binding_protein_817342..817572_POSITIVE 169 65 36 34 3 NC_003454:FN2087|5end_hypothetical_protein_599719..599949_NEGATIVE 167 35 4 107 72 NC_003454:FN1177|5end_hypothetical_protein_1838805..1839035_NEGATIVE 167 70 42 129 102 NC_003454:FN0480|5end_hypothetical_protein_1127454..1127684_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 54 11 60 24 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 196 66 35 41 10 NC_003454:FN0057|3end_Endonuclease_III_693900..694050_POSITIVE 194 36 8 147 114 NC_003454:FN0942|3end_Sensory_Transduction_Protein_Kinase_1596890..1597040_POSITIVE 179 100 52 78 33 NC_003454:FN1115|3end_Hypothetical_membrane-spanning_protein_1759599..1759749_POSITIVE 175 69 27 56 6 NC_003454:FN2100|3end_hypothetical_protein_610316..610466_POSITIVE 175 99 62 119 82 NC_003454:FN1952|3end_Na(+)-linked_D-alanine_glycine_permease_458943..459093_NEGATIVE 173 45 12 38 7 NC_003454:FN1465|3end_Permease_2148941..2149091_POSITIVE 173 15 1 109 94 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 167 35 4 119 84 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 167 70 42 127 100 NC_003454:FN0479|3end_RNA_polymerase_sigma-E_factor_1127532..1127682_POSITIVE 165 42 1 141 100 NC_003454:FN2076|3end_MunI_regulatory_protein_587536..587686_NEGATIVE 162 50 11 113 68 NC_003454:FN1209|3end_Hypothetical_RNA_binding_protein_1868615..1868765_NEGATIVE 157 89 44 41 3 NC_003454:FN0765|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_1421960..1422110_POSITIVE 157 34 8 75 57 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 156 78 41 35 5 NC_003454:FN0697|3end_Alanyl-tRNA_synthetase_1356675..1356825_POSITIVE 156 45 9 132 99 NC_003454:FN0524|3end_DNA_helicase_II_1176884..1177034_NEGATIVE 154 74 46 56 27 NC_003454:FN1935|3end_Adenine-specific_methyltransferase_436060..436210_NEGATIVE 153 51 22 43 14 NC_003454:FN0516|3end_Acriflavin_resistance_protein_E_1167003..1167153_NEGATIVE 153 18 7 133 122 NC_003454:FN1581|3end_DNA_mismatch_repair_protein_mutS_90895..91045_NEGATIVE 152 22 1 97 66 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE