Origin IGS: aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatctttaggaagaaagaagatgcgcccttcttcttccttttttttactgctaagagttgatgcttaaaacgttaaactatatttagatgtcacggatgatgtctattttaaagccaaggaggtttttt Mask Tandem Repeat Region ================================================ aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Find is-nt database================================================ Query_seq: TDE1473:TDE1474|TDE1473:TDE1474:flagellin FlaG, putative:hypothetical protein:<-<-:1521222..1521350 129 aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1473:TDE1474|TDE1473:TDE1474:flagellin FlaG, putative:hypothetical protein:<-<-:1521222..1521350 129 aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1473:TDE1474|TDE1473:TDE1474:flagellin FlaG, putative:hypothetical protein:<-<-:1521222..1521350 129 aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Predict ORF larger than 30AA ================================================ aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt 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================================================ aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1473:TDE1474|TDE1473:TDE1474:flagellin FlaG, putative:hypothetical protein:<-<-:1521222..1521350 129 aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002967_TDE1473_TDE1474|flagellin FlaG, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1521222,1521350]|129 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtnnnnnnnnggaagaagaagggcgcatcttctttcttcctaaagatt aaaaaacctccttggctttaaaatagacatcatccgtgacatctaaatatagtttaacgttttaagcatcaactcttagcagtaaaaaaaaggaagaagaagggcgcatcttctttcttcctaaagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACCUCCUUGGCUUUAAAAUAGACAUCAUCCGUGACAUCUAAAUAUAGUUUAACGUUUUAAGCAUCAACUCUUAGCAGUAAAAAAAAGGAAGAAGAAGGGCGCAUCUUCUUUCUUCCUAAAGAUU ..............(((......((((..(((....)))..))))......((((((....))))))..........)))..........(((((((((((((.....))))).))))))))....... (-23.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUUUAGGAAGAAAGAAGAUGCGCCCUUCUUCUUCCUUUUUUUUACUGCUAAGAGUUGAUGCUUAAAACGUUAAACUAUAUUUAGAUGUCACGGAUGAUGUCUAUUUUAAAGCCAAGGAGGUUUUUU (((((((.(((((((.((((.......)))))))))))...........(((...((((((((.......)))).)))).....(((((((((....)))))))))......)))...))))))).... (-27.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 110 61 201 152 NC_002967:TDE1473|5end_flagellin_FlaG,_putative_1521131..1521361_NEGATIVE 284 118 79 167 123 NC_002967:TDE1899|5end_hypothetical_protein_1921088..1921318_NEGATIVE 269 97 51 67 24 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 258 35 7 35 5 NC_002967:TDE1363|5end_nitroreductase_family_protein_1404635..1404865_NEGATIVE 253 112 90 46 24 NC_002967:TDE2283|5end_permease,_putative_2320917..2321147_NEGATIVE 241 110 68 229 185 NC_002967:TDE2303|5end_hypothetical_protein_2343055..2343285_POSITIVE 233 43 9 197 158 NC_002967:TDE1722|5end_hypothetical_protein_1776085..1776315_POSITIVE 229 43 9 225 191 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 224 97 55 68 22 NC_002967:TDE2615|5end_signal_peptidase_II_2657667..2657897_NEGATIVE 221 102 73 64 31 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 221 120 91 37 1 NC_002967:TDE0436|5end_Recombination_protein_O_492133..492363_NEGATIVE 219 44 7 148 106 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 215 70 26 164 116 NC_002967:TDE0181|5end_methyl-accepting_chemotaxis_protein_215077..215307_NEGATIVE 212 48 5 205 161 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 207 44 11 116 65 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 204 108 66 63 15 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 203 119 79 72 22 NC_002967:TDE1723|5end_hypothetical_protein_1776635..1776865_POSITIVE 203 116 92 47 17 NC_002967:TDE0786|5end_ribosomal_protein_L15_814602..814832_POSITIVE 203 100 57 55 9 NC_002967:TDE0732|5end_hypothetical_protein_772730..772960_NEGATIVE 202 44 7 166 127 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 112 90 38 16 NC_002967:TDE2284|3end_efflux_transporter,_RND_family,_MFP_subunit_2320925..2321075_NEGATIVE 245 116 73 49 3 NC_002967:TDE0708|3end_nitroreductase_family_protein_744495..744645_POSITIVE 239 110 66 108 51 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 224 97 55 55 9 NC_002967:TDE2616|3end_cyclic_nucleotide-binding_protein_2657680..2657830_NEGATIVE 221 66 21 66 20 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 219 44 7 142 100 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 217 120 89 100 67 NC_002967:TDE2327|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2362048..2362198_NEGATIVE 215 70 26 107 59 NC_002967:TDE0182|3end_ABC_transporter,_ATP-binding_protein_215134..215284_NEGATIVE 206 120 91 49 18 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 204 108 66 62 14 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 203 116 92 47 17 NC_002967:TDE0785|3end_ribosomal_protein_L30_814682..814832_POSITIVE 201 69 25 102 57 NC_002967:TDE0380|3end_hypothetical_protein_433982..434132_POSITIVE 199 80 32 137 79 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 199 118 74 61 19 NC_002967:TDE0132|3end_hypothetical_protein_152296..152446_POSITIVE 198 80 42 109 74 NC_002967:TDE1577|3end_lipoprotein,_putative_1625446..1625596_POSITIVE 197 44 9 142 98 NC_002967:TDE0986|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014121..1014271_POSITIVE 196 119 92 39 15 NC_002967:TDE0114|3end_iron-dependent_transcriptional_regulator_133581..133731_NEGATIVE 192 107 73 85 56 NC_002967:TDE0493|3end_hypothetical_protein_548581..548731_NEGATIVE 192 90 44 139 87 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 191 120 91 34 6 NC_002967:TDE0437|3end_PBS_lyase_HEAT-like_repeat_domain_protein_492136..492286_NEGATIVE