Origin IGS: agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attccttttcctcataaattaaataatctttatttttactatagctattatagcaaatatagtttatactgttaaggtattaaataaatattggagaagct Mask Tandem Repeat Region ================================================ agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Find is-nt database================================================ Query_seq: TDE0798:TDE0799|TDE0798:TDE0799:transporter, putative:glycerophosphoryl diester phosphodiesterase, putative:<-->:822648..822748 101 agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0798:TDE0799|TDE0798:TDE0799:transporter, putative:glycerophosphoryl diester phosphodiesterase, putative:<-->:822648..822748 101 agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0798:TDE0799|TDE0798:TDE0799:transporter, putative:glycerophosphoryl diester phosphodiesterase, putative:<-->:822648..822748 101 agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Predict ORF larger than 30AA ================================================ agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat 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: 88 Start: 26 End: 55 .........................CTTAACAGTATAAACTATATTTGCTATAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0798:TDE0799|TDE0798:TDE0799:transporter, putative:glycerophosphoryl diester phosphodiesterase, putative:<-->:822648..822748 101 agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002967_TDE0798_TDE0799|transporter, putative:glycerophosphoryl diester phosphodiesterase, putative|NEGATIVE:POSITIVE|[822648,822748]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat agcttctccaatatttatttaataccttaacagtataaactatatttgctataatagctatagtaaaaataaagattatttaatttatgaggaaaaggaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUCUCCAAUAUUUAUUUAAUACCUUAACAGUAUAAACUAUAUUUGCUAUAAUAGCUAUAGUAAAAAUAAAGAUUAUUUAAUUUAUGAGGAAAAGGAAU ..(((.(((.(((.(((..((((........(((....)))...(((((((((.....))))))))).......))))..)))..)))..))).))).... (-13.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCUUUUCCUCAUAAAUUAAAUAAUCUUUAUUUUUACUAUAGCUAUUAUAGCAAAUAUAGUUUAUACUGUUAAGGUAUUAAAUAAAUAUUGGAGAAGCU ....(((((((.............(((.(((((((.((((...((((...))))....(((((....)))))...))))..))))))).)))))))))).. (-14.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 709 50 1 141 92 NC_002967:TDE0798|5end_transporter,_putative_822557..822787_NEGATIVE 246 100 51 139 94 NC_002967:TDE0710|5end_hypothetical_protein_745432..745662_POSITIVE 223 66 25 60 22 NC_002967:TDE2321|5end_hypothetical_protein_2357301..2357531_NEGATIVE 207 69 25 155 102 NC_002967:TDE1231|5end_hypothetical_protein_1265203..1265433_NEGATIVE 192 70 21 166 108 NC_002967:TDE2006|5end_hypothetical_protein_2024421..2024651_POSITIVE 187 64 23 123 83 NC_002967:TDE2769|5end_flagellar_hook_assembly_protein_2823032..2823262_NEGATIVE 180 47 1 200 153 NC_002967:TDE2014|5end_ankyrin_repeat_protein_2036421..2036651_NEGATIVE 178 46 2 134 93 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 173 100 51 196 152 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 169 63 25 93 49 NC_002967:TDE2087|5end_translation_initiation_factor_IF-1_2115686..2115916_NEGATIVE 166 98 57 212 155 NC_002967:TDE1375|5end_pantetheine-phosphate_adenylyltransferase_1418081..1418311_POSITIVE 165 47 2 136 92 NC_002967:TDE1894|5end_ferredoxin_1914113..1914343_POSITIVE 165 22 2 28 9 NC_002967:TDE1307|5end_hypothetical_protein_1340954..1341184_POSITIVE 165 59 11 129 84 NC_002967:TDE0540|5end_hypothetical_protein_581464..581694_POSITIVE 162 75 32 178 137 NC_002967:TDE2540|5end_lipoprotein,_putative_2567981..2568211_NEGATIVE 160 59 11 230 180 NC_002967:TDE1274|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1309560..1309790_NEGATIVE 157 22 1 58 40 NC_002967:TDE0942|5end_long-chain-fatty-acid--CoA_ligase,_putative_964132..964362_POSITIVE 156 66 24 107 64 NC_002967:TDE1763|5end_hypothetical_protein_1811205..1811435_NEGATIVE 155 25 1 221 199 NC_002967:TDE1217|5end_flagellar_assembly_protein_1249511..1249741_POSITIVE 155 38 3 206 172 NC_002967:TDE0534|5end_hypothetical_protein_576513..576743_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 192 70 21 75 17 NC_002967:TDE2005|3end_hypothetical_protein_2024410..2024560_POSITIVE 187 64 23 111 71 NC_002967:TDE2770|3end_flagellar_hook-length_control_protein_FliK_2823044..2823194_NEGATIVE 178 46 2 141 100 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 167 50 4 139 85 NC_002967:TDE0347|3end_methyl-accepting_chemotaxis_protein_DmcA_388050..388200_NEGATIVE 165 59 11 127 82 NC_002967:TDE0539|3end_hypothetical_protein_581542..581692_POSITIVE 163 66 32 119 84 NC_002967:TDE0417|3end_hypothetical_protein_469489..469639_NEGATIVE 156 66 24 85 42 NC_002967:TDE1764|3end_hypothetical_protein_1811227..1811377_NEGATIVE 153 50 7 141 103 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 152 35 4 148 113 NC_002967:TDE2038|3end_UVR_domain_protein_2067704..2067854_NEGATIVE 148 66 39 27 3 NC_002967:TDE2322|3end_flagellar_protein_FliL-related_protein_2357334..2357484_NEGATIVE 146 99 56 68 24 NC_002967:TDE1466|3end_oxygen-independent_coproporphyrinogen_III_oxidase,_putative_1515517..1515667_POSITIVE 144 34 4 117 87 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 144 14 2 18 6 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 143 50 2 122 80 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 142 33 4 109 79 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 142 27 4 39 14 NC_002967:TDE1353|3end_rod_shape-determining_protein_RodA_1394931..1395081_POSITIVE 142 33 3 107 81 NC_002967:TDE1156|3end_hypothetical_protein_1191621..1191771_NEGATIVE 140 50 7 53 3 NC_002967:TDE2314|3end_hypothetical_protein_2352379..2352529_POSITIVE 139 92 56 143 108 NC_002967:TDE2702|3end_hypothetical_protein_2745832..2745982_NEGATIVE 139 34 4 77 50 NC_002967:TDE1330|3end_conserved_hypothetical_protein_TIGR00244_1365914..1366064_POSITIVE