Origin IGS: aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accagcctccttgtgatatagtaatagtgtaccatatttttaaaaaaaatacacccagaaatggcctttaatataaaaaaatagccgattagactaatcggctatttaaatt Mask Tandem Repeat Region ================================================ aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Find is-nt database================================================ Query_seq: TDE0011:TDE0012|TDE0011:TDE0012:alkyl hydroperoxide reductase/peroxiredoxin:carbon starvation protein CstA, putative:->->:16196..16307 112 aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0011:TDE0012|TDE0011:TDE0012:alkyl hydroperoxide reductase/peroxiredoxin:carbon starvation protein CstA, putative:->->:16196..16307 112 aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0011:TDE0012|TDE0011:TDE0012:alkyl hydroperoxide reductase/peroxiredoxin:carbon starvation protein CstA, putative:->->:16196..16307 112 aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 15 End: 110 .............. M S L I G Y F F I L K A I S G C I F F K N M V H Y Y Y I T R R L .. aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt 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================================================ aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0011:TDE0012|TDE0011:TDE0012:alkyl hydroperoxide reductase/peroxiredoxin:carbon starvation protein CstA, putative:->->:16196..16307 112 aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE0011_TDE0012|alkyl hydroperoxide reductase/peroxiredoxin:carbon starvation protein CstA, putative|POSITIVE:POSITIVE|[16196,16307]|112 HSP 1 e-value: 1.0E-30 bit: 133.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aatttaaatagccgattagtctaatcggctannnnnnnatattaaaggccatttctgggtgtannnnnnnnaaaaatatggtacactattactatatcacaaggaggctggt aatttaaatagccgattagtctaatcggctatttttttatattaaaggccatttctgggtgtattttttttaaaaatatggtacactattactatatcacaaggaggctggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAAAUAGCCGAUUAGUCUAAUCGGCUAUUUUUUUAUAUUAAAGGCCAUUUCUGGGUGUAUUUUUUUUAAAAAUAUGGUACACUAUUACUAUAUCACAAGGAGGCUGGU .....(((((((((((((...))))))))))))).............(((((((((..(((..............((((((((......)))))))))))..))))).)))) (-29.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAGCCUCCUUGUGAUAUAGUAAUAGUGUACCAUAUUUUUAAAAAAAAUACACCCAGAAAUGGCCUUUAAUAUAAAAAAAUAGCCGAUUAGACUAAUCGGCUAUUUAAAUU ..............(((((.(((......))).)))))................(((....)))..............(((((((((((((...)))))))))))))..... (-20.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 50 11 58 12 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 292 60 12 158 104 NC_002967:TDE2206|5end_hypothetical_protein_2245364..2245594_NEGATIVE 290 70 26 167 120 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 269 59 11 70 15 NC_002967:TDE2107|5end_dihydroorotase,_putative_2132874..2133104_NEGATIVE 266 59 13 117 71 NC_002967:TDE0739|5end_hypothetical_protein_775790..776020_POSITIVE 254 57 12 119 75 NC_002967:TDE0767|5end_ribosomal_protein_L3_806355..806585_POSITIVE 253 60 11 188 149 NC_002967:TDE2245|5end_DNA_topoisomerase_IV_subunit_B_2284240..2284470_POSITIVE 248 60 13 192 148 NC_002967:TDE0723|5end_hypothetical_protein_760304..760534_POSITIVE 246 57 11 42 6 NC_002967:TDE2221|5end_hypothetical_protein_2262684..2262914_POSITIVE 240 57 11 66 23 NC_002967:TDE1163|5end_hypothetical_protein_1197930..1198160_NEGATIVE 238 56 12 170 106 NC_002967:TDE2016|5end_hypothetical_protein_2038894..2039124_NEGATIVE 235 48 10 194 157 NC_002967:TDE2159|5end_hypothetical_protein_2193189..2193419_POSITIVE 231 58 24 195 161 NC_002967:TDE1544|5end_mannosyltransferase,_putative_1587154..1587384_POSITIVE 228 57 12 225 173 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 224 50 11 57 22 NC_002967:TDE1740|5end_hypothetical_protein_1792785..1793015_NEGATIVE 224 30 8 77 59 NC_002967:TDE0846|5end_hypothetical_protein_868623..868853_POSITIVE 218 70 26 184 132 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 217 58 11 225 183 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 212 60 22 211 169 NC_002967:TDE2702|5end_hypothetical_protein_2747574..2747804_NEGATIVE 212 60 11 188 131 NC_002967:TDE0240|5end_glycine_reductase_complex_protein_GrdC_274533..274763_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 41 6 95 57 NC_002967:TDE0011|3end_alkyl_hydroperoxide_reductase/peroxiredoxin_16135..16285_POSITIVE 265 50 12 145 102 NC_002967:TDE2207|3end_hypothetical_protein_2245366..2245516_NEGATIVE 256 52 11 47 3 NC_002967:TDE2445|3end_DNA-binding_protein_2474667..2474817_POSITIVE 254 57 12 56 12 NC_002967:TDE0766|3end_30S_ribosomal_protein_S10_806372..806522_POSITIVE 249 50 11 126 86 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 248 41 10 61 19 NC_002967:TDE0138|3end_alkyldihydroxyacetonephosphate_synthase,_putative_160061..160211_POSITIVE 240 57 11 63 20 NC_002967:TDE1164|3end_hypothetical_protein_1197933..1198083_NEGATIVE 233 40 2 94 46 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 231 58 24 131 97 NC_002967:TDE1543|3end_conserved_hypothetical_protein_TIGR00247_1587170..1587320_POSITIVE 229 60 13 144 99 NC_002967:TDE2646|3end_ABC_transporter,_ATP-binding_protein,_putative_2686030..2686180_POSITIVE 229 61 27 45 4 NC_002967:TDE2108|3end_hypothetical_protein_2132902..2133052_NEGATIVE 227 59 11 109 61 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 221 57 13 121 72 NC_002967:TDE2725|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2782240..2782390_NEGATIVE 214 69 23 124 79 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 210 56 20 116 74 NC_002967:TDE0028|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_34056..34206_NEGATIVE 209 45 10 84 42 NC_002967:TDE0139|3end_hypothetical_protein_160121..160271_NEGATIVE 208 49 11 98 56 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 207 49 10 57 10 NC_002967:TDE1884|3end_hypothetical_protein_1905874..1906024_NEGATIVE 207 54 12 59 23 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 203 58 11 113 68 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE