Origin IGS: tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagaccgagaagctgaggttataaaaactaaaaggagttgtctcatttgagaataacggctctttgtcaactgtagtgggttggtggaaaattataccctggagaggaccaaattggttctctccttttaaatattgaaaaaaccattggcagtggacatactttaagactatatatttctgaaactagtttcacaatacaaatattgacatgcaattattaattggtggattttaagttgacatctacaaaggttaatgttagaatacattcaaaaatatatttga Mask Tandem Repeat Region ================================================ tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Find is-nt database================================================ Query_seq: SSA_2026:SSA_2027|SSA_2026:SSA_2027:Cadmium resistance transporter, putative:P-type ATPase-metal/cation transport (probably copper), putative:<-<-:2032912..2033198 287 tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2026:SSA_2027|SSA_2026:SSA_2027:Cadmium resistance transporter, putative:P-type ATPase-metal/cation transport (probably copper), putative:<-<-:2032912..2033198 287 tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2026:SSA_2027|SSA_2026:SSA_2027:Cadmium resistance transporter, putative:P-type ATPase-metal/cation transport (probably copper), putative:<-<-:2032912..2033198 287 tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 17 End: 115 ................ M Y S N I N L C R C Q L K I H Q L I I A C Q Y L Y C E T S F R N I ............................................................................................................................................................................ Protein_Len: 49 Strand: + Start: 72 End: 218 ....................................................................... M H V N I C I V K L V S E I Y S L K V C P L P M V F S I F K R R E P I W S S P G Y N F P P T H Y S ..................................................................... Protein_Len: 57 Strand: + Start: 115 End: 285 .................................................................................................................. M V L K Y V H C Q W F F Q Y L K G E N Q F G P L Q G I I F H Q P T T V D K E P L F S N E T T P F S F Y N L S F S V .. Protein_Len: 36 Strand: - Start: 68 End: 175 ................................................................... Y N C T L I Q I T F S T E S I Y L R L T H G S G I T K E I N L L L S G M ................................................................................................................ tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc 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: 92 Start: 21 End: 50 ....................GTTGACATCTACAAAGGTTAATGTTAGAAT............................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 196 End: 225 ...................................................................................................................................................................................................TTTGTCAACTGTAGTGGGTTGGTGGAAAAT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.1 Tail_Score: -4.28254 Start: 163 End: 187 Full_Region: ggaaaattataccct ggagaggacca aat tggttctctcc ttttaaatattgaaa ..................................................................................................................................................................ggagaggaccaaattggttctctcc.................................................................................................... Find igs database================================================ Query_seq: SSA_2026:SSA_2027|SSA_2026:SSA_2027:Cadmium resistance transporter, putative:P-type ATPase-metal/cation transport (probably copper), putative:<-<-:2032912..2033198 287 tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Intra-Species Hit: Count: 1 Min: 1 Max: 287 Len: 287 Subject: NC_009009_SSA_2026_SSA_2027|Cadmium resistance transporter, putative:P-type ATPase-metal/cation transport (probably copper), putative|NEGATIVE:NEGATIVE|[2032912,2033198]|287 HSP 1 e-value: 1.0E-161 bit: 569.0 Len: 287 Query Start:1 Query End:287 Subject Strand: POSITIVE Subject Start: 1 Subject End: 287 tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc tcaaatatatttttgaatgtattctaacattaacctttgtagatgtcaacttaaaatccaccaattaataattgcatgtcaatatttgtattgtgaaactagtttcagaaatatatagtcttaaagtatgtccactgccaatggttttttcaatatttaaaaggagagaaccaatttggtcctctccagggtataattttccaccaacccactacagttgacaaagagccgttattctcaaatgagacaactccttttagtttttataacctcagcttctcggtctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUAUAUUUUUGAAUGUAUUCUAACAUUAACCUUUGUAGAUGUCAACUUAAAAUCCACCAAUUAAUAAUUGCAUGUCAAUAUUUGUAUUGUGAAACUAGUUUCAGAAAUAUAUAGUCUUAAAGUAUGUCCACUGCCAAUGGUUUUUUCAAUAUUUAAAAGGAGAGAACCAAUUUGGUCCUCUCCAGGGUAUAAUUUUCCACCAACCCACUACAGUUGACAAAGAGCCGUUAUUCUCAAAUGAGACAACUCCUUUUAGUUUUUAUAACCUCAGCUUCUCGGUCUC (((((......))))).((...((((.((........))))))...))...........(((..............(((((((....((((((.(((((((....(((..((((((.........))))))...)))....)))))))..))))))......((((((.(((.....))).)))))).((((..............))))......)))))))..(((..(((((.((.(((.(((....))).))).)).....))))))))........)))... (-53.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGACCGAGAAGCUGAGGUUAUAAAAACUAAAAGGAGUUGUCUCAUUUGAGAAUAACGGCUCUUUGUCAACUGUAGUGGGUUGGUGGAAAAUUAUACCCUGGAGAGGACCAAAUUGGUUCUCUCCUUUUAAAUAUUGAAAAAACCAUUGGCAGUGGACAUACUUUAAGACUAUAUAUUUCUGAAACUAGUUUCACAAUACAAAUAUUGACAUGCAAUUAUUAAUUGGUGGAUUUUAAGUUGACAUCUACAAAGGUUAAUGUUAGAAUACAUUCAAAAAUAUAUUUGA ..((((..........)))).......((.((((((((((((((....))))....))))))..((((.((((((((((...((((........))))..((((((((((.....))))))))))..................))))).))))).))))..)))).))...((((((((.((((....((....(((((....)))))....))...((((((((.((((((.((.....)).))))))...))))))))..........)))).)))))))).... (-69.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 790 140 91 231 182 NC_009009:SSA_2026|5end_Cadmium_resistance_transporter,_putative_2032821..2033051_NEGATIVE 611 50 1 153 104 NC_009009:SSA_2288|5end_Cadmium_resistance_transporter,_putative_2290461..2290691_POSITIVE 310 195 162 166 135 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 281 190 158 145 118 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 271 210 163 170 124 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 270 233 207 180 154 NC_009009:SSA_0732|5end_Transposase,_putative_715896..716126_NEGATIVE 263 204 165 200 151 NC_009009:SSA_1397|5end_hypothetical_protein_1410589..1410819_POSITIVE 262 210 162 196 149 NC_009009:SSA_1051|5end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1065658..1065888_POSITIVE 262 238 197 142 94 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 261 263 222 193 149 NC_009009:SSA_1073|5end_Gamma-glutamyl_phosphate_reductase,_putative_1090886..1091116_POSITIVE 253 220 171 224 164 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 252 266 225 118 74 NC_009009:SSA_1241|5end_Orotidine-5'-phosphate_decarboxylase,_putative_1266201..1266431_NEGATIVE 252 229 181 221 172 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 252 158 117 135 95 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 251 179 131 61 18 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 247 238 201 62 12 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 246 87 42 65 17 NC_009009:SSA_1200|5end_Formate--tetrahydrofolate_ligase,_putative_1225591..1225821_NEGATIVE 245 184 141 104 54 NC_009009:SSA_2138|5end_RNA-binding_protein,_Jag_family,_putative_2139487..2139717_NEGATIVE 245 230 182 57 9 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 243 230 189 184 146 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 620 230 181 69 20 NC_009009:SSA_1482|3end_Pullulanase,_putative_1486949..1487099_NEGATIVE 432 248 202 48 10 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 415 230 207 24 1 NC_009009:SSA_1480|3end_hypothetical_protein_1483960..1484110_NEGATIVE 281 190 158 50 23 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 262 238 197 67 19 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 255 254 216 40 3 NC_009009:SSA_2204|3end_hypothetical_protein_2205507..2205657_POSITIVE 253 240 197 128 75 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 252 158 117 127 87 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 245 184 141 82 32 NC_009009:SSA_2139|3end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2139509..2139659_NEGATIVE 244 185 145 83 51 NC_009009:SSA_0146|3end_DNA_repair_ATPase,_putative_142159..142309_POSITIVE 243 230 189 119 81 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 240 248 204 115 67 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 240 238 198 64 27 NC_009009:SSA_0313|3end_Conserved_uncharacterized_protein_308389..308539_NEGATIVE 236 190 143 78 18 NC_009009:SSA_1828|3end_Glycerol_uptake_facilitator_protein,_putative_1818791..1818941_POSITIVE 234 239 200 61 8 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 234 230 181 50 13 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 231 240 195 68 19 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 230 229 184 129 81 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 230 230 181 126 68 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 230 219 171 67 3 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE