Origin IGS: cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaatacatacctcaatataatttaatagaattagtataaaatgaaataagagctttgtaaaatataaaaaagctatgagagccatagcttttctttatg Mask Tandem Repeat Region ================================================ cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Find is-nt database================================================ Query_seq: SSA_1837:SSA_1839|SSA_1837:SSA_1839:hypothetical protein:Cysteine synthase, putative:->->:1833016..1833115 100 cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1837:SSA_1839|SSA_1837:SSA_1839:hypothetical protein:Cysteine synthase, putative:->->:1833016..1833115 100 cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1837:SSA_1839|SSA_1837:SSA_1839:hypothetical protein:Cysteine synthase, putative:->->:1833016..1833115 100 cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Predict ORF larger than 30AA ================================================ cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct 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: 86 Start: 38 End: 67 .....................................TTTTACAAAGCTCTTATTTCATTTTATACT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1837:SSA_1839|SSA_1837:SSA_1839:hypothetical protein:Cysteine synthase, putative:->->:1833016..1833115 100 cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_009009_SSA_1837_SSA_1839|hypothetical protein:Cysteine synthase, putative|POSITIVE:POSITIVE|[1833016,1833115]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct cataaagaaaagctatggctctcatagcttttttatattttacaaagctcttatttcattttatactaattctattaaattatattgaggtatgtattct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAAGAAAAGCUAUGGCUCUCAUAGCUUUUUUAUAUUUUACAAAGCUCUUAUUUCAUUUUAUACUAAUUCUAUUAAAUUAUAUUGAGGUAUGUAUUCU .(((.((((((((((((.....)))))))))))).)))..((((.(.(((.(((...((((.(((.......))).)))).)))..))).).)))).... (-17.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUACAUACCUCAAUAUAAUUUAAUAGAAUUAGUAUAAAAUGAAAUAAGAGCUUUGUAAAAUAUAAAAAAGCUAUGAGAGCCAUAGCUUUUCUUUAUG ....((((...(((....((((((....)))))).(((........))).)))...))))...(((((((((((((((.....)))))))))..)))))) (-15.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 48 4 156 116 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 240 50 11 170 135 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 227 49 1 56 8 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 223 60 12 155 103 NC_009009:SSA_1347|5end_PhnA_protein,_putative_1365141..1365371_NEGATIVE 222 48 4 188 143 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 220 90 41 149 94 NC_009009:SSA_0302|5end_Phosphoglycerate_kinase,_putative_294890..295120_POSITIVE 220 58 11 128 82 NC_009009:SSA_0149|5end_hypothetical_protein_143574..143804_POSITIVE 217 49 6 49 9 NC_009009:SSA_0837|5end_Glucosyltransferase,_putative_823902..824132_POSITIVE 216 29 9 231 204 NC_009009:SSA_0739|5end_Carbamate_kinase,_putative_721087..721317_POSITIVE 213 58 16 68 25 NC_009009:SSA_2328|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2331483..2331713_POSITIVE 211 57 11 70 21 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 209 58 11 164 128 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 202 31 10 61 34 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 202 50 16 64 34 NC_009009:SSA_2291|5end_hypothetical_protein_2293204..2293434_POSITIVE 201 52 16 106 71 NC_009009:SSA_1531|5end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1539476..1539706_NEGATIVE 201 49 2 223 172 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 199 58 12 118 72 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 198 30 9 231 207 NC_009009:SSA_2253|5end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2249424..2249654_NEGATIVE 198 50 2 164 109 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 197 59 11 194 143 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 48 6 97 57 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 249 48 4 80 40 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 222 48 4 59 14 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE 219 50 7 107 55 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 216 29 9 64 37 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 211 50 9 89 51 NC_009009:SSA_0230|3end_hypothetical_protein_223812..223962_NEGATIVE 211 57 11 50 1 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 208 69 23 99 61 NC_009009:SSA_1497|3end_DCMP_deaminase,_putative_1503068..1503218_NEGATIVE 201 52 16 122 87 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 201 49 2 124 73 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 199 58 12 146 100 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 197 49 5 106 46 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 192 60 11 72 18 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 190 49 6 85 39 NC_009009:SSA_0208|3end_Conserved_uncharacterized_protein_204968..205118_NEGATIVE 189 57 13 67 27 NC_009009:SSA_0881|3end_Lipoprotein,_putative_876949..877099_POSITIVE 188 50 1 71 14 NC_009009:SSA_1087|3end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1106472..1106622_POSITIVE 188 50 12 92 51 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 187 60 18 100 56 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 184 57 11 123 80 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 184 49 13 129 95 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE