Origin IGS: tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatatcctgttcgataagagaacaggatattttgcttggatagaattgctattcaattcatagttgagtactaagttgaaatggacatgttttcaaaaaata Mask Tandem Repeat Region ================================================ tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Find is-nt database================================================ Query_seq: SSA_1839:SSA_1840|SSA_1839:SSA_1840:Cysteine synthase, putative:RNA binding protein, putative:-><-:1834046..1834149 104 tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1839:SSA_1840|SSA_1839:SSA_1840:Cysteine synthase, putative:RNA binding protein, putative:-><-:1834046..1834149 104 tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1839:SSA_1840|SSA_1839:SSA_1840:Cysteine synthase, putative:RNA binding protein, putative:-><-:1834046..1834149 104 tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Predict ORF larger than 30AA ================================================ tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt 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================================================ tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1839:SSA_1840|SSA_1839:SSA_1840:Cysteine synthase, putative:RNA binding protein, putative:-><-:1834046..1834149 104 tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1839_SSA_1840|Cysteine synthase, putative:RNA binding protein, putative|POSITIVE:NEGATIVE|[1834046,1834149]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt tattttttgaaaacatgtccatttcaacttagtactcaactatgaattgaatagcaattctatccaagcaaaatatcctgttctcttatcgaacaggatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUUUGAAAACAUGUCCAUUUCAACUUAGUACUCAACUAUGAAUUGAAUAGCAAUUCUAUCCAAGCAAAAUAUCCUGUUCUCUUAUCGAACAGGAUAUUUU ......((((((.........))))))..((((.....)))).((((((.....)))))).........((((((((((((((.......)))))))))))))) (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUCCUGUUCGAUAAGAGAACAGGAUAUUUUGCUUGGAUAGAAUUGCUAUUCAAUUCAUAGUUGAGUACUAAGUUGAAAUGGACAUGUUUUCAAAAAAUA ((((((((((((((.......))))))))))))))..(((((......((((((((((((..((((.....))))))))).))))).))....)))))...... (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 49 2 107 61 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 242 97 67 163 138 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 229 92 53 75 41 NC_009009:SSA_0077|5end_Oxidoreductase,_putative_80738..80968_POSITIVE 224 100 51 146 92 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 215 43 2 214 168 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 215 96 54 136 87 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 211 97 52 186 133 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 210 82 45 68 21 NC_009009:SSA_1991|5end_Pneumococcal_histidine_triad_protein_A,_putative_1988772..1989002_NEGATIVE 203 98 53 198 162 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 202 99 54 210 162 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 202 70 22 162 104 NC_009009:SSA_0193|5end_CAAX_amino_terminal_protease_family_protein,_putative_194318..194548_POSITIVE 201 87 45 223 179 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 200 70 31 167 113 NC_009009:SSA_0206|5end_hypothetical_protein_204256..204486_POSITIVE 199 85 42 172 129 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 197 98 65 150 104 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 197 98 60 227 194 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 196 87 59 77 51 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 195 100 75 34 8 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 195 70 22 148 99 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 194 92 53 211 172 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 99 52 81 35 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 250 49 2 120 74 NC_009009:SSA_0503|3end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503102..503252_POSITIVE 224 100 51 133 79 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 215 96 54 135 86 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE 209 97 53 79 35 NC_009009:SSA_0448|3end_Excinuclease_ATPase_subunit_A,_putative_449391..449541_POSITIVE 201 97 60 34 1 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 201 84 54 131 99 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 199 85 42 120 77 NC_009009:SSA_1321|3end_Ferrochelatase,_putative_1337246..1337396_NEGATIVE 197 96 51 146 84 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 196 87 59 67 41 NC_009009:SSA_1380|3end_hypothetical_protein_1398538..1398688_NEGATIVE 196 85 55 37 5 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 195 84 47 142 110 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 195 70 22 151 102 NC_009009:SSA_0338|3end_Hydroxymethylglutaryl-CoA_synthase,_putative_332160..332310_NEGATIVE 193 94 54 107 70 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 193 79 35 110 68 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 191 60 17 47 6 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 188 100 52 132 77 NC_009009:SSA_1570|3end_hypothetical_protein_1573137..1573287_POSITIVE 188 100 62 133 84 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 186 98 60 65 12 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 186 99 62 146 113 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE