Origin IGS: atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat .........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 ataggtctgactccttcgttctttataatagatgattagcctgatttcgcttaaaatttaggaattattgctcatatttcatttttaaacatttaaataatcatcattttgtaacacattataacaaaaaaagaaaaattgtcaataaaacaagatgattttttcggttgacaaatatatgtgatgtatattacaatgtagttgttctacaatatgacacatatttcataattttggaggtaaat Mask Tandem Repeat Region ================================================ atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Find is-nt database================================================ Query_seq: SSA_1053:SSA_1054|SSA_1053:SSA_1054:Pyruvate phosphate dikinase, putative:CBS domain protein, putative:<-->:1070159..1070403 245 atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1053:SSA_1054|SSA_1053:SSA_1054:Pyruvate phosphate dikinase, putative:CBS domain protein, putative:<-->:1070159..1070403 245 atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1053:SSA_1054|SSA_1053:SSA_1054:Pyruvate phosphate dikinase, putative:CBS domain protein, putative:<-->:1070159..1070403 245 atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 49 End: 150 ................................................ M V I Y I T Y I C Q P K K S S C F I D N F S F F V I M C Y K M M I I ............................................................................................... atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat 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: 82 Start: 189 End: 218 ............................................................................................................................................................................................ATAGATGATTAGCCTGATTTCGCTTAAAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1053:SSA_1054|SSA_1053:SSA_1054:Pyruvate phosphate dikinase, putative:CBS domain protein, putative:<-->:1070159..1070403 245 atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaatttttctttttttgttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_009009_SSA_1053_SSA_1054|Pyruvate phosphate dikinase, putative:CBS domain protein, putative|NEGATIVE:POSITIVE|[1070159,1070403]|245 HSP 1 e-value: 8.0E-65 bit: 248.0 Len: 125 Query Start:121 Query End:245 Subject Strand: POSITIVE Subject Start: 121 Subject End: 245 ........................................................................................................................gttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat ........................................................................................................................gttataatgtgttacaaaatgatgattatttaaatgtttaaaaatgaaatatgagcaataattcctaaattttaagcgaaatcaggctaatcatctattataaagaacgaaggagtcagacctat HSP 2 e-value: 4.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaa.......................................................................................................................................... atttacctccaaaattatgaaatatgtgtcatattgtagaacaactacattgtaatatacatcacatatatttgtcaaccgaaaaaatcatcttgttttattgacaa.......................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACCUCCAAAAUUAUGAAAUAUGUGUCAUAUUGUAGAACAACUACAUUGUAAUAUACAUCACAUAUAUUUGUCAACCGAAAAAAUCAUCUUGUUUUAUUGACAAUUUUUCUUUUUUUGUUAUAAUGUGUUACAAAAUGAUGAUUAUUUAAAUGUUUAAAAAUGAAAUAUGAGCAAUAAUUCCUAAAUUUUAAGCGAAAUCAGGCUAAUCAUCUAUUAUAAAGAACGAAGGAGUCAGACCUAU .(((..((((.....((((..((.(((((.(((.(((((.....))))).))).))))).))..))))...(((((((..(((.((......)).)))..)))))))...((((((((((((.((.....)).)))))).((((((((......(((((((((..(((.(((.....))).))).....))))))))).........))))))))......))))))....))))..)))..... (-36.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGGUCUGACUCCUUCGUUCUUUAUAAUAGAUGAUUAGCCUGAUUUCGCUUAAAAUUUAGGAAUUAUUGCUCAUAUUUCAUUUUUAAACAUUUAAAUAAUCAUCAUUUUGUAACACAUUAUAACAAAAAAAGAAAAAUUGUCAAUAAAACAAGAUGAUUUUUUCGGUUGACAAAUAUAUGUGAUGUAUAUUACAAUGUAGUUGUUCUACAAUAUGACACAUAUUUCAUAAUUUUGGAGGUAAAU ..........((((....((((((......((((((((((.(((((((............)))))))..))............(((((....)))))))))))))..(((((...........))))).))))))...((((((((.....((((....))))...))))))))..(((((((...(((((.....(((((.....)))))))))).)))))))...........))))...... (-38.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 722 50 1 141 92 NC_009009:SSA_1053|5end_Pyruvate_phosphate_dikinase,_putative_1070068..1070298_NEGATIVE 244 115 72 179 130 NC_009009:SSA_0182|5end_Endoglucanase,_putative_186299..186529_POSITIVE 228 70 22 139 88 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 226 238 195 80 32 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 226 117 71 126 84 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 220 240 204 174 140 NC_009009:SSA_0943|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950846..951076_POSITIVE 210 132 92 119 79 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 207 235 195 227 189 NC_009009:SSA_1639|5end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1642031..1642261_NEGATIVE 207 224 194 87 49 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 205 230 182 182 131 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 200 238 191 177 122 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 199 105 65 140 89 NC_009009:SSA_0963|5end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_971413..971643_POSITIVE 198 126 90 115 76 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 197 234 195 75 46 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 196 240 201 162 127 NC_009009:SSA_1798|5end_hypothetical_protein_1780513..1780743_NEGATIVE 196 230 181 68 22 NC_009009:SSA_0954|5end_hypothetical_protein_958024..958254_POSITIVE 195 150 114 163 127 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 193 237 201 110 75 NC_009009:SSA_0261|5end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_255468..255698_NEGATIVE 192 234 195 205 164 NC_009009:SSA_2148|5end_Alkaline_shock_stress_response_protein,_putative_2150039..2150269_NEGATIVE 191 229 183 197 142 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 115 72 92 43 NC_009009:SSA_0181|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_186292..186442_POSITIVE 231 240 193 59 20 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 221 70 34 45 8 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 216 209 172 66 28 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 207 235 195 150 112 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE 207 224 194 90 52 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 205 230 182 117 66 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 203 238 204 85 49 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 200 233 196 109 77 NC_009009:SSA_2166|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2163873..2164023_NEGATIVE 199 105 65 78 27 NC_009009:SSA_0962|3end_Lactoylglutathione_lyase,_putative_971431..971581_POSITIVE 198 126 90 95 56 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 196 230 181 59 13 NC_009009:SSA_0952|3end_hypothetical_protein_958095..958245_POSITIVE 195 150 114 77 41 NC_009009:SSA_1385|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1402794..1402944_POSITIVE 193 237 201 123 88 NC_009009:SSA_0262|3end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_255455..255605_NEGATIVE 192 119 91 40 10 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 192 240 210 41 11 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 191 239 197 46 1 NC_009009:SSA_0850|3end_Ubiquitin_C-terminal_hydrolase,_putative_837641..837791_POSITIVE 189 235 191 55 18 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 188 216 172 72 16 NC_009009:SSA_0282|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274618..274768_POSITIVE 185 216 173 103 65 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE