Origin IGS: attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctaaacatctccttatttttttagggaacatttcccgtacacattcattctaccacttttgccatattttgtcacggtcaacttgtatatctagcgatgtaaacgtttttacaaacggttcaaaatactgaaaaattaaagaaaatgtggtataatataggatagtttaat Mask Tandem Repeat Region ================================================ attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Find is-nt database================================================ Query_seq: SSA_1220:SSA_1221|SSA_1220:SSA_1221:DNA gyrase A subunit, putative:L-lactate dehydrogenase, putative:<-->:1243923..1244095 173 attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1220:SSA_1221|SSA_1220:SSA_1221:DNA gyrase A subunit, putative:L-lactate dehydrogenase, putative:<-->:1243923..1244095 173 attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1220:SSA_1221|SSA_1220:SSA_1221:DNA gyrase A subunit, putative:L-lactate dehydrogenase, putative:<-->:1243923..1244095 173 attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 9 End: 119 ........ M L Y Y T T F S L I F Q Y F E P F V K T F T S L D I Q V D R D K I W Q K W ...................................................... Protein_Len: 38 Strand: - Start: 44 End: 157 ........................................... Y K S G N T F V N V D S S I C T S R S L I H C F H Y F S H T R S I N G L F M ................ attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa 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: 16 End: 45 ...............ACTGAAAAATTAAAGAAAATGTGGTATAAT................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 96 End: 125 ...............................................................................................CGTGACAAAATATGGCAAAAGTGGTAGAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1220:SSA_1221|SSA_1220:SSA_1221:DNA gyrase A subunit, putative:L-lactate dehydrogenase, putative:<-->:1243923..1244095 173 attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_009009_SSA_1220_SSA_1221|DNA gyrase A subunit, putative:L-lactate dehydrogenase, putative|NEGATIVE:POSITIVE|[1243923,1244095]|173 HSP 1 e-value: 4.0E-81 bit: 301.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctnnnnnnntaaggagatgtttagaa attaaactatcctatattataccacattttctttaatttttcagtattttgaaccgtttgtaaaaacgtttacatcgctagatatacaagttgaccgtgacaaaatatggcaaaagtggtagaatgaatgtgtacgggaaatgttccctaaaaaaataaggagatgtttagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAACUAUCCUAUAUUAUACCACAUUUUCUUUAAUUUUUCAGUAUUUUGAACCGUUUGUAAAAACGUUUACAUCGCUAGAUAUACAAGUUGACCGUGACAAAAUAUGGCAAAAGUGGUAGAAUGAAUGUGUACGGGAAAUGUUCCCUAAAAAAAUAAGGAGAUGUUUAGAA .((((((..((((.((((....((((((((((...(((((((.((((((((...(((((....)))))......((((..(((......)))....)))))))))))).).))))))...)))..)))))))...((((.....))))......))))))))...)))))).. (-36.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAAACAUCUCCUUAUUUUUUUAGGGAACAUUUCCCGUACACAUUCAUUCUACCACUUUUGCCAUAUUUUGUCACGGUCAACUUGUAUAUCUAGCGAUGUAAACGUUUUUACAAACGGUUCAAAAUACUGAAAAAUUAAAGAAAAUGUGGUAUAAUAUAGGAUAGUUUAAU ...(((((...((((((......))))))...................((((((.......(((((((((((...............((((((....))))))..(((((....))))).((((......)))).........))))))))))).....)))))).))))).. (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 869 140 91 231 182 NC_009009:SSA_1220|5end_DNA_gyrase_A_subunit,_putative_1243832..1244062_NEGATIVE 278 139 91 192 148 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 269 149 109 201 161 NC_009009:SSA_1653|5end_hypothetical_protein_1651371..1651601_NEGATIVE 256 96 54 201 160 NC_009009:SSA_2351|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2353507..2353737_NEGATIVE 253 148 105 76 23 NC_009009:SSA_1312|5end_RADC-like_protein,_putative_1329663..1329893_NEGATIVE 239 92 54 184 146 NC_009009:SSA_1146|5end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176453..1176683_POSITIVE 232 101 66 194 154 NC_009009:SSA_0738|5end_Ornithine_carbamoyltransferase,_catabolic,_putative_719904..720134_POSITIVE 230 140 95 220 177 NC_009009:SSA_1799|5end_Acetyltransferase,_putative_1781025..1781255_NEGATIVE 230 100 54 163 106 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 229 65 23 134 95 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 228 139 92 187 142 NC_009009:SSA_0446|5end_hypothetical_protein_445438..445668_NEGATIVE 227 57 11 44 4 NC_009009:SSA_0360|5end_Conserved_uncharacterized_protein_352704..352934_POSITIVE 225 148 108 50 5 NC_009009:SSA_1115|5end_Cytochrome_C-type_biogenesis_protein,_putative_1141614..1141844_POSITIVE 224 44 7 151 115 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 223 81 54 231 201 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 219 139 95 153 117 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 219 84 41 47 9 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 219 127 89 142 110 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 218 148 107 205 168 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 218 150 110 48 9 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 101 66 143 103 NC_009009:SSA_0737|3end_Arginine_deiminase,_putative_719933..720083_POSITIVE 229 65 23 131 92 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 228 166 124 148 97 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 223 117 77 144 94 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 219 139 95 141 105 NC_009009:SSA_1706|3end_Exodeoxyribonuclease,_putative_1697850..1698000_POSITIVE 219 127 89 145 113 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 211 138 95 143 106 NC_009009:SSA_1904|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1898233..1898383_NEGATIVE 208 149 109 83 44 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE 205 138 92 138 97 NC_009009:SSA_0358|3end_hypothetical_protein_351288..351438_NEGATIVE 202 79 36 133 93 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 200 79 40 68 24 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 200 169 121 148 103 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 199 118 77 56 4 NC_009009:SSA_1547|3end_HPr_kinase/phosphorylase,_putative_1550045..1550195_NEGATIVE 199 99 66 149 116 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 198 148 108 40 3 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 198 150 106 72 23 NC_009009:SSA_1907|3end_hypothetical_protein_1900813..1900963_POSITIVE 197 115 75 144 109 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 197 111 74 77 37 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 197 100 54 148 104 NC_009009:SSA_0123|3end_50S_ribosomal_protein_L18P,_putative_116484..116634_POSITIVE 196 120 80 150 113 NC_009009:SSA_0447|3end_Magnesium_and_cobalt_transporter,_putative_445457..445607_NEGATIVE