Origin IGS: tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga .........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 tccttttgtgaagttattaagtagatagggaactctttttgcatagtgaaatccatcatccgtcgaatgaaatgcttctctttctaggacatttgacctattctgaattttagaagggggcttaggttaaaattagtatgcccccccctcaaccaagttcagtttcatctgagcttggtttttctatacctctcctctttcatccctctccgacttaatactttcttttaagccttaaaaatgataaaataagacaaacaaactataggagaacata Mask Tandem Repeat Region ================================================ tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Find is-nt database================================================ Query_seq: SSA_1811:SSA_1812|SSA_1811:SSA_1812:6-phosphogluconate dehydrogenase, putative:Modification methylase, putative:<-<-:1796921..1797197 277 tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1811:SSA_1812|SSA_1811:SSA_1812:6-phosphogluconate dehydrogenase, putative:Modification methylase, putative:<-<-:1796921..1797197 277 tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1811:SSA_1812|SSA_1811:SSA_1812:6-phosphogluconate dehydrogenase, putative:Modification methylase, putative:<-<-:1796921..1797197 277 tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 170 End: 277 ......................................................................................................................................................................... M Q N R S N V L E R E A F H S T D D G F H Y A K R V P Y L L N N F T K G Protein_Len: 43 Strand: - Start: 50 End: 178 ................................................. F F T N L R L P I F S S L Y L F V L S L H F Q V Q N L P P C V L K L R L G R R F N L M ................................................................................................... tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga 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================================================ tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.8 Tail_Score: -4.99638 Start: 100 End: 125 Full_Region: atgcccccccctcaa ccaagttcag tttcat ctgagcttgg tttttctatacctct ...................................................................................................ccaagttcagtttcatctgagcttgg........................................................................................................................................................ Find igs database================================================ Query_seq: SSA_1811:SSA_1812|SSA_1811:SSA_1812:6-phosphogluconate dehydrogenase, putative:Modification methylase, putative:<-<-:1796921..1797197 277 tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Intra-Species Hit: Count: 1 Min: 1 Max: 277 Len: 277 Subject: NC_009009_SSA_1811_SSA_1812|6-phosphogluconate dehydrogenase, putative:Modification methylase, putative|NEGATIVE:NEGATIVE|[1796921,1797197]|277 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 277 Query Start:1 Query End:277 Subject Strand: POSITIVE Subject Start: 1 Subject End: 277 tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgannnnnnnncatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga tatgttctcctatagtttgtttgtcttattttatcatttttaaggcttaaaagaaagtattaagtcggagagggatgaaagaggagaggtatagaaaaaccaagctcagatgaaactgaacttggttgaggggggggcatactaattttaacctaagcccccttctaaaattcagaataggtcaaatgtcctagaaagagaagcatttcattcgacggatgatggatttcactatgcaaaaagagttccctatctacttaataacttcacaaaagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGUUCUCCUAUAGUUUGUUUGUCUUAUUUUAUCAUUUUUAAGGCUUAAAAGAAAGUAUUAAGUCGGAGAGGGAUGAAAGAGGAGAGGUAUAGAAAAACCAAGCUCAGAUGAAACUGAACUUGGUUGAGGGGGGGGCAUACUAAUUUUAACCUAAGCCCCCUUCUAAAAUUCAGAAUAGGUCAAAUGUCCUAGAAAGAGAAGCAUUUCAUUCGACGGAUGAUGGAUUUCACUAUGCAAAAAGAGUUCCCUAUCUACUUAAUAACUUCACAAAAGGA .......((((...........((((((............))))))......(((..((((((((.(((.(((((.............((((((...(((((((.((((......)))).))))))).((((((((((..................))))))))))........((((..((((..((((...(((.((((....)))).)))))))..))))..))))..)))))).........))))).)))))))))))..))).....)))) (-73.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUUUGUGAAGUUAUUAAGUAGAUAGGGAACUCUUUUUGCAUAGUGAAAUCCAUCAUCCGUCGAAUGAAAUGCUUCUCUUUCUAGGACAUUUGACCUAUUCUGAAUUUUAGAAGGGGGCUUAGGUUAAAAUUAGUAUGCCCCCCCCUCAACCAAGUUCAGUUUCAUCUGAGCUUGGUUUUUCUAUACCUCUCCUCUUUCAUCCCUCUCCGACUUAAUACUUUCUUUUAAGCCUUAAAAAUGAUAAAAUAAGACAAACAAACUAUAGGAGAACAUA (((((((((((((.((((((((.((.(((((..............((((......))))..((((((((......((((......)))))))))))).......((....(((((((((((..................)))))).....((((((((((((......)))))))))))).)))))....))..........))))).))..)))))))).))))......(.((((............)))).)..)))))....))))....... (-61.97) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 945 140 91 231 182 NC_009009:SSA_1811|5end_6-phosphogluconate_dehydrogenase,_putative_1796830..1797060_NEGATIVE 336 236 197 223 189 NC_009009:SSA_0131|5end_30S_ribosomal_protein_S11,_putative_120717..120947_POSITIVE 314 230 182 162 105 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 301 138 92 212 178 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 299 139 104 32 3 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 299 137 93 206 150 NC_009009:SSA_0252|5end_hypothetical_protein_245839..246069_NEGATIVE 286 105 66 222 184 NC_009009:SSA_2092|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095975..2096205_NEGATIVE 285 78 32 178 130 NC_009009:SSA_1522|5end_Cell_division_protein_FtsW,_putative_1531962..1532192_NEGATIVE 283 90 50 61 9 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 283 96 54 231 189 NC_009009:SSA_0053|5end_Beta-galactosidase,_putative_56748..56978_POSITIVE 282 160 115 231 169 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 278 219 171 178 128 NC_009009:SSA_1946|5end_Oligopeptide_transport_system_permease_protein,_putative_1938624..1938854_NEGATIVE 278 139 104 38 1 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 276 64 23 201 156 NC_009009:SSA_1959|5end_Undecaprenyl-diphosphatase,_putative_1956431..1956661_NEGATIVE 276 219 171 62 14 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 274 165 123 211 161 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 273 138 100 200 156 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 271 140 91 161 112 NC_009009:SSA_2190|5end_33_kDa_chaperonin,_putative_2191166..2191396_POSITIVE 270 139 101 72 20 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 270 140 93 91 36 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 130 82 72 20 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 321 250 201 151 104 NC_009009:SSA_0871|3end_Cell_division_protein_FtsX,_putative_864627..864777_POSITIVE 299 139 104 39 10 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 276 64 23 61 16 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 276 219 171 71 23 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 274 165 123 76 26 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 270 140 93 94 39 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 270 138 94 114 59 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 269 95 52 72 32 NC_009009:SSA_0802|3end_hypothetical_protein_785228..785378_POSITIVE 269 110 71 57 14 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 268 110 61 145 92 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 266 138 93 90 44 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 264 197 156 52 1 NC_009009:SSA_1667|3end_hypothetical_protein_1667519..1667669_NEGATIVE 264 166 123 51 8 NC_009009:SSA_0777|3end_Glycogen_biosynthesis_protein_GlgD,_putative_760649..760799_POSITIVE 264 114 72 53 9 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 264 176 131 58 15 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 260 90 63 50 16 NC_009009:SSA_1568|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571960..1572110_POSITIVE 260 167 121 115 61 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 259 86 43 135 98 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 256 218 174 148 102 NC_009009:SSA_0036|3end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_42050..42200_NEGATIVE