Origin IGS: gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcattaagtttttatagtcgcaaatatacgcttagcaagaatagataagaaaacaaaagcatttattaggtttaaacaaacttagcgatacagctaaacgtaaatcctaaatacaaaaagagagtataaaattagaatctataaataacttaacctttaaaac Mask Tandem Repeat Region ================================================ gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Find is-nt database================================================ Query_seq: PI1028:PI1029|PI1028:PI1029:glutamate synthase, small subunit:seryl-tRNA synthetase:->->:945912..946077 166 gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1028:PI1029|PI1028:PI1029:glutamate synthase, small subunit:seryl-tRNA synthetase:->->:945912..946077 166 gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1028:PI1029|PI1028:PI1029:glutamate synthase, small subunit:seryl-tRNA synthetase:->->:945912..946077 166 gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Predict ORF larger than 30AA ================================================ gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta 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================================================ gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1028:PI1029|PI1028:PI1029:glutamate synthase, small subunit:seryl-tRNA synthetase:->->:945912..946077 166 gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: pint_PI1028_PI1029|glutamate synthase, small subunit:seryl-tRNA synthetase|POSITIVE:POSITIVE|[945912,946077]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta gttttaaaggttaagttatttatagattctaattttatactctctttttgtatttaggatttacgtttagctgtatcgctaagtttgtttaaacctaataaatgcttttgttttcttatctattcttgctaagcgtatatttgcgactataaaaacttaatgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUAAAGGUUAAGUUAUUUAUAGAUUCUAAUUUUAUACUCUCUUUUUGUAUUUAGGAUUUACGUUUAGCUGUAUCGCUAAGUUUGUUUAAACCUAAUAAAUGCUUUUGUUUUCUUAUCUAUUCUUGCUAAGCGUAUAUUUGCGACUAUAAAAACUUAAUGCUUA ......(((((((((((.(((((((.((((((....((((.........))))))))))..((((((((((.........(((..((..(((....((((((....))))))...)))..))..))))))))))))).........))))))))))))))).))). (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAUUAAGUUUUUAUAGUCGCAAAUAUACGCUUAGCAAGAAUAGAUAAGAAAACAAAAGCAUUUAUUAGGUUUAAACAAACUUAGCGAUACAGCUAAACGUAAAUCCUAAAUACAAAAAGAGAGUAUAAAAUUAGAAUCUAUAAAUAACUUAACCUUUAAAAC ((((..((((((((((((((((.....(((((.(((.((......................)).....(((((((((.......(((((......)))))...)))).))))).........))).)))))......))..))))))).)))))))..)))).... (-24.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 150 104 118 72 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 248 89 43 72 23 pint:PI0453|5end_conserved_hypothetical_protein_426797..427027_POSITIVE 239 147 119 73 46 pint:PI0587|5end_conserved_hypothetical_protein_534416..534646_POSITIVE 239 150 102 159 102 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 234 80 40 188 151 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 233 79 36 179 141 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 232 145 107 88 52 pint:PI0935|5end_collagenase,_protease_866297..866527_POSITIVE 232 117 73 195 158 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 232 117 73 137 100 pint:PI0565|5end_hypothetical_protein_511479..511709_POSITIVE 230 147 104 172 122 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 226 149 104 87 29 pint:PI1483|5end_hypothetical_protein_1404310..1404540_POSITIVE 223 90 41 110 60 pint:PI0730|5end_hypothetical_protein_661685..661915_POSITIVE 220 78 33 222 183 pint:PI0085|5end_RNase_P_protein_component_84440..84670_POSITIVE 219 93 69 58 28 pint:PI1600|5end_conserved_hypothetical_protein_1529269..1529499_POSITIVE 217 136 91 120 81 pint:PI1294|5end_hypothetical_protein_1208490..1208720_POSITIVE 217 148 125 104 76 pint:PI1003|5end_conserved_hypothetical_protein_924694..924924_POSITIVE 217 146 103 48 3 pint:PI0208|5end_possible_peptidase,_M23/M37_family_200676..200906_POSITIVE 216 84 43 64 19 pint:PI1410|5end_conserved_hypothetical_protein_1331579..1331809_POSITIVE 216 134 92 97 57 pint:PI0025|5end_two_component_system_sensor_histidine_kinase_28682..28912_POSITIVE 215 152 113 175 139 pint:PI0664|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_606891..607121_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 146 101 145 94 pint:PI0363|3end_hypothetical_protein_333760..333910_POSITIVE 252 95 62 52 17 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 233 79 36 133 95 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE 233 80 31 149 96 pint:PI0454|3end_hypothetical_protein_426963..427113_POSITIVE 229 147 104 134 84 pint:PI0456|3end_30S_ribosomal_protein_S12_429219..429369_POSITIVE 227 86 42 54 10 pint:PI1291|3end_6-phosphofructokinase_1205706..1205856_POSITIVE 223 90 41 110 60 pint:PI0729|3end_integrase_661765..661915_POSITIVE 217 145 101 71 22 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 214 100 56 56 11 pint:PI1410|3end_conserved_hypothetical_protein_1331949..1332099_POSITIVE 211 148 101 137 84 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 211 79 32 117 47 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 211 90 43 56 7 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 211 81 47 51 23 pint:PI1719|3end_conserved_hypothetical_protein_1636207..1636357_POSITIVE 209 147 101 108 69 pint:PI1025|3end_tRNA_modification_GTPase_942232..942382_POSITIVE 208 89 57 119 83 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 207 145 103 114 73 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 207 149 103 149 100 pint:PI1740|3end_DedA_family_protein_1662316..1662466_POSITIVE 207 120 71 141 101 pint:PI1386|3end_sugar_phosphate_isomerase_1308031..1308181_POSITIVE 207 75 43 81 51 pint:PI1106|3end_conserved_hypothetical_protein_1030869..1031019_POSITIVE 207 137 104 136 104 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE