Origin IGS: cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta .........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 taattcgttcatatgatttatttgtttttattgattttgggtattattcatttgttttttattattatcaattgttcttaccgtttttttgtaaaagcatgatggagatcacttttttaaaaattaaaggcgatttttagataatcttatccagatttgtgatctagttctcagaaattttgtgcattcctgactagtattttgaaaaaatgtttttttaaatacatttgttcattctatgcggcaggtaaaag Mask Tandem Repeat Region ================================================ cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Find is-nt database================================================ Query_seq: AA02226:AA02228|AA02226:AA02228:ABC transporter ATP-binding protein:regulatory protein, sorC family:->->:1514867..1515120 254 cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02226:AA02228|AA02226:AA02228:ABC transporter ATP-binding protein:regulatory protein, sorC family:->->:1514867..1515120 254 cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02226:AA02228|AA02226:AA02228:ABC transporter ATP-binding protein:regulatory protein, sorC family:->->:1514867..1515120 254 cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 118 End: 252 ..................................................................................................................... F D G K I K L F T I E M M S K C F F P L F L Q Y Y Y F V F S Y Y G F D I F V F L D Y S R M .. cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta 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: 81 Start: 183 End: 212 ......................................................................................................................................................................................ATTGATAATAATAAAAAACAAATGAATAAT.......................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 190 End: 219 .............................................................................................................................................................................................TTTGGGTATTATTCATTTGTTTTTTATTAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -2.2 Tail_Score: -5.47821 Start: 43 End: 57 Full_Region: tgcattcctgactag tatttt gaa aaaatg tttttttaaatacat ..........................................tattttgaaaaaatg..................................................................................................................................................................................................... Find igs database================================================ Query_seq: AA02226:AA02228|AA02226:AA02228:ABC transporter ATP-binding protein:regulatory protein, sorC family:->->:1514867..1515120 254 cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttacaaaaaaacggtaagaacaattgataataataaaaaacaaatgaataatacccaaaatcaataaaaacaaataaatcatatgaacgaatta Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: aact_AA02226_AA02228|ABC transporter ATP-binding protein:regulatory protein, sorC family|POSITIVE:POSITIVE|[1514867,1515120]|254 HSP 1 e-value: 1.0E-75 bit: 283.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 cttttacctgccgcatagaatgaacaaatgtatttnnnnnnncattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttac.......................................................................................... cttttacctgccgcatagaatgaacaaatgtatttaaaaaaacattttttcaaaatactagtcaggaatgcacaaaatttctgagaactagatcacaaatctggataagattatctaaaaatcgcctttaatttttaaaaaagtgatctccatcatgcttttac.......................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUACCUGCCGCAUAGAAUGAACAAAUGUAUUUAAAAAAACAUUUUUUCAAAAUACUAGUCAGGAAUGCACAAAAUUUCUGAGAACUAGAUCACAAAUCUGGAUAAGAUUAUCUAAAAAUCGCCUUUAAUUUUUAAAAAAGUGAUCUCCAUCAUGCUUUUAC ............((((.((.((((.((((((..........)))))).)))).........((((((((.......)))))))).....(((((((.(((((.....)))))...(((((((........))))))).....)))))))...))))))...... (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAAGCAUGAUGGAGAUCACUUUUUUAAAAAUUAAAGGCGAUUUUUAGAUAAUCUUAUCCAGAUUUGUGAUCUAGUUCUCAGAAAUUUUGUGCAUUCCUGACUAGUAUUUUGAAAAAAUGUUUUUUUAAAUACAUUUGUUCAUUCUAUGCGGCAGGUAAAAG ......(((..(...(((((((...((((((((((......)))))))))).(((((.....))))).)))))))..(((...)))...)..)))...((((.((.((((..((((.((((((..........)))))).))))....))))))))))...... (-32.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 96 60 219 187 aact:AA00292|5end_dihydrofolate_reductase_201800..202030_POSITIVE 253 96 60 134 102 aact:AA00291|5end_hypothetical_protein_201715..201945_POSITIVE 225 108 63 205 160 aact:AA02659|5end_conserved_hypothetical_protein_1852527..1852757_POSITIVE 216 86 45 125 83 aact:AA02569|5end_hypothetical_protein_1789012..1789242_POSITIVE 216 95 63 65 38 aact:AA01009|5end_universal_stress_protein_A_704443..704673_POSITIVE 205 95 57 163 124 aact:AA02874|5end_hypothetical_protein_2017694..2017924_POSITIVE 204 160 143 192 173 aact:AA00936|5end_ribose_ABC_transporter,_permease_protein,_C-terminal_646289..646519_POSITIVE 201 157 120 44 8 aact:AA01169|5end_hypothetical_protein_801985..802215_POSITIVE 200 159 113 159 109 aact:AA01078|5end_transcriptional_regulator_(probable_MerR_family)_746873..747103_POSITIVE 198 129 100 138 106 aact:AA00894|5end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_619879..620109_POSITIVE 196 128 85 58 8 aact:AA02003|5end_purine_nucleotide_synthesis_repressor_protein_1360633..1360863_POSITIVE 195 85 45 214 172 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 195 98 62 207 172 aact:AA01170|5end_hypothetical_protein_802464..802694_POSITIVE 195 103 61 200 157 aact:AA00789|5end_DNA_topoisomerase_III_540486..540716_POSITIVE 195 103 61 65 22 aact:AA00788|5end_hypothetical_protein_540351..540581_POSITIVE 194 126 81 229 189 aact:AA02626|5end_conserved_hypothetical_protein_1828331..1828561_POSITIVE 194 30 5 176 146 aact:AA00887|5end_hypothetical_protein_616739..616969_POSITIVE 194 22 7 173 152 aact:AA00384|5end_conserved_hypothetical_protein_(possible_nitrogen_fixation_protein)_260108..260338_POSITIVE 193 22 6 215 199 aact:AA01241|5end_30S_ribosomal_protein_S4_845294..845524_POSITIVE 191 105 64 230 182 aact:AA02473|5end_conserved_hypothetical_protein_1708571..1708801_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 228 91 60 147 120 aact:AA00290|3end_conserved_hypothetical_protein_201813..201963_POSITIVE 204 160 143 151 132 aact:AA00935|3end_ribose_ABC_transporter,_permease_protein,_N-terminal_646328..646478_POSITIVE 200 159 113 76 26 aact:AA01077|3end_transposase_746870..747020_POSITIVE 198 129 100 138 106 aact:AA00892|3end_selenocysteine-specific_elongation_factor_(SelB_translation_factor)_619959..620109_POSITIVE 195 85 45 139 97 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 190 99 52 81 37 aact:AA00675|3end_glutaredoxin_2_463248..463398_POSITIVE 185 130 81 76 23 aact:AA01681|3end_molybdate-binding_periplasmic_protein_1135670..1135820_POSITIVE 184 159 121 122 90 aact:AA02160|3end_conserved_hypothetical_protein_1478929..1479079_POSITIVE 184 130 81 151 102 aact:AA01746|3end_thiol:disulfide_interchange_protein_1181396..1181546_POSITIVE 184 128 83 119 78 aact:AA01692|3end_hexulose-6-phosphate_synthase_1149929..1150079_POSITIVE 180 104 63 60 18 aact:AA01523|3end_conserved_hypothetical_protein_1023569..1023719_POSITIVE 180 157 120 93 60 aact:AA00198|3end_conserved_hypothetical_protein_(Cytosine_deaminase-related_enzyme)_138643..138793_POSITIVE 178 160 114 108 61 aact:AA01983|3end_maltose_regulon_positive_regulatory_protein_1344738..1344888_POSITIVE 178 132 95 111 78 aact:AA01341|3end_acriflavine_resistance_protein_910131..910281_POSITIVE 175 45 8 55 13 aact:AA00311|3end_L-fuculose-phosphate_aldolase_212143..212293_POSITIVE 174 160 115 86 41 aact:AA02037|3end_hypothetical_protein_1387052..1387202_POSITIVE 174 160 143 101 84 aact:AA01657|3end_maltose_high-affinity_receptor_1124095..1124245_POSITIVE 173 109 64 121 68 aact:AA01744|3end_peptide_chain_release_factor_RF-2_1180352..1180502_POSITIVE 171 104 61 49 9 aact:AA01037|3end_hypothetical_protein_723912..724062_POSITIVE 169 129 81 117 67 aact:AA01136|3end_hypothetical_protein_778502..778652_POSITIVE