Origin IGS: tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat .........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 ataaagccctaaatatgaaaaatgagtcgcaagattttagcggaaatcagctcaaatagaaaatgttaatttccgaaacgttttgcaagcgaaccgcactttatgatctaggtcacaaaaccgtttttctgtttgtaatttcggttcatagattcgtttaccagtgctagaatctggttaatcttgttaatcattaagaggtaatcaca Mask Tandem Repeat Region ================================================ tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Find is-nt database================================================ Query_seq: AA01717:AA01718|AA01717:AA01718:fumarate hydratase, class II:DNA polymerase III, chi subunit:->->:1162721..1162929 209 tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01717:AA01718|AA01717:AA01718:fumarate hydratase, class II:DNA polymerase III, chi subunit:->->:1162721..1162929 209 tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01717:AA01718|AA01717:AA01718:fumarate hydratase, class II:DNA polymerase III, chi subunit:->->:1162721..1162929 209 tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 57 End: 155 ........................................................ M Y E P K L Q T E K R F C D L D H K V R F A C K T F R K L T F S I ...................................................... Protein_Len: 35 Strand: - Start: 43 End: 147 .......................................... C Q Y V F R H V S I V F L F V T K H G L D Y L A T R K C F T E S I L M .............................................................. tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat 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: 84 Start: 147 End: 176 ..................................................................................................................................................TTTTCTATTTGAGCTGATTTCCGCTAAAAT................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 37 End: 66 ....................................GTTCATAGATTCGTTTACCAGTGCTAGAAT............................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01717:AA01718|AA01717:AA01718:fumarate hydratase, class II:DNA polymerase III, chi subunit:->->:1162721..1162929 209 tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: aact_AA01717_AA01718|fumarate hydratase, class II:DNA polymerase III, chi subunit|POSITIVE:POSITIVE|[1162721,1162929]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat tgtgattacctcttaatgattaacaagattaaccagattctagcactggtaaacgaatctatgaaccgaaattacaaacagaaaaacggttttgtgacctagatcataaagtgcggttcgcttgcaaaacgtttcggaaattaacattttctatttgagctgatttccgctaaaatcttgcgactcatttttcatatttagggctttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGAUUACCUCUUAAUGAUUAACAAGAUUAACCAGAUUCUAGCACUGGUAAACGAAUCUAUGAACCGAAAUUACAAACAGAAAAACGGUUUUGUGACCUAGAUCAUAAAGUGCGGUUCGCUUGCAAAACGUUUCGGAAAUUAACAUUUUCUAUUUGAGCUGAUUUCCGCUAAAAUCUUGCGACUCAUUUUUCAUAUUUAGGGCUUUAU (((((((...((.....))....(((((((.(((((.........))))).....))))).))......))))))).((((((......))))))..(((((((...((((((.(((.(((..(..........(((((((((.....(((.....))).))))))))).......)..))))))))))))....)))))))....... (-36.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAGCCCUAAAUAUGAAAAAUGAGUCGCAAGAUUUUAGCGGAAAUCAGCUCAAAUAGAAAAUGUUAAUUUCCGAAACGUUUUGCAAGCGAACCGCACUUUAUGAUCUAGGUCACAAAACCGUUUUUCUGUUUGUAAUUUCGGUUCAUAGAUUCGUUUACCAGUGCUAGAAUCUGGUUAAUCUUGUUAAUCAUUAAGAGGUAAUCACA .......(((....((((.((((((((((((((((.....(((((((.(((.............))).)))))))....)))))))....((((((....(((..(..((((..((......))...)))).)..)))...))))))...)))))))))(((((.........)))))............))))....)))........ (-45.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 182 153 204 174 aact:AA02533|5end_zinc_protease;_peptidase_1762010..1762240_POSITIVE 311 146 106 115 78 aact:AA02623|5end_dTDP-D-glucose_4,6-dehydratase_1827300..1827530_POSITIVE 311 137 93 230 180 aact:AA00208|5end_D-ribose_ABC_transporter,_permease_protein_/_Galactoside_transport_system_permease_protein_144097..144327_POSITIVE 300 134 97 180 143 aact:AA01173|5end_VapD-homolog_803850..804080_POSITIVE 298 134 94 140 95 aact:AA00766|5end_heat_shock_protein_B25.3_(HSP-70_cofactor)_527384..527614_POSITIVE 297 139 93 78 24 aact:AA00764|5end_hemoglobin_binding_protein_A_526848..527078_POSITIVE 286 138 92 168 108 aact:AA01161|5end_araC-like_transcriptional_regulator_794121..794351_POSITIVE 281 140 98 150 101 aact:AA02249|5end_thiamine_biosynthesis_protein_1528365..1528595_POSITIVE 280 126 83 106 53 aact:AA02832|5end_outer_membrane_integrity_protein_1990044..1990274_POSITIVE 280 126 87 212 172 aact:AA00918|5end_hypothetical_protein_630044..630274_POSITIVE 278 138 98 53 13 aact:AA02357|5end_bifunctional_protein:_aspartokinase_I;_homoserine_dehydrogenaseI_1614668..1614898_POSITIVE 276 136 91 47 9 aact:AA02399|5end_30S_ribosomal_protein_S21_1650900..1651130_POSITIVE 275 138 103 38 3 aact:AA02313|5end_conserved_hypothetical_protein_1580156..1580386_POSITIVE 272 127 87 152 103 aact:AA02553|5end_acylphosphatase_1779321..1779551_POSITIVE 272 125 89 195 163 aact:AA00529|5end_outer_membrane_protein,_Omp_18/16_361730..361960_POSITIVE 269 150 103 78 26 aact:AA00415|5end_D-methionine_ABC_transporter,_ATP-binding_protein_281650..281880_POSITIVE 268 170 123 110 66 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 267 117 76 198 153 aact:AA00205|5end_ribose_ABC_transporter_protein_/_high_affinity_D-ribose_transport_protein_142162..142392_POSITIVE 267 127 86 40 3 aact:AA00071|5end_conserved_hypothetical_protein_(possible_zinc_protease)_53463..53693_POSITIVE 266 123 95 151 118 aact:AA00254|5end_penicillin-binding_protein_5_177579..177809_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 182 153 123 93 aact:AA02532|3end_conserved_hypothetical_protein_1762009..1762159_POSITIVE 306 125 81 90 34 aact:AA00943|3end_conserved_hypothetical_protein_654542..654692_POSITIVE 300 134 97 97 60 aact:AA01172|3end_conserved_hypothetical_protein_803847..803997_POSITIVE 281 140 98 60 11 aact:AA02246|3end_peptidase_E_1528355..1528505_POSITIVE 280 126 83 68 15 aact:AA02830|3end_colicin_tolerance_protein_1990086..1990236_POSITIVE 275 138 103 42 7 aact:AA02312|3end_conserved_hypothetical_protein_1580240..1580390_POSITIVE 272 125 89 88 56 aact:AA00528|3end_conserved_hypothetical_protein_361703..361853_POSITIVE 266 123 95 128 95 aact:AA00253|3end_hypothetical_protein_177636..177786_POSITIVE 265 137 91 79 30 aact:AA02305|3end_guanosine-3',5'-bis(diphosphate)3'-_pyrophosphohydrolase_1576978..1577128_POSITIVE 262 160 112 52 7 aact:AA02827|3end_conserved_hypothetical_protein_1987619..1987769_POSITIVE 260 138 110 125 96 aact:AA02946|3end_virulence_factor_protein_2060870..2061020_POSITIVE 258 139 93 46 6 aact:AA02560|3end_integral_membrane_protein_1783630..1783780_POSITIVE 257 148 104 97 48 aact:AA02196|3end_oxaloacetate_decarboxylase_beta_chain_1497692..1497842_POSITIVE 257 170 130 49 4 aact:AA01767|3end_conserved_hypothetical_protein_1192961..1193111_POSITIVE 255 147 109 49 17 aact:AA00355|3end_DNA-directed_RNA_polymerase_beta_chain_(transcriptase_beta_chain)_238911..239061_POSITIVE 254 138 95 64 24 aact:AA00806|3end_fumarate_reductase_15_kD_hydrophobic_protein_552834..552984_POSITIVE 253 145 108 104 58 aact:AA02142|3end_outer_membrane_protein_OprM_precursor_1467532..1467682_POSITIVE 253 77 31 105 53 aact:AA01568|3end_dipeptide_transport_system_ATP-binding_protein_1056932..1057082_POSITIVE 252 128 85 69 20 aact:AA01744|3end_peptide_chain_release_factor_RF-2_1180352..1180502_POSITIVE 250 137 91 74 20 aact:AA00933|3end_ribose_ABC_transporter,_ATP-binding_protein_645197..645347_POSITIVE