Origin IGS: taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaactcctcacctttatagtttgtttataatttcctcacaaagcgttaaacattacttttattcgattcggtattctctttacaaccaacacaaaaaccgaactctaagatataaaaagctta Mask Tandem Repeat Region ================================================ taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Find is-nt database================================================ Query_seq: AA01011:AA01012|AA01011:AA01012:alanyl-tRNA synthetase (alanine--tRNA ligase):probable carbon storage regulator homolog:->->:707830..707954 125 taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01011:AA01012|AA01011:AA01012:alanyl-tRNA synthetase (alanine--tRNA ligase):probable carbon storage regulator homolog:->->:707830..707954 125 taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01011:AA01012|AA01011:AA01012:alanyl-tRNA synthetase (alanine--tRNA ligase):probable carbon storage regulator homolog:->->:707830..707954 125 taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 2 End: 103 . L K K Y R L T R N K H Q N Y L S Y R I S Y F Y H K V S Q S S I I F M ...................... taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat 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================================================ taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01011:AA01012|AA01011:AA01012:alanyl-tRNA synthetase (alanine--tRNA ligase):probable carbon storage regulator homolog:->->:707830..707954 125 taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: aact_AA01011_AA01012|alanyl-tRNA synthetase (alanine--tRNA ligase):probable carbon storage regulator homolog|POSITIVE:POSITIVE|[707830,707954]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat taagctttttatatcttagagttcggtttttgtgttggttgtaaagagaataccgaatcgaataaaagtaatgtttaacgctttgtgaggaaattataaacaaactataaaggtgaggagtttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCUUUUUAUAUCUUAGAGUUCGGUUUUUGUGUUGGUUGUAAAGAGAAUACCGAAUCGAAUAAAAGUAAUGUUUAACGCUUUGUGAGGAAAUUAUAAACAAACUAUAAAGGUGAGGAGUUUAU ((((((((((((....(((.(((((((((..(((((..((....))..))))).)))))))))................(.(((((((.....))))))))...))).....)))))))))))). (-24.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAACUCCUCACCUUUAUAGUUUGUUUAUAAUUUCCUCACAAAGCGUUAAACAUUACUUUUAUUCGAUUCGGUAUUCUCUUUACAACCAACACAAAAACCGAACUCUAAGAUAUAAAAAGCUUA ..............((((((...((((((...(((......)))....))))))............((((((((........................)))))).)).....))))))....... ( -9.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 41 4 186 152 aact:AA02568|5end_sugar_phosphotransferase_component_II_B_1788379..1788609_POSITIVE 270 64 21 104 59 aact:AA00528|5end_conserved_hypothetical_protein_361396..361626_POSITIVE 266 69 21 118 66 aact:AA00766|5end_heat_shock_protein_B25.3_(HSP-70_cofactor)_527384..527614_POSITIVE 252 40 7 191 156 aact:AA02966|5end_conserved_hypothetical_protein_2074223..2074453_POSITIVE 252 40 7 37 2 aact:AA02965|5end_hypothetical_protein_2074069..2074299_POSITIVE 252 64 22 171 123 aact:AA00321|5end_hypothetical_protein_219054..219284_POSITIVE 250 62 21 77 31 aact:AA02507|5end_penicillin-insensitive_murein_endopeptidase_A_1740058..1740288_POSITIVE 238 87 53 78 52 aact:AA01861|5end_phosphomethylpyrimidine_kinase_1251806..1252036_POSITIVE 231 55 15 155 99 aact:AA02485|5end_outer_membrane_protein_100_1722950..1723180_POSITIVE 226 60 18 193 144 aact:AA03003|5end_GTP-binding_membrane_protein_2096544..2096774_POSITIVE 226 60 18 72 23 aact:AA03002|5end_hypothetical_protein_2096423..2096653_POSITIVE 221 66 29 183 149 aact:AA01421|5end_phosphoglycolate_phosphatase_955055..955285_POSITIVE 220 41 7 32 1 aact:AA02567|5end_hypothetical_protein_(possible_inner_membrane_protein)_1788225..1788455_POSITIVE 217 68 21 156 113 aact:AA02735|5end_DNA_repair_protein_1915974..1916204_POSITIVE 217 43 18 90 64 aact:AA01107|5end_adenylosuccinate_lyase_762310..762540_POSITIVE 215 69 25 208 167 aact:AA02870|5end_conserved_hypothetical_protein_2014123..2014353_POSITIVE 214 99 59 93 53 aact:AA01081|5end_hypothetical_protein_747804..748034_POSITIVE 212 57 13 183 143 aact:AA03000|5end_uracil-DNA_glycosylase_(UDG)_2095076..2095306_POSITIVE 212 49 5 146 106 aact:AA01374|5end_tRNA/rRNA_methyltransferase_930283..930513_POSITIVE 211 60 11 66 15 aact:AA02140|5end_ABC_transporter_ATP-binding_protein_1462144..1462374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 64 21 91 46 aact:AA00527|3end_ATP-dependent_DNA_helicase_361463..361613_POSITIVE 252 64 22 86 38 aact:AA00318|3end_hypothetical_protein_219049..219199_POSITIVE 250 62 21 70 24 aact:AA02506|3end_possible_transmembrane_protein_1740131..1740281_POSITIVE 238 87 53 82 56 aact:AA01859|3end_hypothetical_protein_1251890..1252040_POSITIVE 236 60 23 151 122 aact:AA01303|3end_competence_protein_A_882882..883032_POSITIVE 236 56 16 107 65 aact:AA00943|3end_conserved_hypothetical_protein_654542..654692_POSITIVE 228 60 18 60 2 aact:AA00151|3end_polynucleotide_phosphorylase_111071..111221_POSITIVE 226 60 18 56 7 aact:AA03001|3end_probable_glycyl_radical_protein/pyruvate-formate_lyase_2096487..2096637_POSITIVE 221 70 21 73 26 aact:AA01875|3end_PTS_system,_glucose-specific_enzyme_II,_A_component_1263506..1263656_POSITIVE 217 43 18 63 37 aact:AA01106|3end_conserved_hypothetical_protein_762363..762513_POSITIVE 217 59 26 150 111 aact:AA01041|3end_hypothetical_protein_725055..725205_POSITIVE 217 59 26 41 2 aact:AA01040|3end_possible_lipoprotein_724946..725096_POSITIVE 214 99 59 93 53 aact:AA01080|3end_hypothetical_protein_747884..748034_POSITIVE 212 49 5 146 106 aact:AA01372|3end_ribonuclease_r,_virulence_associated_protein_930363..930513_POSITIVE 211 60 11 60 9 aact:AA02139|3end_possible_membrane_protein_1462218..1462368_POSITIVE 203 65 21 53 19 aact:AA02204|3end_hypothetical_protein_1501262..1501412_POSITIVE 203 55 13 71 18 aact:AA02087|3end_1,4-alpha-glucan_branching_enzyme_1421206..1421356_POSITIVE 203 57 15 71 12 aact:AA00081|3end_fatty_acid_metabolism_regulator_protein_60767..60917_POSITIVE 200 47 2 47 8 aact:AA02278|3end_conserved_hypothetical_protein_1551033..1551183_POSITIVE 199 90 41 82 26 aact:AA00692|3end_conserved_hypothetical_protein_474515..474665_POSITIVE