Origin IGS: tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattttcactccaagtcattataaataatcacttattttggacttgtggtgaacaagtcctttttttgcaaaaatcttagcctgctgctgaatttaattatttatttttaagatattataggtgcattgtattatatgatggtagaatactctcttttctactcattaaaataaa Mask Tandem Repeat Region ================================================ tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Find is-nt database================================================ Query_seq: AA00948:AA00949|AA00948:AA00949:probable ECF-family RNA polymerase sigma factor:hypothetical protein:->->:656184..656359 176 tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00948:AA00949|AA00948:AA00949:probable ECF-family RNA polymerase sigma factor:hypothetical protein:->->:656184..656359 176 tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00948:AA00949|AA00948:AA00949:probable ECF-family RNA polymerase sigma factor:hypothetical protein:->->:656184..656359 176 tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Predict ORF larger than 30AA ================================================ tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta 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================================================ tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.8 Tail_Score: -5.40474 Start: 116 End: 136 Full_Region: ataatcacttatttt ggacttgt ggtga acaagtcc tttttttgcaaaaat ...................................................................................................................ggacttgtggtgaacaagtcc........................................ Find igs database================================================ Query_seq: AA00948:AA00949|AA00948:AA00949:probable ECF-family RNA polymerase sigma factor:hypothetical protein:->->:656184..656359 176 tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: aact_AA00948_AA00949|probable ECF-family RNA polymerase sigma factor:hypothetical protein|POSITIVE:POSITIVE|[656184,656359]|176 HSP 1 e-value: 7.0E-83 bit: 307.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcnnnnnnnggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta tttattttaatgagtagaaaagagagtattctaccatcatataatacaatgcacctataatatcttaaaaataaataattaaattcagcagcaggctaagatttttgcaaaaaaaggacttgttcaccacaagtccaaaataagtgattatttataatgacttggagtgaaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUUUAAUGAGUAGAAAAGAGAGUAUUCUACCAUCAUAUAAUACAAUGCACCUAUAAUAUCUUAAAAAUAAAUAAUUAAAUUCAGCAGCAGGCUAAGAUUUUUGCAAAAAAAGGACUUGUUCACCACAAGUCCAAAAUAAGUGAUUAUUUAUAAUGACUUGGAGUGAAAAUUA ((((((((.(((.((((((.........)))))))))(((........)))................))))))))...........(((.....)))..((((((..(.......((((((((.....))))))))....(((((.((((....)))).)))))..)..)))))). (-31.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUCACUCCAAGUCAUUAUAAAUAAUCACUUAUUUUGGACUUGUGGUGAACAAGUCCUUUUUUUGCAAAAAUCUUAGCCUGCUGCUGAAUUUAAUUAUUUAUUUUUAAGAUAUUAUAGGUGCAUUGUAUUAUAUGAUGGUAGAAUACUCUCUUUUCUACUCAUUAAAAUAAA ....................(((((((((((((((((...((((((((.....))))))))...........((((.(((((.....)))))))))......................))))))).))))).)))))(((((((((((.........)))))).)))))....... (-33.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 129 84 225 186 aact:AA01140|5end_anaerobic_dimethyl_sulfoxide_reductase,_chain_C_781610..781840_POSITIVE 238 130 86 152 110 aact:AA01619|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthase)_1094422..1094652_POSITIVE 231 139 93 179 125 aact:AA01962|5end_recombination_protein_rec2_1326200..1326430_POSITIVE 224 127 82 73 30 aact:AA01422|5end_cell_division_protein_E,_ABC_system_ATP-binding_protein_956009..956239_POSITIVE 222 122 81 211 157 aact:AA02807|5end_leukotoxin_activator_(leukotoxin_C)_1977102..1977332_POSITIVE 218 126 84 74 32 aact:AA02784|5end_NAD+_dependent_acetaldehyde-alcohol_dehydrogenase,_iron-containing_1949101..1949331_POSITIVE 217 110 86 82 53 aact:AA00819|5end_D-alanyl-D-alanine_carboxypeptidase_562644..562874_POSITIVE 215 121 88 147 105 aact:AA01527|5end_hypothetical_protein_1025704..1025934_POSITIVE 215 56 24 81 47 aact:AA00596|5end_uridylate_kinase_407496..407726_POSITIVE 212 125 83 81 43 aact:AA01610|5end_hypothetical_protein_1088811..1089041_POSITIVE 212 130 84 162 121 aact:AA00892|5end_selenocysteine-specific_elongation_factor_(SelB_translation_factor)_618023..618253_POSITIVE 212 66 34 112 79 aact:AA00574|5end_regulatory_protein_392113..392343_POSITIVE 207 125 85 136 100 aact:AA00506|5end_ATP-dependent_RNA_helicase_protein_351681..351911_POSITIVE 203 140 91 219 180 aact:AA02704|5end_dihydrolipoamide_succinyltransferase_1885495..1885725_POSITIVE 203 140 91 89 50 aact:AA02703|5end_hypothetical_protein_1885365..1885595_POSITIVE 202 136 91 43 1 aact:AA01453|5end_D-xylose_isomerase_973457..973687_POSITIVE 199 170 127 182 129 aact:AA00631|5end_hypothetical_protein_433678..433908_POSITIVE 198 130 88 65 37 aact:AA02959|5end_pyrroline-5-carboxylate_(P5C)_reductase_2070540..2070770_POSITIVE 198 125 86 183 141 aact:AA00606|5end_membrane-associated_zinc_metalloprotease_411808..412038_POSITIVE 197 119 83 195 169 aact:AA02168|5end_possible_protease;_heat_shock_protein_1483529..1483759_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 135 91 129 86 aact:AA00227|3end_hypothetical_sequence_156642..156792_POSITIVE 238 130 86 48 6 aact:AA01618|3end_lipoprotein_releasing_system_transmembrane_protein_1094398..1094548_POSITIVE 231 139 93 129 75 aact:AA01961|3end_lipid_A_export_ATP-binding/permease_protein_msbA_1326230..1326380_POSITIVE 225 129 84 148 103 aact:AA01453|3end_D-xylose_isomerase_974853..975003_POSITIVE 212 130 84 113 72 aact:AA00890|3end_conserved_hypothetical_protein_618054..618204_POSITIVE 207 125 85 108 72 aact:AA00505|3end_hypothetical_protein_351733..351883_POSITIVE 202 130 82 147 102 aact:AA02409|3end_DNA_ligase_1655404..1655554_POSITIVE 197 119 83 60 34 aact:AA02167|3end_hypothetical_protein_1483474..1483624_POSITIVE 197 137 94 149 93 aact:AA02003|3end_purine_nucleotide_synthesis_repressor_protein_1361708..1361858_POSITIVE 196 124 85 123 88 aact:AA00134|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_(menaquinone_biosynthetic_protein)_96329..96479_POSITIVE 195 123 84 92 55 aact:AA02674|3end_formate_dehydrogenase-related_protein_1860732..1860882_POSITIVE 195 123 85 92 58 aact:AA01488|3end_ATP_synthase_F0,_subunit_b_1001223..1001373_POSITIVE 194 136 91 84 46 aact:AA02675|3end_formate_dehydrogenase_alpha_subunit_1861699..1861849_POSITIVE 194 108 85 70 47 aact:AA02668|3end_gluconate_permease_1858121..1858271_POSITIVE 194 124 86 67 30 aact:AA02301|3end_chorismate_lyase_1572795..1572945_POSITIVE 193 122 81 80 38 aact:AA01056|3end_conserved_hypothetical_protein_734168..734318_POSITIVE 193 137 95 143 104 aact:AA00448|3end_C-terminal_region_of_competence_protein_M_313058..313208_POSITIVE 191 108 84 133 100 aact:AA03003|3end_GTP-binding_membrane_protein_2098447..2098597_POSITIVE 191 170 130 149 109 aact:AA00028|3end_conserved_hypothetical_protein_(possible_type_III_restriction-modification_system_restriction_subunit)_23293..23443_POSITIVE 189 156 114 76 29 aact:AA01631|3end_dihydrodipicolinate_reductase_1103915..1104065_POSITIVE