Origin IGS: aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta .........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.........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 taaatttcctcaacgaataaacagttcgaagatttttggttaataaaaaagcctgtttaaatatacaggcttcatgctataatttttcgcaatgctcttacgagcagaggcggactctactaatgatagtccgccagttgccgctgttgggctagattagtagatccttgttataatcataaggataaaaatatgattaaattttttattaaattggtcatcattattctactttgcctgttattgaaaagtagcactggctcatagtaattgatgccgcaaggaatggttatcgccattccttgttttttattttatgacttgcccgaaaataagtcaaacaccgccttctttcggcgcttaataagtttcaatttttggcatagcccaaggtttttcttgaaaaagatatttatcgtattaatatttatacttatattttaaatgtgattattcataaaggtagagcttt Mask Tandem Repeat Region ================================================ aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Find is-nt database================================================ Query_seq: AA02776:AA02777|AA02776:AA02777:conserved hypothetical protein:tRNA-guanine transglycosylase:->->:1940967..1941438 472 aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02776:AA02777|AA02776:AA02777:conserved hypothetical protein:tRNA-guanine transglycosylase:->->:1940967..1941438 472 aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02776:AA02777|AA02776:AA02777:conserved hypothetical protein:tRNA-guanine transglycosylase:->->:1940967..1941438 472 aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 36 End: 155 ................................... M S I N I N T I N I F F K K N L G L C Q K L K L I K R R K K A V F D L F S G K S ............................................................................................................................................................................................................................................................................................................................. Protein_Len: 40 Strand: + Start: 174 End: 293 ............................................................................................................................................................................. M A I T I P C G I N Y Y E P V L L F N N R Q S R I M M T N L I K N L I I F L S L ................................................................................................................................................................................... Protein_Len: 39 Strand: - Start: 321 End: 437 ................................................................................................................................................................................................................................................................................................................................ G L L P L Q R V I M L L T R R Q E Y S C Q S F N Y C S A Q I N L C A K K N V M ................................... Protein_Len: 57 Strand: - Start: 32 End: 202 ............................... F I L I F I L V I F I K K L F F R P S H W F N F S I L R R F F A T N S K N E P L D Y F L F C P I A I V M G Q P M M .............................................................................................................................................................................................................................................................................. aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta 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: 87 Start: 132 End: 161 ...................................................................................................................................TTTGACTTATTTTCGGGCAAGTCATAAAAT....................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.7 Tail_Score: -5.86976 Start: 168 End: 193 Full_Region: tagtaattgatgccg caaggaatggt tatc gccattccttg ttttttattttatga .......................................................................................................................................................................caaggaatggttatcgccattccttg....................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 88 HP_score: -6.4 Tail_Score: -5.4505 Start: 403 End: 422 Full_Region: AAATTATAGCATGAA GCCTGTAT ATTT AAACAGGC TTTTTTATTAACCAA ..................................................................................................................................................................................................................................................................................................................................................................................................................GCCTGTATATTTAAACAGGC.................................................. Find igs database================================================ Query_seq: AA02776:AA02777|AA02776:AA02777:conserved hypothetical protein:tRNA-guanine transglycosylase:->->:1940967..1941438 472 aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Intra-Species Hit: Count: 1 Min: 1 Max: 472 Len: 472 Subject: aact_AA02776_AA02777|conserved hypothetical protein:tRNA-guanine transglycosylase|POSITIVE:POSITIVE|[1940967,1941438]|472 HSP 1 e-value: 0.0 bit: 936.0 Len: 472 Query Start:1 Query End:472 Subject Strand: POSITIVE Subject Start: 1 Subject End: 472 aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta aaagctctacctttatgaataatcacatttaaaatataagtataaatattaatacgataaatatctttttcaagaaaaaccttgggctatgccaaaaattgaaacttattaagcgccgaaagaaggcggtgtttgacttattttcgggcaagtcataaaataaaaaacaaggaatggcgataaccattccttgcggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgattataacaaggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttgaggaaattta Inter-species Hit: Count: 2 Min: 159 Max: 462 Len: 304 Subject: NC_000907_HI0244_HI0245|queuine tRNA-ribosyltransferase:S-adenosylmethionine:tRNA ribosyltransferase-isomerase|NEGATIVE:NEGATIVE|[272749, 273091]|343 HSP 1 e-value: 5.0E-52 bit: 206.0 Len: 304 Query Start:159 Query End:462 Subject Strand: NEGATIVE Subject Start: 9 Subject End: 312 ..............................................................................................................................................................aataaaaaacaaggaatggcgataaccattccttg-cggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgatta-taaca-----aggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttg.......... ..............................................................................................................................................................aataaagaacaagagatggcggtaaccatctcttgtcggcatcaactactaatagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaacttaatcataaatttagtcatatttttatccttagtatgattaacaaactcaggatctacgaa-atagcccgacagcggcaactggcggactatc-ttagtaga-tccgcctctgctc-aaagagcattg-aaaatatgatatcacaaagcctgtattttttaacaggcttttttgttta--aaaaatcttcgaactgtttattcgttg.......... Subject: NC_007146_NTHI0350_NTHI0351|queuine tRNA-ribosyltransferase:S-adenosylmethionine:tRNA ribosyltransferase-isomerase|NEGATIVE:NEGATIVE|[334800, 335143]|344 HSP 1 e-value: 2.0E-51 bit: 204.0 Len: 304 Query Start:159 Query End:462 Subject Strand: NEGATIVE Subject Start: 9 Subject End: 313 ..............................................................................................................................................................aataaaaaacaaggaatggcgataaccattccttg-cggcatcaattactatgagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaatttaataaaaaatttaatcatatttttatccttatgatta-taaca-----aggatctactaatctagcccaacagcggcaactggcggactatcattagtagagtccgcctctgctcgtaagagcattgcgaaaaattatagcatgaagcctgtatatttaaacaggcttttttattaaccaaaaatcttcgaactgtttattcgttg.......... ..............................................................................................................................................................aataaagaacaagagatggcggtaaccatctcttgtcggcatcaactactaatagccagtgctacttttcaataacaggcaaagtagaataatgatgaccaacttaatcataaatttagtcatatttttatccttagtatgattaacaaactcaggatctacgaa-atagcccgacagcggcaactggcggactatc-ttagtaga-tccgcctctgctc-aaagagcattg-aaaatatgatatcacaaagcctgtattttttaacaggcttttttgttca-aaaaaatcttcgaactgtttattcgttg.......... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAAAACAAGGAAUGGCGAUAACCAUUCCUUGCGGCAUCAAUUACUAUGAGCCAGUGCUACUUUUCAAUAACAGGCAAAGUAGAAUAAUGAUGACCAAUUUAAUAAAAAAUUUAAUCAUAUUUUUAUCCUUAUGAUUAUAACAAGGAUCUACUAAUCUAGCCCAACAGCGGCAACUGGCGGACUAUCAUUAGUAGAGUCCGCCUCUGCUCGUAAGAGCAUUGCGAAAAAUUAUAGCAUGAAGCCUGUAUAUUUAAACAGGCUUUUUUAUUAACCAAAAAUCUUCGAACUGUUUAUUCGUUG (((((((..((((((((((......)))))))))).(((.(((.......)))))).((((((.(((((......((((....................................((((((((..........))))))))......((((((((((((.(((.((..(((......)))..)).)))..))))))))).))))))).(((((....)))))....)))))....)))))).((((((((........))))))))))))))).............((((.......))))... (-79.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACGAAUAAACAGUUCGAAGAUUUUUGGUUAAUAAAAAAGCCUGUUUAAAUAUACAGGCUUCAUGCUAUAAUUUUUCGCAAUGCUCUUACGAGCAGAGGCGGACUCUACUAAUGAUAGUCCGCCAGUUGCCGCUGUUGGGCUAGAUUAGUAGAUCCUUGUUAUAAUCAUAAGGAUAAAAAUAUGAUUAAAUUUUUUAUUAAAUUGGUCAUCAUUAUUCUACUUUGCCUGUUAUUGAAAAGUAGCACUGGCUCAUAGUAAUUGAUGCCGCAAGGAAUGGUUAUCGCCAUUCCUUGUUUUUUAUU ...(((((.....)))))..((((.....(((((((((((((((((........)))))).(((((.........(((((..(((((....)))))...))))).(((((((((..(((((((.((((....)))).))))))).)))))))))(((((((.......)))))))......))))).....)))))))))))...))))..(((((...((((..((((((((((....)))))))..)))....))))..)))))..((((((((((((....))))))))))))........ (-98.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 210 165 113 61 aact:AA00574|5end_regulatory_protein_392113..392343_POSITIVE 371 210 163 82 29 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 364 201 161 172 134 aact:AA02929|5end_hypothetical_protein_2049189..2049419_POSITIVE 364 220 171 191 127 aact:AA02688|5end_hydrogenase_4_component_E_1873977..1874207_POSITIVE 348 206 165 77 27 aact:AA02692|5end_hydrogenase_4_subunit;_hydrogenase_3_subunit_1876324..1876554_POSITIVE 345 210 163 215 181 aact:AA02405|5end_conserved_hypothetical_protein_1652430..1652660_POSITIVE 345 210 163 163 129 aact:AA02404|5end_hypothetical_protein_1652378..1652608_POSITIVE 336 193 151 150 103 aact:AA00348|5end_50S_ribosomal_protein_L1_232570..232800_POSITIVE 335 188 149 45 14 aact:AA00592|5end_conserved_hypothetical_protein_(membrane/transport_protein)_405536..405766_POSITIVE 334 216 171 78 36 aact:AA01928|5end_ATP-dependent_RNA_helicase_1301986..1302216_POSITIVE 334 217 171 228 187 aact:AA00040|5end_thiol:disulfide_interchange_protein_31358..31588_POSITIVE 327 208 169 161 121 aact:AA00582|5end_conserved_hypothetical_protein_397904..398134_POSITIVE 326 240 197 152 107 aact:AA02137|5end_transcriptional_regulators_(TetR/AcrR_family)_1460453..1460683_POSITIVE 326 185 148 214 168 aact:AA02025|5end_hypothetical_protein_1378667..1378897_POSITIVE 320 209 167 152 110 aact:AA00849|5end_MraZ_cell_division_protein_586038..586268_POSITIVE 319 208 162 109 52 aact:AA01753|5end_conserved_hypothetical_protein_1185322..1185552_POSITIVE 317 205 162 218 171 aact:AA01299|5end_competence_protein_C_880946..881176_POSITIVE 317 227 181 76 27 aact:AA00190|5end_triosephosphate_isomerase_134088..134318_POSITIVE 317 206 164 45 10 aact:AA00132|5end_conserved_hypothetical_protein_(possible_regulator_protein,_VirR_family)_94938..95168_POSITIVE 312 216 173 116 64 aact:AA01710|5end_ribosomal_protein_S6_modification_protein_1159348..1159578_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 201 161 147 109 aact:AA02928|3end_conserved_hypothetical_protein_2049244..2049394_POSITIVE 345 210 163 147 113 aact:AA02402|3end_O-sialoglycoprotein_endopeptidase_1652442..1652592_POSITIVE 336 193 151 142 95 aact:AA00347|3end_50S_ribosomal_protein_L11_232642..232792_POSITIVE 327 208 169 143 103 aact:AA00581|3end_thiosulfate_sulfurtransferase_(rhodanese)_397966..398116_POSITIVE 326 240 197 95 50 aact:AA02136|3end_aspartate_aminotransferase_1460476..1460626_POSITIVE 320 195 157 150 99 aact:AA02687|3end_hydrogenase-4_component_D_1874043..1874193_POSITIVE 319 208 162 99 42 aact:AA01751|3end_conserved_hypothetical_protein_1185392..1185542_POSITIVE 314 190 145 79 38 aact:AA01357|3end_5-formyltetrahydrofolate_cyclo-ligase-family_protein_919785..919935_POSITIVE 311 209 163 55 2 aact:AA02492|3end_glutathione_S-transferase_1730054..1730204_POSITIVE 302 185 143 77 29 aact:AA01059|3end_orotate_phosphoribosyltransferase_735773..735923_POSITIVE 301 218 171 79 16 aact:AA02990|3end_beta_hexosaminadase_2090596..2090746_POSITIVE 300 184 151 134 98 aact:AA01107|3end_adenylosuccinate_lyase_763754..763904_POSITIVE 294 206 163 144 103 aact:AA00943|3end_conserved_hypothetical_protein_654542..654692_POSITIVE 291 204 161 115 76 aact:AA01158|3end_ribosome_associated_heat_shock_protein_15_homolog_792892..793042_POSITIVE 291 213 171 38 1 aact:AA00847|3end_S-adenosyl-dependent_methyltransferase_586005..586155_POSITIVE 290 185 161 146 116 aact:AA02275|3end_conserved_hypothetical_protein_1549955..1550105_POSITIVE 287 206 162 72 31 aact:AA00525|3end_hypothetical_protein_359459..359609_POSITIVE 286 210 161 142 101 aact:AA03008|3end_GTP-binding_protein_era_homolog_(GTPase)_2101072..2101222_POSITIVE 285 204 161 72 19 aact:AA00446|3end_transposase_311566..311716_POSITIVE 284 217 174 140 95 aact:AA02217|3end_deoxyribose-phosphate_aldolase_1509835..1509985_POSITIVE