Origin IGS: taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg .........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 catcaagcgtctgcatacacaaaagttctgtaatgtatgcagacgcttgtcaatattatggtgtcgatataatagatgtttatgattttgctttgccagacgtattttaatttatacaggtatacaaaaccaatccgacagtttttcgcatctcaaaaaattctttgcgttctttgcgccccctgcggttaaataccgacccccagctgtccctgccggcaactttcccctttaattgattttttcccgtctttgtgataaactttcaagcggttaaaggattgaaaattta Mask Tandem Repeat Region ================================================ taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Find is-nt database================================================ Query_seq: TDE0438:TDE0439|TDE0438:TDE0439:queuine tRNA-ribosyltransferase:hypothetical protein:<-<-:494902..495193 292 taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0438:TDE0439|TDE0438:TDE0439:queuine tRNA-ribosyltransferase:hypothetical protein:<-<-:494902..495193 292 taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0438:TDE0439|TDE0438:TDE0439:queuine tRNA-ribosyltransferase:hypothetical protein:<-<-:494902..495193 292 taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 71 End: 178 ...................................................................... M P A G T A G G R Y L T A G G A K N A K N F L R C E K L S D W F C I P V .................................................................................................................. Protein_Len: 50 Strand: + Start: 34 End: 183 ................................. M T K T G K N Q L K G K V A G R D S W G S V F N R R G R K E R K E F F E M R K T V G L V L Y T C I N ............................................................................................................. Protein_Len: 44 Strand: + Start: 159 End: 287 .............................................................................................................................................................. M G F V Y L Y K L K Y V W Q S K I I N I Y Y I D T I I L T S V C I H Y R T F V Y A D A * ..... Protein_Len: 37 Strand: + Start: 182 End: 292 ..................................................................................................................................................................................... M K I R L A K Q N H K H L L Y R H H N I D K R L H T L Q N F C V C R R L M Protein_Len: 31 Strand: - Start: 186 End: 278 ......................................................................................................................................................................................... F V D P L A F D Y V D I I D V G Y Y Q C A D A Y M V S S K H M .............. Protein_Len: 38 Strand: - Start: 104 End: 217 ....................................................................................................... G C P A C L V C L I K Q S A F F Q R I P K T Y R Y L N F Y T Q C L L I M F M ........................................................................... Protein_Len: 43 Strand: - Start: 61 End: 189 ............................................................ L P F N G A P V A P P R Y K V A P P A F F A F F K K L H S F S D S Q N Q I G T Y I L M ....................................................................................................... Protein_Len: 41 Strand: - Start: 57 End: 179 ........................................................ N F P F T A P L S L Q P D T N L R L P R L S R L S N K S I R F V T P N T K Y V Q M ................................................................................................................. taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg 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: 83 Start: 29 End: 58 ............................ATTGATTTTTTCCCGTCTTTGTGATAAACT.......................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0438:TDE0439|TDE0438:TDE0439:queuine tRNA-ribosyltransferase:hypothetical protein:<-<-:494902..495193 292 taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: NC_002967_TDE0438_TDE0439|queuine tRNA-ribosyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[494902,495193]|292 HSP 1 e-value: 1.0E-164 bit: 579.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg taaattttcaatcctttaaccgcttgaaagtttatcacaaagacgggaaaaaatcaattaaaggggaaagttgccggcagggacagctgggggtcggtatttaaccgcagggggcgcaaagaacgcaaagaattttttgagatgcgaaaaactgtcggattggttttgtatacctgtataaattaaaatacgtctggcaaagcaaaatcataaacatctattatatcgacaccataatattgacaagcgtctgcatacattacagaacttttgtgtatgcagacgcttgatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUUUCAAUCCUUUAACCGCUUGAAAGUUUAUCACAAAGACGGGAAAAAAUCAAUUAAAGGGGAAAGUUGCCGGCAGGGACAGCUGGGGGUCGGUAUUUAACCGCAGGGGGCGCAAAGAACGCAAAGAAUUUUUUGAGAUGCGAAAAACUGUCGGAUUGGUUUUGUAUACCUGUAUAAAUUAAAAUACGUCUGGCAAAGCAAAAUCAUAAACAUCUAUUAUAUCGACACCAUAAUAUUGACAAGCGUCUGCAUACAUUACAGAACUUUUGUGUAUGCAGACGCUUGAUG ..(((((((...(((((((((((((..............))).)))...........))))))).))))))).(((((.......)))))((((((((((....((((((....((((.......(((((....)))))...)))).....))).)))..(((((((((...(((((((........)))))...))....)))))))))............)))))))).))..........(((((((((((((((((............)))))))))))))))))... (-82.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCAAGCGUCUGCAUACACAAAAGUUCUGUAAUGUAUGCAGACGCUUGUCAAUAUUAUGGUGUCGAUAUAAUAGAUGUUUAUGAUUUUGCUUUGCCAGACGUAUUUUAAUUUAUACAGGUAUACAAAACCAAUCCGACAGUUUUUCGCAUCUCAAAAAAUUCUUUGCGUUCUUUGCGCCCCCUGCGGUUAAAUACCGACCCCCAGCUGUCCCUGCCGGCAACUUUCCCCUUUAAUUGAUUUUUUCCCGUCUUUGUGAUAAACUUUCAAGCGGUUAAAGGAUUGAAAAUUUA ...((((((((((((((((..............)))))))))))))))).(((.(((((((..((.........))..).)))))).)))..(((((....((((........)))).(((.......))).....(((((((.......................((((.....))))......((((.....))))......)))))))......))))).((((.((((((((((..........(((.....)))...........))))))))))...))))..... (-69.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1153 120 71 211 162 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 677 138 91 203 156 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 512 138 91 109 63 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 496 131 91 230 190 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 476 145 101 48 3 NC_002967:TDE1905|5end_hypothetical_protein_1923877..1924107_NEGATIVE 442 126 86 180 131 NC_002967:TDE2264|5end_ABC_transporter,_ATP-binding/permease_protein_2302033..2302263_NEGATIVE 442 130 88 193 149 NC_002967:TDE0162|5end_hypothetical_protein_187898..188128_POSITIVE 413 141 103 44 7 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 409 125 88 95 61 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 409 125 88 171 137 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 401 137 91 221 175 NC_002967:TDE1345|5end_DNA_primase_1383439..1383669_POSITIVE 400 145 102 167 127 NC_002967:TDE2242|5end_antigen,_putative_2282034..2282264_NEGATIVE 398 133 99 155 121 NC_002967:TDE0597|5end_hypothetical_protein_637212..637442_NEGATIVE 395 142 103 146 108 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 390 116 71 188 145 NC_002967:TDE0213|5end_TPR_domain_protein_249460..249690_NEGATIVE 387 119 71 169 124 NC_002967:TDE2576|5end_RNA_pseudouridylate_synthase_family_protein_2601672..2601902_POSITIVE 374 117 72 226 179 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 374 78 31 229 179 NC_002967:TDE0193|5end_hypothetical_protein_230589..230819_NEGATIVE 366 116 73 83 30 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 362 139 94 74 21 NC_002967:TDE2089|5end_signal_recognition_particle_protein_2117563..2117793_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 476 140 98 66 21 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 442 116 73 147 96 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 430 136 93 136 90 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 401 137 91 52 6 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 395 142 103 82 44 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 390 116 71 143 100 NC_002967:TDE0214|3end_hypothetical_protein_249505..249655_NEGATIVE 387 119 71 129 84 NC_002967:TDE2575|3end_hypothetical_protein_2601712..2601862_POSITIVE 383 120 73 74 19 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 376 117 73 146 96 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 374 78 31 79 29 NC_002967:TDE0194|3end_hypothetical_protein_230739..230889_NEGATIVE 369 118 75 147 98 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 362 139 94 74 21 NC_002967:TDE2090|3end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2117563..2117713_NEGATIVE 358 98 61 49 20 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 356 117 74 143 108 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 354 112 72 76 28 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 352 135 99 92 55 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 350 108 61 70 20 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 349 116 73 146 96 NC_002967:TDE2495|3end_hypothetical_protein_2518735..2518885_NEGATIVE 348 93 60 51 16 NC_002967:TDE0158|3end_hypothetical_protein_185724..185874_NEGATIVE 343 115 73 146 96 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE