Origin IGS: aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc .........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 gaaaaacagcttttttccgccttacgatttgtgtataaactgcttacaatccatgagaccatttagagtcacacctcttcttatcgggttatcagttggtctccataggctttgggagtaggaaagcacgaatgtcccatagaagagcattgcgccccttcgtcctattgctctcgctgtactcatggtcagccctagatagagaggctttagcttcgctgcaattcgccatcagccatcacacaaaatcacggatgagccacacatgagacctttgcacagggcaaccgcatcaaaaatttcgagaaaatacaagttgctaattttcaaatgattgcatttcggagattatactcaaagataaagaatatactcaaaactatgattgataatcaggtacttacattttgatgcggttgccctgcctccacctccttatttttcaaaggtctcgagtttatatatatatttgtctagttgtaatatatgtaggtt Mask Tandem Repeat Region ================================================ aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Find is-nt database================================================ Query_seq: PG0742:PG0744|PG0742:PG0744:antigen PgaA:RNA methyltransferase, TrmH family:<-<-:790728..791222 495 aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0742:PG0744|PG0742:PG0744:antigen PgaA:RNA methyltransferase, TrmH family:<-<-:790728..791222 495 aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0742:PG0744|PG0742:PG0744:antigen PgaA:RNA methyltransferase, TrmH family:<-<-:790728..791222 495 aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 166 End: 261 ..................................................................................................................................................................... M K I S N L Y F L E I F D A V A L C K G L M C G S S V I L C D G .......................................................................................................................................................................................................................................... Protein_Len: 47 Strand: + Start: 261 End: 401 .................................................................................................................................................................................................................................................................... M M A N C S E A K A S L S R A D H E Y S E S N R T K G R N A L L W D I R A F L L P K P M E T N .............................................................................................. Protein_Len: 60 Strand: + Start: 271 End: 471 .............................................................................................................................................................................................................................................................................. M A A K L K P L Y L G L T M S T A R A I G R R G A M L F Y G T F V L S Y S Q S L W R P T D N P I R R G V T L N G L M D C ........................ Protein_Len: 30 Strand: - Start: 378 End: 467 ......................................................................................................................................................................................................................................................................................................................................................................................... E W L R H L G V S L G I L L P T V R F P R M S Q L C N I C M ............................ Protein_Len: 57 Strand: - Start: 230 End: 400 ..................................................................................................................................................................................................................................... T H S M R S K T H H S I A F Q L S A L A E R D L A S W S Y L S L L L V F P R L A R R H S M R A K R S G F G I S V M ............................................................................................... Protein_Len: 36 Strand: - Start: 165 End: 272 .................................................................................................................................................................... K F I L L K Y K R S I K S A T A R H L P R M H P E D T I K H S P Q H R M ............................................................................................................................................................................................................................... Protein_Len: 39 Strand: - Start: 88 End: 204 ....................................................................................... F T L V Q N D I M T K L I N K I K S Y L R R F A I M Q F N A V Q I K E F N K M ................................................................................................................................................................................................................................................................................................... Protein_Len: 36 Strand: - Start: 3 End: 110 .. R C I N C S S L Y I Y L S S V K S F Y P P P P L A V A D F H L Y R I I M ................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 30 Strand: - Start: 2 End: 91 . G V Y I V V L C I Y I Y V R S R Q F I L L H L C P L R M L M .................................................................................................................................................................................................................................................................................................................................................................................................................... aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc 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================================================ aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0742:PG0744|PG0742:PG0744:antigen PgaA:RNA methyltransferase, TrmH family:<-<-:790728..791222 495 aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Intra-Species Hit: Count: 1 Min: 1 Max: 495 Len: 495 Subject: NC_002950_PG0742_PG0744|antigen PgaA:RNA methyltransferase, TrmH family|NEGATIVE:NEGATIVE|[790728,791222]|495 HSP 1 e-value: 0.0 bit: 981.0 Len: 495 Query Start:1 Query End:495 Subject Strand: POSITIVE Subject Start: 1 Subject End: 495 aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc aacctacatatattacaactagacaaatatatatataaactcgagacctttgaaaaataaggaggtggaggcagggcaaccgcatcaaaatgtaagtacctgattatcaatcatagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgtgcaaaggtctcatgtgtggctcatccgtgattttgtgtgatggctgatggcgaattgcagcgaagctaaagcctctctatctagggctgaccatgagtacagcgagagcaataggacgaaggggcgcaatgctcttctatgggacattcgtgctttcctactcccaaagcctatggagaccaactgataacccgataagaagaggtgtgactctaaatggtctcatggattgtaagcagtttatacacaaatcgtaaggcggaaaaaagctgtttttc Inter-species Hit: Count: 1 Min: 113 Max: 217 Len: 105 Subject: tfor_TF0891_TF0892|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[940856,940975]|120 HSP 1 e-value: 8.0E-48 bit: 192.0 Len: 105 Query Start:113 Query End:217 Subject Strand: POSITIVE Subject Start: 3 Subject End: 107 ................................................................................................................atagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgt...................................................................................................................................................................................................................................................................................... ................................................................................................................atagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgt...................................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUUUGAGUAUAUUCUUUAUCUUUGAGUAUAAUCUCCGAAAUGCAAUCAUUUGAAAAUUAGCAACUUGUAUUUUCUCGAAAUUUUUGAUGCGGUUGCCCUGU ...(((((((((((((((.........)))))))..)).))))))..................((((((.(((((..............)))))))))))..... (-16.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGGGCAACCGCAUCAAAAAUUUCGAGAAAAUACAAGUUGCUAAUUUUCAAAUGAUUGCAUUUCGGAGAUUAUACUCAAAGAUAAAGAAUAUACUCAAAACUAU ...((....))..............(((..............(((((((((((((....))))).))))))))...((.........)).....)))........ (-13.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 28 1 231 204 NC_002950:PG0742|5end_antigen_PgaA_790637..790867_NEGATIVE 228 100 56 124 69 NC_002950:PG1061|5end_ISPg6,_transposase_1129818..1130048_NEGATIVE 225 100 63 105 68 NC_002950:PG0876|5end_tRNA_modification_GTPase_940806..941036_NEGATIVE 224 78 36 54 14 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 223 67 25 226 176 NC_002950:PG2165|5end_glycyl-tRNA_synthetase_2271669..2271899_NEGATIVE 221 43 1 126 82 NC_002950:PG0719|5end_sensor_histidine_kinase_772979..773209_NEGATIVE 220 78 36 54 14 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 220 56 16 143 94 NC_002950:PG0293|5end_secretion_activator_protein,_putative_328671..328901_NEGATIVE 220 78 36 54 14 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 219 100 64 136 96 NC_002950:PG0319|5end_hypothetical_protein_352949..353179_POSITIVE 218 100 57 147 99 NC_002950:PG0156|5end_modification_methylase,_HemK_family_178828..179058_POSITIVE 215 98 53 62 14 NC_002950:PG0354|5end_hypothetical_protein_389283..389513_NEGATIVE 212 100 62 49 7 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 206 100 63 111 80 NC_002950:PG0997|5end_transcriptional_regulator,_putative_1056666..1056896_POSITIVE 201 47 8 197 150 NC_002950:PG2179|5end_NADH-ubiquinone_oxidoreductase_2287806..2288036_NEGATIVE 200 96 69 56 32 NC_002950:PG2060|5end_thymidylate_synthase_2157573..2157803_POSITIVE 198 100 52 179 133 NC_002950:PG2082|5end_POT_family_protein_2183384..2183614_NEGATIVE 198 42 5 75 40 NC_002950:PG1073|5end_D-lysine_5,6-aminomutase,_alpha_subunit_1140395..1140625_POSITIVE 198 69 27 198 160 NC_002950:PG0377|5end_30S_ribosomal_protein_S2_406920..407150_POSITIVE 197 100 74 173 141 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 95 56 120 81 NC_002950:PG0530|3end_carbamoyl-phosphate_synthase,_large_subunit_579036..579186_POSITIVE 225 100 63 73 36 NC_002950:PG0877|3end_hypothetical_protein_940838..940988_NEGATIVE 221 43 1 129 85 NC_002950:PG0720|3end_DNA-binding_response_regulator_772976..773126_NEGATIVE 212 100 62 44 2 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 208 47 1 51 5 NC_002950:PG0161|3end_hypothetical_protein_184267..184417_NEGATIVE 203 100 61 110 67 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 200 39 1 55 13 NC_002950:PG1026|3end_hypothetical_protein_1088988..1089138_POSITIVE 198 42 5 47 12 NC_002950:PG1072|3end_MutS_family_protein_1140447..1140597_POSITIVE 198 69 27 63 25 NC_002950:PG0376|3end_30S_ribosomal_protein_S9_406865..407015_POSITIVE 196 44 2 63 19 NC_002950:PG0532|3end_hypothetical_protein_581249..581399_NEGATIVE 194 79 36 101 67 NC_002950:PG1135|3end_bacterial_sugar_transferase_1216554..1216704_POSITIVE 192 96 52 148 107 NC_002950:PG2083|3end_hypothetical_protein_2183410..2183560_NEGATIVE 192 99 53 127 76 NC_002950:PG1094|3end_phosphomannomutase_1160221..1160371_POSITIVE 191 90 45 109 71 NC_002950:PG1764|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_1851796..1851946_NEGATIVE 189 98 51 74 24 NC_002950:PG0879|3end_hypothetical_protein_941931..942081_NEGATIVE 188 100 55 51 2 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 188 99 61 130 91 NC_002950:PG0685|3end_ABC_transporter,_ATP-binding_protein_740855..741005_POSITIVE 188 79 35 64 19 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 187 58 11 98 54 NC_002950:PG1798|3end_immunoreactive_46_kDa_antigen_PG99_1893028..1893178_NEGATIVE 186 100 63 59 17 NC_002950:PG0624|3end_hypothetical_protein_678664..678814_POSITIVE