Origin IGS: tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat .........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 ataataagaatttgtactgcacctaaaatcttggacacaagattggaggtgcagtttttttcaattatttaatacagtttgctttttattcgtgataaaggtacaaaaaataaaaataaacattgactatttaatataaaaaaagttaaaatgtaaacatgaaataattttaaaattaaatattttaataaagggggca Mask Tandem Repeat Region ================================================ tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Find is-nt database================================================ Query_seq: FN1546:FN1547|FN1546:FN1547:translation elongation factor EF-G:PTS permease for N-acetylglucosamine and glucose:<-<-:61692..61890 199 tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1546:FN1547|FN1546:FN1547:translation elongation factor EF-G:PTS permease for N-acetylglucosamine and glucose:<-<-:61692..61890 199 tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1546:FN1547|FN1546:FN1547:translation elongation factor EF-G:PTS permease for N-acetylglucosamine and glucose:<-<-:61692..61890 199 tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 24 End: 128 ....................... M L K L F H V Y I L T F F I L N S Q C L F L F F V P L S R I K S K L Y ....................................................................... Protein_Len: 40 Strand: - Start: 64 End: 183 ............................................................... I L Y D I N I K I K Q V K I V F L F C V T N F L Q F F S C R W D Q T W S K L H M ................ tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat 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================================================ tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1546:FN1547|FN1546:FN1547:translation elongation factor EF-G:PTS permease for N-acetylglucosamine and glucose:<-<-:61692..61890 199 tgccccctttattaaaatatttaattttaaaattatttcatgtttacattttaactttttttatattaaatagtcaatgtttatttttattttttgtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Intra-Species Hit: Count: 1 Min: 96 Max: 199 Len: 104 Subject: NC_003454_FN1546_FN1547|translation elongation factor EF-G:PTS permease for N-acetylglucosamine and glucose|NEGATIVE:NEGATIVE|[61692,61890]|199 HSP 1 e-value: 7.0E-40 bit: 165.0 Len: 104 Query Start:96 Query End:199 Subject Strand: POSITIVE Subject Start: 96 Subject End: 199 ...............................................................................................gtacctttatcacgaataaaaagcaaactgtattaaataattgnnnnnnnctgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat ...............................................................................................gtacctttatcacgaataaaaagcaaactgtattaaataattgaaaaaaactgcacctccaatcttgtgtccaagattttaggtgcagtacaaattcttattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUACCUUUAUCACGAAUAAAAAGCAAACUGUAUUAAAUAAUUGAAAAAAACUGCACCUCCAAUCUUGUGUCCAAGAUUUUAGGUGCAGUACAAAUUCUUAUUAU .............((((.....((.....))..................(((((((((..(((((((....)))))))..)))))))))....))))....... (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAAGAAUUUGUACUGCACCUAAAAUCUUGGACACAAGAUUGGAGGUGCAGUUUUUUUCAAUUAUUUAAUACAGUUUGCUUUUUAUUCGUGAUAAAGGUAC .......(((.....(((((((((..(((((((....)))))))..)))))))))....))).................(((((((..........))))))). (-29.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 727 89 44 135 90 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 727 89 44 135 90 NC_003454:FN0485|5end_Transposase_1130267..1130497_POSITIVE 718 89 45 222 178 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 702 88 45 123 80 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 702 88 45 135 92 NC_003454:FN1887|5end_Transposase_371671..371901_POSITIVE 695 89 42 137 91 NC_003454:FN1443|5end_Transposase_2111518..2111748_NEGATIVE 695 89 42 137 91 NC_003454:FN0786|5end_Transposase_1442465..1442695_POSITIVE 695 89 42 137 91 NC_003454:FN0135|5end_Transposase_770238..770468_POSITIVE 608 45 1 231 187 NC_003454:FN1546|5end_translation_elongation_factor_EF-G_61601..61831_NEGATIVE 597 89 50 208 170 NC_003454:FN0210|5end_Transcriptional_regulator,_COPG_family_836998..837228_POSITIVE 398 89 49 201 161 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 398 89 49 71 31 NC_003454:FN0839|5end_hypothetical_protein_1501426..1501656_NEGATIVE 392 71 43 231 203 NC_003454:FN0234|5end_hypothetical_protein_859499..859729_NEGATIVE 231 84 43 101 48 NC_003454:FN1236|5end_Choline_transport_protein_1893480..1893710_NEGATIVE 222 79 52 120 96 NC_003454:FN0219|5end_Autolysin_response_regulator_843316..843546_NEGATIVE 221 99 56 164 106 NC_003454:FN1754|5end_thiazole_synthase_251117..251347_NEGATIVE 218 85 52 222 189 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 217 79 52 181 152 NC_003454:FN0045|5end_Shikimate_5-dehydrogenase_683012..683242_POSITIVE 210 68 21 191 141 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 205 98 51 183 143 NC_003454:FN1640|5end_LSU_ribosomal_protein_L22P_138517..138747_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 727 89 44 60 15 NC_003454:FN0484|3end_Lipase_1130272..1130422_POSITIVE 726 90 43 84 36 NC_003454:FN1905|3end_168_kDa_surface-layer_protein_precursor_393653..393803_NEGATIVE 718 89 45 63 19 NC_003454:FN1973|3end_Translation_initiation_inhibitor_472230..472380_NEGATIVE 702 88 45 138 95 NC_003454:FN1886|3end_hypothetical_protein_371754..371904_POSITIVE 692 89 43 74 28 NC_003454:FN0235|3end_ABC_transporter_ATP-binding_protein_859674..859824_NEGATIVE 668 89 49 80 40 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 613 95 51 86 42 NC_003454:FN1221|3end_hypothetical_protein_1881290..1881440_POSITIVE 486 89 48 85 44 NC_003454:FN1500|3end_Nickel_transport_ATP-binding_protein_nikE_5193..5343_NEGATIVE 461 89 41 83 33 NC_003454:FN1545|3end_Ferredoxin_like_protein_59497..59647_POSITIVE 460 89 41 81 28 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 434 89 42 69 23 NC_003454:FN0178|3end_UNC-44_ankyrins_802390..802540_NEGATIVE 427 92 51 46 5 NC_003454:FN1019|3end_3-hydroxybutyryl-CoA_dehydrogenase_1672945..1673095_NEGATIVE 405 99 51 98 50 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 390 89 46 76 33 NC_003454:FN1546|3end_translation_elongation_factor_EF-G_59529..59679_NEGATIVE 373 89 44 70 25 NC_003454:FN1144|3end_hypothetical_protein_1793403..1793553_NEGATIVE 373 89 42 70 29 NC_003454:FN0435|3end_Purine_nucleoside_phosphorylase_1077821..1077971_POSITIVE 364 89 41 77 29 NC_003454:FN1498|3end_Integral_membrane_protein_3542..3692_POSITIVE 333 90 46 85 48 NC_003454:FN0436|3end_Urea_carboxylase_1077851..1078001_NEGATIVE 328 89 49 79 39 NC_003454:FN1499|3end_Cell_surface_protein_5166..5316_POSITIVE 316 89 45 80 44 NC_003454:FN0980|3end_hypothetical_protein_1632815..1632965_POSITIVE