Origin IGS: tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtatatatcttttacgaatcatgcagcaaatataataatttccgaatagatataaaaaaaggcctctattgaggcctttttaacatttatggcaaatcggaatatca Mask Tandem Repeat Region ================================================ tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Find is-nt database================================================ Query_seq: TF1018:TF1019|TF1018:TF1019:50S ribosomal protein L9:N-acetylmuramoyl-L-alanine amidase:->->:1075399..1075506 108 tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1018:TF1019|TF1018:TF1019:50S ribosomal protein L9:N-acetylmuramoyl-L-alanine amidase:->->:1075399..1075506 108 tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1018:TF1019|TF1018:TF1019:50S ribosomal protein L9:N-acetylmuramoyl-L-alanine amidase:->->:1075399..1075506 108 tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Predict ORF larger than 30AA ================================================ tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg 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: 82 Start: 69 End: 98 ....................................................................TTTTACGAATCATGCAGCAAATATAATAAT.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.4 Tail_Score: -4.72486 Start: 32 End: 47 Full_Region: atagatataaaaaaa ggcctc tatt gaggcc tttttaacatttatg ...............................ggcctctattgaggcc............................................................. Find igs database================================================ Query_seq: TF1018:TF1019|TF1018:TF1019:50S ribosomal protein L9:N-acetylmuramoyl-L-alanine amidase:->->:1075399..1075506 108 tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: tfor_TF1018_TF1019|50S ribosomal protein L9:N-acetylmuramoyl-L-alanine amidase|POSITIVE:POSITIVE|[1075399,1075506]|108 HSP 1 e-value: 1.0E-42 bit: 172.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 tgatattccgatttgccataaatgttaaaaaggcctcaatagaggccnnnnnnnatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg tgatattccgatttgccataaatgttaaaaaggcctcaatagaggcctttttttatatctattcggaaattattatatttgctgcatgattcgtaaaagatatatacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUUCCGAUUUGCCAUAAAUGUUAAAAAGGCCUCAAUAGAGGCCUUUUUUUAUAUCUAUUCGGAAAUUAUUAUAUUUGCUGCAUGAUUCGUAAAAGAUAUAUACG .....((((((......(((.((((.(((((((((((....)))))))))))..)))).))))))))).....(((((((..(((.......)))..))))))).... (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUAUAUCUUUUACGAAUCAUGCAGCAAAUAUAAUAAUUUCCGAAUAGAUAUAAAAAAAGGCCUCUAUUGAGGCCUUUUUAACAUUUAUGGCAAAUCGGAAUAUCA ((((.........)))).......................((((((.....((((((((((((((((....)))))))))).....)))))).....))))))..... (-26.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 49 4 79 34 tfor:TF2797|5end_cytochrome_d_oxidase,_subunit_I_2982450..2982680_POSITIVE 275 65 29 44 6 tfor:TF2473|5end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2650470..2650700_POSITIVE 255 76 31 107 47 tfor:TF1120|5end_conserved_hypothetical_protein_1194004..1194234_POSITIVE 244 67 29 187 146 tfor:TF3050|5end_conserved_hypothetical_protein_3277041..3277271_POSITIVE 237 47 7 56 11 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 236 100 59 208 159 tfor:TF0825|5end_hypothetical_protein_883597..883827_POSITIVE 235 50 3 75 28 tfor:TF1448|5end_possible_competence_protein_1531711..1531941_POSITIVE 233 95 61 230 197 tfor:TF0045|5end_outer_membrane_protein,_TonB_dependent_receptor_49626..49856_POSITIVE 226 58 12 118 57 tfor:TF3118|5end_conserved_hypothetical_protein_3352373..3352603_POSITIVE 226 49 1 125 74 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 226 49 1 125 74 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 220 46 8 39 1 tfor:TF2281|5end_hypothetical_protein_2439574..2439804_POSITIVE 220 45 9 110 79 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 219 67 34 171 137 tfor:TF2308|5end_conserved_hypothetical_protein_2466932..2467162_POSITIVE 219 100 64 180 141 tfor:TF0756|5end_GDP-mannose_dehydratase_803171..803401_POSITIVE 218 86 45 49 6 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 217 66 30 115 78 tfor:TF1763|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_1900406..1900636_POSITIVE 216 50 9 73 24 tfor:TF2380|5end_hemagglutinin_2545012..2545242_POSITIVE 215 47 4 44 8 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 213 47 9 82 47 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 68 27 85 39 tfor:TF1018|3end_50S_ribosomal_protein_L9_1075338..1075488_POSITIVE 287 49 4 49 4 tfor:TF2796|3end_cytochrome_D_ubiquinol_oxidase,_subunit_II_2982500..2982650_POSITIVE 255 76 31 91 31 tfor:TF1119|3end_arylsulfatase_regulator:_Fe-S_oxidoreductase_1194068..1194218_POSITIVE 235 50 3 48 1 tfor:TF1447|3end_D-ribulose-phosphate-3_epimerase_1531764..1531914_POSITIVE 226 58 12 78 17 tfor:TF3116|3end_conserved_hypothetical_protein_3352413..3352563_POSITIVE 226 49 1 92 41 tfor:TF1577|3end_hypothetical_protein_1686234..1686384_POSITIVE 222 68 31 46 9 tfor:TF0358|3end_hypothetical_protein_376304..376454_POSITIVE 219 67 34 74 40 tfor:TF2306|3end_hypothetical_protein_2466915..2467065_POSITIVE 219 100 64 89 50 tfor:TF0755|3end_conserved_hypothetical_protein_803160..803310_POSITIVE 216 50 9 73 24 tfor:TF2379|3end_phosphoribosylformylglycinamidine_cyclo-ligase_(AIR_synthase)_2545092..2545242_POSITIVE 216 54 15 65 18 tfor:TF1527|3end_hypothetical_protein_1633056..1633206_POSITIVE 213 66 21 99 57 tfor:TF1996|3end_ATP-dependent_exonuclease_SbcC_2151591..2151741_POSITIVE 212 93 55 124 84 tfor:TF1607|3end_conserved_hypothetical_protein_1725838..1725988_POSITIVE 211 69 27 71 13 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE 210 69 31 82 38 tfor:TF1664|3end_conserved_hypothetical_protein_1779206..1779356_POSITIVE 209 46 1 95 48 tfor:TF1689|3end_conserved_hypothetical_protein_1806614..1806764_POSITIVE 209 66 21 49 11 tfor:TF0043|3end_conserved_hypothetical_protein_48397..48547_POSITIVE 208 69 28 82 45 tfor:TF1598|3end_conserved_hypothetical_protein_1713659..1713809_POSITIVE 206 47 6 67 25 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 206 67 29 63 18 tfor:TF0144|3end_hypothetical_protein_151483..151633_POSITIVE