Origin IGS: aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtcaaatatctatacctttgtagaggttgtgtgccaacctatgcacacaccggaacgagagtctgcgccgtaagccgtttttttatggctctgcctcccaaagataaacaatcgtt Mask Tandem Repeat Region ================================================ aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Find is-nt database================================================ Query_seq: PG1731:PG1732|PG1731:PG1732:3-dehydroquinate dehydratase:integrase/recombinase XerD:<-->:1820194..1820310 117 aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1731:PG1732|PG1731:PG1732:3-dehydroquinate dehydratase:integrase/recombinase XerD:<-->:1820194..1820310 117 aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1731:PG1732|PG1731:PG1732:3-dehydroquinate dehydratase:integrase/recombinase XerD:<-->:1820194..1820310 117 aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 6 End: 104 ..... M F I F G R Q S H K K T A Y G A D S R S G V C I G W H T T S T K V ............. aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca 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================================================ aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1731:PG1732|PG1731:PG1732:3-dehydroquinate dehydratase:integrase/recombinase XerD:<-->:1820194..1820310 117 aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_002950_PG1731_PG1732|3-dehydroquinate dehydratase:integrase/recombinase XerD|NEGATIVE:POSITIVE|[1820194,1820310]|117 HSP 1 e-value: 7.0E-48 bit: 190.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 aacgattgtttatctttgggaggcagagccatnnnnnnncggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca aacgattgtttatctttgggaggcagagccataaaaaaacggcttacggcgcagactctcgttccggtgtgtgcataggttggcacacaacctctacaaaggtatagatatttgaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGAUUGUUUAUCUUUGGGAGGCAGAGCCAUAAAAAAACGGCUUACGGCGCAGACUCUCGUUCCGGUGUGUGCAUAGGUUGGCACACAACCUCUACAAAGGUAUAGAUAUUUGACA ..(((.(((((((((((((((((..(((((..........))))).(((.((........)).))).(((((((........))))))).))))).))))))))..)))).)))... (-36.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCAAAUAUCUAUACCUUUGUAGAGGUUGUGUGCCAACCUAUGCACACACCGGAACGAGAGUCUGCGCCGUAAGCCGUUUUUUUAUGGCUCUGCCUCCCAAAGAUAAACAAUCGUU ................(((((..(((((.((((((........))))))..((((.(....))))).((((((((.......))))))))...))))).)))))............. (-30.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1079 90 41 181 132 NC_002950:PG1731|5end_3-dehydroquinate_dehydratase_1820103..1820333_NEGATIVE 402 86 41 189 145 NC_002950:PG1852|5end_exonuclease_1951973..1952203_NEGATIVE 399 84 41 71 32 NC_002950:PG2038|5end_N-acetylmuramoyl-L-alanine_amidase,_putative_2138207..2138437_NEGATIVE 385 67 21 55 4 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 365 76 40 214 169 NC_002950:PG0351|5end_hypothetical_protein_386774..387004_POSITIVE 361 55 13 70 14 NC_002950:PG1269|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_1349201..1349431_NEGATIVE 357 82 42 60 23 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 350 88 42 220 173 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 346 84 43 157 99 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 344 70 22 201 160 NC_002950:PG2070|5end_hypothetical_protein_2165541..2165771_POSITIVE 344 68 27 104 58 NC_002950:PG0337|5end_hypothetical_protein_371529..371759_NEGATIVE 340 85 41 199 149 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 340 87 47 48 1 NC_002950:PG0522|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_566901..567131_NEGATIVE 339 68 22 215 153 NC_002950:PG0130|5end_phosphoglyceromutase_152668..152898_NEGATIVE 338 83 48 68 31 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 337 84 42 209 152 NC_002950:PG1993|5end_excinuclease_ABC,_C_subunit_2083321..2083551_POSITIVE 337 85 41 59 11 NC_002950:PG0924|5end_5'-nucleotidase,_lipoprotein_e(P4)_family_983668..983898_NEGATIVE 337 89 42 56 12 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 335 72 40 200 167 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 333 83 42 63 20 NC_002950:PG0927|5end_conserved_hypothetical_protein_TIGR00150_985050..985280_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 89 41 90 33 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 357 82 42 56 19 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 349 60 18 41 5 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 341 79 40 86 48 NC_002950:PG0474|3end_low-specificity_L-threonine_aldolase_515011..515161_NEGATIVE 340 87 47 51 4 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 337 85 41 62 14 NC_002950:PG0925|3end_thymidine_kinase_983665..983815_NEGATIVE 333 83 42 51 8 NC_002950:PG0928|3end_response_regulator_985062..985212_NEGATIVE 332 70 22 114 51 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 331 85 47 66 25 NC_002950:PG1408|3end_heavy_metal_efflux_pump,_CzcD_family_1492906..1493056_POSITIVE 325 69 21 111 61 NC_002950:PG0628|3end_ABC_transporter,_ATP-binding_protein_681684..681834_NEGATIVE 324 80 39 84 40 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 323 60 13 125 72 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 321 97 53 144 93 NC_002950:PG0303|3end_ferredoxin_339603..339753_POSITIVE 319 79 39 73 23 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 319 69 21 67 18 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 319 65 23 142 82 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 318 97 51 111 58 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 318 77 36 122 67 NC_002950:PG0978|3end_shikimate_5-dehydrogenase_1040862..1041012_POSITIVE 314 60 18 47 4 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 312 89 41 151 105 NC_002950:PG2205|3end_2-dehydropantoate_2-reductase_2317145..2317295_POSITIVE