Origin IGS: aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcgaattgccttgccgataaaacattgcagttttttctcctttcggccatactttttatatcggaggatatataaaagtattggttatagacagtaagacagtaacggcgcttattctaaaaattttcct Mask Tandem Repeat Region ================================================ aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Find is-nt database================================================ Query_seq: TDE1112:TDE1113|TDE1112:TDE1113:adenylate kinase:hypothetical protein:-><-:1147688..1147818 131 aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1112:TDE1113|TDE1112:TDE1113:adenylate kinase:hypothetical protein:-><-:1147688..1147818 131 aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1112:TDE1113|TDE1112:TDE1113:adenylate kinase:hypothetical protein:-><-:1147688..1147818 131 aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 37 End: 126 .................................... Q R Y G I S K Y I R R Y L F Y P R F S F F S C H K I P L A M ..... Protein_Len: 35 Strand: - Start: 3 End: 107 .. F I K L I L A T V T K S D I V L V K I Y G G I Y F T H G F P S F V A M ........................ aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct 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================================================ aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1112:TDE1113|TDE1112:TDE1113:adenylate kinase:hypothetical protein:-><-:1147688..1147818 131 aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_002967_TDE1112_TDE1113|adenylate kinase:hypothetical protein|POSITIVE:NEGATIVE|[1147688,1147818]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct aggaaaatttttagaataagcgccgttactgtcttactgtctataaccaatacttttatatatcctccgatataaaaagtatggccgaaaggagaaaaaactgcaatgttttatcggcaaggcaattcgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAAAAUUUUUAGAAUAAGCGCCGUUACUGUCUUACUGUCUAUAACCAAUACUUUUAUAUAUCCUCCGAUAUAAAAAGUAUGGCCGAAAGGAGAAAAAACUGCAAUGUUUUAUCGGCAAGGCAAUUCGCU ..................((((.......((((((.(((.......(((.(((((((.((((((....))))))))))))))))((....))....(((((......)))))..))).))))))...)))) (-26.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAAUUGCCUUGCCGAUAAAACAUUGCAGUUUUUUCUCCUUUCGGCCAUACUUUUUAUAUCGGAGGAUAUAUAAAAGUAUUGGUUAUAGACAGUAAGACAGUAACGGCGCUUAUUCUAAAAAUUUUCCU ((((.((((.(((((.((.(((((......))))).)).......((((((((((((((((((....)))))).))))))).))))).......))))).)))).....)))).................. (-28.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 68 22 101 39 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 306 121 81 52 13 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 296 69 21 105 52 NC_002967:TDE0536|5end_hypothetical_protein_578864..579094_NEGATIVE 284 69 25 195 152 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 279 120 77 188 146 NC_002967:TDE1321|5end_conserved_hypothetical_protein_TIGR00257_1359335..1359565_POSITIVE 276 95 51 116 76 NC_002967:TDE1499|5end_adenylosuccinate_lyase,_putative_1545266..1545496_POSITIVE 275 66 21 99 52 NC_002967:TDE1495|5end_hypothetical_protein_1540216..1540446_NEGATIVE 270 48 2 161 109 NC_002967:TDE0910|5end_hypothetical_protein_928774..929004_POSITIVE 270 120 76 91 51 NC_002967:TDE0523|5end_hypothetical_protein_569831..570061_NEGATIVE 269 68 21 103 57 NC_002967:TDE2417|5end_nitroimidazole_resistance_protein,_putative_2443288..2443518_NEGATIVE 264 130 83 52 4 NC_002967:TDE2673|5end_hypothetical_protein_2712377..2712607_NEGATIVE 262 124 85 148 105 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 262 123 82 219 170 NC_002967:TDE1947|5end_ABC_transporter,_permease_protein_1963449..1963679_NEGATIVE 260 90 54 69 31 NC_002967:TDE2101|5end_hypothetical_protein_2126619..2126849_NEGATIVE 258 128 101 45 19 NC_002967:TDE1381|5end_V-type_ATP_synthase_subunit_E_1421905..1422135_NEGATIVE 254 129 84 226 178 NC_002967:TDE2655|5end_hypothetical_protein_2693070..2693300_NEGATIVE 254 128 86 177 131 NC_002967:TDE1178|5end_iron_compound_ABC_transporter,_ATP-binding_protein_1207913..1208143_NEGATIVE 252 129 85 41 4 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 250 94 64 40 12 NC_002967:TDE2537|5end_hypothetical_protein_2563266..2563496_POSITIVE 249 130 85 221 176 NC_002967:TDE2622|5end_ABC_transporter,_ATP-binding_protein_2663590..2663820_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 121 82 39 1 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 271 123 82 91 55 NC_002967:TDE0044|3end_ABC_transporter,_ATP-binding_protein_51660..51810_NEGATIVE 269 68 21 61 15 NC_002967:TDE2418|3end_hypothetical_protein_2443330..2443480_NEGATIVE 265 129 81 57 6 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 262 124 85 151 108 NC_002967:TDE2597|3end_ribulose-phosphate_3-epimerase_2632036..2632186_NEGATIVE 260 90 54 72 34 NC_002967:TDE2102|3end_hypothetical_protein_2126616..2126766_NEGATIVE 259 128 84 96 57 NC_002967:TDE1184|3end_hypothetical_protein_1211521..1211671_POSITIVE 250 94 64 35 7 NC_002967:TDE2536|3end_hypothetical_protein_2563341..2563491_POSITIVE 248 101 67 79 45 NC_002967:TDE2240|3end_hypothetical_protein_2277625..2277775_NEGATIVE 248 130 84 79 30 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 242 104 64 94 54 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 240 68 22 102 54 NC_002967:TDE2363|3end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2397472..2397622_NEGATIVE 240 128 85 59 8 NC_002967:TDE1442|3end_histidyl-tRNA_synthetase_1488842..1488992_POSITIVE 233 122 83 148 112 NC_002967:TDE2324|3end_DNA-binding_response_regulator_2359921..2360071_POSITIVE 233 43 2 151 108 NC_002967:TDE0909|3end_type_II_DNA_modification_methyltransferase_M.TdeIII_928853..929003_POSITIVE 233 118 74 49 15 NC_002967:TDE0138|3end_alkyldihydroxyacetonephosphate_synthase,_putative_160061..160211_POSITIVE 230 118 75 66 8 NC_002967:TDE2586|3end_DNA_polymerase_III_subunits_gamma_and_tau_2620251..2620401_NEGATIVE 230 130 84 70 28 NC_002967:TDE1038|3end_hypothetical_protein_1065405..1065555_NEGATIVE 229 130 83 71 20 NC_002967:TDE0243|3end_ABC_transporter,_ATP-binding_protein_276026..276176_NEGATIVE 228 129 82 59 4 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE