Origin IGS: cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atagtttccttcctccaatatttaagatattatcatacaaacacataaaattcaaggggaaaatggagatgttttagttttatttaattaaaactcgtcgtcagctttgctgatgtg Mask Tandem Repeat Region ================================================ cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Find is-nt database================================================ Query_seq: TDE1588:TDE1589|TDE1588:TDE1589:tryptophanyl-tRNA synthetase:purine-binding chemotaxis protein:->->:1637027..1637143 117 cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1588:TDE1589|TDE1588:TDE1589:tryptophanyl-tRNA synthetase:purine-binding chemotaxis protein:->->:1637027..1637143 117 cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1588:TDE1589|TDE1588:TDE1589:tryptophanyl-tRNA synthetase:purine-binding chemotaxis protein:->->:1637027..1637143 117 cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Predict ORF larger than 30AA ================================================ cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat 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: 62 End: 91 .............................................................CTTGAATTTTATGTGTTTGTATGATAATAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1588:TDE1589|TDE1588:TDE1589:tryptophanyl-tRNA synthetase:purine-binding chemotaxis protein:->->:1637027..1637143 117 cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_002967_TDE1588_TDE1589|tryptophanyl-tRNA synthetase:purine-binding chemotaxis protein|POSITIVE:POSITIVE|[1637027,1637143]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat cacatcagcaaagctgacgacgagttttaattaaataaaactaaaacatctccattttccccttgaattttatgtgtttgtatgataatatcttaaatattggaggaaggaaactat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACAUCAGCAAAGCUGACGACGAGUUUUAAUUAAAUAAAACUAAAACAUCUCCAUUUUCCCCUUGAAUUUUAUGUGUUUGUAUGAUAAUAUCUUAAAUAUUGGAGGAAGGAAACUAU ..(.(((((...))))).)...(((((((......))))))).............(((((((((.(((((((.(((((........)))))..)))).))).))))..))))).... (-19.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUUCCUUCCUCCAAUAUUUAAGAUAUUAUCAUACAAACACAUAAAAUUCAAGGGGAAAAUGGAGAUGUUUUAGUUUUAUUUAAUUAAAACUCGUCGUCAGCUUUGCUGAUGUG ...((((((((((((....((((........................))))....))))))...))))))(((((((((......)))))))))....(((((((...))))))).. (-22.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 28 4 190 166 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 239 90 47 209 153 NC_002967:TDE1962|5end_hypothetical_protein_1975204..1975434_NEGATIVE 233 60 12 102 44 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 232 92 52 131 88 NC_002967:TDE0223|5end_hypothetical_protein_255904..256134_NEGATIVE 224 76 34 115 77 NC_002967:TDE0176|5end_hypothetical_protein_209798..210028_NEGATIVE 218 110 75 145 113 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 217 80 44 64 28 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 216 106 63 195 150 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 215 76 44 190 163 NC_002967:TDE0561|5end_hypothetical_protein_594245..594475_POSITIVE 215 76 44 107 80 NC_002967:TDE0560|5end_hypothetical_protein_594162..594392_POSITIVE 214 110 91 26 4 NC_002967:TDE1317|5end_hypothetical_protein_1355464..1355694_NEGATIVE 213 30 6 72 52 NC_002967:TDE2257|5end_5'-nucleotidase_family_protein_2295104..2295334_NEGATIVE 211 82 54 217 191 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 210 87 47 141 80 NC_002967:TDE1521|5end_fumarate_hydratase_1567211..1567441_POSITIVE 197 28 5 50 28 NC_002967:TDE1472|5end_flagellar_hook-associated_protein_1520715..1520945_NEGATIVE 196 110 75 224 183 NC_002967:TDE2672|5end_TPR_domain_protein_2710210..2710440_POSITIVE 196 47 2 51 12 NC_002967:TDE1508|5end_hypothetical_protein_1555976..1556206_POSITIVE 193 110 61 148 100 NC_002967:TDE2337|5end_aminopeptidase_2373295..2373525_POSITIVE 192 83 43 191 146 NC_002967:TDE2292|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_2328818..2329048_POSITIVE 191 89 50 130 99 NC_002967:TDE1094|5end_hypothetical_protein_1128065..1128295_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 28 4 90 66 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 263 46 4 134 81 NC_002967:TDE2642|3end_hypothetical_protein_2682111..2682261_NEGATIVE 224 28 4 54 30 NC_002967:TDE2000|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2019639..2019789_POSITIVE 224 76 34 122 84 NC_002967:TDE0177|3end_hypothetical_protein_209791..209941_NEGATIVE 218 110 75 130 98 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 210 87 47 126 65 NC_002967:TDE1520|3end_fumarate_hydratase_1567276..1567426_POSITIVE 200 78 47 33 4 NC_002967:TDE2169|3end_hypothetical_protein_2201509..2201659_POSITIVE 194 82 48 61 38 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 192 83 48 52 17 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 191 89 50 143 112 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 190 23 4 137 114 NC_002967:TDE1034|3end_magnesium_and_cobalt_transporter,_putative_1063466..1063616_POSITIVE 190 37 3 68 36 NC_002967:TDE0876|3end_hypothetical_protein_898339..898489_NEGATIVE 189 79 50 91 62 NC_002967:TDE2170|3end_hypothetical_protein_2201606..2201756_NEGATIVE 189 92 57 37 2 NC_002967:TDE0224|3end_hypothetical_protein_255998..256148_NEGATIVE 185 82 52 109 79 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 181 97 53 121 77 NC_002967:TDE2580|3end_GGDEF_domain_protein_2610850..2611000_POSITIVE 180 60 12 108 58 NC_002967:TDE2364|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398329_NEGATIVE 179 61 44 148 132 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 179 77 39 91 50 NC_002967:TDE0002|3end_DNA_gyrase,_B_subunit_3540..3690_POSITIVE 178 54 12 125 89 NC_002967:TDE0444|3end_glutamine_amidotransferase_class-I_domain_protein_499771..499921_POSITIVE