Origin IGS: cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgtctgctttctttcgtaacgggcagcaaaggtacgaaaaccctttccgtctgccatcataaaatgattataataataggtatacggtatctatcggcagctacccgaccccaag Mask Tandem Repeat Region ================================================ cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Find is-nt database================================================ Query_seq: TF1046:TF1047|TF1046:TF1047:hypothetical protein:tRNA pseudouridylate synthetase A (pseudouridylate synthase I):->->:1108507..1108622 116 cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1046:TF1047|TF1046:TF1047:hypothetical protein:tRNA pseudouridylate synthetase A (pseudouridylate synthase I):->->:1108507..1108622 116 cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1046:TF1047|TF1046:TF1047:hypothetical protein:tRNA pseudouridylate synthetase A (pseudouridylate synthase I):->->:1108507..1108622 116 cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 26 End: 115 ......................... M P Y T Y Y Y N H F M M A D G K G F R T F A A R Y E R K Q T . Protein_Len: 37 Strand: - Start: 2 End: 112 . Q P R T A A S L Y R I G I I I I M K H H C V S L T K T G K S G T V F S L M .... cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt 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================================================ cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1046:TF1047|TF1046:TF1047:hypothetical protein:tRNA pseudouridylate synthetase A (pseudouridylate synthase I):->->:1108507..1108622 116 cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: tfor_TF1046_TF1047|hypothetical protein:tRNA pseudouridylate synthetase A (pseudouridylate synthase I)|POSITIVE:POSITIVE|[1108507,1108622]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt cttggggtcgggtagctgccgatagataccgtatacctattattataatcattttatgatggcagacggaaagggttttcgtacctttgctgcccgttacgaaagaaagcagacgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGGGGUCGGGUAGCUGCCGAUAGAUACCGUAUACCUAUUAUUAUAAUCAUUUUAUGAUGGCAGACGGAAAGGGUUUUCGUACCUUUGCUGCCCGUUACGAAAGAAAGCAGACGU (((..(..((((((((............((((....((.(((((((((.....))))))))).)))))).((((((......))))))))))))))...)..)))........... (-31.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUCUGCUUUCUUUCGUAACGGGCAGCAAAGGUACGAAAACCCUUUCCGUCUGCCAUCAUAAAAUGAUUAUAAUAAUAGGUAUACGGUAUCUAUCGGCAGCUACCCGACCCCAAG ....................((((.(((...(((......)))..........(((.((((...))))........((((((((...)))))))).))).))).))))........ (-22.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 97 61 181 144 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 384 110 65 52 2 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 369 109 61 62 8 tfor:TF1427|5end_penicillin-binding_protein_2_1511349..1511579_POSITIVE 364 37 1 223 191 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 364 110 61 208 157 tfor:TF1651|5end_integrase_1761296..1761526_POSITIVE 327 96 59 185 141 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 326 44 1 62 24 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 325 110 65 60 1 tfor:TF0939|5end_ISPg1_transposase,_IS1106-related_transposase_979956..980186_POSITIVE 324 84 55 36 5 tfor:TF1452|5end_conserved_hypothetical_protein;_possible_transglutaminase-like_enzyme_1537529..1537759_POSITIVE 323 38 4 210 168 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 320 94 52 49 2 tfor:TF1881|5end_hypothetical_protein_2033412..2033642_POSITIVE 319 94 62 227 189 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 318 94 51 166 120 tfor:TF0140|5end_exodeoxyribonuclease_VII,_small_subunit_148203..148433_POSITIVE 312 96 58 202 150 tfor:TF0234|5end_5,10-methylenetetrahydrofolate_reductase_260482..260712_POSITIVE 310 101 61 134 95 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 310 110 65 88 26 tfor:TF1439|5end_outer_membrane_protein,_TonB_dependent_receptor_1522479..1522709_POSITIVE 309 95 61 200 164 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 306 98 58 48 1 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 306 37 4 208 172 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 306 102 61 72 28 tfor:TF1689|5end_conserved_hypothetical_protein_1805068..1805298_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 97 61 147 110 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 376 108 61 135 94 tfor:TF1740|3end_hypothetical_protein_1869192..1869342_POSITIVE 363 96 54 102 52 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 358 109 67 60 11 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 327 96 59 109 65 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 326 44 1 45 7 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE 323 38 4 140 98 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 306 98 58 48 1 tfor:TF2819|3end_N-acetyl-gamma-glutamylphosphate_reductase_3009956..3010106_POSITIVE 299 110 62 122 71 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 297 100 58 99 57 tfor:TF1851|3end_methionine_synthase_I_2004681..2004831_POSITIVE 296 105 65 146 118 tfor:TF0969|3end_oxidoreductase_1020439..1020589_POSITIVE 296 97 58 73 26 tfor:TF0249|3end_3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl_carrier_protein)_dehydratase_279256..279406_POSITIVE 295 98 58 43 4 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 295 108 61 83 29 tfor:TF2001|3end_conserved_hypothetical_protein_2155931..2156081_POSITIVE 294 99 55 117 65 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 290 34 4 151 127 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 288 108 73 113 75 tfor:TF1935|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2083881..2084031_POSITIVE 286 100 56 151 97 tfor:TF0456|3end_conserved_hypothetical_protein_474172..474322_POSITIVE 285 93 51 151 106 tfor:TF0139|3end_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_(MEP_cytidylyltransferase)_(MCT)_148269..148419_POSITIVE 281 104 62 82 42 tfor:TF2099|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2273419..2273569_POSITIVE