Origin IGS: aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattccttattatgatgatgtccggaaggtctgcatgtttttcgaagcggagaggtgcataaagtcgacttttttgcttacttttgcgaggtttaaaaggtaaaaaacctgttt Mask Tandem Repeat Region ================================================ aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Find is-nt database================================================ Query_seq: TF2004:TF2006|TF2004:TF2006:thymidylate synthase:uracil permease:->->:2157304..2157418 115 aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2004:TF2006|TF2004:TF2006:thymidylate synthase:uracil permease:->->:2157304..2157418 115 aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2004:TF2006|TF2004:TF2006:thymidylate synthase:uracil permease:->->:2157304..2157418 115 aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 15 End: 113 .............. R K F R A F T L L F T S K I C R E A E F F M C V K R V D D Y Y P M .. aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta 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================================================ aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2004:TF2006|TF2004:TF2006:thymidylate synthase:uracil permease:->->:2157304..2157418 115 aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: tfor_TF2004_TF2006|thymidylate synthase:uracil permease|POSITIVE:POSITIVE|[2157304,2157418]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta aaacaggttttttaccttttaaacctcgcaaaagtaagcaaaaaagtcgactttatgcacctctccgcttcgaaaaacatgcagaccttccggacatcatcataataaggaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGGUUUUUUACCUUUUAAACCUCGCAAAAGUAAGCAAAAAAGUCGACUUUAUGCACCUCUCCGCUUCGAAAAACAUGCAGACCUUCCGGACAUCAUCAUAAUAAGGAAUUA ....((((((..........)))))).((((((((..((......))..))))).))).(((....((............))...((....))..............)))..... (-14.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCCUUAUUAUGAUGAUGUCCGGAAGGUCUGCAUGUUUUUCGAAGCGGAGAGGUGCAUAAAGUCGACUUUUUUGCUUACUUUUGCGAGGUUUAAAAGGUAAAAAACCUGUUU .....((((......(((....((....))....)))........((((((((((((((.....))..))))))))))))........))))......((((.....)))).... (-24.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 97 60 178 133 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 340 93 51 72 19 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 322 98 60 67 29 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 321 93 58 42 1 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 317 72 33 80 46 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 315 100 51 161 105 tfor:TF2887|5end_phosphomannomutase/phosphoglucomutase_3076327..3076557_POSITIVE 313 92 55 86 39 tfor:TF0409|5end_conserved_hypothetical_protein_426240..426470_POSITIVE 308 90 48 53 1 tfor:TF1229|5end_hypothetical_protein_1314619..1314849_POSITIVE 305 94 57 51 10 tfor:TF1951|5end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2100792..2101022_POSITIVE 301 98 52 63 15 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 293 100 60 189 148 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 293 90 46 101 48 tfor:TF0665|5end_conserved_hypothetical_protein_709497..709727_POSITIVE 290 98 59 142 95 tfor:TF2594|5end_hypothetical_protein_2764176..2764406_POSITIVE 288 99 59 71 17 tfor:TF1741|5end_conserved_hypothetical_protein_1869304..1869534_POSITIVE 282 96 52 183 127 tfor:TF3093|5end_30S_ribosomal_protein_S2_3325244..3325474_POSITIVE 281 94 51 99 40 tfor:TF2286|5end_hypothetical_protein_2440901..2441131_POSITIVE 281 94 56 130 79 tfor:TF0312|5end_outer_membrane_protein_336473..336703_POSITIVE 277 95 58 198 156 tfor:TF1808|5end_DNA_processing_protein_subunit_A_1949356..1949586_POSITIVE 276 98 57 201 150 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 276 110 61 96 40 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 97 60 129 84 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 340 93 51 61 8 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 317 72 33 72 38 tfor:TF2015|3end_N6-adenine-specific_DNA_methylase_2173020..2173170_POSITIVE 313 92 55 90 43 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 295 95 51 59 13 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 293 90 46 94 41 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 290 98 59 128 81 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 281 94 51 142 83 tfor:TF2285|3end_hypothetical_protein_2441024..2441174_POSITIVE 276 110 61 79 23 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 273 85 45 81 41 tfor:TF2533|3end_adenylosuccinate_synthetase_2717014..2717164_POSITIVE 272 86 41 120 77 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 270 70 23 66 19 tfor:TF0765|3end_conserved_hypothetical_protein_812014..812164_POSITIVE 269 97 57 146 101 tfor:TF2904|3end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3102204..3102354_POSITIVE 269 97 66 73 47 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 265 89 46 97 61 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 265 100 55 134 82 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 264 83 47 150 118 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 263 68 23 65 22 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 261 70 23 74 17 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 261 92 53 98 56 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE