Origin IGS: tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagcagacagctcccataccgattgatccgtccgatggactgagactttatcaaatatcaccaatgatttcctccatgtgtgaattgtgaataatgttaaataatgataatagtggcgaatctctgaatatttcactataaaataattacctttgcatcataataaatcataaaatcatcaagtcgtttgatca Mask Tandem Repeat Region ================================================ tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Find is-nt database================================================ Query_seq: TF1741:TF1742|TF1741:TF1742:conserved hypothetical protein:TPR repeat-containing protein:->->:1873074..1873268 195 tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1741:TF1742|TF1741:TF1742:conserved hypothetical protein:TPR repeat-containing protein:->->:1873074..1873268 195 tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1741:TF1742|TF1741:TF1742:conserved hypothetical protein:TPR repeat-containing protein:->->:1873074..1873268 195 tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 56 End: 193 ....................................................... M V K Y S E I R H Y Y H Y L T L F T I H T W R K S L V I F D K V S V H R T D Q S V W E L S A .. tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca 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================================================ tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1741:TF1742|TF1741:TF1742:conserved hypothetical protein:TPR repeat-containing protein:->->:1873074..1873268 195 tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: tfor_TF1741_TF1742|conserved hypothetical protein:TPR repeat-containing protein|POSITIVE:POSITIVE|[1873074,1873268]|195 HSP 1 e-value: 1.0E-106 bit: 387.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca tgatcaaacgacttgatgattttatgatttattatgatgcaaaggtaattattttatagtgaaatattcagagattcgccactattatcattatttaacattattcacaattcacacatggaggaaatcattggtgatatttgataaagtctcagtccatcggacggatcaatcggtatgggagctgtctgctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCAAACGACUUGAUGAUUUUAUGAUUUAUUAUGAUGCAAAGGUAAUUAUUUUAUAGUGAAAUAUUCAGAGAUUCGCCACUAUUAUCAUUAUUUAACAUUAUUCACAAUUCACACAUGGAGGAAAUCAUUGGUGAUAUUUGAUAAAGUCUCAGUCCAUCGGACGGAUCAAUCGGUAUGGGAGCUGUCUGCUCA (((((....(((((....(((((((....((..(((((((....)).)))))..))..)))))))..(((((...((((((...(((........))).....(((....((((....)))).))).....))))))..)))))..)))))...((((...)))).)))))..........((((.....)))). (-37.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCAGACAGCUCCCAUACCGAUUGAUCCGUCCGAUGGACUGAGACUUUAUCAAAUAUCACCAAUGAUUUCCUCCAUGUGUGAAUUGUGAAUAAUGUUAAAUAAUGAUAAUAGUGGCGAAUCUCUGAAUAUUUCACUAUAAAAUAAUUACCUUUGCAUCAUAAUAAAUCAUAAAAUCAUCAAGUCGUUUGAUCA .((((.....)))).......(((..(...((((...))))...(((((.........((((..(((........)))..))))(((((((....(((....((((....(((((((................)))))))......)))).....))))))))))................)))))..)..))). (-29.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 183 147 90 45 tfor:TF2198|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2372906..2373136_POSITIVE 360 189 141 163 107 tfor:TF2774|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959133..2959363_POSITIVE 357 178 133 198 140 tfor:TF1782|5end_conserved_hypothetical_protein_1922003..1922233_POSITIVE 347 186 153 139 106 tfor:TF1898|5end_RNA_polymerase_ECF-type_sigma_factor_2052115..2052345_POSITIVE 339 188 153 144 100 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 337 188 141 157 88 tfor:TF1554|5end_UDP-glucose_dehydrogenase_1659623..1659853_POSITIVE 331 188 146 151 106 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 329 168 121 67 17 tfor:TF1785|5end_histidine_ammonia-lyase_1924494..1924724_POSITIVE 320 189 154 205 176 tfor:TF1812|5end_tryptophan_synthase,_beta_chain_1952696..1952926_POSITIVE 320 189 154 32 3 tfor:TF1811|5end_hypothetical_protein_1952523..1952753_POSITIVE 318 189 149 205 156 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 317 182 149 127 87 tfor:TF0633|5end_hypothetical_protein_668922..669152_POSITIVE 314 190 141 154 100 tfor:TF2836|5end_methyltransferase_3027394..3027624_POSITIVE 313 187 145 162 113 tfor:TF0517|5end_TPR-repeat-containing_protein_540621..540851_POSITIVE 312 189 158 49 10 tfor:TF0320|5end_dihydroorotase_346062..346292_POSITIVE 310 187 141 186 130 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 308 190 141 226 160 tfor:TF3125|5end_recombination/repair_protein_3359808..3360038_POSITIVE 308 185 155 57 26 tfor:TF0396|5end_conserved_hypothetical_protein_417018..417248_POSITIVE 307 186 149 64 25 tfor:TF1942|5end_conserved_hypothetical_protein_2090129..2090359_POSITIVE 300 180 132 180 134 tfor:TF0584|5end_phosphopantetheinyl_transferase_613755..613985_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 183 147 50 5 tfor:TF2197|3end_conserved_hypothetical_protein_2372946..2373096_POSITIVE 347 186 153 51 18 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 337 188 141 135 66 tfor:TF1553|3end_copper_homeostasis_protein_1659681..1659831_POSITIVE 330 186 149 145 109 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 310 187 141 149 93 tfor:TF0969|3end_oxidoreductase_1020439..1020589_POSITIVE 303 190 141 49 2 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 297 187 158 31 4 tfor:TF1398|3end_conserved_hypothetical_protein_1473701..1473851_POSITIVE 295 179 133 146 102 tfor:TF1677|3end_ATP_synthase,_beta_subunit_1790921..1791071_POSITIVE 293 190 146 146 99 tfor:TF2473|3end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2652010..2652160_POSITIVE 293 190 150 137 99 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 289 183 142 136 94 tfor:TF2021|3end_hypothetical_protein_2178588..2178738_POSITIVE 288 189 153 50 11 tfor:TF2590|3end_transposase_2757566..2757716_POSITIVE 287 189 154 63 25 tfor:TF1807|3end_thioesterase_family_protein_1949425..1949575_POSITIVE 284 168 123 49 1 tfor:TF1784|3end_conserved_hypothetical_protein;_possible_formiminotransferase-cyclodeaminase_1924556..1924706_POSITIVE 280 189 141 67 21 tfor:TF2058|3end_possible_ATP-dependent_DNA_helicase_2223798..2223948_POSITIVE 278 188 145 81 39 tfor:TF2937|3end_translation_elongation_factor_Tu_3140502..3140652_POSITIVE 278 166 121 109 54 tfor:TF2181|3end_conserved_hypothetical_protein_2354963..2355113_POSITIVE 278 188 152 129 97 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 274 174 145 130 103 tfor:TF2683|3end_translation_initiation_factor_IF-2_2860756..2860906_POSITIVE 274 189 161 137 103 tfor:TF2526|3end_outer_membrane_protein,_TonB_dependent_receptor_2709007..2709157_POSITIVE