Origin IGS: atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattaaaagccggtgacttttctttaaacattcagaaacgatagcgcatagtggttttatccataagaaaaagaatttatttctttaagaaagacctgcaatttgagggaggatagactgcagaaataggcagctaccggaaaataaacaaacgagaataagggat Mask Tandem Repeat Region ================================================ atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Find is-nt database================================================ Query_seq: TF2055:TF2056|TF2055:TF2056:UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase:conserved hypothetical protein:->->:2220845..2221011 167 atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2055:TF2056|TF2055:TF2056:UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase:conserved hypothetical protein:->->:2220845..2221011 167 atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2055:TF2056|TF2055:TF2056:UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase:conserved hypothetical protein:->->:2220845..2221011 167 atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Predict ORF larger than 30AA ================================================ atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta 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================================================ atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2055:TF2056|TF2055:TF2056:UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase:conserved hypothetical protein:->->:2220845..2221011 167 atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: tfor_TF2055_TF2056|UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase:conserved hypothetical protein|POSITIVE:POSITIVE|[2220845,2221011]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta atcccttattctcgtttgtttattttccggtagctgcctatttctgcagtctatcctccctcaaattgcaggtctttcttaaagaaataaattctttttcttatggataaaaccactatgcgctatcgtttctgaatgtttaaagaaaagtcaccggcttttaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCCUUAUUCUCGUUUGUUUAUUUUCCGGUAGCUGCCUAUUUCUGCAGUCUAUCCUCCCUCAAAUUGCAGGUCUUUCUUAAAGAAAUAAAUUCUUUUUCUUAUGGAUAAAACCACUAUGCGCUAUCGUUUCUGAAUGUUUAAAGAAAAGUCACCGGCUUUUAAUUA ..............((((..(((((..(((((((.((.....((((((((..............))))))))....(((..((((((.........))))))..)))............))))))))).....)))))..)))).((((((.....))))))..... (-27.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAAAAGCCGGUGACUUUUCUUUAAACAUUCAGAAACGAUAGCGCAUAGUGGUUUUAUCCAUAAGAAAAAGAAUUUAUUUCUUUAAGAAAGACCUGCAAUUUGAGGGAGGAUAGACUGCAGAAAUAGGCAGCUACCGGAAAAUAAACAAACGAGAAUAAGGGAU ..........((((((..(((((((((((...((......))....(((....((((((.((...((((((.........))))))...)))))))))))..))))))))))).....((((........)))).)))))).......................... (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 69 23 185 137 tfor:TF1245|5end_LemA_protein_1328822..1329052_POSITIVE 345 68 26 73 18 tfor:TF0288|5end_conserved_hypothetical_protein_317474..317704_POSITIVE 337 70 27 54 10 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 335 62 22 210 158 tfor:TF2344|5end_ATP/GTP_binding_protein_2507422..2507652_POSITIVE 317 52 11 68 20 tfor:TF0096|5end_tRNA-guanine_transglycosylase_(queuine_tRNA-ribosyltransferase)_106971..107201_POSITIVE 315 69 23 116 66 tfor:TF1254|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_1336248..1336478_POSITIVE 312 58 11 197 147 tfor:TF1923|5end_conserved_hypothetical_protein;_possible_phosphoserine_phosphatase_2072259..2072489_POSITIVE 305 47 2 187 139 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 304 59 11 70 15 tfor:TF1386|5end_hypothetical_protein_1460103..1460333_POSITIVE 292 48 4 59 7 tfor:TF1602|5end_L-aspartate_oxidase_1715579..1715809_POSITIVE 292 60 12 228 172 tfor:TF0528|5end_two-component_system_sensor_histidine_kinase_552357..552587_POSITIVE 291 61 27 222 180 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 290 78 34 50 6 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 289 60 11 208 138 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 289 45 10 176 144 tfor:TF1291|5end_response_regulator_(fimR__protein)_1371959..1372189_POSITIVE 287 78 33 231 189 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 287 69 23 79 20 tfor:TF0722|5end_pyruvate_dehydrogenase_E3_component(dihydrolipoamide_dehydrogenase)_772873..773103_POSITIVE 286 59 12 55 5 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 285 59 13 198 144 tfor:TF2786|5end_hypothetical_protein_2969851..2970081_POSITIVE 285 70 27 54 13 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 69 23 96 48 tfor:TF1244|3end_hypothetical_protein_1328813..1328963_POSITIVE 298 52 12 62 11 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE 297 46 4 45 1 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 285 70 27 58 17 tfor:TF2218|3end_two-component_system_response_regulator_2390928..2391078_POSITIVE 283 158 113 57 10 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 278 56 11 56 16 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 278 47 5 45 13 tfor:TF2223|3end_CTn_excision__protein_2394632..2394782_POSITIVE 276 60 13 150 109 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 274 80 32 96 33 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 274 38 1 67 29 tfor:TF2153|3end_6-phosphofructokinase_2329172..2329322_POSITIVE 274 68 27 85 46 tfor:TF0263|3end_ISPg3_(IS195)_transposase_292654..292804_POSITIVE 273 48 1 138 93 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 265 65 28 68 34 tfor:TF0079|3end_conserved_hypothetical_protein_86273..86423_POSITIVE 264 78 46 74 36 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 263 53 12 137 98 tfor:TF2331|3end_conserved_hypothetical_protein_2491767..2491917_POSITIVE 263 43 8 56 12 tfor:TF0933|3end_conserved_hypothetical_protein;_possible_DNA_repair_protein_974627..974777_POSITIVE 262 56 12 58 16 tfor:TF1758|3end_conserved_hypothetical_protein_1895544..1895694_POSITIVE 262 48 13 43 11 tfor:TF0185|3end_4-alpha-glucanotransferase_(amylomaltase)_199256..199406_POSITIVE 261 72 33 151 100 tfor:TF2570|3end_50S_ribosomal_protein_L18_2742619..2742769_POSITIVE 261 52 21 48 15 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE