Origin IGS: taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta .........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 taaaatatgcaaaaaataaaccgcacttgtcgtctgcggcctaaaagttgaatagcacaactaaccaattaaggtacgcagcacacgtgcggttttattttatcgctattttttcagtatcactcggcacagtagacaaaaaatctaacatacctccgcagtaccaagctgcatagcggtattggccacataattttctcggtggttttta Mask Tandem Repeat Region ================================================ taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Find is-nt database================================================ Query_seq: AA00316:AA00317|AA00316:AA00317:conserved hypothetical protein:DNA mismatch repair protein:->->:215401..215611 211 taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00316:AA00317|AA00316:AA00317:conserved hypothetical protein:DNA mismatch repair protein:->->:215401..215611 211 taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00316:AA00317|AA00316:AA00317:conserved hypothetical protein:DNA mismatch repair protein:->->:215401..215611 211 taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 39 End: 164 ...................................... A A Q Y Q P P I N S K K D V T G L S V S F I A I F Y F R V H A A Y R L Q N T T S N M ............................................... taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta 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================================================ taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -2.3 Tail_Score: -5.19275 Start: 120 End: 133 Full_Region: accaattaaggtacg cagca cacg tgcgg ttttattttatcgct .......................................................................................................................cagcacacgtgcgg.............................................................................. TransTerm Strand: + Conf: 71 HP_score: -2.3 Tail_Score: -5.19916 Start: 169 End: 195 Full_Region: GTGCTATTCAACTTT TAGGCCGCA GACGACAAG TGCGGTTTA TTTTTTGCATATTTT ........................................................................................................................................................................TAGGCCGCAGACGACAAGTGCGGTTTA................ TransTerm Strand: + Conf: 71 HP_score: -3.1 Tail_Score: -5.0666 Start: 173 End: 191 Full_Region: TATTCAACTTTTAGG CCGCA GACGACAAG TGCGG TTTATTTTTTGCATA ............................................................................................................................................................................CCGCAGACGACAAGTGCGG.................... Find igs database================================================ Query_seq: AA00316:AA00317|AA00316:AA00317:conserved hypothetical protein:DNA mismatch repair protein:->->:215401..215611 211 taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: aact_AA00316_AA00317|conserved hypothetical protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[215401,215611]|211 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 211 Query Start:1 Query End:211 Subject Strand: POSITIVE Subject Start: 1 Subject End: 211 taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta taaaaaccaccgagaaaattatgtggccaataccgctatgcagcttggtactgcggaggtatgttagattttttgtctactgtgccgagtgatactgaaaaaatagcgataaaataaaaccgcacgtgtgctgcgtaccttaattggttagttgtgctattcaacttttaggccgcagacgacaagtgcggtttattttttgcatatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACCACCGAGAAAAUUAUGUGGCCAAUACCGCUAUGCAGCUUGGUACUGCGGAGGUAUGUUAGAUUUUUUGUCUACUGUGCCGAGUGAUACUGAAAAAAUAGCGAUAAAAUAAAACCGCACGUGUGCUGCGUACCUUAAUUGGUUAGUUGUGCUAUUCAACUUUUAGGCCGCAGACGACAAGUGCGGUUUAUUUUUUGCAUAUUUUA ........((((((........((((......)))).......))))))...((...(((((..(((((.....)))))..)))))..)).........((((((((((.((((((((.((((((.(((((((((..(((...(((..(((.....)))..))).....))).))))).).))).)))))))))))))))))).)))))). (-62.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAUGCAAAAAAUAAACCGCACUUGUCGUCUGCGGCCUAAAAGUUGAAUAGCACAACUAACCAAUUAAGGUACGCAGCACACGUGCGGUUUUAUUUUAUCGCUAUUUUUUCAGUAUCACUCGGCACAGUAGACAAAAAAUCUAACAUACCUCCGCAGUACCAAGCUGCAUAGCGGUAUUGGCCACAUAAUUUUCUCGGUGGUUUUUA .((((((.((..((((((((((((((.(((.(.(((((((((...(((((..(((.....)))..))))).)))).))))))))).)))))).))))))))...))))))))..(((((((.((.((.....((((.......)))).....))...(((((.....)))))..)).)))))))(((((............)))))..... (-57.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 179 135 45 1 aact:AA01176|5end_hypothetical_protein_806309..806539_POSITIVE 391 57 18 48 6 aact:AA00596|5end_uridylate_kinase_407496..407726_POSITIVE 368 190 141 138 87 aact:AA00145|5end_probable_degenerate_transposase_fragment_105046..105276_POSITIVE 363 200 151 88 41 aact:AA02681|5end_hypothetical_protein_1865749..1865979_POSITIVE 361 120 71 161 108 aact:AA02001|5end_conserved_hypothetical_protein_1359842..1360072_POSITIVE 355 65 23 163 121 aact:AA02091|5end_hypothetical_protein_1424441..1424671_POSITIVE 353 63 24 78 41 aact:AA01184|5end_hypothetical_protein_810838..811068_POSITIVE 351 179 131 62 17 aact:AA02419|5end_hypothetical_protein_1661731..1661961_POSITIVE 346 160 114 226 182 aact:AA00564|5end_elongation_factor_G_387755..387985_POSITIVE 327 210 163 129 81 aact:AA00260|5end_conserved_hypothetical_protein_183315..183545_POSITIVE 326 204 171 159 115 aact:AA01692|5end_hexulose-6-phosphate_synthase_1149178..1149408_POSITIVE 325 62 22 200 153 aact:AA01553|5end_conserved_hypothetical_protein_1039220..1039450_POSITIVE 323 157 119 200 161 aact:AA00451|5end_hypothetical_protein_315068..315298_POSITIVE 321 192 153 176 133 aact:AA02369|5end_conserved_hypothetical_protein_1624248..1624478_POSITIVE 321 67 24 70 13 aact:AA00531|5end_DNA_polymerase_I_362621..362851_POSITIVE 317 200 156 126 74 aact:AA02465|5end_glucosamine-6-phosphate_isomerase_1704005..1704235_POSITIVE 317 78 33 223 172 aact:AA01620|5end_hypothetical_protein_1095513..1095743_POSITIVE 314 192 155 45 7 aact:AA02239|5end_molybdopterin_biosynthesis_protein_D_1523216..1523446_POSITIVE 313 64 26 49 12 aact:AA00069|5end_conserved_hypothetical_protein_52465..52695_POSITIVE 312 60 11 188 120 aact:AA01538|5end_conserved_hypothetical_protein_1031527..1031757_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 179 131 51 5 aact:AA01175|3end_6-phosphogluconate_dehydrogenase_806395..806545_POSITIVE 363 200 151 70 23 aact:AA02679|3end_formate_dehydrogenase,_gamma_subunit_1865811..1865961_POSITIVE 356 164 130 140 108 aact:AA02629|3end_hypothetical_protein_1830274..1830424_POSITIVE 353 63 24 62 25 aact:AA01183|3end_conserved_hypothetical_protein_810902..811052_POSITIVE 351 179 131 62 17 aact:AA02418|3end_peptidyl-tRNA_hydrolase_1661811..1661961_POSITIVE 340 200 152 77 17 aact:AA01090|3end_leucyl-tRNA_synthetase,_leucyl-tRNA_ligase_756213..756363_POSITIVE 333 87 43 129 81 aact:AA00254|3end_penicillin-binding_protein_5_178774..178924_POSITIVE 327 210 163 66 18 aact:AA00259|3end_conserved_hypothetical_protein_183332..183482_POSITIVE 321 192 153 134 91 aact:AA02368|3end_conserved_hypothetical_protein_1624286..1624436_POSITIVE 317 200 156 135 83 aact:AA02464|3end_hypothetical_protein_1704094..1704244_POSITIVE 314 192 155 41 3 aact:AA02237|3end_molybdopterin_biosynthesis_protein_E_chain_1523292..1523442_POSITIVE 305 204 164 43 5 aact:AA01690|3end_penicillin-binding_protein_1C_1149142..1149292_POSITIVE 304 128 81 80 21 aact:AA01747|3end_single-stranded-DNA-specific_exonuclease_1183130..1183280_POSITIVE 303 66 26 87 45 aact:AA01805|3end_electron_transport_complex_protein_1216773..1216923_POSITIVE 303 193 153 144 101 aact:AA00557|3end_nitrate/nitrite_sensor_protein_382188..382338_POSITIVE 300 201 161 131 88 aact:AA00253|3end_hypothetical_protein_177636..177786_POSITIVE 299 199 164 67 32 aact:AA02936|3end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2056373..2056523_POSITIVE 299 167 122 100 51 aact:AA01048|3end_iron_binding_protein_afuA,_periplasmic_protein_730497..730647_POSITIVE 297 150 105 149 110 aact:AA00563|3end_elongation_factor_Tu_387768..387918_POSITIVE 295 70 25 56 8 aact:AA01411|3end_stationary-phase_survival_protein_951817..951967_POSITIVE