Origin IGS: aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattcaattcataaaataaatgaaatatttgaaattgacacatattccttttcgctttaatttgaaccaacgtatccgactgatgaaaacacgaggcaacttt Mask Tandem Repeat Region ================================================ aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Find is-nt database================================================ Query_seq: AA01774:AA01775|AA01774:AA01775:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:1196037..1196140 104 aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01774:AA01775|AA01774:AA01775:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:1196037..1196140 104 aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01774:AA01775|AA01774:AA01775:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:1196037..1196140 104 aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 5 End: 97 .... M P R V F I S R I R W F K L K R K G I C V N F K Y F I Y F M N ....... aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 41 End: 70 ........................................ATTGACACATATTCCTTTTCGCTTTAATTT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01774:AA01775|AA01774:AA01775:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:1196037..1196140 104 aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: aact_AA01774_AA01775|5,10-methylenetetrahydrofolate reductase:hypothetical protein|POSITIVE:POSITIVE|[1196037,1196140]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta aaagttgcctcgtgttttcatcagtcggatacgttggttcaaattaaagcgaaaaggaatatgtgtcaatttcaaatatttcatttattttatgaattgaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUGCCUCGUGUUUUCAUCAGUCGGAUACGUUGGUUCAAAUUAAAGCGAAAAGGAAUAUGUGUCAAUUUCAAAUAUUUCAUUUAUUUUAUGAAUUGAAUUA ......(((.(((((((.........)))))))..)))((((..(((((..((..(((((((.((.......)).))))))).))..)))))....)))).... (-13.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCAAUUCAUAAAAUAAAUGAAAUAUUUGAAAUUGACACAUAUUCCUUUUCGCUUUAAUUUGAACCAACGUAUCCGACUGAUGAAAACACGAGGCAACUUU ...((((.(((((.......)))))......((((..((.......))..))))..............................)))).....(((....))). ( -7.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 59 12 197 143 aact:AA00089|5end_S-adenosylmethionine_synthase;_methionine_adenosyltransferase_66518..66748_POSITIVE 295 40 5 180 154 aact:AA00528|5end_conserved_hypothetical_protein_361396..361626_POSITIVE 286 50 5 83 39 aact:AA00990|5end_conserved_hypothetical_protein_692559..692789_POSITIVE 271 33 6 144 106 aact:AA02939|5end_phosphoserine_phosphatase_2056881..2057111_POSITIVE 255 66 25 85 39 aact:AA00041|5end_cytochrome_c-type_biogenesis_protein_31881..32111_POSITIVE 253 38 4 186 146 aact:AA01630|5end_threonine_efflux_protein_1102381..1102611_POSITIVE 247 50 5 41 6 aact:AA02600|5end_conserved_hypothetical_protein_1810672..1810902_POSITIVE 245 33 4 48 18 aact:AA00345|5end_transcription_antitermination_protein_231430..231660_POSITIVE 240 67 25 83 33 aact:AA02157|5end_TonB-dependent_outer_membrane_receptor_1475251..1475481_POSITIVE 240 48 1 55 3 aact:AA01398|5end_KDO_kinase_944889..945119_POSITIVE 240 38 5 219 180 aact:AA00259|5end_conserved_hypothetical_protein_182788..183018_POSITIVE 239 37 3 229 187 aact:AA02978|5end_sufI_protein_precursor_homolog_2081813..2082043_POSITIVE 239 50 5 98 48 aact:AA00534|5end_hypothetical_protein_365419..365649_POSITIVE 233 42 12 211 184 aact:AA01735|5end_hypothetical_protein_1172533..1172763_POSITIVE 231 37 6 54 17 aact:AA01419|5end_D-ribulose-phosphate-3_epimerase_954378..954608_POSITIVE 230 50 6 206 156 aact:AA02342|5end_ISRSO11/IS150_related_transposase,_orfB_1599565..1599795_POSITIVE 230 50 6 87 37 aact:AA02341|5end_hypothetical_protein_1599446..1599676_POSITIVE 230 50 6 206 156 aact:AA02117|5end_probable_transposase_1445207..1445437_POSITIVE 230 50 6 87 37 aact:AA02116|5end_hypothetical_protein_1445088..1445318_POSITIVE 230 50 4 78 35 aact:AA01891|5end_pyridoxine_kinase_1275922..1276152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 67 22 52 3 aact:AA01646|3end_hypothetical_protein_1115262..1115412_POSITIVE 286 50 5 88 44 aact:AA00989|3end_hypothetical_protein_692644..692794_POSITIVE 271 33 6 130 92 aact:AA02937|3end_conserved_hypothetical_protein_2056947..2057097_POSITIVE 269 60 12 146 104 aact:AA00497|3end_hexose_phosphate_transport_system_regulatory_protein;_regulator_of_uhpT_expression_346479..346629_POSITIVE 255 66 25 89 43 aact:AA00040|3end_thiol:disulfide_interchange_protein_31965..32115_POSITIVE 250 57 11 143 87 aact:AA02002|3end_hypothetical_protein_1360407..1360557_POSITIVE 247 41 4 133 95 aact:AA02208|3end_tryptophan_synthase,__alpha_subunit_1503996..1504146_POSITIVE 245 33 4 43 13 aact:AA00344|3end_preprotein_translocase_secE_subunit_231505..231655_POSITIVE 240 67 25 78 28 aact:AA02156|3end_conserved_hypothetical_protein_1475326..1475476_POSITIVE 239 50 5 121 71 aact:AA00533|3end_conserved_hypothetical_protein_365522..365672_POSITIVE 236 37 3 53 27 aact:AA02242|3end_molybdenum_cofactor_biosynthesis_protein_A_1525088..1525238_POSITIVE 230 57 12 57 10 aact:AA01839|3end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1237291..1237441_POSITIVE 230 38 1 147 105 aact:AA01379|3end_glycerophosphoryl_diester_phosphodiesterase_(protein_D)_934188..934338_POSITIVE 230 50 6 106 56 aact:AA01267|3end_degenerate_transposase_fragment_862610..862760_POSITIVE 226 54 11 101 54 aact:AA01861|3end_phosphomethylpyrimidine_kinase_1252107..1252257_POSITIVE 224 42 2 53 14 aact:AA02959|3end_pyrroline-5-carboxylate_(P5C)_reductase_2070976..2071126_POSITIVE 220 38 4 132 99 aact:AA01374|3end_tRNA/rRNA_methyltransferase_931097..931247_POSITIVE 220 38 1 138 100 aact:AA00269|3end_3-oxoacyl-(acyl-carrier-protein)_reductase/short-chain_alcohol_dehydrogenase_189413..189563_POSITIVE 219 37 4 55 11 aact:AA01700|3end_hexulose-6-phosphate_isomerase_1155472..1155622_POSITIVE 219 39 5 107 77 aact:AA00474|3end_cell_division_protein_Y_(GTP-binding_signal_recognition_particle)_331724..331874_POSITIVE