Origin IGS: caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttttccaatctcaaaatgaatattattgcctgttatatatttaacaggcttttttcttttctaacaaactttttatcattctttcagttaagttcctacaaagttttttaaataattttatataaagtattgaaaataaaagaaatatttttttaagatagaacaaatttattttttaattgttatctatatttttctatgctaattgtgttaaaatgcttgcaataaataaagcaggaggaaagaaagatgaaaaaattattaactatattaggattg Mask Tandem Repeat Region ================================================ caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Find is-nt database================================================ Query_seq: FN2081:FN2082|FN2081:FN2082:ABC transporter substrate-binding protein:Formate--tetrahydrofolate ligase:<-<-:593065..593346 282 caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2081:FN2082|FN2081:FN2082:ABC transporter substrate-binding protein:Formate--tetrahydrofolate ligase:<-<-:593065..593346 282 caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2081:FN2082|FN2081:FN2082:ABC transporter substrate-binding protein:Formate--tetrahydrofolate ligase:<-<-:593065..593346 282 caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 108 End: 236 ........................................................................................................... M N L F Y L K K I F L L F S I L Y I K L F K K L C R N L T E R M I K S L L E K K K A C .............................................. Protein_Len: 31 Strand: - Start: 172 End: 264 ........................................................................................................................................................................... F V K Y S S L Q F F S L F N T L F S F L R N F I Y C A I I N M .................. Protein_Len: 33 Strand: - Start: 2 End: 100 . I R I Y N I I K E D K K G G A K N I A L M K V C N A Y F F I S L M ...................................................................................................................................................................................... caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt 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================================================ caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2081:FN2082|FN2081:FN2082:ABC transporter substrate-binding protein:Formate--tetrahydrofolate ligase:<-<-:593065..593346 282 caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatcttaaaaaaatatttcttttattttcaatactttatataaaattatttaaaaaactttgtaggaacttaactgaaagaatgataaaaagtttgttagaaaagaaaaaagcctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 282 Len: 282 Subject: NC_003454_FN2081_FN2082|ABC transporter substrate-binding protein:Formate--tetrahydrofolate ligase|NEGATIVE:NEGATIVE|[593065,593346]|282 HSP 1 e-value: 9.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatctt............................................................................................................................................................. caatcctaatatagttaataattttttcatctttctttcctcctgctttatttattgcaagcattttaacacaattagcatagaaaaatatagataacaattaaaaaataaatttgttctatctt............................................................................................................................................................. HSP 2 e-value: 1.0E-20 bit: 101.0 Len: 51 Query Start:232 Query End:282 Subject Strand: POSITIVE Subject Start: 232 Subject End: 282 .......................................................................................................................................................................................................................................cctgttaaatatataacaggcaataatattcattttgagattggaaaaatt .......................................................................................................................................................................................................................................cctgttaaatatataacaggcaataatattcattttgagattggaaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUCCUAAUAUAGUUAAUAAUUUUUUCAUCUUUCUUUCCUCCUGCUUUAUUUAUUGCAAGCAUUUUAACACAAUUAGCAUAGAAAAAUAUAGAUAACAAUUAAAAAAUAAAUUUGUUCUAUCUUAAAAAAAUAUUUCUUUUAUUUUCAAUACUUUAUAUAAAAUUAUUUAAAAAACUUUGUAGGAACUUAACUGAAAGAAUGAUAAAAAGUUUGUUAGAAAAGAAAAAAGCCUGUUAAAUAUAUAACAGGCAAUAAUAUUCAUUUUGAGAUUGGAAAAAUU (((((.(((.....(((((((.(((((.(((.(((((((.((((((.(((((((((((...................))).........))))))))........((((((.(((((...........((((((.......))))))...........))))).))))))..........))))))........))))))).))).))))).)))))))...........((((((((......)))))))).............))).)))))........ (-42.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUCCAAUCUCAAAAUGAAUAUUAUUGCCUGUUAUAUAUUUAACAGGCUUUUUUCUUUUCUAACAAACUUUUUAUCAUUCUUUCAGUUAAGUUCCUACAAAGUUUUUUAAAUAAUUUUAUAUAAAGUAUUGAAAAUAAAAGAAAUAUUUUUUUAAGAUAGAACAAAUUUAUUUUUUAAUUGUUAUCUAUAUUUUUCUAUGCUAAUUGUGUUAAAAUGCUUGCAAUAAAUAAAGCAGGAGGAAAGAAAGAUGAAAAAAUUAUUAACUAUAUUAGGAUUG ........(((((..((.(((.........((((((((......))))))))....................((((((((.(((((((.............................((((((((((((((((.(((((....(((((((...((..((((((((.....))))))))..)).)))).)))....))))).)))))..))))).)))))).(((((..........)))))..))))))).))))))))..........))).))..))))) (-50.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 782 80 31 171 122 NC_003454:FN2081|5end_ABC_transporter_substrate-binding_protein_592974..593204_NEGATIVE 351 44 2 104 69 NC_003454:FN2118|5end_Hypothetical_exported_24-amino_acid_repeat_protein_627024..627254_NEGATIVE 348 43 4 104 59 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 332 44 4 188 155 NC_003454:FN2110|5end_Hypothetical_exported_24-amino_acid_repeat_protein_622330..622560_NEGATIVE 286 44 5 142 111 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 272 41 4 105 62 NC_003454:FN0252|5end_hypothetical_protein_874193..874423_POSITIVE 272 41 4 105 62 NC_003454:FN2060|5end_hypothetical_protein_573649..573879_NEGATIVE 272 41 4 105 62 NC_003454:FN2049|5end_hypothetical_protein_559573..559803_NEGATIVE 269 44 8 104 66 NC_003454:FN2117|5end_Hypothetical_exported_24-amino_acid_repeat_protein_626259..626489_NEGATIVE 255 44 2 141 108 NC_003454:FN0024|5end_Hypothetical_exported_24-amino_acid_repeat_protein_663051..663281_POSITIVE 250 42 2 104 69 NC_003454:FN2120|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628930..629160_NEGATIVE 240 64 35 152 125 NC_003454:FN2094|5end_General_secretion_pathway_protein_F_604839..605069_NEGATIVE 239 48 4 104 50 NC_003454:FN1971|5end_Hemin_receptor_471106..471336_NEGATIVE 239 69 24 203 147 NC_003454:FN1613|5end_hypothetical_protein_123486..123716_NEGATIVE 237 78 31 48 8 NC_003454:FN1365|5end_GTP-binding_protein_2016739..2016969_NEGATIVE 237 50 4 108 62 NC_003454:FN1724|5end_Potassium_uptake_protein_KtrA_223310..223540_NEGATIVE 236 78 31 157 95 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 234 50 4 147 110 NC_003454:FN0846|5end_hypothetical_protein_1504242..1504472_POSITIVE 233 44 4 109 68 NC_003454:FN1597|5end_peptidyl-tRNA_hydrolase_107810..108040_NEGATIVE 231 60 14 66 18 NC_003454:FN0855|5end_glucose-1-phosphate_adenylyltransferase_1514662..1514892_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 44 2 92 57 NC_003454:FN2119|3end_Hypothetical_exported_24-amino_acid_repeat_protein_627036..627186_NEGATIVE 332 44 4 84 51 NC_003454:FN2111|3end_Hypothetical_exported_24-amino_acid_repeat_protein_622434..622584_NEGATIVE 286 44 5 72 41 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 272 41 4 88 45 NC_003454:FN0251|3end_Hypothetical_membrane-spanning_Protein_874256..874406_POSITIVE 272 41 4 88 45 NC_003454:FN2061|3end_Hypothetical_membrane-spanning_protein_573666..573816_NEGATIVE 272 41 4 88 45 NC_003454:FN2050|3end_Hypothetical_membrane-spanning_protein_559590..559740_NEGATIVE 269 44 8 76 38 NC_003454:FN2118|3end_Hypothetical_exported_24-amino_acid_repeat_protein_626287..626437_NEGATIVE 237 50 4 93 47 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 236 78 31 140 78 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 236 59 35 151 128 NC_003454:FN2095|3end_General_secretion_pathway_protein_E_604836..604986_NEGATIVE 234 50 4 49 12 NC_003454:FN0845|3end_hypothetical_protein_1504224..1504374_POSITIVE 230 47 4 140 101 NC_003454:FN0043|3end_Hypothetical_exported_24-amino_acid_repeat_protein_682818..682968_POSITIVE 225 66 21 121 65 NC_003454:FN0452|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1097602..1097752_POSITIVE 222 56 22 76 42 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 220 67 32 46 10 NC_003454:FN0856|3end_glycogen_branching_enzyme_1514689..1514839_NEGATIVE 218 57 11 104 48 NC_003454:FN0207|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_835026..835176_POSITIVE 216 44 11 92 62 NC_003454:FN1190|3end_Probable_cadmium-transporting_ATPase_1853964..1854114_POSITIVE 215 44 4 84 41 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 214 53 11 96 54 NC_003454:FN1528|3end_hypothetical_protein_42588..42738_NEGATIVE 213 44 4 89 44 NC_003454:FN0659|3end_ABC_transporter_permease_protein_1315690..1315840_NEGATIVE