Origin IGS: aaaaataaaatgagttgttgcaatattataaagtaaaaatagtttgttactgagtagatttcttaacggataaaaattaagaattcgctgtaaattctaccaactcgctatgctcagacacgtcgagatttactcggctcattctatttaattttcatcctaaaatctacattcgtaactcacttattttttacttttagattaatagtttaaatttgcaacaacctcatatttgttttta .........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 taaaaacaaatatgaggttgttgcaaatttaaactattaatctaaaagtaaaaaataagtgagttacgaatgtagattttaggatgaaaattaaatagaatgagccgagtaaatctcgacgtgtctgagcatagcgagttggtagaatttacagcgaattcttaatttttatccgttaagaaatctactcagtaacaaactatttttactttataatattgcaacaactcattttattttt Mask Tandem Repeat Region ================================================ aaaaataaaatgagttgttgcaatattataaagtaaaaatagtttgttactgagtagatttcttaacggataaaaattaagaattcgctgtaaattctaccaactcgctatgctcagacacgtcgagatttactcggctcattctatttaattttcatcctaaaatctacattcgtaactcacttattttttacttttagattaatagtttaaatttgcaacaacctcatatttgttttta Find is-nt database================================================ Query_seq: FN1651:FN1652|FN1651:FN1652:Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA:<-<-:145890..146130 241 aaaaataaaatgagttgttgcaatattataaagtaaaaatagtttgttactgagtagatttcttaacggataaaaattaagaattcgctgtaaattctaccaactcgctatgctcagacacgtcgagatttactcggctcattctatttaattttcatcctaaaatctacattcgtaactcacttattttttacttttagattaatagtttaaatttgcaacaacctcatatttgttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1651:FN1652|FN1651:FN1652:Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA:<-<-:145890..146130 241 aaaaataaaatgagttgttgcaatattataaagtaaaaatagtttgttactgagtagatttcttaacggataaaaattaagaattcgctgtaaattctaccaactcgctatgctcagacacgtcgagatttactcggctcattctatttaattttcatcctaaaatctacattcgtaactcacttattttttacttttagattaatagtttaaatttgcaacaacctcatatttgttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1651:FN1652|FN1651:FN1652:Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA:<-<-:145890..146130 241 aaaaataaaatgagttgttgcaatattataaagtaaaaatagtttgttactgagtagatttcttaacggataaaaattaagaattcgctgtaaattctaccaactcgctatgctcagacacgtcgagatttactcggctcattctatttaattttcatcctaaaatctacattcgtaactcacttattttttacttttagattaatagtttaaatttgcaacaacctcatatttgttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 44 Max: 194 Len: 151 Subject: UniRef90_Q8RGV6 Cluster: Hypothetical cytosolic protein; n=1; Fusobacterium nucleatum subsp. nucleatum|Rep: Hypothetical cytosolic protein - Fusobacterium nucleatum subsp. nucleatum HSP 1 e-value: 1.0E-7 bit: 42.4 Len: 81 Query Start:114 Query End:194 Subject Strand: null Subject Start: 27 Subject End: 53 ................................................................................................................. S D T S R F T R L I L F N F H P K I Y I R N S L I F Y ............................................... ................................................................................................................. S N K S R F A W L I L F N F L S K I Y I R N S L I F Y ............................................... HSP 2 e-value: 1.0E-7 bit: 35.0 Len: 66 Query Start:44 Query End:109 Subject Strand: null Subject Start: 1 Subject End: 22 ........................................... L L L S R F L N G * K L R I R C K F Y Q L A .................................................................................................................................... ........................................... M L L S R F L N D K K L R I R C K F D K L A .................................................................................................................................... aaaaataaaatgagttgttgcaatattataaagtaaaaatagtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttttagattaatagtttaaatttgcaacaacctcatatttgttttta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 94 End: 210 ............................................................................................. M L P T R Y A Q T R R D L L G S F Y L I F I L K S T F V T H L F F T F R L I V ............................... aaaaataaaatgagttgttgcaatattataaagtaaaaatagtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttttagattaatagtttaaatttgcaacaacctcatatttgttttta 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================================================ aaaaataaaatgagttgttgcaatattataaagtaaaaatagtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttttagattaatagtttaaatttgcaacaacctcatatttgttttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1651:FN1652|FN1651:FN1652:Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA:<-<-:145890..146130 241 aaaaataaaatgagttgttgcaatattataaagtaaaaatagtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttttagattaatagtttaaatttgcaacaacctcatatttgttttta Intra-Species Hit: Count: 1 Min: 1 Max: 241 Len: 241 Subject: NC_003454_FN1651_FN1652|Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA|NEGATIVE:NEGATIVE|[145890,146130]|241 HSP 1 e-value: 3.0E-18 bit: 93.7 Len: 47 Query Start:195 Query End:241 Subject Strand: POSITIVE Subject Start: 195 Subject End: 241 ..................................................................................................................................................................................................ttttagattaatagtttaaatttgcaacaacctcatatttgttttta ..................................................................................................................................................................................................ttttagattaatagtttaaatttgcaacaacctcatatttgttttta HSP 2 e-value: 6.0E-16 bit: 85.7 Len: 43 Query Start:1 Query End:43 Subject Strand: POSITIVE Subject Start: 1 Subject End: 43 aaaaataaaatgagttgttgcaatattataaagtaaaaatagt...................................................................................................................................................................................................... aaaaataaaatgagttgttgcaatattataaagtaaaaatagt...................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAAAAUGAGUUGUUGCAAUAUUAUAAAGUAAAAAUAGUUUGUUACUGAGUAGAUUUCUUAACGGAUAAAAAUUAAGAAUUCGCUGUAAAUUCUACCAACUCGCUAUGCUCAGACACGUCGAGAUUUACUCGGCUCAUUCUAUUUAAUUUUCAUCCUAAAAUCUACAUUCGUAACUCACUUAUUUUUUACUUUUAGAUUAAUAGUUUAAAUUUGCAACAACCUCAUAUUUGUUUUUA (((((((((((((((((((((((.......(((((((((.(((..(((((.((((((((((......((((.((((((((((((..(((((((((........((((...((......))...))))))))))..)))..)))))...))))))).))))..)))))))).)).)))))..)))...)))))))))((((((.....))))))..))))))))).))))).))))))))). (-60.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACAAAUAUGAGGUUGUUGCAAAUUUAAACUAUUAAUCUAAAAGUAAAAAAUAAGUGAGUUACGAAUGUAGAUUUUAGGAUGAAAAUUAAAUAGAAUGAGCCGAGUAAAUCUCGACGUGUCUGAGCAUAGCGAGUUGGUAGAAUUUACAGCGAAUUCUUAAUUUUUAUCCGUUAAGAAAUCUACUCAGUAACAAACUAUUUUUACUUUAUAAUAUUGCAACAACUCAUUUUAUUUUU .(((((.(((.(((((.(((((((((..((((....))))....((((((((((...(((..(((((....(((((((((.((((((((((((...(((((..((...((((((((((..((((....))))..))))........)))))).))..))))))))))))))))).....)))))))))...)))))..))).))))))))))......))))))))))))))))).))))) (-66.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 949 140 91 231 182 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 620 90 41 73 24 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 599 168 121 117 68 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 518 109 61 194 146 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 455 97 53 227 182 NC_003454:FN0798|5end_Fructose-1,6-bisphosphatase_1455835..1456065_POSITIVE 380 90 41 67 18 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 380 90 41 228 179 NC_003454:FN1603|5end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_113661..113891_NEGATIVE 308 70 21 141 89 NC_003454:FN1440|5end_1-phosphofructokinase_2107238..2107468_POSITIVE 247 160 111 228 179 NC_003454:FN2058|5end_Fusobacterium_outer_membrane_protein_family_571095..571325_NEGATIVE 241 128 83 194 144 NC_003454:FN1909|5end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_402710..402940_NEGATIVE 239 160 113 193 137 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 233 109 66 189 138 NC_003454:FN1468|5end_Flavoredoxin_2150385..2150615_NEGATIVE 233 200 151 85 44 NC_003454:FN0462|5end_DNA_mismatch_repair_protein_mutL_1107184..1107414_POSITIVE 218 89 41 172 119 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 210 186 142 94 46 NC_003454:FN1932|5end_Dephospho-CoA_kinase_432999..433229_NEGATIVE 209 139 95 50 11 NC_003454:FN1159|5end_fructose_1,6-bisphosphatase_II_1814731..1814961_POSITIVE 205 160 115 175 128 NC_003454:FN0643|5end_hypothetical_protein_1299871..1300101_NEGATIVE 204 106 67 198 161 NC_003454:FN1167|5end_beta-methylgalactoside_transporter_inner_membrane_component_1825538..1825768_POSITIVE 203 169 129 191 149 NC_003454:FN0385|5end_hypothetical_protein_1017920..1018150_POSITIVE 203 90 41 211 163 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 498 180 131 70 21 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 427 168 125 54 11 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 308 70 21 68 16 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 281 227 183 74 28 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 255 46 1 63 19 NC_003454:FN1055|3end_Cysteine_synthase_1702490..1702640_NEGATIVE 240 166 135 32 1 NC_003454:FN0796|3end_pyruvate_phosphate_dikinase_1455643..1455793_POSITIVE 225 239 193 92 51 NC_003454:FN1907|3end_Thymidylate_synthase_400546..400696_POSITIVE 218 89 41 65 12 NC_003454:FN0080|3end_ethanolamine_ammonia-lyase_small_subunit_720008..720158_POSITIVE 211 179 131 143 92 NC_003454:FN1364|3end_LSU_ribosomal_protein_L32P_2015382..2015532_NEGATIVE 210 186 142 93 45 NC_003454:FN1933|3end_hypothetical_protein_433000..433150_NEGATIVE 209 139 95 53 14 NC_003454:FN1158|3end_hypothetical_protein_1814814..1814964_POSITIVE 207 239 191 76 26 NC_003454:FN0528|3end_Cold_shock_protein_1184746..1184896_POSITIVE 206 199 153 59 16 NC_003454:FN2094|3end_General_secretion_pathway_protein_F_603799..603949_NEGATIVE 201 230 183 146 90 NC_003454:FN1813|3end_Manganese-binding_protein_293772..293922_NEGATIVE 199 160 112 51 5 NC_003454:FN0156|3end_Phosphopantetheine_adenylyltransferase_784974..785124_POSITIVE 197 170 123 99 56 NC_003454:FN1318|3end_RNA_polymerase_sigma_factor_rpoD_1971101..1971251_NEGATIVE 196 228 200 29 4 NC_003454:FN1476|3end_N-acetylmannosamine-6-phosphate_2-epimerase_2159426..2159576_POSITIVE 195 230 184 82 37 NC_003454:FN0405|3end_tryptophanyl-tRNA_synthetase_1042465..1042615_NEGATIVE 193 198 168 139 103 NC_003454:FN0915|3end_PTS_system,_N-acetylglucosamine-specific_IIA_component_1571543..1571693_NEGATIVE 192 238 197 141 104 NC_003454:FN1421|3end_Pyruvate-flavodoxin_oxidoreductase_2086957..2087107_POSITIVE