Origin IGS: tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gacatataatagtgatgatggaataaattttctatcatcatttttttataaaaaagttgagataataagatattcttgttaaaatcaaataaatacaagtataaacaagaaaggaagttgggctataatgttaaaaagagtggtaatgttaata Mask Tandem Repeat Region ================================================ tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Find is-nt database================================================ Query_seq: FN2115:FN2116|FN2115:FN2116:hypothetical protein:Hypothetical exported 24-amino acid repeat protein:<-<-:624934..625087 154 tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2115:FN2116|FN2115:FN2116:hypothetical protein:Hypothetical exported 24-amino acid repeat protein:<-<-:624934..625087 154 tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2115:FN2116|FN2115:FN2116:hypothetical protein:Hypothetical exported 24-amino acid repeat protein:<-<-:624934..625087 154 tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 57 End: 152 ........................................................ M Y L F D F N K N I L L S Q L F Y K K M M I E N L F H H H Y Y M .. tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc 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: 89 Start: 70 End: 99 .....................................................................GTTGAGATAATAAGATATTCTTGTTAAAAT....................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 120 End: 149 .......................................................................................................................ATAGAAAATTTATTCCATCATCACTATTAT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2115:FN2116|FN2115:FN2116:hypothetical protein:Hypothetical exported 24-amino acid repeat protein:<-<-:624934..625087 154 tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: NC_003454_FN2115_FN2116|hypothetical protein:Hypothetical exported 24-amino acid repeat protein|NEGATIVE:NEGATIVE|[624934,625087]|154 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttatnnnnnnntgatgatagaaaatttattccatcatcactattatatgtc tattaacattaccactctttttaacattatagcccaacttcctttcttgtttatacttgtatttatttgattttaacaagaatatcttattatctcaacttttttataaaaaaatgatgatagaaaatttattccatcatcactattatatgtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAACAUUACCACUCUUUUUAACAUUAUAGCCCAACUUCCUUUCUUGUUUAUACUUGUAUUUAUUUGAUUUUAACAAGAAUAUCUUAUUAUCUCAACUUUUUUAUAAAAAAAUGAUGAUAGAAAAUUUAUUCCAUCAUCACUAUUAUAUGUC .......................((((.((((...........((((((((.......................))))))))................................(((((((.(((......))).)))))))))))...)))). (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUAUAAUAGUGAUGAUGGAAUAAAUUUUCUAUCAUCAUUUUUUUAUAAAAAAGUUGAGAUAAUAAGAUAUUCUUGUUAAAAUCAAAUAAAUACAAGUAUAAACAAGAAAGGAAGUUGGGCUAUAAUGUUAAAAAGAGUGGUAAUGUUAAUA ....(((((.(((((((((((((......)))))))))))))...)))))......((((..(((((((.....)))))))...)))).........(((...(((..........)))..))).((((((((..(....)..))))))))... (-28.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 782 60 11 151 102 NC_003454:FN2115|5end_hypothetical_protein_624843..625073_NEGATIVE 306 140 93 91 38 NC_003454:FN0812|5end_Hypothetical_cytosolic_protein_1471051..1471281_POSITIVE 293 140 93 198 143 NC_003454:FN0275|5end_Transposase_901560..901790_NEGATIVE 277 78 31 136 85 NC_003454:FN0710|5end_hypothetical_protein_1368875..1369105_POSITIVE 250 140 93 201 144 NC_003454:FN0599|5end_Transposase_1253833..1254063_POSITIVE 242 43 7 62 29 NC_003454:FN1092|5end_hypothetical_protein_1737267..1737497_POSITIVE 220 150 115 184 153 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 217 68 32 133 86 NC_003454:FN1930|5end_Phosphatidylglycerophosphatase_A_430259..430489_NEGATIVE 215 58 12 224 166 NC_003454:FN1914|5end_Anti-sigma_F_factor_antagonist_411990..412220_NEGATIVE 213 74 37 153 114 NC_003454:FN0905|5end_hypothetical_protein_1564086..1564316_NEGATIVE 213 43 15 30 1 NC_003454:FN0680|5end_Ribulose-phosphate_3-epimerase_1335455..1335685_POSITIVE 212 147 118 183 152 NC_003454:FN1910|5end_hypothetical_protein_403208..403438_NEGATIVE 207 77 38 201 164 NC_003454:FN2128|5end_RECF_protein_639585..639815_NEGATIVE 205 80 38 140 101 NC_003454:FN0928|5end_O-sialoglycoprotein_endopeptidase_1583026..1583256_NEGATIVE 202 49 13 52 13 NC_003454:FN0104|5end_Acetyltransferase_739896..740126_NEGATIVE 200 51 15 120 75 NC_003454:FN1638|5end_50S_ribosomal_protein_L16_137501..137731_NEGATIVE 199 56 11 218 164 NC_003454:FN1726|5end_Na+_driven_multidrug_efflux_pump_226059..226289_NEGATIVE 199 80 38 48 7 NC_003454:FN1527|5end_hypothetical_protein_42572..42802_NEGATIVE 198 70 23 170 125 NC_003454:FN1780|5end_hypothetical_protein_261664..261894_NEGATIVE 197 54 12 221 179 NC_003454:FN1264|5end_hypothetical_protein_1920766..1920996_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 140 93 68 15 NC_003454:FN0811|3end_hypothetical_protein_1471108..1471258_POSITIVE 277 78 31 69 18 NC_003454:FN0709|3end_Virulence_factor_mviN_1368888..1369038_POSITIVE 242 43 7 53 20 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 227 74 39 118 83 NC_003454:FN1527|3end_hypothetical_protein_42183..42333_NEGATIVE 217 68 32 133 86 NC_003454:FN1931|3end_Protease_430259..430409_NEGATIVE 213 74 37 115 76 NC_003454:FN0906|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1564124..1564274_NEGATIVE 212 147 118 142 111 NC_003454:FN1911|3end_Outer_membrane_protein_403249..403399_NEGATIVE 206 48 14 135 97 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE 201 147 106 58 15 NC_003454:FN0299|3end_Aspartyl-tRNA_synthetase_934251..934401_POSITIVE 201 146 104 44 1 NC_003454:FN0254|3end_Fusobacterium_outer_membrane_protein_family_881390..881540_POSITIVE 200 51 15 117 72 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 198 74 31 114 73 NC_003454:FN0430|3end_50S_ribosomal_protein_L19_1071791..1071941_POSITIVE 198 70 23 102 57 NC_003454:FN1781|3end_LytB_protein_261732..261882_NEGATIVE 196 60 16 108 68 NC_003454:FN1789|3end_Na+_driven_multidrug_efflux_pump_271579..271729_POSITIVE 195 50 7 117 73 NC_003454:FN1343|3end_seC-independent_protein_TATD_1996456..1996606_NEGATIVE 192 57 15 92 58 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE 192 59 14 134 76 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 189 150 125 57 31 NC_003454:FN0592|3end_ATP-dependent_DNA_helicase_pcrA_1247999..1248149_POSITIVE 189 45 5 108 60 NC_003454:FN1696|3end_UDP-4-dehydro-6-deoxy-2-acetamido-D-glucose_4-reductase_190876..191026_NEGATIVE 186 50 17 64 26 NC_003454:FN1366|3end_Triosephosphate_isomerase_2016763..2016913_NEGATIVE