Origin IGS: taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata .........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 tattatcctccatttttctttaataccataaatctatgaaaacacaatatcacttttttgtcttctatttgttttgcaaaatattgagtctatataaaactattaacttaatatagtactatctgattttccctattatacactttttttttattatagaaaagaaaaattaagatttggtaaaaatttagtaaaatttcttattttaaattttaaaatacttttaataaatggaataaacaaaaaaccgataaagaattttacttctaaatcggttttatttcttcttgataaattatgattgagagttagtcacttacaataacaatgttatatttta Mask Tandem Repeat Region ================================================ taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Find is-nt database================================================ Query_seq: FN1138:FN1139|FN1138:FN1139:Hypothetical cytosolic protein:Activator of (R)-2-hydroxyglutaryl-CoA dehydratase:->->:1786041..1786380 340 taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1138:FN1139|FN1138:FN1139:Hypothetical cytosolic protein:Activator of (R)-2-hydroxyglutaryl-CoA dehydratase:->->:1786041..1786380 340 taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1138:FN1139|FN1138:FN1139:Hypothetical cytosolic protein:Activator of (R)-2-hydroxyglutaryl-CoA dehydratase:->->:1786041..1786380 340 taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 89 End: 184 ........................................................................................ M G F L F I P F I K S I L K F K I R N F T K F L P N L N F S F L ............................................................................................................................................................ Protein_Len: 60 Strand: - Start: 43 End: 228 .......................................... D L L F L V S K S T F N K I P K K N I G N I L L I K F N L I L F K V L N K G F R L K E K R Y Y F F L T Y Y P F D S L V M ................................................................................................................ taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata 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: 83 Start: 184 End: 213 .......................................................................................................................................................................................TTTCCCTATTATACACTTTTTTTTTATTAT............................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 177 End: 206 ................................................................................................................................................................................CTTTTCTATAATAAAAAAAAAGTGTATAAT...................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -2.8 Tail_Score: -4.48713 Start: 61 End: 98 Full_Region: taaatggaataaaca aaaaaccgataaagaa ttttac ttctaaatcggtttta tttcttcttgataaa ............................................................aaaaaccgataaagaattttacttctaaatcggtttta.................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 72 HP_score: -2.7 Tail_Score: -5.80003 Start: 66 End: 93 Full_Region: CAAGAAGAAATAAAA CCGATTTAGAA GTAAAA TTCTTTATCGG TTTTTTGTTTATTCC .................................................................CCGATTTAGAAGTAAAATTCTTTATCGG....................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 62 HP_score: -2.7 Tail_Score: -5.18297 Start: 66 End: 93 Full_Region: ggaataaacaaaaaa ccgataaagaa ttttac ttctaaatcgg ttttatttcttcttg .................................................................ccgataaagaattttacttctaaatcgg....................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN1138:FN1139|FN1138:FN1139:Hypothetical cytosolic protein:Activator of (R)-2-hydroxyglutaryl-CoA dehydratase:->->:1786041..1786380 340 taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaagtaaaattctttatcggttttttgtttattccatttattaaaagtattttaaaatttaaaataagaaattttactaaatttttaccaaatcttaatttttcttttctataataaaaaaaaagtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: NC_003454_FN1138_FN1139|Hypothetical cytosolic protein:Activator of (R)-2-hydroxyglutaryl-CoA dehydratase|POSITIVE:POSITIVE|[1786041,1786380]|340 HSP 1 e-value: 2.0E-75 bit: 283.0 Len: 143 Query Start:198 Query End:340 Subject Strand: POSITIVE Subject Start: 198 Subject End: 340 .....................................................................................................................................................................................................gtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata .....................................................................................................................................................................................................gtgtataatagggaaaatcagatagtactatattaagttaatagttttatatagactcaatattttgcaaaacaaatagaagacaaaaaagtgatattgtgttttcatagatttatggtattaaagaaaaatggaggataata HSP 2 e-value: 5.0E-36 bit: 153.0 Len: 77 Query Start:1 Query End:77 Subject Strand: POSITIVE Subject Start: 1 Subject End: 77 taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaag....................................................................................................................................................................................................................................................................... taaaatataacattgttattgtaagtgactaactctcaatcataatttatcaagaagaaataaaaccgatttagaag....................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAUAACAUUGUUAUUGUAAGUGACUAACUCUCAAUCAUAAUUUAUCAAGAAGAAAUAAAACCGAUUUAGAAGUAAAAUUCUUUAUCGGUUUUUUGUUUAUUCCAUUUAUUAAAAGUAUUUUAAAAUUUAAAAUAAGAAAUUUUACUAAAUUUUUACCAAAUCUUAAUUUUUCUUUUCUAUAAUAAAAAAAAAGUGUAUAAUAGGGAAAAUCAGAUAGUACUAUAUUAAGUUAAUAGUUUUAUAUAGACUCAAUAUUUUGCAAAACAAAUAGAAGACAAAAAAGUGAUAUUGUGUUUUCAUAGAUUUAUGGUAUUAAAGAAAAAUGGAGGAUAAUA ((((((((...(((((.((((..(((.....)))..)))).))))).......(((.(((((((((((((..((((......))))..))))))..))))))).)))............))))))))............((((((((....)))))))).....(((((.((((((((((..(((.(((((.......((((.((((..((.......((((.(((((.........))))).))))......))..)))).)))).........(((((((...((......)).))))))).....))))).)))..))))))))))..))))).... (-59.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAUCCUCCAUUUUUCUUUAAUACCAUAAAUCUAUGAAAACACAAUAUCACUUUUUUGUCUUCUAUUUGUUUUGCAAAAUAUUGAGUCUAUAUAAAACUAUUAACUUAAUAUAGUACUAUCUGAUUUUCCCUAUUAUACACUUUUUUUUUAUUAUAGAAAAGAAAAAUUAAGAUUUGGUAAAAAUUUAGUAAAAUUUCUUAUUUUAAAUUUUAAAAUACUUUUAAUAAAUGGAAUAAACAAAAAACCGAUAAAGAAUUUUACUUCUAAAUCGGUUUUAUUUCUUCUUGAUAAAUUAUGAUUGAGAGUUAGUCACUUACAAUAACAAUGUUAUAUUUUA ..(((((.(((((((.....(((((....(((((..((((((((.((((..((......))....)))))))))).))..(((((((((..(((......)))..)))))))))..........)))))....)))))....(((((((........))))))).....((((((((((((((((((((....)))))).))))..))))))))))............)))))))........(((((((((..((((......))))..)))))))))..........)))))......((((.((((.....)))).))))................. (-47.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 176 138 134 95 NC_003454:FN1261|5end_Two-component_response_regulator_1917871..1918101_NEGATIVE 247 195 154 117 80 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 237 205 161 167 120 NC_003454:FN1202|5end_NAD(+)_synthetase_1862298..1862528_NEGATIVE 205 187 145 148 107 NC_003454:FN1441|5end_PTS_system,_fructose-specific_IIABC_component_2108211..2108441_POSITIVE 200 125 83 183 144 NC_003454:FN0120|5end_hypothetical_protein_752891..753121_NEGATIVE 200 255 212 195 156 NC_003454:FN1699|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_194851..195081_NEGATIVE 198 170 121 109 62 NC_003454:FN0879|5end_ABC_transporter_integral_membrane_protein_1540946..1541176_NEGATIVE 198 110 64 91 43 NC_003454:FN0826|5end_periplasmic_component_of_efflux_system_1486495..1486725_POSITIVE 198 336 291 139 99 NC_003454:FN0790|5end_Xylose_repressor_1446457..1446687_NEGATIVE 194 126 90 58 18 NC_003454:FN0863|5end_hypothetical_protein_1522574..1522804_NEGATIVE 190 151 111 185 147 NC_003454:FN1141|5end_Formate_transporter_1791263..1791493_NEGATIVE 184 110 74 91 54 NC_003454:FN1048|5end_Hypothetical_membrane-spanning_protein_1697911..1698141_POSITIVE 183 124 90 183 138 NC_003454:FN0630|5end_PTS_system,_IIC_component_1289857..1290087_NEGATIVE 183 124 84 52 15 NC_003454:FN2047|5end_Fusobacterium_outer_membrane_protein_family_556383..556613_NEGATIVE 183 54 13 178 140 NC_003454:FN1502|5end_Nickel_transport_system_permease_protein_nikC_7522..7752_NEGATIVE 182 206 162 127 82 NC_003454:FN1988|5end_Tyrosine_phenol-lyase_490918..491148_POSITIVE 180 215 171 48 6 NC_003454:FN1996|5end_Transporter_498955..499185_POSITIVE 179 124 83 150 115 NC_003454:FN1323|5end_Thymidylate_kinase_1979152..1979382_NEGATIVE 178 297 262 193 157 NC_003454:FN1145|5end_Oligoendopeptidase_F_1795931..1796161_NEGATIVE 177 99 67 199 166 NC_003454:FN1849|5end_Coenzyme_F390_synthetase_337934..338164_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 43 4 114 76 NC_003454:FN1305|3end_Hypothetical_cytosolic_protein_1961620..1961770_POSITIVE 205 187 145 119 78 NC_003454:FN1440|3end_1-phosphofructokinase_2108262..2108412_POSITIVE 204 202 161 151 107 NC_003454:FN1203|3end_GTP-binding_protein_1862311..1862461_NEGATIVE 198 170 121 93 46 NC_003454:FN0880|3end_ABC_transporter_ATP-binding_protein_1540962..1541112_NEGATIVE 194 126 90 70 30 NC_003454:FN0864|3end_hypothetical_protein_1522562..1522712_NEGATIVE 190 253 214 138 103 NC_003454:FN1783|3end_Ethanolamine_utilization_protein_eutJ_265530..265680_POSITIVE 184 110 74 71 34 NC_003454:FN1047|3end_Hypothetical_membrane-spanning_protein_1697971..1698121_POSITIVE 180 215 171 51 9 NC_003454:FN1995|3end_hypothetical_protein_499038..499188_POSITIVE 178 297 262 44 8 NC_003454:FN1146|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1796080..1796230_NEGATIVE 175 228 184 57 12 NC_003454:FN0299|3end_Aspartyl-tRNA_synthetase_934251..934401_POSITIVE 174 110 79 79 46 NC_003454:FN1268|3end_Methionyl-tRNA_synthetase_1923683..1923833_NEGATIVE 173 189 144 139 93 NC_003454:FN0855|3end_glucose-1-phosphate_adenylyltransferase_1513508..1513658_NEGATIVE 173 99 53 85 32 NC_003454:FN0257|3end_Transporter_884107..884257_POSITIVE 173 110 61 81 27 NC_003454:FN1649|3end_Oligopeptide_transport_ATP-binding_protein_oppD_143327..143477_NEGATIVE 171 189 154 143 109 NC_003454:FN1603|3end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_111610..111760_NEGATIVE 170 133 92 71 34 NC_003454:FN1191|3end_hypothetical_protein_1854729..1854879_POSITIVE 169 116 85 116 86 NC_003454:FN0087|3end_Ethanolamine_utilization_protein_eutN_724954..725104_POSITIVE 169 126 82 132 79 NC_003454:FN0066|3end_Two_component_system_histidine_kinase_704620..704770_POSITIVE 169 265 244 134 111 NC_003454:FN1543|3end_Ubiquinone/menaquinone_biosynthesis_methyltransferase_UBIE_57889..58039_POSITIVE 166 129 82 105 51 NC_003454:FN1343|3end_seC-independent_protein_TATD_1996456..1996606_NEGATIVE