Origin IGS: actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattctccatttctaattattttttattatttaaaatcatcattaactactaagatatttaagttagaattcctatattatttactatactacctataaacaattatttataggtagcatagcaacaatatttttatttagt Mask Tandem Repeat Region ================================================ actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Find is-nt database================================================ Query_seq: FN0204:FN0205|FN0204:FN0205:Glutaconyl-CoA decarboxylase A subunit:Sodium/glutamate symport carrier protein:->->:831467..831608 142 actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0204:FN0205|FN0204:FN0205:Glutaconyl-CoA decarboxylase A subunit:Sodium/glutamate symport carrier protein:->->:831467..831608 142 actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0204:FN0205|FN0204:FN0205:Glutaconyl-CoA decarboxylase A subunit:Sodium/glutamate symport carrier protein:->->:831467..831608 142 actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Predict ORF larger than 30AA ================================================ actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt 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================================================ actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -11.5 Tail_Score: -2.6381 Start: 17 End: 62 Full_Region: CTAAATAAAAATATT GTTGCTATGCTACCTATAAAT AATT GTTTATAGGTAGTATAGTAAA TAATATAGGAATTCT ................GTTGCTATGCTACCTATAAATAATTGTTTATAGGTAGTATAGTAAA................................................................................ Find igs database================================================ Query_seq: FN0204:FN0205|FN0204:FN0205:Glutaconyl-CoA decarboxylase A subunit:Sodium/glutamate symport carrier protein:->->:831467..831608 142 actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_003454_FN0204_FN0205|Glutaconyl-CoA decarboxylase A subunit:Sodium/glutamate symport carrier protein|POSITIVE:POSITIVE|[831467,831608]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt actaaataaaaatattgttgctatgctacctataaataattgtttataggtagtatagtaaataatataggaattctaacttaaatatcttagtagttaatgatgattttaaataataaaaaataattagaaatggagaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAAAUAAAAAUAUUGUUGCUAUGCUACCUAUAAAUAAUUGUUUAUAGGUAGUAUAGUAAAUAAUAUAGGAAUUCUAACUUAAAUAUCUUAGUAGUUAAUGAUGAUUUUAAAUAAUAAAAAAUAAUUAGAAAUGGAGAAUU ...........((((((((((((((((((((((((((....)))))))))))))))))).))))))))...................((((....(((..((((.(((((.........))))).))))..))).))))... (-33.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCUCCAUUUCUAAUUAUUUUUUAUUAUUUAAAAUCAUCAUUAACUACUAAGAUAUUUAAGUUAGAAUUCCUAUAUUAUUUACUAUACUACCUAUAAACAAUUAUUUAUAGGUAGCAUAGCAACAAUAUUUUUAUUUAGU ..........((((((((((.(((((.((.((((........)))).)).))))).))...))))))))...............((((.(((((((((((......))))))))))).)))).................... (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 75 35 145 104 NC_003454:FN1199|5end_DNA_polymerase_IV_1859061..1859291_POSITIVE 191 90 44 189 144 NC_003454:FN0713|5end_Chromate_transport_protein_1371333..1371563_POSITIVE 179 82 43 183 149 NC_003454:FN1489|5end_Methionyl-tRNA_formyltransferase_2171833..2172063_NEGATIVE 179 60 11 222 170 NC_003454:FN1249|5end_Transcriptional_regulator,_DeoR_family_1906241..1906471_NEGATIVE 178 115 71 81 27 NC_003454:FN1849|5end_Coenzyme_F390_synthetase_337934..338164_POSITIVE 174 64 29 65 35 NC_003454:FN0745|5end_metal_dependent_phosphohydrolase_1403275..1403505_POSITIVE 174 29 11 131 113 NC_003454:FN0657|5end_Acetyltransferase_1314266..1314496_POSITIVE 173 51 12 137 90 NC_003454:FN1088|5end_NADH_oxidase_1731708..1731938_POSITIVE 172 50 18 179 146 NC_003454:FN1828|5end_LSU_ribosomal_protein_L9P_317700..317930_NEGATIVE 165 96 53 49 7 NC_003454:FN0604|5end_Proton/sodium-aspartate_symport_protein_1258570..1258800_POSITIVE 164 63 31 217 187 NC_003454:FN1374|5end_Transcriptional_regulator_2022301..2022531_NEGATIVE 164 59 14 66 15 NC_003454:FN0748|5end_hypothetical_protein_1407543..1407773_NEGATIVE 162 99 52 71 21 NC_003454:FN0641|5end_Methyltransferase_1298978..1299208_NEGATIVE 161 95 53 62 17 NC_003454:FN1001|5end_Dethiobiotin_synthetase_1656011..1656241_POSITIVE 161 46 21 181 153 NC_003454:FN0973|5end_Histidinol-phosphate_aminotransferase_1626699..1626929_NEGATIVE 160 79 40 48 3 NC_003454:FN1052|5end_hypothetical_protein_1700520..1700750_POSITIVE 159 103 65 114 76 NC_003454:FN1307|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_1963377..1963607_POSITIVE 159 37 17 24 3 NC_003454:FN1303|5end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1960284..1960514_NEGATIVE 159 60 15 74 24 NC_003454:FN0833|5end_hypothetical_protein_1494853..1495083_POSITIVE 158 76 51 162 138 NC_003454:FN1682|5end_Heteropolysaccharide_repeat_unit_export_protein_178523..178753_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 568 60 12 72 23 NC_003454:FN0204|3end_Glutaconyl-CoA_decarboxylase_A_subunit_831406..831556_POSITIVE 210 58 12 52 11 NC_003454:FN1409|3end_Transporter_2069832..2069982_POSITIVE 174 64 29 68 38 NC_003454:FN0744|3end_metal_dependent_phosphohydrolase_1403358..1403508_POSITIVE 164 60 15 65 15 NC_003454:FN1017|3end_hypothetical_protein_1672164..1672314_POSITIVE 164 115 79 50 3 NC_003454:FN1848|3end_Metal_dependent_hydrolase_337983..338133_POSITIVE 162 56 17 149 111 NC_003454:FN0954|3end_Hypothetical_cytosolic_protein_1610369..1610519_NEGATIVE 162 99 52 58 8 NC_003454:FN0642|3end_hypothetical_protein_1298991..1299141_NEGATIVE 161 95 53 72 27 NC_003454:FN1000|3end_biotin_synthase_1656101..1656251_POSITIVE 159 103 65 111 73 NC_003454:FN1306|3end_Methyltransferase_1963454..1963604_POSITIVE 159 78 35 62 22 NC_003454:FN0387|3end_Fusobacterium_outer_membrane_protein_family_1026596..1026746_POSITIVE 158 76 51 136 112 NC_003454:FN1683|3end_Acetyltransferase_178549..178699_NEGATIVE 155 104 66 40 7 NC_003454:FN0159|3end_hypothetical_protein_788329..788479_POSITIVE 154 79 36 107 63 NC_003454:FN0917|3end_hypothetical_protein_1573643..1573793_POSITIVE 151 77 38 47 1 NC_003454:FN0181|3end_hypothetical_protein_805457..805607_NEGATIVE 151 60 17 112 72 NC_003454:FN1621|3end_elongation_factor_Ts_129655..129805_POSITIVE 150 50 18 132 101 NC_003454:FN0362|3end_ATP_synthase_B_chain,_sodium_ion_specific_992902..993052_NEGATIVE 149 81 48 77 35 NC_003454:FN0192|3end_Dipeptide-binding_protein_818969..819119_POSITIVE 149 50 20 52 10 NC_003454:FN1928|3end_Transcriptional_regulator,_MerR_family_427964..428114_NEGATIVE 148 73 48 99 75 NC_003454:FN1176|3end_Hypothetical_cytosolic_protein_1837506..1837656_NEGATIVE 146 56 11 114 53 NC_003454:FN1163|3end_Thioredoxin_reductase_1821810..1821960_POSITIVE