Origin IGS: atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaagttaagggttattgtaaatttgcaatagcccttattttttgttttacaaattataacaagtatggtatacttaaattagttctatttagaactaatttaaaaggtgaataaaaggactgatatat Mask Tandem Repeat Region ================================================ atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Find is-nt database================================================ Query_seq: FN2010:FN2011|FN2010:FN2011:Transcriptional regulator, MarR family:Valyl-tRNA synthetase:<-<-:510393..510522 130 atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2010:FN2011|FN2010:FN2011:Transcriptional regulator, MarR family:Valyl-tRNA synthetase:<-<-:510393..510522 130 atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2010:FN2011|FN2010:FN2011:Transcriptional regulator, MarR family:Valyl-tRNA synthetase:<-<-:510393..510522 130 atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Predict ORF larger than 30AA ================================================ atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat 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: 85 Start: 55 End: 84 ......................................................TTTTACAAATTATAACAAGTATGGTATACT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -8.0 Tail_Score: -3.55761 Start: 31 End: 50 Full_Region: tatggtatacttaaa ttagttct attt agaactaa tttaaaaggtgaata ..............................ttagttctatttagaactaa................................................................................ Find igs database================================================ Query_seq: FN2010:FN2011|FN2010:FN2011:Transcriptional regulator, MarR family:Valyl-tRNA synthetase:<-<-:510393..510522 130 atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_003454_FN2010_FN2011|Transcriptional regulator, MarR family:Valyl-tRNA synthetase|NEGATIVE:NEGATIVE|[510393,510522]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat atatatcagtccttttattcaccttttaaattagttctaaatagaactaatttaagtataccatacttgttataatttgtaaaacaaaaaataagggctattgcaaatttacaataacccttaactttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUCAGUCCUUUUAUUCACCUUUUAAAUUAGUUCUAAAUAGAACUAAUUUAAGUAUACCAUACUUGUUAUAAUUUGUAAAACAAAAAAUAAGGGCUAUUGCAAAUUUACAAUAACCCUUAACUUUAU ............((((((.......(((((((((((((....))))))))))))).((((.((....)).))))....)))))).......((((((.(((((........))))).))))))....... (-24.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAGUUAAGGGUUAUUGUAAAUUUGCAAUAGCCCUUAUUUUUUGUUUUACAAAUUAUAACAAGUAUGGUAUACUUAAAUUAGUUCUAUUUAGAACUAAUUUAAAAGGUGAAUAAAAGGACUGAUAUAU .......((((((((((((((....)))))))))))))).(((((((((.((..((((((.....))))))....(((((((((((((....)))))))))))))...)))))))))))........... (-35.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 130 81 221 172 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 233 124 85 230 187 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 232 120 87 72 38 NC_003454:FN1260|5end_Sensory_Transduction_Protein_Kinase_1917146..1917376_NEGATIVE 229 121 86 198 159 NC_003454:FN0374|5end_Single-stranded-DNA-specific_exonuclease_recJ_1002654..1002884_POSITIVE 214 130 87 184 135 NC_003454:FN0847|5end_TPR-repeat-containing_proteins_1505253..1505483_POSITIVE 210 120 86 43 5 NC_003454:FN0531|5end_hypothetical_protein_1186389..1186619_POSITIVE 208 118 86 149 120 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 207 48 5 100 51 NC_003454:FN0763|5end_Transporter,_LysE_family_1420169..1420399_POSITIVE 199 48 10 103 71 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 190 115 83 194 152 NC_003454:FN0799|5end_Isoamylase_1459826..1460056_NEGATIVE 188 46 7 110 76 NC_003454:FN0817|5end_ABC_transporter_ATP-binding_protein_1476448..1476678_POSITIVE 182 38 10 59 23 NC_003454:FN1092|5end_hypothetical_protein_1737267..1737497_POSITIVE 182 108 61 50 1 NC_003454:FN0939|5end_Hypothetical_membrane-spanning_protein_1592919..1593149_NEGATIVE 180 129 91 52 17 NC_003454:FN0069|5end_glycyl-tRNA_synthetase_alpha_subunit_707809..708039_POSITIVE 178 57 13 150 109 NC_003454:FN1695|5end_Probable_quinovosaminephosphotransferae_190861..191091_NEGATIVE 176 120 76 211 163 NC_003454:FN1337|5end_hypothetical_protein_1991481..1991711_NEGATIVE 176 58 11 72 23 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 173 128 94 221 181 NC_003454:FN1488|5end_Methenyltetrahydrofolate_cyclohydrolase_2170886..2171116_NEGATIVE 173 128 88 150 111 NC_003454:FN1160|5end_SWF/SNF_family_helicase_1815836..1816066_POSITIVE 171 119 73 144 102 NC_003454:FN0780|5end_Hypothetical_membrane-spanning_protein_1437490..1437720_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 111 79 59 26 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 232 120 87 48 14 NC_003454:FN1261|3end_Two-component_response_regulator_1917170..1917320_NEGATIVE 231 122 88 104 66 NC_003454:FN1044|3end_hypothetical_protein_1694453..1694603_NEGATIVE 217 120 78 56 1 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 214 130 87 87 38 NC_003454:FN0846|3end_hypothetical_protein_1505236..1505386_POSITIVE 210 120 86 147 109 NC_003454:FN0531|3end_hypothetical_protein_1186573..1186723_POSITIVE 208 118 86 41 12 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 198 128 86 79 28 NC_003454:FN0225|3end_Gluconate_permease_851715..851865_NEGATIVE 195 122 82 75 37 NC_003454:FN0658|3end_ABC_transporter_substrate-binding_protein_1314890..1315040_NEGATIVE 190 115 83 73 31 NC_003454:FN0800|3end_Amino_acid-binding_protein_1459947..1460097_NEGATIVE 188 46 7 37 3 NC_003454:FN0816|3end_dehydrogenase_with_MaoC-like_domain_1476455..1476605_POSITIVE 188 109 93 60 44 NC_003454:FN0637|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1295636..1295786_NEGATIVE 186 104 78 81 55 NC_003454:FN2109|3end_UDP-glucose_4-epimerase_621917..622067_POSITIVE 184 119 74 76 26 NC_003454:FN0749|3end_hypothetical_protein_1407712..1407862_NEGATIVE 182 38 10 50 14 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 180 129 91 48 13 NC_003454:FN0068|3end_Lipoprotein_signal_peptidase_707885..708035_POSITIVE 178 123 87 100 65 NC_003454:FN0879|3end_ABC_transporter_integral_membrane_protein_1540161..1540311_NEGATIVE 178 80 42 137 92 NC_003454:FN1905|3end_168_kDa_surface-layer_protein_precursor_393653..393803_NEGATIVE 178 57 13 135 94 NC_003454:FN1696|3end_UDP-4-dehydro-6-deoxy-2-acetamido-D-glucose_4-reductase_190876..191026_NEGATIVE 177 38 1 136 96 NC_003454:FN1449|3end_Fusobacterium_outer_membrane_protein_family_2118612..2118762_NEGATIVE