Origin IGS: ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttatcaccttttttattataacatattttttaaataataggacataaaaggacaaatttaaaagaatttgcaattttttataaaacttgttaacctaaacaagtaatgaaaa Mask Tandem Repeat Region ================================================ ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Find is-nt database================================================ Query_seq: FN0686:FN0687|FN0686:FN0687:Integral membrane protein:hypothetical protein:<-->:1342589..1342702 114 ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0686:FN0687|FN0686:FN0687:Integral membrane protein:hypothetical protein:<-->:1342589..1342702 114 ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0686:FN0687|FN0686:FN0687:Integral membrane protein:hypothetical protein:<-->:1342589..1342702 114 ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Predict ORF larger than 30AA ================================================ ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa 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: 50 End: 79 .................................................TTTTAAATTTGTCCTTTTATGTCCTATTAT................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 17 End: 46 ................TTTGCAATTTTTTATAAAACTTGTTAACCT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.8 Tail_Score: -3.23165 Start: 43 End: 60 Full_Region: TTTTATAAAAAATTG CAAATT CTTTTA AATTTG TCCTTTTATGTCCTA ..........................................CAAATTCTTTTAAATTTG...................................................... Find igs database================================================ Query_seq: FN0686:FN0687|FN0686:FN0687:Integral membrane protein:hypothetical protein:<-->:1342589..1342702 114 ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_003454_FN0686_FN0687|Integral membrane protein:hypothetical protein|NEGATIVE:POSITIVE|[1342589,1342702]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa ttttcattacttgtttaggttaacaagttttataaaaaattgcaaattcttttaaatttgtccttttatgtcctattatttaaaaaatatgttataataaaaaaggtgataaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCAUUACUUGUUUAGGUUAACAAGUUUUAUAAAAAAUUGCAAAUUCUUUUAAAUUUGUCCUUUUAUGUCCUAUUAUUUAAAAAAUAUGUUAUAAUAAAAAAGGUGAUAAAA .....(((((((.((((...(((((.(((((.((((.(((.(((((((......))))))).............))).)))).))))).)))))...))))..))))))).... (-14.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUCACCUUUUUUAUUAUAACAUAUUUUUUAAAUAAUAGGACAUAAAAGGACAAAUUUAAAAGAAUUUGCAAUUUUUUAUAAAACUUGUUAACCUAAACAAGUAAUGAAAA ........(((((((((((((..............))))))).....)))))).(((((((....)))))))....(((((((...(((((((......))))))).))))))) (-14.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 633 50 1 141 92 NC_003454:FN0686|5end_Integral_membrane_protein_1342498..1342728_NEGATIVE 320 80 31 192 145 NC_003454:FN1359|5end_Dipeptide-binding_protein_2010637..2010867_POSITIVE 247 81 41 205 174 NC_003454:FN1640|5end_LSU_ribosomal_protein_L22P_138517..138747_NEGATIVE 213 89 42 120 72 NC_003454:FN0818|5end_DNA-binding_protein_HU_1477034..1477264_NEGATIVE 212 77 40 211 168 NC_003454:FN1702|5end_undecaprenyl_pyrophosphate_phosphatase_197964..198194_NEGATIVE 211 43 1 190 155 NC_003454:FN1482|5end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2165992..2166222_NEGATIVE 186 82 48 167 129 NC_003454:FN1667|5end_dTDP-glucose_4,6-dehydratase_164472..164702_NEGATIVE 184 83 45 230 196 NC_003454:FN1630|5end_SSU_ribosomal_protein_S8P_134931..135161_NEGATIVE 183 46 12 182 144 NC_003454:FN0799|5end_Isoamylase_1459826..1460056_NEGATIVE 183 47 1 195 142 NC_003454:FN0175|5end_Cell_division_inhibitor_MinC_800505..800735_POSITIVE 176 34 1 59 33 NC_003454:FN1123|5end_Thioredoxin-like_protein_1767478..1767708_POSITIVE 174 81 43 93 55 NC_003454:FN1105|5end_hypothetical_protein_1750041..1750271_POSITIVE 173 80 36 95 42 NC_003454:FN0008|5end_quinolinate_synthetase_648010..648240_POSITIVE 167 63 40 217 194 NC_003454:FN1209|5end_Hypothetical_RNA_binding_protein_1868914..1869144_NEGATIVE 167 75 47 224 196 NC_003454:FN0286|5end_hypothetical_protein_914425..914655_NEGATIVE 167 108 61 152 101 NC_003454:FN1589|5end_LexA_repressor_99792..100022_POSITIVE 166 74 45 47 21 NC_003454:FN0855|5end_glucose-1-phosphate_adenylyltransferase_1514662..1514892_NEGATIVE 166 80 49 95 58 NC_003454:FN2039|5end_50S_ribosomal_protein_L1_548557..548787_NEGATIVE 165 50 6 163 110 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 164 77 47 49 22 NC_003454:FN0709|5end_Virulence_factor_mviN_1367339..1367569_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 80 40 76 31 NC_003454:FN0742|3end_hypothetical_protein_1400671..1400821_POSITIVE 183 46 12 61 23 NC_003454:FN0800|3end_Amino_acid-binding_protein_1459947..1460097_NEGATIVE 183 47 1 73 20 NC_003454:FN0174|3end_Enoyl-[acyl-carrier-protein]_reductase_800463..800613_POSITIVE 174 81 43 89 51 NC_003454:FN1104|3end_Holliday_junction_DNA_helicase_ruvA_1750117..1750267_POSITIVE 174 78 40 143 108 NC_003454:FN0688|3end_hypothetical_protein_1344609..1344759_POSITIVE 173 83 41 126 77 NC_003454:FN0211|3end_Plasmid_addiction_system_poison_protein_837570..837720_POSITIVE 168 80 32 95 43 NC_003454:FN1087|3end_hypothetical_protein_1731616..1731766_POSITIVE 167 108 61 77 26 NC_003454:FN1588|3end_hypothetical_protein_99797..99947_POSITIVE 164 77 47 55 28 NC_003454:FN0708|3end_Hypothetical_cytosolic_protein_1367425..1367575_POSITIVE 162 109 64 108 54 NC_003454:FN0729|3end_Phosphoglycerate_mutase_1387120..1387270_POSITIVE 162 44 1 44 4 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 161 89 48 74 28 NC_003454:FN1707|3end_Aldose_1-epimerase_203268..203418_POSITIVE 160 74 47 151 118 NC_003454:FN0254|3end_Fusobacterium_outer_membrane_protein_family_881390..881540_POSITIVE 160 63 26 122 84 NC_003454:FN1886|3end_hypothetical_protein_371754..371904_POSITIVE 158 39 1 147 98 NC_003454:FN1292|3end_hypothetical_protein_1949443..1949593_NEGATIVE 158 74 34 131 76 NC_003454:FN1237|3end_Choline_kinase_1893453..1893603_NEGATIVE 157 88 45 99 43 NC_003454:FN1105|3end_hypothetical_protein_1750618..1750768_POSITIVE 157 77 39 121 80 NC_003454:FN0065|3end_Transcription_accessory_protein_(S1_RNA_binding_domain)_702184..702334_POSITIVE 156 73 46 124 95 NC_003454:FN0552|3end_Serine_racemase_1203606..1203756_NEGATIVE 155 77 40 57 18 NC_003454:FN1929|3end_Competence-damage_protein_cinA_428525..428675_NEGATIVE