Origin IGS: aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag .........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 ctttataattaaattagcactaaccctagtgtatatagattattatttcccaaaagaaggttgaaattttcaatcttctttttatttgttataaaataaaaatgtgttagaatatataataaatattctaaataaaattcgcagatgctgtctgtggaatgtaaatatttataggaggatttt Mask Tandem Repeat Region ================================================ aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Find is-nt database================================================ Query_seq: FN1448:FN1449|FN1448:FN1449:Hypothetical cytosolic protein:Fusobacterium outer membrane protein family:<-<-:2118519..2118701 183 aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1448:FN1449|FN1448:FN1449:Hypothetical cytosolic protein:Fusobacterium outer membrane protein family:<-<-:2118519..2118701 183 aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1448:FN1449|FN1448:FN1449:Hypothetical cytosolic protein:Fusobacterium outer membrane protein family:<-<-:2118519..2118701 183 aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 38 End: 172 ..................................... M C E F Y L E Y L L Y I L T H F Y F I T N K K K I E N F N L L L G N N N L Y T L G L V L I ........... aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag 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: 81 Start: 87 End: 116 ......................................................................................TTTCAATCTTCTTTTTATTTGTTATAAAAT................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 89 End: 118 ........................................................................................ATTTTCAATCTTCTTTTTATTTGTTATAAA................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.0 Tail_Score: -5.50774 Start: 106 End: 128 Full_Region: tattatttcccaaaa gaaggttgaa att ttcaatcttc tttttatttgttata .........................................................................................................gaaggttgaaattttcaatcttc....................................................... Find igs database================================================ Query_seq: FN1448:FN1449|FN1448:FN1449:Hypothetical cytosolic protein:Fusobacterium outer membrane protein family:<-<-:2118519..2118701 183 aaaatcctcctataaatatttacattccacagacagcatctgcgaattttatttagaatatttattatatattctaacacatttttattttataacaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_003454_FN1448_FN1449|Hypothetical cytosolic protein:Fusobacterium outer membrane protein family|NEGATIVE:NEGATIVE|[2118519,2118701]|183 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 89 Query Start:95 Query End:183 Subject Strand: POSITIVE Subject Start: 95 Subject End: 183 ..............................................................................................acaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag ..............................................................................................acaaataaaaagaagattgaaaatttcaaccttcttttgggaaataataatctatatacactagggttagtgctaatttaattataaag HSP 2 e-value: 3.0E-17 bit: 89.7 Len: 45 Query Start:1 Query End:45 Subject Strand: POSITIVE Subject Start: 1 Subject End: 45 aaaatcctcctataaatatttacattccacagacagcatctgcga.......................................................................................................................................... aaaatcctcctataaatatttacattccacagacagcatctgcga.......................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCCUCCUAUAAAUAUUUACAUUCCACAGACAGCAUCUGCGAAUUUUAUUUAGAAUAUUUAUUAUAUAUUCUAACACAUUUUUAUUUUAUAACAAAUAAAAAGAAGAUUGAAAAUUUCAACCUUCUUUUGGGAAAUAAUAAUCUAUAUACACUAGGGUUAGUGCUAAUUUAAUUAUAAAG ....(((...((((((.......((((..((((.....)))).)))).....(((((((((.......)))))))))...........)))))).......((((((((.((((.....)))).)))))))).)))................(((((....)))))................. (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUAAUUAAAUUAGCACUAACCCUAGUGUAUAUAGAUUAUUAUUUCCCAAAAGAAGGUUGAAAUUUUCAAUCUUCUUUUUAUUUGUUAUAAAAUAAAAAUGUGUUAGAAUAUAUAAUAAAUAUUCUAAAUAAAAUUCGCAGAUGCUGUCUGUGGAAUGUAAAUAUUUAUAGGAGGAUUUU ....((((((......((((((....)))))).....))))))..(((((.(((((((((((((.....))))))))))))).................((((((.(((((((((.......)))))))))......(((((((((...)))))))))......))))))...)))))..... (-39.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 50 1 141 92 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 469 166 126 185 142 NC_003454:FN1891|5end_Glycerophosphoryl_diester_phosphodiesterase_374294..374524_NEGATIVE 353 150 101 189 137 NC_003454:FN2046|5end_Acetyltransferase_551360..551590_NEGATIVE 253 168 126 108 68 NC_003454:FN0743|5end_ATP-dependent_helicase,_DinG_family_1400850..1401080_POSITIVE 219 60 20 212 172 NC_003454:FN1532|5end_murein_hydrolase_exporter_45319..45549_NEGATIVE 216 50 4 196 142 NC_003454:FN1622|5end_Uridylate_kinase_129640..129870_POSITIVE 209 158 118 101 59 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 208 90 47 226 177 NC_003454:FN1125|5end_LemA_protein_1769811..1770041_NEGATIVE 208 43 8 112 75 NC_003454:FN0188|5end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_812276..812506_POSITIVE 201 139 111 77 43 NC_003454:FN0814|5end_Propionate_CoA-transferase_1472717..1472947_POSITIVE 200 127 84 144 105 NC_003454:FN2128|5end_RECF_protein_639585..639815_NEGATIVE 200 45 6 66 24 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 196 149 114 124 92 NC_003454:FN0527|5end_Alanyl-tRNA_synthetase_1184098..1184328_NEGATIVE 193 50 6 154 99 NC_003454:FN1533|5end_Electron_transfer_flavoprotein_alpha-subunit_46321..46551_NEGATIVE 190 40 5 126 96 NC_003454:FN0285|5end_RNA_binding_protein_914171..914401_NEGATIVE 186 50 5 147 101 NC_003454:FN0584|5end_hypothetical_protein_1239444..1239674_POSITIVE 186 166 122 210 147 NC_003454:FN0477|5end_Cell_wall_endopeptidase_family_M23/M37_1124872..1125102_POSITIVE 186 136 122 231 217 NC_003454:FN1553|5end_Transporter_68538..68768_NEGATIVE 185 41 5 216 182 NC_003454:FN1831|5end_Nitrogen_assimilation_regulatory_protein_321423..321653_NEGATIVE 185 62 25 62 28 NC_003454:FN1590|5end_Hypothetical_lipoprotein_101804..102034_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 570 166 122 81 36 NC_003454:FN1554|3end_Fusobacterium_outer_membrane_protein_family_68719..68869_NEGATIVE 469 166 126 67 24 NC_003454:FN1893|3end_Fusobacterium_outer_membrane_protein_family_374412..374562_NEGATIVE 353 150 101 58 6 NC_003454:FN2047|3end_Fusobacterium_outer_membrane_protein_family_551491..551641_NEGATIVE 216 50 4 131 77 NC_003454:FN1621|3end_elongation_factor_Ts_129655..129805_POSITIVE 208 43 8 55 18 NC_003454:FN0187|3end_Thiol:disulfide_interchange_protein_tlpA_812299..812449_POSITIVE 200 127 84 129 90 NC_003454:FN2129|3end_Hypothetical_cytosolic_protein_639600..639750_NEGATIVE 193 50 6 142 87 NC_003454:FN1534|3end_Electron_transfer_flavoprotein_beta-subunit_46333..46483_NEGATIVE 190 40 5 114 84 NC_003454:FN0286|3end_hypothetical_protein_914183..914333_NEGATIVE 186 114 78 51 16 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE 186 50 5 141 95 NC_003454:FN0583|3end_hypothetical_protein_1239518..1239668_POSITIVE 184 37 5 131 86 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 183 53 23 72 42 NC_003454:FN0979|3end_hypothetical_protein_1632544..1632694_POSITIVE 179 168 125 63 14 NC_003454:FN0195|3end_Dipeptide_transport_ATP-binding_protein_dppD_822407..822557_POSITIVE 177 48 5 133 86 NC_003454:FN0025|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664326..664476_POSITIVE 175 71 39 33 2 NC_003454:FN1302|3end_hypothetical_protein_1959667..1959817_POSITIVE 175 168 123 97 54 NC_003454:FN1657|3end_SSU_ribosomal_protein_S6P_152805..152955_NEGATIVE 175 45 5 131 83 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 174 33 4 137 98 NC_003454:FN0524|3end_DNA_helicase_II_1176884..1177034_NEGATIVE 172 45 17 122 92 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 170 74 34 96 61 NC_003454:FN0987|3end_Amidophosphoribosyltransferase_1638864..1639014_NEGATIVE