Origin IGS: actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttataaattagcaaaaaagtggataatgtagtataagataaatttacagtatccactttatttttttatattgtttttgcaattaattattttttagtctatacttaatattagcgaagatttacaaaaataaattaggaggatagt Mask Tandem Repeat Region ================================================ actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Find is-nt database================================================ Query_seq: FN1145:FN1146|FN1145:FN1146:Oligoendopeptidase F:Hypothetical exported 24-amino acid repeat protein:<-<-:1796022..1796169 148 actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1145:FN1146|FN1145:FN1146:Oligoendopeptidase F:Hypothetical exported 24-amino acid repeat protein:<-<-:1796022..1796169 148 actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1145:FN1146|FN1145:FN1146:Oligoendopeptidase F:Hypothetical exported 24-amino acid repeat protein:<-<-:1796022..1796169 148 actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Predict ORF larger than 30AA ================================================ actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa 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: 84 Start: 43 End: 72 ..........................................TTTGCAATTAATTATTTTTTAGTCTATACT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -2.1 Tail_Score: -5.86465 Start: 88 End: 133 Full_Region: tttataaattagcaa aaaagtggataatgtagtata aga taaatttacagtatccacttta tttttttatattgtt .......................................................................................aaaagtggataatgtagtataagataaatttacagtatccacttta............... Find igs database================================================ Query_seq: FN1145:FN1146|FN1145:FN1146:Oligoendopeptidase F:Hypothetical exported 24-amino acid repeat protein:<-<-:1796022..1796169 148 actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagactaaaaaataattaattgcaaaaacaatataaaaaaataaagtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_003454_FN1145_FN1146|Oligoendopeptidase F:Hypothetical exported 24-amino acid repeat protein|NEGATIVE:NEGATIVE|[1796022,1796169]|148 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 57 Query Start:92 Query End:148 Subject Strand: POSITIVE Subject Start: 92 Subject End: 148 ...........................................................................................gtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa ...........................................................................................gtggatactgtaaatttatcttatactacattatccacttttttgctaatttataaa HSP 2 e-value: 6.0E-21 bit: 101.0 Len: 51 Query Start:1 Query End:51 Subject Strand: POSITIVE Subject Start: 1 Subject End: 51 actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagac................................................................................................. actatcctcctaatttatttttgtaaatcttcgctaatattaagtatagac................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUCCUCCUAAUUUAUUUUUGUAAAUCUUCGCUAAUAUUAAGUAUAGACUAAAAAAUAAUUAAUUGCAAAAACAAUAUAAAAAAAUAAAGUGGAUACUGUAAAUUUAUCUUAUACUACAUUAUCCACUUUUUUGCUAAUUUAUAAA ..............((((((((.....(((..(((.......)))..)))...))))))))......(((((((................((((((((.((((..............)))).)))))))))))))))........... (-21.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAAAUUAGCAAAAAAGUGGAUAAUGUAGUAUAAGAUAAAUUUACAGUAUCCACUUUAUUUUUUUAUAUUGUUUUUGCAAUUAAUUAUUUUUUAGUCUAUACUUAAUAUUAGCGAAGAUUUACAAAAAUAAAUUAGGAGGAUAGU .................(((((((((.(((((............))))).)))))))))((((((((((.(((((....)))))...((((((((.(((((...((.......))...)))))...))))))))..)))))))))).. (-24.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 725 140 91 231 182 NC_003454:FN1145|5end_Oligoendopeptidase_F_1795931..1796161_NEGATIVE 220 49 3 150 97 NC_003454:FN0012|5end_DNA_topology_modulation_protein_FLAR-related_protein_652114..652344_NEGATIVE 208 29 2 122 92 NC_003454:FN0732|5end_hypothetical_protein_1388270..1388500_POSITIVE 208 48 6 144 100 NC_003454:FN0339|5end_hypothetical_protein_972035..972265_POSITIVE 207 36 6 48 15 NC_003454:FN0476|5end_transcription_termination_factor_Rho_1123450..1123680_POSITIVE 207 41 1 130 96 NC_003454:FN1867|5end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_359597..359827_NEGATIVE 202 25 5 118 98 NC_003454:FN0052|5end_Arsenate_reductase_688849..689079_POSITIVE 201 31 2 209 182 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 195 41 2 140 99 NC_003454:FN0596|5end_hypothetical_protein_1250001..1250231_POSITIVE 194 36 5 121 95 NC_003454:FN0519|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1171669..1171899_NEGATIVE 194 48 5 97 54 NC_003454:FN0334|5end_Aspartate/aromatic_aminotransferase_969066..969296_NEGATIVE 194 140 99 113 70 NC_003454:FN1780|5end_hypothetical_protein_261664..261894_NEGATIVE 194 69 31 224 184 NC_003454:FN1523|5end_Dipeptide-binding_protein_28207..28437_POSITIVE 193 50 3 146 97 NC_003454:FN1113|5end_Dipeptide_transport_system_permease_protein_dppB_1757915..1758145_NEGATIVE 191 35 3 143 99 NC_003454:FN0466|5end_Lysyl-tRNA_synthetase_1111301..1111531_POSITIVE 189 50 5 124 62 NC_003454:FN1335|5end_Protein_translocase_subunit_YajC_1989011..1989241_NEGATIVE 189 45 5 136 95 NC_003454:FN0775|5end_putative_aminopeptidase_2_1430568..1430798_POSITIVE 189 54 13 58 17 NC_003454:FN0410|5end_6-phosphofructokinase_1047230..1047460_POSITIVE 187 50 5 175 129 NC_003454:FN2081|5end_ABC_transporter_substrate-binding_protein_592974..593204_NEGATIVE 187 50 2 146 102 NC_003454:FN1992|5end_Ribose-phosphate_pyrophosphokinase_495965..496195_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 29 2 105 75 NC_003454:FN0731|3end_hypothetical_protein_1388333..1388483_POSITIVE 208 48 6 126 82 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 207 41 1 112 78 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 201 31 2 56 29 NC_003454:FN1271|3end_Protease_IV_1926745..1926895_NEGATIVE 195 41 2 140 99 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE 194 36 5 112 86 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 194 140 99 45 2 NC_003454:FN1781|3end_LytB_protein_261732..261882_NEGATIVE 191 35 3 120 76 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 189 54 13 46 5 NC_003454:FN0409|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_alpha_1047298..1047448_POSITIVE 187 50 2 144 100 NC_003454:FN1991|3end_Glucosamine-1-phosphate_acetyltransferase_496043..496193_POSITIVE 186 121 83 79 37 NC_003454:FN1080|3end_Export_ABC_transporter_1727308..1727458_POSITIVE 186 128 89 109 67 NC_003454:FN0469|3end_Copper_homeostasis_protein_cutC_1114614..1114764_POSITIVE 182 139 99 47 8 NC_003454:FN1518|3end_RNA_polymerase_sigma-70_factor_23463..23613_NEGATIVE 180 49 8 125 88 NC_003454:FN0715|3end_hypothetical_protein_1374056..1374206_POSITIVE 178 48 2 121 71 NC_003454:FN1105|3end_hypothetical_protein_1750618..1750768_POSITIVE 178 47 1 138 93 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 175 50 1 59 13 NC_003454:FN1404|3end_Imidazolonepropionase_2064366..2064516_POSITIVE 175 41 6 115 87 NC_003454:FN1534|3end_Electron_transfer_flavoprotein_beta-subunit_46333..46483_NEGATIVE 173 48 6 142 101 NC_003454:FN1459|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase_2140275..2140425_NEGATIVE 172 35 2 107 75 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE