Origin IGS: catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattaatatgggggaaacttatatgagaaaaaaatttaaaatgttattattagctattggagtattaactttattttcagcttgttcatcttattatactcgtgaggaagaatatgcaagaaatatg Mask Tandem Repeat Region ================================================ catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Find is-nt database================================================ Query_seq: FN1146:FN1147|FN1146:FN1147:Hypothetical exported 24-amino acid repeat protein:hypothetical protein:<-<-:1796557..1796683 127 catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1146:FN1147|FN1146:FN1147:Hypothetical exported 24-amino acid repeat protein:hypothetical protein:<-<-:1796557..1796683 127 catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1146:FN1147|FN1146:FN1147:Hypothetical exported 24-amino acid repeat protein:hypothetical protein:<-<-:1796557..1796683 127 catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 1 End: 126 M N R A Y E E E R T Y Y S S C A S F L T L V G I A L L L M K F K K R M Y T E G M N M . catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt 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================================================ catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1146:FN1147|FN1146:FN1147:Hypothetical exported 24-amino acid repeat protein:hypothetical protein:<-<-:1796557..1796683 127 catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_003454_FN1146_FN1147|Hypothetical exported 24-amino acid repeat protein:hypothetical protein|NEGATIVE:NEGATIVE|[1796557,1796683]|127 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaannnnnnnctcatataagtttcccccatattaatt catatttcttgcatattcttcctcacgagtataataagatgaacaagctgaaaataaagttaatactccaatagctaataataacattttaaatttttttctcatataagtttcccccatattaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUUUCUUGCAUAUUCUUCCUCACGAGUAUAAUAAGAUGAACAAGCUGAAAAUAAAGUUAAUACUCCAAUAGCUAAUAAUAACAUUUUAAAUUUUUUUCUCAUAUAAGUUUCCCCCAUAUUAAUU ......(((((.((((((........))))))..)))))......(((((.......(((....)))....)))))................................................... ( -8.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAUAUGGGGGAAACUUAUAUGAGAAAAAAAUUUAAAAUGUUAUUAUUAGCUAUUGGAGUAUUAACUUUAUUUUCAGCUUGUUCAUCUUAUUAUACUCGUGAGGAAGAAUAUGCAAGAAAUAUG .....(((((((.....)))))))..(((((...........((((....))))...((((((....))))))))))).((.(((((.((((((.......))))))..))))).)).......... (-17.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 812 50 1 141 92 NC_003454:FN1146|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1796466..1796696_NEGATIVE 262 50 8 126 85 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 234 120 71 102 45 NC_003454:FN1652|5end_Oligopeptide-binding_protein_oppA_147540..147770_NEGATIVE 230 77 31 88 43 NC_003454:FN0921|5end_hypothetical_protein_1576482..1576712_NEGATIVE 222 50 5 227 179 NC_003454:FN1578|5end_hypothetical_protein_88796..89026_NEGATIVE 221 56 18 105 57 NC_003454:FN1886|5end_hypothetical_protein_371399..371629_POSITIVE 217 48 2 67 24 NC_003454:FN1466|5end_hypothetical_protein_2148862..2149092_POSITIVE 216 119 73 103 56 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 214 19 1 47 29 NC_003454:FN1243|5end_Glycosyl_transferase_1900484..1900714_NEGATIVE 212 120 71 86 27 NC_003454:FN0427|5end_Orotate_phosphoribosyltransferase_1069405..1069635_POSITIVE 208 120 73 148 104 NC_003454:FN1296|5end_hypothetical_protein_1954141..1954371_NEGATIVE 207 49 1 84 43 NC_003454:FN1723|5end_glucose-inhibited_division_protein_A_222645..222875_NEGATIVE 205 44 5 87 45 NC_003454:FN0234|5end_hypothetical_protein_859499..859729_NEGATIVE 205 70 23 204 154 NC_003454:FN0082|5end_Ethanolamine_utilization_protein_eutM_720699..720929_POSITIVE 201 81 43 79 35 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 200 118 73 127 87 NC_003454:FN0459|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1104609..1104839_POSITIVE 199 50 5 63 22 NC_003454:FN1274|5end_Acriflavin_resistance_protein_E_1930613..1930843_POSITIVE 198 112 85 117 89 NC_003454:FN0346|5end_hypothetical_protein_979267..979497_NEGATIVE 198 40 2 62 34 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 196 90 47 86 45 NC_003454:FN0264|5end_hypothetical_protein_890862..891092_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 50 8 49 8 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 225 76 33 82 43 NC_003454:FN1276|3end_hypothetical_protein_1935280..1935430_POSITIVE 217 48 2 66 23 NC_003454:FN1465|3end_Permease_2148941..2149091_POSITIVE 214 19 1 42 24 NC_003454:FN1244|3end_Polysaccharide_deacetylase_1900489..1900639_NEGATIVE 212 120 71 114 55 NC_003454:FN0426|3end_Orotidine_5'-phosphate_decarboxylase_1069513..1069663_POSITIVE 208 120 73 72 28 NC_003454:FN1297|3end_Methionine_aminopeptidase_1954217..1954367_NEGATIVE 207 49 1 75 34 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 200 118 73 83 43 NC_003454:FN0458|3end_hypothetical_protein_1104645..1104795_POSITIVE 198 112 85 130 102 NC_003454:FN0347|3end_phosphatidylserine_decarboxylase_979254..979404_NEGATIVE 198 40 2 65 37 NC_003454:FN1969|3end_Hemin_transport_system_permease_protein_hmuU_467186..467336_NEGATIVE 193 32 4 135 103 NC_003454:FN0688|3end_hypothetical_protein_1344609..1344759_POSITIVE 189 33 12 115 95 NC_003454:FN0794|3end_hypothetical_protein_1451840..1451990_NEGATIVE 184 49 8 136 96 NC_003454:FN1626|3end_LSU_ribosomal_protein_L30P_132864..133014_NEGATIVE 182 51 18 87 52 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 182 120 71 112 63 NC_003454:FN0267|3end_ATP-NAD_kinase_894431..894581_POSITIVE 181 120 78 104 68 NC_003454:FN0833|3end_hypothetical_protein_1496552..1496702_POSITIVE 180 119 82 38 8 NC_003454:FN0534|3end_hypothetical_protein_1189366..1189516_POSITIVE 179 120 103 147 129 NC_003454:FN0702|3end_N-acyl-L-amino_acid_amidohydrolase_1360925..1361075_NEGATIVE 175 77 33 81 37 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 173 33 2 149 111 NC_003454:FN2090|3end_hypothetical_protein_601536..601686_NEGATIVE