Origin IGS: tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca .........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 tgaaattcctcctgtaaaattaatattaagaaataactgttatattttaccacaaattttctaaatattaataatttttaattatgatttacaatatattgtatgatataatataaaataaaataaatttttactttaattaaatagctaaaaatgttatactctttaagttgaatacaaggaggtattaaa Mask Tandem Repeat Region ================================================ tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Find is-nt database================================================ Query_seq: FN1703:FN1704|FN1703:FN1704:ADP-L-glycero-D-manno-heptose-6-epimerase:Serine protease:<-->:199083..199274 192 tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1703:FN1704|FN1703:FN1704:ADP-L-glycero-D-manno-heptose-6-epimerase:Serine protease:<-->:199083..199274 192 tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1703:FN1704|FN1703:FN1704:ADP-L-glycero-D-manno-heptose-6-epimerase:Serine protease:<-->:199083..199274 192 tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 5 End: 112 .... M P P C I Q L K E Y N I F S Y L I K V K I Y F I L Y Y I I Q Y I V N H N ................................................................................ tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca 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================================================ tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.8 Tail_Score: -3.34902 Start: 55 End: 79 Full_Region: TTTTAGCTATTTAAT TAAAGTAAAA ATTTA TTTTATTTTA TATTATATCATACAA ......................................................TAAAGTAAAAATTTATTTTATTTTA................................................................................................................. Find igs database================================================ Query_seq: FN1703:FN1704|FN1703:FN1704:ADP-L-glycero-D-manno-heptose-6-epimerase:Serine protease:<-->:199083..199274 192 tttaatacctccttgtattcaacttaaagagtataacatttttagctatttaattaaagtaaaaatttattttattttatattatatcatacaatatattgtaaatcataattaaaaattattaatatttagaaaatttgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca Intra-Species Hit: Count: 1 Min: 1 Max: 192 Len: 192 Subject: NC_003454_FN1703_FN1704|ADP-L-glycero-D-manno-heptose-6- epimerase:Serine protease|NEGATIVE:POSITIVE|[199083,199274]|192 HSP 1 e-value: 1.0E-22 bit: 107.0 Len: 54 Query Start:139 Query End:192 Subject Strand: POSITIVE Subject Start: 139 Subject End: 192 ..........................................................................................................................................tgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca ..........................................................................................................................................tgtggtaaaatataacagttatttcttaatattaattttacaggaggaatttca HSP 2 e-value: 2.0E-12 bit: 73.8 Len: 37 Query Start:1 Query End:37 Subject Strand: POSITIVE Subject Start: 1 Subject End: 37 tttaatacctccttgtattcaacttaaagagtataac........................................................................................................................................................... tttaatacctccttgtattcaacttaaagagtataac........................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUACCUCCUUGUAUUCAACUUAAAGAGUAUAACAUUUUUAGCUAUUUAAUUAAAGUAAAAAUUUAUUUUAUUUUAUAUUAUAUCAUACAAUAUAUUGUAAAUCAUAAUUAAAAAUUAUUAAUAUUUAGAAAAUUUGUGGUAAAAUAUAACAGUUAUUUCUUAAUAUUAAUUUUACAGGAGGAAUUUCA .......(((((((((((((........)))))))..((((((((.(((.....((((((((....)))))))).((((((.(((((......))))).))))))..))).)))))))).(((((((((.(((((..((((...........))))...))))).))))))))).....))))))....... (-32.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAUUCCUCCUGUAAAAUUAAUAUUAAGAAAUAACUGUUAUAUUUUACCACAAAUUUUCUAAAUAUUAAUAAUUUUUAAUUAUGAUUUACAAUAUAUUGUAUGAUAUAAUAUAAAAUAAAAUAAAUUUUUACUUUAAUUAAAUAGCUAAAAAUGUUAUACUCUUUAAGUUGAAUACAAGGAGGUAUUAAA ...(((.(((((((((..(((((((((.(((((....(((...........)))...))))).)))))))))...................((((.((..(((((((((....((((.(((((.....))))).)))).(((......)))..)))))))))....)).))))..))).)))))).)))... (-29.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 698 50 1 141 92 NC_003454:FN1703|5end_ADP-L-glycero-D-manno-heptose-6-epimerase_198992..199222_NEGATIVE 198 46 5 138 97 NC_003454:FN0606|5end_Translation_initiation_inhibitor_1261014..1261244_POSITIVE 198 150 108 187 144 NC_003454:FN1975|5end_ATP-dependent_RNA_helicase_475599..475829_POSITIVE 195 153 117 226 197 NC_003454:FN0296|5end_Hypothetical_cytosolic_protein_929789..930019_NEGATIVE 194 30 8 122 102 NC_003454:FN0067|5end_Isoleucyl-tRNA_synthetase_704537..704767_POSITIVE 192 48 6 140 98 NC_003454:FN0472|5end_flavodoxin_1118165..1118395_NEGATIVE 191 70 21 67 14 NC_003454:FN1781|5end_LytB_protein_264215..264445_NEGATIVE 190 44 8 176 130 NC_003454:FN0350|5end_hypothetical_protein_982372..982602_POSITIVE 188 165 122 143 101 NC_003454:FN0598|5end_Phospholipid-lipopolysaccharide_ABC_transporter_1251881..1252111_POSITIVE 188 99 58 191 150 NC_003454:FN0262|5end_Formate_acetyltransferase_889807..890037_NEGATIVE 179 190 141 131 80 NC_003454:FN1638|5end_50S_ribosomal_protein_L16_137501..137731_NEGATIVE 175 51 13 227 198 NC_003454:FN0511|5end_D-lactate_dehydrogenase_1160285..1160515_POSITIVE 175 51 13 225 196 NC_003454:FN1881|5end_Esterase_368639..368869_NEGATIVE 174 57 11 100 45 NC_003454:FN1828|5end_LSU_ribosomal_protein_L9P_317700..317930_NEGATIVE 173 46 12 98 56 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 173 47 6 200 161 NC_003454:FN1709|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_205415..205645_POSITIVE 167 92 58 144 116 NC_003454:FN0370|5end_Signal_peptidase_I_999832..1000062_NEGATIVE 167 146 105 165 130 NC_003454:FN2084|5end_Permease_595708..595938_POSITIVE 164 18 5 108 95 NC_003454:FN1463|5end_pyridoxine_biosynthesis_protein_2145002..2145232_POSITIVE 163 43 5 136 96 NC_003454:FN1670|5end_Choline_kinase_168266..168496_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 198 46 5 141 100 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 194 30 8 125 105 NC_003454:FN0066|3end_Two_component_system_histidine_kinase_704620..704770_POSITIVE 191 70 21 61 8 NC_003454:FN1782|3end_Phosphocarrier_protein_HPr_264221..264371_NEGATIVE 190 44 8 60 14 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE 188 165 122 146 104 NC_003454:FN0597|3end_Lipid-A-disaccharide_synthase_1251964..1252114_POSITIVE 179 190 141 128 77 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 175 162 126 145 92 NC_003454:FN0799|3end_Isoamylase_1457889..1458039_NEGATIVE 174 57 11 83 28 NC_003454:FN1829|3end_hypothetical_protein_317717..317867_NEGATIVE 173 46 12 86 44 NC_003454:FN1103|3end_Excinuclease_ABC_subunit_A_1749521..1749671_POSITIVE 172 165 129 103 53 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 166 47 6 96 47 NC_003454:FN0787|3end_Transposase_1443908..1444058_POSITIVE 165 46 8 148 115 NC_003454:FN1981|3end_Transposase_483747..483897_POSITIVE 162 60 11 73 14 NC_003454:FN1457|3end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2137903..2138053_NEGATIVE 162 50 3 124 77 NC_003454:FN0754|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1413183..1413333_NEGATIVE 161 165 121 134 90 NC_003454:FN1780|3end_hypothetical_protein_260921..261071_NEGATIVE 160 24 8 145 129 NC_003454:FN2114|3end_hypothetical_protein_624010..624160_NEGATIVE 157 48 8 134 87 NC_003454:FN0596|3end_hypothetical_protein_1250884..1251034_POSITIVE 156 186 158 109 74 NC_003454:FN0847|3end_TPR-repeat-containing_proteins_1507132..1507282_POSITIVE 156 47 7 120 80 NC_003454:FN0121|3end_hypothetical_protein_752908..753058_NEGATIVE 153 89 60 39 8 NC_003454:FN0714|3end_NADH_oxidase_1373086..1373236_POSITIVE