Origin IGS: tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatactcctccaaatatttttaaaataaatgtaaaatatttattttgtatatattataatcataaaaaaatttttttcaagtattattaaaaaaatataaataatatgtatctaatattttttttaataatatttgtttaaaaaaatacataaaactgtataaattaaaagactttttttctgaatatctatatttttcgacactaaaaaaatataaatattataaaaagatattgacttatgtattgtttggatatataataacacaaacaaattaaagtgataaacaaataaacagtttttattattaggaggaggtatgtatgaaa Mask Tandem Repeat Region ================================================ tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Find is-nt database================================================ Query_seq: FN1899:FN1900|FN1899:FN1900:Hypothetical lipoprotein:pfoS/R:<-->:388055..388383 329 tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1899:FN1900|FN1899:FN1900:Hypothetical lipoprotein:pfoS/R:<-->:388055..388383 329 tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1899:FN1900|FN1899:FN1900:Hypothetical lipoprotein:pfoS/R:<-->:388055..388383 329 tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 22 End: 123 ..................... M I K T V Y L F I T L I C L C Y Y I S K Q Y I S Q Y L F I I F I F F .............................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 9 End: 203 ........ M P P P N N K N C L F V Y H F N L F V L L Y I Q T I H K S I S F Y N I Y I F L V S K N I D I Q K K S L L I Y T V L C I F .............................................................................................................................. Protein_Len: 53 Strand: - Start: 55 End: 213 ...................................................... N T Q T I I Y G F L V Y T L I K K Y Y K Y K K L T S F Y L Y E S F F D K L K Y L K I Y K K L C I N N F F M .................................................................................................................... tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt 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: 88 Start: 68 End: 97 ...................................................................ATTGACTTATGTATTGTTTGGATATATAAT........................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 43 End: 72 ..........................................TTTATCACTTTAATTTGTTTGTGTTATTAT................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -3.5 Tail_Score: -5.58454 Start: 105 End: 117 Full_Region: AAGTCAATATCTTTT TATAA TAT TTATA TTTTTTTAGTGTCGA ........................................................................................................TATAATATTTATA.................................................................................................................................................................................................................... TransTerm Strand: - Conf: 44 HP_score: -3.2 Tail_Score: -3.54543 Start: 194 End: 252 Full_Region: taaaaaaattttttt caagtattattaaaaaaatataaata atatg tatctaatattttttttaataatatttg tttaaaaaaatacat .................................................................................................................................................................................................caagtattattaaaaaaatataaataatatgtatctaatattttttttaataatatttg............................................................................. Find igs database================================================ Query_seq: FN1899:FN1900|FN1899:FN1900:Hypothetical lipoprotein:pfoS/R:<-->:388055..388383 329 tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcagaaaaaaagtcttttaatttatacagttttatgtatttttttaaacaaatattattaaaaaaaatattagatacatattatttatatttttttaataatacttgaaaaaaatttttttatgattataatatatacaaaataaatattttacatttattttaaaaatatttggaggagtatt Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_003454_FN1899_FN1900|Hypothetical lipoprotein:pfoS/R|NEGATIVE:POSITIVE|[388055,388383]|329 HSP 1 e-value: 2.0E-66 bit: 254.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatannnnnnnagtgtcgaaaaatatagatattcag.................................................................................................................................................................................... tttcatacatacctcctcctaataataaaaactgtttatttgtttatcactttaatttgtttgtgttattatatatccaaacaatacataagtcaatatctttttataatatttatatttttttagtgtcgaaaaatatagatattcag.................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAUACAUACCUCCUCCUAAUAAUAAAAACUGUUUAUUUGUUUAUCACUUUAAUUUGUUUGUGUUAUUAUAUAUCCAAACAAUACAUAAGUCAAUAUCUUUUUAUAAUAUUUAUAUUUUUUUAGUGUCGAAAAAUAUAGAUAUUCAG ........................(((((((.((((.((((((.(((..........((((((..(........)..))))))))).)))))).))))..)))))))((((((((((((((((.......))))))))))))))))... (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAUAUCUAUAUUUUUCGACACUAAAAAAAUAUAAAUAUUAUAAAAAGAUAUUGACUUAUGUAUUGUUUGGAUAUAUAAUAACACAAACAAAUUAAAGUGAUAAACAAAUAAACAGUUUUUAUUAUUAGGAGGAGGUAUGUAUGAAA ...(((((.(((((((((.........))))))))).)))))......(.(((((..(((.....(((((((..............))))))).....(((((((((.............)))))))))..)))..))))).)...... (-18.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 709 50 1 141 92 NC_003454:FN1899|5end_Hypothetical_lipoprotein_387964..388194_NEGATIVE 258 43 1 131 86 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 252 110 64 113 65 NC_003454:FN0575|5end_hypothetical_protein_1225331..1225561_POSITIVE 228 60 13 162 101 NC_003454:FN0370|5end_Signal_peptidase_I_999832..1000062_NEGATIVE 207 46 5 120 86 NC_003454:FN0319|5end_Citrate_(pro-3S)-lyase_ligase_956855..957085_NEGATIVE 207 48 2 143 87 NC_003454:FN1866|5end_Lysine_2,3-aminomutase_358440..358670_NEGATIVE 206 43 2 124 87 NC_003454:FN1063|5end_N-acyl-L-amino_acid_amidohydrolase_1709325..1709555_POSITIVE 203 60 13 87 45 NC_003454:FN0189|5end_Two-component_response_regulator_yesN_813203..813433_POSITIVE 202 60 14 156 98 NC_003454:FN1170|5end_Pyruvate-flavodoxin_oxidoreductase_1832273..1832503_NEGATIVE 196 74 31 121 71 NC_003454:FN0624|5end_NA+/H+_antiporter_NHAC_1284329..1284559_NEGATIVE 194 20 1 106 86 NC_003454:FN1869|5end_hypothetical_protein_360839..361069_NEGATIVE 193 59 13 141 96 NC_003454:FN0280|5end_hypothetical_protein_907752..907982_NEGATIVE 192 50 7 131 88 NC_003454:FN0150|5end_Acyl_carrier_protein_778453..778683_POSITIVE 192 46 2 130 87 NC_003454:FN1978|5end_Cell_division_protein_ftsH_479479..479709_POSITIVE 192 129 94 187 153 NC_003454:FN1516|5end_hypothetical_protein_20858..21088_NEGATIVE 191 47 2 152 114 NC_003454:FN0573|5end_hypothetical_protein_1222518..1222748_POSITIVE 191 36 1 34 2 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 189 42 2 124 87 NC_003454:FN1463|5end_pyridoxine_biosynthesis_protein_2145002..2145232_POSITIVE 189 19 1 74 53 NC_003454:FN1657|5end_SSU_ribosomal_protein_S6P_153122..153352_NEGATIVE 189 51 12 146 96 NC_003454:FN1540|5end_Iron-sulfur_cluster-binding_protein_53055..53285_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 203 60 13 56 14 NC_003454:FN0188|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_813252..813402_POSITIVE 202 60 14 64 6 NC_003454:FN1171|3end_Acetate_kinase_1832365..1832515_NEGATIVE 196 74 31 131 81 NC_003454:FN0625|3end_Aspartate_aminotransferase_1284319..1284469_NEGATIVE 193 59 13 128 83 NC_003454:FN0281|3end_DNA_polymerase_III_alpha_subunit_907765..907915_NEGATIVE 192 50 7 63 20 NC_003454:FN0149|3end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_778465..778615_POSITIVE 192 46 2 133 90 NC_003454:FN1977|3end_Cell_cycle_protein_MesJ_479562..479712_POSITIVE 189 51 12 103 53 NC_003454:FN1539|3end_Iron-sulfur_cluster-binding_protein_53092..53242_POSITIVE 185 129 93 147 113 NC_003454:FN2102|3end_ABC_transporter_ATP-binding_protein_613152..613302_POSITIVE 183 23 1 90 65 NC_003454:FN0731|3end_hypothetical_protein_1388333..1388483_POSITIVE 183 129 86 116 74 NC_003454:FN0419|3end_aspartate_carbamoyltransferase_catalytic_subunit_1060707..1060857_POSITIVE 180 47 1 89 37 NC_003454:FN1036|3end_hypothetical_protein_1689478..1689628_POSITIVE 180 130 89 114 71 NC_003454:FN0109|3end_hypothetical_protein_744333..744483_NEGATIVE 175 50 14 103 65 NC_003454:FN0114|3end_GrpE_protein_748302..748452_POSITIVE 172 29 12 120 104 NC_003454:FN1920|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_415879..416029_NEGATIVE 170 128 81 149 95 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 170 129 87 84 41 NC_003454:FN1614|3end_MG(2+)_chelatase_family_protein_123509..123659_NEGATIVE 168 49 5 110 73 NC_003454:FN1247|3end_LOS_biosynthesis_enzyme_LBGB_1903205..1903355_NEGATIVE 168 48 1 108 75 NC_003454:FN1837|3end_putative_nucleotide-binding_protein_326725..326875_NEGATIVE 167 77 46 147 109 NC_003454:FN1878|3end_hypothetical_protein_367086..367236_POSITIVE 167 49 1 127 68 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE