Origin IGS: tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaaaataactcattactgagtagattttttatctaaaatctacattcgtaattcgtttatttttatttattaataatatatgattaaggaaaataaggtacagtagaggaagcgattaaaaataatttagatacagaagggaagattttaaa Mask Tandem Repeat Region ================================================ tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Find is-nt database================================================ Query_seq: FN1350:FN1351|FN1350:FN1351:Integral membrane protein:15 kDa lipoprotein precursor:<-<-:2002887..2003039 153 tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1350:FN1351|FN1350:FN1351:Integral membrane protein:15 kDa lipoprotein precursor:<-<-:2002887..2003039 153 tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1350:FN1351|FN1350:FN1351:Integral membrane protein:15 kDa lipoprotein precursor:<-<-:2002887..2003039 153 tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Predict ORF larger than 30AA ================================================ tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg 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================================================ tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1350:FN1351|FN1350:FN1351:Integral membrane protein:15 kDa lipoprotein precursor:<-<-:2002887..2003039 153 tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_003454_FN1350_FN1351|Integral membrane protein:15 kDa lipoprotein precursor|NEGATIVE:NEGATIVE|[2002887,2003039]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg tttaaaatcttcccttctgtatctaaattatttttaatcgcttcctctactgtaccttattttccttaatcatatattattaataaataaaaataaacgaattacgaatgtagattttagataaaaaatctactcagtaatgagttatttttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAAUCUUCCCUUCUGUAUCUAAAUUAUUUUUAAUCGCUUCCUCUACUGUACCUUAUUUUCCUUAAUCAUAUAUUAUUAAUAAAUAAAAAUAAACGAAUUACGAAUGUAGAUUUUAGAUAAAAAAUCUACUCAGUAAUGAGUUAUUUUUG ((((((((((....(((.(((......(((((((((...((..........))............(((((........)))))....)))))))))......))))))...))))))))))..((((((..(((((....))))).)))))). (-19.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAAUAACUCAUUACUGAGUAGAUUUUUUAUCUAAAAUCUACAUUCGUAAUUCGUUUAUUUUUAUUUAUUAAUAAUAUAUGAUUAAGGAAAAUAAGGUACAGUAGAGGAAGCGAUUAAAAAUAAUUUAGAUACAGAAGGGAAGAUUUUAAA ..(((((..(((.((.(((.(((((((((......)))))))))..((((..(((.(((((((((((((.(((((........)))))...)))))))....)))))).)))))))..................))))))))...)))))... (-24.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 795 60 11 151 102 NC_003454:FN1350|5end_Integral_membrane_protein_2002796..2003026_NEGATIVE 583 150 102 210 162 NC_003454:FN0423|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1066328..1066558_POSITIVE 505 143 101 231 189 NC_003454:FN1347|5end_Hypothetical_cytosolic_protein_2000300..2000530_NEGATIVE 485 150 101 206 153 NC_003454:FN2080|5end_ABC_transporter_integral_membrane_protein_591957..592187_NEGATIVE 358 150 106 202 154 NC_003454:FN0921|5end_hypothetical_protein_1576482..1576712_NEGATIVE 248 67 21 114 54 NC_003454:FN0395|5end_Transporter_1033106..1033336_POSITIVE 247 150 126 98 74 NC_003454:FN0171|5end_Hypothetical_cytosolic_protein_796548..796778_POSITIVE 246 68 21 74 27 NC_003454:FN0950|5end_Precorrin-6X_reductase_1607775..1608005_NEGATIVE 235 54 14 115 70 NC_003454:FN1545|5end_Ferredoxin_like_protein_59133..59363_POSITIVE 233 49 7 84 50 NC_003454:FN0197|5end_Methyltransferase_822664..822894_POSITIVE 232 65 38 64 36 NC_003454:FN0852|5end_Hydrolase_1510224..1510454_POSITIVE 224 50 7 98 56 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 223 56 28 117 88 NC_003454:FN0700|5end_Protein_translocase_subunit_secF_1358286..1358516_POSITIVE 223 65 27 128 90 NC_003454:FN0584|5end_hypothetical_protein_1239444..1239674_POSITIVE 220 67 31 163 132 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 217 49 15 107 71 NC_003454:FN0549|5end_O-sialoglycoprotein_endopeptidase_1201326..1201556_POSITIVE 214 57 11 100 55 NC_003454:FN1591|5end_RNFB-related_protein_103135..103365_NEGATIVE 210 66 22 100 51 NC_003454:FN1764|5end_Enolase_257997..258227_NEGATIVE 209 127 84 216 173 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 208 56 11 148 94 NC_003454:FN0357|5end_ATP_synthase_epsilon_chain,_sodium_ion_specific_988276..988506_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 583 150 102 85 37 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 570 150 101 68 19 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 485 150 101 88 35 NC_003454:FN2081|3end_ABC_transporter_substrate-binding_protein_592075..592225_NEGATIVE 358 150 106 96 48 NC_003454:FN0922|3end_Homoserine_kinase_1576588..1576738_NEGATIVE 257 65 28 122 85 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 248 67 21 75 15 NC_003454:FN0394|3end_Outer_membrane_protein_1033147..1033297_POSITIVE 247 150 126 83 59 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 246 68 21 102 55 NC_003454:FN0951|3end_Precorrin-3B_C17-methyltransferase_1607747..1607897_NEGATIVE 235 54 14 112 67 NC_003454:FN1544|3end_Probable_electron_transfer_flavoprotein-quinone_oxidoreductase_ydiS_59210..59360_POSITIVE 233 49 7 87 53 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 232 150 119 52 21 NC_003454:FN1428|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2096860..2097010_NEGATIVE 229 65 40 28 3 NC_003454:FN0851|3end_Biotin_synthesis_protein_bioC_1510268..1510418_POSITIVE 223 56 28 117 88 NC_003454:FN0699|3end_Protein_translocase_subunit_secD_1358366..1358516_POSITIVE 223 65 27 122 84 NC_003454:FN0583|3end_hypothetical_protein_1239518..1239668_POSITIVE 217 49 15 110 74 NC_003454:FN0548|3end_Regulatory_protein_recX_1201409..1201559_POSITIVE 217 146 105 72 27 NC_003454:FN0071|3end_GTP_cyclohydrolase_I_711605..711755_POSITIVE 214 57 11 73 28 NC_003454:FN1592|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103162..103312_NEGATIVE 210 66 22 74 25 NC_003454:FN1765|3end_pyruvate_kinase_258023..258173_NEGATIVE 208 56 11 138 84 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 207 43 7 119 77 NC_003454:FN0850|3end_Hypothetical_cytosolic_protein_1509583..1509733_POSITIVE