Origin IGS: cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataatttaaagaaaacactagaaatgtatttataaatctagtgtttttattttctatatcttattttaataatatattgacatatcaatatattagatatataatagcaaaaatatataaaattgaattgtaagaaaaaactttaattgtaaaggaggaaataggtatgaag Mask Tandem Repeat Region ================================================ cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Find is-nt database================================================ Query_seq: FN1590:FN1591|FN1590:FN1591:Hypothetical lipoprotein:RNFB-related protein:<-<-:101895..102067 173 cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1590:FN1591|FN1590:FN1591:Hypothetical lipoprotein:RNFB-related protein:<-<-:101895..102067 173 cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1590:FN1591|FN1590:FN1591:Hypothetical lipoprotein:RNFB-related protein:<-<-:101895..102067 173 cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 43 End: 141 .......................................... L E I K Y I K A I I Y R I Y Q Y T L I N N F Y S I S F L F V L N M ................................ cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt 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: 92 Start: 68 End: 97 ...................................................................ATTGACATATCAATATATTAGATATATAAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1590:FN1591|FN1590:FN1591:Hypothetical lipoprotein:RNFB-related protein:<-<-:101895..102067 173 cttcatacctatttcctcctttacaattaaagttttttcttacaattcaattttatatatttttgctattatatatctaatatattgatatgtcaatatattattaaaataagatatagaaaataaaaacactagatttataaatacatttctagtgttttctttaaattatt Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_003454_FN1590_FN1591|Hypothetical lipoprotein:RNFB-related protein|NEGATIVE:NEGATIVE|[101895,102067]|173 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 44 Query Start:130 Query End:173 Subject Strand: POSITIVE Subject Start: 130 Subject End: 173 .................................................................................................................................cactagatttataaatacatttctagtgttttctttaaattatt .................................................................................................................................cactagatttataaatacatttctagtgttttctttaaattatt HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 cttcatacctatttcctcctttacaattaaag............................................................................................................................................. cttcatacctatttcctcctttacaattaaag............................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCAUACCUAUUUCCUCCUUUACAAUUAAAGUUUUUUCUUACAAUUCAAUUUUAUAUAUUUUUGCUAUUAUAUAUCUAAUAUAUUGAUAUGUCAAUAUAUUAUUAAAAUAAGAUAUAGAAAAUAAAAACACUAGAUUUAUAAAUACAUUUCUAGUGUUUUCUUUAAAUUAUU ..........................((((((..((((((......((.....((((((..........))))))..(((((((((((....))))))))))).........))...))))))..(((((((((((..............)))))))))))))))))...... (-26.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUUAAAGAAAACACUAGAAAUGUAUUUAUAAAUCUAGUGUUUUUAUUUUCUAUAUCUUAUUUUAAUAAUAUAUUGACAUAUCAAUAUAUUAGAUAUAUAAUAGCAAAAAUAUAUAAAAUUGAAUUGUAAGAAAAAACUUUAAUUGUAAAGGAGGAAAUAGGUAUGAAG ............(((((((((((..(((....)))..)))))))))))((((((((...((((((((((((((((((((((....)))))))))))..((((((..........))))))...)))))..)))))).....(((((....))))).))))))))......... (-31.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 702 50 1 141 92 NC_003454:FN1590|5end_Hypothetical_lipoprotein_101804..102034_NEGATIVE 256 115 71 222 184 NC_003454:FN0121|5end_hypothetical_protein_753300..753530_NEGATIVE 227 34 1 61 32 NC_003454:FN1111|5end_Dipeptide-binding_protein_1756181..1756411_NEGATIVE 221 100 51 196 149 NC_003454:FN1251|5end_High-affinity_iron_permease_1908008..1908238_POSITIVE 219 58 11 152 96 NC_003454:FN1464|5end_1-deoxy-D-xylulose-5-phosphate_synthase_2147705..2147935_NEGATIVE 215 30 9 131 109 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 213 36 1 56 13 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 213 120 79 168 123 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 207 110 67 187 137 NC_003454:FN1411|5end_Threonine_dehydratase_2070730..2070960_POSITIVE 207 70 25 227 183 NC_003454:FN2007|5end_Glutathione_peroxidase_507476..507706_NEGATIVE 207 161 132 44 16 NC_003454:FN1794|5end_Phosphocarrier_protein_HPr_275591..275821_NEGATIVE 206 29 1 72 40 NC_003454:FN1723|5end_glucose-inhibited_division_protein_A_222645..222875_NEGATIVE 202 25 2 104 81 NC_003454:FN1421|5end_Pyruvate-flavodoxin_oxidoreductase_2083305..2083535_POSITIVE 200 48 8 94 54 NC_003454:FN0163|5end_5-methyltetrahydrofolate--homocysteine_methyltransferase_791318..791548_POSITIVE 199 100 51 150 96 NC_003454:FN0668|5end_High-affinity_zinc_uptake_system_protein_znuA_precursor_1323969..1324199_POSITIVE 198 25 1 111 86 NC_003454:FN0257|5end_Transporter_882516..882746_POSITIVE 198 47 8 128 87 NC_003454:FN1536|5end_(S)-2-hydroxy-acid_oxidase_chain_D_49718..49948_NEGATIVE 197 40 2 148 108 NC_003454:FN0579|5end_Hypothetical_cytosolic_protein_1229803..1230033_POSITIVE 197 36 2 197 161 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 196 75 33 214 167 NC_003454:FN0857|5end_Glycogen_phosphorylase_1518922..1519152_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 34 1 77 48 NC_003454:FN1112|3end_Dipeptide_transport_system_permease_protein_dppC_1756165..1756315_NEGATIVE 211 48 10 116 75 NC_003454:FN0561|3end_Proline_synthetase_associated_protein_1214906..1215056_POSITIVE 207 70 25 106 62 NC_003454:FN2008|3end_Glycine_betaine_transport_ATP-binding_protein_507597..507747_NEGATIVE 206 29 1 63 31 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 202 25 2 35 12 NC_003454:FN1420|3end_NA+/H+_antiporter_NHAC_2083316..2083466_POSITIVE 197 40 2 130 90 NC_003454:FN0578|3end_ATP-dependent_DNA_helicase_recQ_1229865..1230015_POSITIVE 196 75 33 149 102 NC_003454:FN0858|3end_4-alpha-glucanotransferase_1518987..1519137_NEGATIVE 196 73 33 109 77 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE 196 46 1 117 70 NC_003454:FN0151|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_780092..780242_POSITIVE 193 53 11 92 49 NC_003454:FN0318|3end_CITX_protein_955285..955435_NEGATIVE 191 47 2 108 59 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 191 79 31 121 68 NC_003454:FN0238|3end_hypothetical_protein_862382..862532_NEGATIVE 190 40 2 112 65 NC_003454:FN1474|3end_N-acetylmannosamine_kinase_2157843..2157993_POSITIVE 188 49 1 122 89 NC_003454:FN0969|3end_hypothetical_protein_1621806..1621956_NEGATIVE 186 40 2 106 75 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 185 50 13 114 85 NC_003454:FN1349|3end_ABC_transporter_permease_protein_2001150..2001300_NEGATIVE 180 49 2 112 67 NC_003454:FN1012|3end_HPr_kinase/phosphorylase_1665680..1665830_NEGATIVE 180 50 2 73 29 NC_003454:FN2098|3end_MRP-family_nucleotide-binding_protein_607373..607523_NEGATIVE 177 38 1 104 58 NC_003454:FN0916|3end_hypothetical_protein_1572065..1572215_NEGATIVE 177 81 45 142 105 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE