Origin IGS: accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta .........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 taaatttgtaattaatatagacaaatttttataaaaatgatatatttagtacaacataatacaaaatctatctacaaaattataaggtttaaaaagttatgaaacaagtttttaatttattataacggatacaatgtgaataataaaatttttttaatttctcattgtattaacaaggtaaaaaaattatattatggaggttttggt Mask Tandem Repeat Region ================================================ accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Find is-nt database================================================ Query_seq: FN1860:FN1861|FN1860:FN1861:NA+/H+ antiporter NHAC:L-lysine permease:<-<-:351568..351774 207 accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1860:FN1861|FN1860:FN1861:NA+/H+ antiporter NHAC:L-lysine permease:<-<-:351568..351774 207 accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1860:FN1861|FN1860:FN1861:NA+/H+ antiporter NHAC:L-lysine permease:<-<-:351568..351774 207 accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 G F G G Y Y L K K V K N I C H S I L F I K N N V N Y G N Y Y M .................................................................................................................. accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta 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: 87 Start: 60 End: 89 ...........................................................TTTTATTATTCACATTGTATCCGTTATAAT...................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 100 End: 129 ...................................................................................................CTTGTTTCATAACTTTTTAAACCTTATAAT.............................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 162 End: 191 .................................................................................................................................................................ATAGACAAATTTTTATAAAAATGATATATT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1860:FN1861|FN1860:FN1861:NA+/H+ antiporter NHAC:L-lysine permease:<-<-:351568..351774 207 accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: NC_003454_FN1860_FN1861|NA+/H+ antiporter NHAC:L-lysine permease|NEGATIVE:NEGATIVE|[351568,351774]|207 HSP 1 e-value: 8.0E-89 bit: 327.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 accaaaacctccataatataannnnnnnaccttgttaatacaatgagaaattnnnnnnnttttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta accaaaacctccataatataatttttttaccttgttaatacaatgagaaattaaaaaaattttattattcacattgtatccgttataataaattaaaaacttgtttcataactttttaaaccttataattttgtagatagattttgtattatgttgtactaaatatatcatttttataaaaatttgtctatattaattacaaattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAAAACCUCCAUAAUAUAAUUUUUUUACCUUGUUAAUACAAUGAGAAAUUAAAAAAAUUUUAUUAUUCACAUUGUAUCCGUUAUAAUAAAUUAAAAACUUGUUUCAUAACUUUUUAAACCUUAUAAUUUUGUAGAUAGAUUUUGUAUUAUGUUGUACUAAAUAUAUCAUUUUUAUAAAAAUUUGUCUAUAUUAAUUACAAAUUUA ............((((((.((((((((((.((..((.....))..))....)))))))))).)))))).....(((((...(((((((....(((((((.((((...)))).)))))))...)))))))..(((((((((((((((((..(((.((((.....)))).)))...))).)))))))))))))).....)))))..... (-30.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUUGUAAUUAAUAUAGACAAAUUUUUAUAAAAAUGAUAUAUUUAGUACAACAUAAUACAAAAUCUAUCUACAAAAUUAUAAGGUUUAAAAAGUUAUGAAACAAGUUUUUAAUUUAUUAUAACGGAUACAAUGUGAAUAAUAAAAUUUUUUUAAUUUCUCAUUGUAUUAACAAGGUAAAAAAAUUAUAUUAUGGAGGUUUUGGU .....(((((...((((((.....(((((....)))))..))))))...))))).......((((((((.....((....(((((..(((.....(((((((...((((.....)))).))))))).(((((((((.(((...((((.....))))..))).)))))))))..........)))..)))))...)).)))))))).. (-30.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 50 1 141 92 NC_003454:FN1860|5end_NA+/H+_antiporter_NHAC_351477..351707_NEGATIVE 226 138 98 103 65 NC_003454:FN0038|5end_hypothetical_protein_678499..678729_NEGATIVE 224 130 81 77 25 NC_003454:FN1724|5end_Potassium_uptake_protein_KtrA_223310..223540_NEGATIVE 202 136 98 124 77 NC_003454:FN1878|5end_hypothetical_protein_366707..366937_POSITIVE 198 139 101 122 83 NC_003454:FN1199|5end_DNA_polymerase_IV_1859061..1859291_POSITIVE 190 60 25 230 189 NC_003454:FN0517|5end_Outer_membrane_protein_tolC_1169435..1169665_NEGATIVE 185 46 7 135 97 NC_003454:FN1943|5end_Tryptophanase_444851..445081_POSITIVE 183 169 128 88 46 NC_003454:FN0817|5end_ABC_transporter_ATP-binding_protein_1476448..1476678_POSITIVE 183 200 152 132 77 NC_003454:FN1938|5end_hypothetical_protein_438416..438646_NEGATIVE 180 177 131 97 42 NC_003454:FN0416|5end_Type_III_restriction-modification_system_methylation_subunit_1054300..1054530_POSITIVE 178 46 1 231 176 NC_003454:FN0295|5end_Transketolase_927986..928216_POSITIVE 176 107 67 144 106 NC_003454:FN0595|5end_UDP-N-acetylglucosamine_acyltransferase_1249228..1249458_POSITIVE 175 145 104 124 86 NC_003454:FN0879|5end_ABC_transporter_integral_membrane_protein_1540946..1541176_NEGATIVE 174 108 63 149 112 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 174 42 2 173 138 NC_003454:FN1709|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_205415..205645_POSITIVE 171 42 5 129 96 NC_003454:FN1301|5end_ABC_transporter_ATP-binding_protein_1957669..1957899_POSITIVE 171 167 122 152 101 NC_003454:FN0667|5end_Na+_driven_multidrug_efflux_pump_1323624..1323854_NEGATIVE 170 58 11 197 155 NC_003454:FN0321|5end_heat_shock_protein_90_957634..957864_POSITIVE 168 190 142 104 53 NC_003454:FN0724|5end_flavodoxin_1384167..1384397_NEGATIVE 168 30 3 122 99 NC_003454:FN0575|5end_hypothetical_protein_1225331..1225561_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 130 81 62 10 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 186 110 62 111 70 NC_003454:FN1114|3end_hypothetical_protein_1758686..1758836_POSITIVE 176 107 67 126 88 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE 175 145 104 108 70 NC_003454:FN0880|3end_ABC_transporter_ATP-binding_protein_1540962..1541112_NEGATIVE 171 42 5 39 6 NC_003454:FN1300|3end_Integral_membrane_protein_1957659..1957809_POSITIVE 170 58 11 45 3 NC_003454:FN0320|3end_Hypothetical_cytosolic_protein_957562..957712_POSITIVE 168 35 4 106 74 NC_003454:FN1125|3end_LemA_protein_1769260..1769410_NEGATIVE 168 190 142 90 39 NC_003454:FN0725|3end_Molybdopterin_biosynthesis_MoeB_protein_1384181..1384331_NEGATIVE 168 157 111 62 15 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 163 189 154 64 27 NC_003454:FN1134|3end_Hypothetical_cytosolic_protein_1782042..1782192_POSITIVE 163 36 7 108 82 NC_003454:FN0329|3end_50S_ribosomal_protein_L13_964647..964797_POSITIVE 159 175 131 64 19 NC_003454:FN0031|3end_hypothetical_protein_667899..668049_NEGATIVE 158 175 141 91 58 NC_003454:FN1401|3end_urocanate_hydratase_2060426..2060576_POSITIVE 157 40 1 53 14 NC_003454:FN1618|3end_hypothetical_protein_126666..126816_NEGATIVE 157 118 79 148 103 NC_003454:FN1611|3end_Competence_protein_120597..120747_NEGATIVE 155 43 1 111 76 NC_003454:FN0643|3end_hypothetical_protein_1299434..1299584_NEGATIVE 154 23 5 112 93 NC_003454:FN1561|3end_Hypothetical_cytosolic_protein_83032..83182_NEGATIVE 153 200 151 42 6 NC_003454:FN1695|3end_Probable_quinovosaminephosphotransferae_190169..190319_NEGATIVE 152 60 29 38 1 NC_003454:FN0518|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1169627..1169777_NEGATIVE 151 50 8 49 15 NC_003454:FN0466|3end_Lysyl-tRNA_synthetase_1112862..1113012_POSITIVE