Origin IGS: aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa .........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 ttagaatatcacttaattaataccaaataattgggactgttatatacttataaatatttttgttttatatgaaataaaaatgttttaaatgtgacagtcttattttttatctaataaaaaatattgacaattaagtaaaaaaatcataatatatgatatgtaatatattacatatcatatatttaaaaataggagggaaagattatgctaatt Mask Tandem Repeat Region ================================================ aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Find is-nt database================================================ Query_seq: FN0877:FN0878|FN0877:FN0878:Sodium/proline symporter:Transcriptional regulator, GntR family:<-<-:1538964..1539176 213 aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0877:FN0878|FN0877:FN0878:Sodium/proline symporter:Transcriptional regulator, GntR family:<-<-:1538964..1539176 213 aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0877:FN0878|FN0877:FN0878:Sodium/proline symporter:Transcriptional regulator, GntR family:<-<-:1538964..1539176 213 aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Predict ORF larger than 30AA ================================================ aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa 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: 86 Start: 62 End: 91 .............................................................ATTGACAATTAAGTAAAAAAATCATAATAT.......................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 83 End: 112 ..................................................................................ATTGTCAATATTTTTTATTAGATAAAAAAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.7 Tail_Score: -5.66868 Start: 28 End: 70 Full_Region: CTTTCCCTCCTATTT TTAAATATATGATATGTAA TATA TTACATATCATATATTATGA TTTTTTTACTTAATT ...........................TTAAATATATGATATGTAATATATTACATATCATATATTATGA............................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.4 Tail_Score: -3.86495 Start: 33 End: 64 Full_Region: CCTCCTATTTTTAAA TATATGATATGTAA TATA TTACATATCATATA TTATGATTTTTTTAC ................................TATATGATATGTAATATATTACATATCATATA..................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.4 Tail_Score: -3.57144 Start: 33 End: 64 Full_Region: gtaaaaaaatcataa tatatgatatgtaa tata ttacatatcatata tttaaaaataggagg ................................tatatgatatgtaatatattacatatcatata..................................................................................................................................................... Find igs database================================================ Query_seq: FN0877:FN0878|FN0877:FN0878:Sodium/proline symporter:Transcriptional regulator, GntR family:<-<-:1538964..1539176 213 aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: NC_003454_FN0877_FN0878|Sodium/proline symporter:Transcriptional regulator, GntR family|NEGATIVE:NEGATIVE|[1538964,1539176]|213 HSP 1 e-value: 1.0E-105 bit: 381.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgannnnnnnacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa aattagcataatctttccctcctatttttaaatatatgatatgtaatatattacatatcatatattatgatttttttacttaattgtcaatattttttattagataaaaaataagactgtcacatttaaaacatttttatttcatataaaacaaaaatatttataagtatataacagtcccaattatttggtattaattaagtgatattctaa HSP 2 e-value: 8.0E-12 bit: 71.9 Len: 36 Query Start:31 Query End:66 Subject Strand: NEGATIVE Subject Start: 31 Subject End: 66 ..............................aatatatgatatgtaatatattacatatcatatatt................................................................................................................................................... ..............................aatatatgatatgtaatatattacatatcatatatt................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAGCAUAAUCUUUCCCUCCUAUUUUUAAAUAUAUGAUAUGUAAUAUAUUACAUAUCAUAUAUUAUGAUUUUUUUACUUAAUUGUCAAUAUUUUUUAUUAGAUAAAAAAUAAGACUGUCACAUUUAAAACAUUUUUAUUUCAUAUAAAACAAAAAUAUUUAUAAGUAUAUAACAGUCCCAAUUAUUUGGUAUUAAUUAAGUGAUAUUCUAA ..((((.(((....................((((((((((((((((....)))))))))))))))).........(((((((((((....((((((((((...)))))))))).((((((...((((((((.((((((.(((......))).)))))).))).))))).....))))))((((....))))...)))))))))))))).)))) (-38.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGAAUAUCACUUAAUUAAUACCAAAUAAUUGGGACUGUUAUAUACUUAUAAAUAUUUUUGUUUUAUAUGAAAUAAAAAUGUUUUAAAUGUGACAGUCUUAUUUUUUAUCUAAUAAAAAAUAUUGACAAUUAAGUAAAAAAAUCAUAAUAUAUGAUAUGUAAUAUAUUACAUAUCAUAUAUUUAAAAAUAGGAGGGAAAGAUUAUGCUAAUU ((((...(((((((((((....((((....))))(((((((((((..(((.(((((((((((((((....))))))))))))))))))))))))))))).((((((((((...)))))))))).....))))))))...........((((((((((((((((....)))))))))))))))).................)))....)))).. (-50.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 670 60 11 151 102 NC_003454:FN0877|5end_Sodium/proline_symporter_1538873..1539103_NEGATIVE 250 37 3 139 106 NC_003454:FN0465|5end_hypothetical_protein_1110046..1110276_POSITIVE 238 40 7 127 89 NC_003454:FN1268|5end_Methionyl-tRNA_synthetase_1925593..1925823_NEGATIVE 236 29 2 114 84 NC_003454:FN1638|5end_50S_ribosomal_protein_L16_137501..137731_NEGATIVE 220 23 6 106 88 NC_003454:FN0362|5end_ATP_synthase_B_chain,_sodium_ion_specific_993393..993623_NEGATIVE 213 44 7 124 89 NC_003454:FN0495|5end_Acetyl-CoA_acetyltransferase_1139567..1139797_POSITIVE 211 58 12 140 94 NC_003454:FN1597|5end_peptidyl-tRNA_hydrolase_107810..108040_NEGATIVE 205 36 5 119 87 NC_003454:FN1465|5end_Permease_2147986..2148216_POSITIVE 200 29 3 114 85 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 198 49 12 169 113 NC_003454:FN1032|5end_hypothetical_protein_1686348..1686578_NEGATIVE 198 206 163 229 185 NC_003454:FN0041|5end_hypothetical_protein_680807..681037_NEGATIVE 198 50 3 133 81 NC_003454:FN2053|5end_Serine/threonine_sodium_symporter_562415..562645_NEGATIVE 197 42 2 111 71 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 194 22 3 89 66 NC_003454:FN1134|5end_Hypothetical_cytosolic_protein_1781495..1781725_POSITIVE 194 50 11 169 125 NC_003454:FN0350|5end_hypothetical_protein_982372..982602_POSITIVE 193 26 7 107 89 NC_003454:FN0298|5end_Histidyl-tRNA_synthetase_931133..931363_POSITIVE 191 46 1 129 82 NC_003454:FN0357|5end_ATP_synthase_epsilon_chain,_sodium_ion_specific_988276..988506_NEGATIVE 189 26 4 101 76 NC_003454:FN1621|5end_elongation_factor_Ts_128673..128903_POSITIVE 188 55 12 142 93 NC_003454:FN0186|5end_Cytochrome_c-type_biogenesis_protein_ccdA_810853..811083_POSITIVE 186 209 166 165 124 NC_003454:FN0231|5end_hypothetical_protein_857351..857581_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 37 3 100 67 NC_003454:FN0464|3end_hypothetical_protein_1110087..1110237_POSITIVE 239 105 61 65 16 NC_003454:FN0106|3end_hypothetical_protein_741462..741612_POSITIVE 238 40 7 107 69 NC_003454:FN1269|3end_Hypothetical_lipoprotein_1925613..1925763_NEGATIVE 237 40 3 40 3 NC_003454:FN0803|3end_trifunctional_thioredoxin/methionine_sulfoxide_reductase_A/B_protein_1462450..1462600_NEGATIVE 236 29 2 111 81 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 220 23 6 65 47 NC_003454:FN0363|3end_ATP_synthase_C_chain,_sodium_ion_specific_993434..993584_NEGATIVE 213 44 7 65 30 NC_003454:FN0494|3end_Short_chain_dehydrogenase_1139588..1139738_POSITIVE 200 29 3 112 83 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 196 203 163 86 46 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 194 50 11 53 9 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE 193 26 7 95 77 NC_003454:FN0297|3end_ATPase_associated_with_chromosome_architecture/replication_931201..931351_POSITIVE 191 46 1 119 72 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 189 26 4 67 42 NC_003454:FN1620|3end_30S_ribosomal_protein_S2_128719..128869_POSITIVE 188 196 156 90 53 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 184 29 2 87 58 NC_003454:FN0610|3end_hypothetical_protein_1268362..1268512_POSITIVE 183 57 11 124 78 NC_003454:FN0292|3end_Hemolysin_activator_protein_precursor_925011..925161_NEGATIVE 180 120 73 143 95 NC_003454:FN1191|3end_hypothetical_protein_1854729..1854879_POSITIVE 179 60 11 130 74 NC_003454:FN0021|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_660854..661004_POSITIVE 177 57 14 85 41 NC_003454:FN0239|3end_hypothetical_protein_863923..864073_POSITIVE 176 37 11 81 59 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE