Origin IGS: ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaattgttaaatttttgttaaataagaatctaatagaggctgttgcatttttcaaatatttgcaacagcctattttaagattttaaagagagggtcataatgaaagattttttaaaaaaatttgaa Mask Tandem Repeat Region ================================================ ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Find is-nt database================================================ Query_seq: FN1257:FN1258|FN1257:FN1258:C4-dicarboxylate transporter small subunit:C4-dicarboxylate-binding protein:<-<-:1913755..1913881 127 ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1257:FN1258|FN1257:FN1258:C4-dicarboxylate transporter small subunit:C4-dicarboxylate-binding protein:<-<-:1913755..1913881 127 ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1257:FN1258|FN1257:FN1258:C4-dicarboxylate transporter small subunit:C4-dicarboxylate-binding protein:<-<-:1913755..1913881 127 ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Predict ORF larger than 30AA ================================================ ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa 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: 85 Start: 71 End: 100 ......................................................................TTTGAAAAATGCAACAGCCTCTATTAGATT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -7.7 Tail_Score: -3.73411 Start: 57 End: 89 Full_Region: taagaatctaataga ggctgttgcattttt caa atatttgcaacagcc tattttaagatttta ........................................................ggctgttgcatttttcaaatatttgcaacagcc...................................... Find igs database================================================ Query_seq: FN1257:FN1258|FN1257:FN1258:C4-dicarboxylate transporter small subunit:C4-dicarboxylate-binding protein:<-<-:1913755..1913881 127 ttcaaatttttttaaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Intra-Species Hit: Count: 1 Min: 14 Max: 127 Len: 114 Subject: NC_003454_FN1257_FN1258|C4-dicarboxylate transporter small subunit:C4-dicarboxylate-binding protein|NEGATIVE:NEGATIVE|[1913755,1913881]|127 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:14 Query End:127 Subject Strand: POSITIVE Subject Start: 14 Subject End: 127 .............aaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa .............aaaaaatctttcattatgaccctctctttaaaatcttaaaataggctgttgcaaatatttgaaaaatgcaacagcctctattagattcttatttaacaaaaatttaacaattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUCUUUCAUUAUGACCCUCUCUUUAAAAUCUUAAAAUAGGCUGUUGCAAAUAUUUGAAAAAUGCAACAGCCUCUAUUAGAUUCUUAUUUAACAAAAAUUUAACAAUUAA ...............................(((((......(((((((((((.............))))))))))).....)))))........................... (-19.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUGUUAAAUUUUUGUUAAAUAAGAAUCUAAUAGAGGCUGUUGCAUUUUUCAAAUAUUUGCAACAGCCUAUUUUAAGAUUUUAAAGAGAGGGUCAUAAUGAAAGAUUUUUU ........................((((((((.....(((((((((((.............))))))))))).......((((((......))))))........)))))))). (-26.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 797 90 41 194 145 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 354 87 44 178 131 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 346 77 36 141 109 NC_003454:FN1160|5end_SWF/SNF_family_helicase_1815836..1816066_POSITIVE 293 77 43 141 115 NC_003454:FN1660|5end_ATP-dependent_DNA_helicase_recG_157908..158138_NEGATIVE 289 89 43 162 121 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 260 78 34 89 54 NC_003454:FN2106|5end_Transporter_616458..616688_POSITIVE 256 97 55 123 71 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 253 103 62 153 123 NC_003454:FN1944|5end_Sodium-dependent_tryptophan_transporter_446567..446797_POSITIVE 251 79 37 172 113 NC_003454:FN1806|5end_Integral_membrane_protein_287724..287954_POSITIVE 245 78 35 44 2 NC_003454:FN0531|5end_hypothetical_protein_1186389..1186619_POSITIVE 243 109 67 196 150 NC_003454:FN1935|5end_Adenine-specific_methyltransferase_437061..437291_NEGATIVE 241 79 34 136 93 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 229 90 41 146 96 NC_003454:FN0133|5end_hypothetical_protein_769121..769351_POSITIVE 226 79 34 70 16 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 223 52 17 149 99 NC_003454:FN0880|5end_ABC_transporter_ATP-binding_protein_1541978..1542208_NEGATIVE 222 45 3 146 99 NC_003454:FN0821|5end_hypothetical_protein_1480859..1481089_POSITIVE 220 80 38 199 161 NC_003454:FN0374|5end_Single-stranded-DNA-specific_exonuclease_recJ_1002654..1002884_POSITIVE 217 69 22 146 95 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 215 57 11 87 39 NC_003454:FN1295|5end_Acetyltransferase_1953565..1953795_NEGATIVE 212 70 21 148 96 NC_003454:FN0595|5end_UDP-N-acetylglucosamine_acyltransferase_1249228..1249458_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 89 44 100 40 NC_003454:FN1907|3end_Thymidylate_synthase_400546..400696_POSITIVE 354 87 44 70 23 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 352 79 33 65 6 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 346 77 36 76 44 NC_003454:FN1159|3end_fructose_1,6-bisphosphatase_II_1815851..1816001_POSITIVE 343 90 44 91 52 NC_003454:FN0405|3end_tryptophanyl-tRNA_synthetase_1042465..1042615_NEGATIVE 317 90 42 89 47 NC_003454:FN0515|3end_Acriflavin_resistance_protein_D_1163938..1164088_NEGATIVE 306 79 43 91 55 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE 296 79 43 63 16 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE 295 79 38 83 35 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 293 81 43 88 53 NC_003454:FN1080|3end_Export_ABC_transporter_1727308..1727458_POSITIVE 293 77 43 86 60 NC_003454:FN1661|3end_Hypothetical_cytosolic_protein_157963..158113_NEGATIVE 289 89 43 85 44 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 287 79 43 67 20 NC_003454:FN0528|3end_Cold_shock_protein_1184746..1184896_POSITIVE 282 75 37 80 46 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE 277 75 43 81 53 NC_003454:FN1276|3end_hypothetical_protein_1935280..1935430_POSITIVE 275 79 36 83 40 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE 273 90 43 100 39 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 264 94 52 96 52 NC_003454:FN0026|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664832..664982_POSITIVE 259 79 44 84 55 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 256 80 38 58 12 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE