Origin IGS: taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaatcctcctttaatattttaaaatttatatagtttttaaactaataattaaattgtaatcattacaaatacataatactatatctgagttatcttgtcaagtattatttttaaaaattttta Mask Tandem Repeat Region ================================================ taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Find is-nt database================================================ Query_seq: FN1982:FN1983|FN1982:FN1983:hypothetical protein:Alkyl hydroperoxide reductase C22 protein:->->:484633..484758 126 taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1982:FN1983|FN1982:FN1983:hypothetical protein:Alkyl hydroperoxide reductase C22 protein:->->:484633..484758 126 taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1982:FN1983|FN1982:FN1983:hypothetical protein:Alkyl hydroperoxide reductase C22 protein:->->:484633..484758 126 taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Predict ORF larger than 30AA ================================================ taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt 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: 88 Start: 22 End: 51 .....................CTTGACAAGATAACTCAGATATAGTATTAT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 36 HP_score: -2.9 Tail_Score: -2.7395 Start: 59 End: 81 Full_Region: AGTATTATGTATTTG TAATGATTA CAATT TAATTATTA GTTTAAAAACTATAT ..........................................................TAATGATTACAATTTAATTATTA............................................. Find igs database================================================ Query_seq: FN1982:FN1983|FN1982:FN1983:hypothetical protein:Alkyl hydroperoxide reductase C22 protein:->->:484633..484758 126 taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_003454_FN1982_FN1983|hypothetical protein:Alkyl hydroperoxide reductase C22 protein|POSITIVE:POSITIVE|[484633,484758]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt taaaaatttttaaaaataatacttgacaagataactcagatatagtattatgtatttgtaatgattacaatttaattattagtttaaaaactatataaattttaaaatattaaaggaggatttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUUUUUAAAAAUAAUACUUGACAAGAUAACUCAGAUAUAGUAUUAUGUAUUUGUAAUGAUUACAAUUUAAUUAUUAGUUUAAAAACUAUAUAAAUUUUAAAAUAUUAAAGGAGGAUUUAUU ......((((((((.((((((((......((....))......)))))))).......(((((((((.....))))))))).))))))))....(((((((((.............))))))))). (-12.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAUCCUCCUUUAAUAUUUUAAAAUUUAUAUAGUUUUUAAACUAAUAAUUAAAUUGUAAUCAUUACAAAUACAUAAUACUAUAUCUGAGUUAUCUUGUCAAGUAUUAUUUUUAAAAAUUUUUA .((((((.....(((((....)))))))))))..((((((((((............(((((.....)))))....((((((((..((..((....))..))..)))))))).)))))))))).... (-11.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 59 19 48 3 NC_003454:FN0802|5end_Amino_acid_transport_system_permease_protein_1462136..1462366_NEGATIVE 203 66 29 224 179 NC_003454:FN2014|5end_ATP-dependent_protease_La_516974..517204_NEGATIVE 187 50 20 231 199 NC_003454:FN0246|5end_hypothetical_protein_870797..871027_NEGATIVE 184 60 11 219 171 NC_003454:FN2065|5end_Transcriptional_repressor_575850..576080_POSITIVE 183 88 43 147 102 NC_003454:FN0614|5end_Export_ABC_transporter_1271447..1271677_POSITIVE 167 119 87 198 173 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 163 70 22 80 27 NC_003454:FN0514|5end_hypothetical_protein_1163431..1163661_POSITIVE 155 65 23 206 168 NC_003454:FN0048|5end_4-nitrophenylphosphatase_686043..686273_NEGATIVE 152 60 19 83 35 NC_003454:FN1064|5end_hypothetical_protein_1710528..1710758_POSITIVE 144 50 23 120 94 NC_003454:FN0558|5end_TraT_complement_resistance_protein_precursor_1210682..1210912_POSITIVE 144 67 26 102 74 NC_003454:FN0247|5end_Hypothetical_cytosolic_protein_870707..870937_POSITIVE 143 64 22 227 186 NC_003454:FN1313|5end_Oligopeptide-binding_protein_oppA_1967053..1967283_POSITIVE 143 47 16 167 134 NC_003454:FN1987|5end_Transcriptional_regulator,_GntR_family_490668..490898_NEGATIVE 142 104 62 100 58 NC_003454:FN1398|5end_Amino_acid_carrier_protein_alsT_2052808..2053038_POSITIVE 142 66 26 50 11 NC_003454:FN1167|5end_beta-methylgalactoside_transporter_inner_membrane_component_1825538..1825768_POSITIVE 141 100 51 176 132 NC_003454:FN0224|5end_excinuclease_ABC_subunit_B_849602..849832_POSITIVE 139 83 51 199 170 NC_003454:FN0248|5end_hypothetical_protein_871562..871792_POSITIVE 136 58 39 149 131 NC_003454:FN0669|5end_High-affinity_zinc_uptake_system_ATP-binding_protein_znuC_1324931..1325161_POSITIVE 136 85 57 102 73 NC_003454:FN0244|5end_COP_associated_protein_868115..868345_POSITIVE 135 88 46 92 49 NC_003454:FN0918|5end_hypothetical_protein_1574237..1574467_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 152 60 19 64 16 NC_003454:FN1063|3end_N-acyl-L-amino_acid_amidohydrolase_1710589..1710739_POSITIVE 152 57 29 151 127 NC_003454:FN2076|3end_MunI_regulatory_protein_587536..587686_NEGATIVE 147 59 21 119 75 NC_003454:FN0451|3end_hypothetical_protein_1095427..1095577_POSITIVE 146 69 33 151 113 NC_003454:FN1823|3end_Transcriptional_regulator,_TetR_family_312270..312420_POSITIVE 141 100 51 150 106 NC_003454:FN0223|3end_COME_operon_protein_3_849656..849806_POSITIVE 139 83 51 135 106 NC_003454:FN0247|3end_Hypothetical_cytosolic_protein_871578..871728_POSITIVE 138 58 41 71 54 NC_003454:FN0803|3end_trifunctional_thioredoxin/methionine_sulfoxide_reductase_A/B_protein_1462450..1462600_NEGATIVE 136 58 39 125 107 NC_003454:FN0668|3end_High-affinity_zinc_uptake_system_protein_znuA_precursor_1324987..1325137_POSITIVE 135 56 28 64 36 NC_003454:FN1447|3end_Transposase_2117342..2117492_POSITIVE 131 104 71 42 7 NC_003454:FN1397|3end_glutaminase_2052830..2052980_POSITIVE 130 120 78 54 4 NC_003454:FN1880|3end_Dihydropteridine_reductase_368211..368361_POSITIVE 128 56 27 150 123 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 126 48 25 66 42 NC_003454:FN1839|3end_glycerol_kinase_329845..329995_POSITIVE 126 67 21 69 17 NC_003454:FN1586|3end_O-succinylbenzoate-CoA_synthase_97415..97565_NEGATIVE 124 104 61 62 23 NC_003454:FN1184|3end_hypothetical_protein_1846208..1846358_NEGATIVE 124 74 34 66 22 NC_003454:FN1067|3end_Tetratricopeptide_repeat_family_protein_1713879..1714029_POSITIVE 123 68 21 131 89 NC_003454:FN0238|3end_hypothetical_protein_862382..862532_NEGATIVE 122 65 42 63 38 NC_003454:FN0380|3end_hypothetical_protein_1012361..1012511_POSITIVE 121 53 11 53 12 NC_003454:FN1445|3end_DNA_helicase_2115953..2116103_POSITIVE 118 90 44 104 44 NC_003454:FN1308|3end_Phosphatidate_cytidylyltransferase_1964861..1965011_POSITIVE