Origin IGS: ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttactcattttatattcataaattcaagttttagaattgactatatacttaattcctgttataataaaagcaaagtaatcaatctattgactaaaaataataggaggtcaaaa Mask Tandem Repeat Region ================================================ ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Find is-nt database================================================ Query_seq: TDE2120:TDE2121|TDE2120:TDE2121:glycine reductase complex proprotein GrdE2:hypothetical protein:<-<-:2154085..2154201 117 ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2120:TDE2121|TDE2120:TDE2121:glycine reductase complex proprotein GrdE2:hypothetical protein:<-<-:2154085..2154201 117 ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2120:TDE2121|TDE2120:TDE2121:glycine reductase complex proprotein GrdE2:hypothetical protein:<-<-:2154085..2154201 117 ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 K S R R N N K T L L N I V K S K N Y C S N L I Y D I R F S S N I F M ............... ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt 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: 95 Start: 49 End: 78 ................................................ATTGACTATATACTTAATTCCTGTTATAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2120:TDE2121|TDE2120:TDE2121:glycine reductase complex proprotein GrdE2:hypothetical protein:<-<-:2154085..2154201 117 ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_002967_TDE2120_TDE2121|glycine reductase complex proprotein GrdE2:hypothetical protein|NEGATIVE:NEGATIVE|[2154085,2154201]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt ttttgacctcctattatttttagtcaatagattgattactttgcttttattataacaggaattaagtatatagtcaattctaaaacttgaatttatgaatataaaatgagtaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGACCUCCUAUUAUUUUUAGUCAAUAGAUUGAUUACUUUGCUUUUAUUAUAACAGGAAUUAAGUAUAUAGUCAAUUCUAAAACUUGAAUUUAUGAAUAUAAAAUGAGUAAAAUU .......(((...((((.((((.(((((((((((((((...(((((..(((........))).)))))..))))))).))))....)))).....)))).))))...)))....... (-14.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUACUCAUUUUAUAUUCAUAAAUUCAAGUUUUAGAAUUGACUAUAUACUUAAUUCCUGUUAUAAUAAAAGCAAAGUAAUCAAUCUAUUGACUAAAAAUAAUAGGAGGUCAAAA ..............(((((.....(((((........)))))....))))).....((((((((((........(((((........)).))).......))))))))))....... (-13.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 696 50 1 141 92 NC_002967:TDE2120|5end_glycine_reductase_complex_proprotein_GrdE2_2153994..2154224_NEGATIVE 208 61 22 172 122 NC_002967:TDE2784|5end_hypothetical_protein_2836838..2837068_POSITIVE 208 44 3 129 93 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 199 44 7 148 112 NC_002967:TDE1327|5end_hypothetical_protein_1362949..1363179_NEGATIVE 194 39 1 129 92 NC_002967:TDE0842|5end_cytoplasmic_filament_protein_A_861715..861945_POSITIVE 191 32 2 131 91 NC_002967:TDE1956|5end_hypothetical_protein_1971114..1971344_POSITIVE 190 90 43 107 66 NC_002967:TDE1699|5end_hypothetical_protein_1757920..1758150_NEGATIVE 189 31 7 177 155 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 189 48 6 49 15 NC_002967:TDE1266|5end_phosphoribosylaminoimidazole_synthetase_1301588..1301818_NEGATIVE 185 61 21 174 131 NC_002967:TDE0196|5end_hypothetical_protein_232571..232801_POSITIVE 183 91 52 111 72 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 183 48 7 71 30 NC_002967:TDE0490|5end_hypothetical_protein_546793..547023_NEGATIVE 180 44 3 57 12 NC_002967:TDE2166|5end_hydrogenase_nickel_insertion_protein_HypA_2198084..2198314_NEGATIVE 179 50 8 72 40 NC_002967:TDE1751|5end_ribosomal_protein_L21_1804142..1804372_NEGATIVE 178 42 1 149 102 NC_002967:TDE1700|5end_hypothetical_protein_1758040..1758270_POSITIVE 176 67 31 111 68 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 175 46 3 148 93 NC_002967:TDE1361|5end_hypothetical_protein_1400688..1400918_POSITIVE 174 59 13 202 144 NC_002967:TDE2775|5end_lipoprotein,_putative_2826196..2826426_POSITIVE 174 57 17 204 154 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 173 50 1 159 93 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 199 44 7 135 99 NC_002967:TDE1328|3end_hypothetical_protein_1362962..1363112_NEGATIVE 189 31 7 25 3 NC_002967:TDE2668|3end_serine_hydroxymethyltransferase_2704546..2704696_NEGATIVE 178 48 7 128 82 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 175 46 3 61 6 NC_002967:TDE1360|3end_xanthine/uracil_permease_family_protein_1400681..1400831_POSITIVE 169 70 40 112 81 NC_002967:TDE2767|3end_flagellar_protein-related_protein_2820896..2821046_NEGATIVE 169 100 55 86 45 NC_002967:TDE1531|3end_hypothetical_protein_1576609..1576759_POSITIVE 169 44 4 31 1 NC_002967:TDE0465|3end_PIN_domain_protein_518268..518418_NEGATIVE 168 90 41 77 29 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE 167 74 32 136 87 NC_002967:TDE0803|3end_hypothetical_protein_826875..827025_POSITIVE 164 70 29 124 77 NC_002967:TDE1007|3end_flagellar_basal-body_rod_protein_FlgG_1032135..1032285_POSITIVE 163 47 3 129 82 NC_002967:TDE2550|3end_hypothetical_protein_2575520..2575670_NEGATIVE 162 48 19 103 78 NC_002967:TDE1110|3end_lipoprotein,_putative_1145671..1145821_POSITIVE 161 64 34 60 26 NC_002967:TDE1467|3end_HD_domain_protein_1515491..1515641_NEGATIVE 161 60 27 55 21 NC_002967:TDE0500|3end_hypothetical_protein_553564..553714_NEGATIVE 160 50 5 140 95 NC_002967:TDE2271|3end_HAM1_protein_2308481..2308631_NEGATIVE 160 97 65 147 112 NC_002967:TDE2171|3end_hypothetical_protein_2201777..2201927_NEGATIVE 159 47 7 107 63 NC_002967:TDE1510|3end_hypothetical_protein_1558528..1558678_POSITIVE 158 35 4 106 75 NC_002967:TDE2491|3end_DNA_polymerase_domain_protein_2514705..2514855_NEGATIVE 157 46 3 99 57 NC_002967:TDE2495|3end_hypothetical_protein_2518735..2518885_NEGATIVE 157 42 8 149 113 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE