Origin IGS: atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtcctcctaaatatctccttaaatatatcagtttttcgcattttaatcaagatgtacatctaaaccgagatattttctaaaaaaatcttaaaaaccttgaaataggtctagaaacggtctatactgtat Mask Tandem Repeat Region ================================================ atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Find is-nt database================================================ Query_seq: TDE0742:TDE0743|TDE0742:TDE0743:hypothetical protein:thioredoxin reductase:<-->:778726..778857 132 atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0742:TDE0743|TDE0742:TDE0743:hypothetical protein:thioredoxin reductase:<-->:778726..778857 132 atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0742:TDE0743|TDE0742:TDE0743:hypothetical protein:thioredoxin reductase:<-->:778726..778857 132 atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Predict ORF larger than 30AA ================================================ atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt 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: 83 Start: 5 End: 34 ....CTTGAAATAGGTCTAGAAACGGTCTATACT.................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 79 End: 108 ..............................................................................CTTGATTAAAATGCGAAAAACTGATATATT........................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0742:TDE0743|TDE0742:TDE0743:hypothetical protein:thioredoxin reductase:<-->:778726..778857 132 atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_002967_TDE0742_TDE0743|hypothetical protein:thioredoxin reductase|NEGATIVE:POSITIVE|[778726,778857]|132 HSP 1 e-value: 9.0E-57 bit: 220.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 atacagtatagaccgtttctagacctatttcaaggtttttaagannnnnnnagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt atacagtatagaccgtttctagacctatttcaaggtttttaagatttttttagaaaatatctcggtttagatgtacatcttgattaaaatgcgaaaaactgatatatttaaggagatatttaggaggacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAGUAUAGACCGUUUCUAGACCUAUUUCAAGGUUUUUAAGAUUUUUUUAGAAAAUAUCUCGGUUUAGAUGUACAUCUUGAUUAAAAUGCGAAAAACUGAUAUAUUUAAGGAGAUAUUUAGGAGGACUUU .((((...(((((((.....((((((......))))))...((((.(((.....))).)))))))))))..)))).......................((((.((((((....))))))))))......... (-20.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCCUCCUAAAUAUCUCCUUAAAUAUAUCAGUUUUUCGCAUUUUAAUCAAGAUGUACAUCUAAACCGAGAUAUUUUCUAAAAAAAUCUUAAAAACCUUGAAAUAGGUCUAGAAACGGUCUAUACUGUAU ..((.((....(((((((((...((((......))))...(((((((....)))))))...........)))))))))..........(((.....((((......))))..)))...)).))......... (-17.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 748 130 81 221 172 NC_002967:TDE0742|5end_hypothetical_protein_778635..778865_NEGATIVE 239 44 3 50 8 NC_002967:TDE2557|5end_hypothetical_protein_2583383..2583613_NEGATIVE 231 69 21 148 101 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 229 49 6 118 76 NC_002967:TDE1221|5end_glycosyl_hydrolase,_family_3_1254796..1255026_POSITIVE 226 70 28 168 127 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 211 58 13 141 98 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 208 85 42 229 192 NC_002967:TDE1073|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1103515..1103745_POSITIVE 206 40 2 230 196 NC_002967:TDE0714|5end_capsular_polysaccharide_biosynthesis_protein_747633..747863_POSITIVE 205 78 32 223 172 NC_002967:TDE2135|5end_hypothetical_protein_2164586..2164816_POSITIVE 205 78 32 84 33 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 205 40 1 175 136 NC_002967:TDE0891|5end_transcriptional_regulator,_putative_907592..907822_POSITIVE 204 79 31 143 92 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 202 32 1 196 166 NC_002967:TDE2261|5end_hypothetical_protein_2298013..2298243_NEGATIVE 200 53 13 87 34 NC_002967:TDE0182|5end_ABC_transporter,_ATP-binding_protein_216783..217013_NEGATIVE 199 48 12 31 2 NC_002967:TDE2207|5end_hypothetical_protein_2246634..2246864_NEGATIVE 199 70 21 101 37 NC_002967:TDE1967|5end_hypothetical_protein_1981557..1981787_POSITIVE 199 46 5 218 179 NC_002967:TDE1578|5end_phosphoesterase,_putative_1625370..1625600_POSITIVE 195 32 5 41 13 NC_002967:TDE1394|5end_hypothetical_protein_1433084..1433314_POSITIVE 194 58 14 205 154 NC_002967:TDE2663|5end_isoleucyl-tRNA_synthetase_2701918..2702148_NEGATIVE 194 57 13 207 158 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 69 21 142 95 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 229 49 6 104 62 NC_002967:TDE1220|3end_hypothetical_protein_1254862..1255012_POSITIVE 228 67 31 133 84 NC_002967:TDE0100|3end_hypothetical_protein_116974..117124_NEGATIVE 212 127 90 98 67 NC_002967:TDE1434|3end_hypothetical_protein_1478238..1478388_NEGATIVE 211 58 13 148 105 NC_002967:TDE0576|3end_glutamyl-tRNA(Gln)_amidotransferase,_A_subunit_607726..607876_NEGATIVE 210 90 42 75 33 NC_002967:TDE1072|3end_lipoprotein,_putative_1103436..1103586_POSITIVE 209 66 24 134 90 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 205 40 1 107 68 NC_002967:TDE0890|3end_hypothetical_protein_907604..907754_POSITIVE 204 79 31 137 86 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 203 40 2 132 86 NC_002967:TDE1681|3end_V-type_ATP_synthase_subunit_D_1732923..1733073_NEGATIVE 200 53 13 87 34 NC_002967:TDE0183|3end_ABC_transporter,_permease_protein_216783..216933_NEGATIVE 199 70 21 94 30 NC_002967:TDE1966|3end_trypsin_domain/PDZ_domain_protein_1981630..1981780_POSITIVE 195 32 5 44 16 NC_002967:TDE1393|3end_hypothetical_protein_1433167..1433317_POSITIVE 193 46 10 38 10 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 189 47 3 133 79 NC_002967:TDE1968|3end_cell_division_protein_FtsJ_1982493..1982643_NEGATIVE 188 54 12 124 79 NC_002967:TDE0216|3end_hypothetical_protein_252620..252770_POSITIVE 186 45 14 84 53 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 185 67 32 103 65 NC_002967:TDE0980|3end_asparaginyl-tRNA_synthetase_1003979..1004129_NEGATIVE 183 93 62 70 37 NC_002967:TDE1697|3end_phosphoglycerate_mutase_1755516..1755666_NEGATIVE 182 35 6 63 35 NC_002967:TDE2154|3end_50S_ribosomal_protein_L20_2189575..2189725_NEGATIVE