Origin IGS: gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatcctccatacataattctattatagtttatgcatatagtcaatagtgattatatgtctttgtcaagactattaccggaaagccgaaaatagcgttatttttatac Mask Tandem Repeat Region ================================================ gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Find is-nt database================================================ Query_seq: TDE0195:TDE0196|TDE0195:TDE0196:acetyltransferase, GNAT family:hypothetical protein:<-->:232602..232710 109 gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0195:TDE0196|TDE0195:TDE0196:acetyltransferase, GNAT family:hypothetical protein:<-->:232602..232710 109 gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0195:TDE0196|TDE0195:TDE0196:acetyltransferase, GNAT family:hypothetical protein:<-->:232602..232710 109 gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Predict ORF larger than 30AA ================================================ gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa 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: 63 End: 92 ..............................................................ATTGACTATATGCATAAACTATAATAGAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0195:TDE0196|TDE0195:TDE0196:acetyltransferase, GNAT family:hypothetical protein:<-->:232602..232710 109 gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE0195_TDE0196|acetyltransferase, GNAT family:hypothetical protein|NEGATIVE:POSITIVE|[232602,232710]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa gtataaaaataacgctattttcggctttccggtaatagtcttgacaaagacatataatcactattgactatatgcataaactataatagaattatgtatggaggataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAAAAAUAACGCUAUUUUCGGCUUUCCGGUAAUAGUCUUGACAAAGACAUAUAAUCACUAUUGACUAUAUGCAUAAACUAUAAUAGAAUUAUGUAUGGAGGAUAAA ...............(((((((........(((.((((((((....))))).))).)))...........(((((((((.(((...)))..)))))))))))))))).. (-16.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCCUCCAUACAUAAUUCUAUUAUAGUUUAUGCAUAUAGUCAAUAGUGAUUAUAUGUCUUUGUCAAGACUAUUACCGGAAAGCCGAAAAUAGCGUUAUUUUUAUAC ..............(((((.(((((.((((((..(((((((((((....)))))))))))........))))))....(((....)))..))))).)))))........ (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 70 21 161 112 NC_002967:TDE0195|5end_acetyltransferase,_GNAT_family_232511..232741_NEGATIVE 281 56 17 160 109 NC_002967:TDE1316|5end_hypothetical_protein_1354741..1354971_POSITIVE 274 43 8 143 114 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 273 45 9 199 162 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 252 41 18 66 40 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 249 67 21 199 151 NC_002967:TDE1375|5end_pantetheine-phosphate_adenylyltransferase_1418081..1418311_POSITIVE 240 38 1 39 3 NC_002967:TDE1463|5end_hypothetical_protein_1513072..1513302_NEGATIVE 234 49 14 71 45 NC_002967:TDE2451|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2479832..2480062_POSITIVE 230 42 14 213 180 NC_002967:TDE1502|5end_chorismate_mutase_1550920..1551150_POSITIVE 230 49 11 143 96 NC_002967:TDE0775|5end_ribosomal_protein_L29_810597..810827_POSITIVE 227 51 20 57 21 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 227 46 7 81 37 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 223 68 21 192 137 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 222 49 9 158 119 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 221 46 14 168 135 NC_002967:TDE1887|5end_TPR_domain_protein_1909133..1909363_NEGATIVE 218 52 16 159 124 NC_002967:TDE1103|5end_hypothetical_protein_1136360..1136590_POSITIVE 218 68 21 114 64 NC_002967:TDE0494|5end_hypothetical_protein_550515..550745_NEGATIVE 218 43 12 183 147 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 216 34 12 177 146 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 215 51 20 221 190 NC_002967:TDE1068|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1096686..1096916_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 43 8 140 111 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 238 38 9 35 3 NC_002967:TDE1464|3end_SsrA-binding_protein_1513076..1513226_NEGATIVE 234 49 14 46 20 NC_002967:TDE2450|3end_ankyrin_repeat_protein_2479887..2480037_POSITIVE 230 42 14 135 102 NC_002967:TDE1501|3end_pyruvate_phosphate_dikinase_1550922..1551072_POSITIVE 230 49 11 130 83 NC_002967:TDE0774|3end_50S_ribosomal_protein_L16_810664..810814_POSITIVE 227 51 20 60 24 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 222 49 9 49 10 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 218 68 21 117 67 NC_002967:TDE0495|3end_hypothetical_protein_550512..550662_NEGATIVE 211 35 18 87 68 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 211 46 13 42 4 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 209 60 12 149 96 NC_002967:TDE2751|3end_hypothetical_protein_2809194..2809344_POSITIVE 208 32 17 130 115 NC_002967:TDE1945|3end_hypothetical_protein_1961119..1961269_NEGATIVE 208 57 12 149 105 NC_002967:TDE1932|3end_hypothetical_protein_1949131..1949281_NEGATIVE 205 42 14 150 119 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 203 42 12 53 23 NC_002967:TDE2152|3end_hypothetical_protein_2188804..2188954_NEGATIVE 203 33 15 139 121 NC_002967:TDE2126|3end_hypothetical_protein_2159843..2159993_POSITIVE 203 33 13 82 61 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 200 40 12 48 22 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 200 42 22 31 7 NC_002967:TDE0606|3end_ParB_family_protein_643239..643389_NEGATIVE 199 50 19 71 26 NC_002967:TDE1252|3end_lipoprotein,_putative_1287094..1287244_POSITIVE