Origin IGS: aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcatatatcctactatttttaagcaaaaacggcaatagatataaaaaaaatacttacatccggttgaaaatatgttaatagtgggctatacttatataaaatatacgattatgcttttaaataaaattttatcttggaggataatt Mask Tandem Repeat Region ================================================ aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Find is-nt database================================================ Query_seq: TDE2674:TDE2675|TDE2674:TDE2675:hypothetical protein:hypothetical protein:<-->:2713368..2713513 146 aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2674:TDE2675|TDE2674:TDE2675:hypothetical protein:hypothetical protein:<-->:2713368..2713513 146 aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2674:TDE2675|TDE2674:TDE2675:hypothetical protein:hypothetical protein:<-->:2713368..2713513 146 aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Predict ORF larger than 30AA ================================================ aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc 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: 86 Start: 55 End: 84 ......................................................GTTGAAAATATGTTAATAGTGGGCTATACT.............................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 111 End: 140 ..............................................................................................................ATTGCCGTTTTTGCTTAAAAATAGTAGGAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2674:TDE2675|TDE2674:TDE2675:hypothetical protein:hypothetical protein:<-->:2713368..2713513 146 aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002967_TDE2674_TDE2675|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2713368,2713513]|146 HSP 1 e-value: 3.0E-63 bit: 242.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtannnnnnnnatatctattgccgtttttgcttaaaaatagtaggatatatgc aattatcctccaagataaaattttatttaaaagcataatcgtatattttatataagtatagcccactattaacatattttcaaccggatgtaagtattttttttatatctattgccgtttttgcttaaaaatagtaggatatatgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUCCUCCAAGAUAAAAUUUUAUUUAAAAGCAUAAUCGUAUAUUUUAUAUAAGUAUAGCCCACUAUUAACAUAUUUUCAACCGGAUGUAAGUAUUUUUUUUAUAUCUAUUGCCGUUUUUGCUUAAAAAUAGUAGGAUAUAUGC ..(((((......)))))..............(((((....(((((((.....))))))).((.((((((...............(((((((((.......)))))))))...((.......)).....)))))).))...))))) (-21.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUAUAUCCUACUAUUUUUAAGCAAAAACGGCAAUAGAUAUAAAAAAAAUACUUACAUCCGGUUGAAAAUAUGUUAAUAGUGGGCUAUACUUAUAUAAAAUAUACGAUUAUGCUUUUAAAUAAAAUUUUAUCUUGGAGGAUAAUU ...((((.(((((((((..((..(((...(((....((.(((.......))))).....))).)))......))..))))))))).))))................((((((.((((...((((....))))...)))).)))))) (-21.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 749 100 51 191 142 NC_002967:TDE2674|5end_hypothetical_protein_2713277..2713507_NEGATIVE 236 118 79 135 87 NC_002967:TDE1578|5end_phosphoesterase,_putative_1625370..1625600_POSITIVE 226 120 80 183 148 NC_002967:TDE0257|5end_hypothetical_protein_292098..292328_NEGATIVE 221 92 51 208 175 NC_002967:TDE2669|5end_CDP-alcohol_phosphatidyltransferase_family_protein_2706943..2707173_NEGATIVE 218 138 91 76 29 NC_002967:TDE2728|5end_hypothetical_protein_2785607..2785837_POSITIVE 218 46 3 152 107 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 213 123 82 116 70 NC_002967:TDE0212|5end_hypothetical_protein_248235..248465_NEGATIVE 211 137 102 161 125 NC_002967:TDE2712|5end_hypothetical_protein_2769008..2769238_POSITIVE 210 79 37 214 170 NC_002967:TDE0194|5end_hypothetical_protein_231881..232111_NEGATIVE 209 130 85 176 129 NC_002967:TDE0158|5end_hypothetical_protein_185948..186178_NEGATIVE 206 123 84 160 110 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 205 127 83 132 86 NC_002967:TDE0298|5end_hypothetical_protein_327963..328193_POSITIVE 204 124 82 120 65 NC_002967:TDE1897|5end_phosphoribosylglycinamide_formyltransferase_1918109..1918339_NEGATIVE 204 126 83 78 29 NC_002967:TDE0856|5end_L-fuculose_phosphate_aldolase,_putative_877111..877341_POSITIVE 202 126 81 201 145 NC_002967:TDE2774|5end_hypothetical_protein_2825994..2826224_POSITIVE 200 140 106 197 162 NC_002967:TDE1997|5end_hypothetical_protein_2014796..2015026_POSITIVE 200 124 83 94 35 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 199 124 81 134 77 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 197 125 83 108 56 NC_002967:TDE1632|5end_citrate_lyase,_beta_subunit_1682438..1682668_NEGATIVE 197 97 54 111 80 NC_002967:TDE0701|5end_hypothetical_protein_737247..737477_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 122 83 105 64 NC_002967:TDE1238|3end_translocase_1271245..1271395_POSITIVE 248 127 82 151 105 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 236 118 79 131 83 NC_002967:TDE1577|3end_lipoprotein,_putative_1625446..1625596_POSITIVE 226 120 80 149 114 NC_002967:TDE0258|3end_methlytransferase,_UbiE/COQ5_family_292132..292282_NEGATIVE 218 46 3 150 105 NC_002967:TDE2137|3end_hypothetical_protein_2171709..2171859_POSITIVE 214 103 62 151 103 NC_002967:TDE1291|3end_HD_domain_protein_1328638..1328788_NEGATIVE 212 118 81 39 6 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 211 137 102 64 28 NC_002967:TDE2711|3end_hypothetical_protein_2768991..2769141_POSITIVE 206 123 84 127 77 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 204 124 82 107 52 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 204 126 83 72 23 NC_002967:TDE0855|3end_DNA-binding_response_regulator_877185..877335_POSITIVE 198 126 84 111 71 NC_002967:TDE0013|3end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_17758..17908_NEGATIVE 197 139 112 132 107 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 197 125 83 118 66 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 197 97 54 114 83 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE 192 117 78 104 55 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 192 77 37 151 109 NC_002967:TDE0195|3end_acetyltransferase,_GNAT_family_231942..232092_NEGATIVE 191 126 84 68 13 NC_002967:TDE0678|3end_hypothetical_protein_716438..716588_POSITIVE 188 127 81 116 77 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 187 118 75 138 92 NC_002967:TDE0836|3end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_855527..855677_NEGATIVE