Origin IGS: atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaatagctcctgaatttgttttatttatcttattttcggcattataacagccttacattaaagacagattttagtatttagttacaaaacaccataatatccgtaaattaaggcacgaattagaatttactcaattttataggtatcgtcaagaggataaacaaaatactattgaccgatcataaaaccaatgttacaatatagctatagttattatgaggaggaaaaatat Mask Tandem Repeat Region ================================================ atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Find is-nt database================================================ Query_seq: TDE1102:TDE1103|TDE1102:TDE1103:hypothetical protein:hypothetical protein:<-->:1136266..1136499 234 atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1102:TDE1103|TDE1102:TDE1103:hypothetical protein:hypothetical protein:<-->:1136266..1136499 234 atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1102:TDE1103|TDE1102:TDE1103:hypothetical protein:hypothetical protein:<-->:1136266..1136499 234 atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Predict ORF larger than 30AA ================================================ atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt 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: 33 End: 62 ................................ATTGACCGATCATAAAACCAATGTTACAAT............................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 80 End: 109 ...............................................................................CTTGACGATACCTATAAAATTGAGTAAATT............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1102:TDE1103|TDE1102:TDE1103:hypothetical protein:hypothetical protein:<-->:1136266..1136499 234 atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: NC_002967_TDE1102_TDE1103|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1136266,1136499]|234 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt atatttttcctcctcataataactatagctatattgtaacattggttttatgatcggtcaatagtattttgtttatcctcttgacgatacctataaaattgagtaaattctaattcgtgccttaatttacggatattatggtgttttgtaactaaatactaaaatctgtctttaatgtaaggctgttataatgccgaaaataagataaataaaacaaattcaggagctattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUUUCCUCCUCAUAAUAACUAUAGCUAUAUUGUAACAUUGGUUUUAUGAUCGGUCAAUAGUAUUUUGUUUAUCCUCUUGACGAUACCUAUAAAAUUGAGUAAAUUCUAAUUCGUGCCUUAAUUUACGGAUAUUAUGGUGUUUUGUAACUAAAUACUAAAAUCUGUCUUUAAUGUAAGGCUGUUAUAAUGCCGAAAAUAAGAUAAAUAAAACAAAUUCAGGAGCUAUUUUU ........................((((((.(((((((((.(..((((((((((((.((((.((.((.......)).)).))))))))...))))))))..)................((((((..(((.(((((((.((((((((.......)))))))).)))..)))).)))..)))))).)))))))))..........((..............))...)))))).... (-40.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAGCUCCUGAAUUUGUUUUAUUUAUCUUAUUUUCGGCAUUAUAACAGCCUUACAUUAAAGACAGAUUUUAGUAUUUAGUUACAAAACACCAUAAUAUCCGUAAAUUAAGGCACGAAUUAGAAUUUACUCAAUUUUAUAGGUAUCGUCAAGAGGAUAAACAAAAUACUAUUGACCGAUCAUAAAACCAAUGUUACAAUAUAGCUAUAGUUAUUAUGAGGAGGAAAAAUAU ........((((......((((((.((((((((......(((.........)))..........(((........(((......))).....(((((((.....(((((((..............)))))))......)))).)))...)))...)))))))).))))))...........(((((((((....((((.....))))....))).))))))))))......... (-33.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 780 90 41 181 132 NC_002967:TDE1102|5end_hypothetical_protein_1136175..1136405_NEGATIVE 265 50 7 210 161 NC_002967:TDE1177|5end_flavodoxin_family_protein_1207097..1207327_NEGATIVE 258 95 54 71 24 NC_002967:TDE2354|5end_hypothetical_protein_2390395..2390625_POSITIVE 254 72 35 161 121 NC_002967:TDE1498|5end_hypothetical_protein_1543669..1543899_POSITIVE 254 92 51 177 127 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 251 121 83 224 189 NC_002967:TDE0535|5end_ABC_transporter,_ATP-binding_protein_577323..577553_POSITIVE 246 86 44 109 61 NC_002967:TDE1067|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095701..1095931_NEGATIVE 244 108 61 63 9 NC_002967:TDE1337|5end_hypothetical_protein_1374806..1375036_NEGATIVE 237 148 107 170 118 NC_002967:TDE2283|5end_permease,_putative_2320917..2321147_NEGATIVE 237 149 111 129 97 NC_002967:TDE0735|5end_hypothetical_protein_775003..775233_NEGATIVE 222 200 154 102 56 NC_002967:TDE1966|5end_trypsin_domain/PDZ_domain_protein_1980273..1980503_POSITIVE 221 35 1 148 113 NC_002967:TDE2135|5end_hypothetical_protein_2164586..2164816_POSITIVE 221 35 1 148 113 NC_002967:TDE1991|5end_hypothetical_protein_2009398..2009628_NEGATIVE 218 45 6 45 12 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 218 80 33 178 123 NC_002967:TDE0969|5end_hypothetical_protein_993260..993490_POSITIVE 218 202 167 185 149 NC_002967:TDE0196|5end_hypothetical_protein_232571..232801_POSITIVE 214 187 141 204 156 NC_002967:TDE2501|5end_response_regulator_2524773..2525003_POSITIVE 213 209 166 225 176 NC_002967:TDE2364|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398949..2399179_NEGATIVE 213 133 98 157 122 NC_002967:TDE1559|5end_hypothetical_protein_1610723..1610953_POSITIVE 211 149 114 219 176 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 95 54 52 5 NC_002967:TDE2353|3end_flagellar_hook-associated_protein_2390456..2390606_POSITIVE 254 72 35 116 76 NC_002967:TDE1497|3end_hypothetical_protein_1543704..1543854_POSITIVE 246 86 44 116 68 NC_002967:TDE1068|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095694..1095844_NEGATIVE 239 197 167 36 4 NC_002967:TDE2513|3end_glucose-inhibited_division_protein_B_2539888..2540038_POSITIVE 237 149 111 132 100 NC_002967:TDE0736|3end_hypothetical_protein_775000..775150_NEGATIVE 221 35 1 104 69 NC_002967:TDE2134|3end_hypothetical_protein_2164622..2164772_POSITIVE 215 90 41 125 84 NC_002967:TDE0559|3end_hypothetical_protein_594126..594276_POSITIVE 210 197 160 78 49 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 209 49 4 100 62 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 208 149 101 114 60 NC_002967:TDE1129|3end_lipoprotein,_putative_1162523..1162673_POSITIVE 205 119 71 114 59 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 202 200 166 44 8 NC_002967:TDE2618|3end_PHP_domain_protein_2660347..2660497_POSITIVE 201 79 34 57 1 NC_002967:TDE0262|3end_hypothetical_protein_295227..295377_NEGATIVE 199 88 42 83 38 NC_002967:TDE2329|3end_hypothetical_protein_2366347..2366497_NEGATIVE 198 204 174 57 31 NC_002967:TDE1947|3end_ABC_transporter,_permease_protein_1962517..1962667_NEGATIVE 198 198 177 64 43 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 198 205 179 68 39 NC_002967:TDE1545|3end_phosphoribosyl_transferase_domain_protein_1589012..1589162_POSITIVE 195 200 159 138 105 NC_002967:TDE0053|3end_flagellar_biosynthetic_protein_FliR_62467..62617_POSITIVE 194 88 42 127 91 NC_002967:TDE1682|3end_V-type_ATP_synthase_subunit_B_1733548..1733698_NEGATIVE 193 141 101 75 23 NC_002967:TDE0790|3end_30S_ribosomal_protein_S11_817411..817561_POSITIVE