Origin IGS: caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg .........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 catagactcctcctgtcaaagtctttttaatttgcaattcaattatcaattaccaattacccattatccattggaattggattgacttgtcccaatcctcaaggacattccgaagcacagtaacggacgctccgtcattagtttaacggtcagaccgttattatgctgacggctagtccgtcattatgctgatgtacattccgttatcagcttaacggtcttcccgtcattatactgacggcaggagcgtacattttg Mask Tandem Repeat Region ================================================ caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Find is-nt database================================================ Query_seq: TDE0570:TDE0571|TDE0570:TDE0571:hypothetical protein:hypothetical protein:->->:601017..601274 258 caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0570:TDE0571|TDE0570:TDE0571:hypothetical protein:hypothetical protein:->->:601017..601274 258 caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0570:TDE0571|TDE0570:TDE0571:hypothetical protein:hypothetical protein:->->:601017..601274 258 caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 116 End: 229 ................................................................................................................... V L S P A D T V T S R F T R S S Q S L D I W N W H I I P L Q Y N I I S N C M ............................. caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.2 Tail_Score: -3.40403 Start: 30 End: 46 Full_Region: attccgttatcagct taacgg tcttc ccgtca ttatactgacggcag .............................taacggtcttcccgtca.................................................................................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -9.5 Tail_Score: -3.4072 Start: 99 End: 115 Full_Region: gctccgtcattagtt taacggt cag accgtta ttatgctgacggcta ..................................................................................................taacggtcagaccgtta............................................................................................................................................... TransTerm Strand: + Conf: 41 HP_score: -2.1 Tail_Score: -2.81815 Start: 179 End: 206 Full_Region: TTGGGACAAGTCAAT CCAATTCCAAT GGATA ATGGGTAATTGG TAATTGATAATTGAA ..................................................................................................................................................................................CCAATTCCAATGGATAATGGGTAATTGG.................................................... Find igs database================================================ Query_seq: TDE0570:TDE0571|TDE0570:TDE0571:hypothetical protein:hypothetical protein:->->:601017..601274 258 caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: NC_002967_TDE0570_TDE0571|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[601017,601274]|258 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg caaaatgtacgctcctgccgtcagtataatgacgggaagaccgttaagctgataacggaatgtacatcagcataatgacggactagccgtcagcataataacggtctgaccgttaaactaatgacggagcgtccgttactgtgcttcggaatgtccttgaggattgggacaagtcaatccaattccaatggataatgggtaattggtaattgataattgaattgcaaattaaaaagactttgacaggaggagtctatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAUGUACGCUCCUGCCGUCAGUAUAAUGACGGGAAGACCGUUAAGCUGAUAACGGAAUGUACAUCAGCAUAAUGACGGACUAGCCGUCAGCAUAAUAACGGUCUGACCGUUAAACUAAUGACGGAGCGUCCGUUACUGUGCUUCGGAAUGUCCUUGAGGAUUGGGACAAGUCAAUCCAAUUCCAAUGGAUAAUGGGUAAUUGGUAAUUGAUAAUUGAAUUGCAAAUUAAAAAGACUUUGACAGGAGGAGUCUAUG ....(((((((.(((.(..((((((....((((((.....)))))).))))))..)))).))))))).((((((.((((((((...((((((......((((((.....))))))......))))))...)))))))).))))))......((((((((.(((((((((....))...)))))))))).))))).....(((((.((((((.(....).)))))).)))))...(((((((.......)))))))... (-88.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAGACUCCUCCUGUCAAAGUCUUUUUAAUUUGCAAUUCAAUUAUCAAUUACCAAUUACCCAUUAUCCAUUGGAAUUGGAUUGACUUGUCCCAAUCCUCAAGGACAUUCCGAAGCACAGUAACGGACGCUCCGUCAUUAGUUUAACGGUCAGACCGUUAUUAUGCUGACGGCUAGUCCGUCAUUAUGCUGAUGUACAUUCCGUUAUCAGCUUAACGGUCUUCCCGUCAUUAUACUGACGGCAGGAGCGUACAUUUUG ....(((.......)))...((((((.....((((((.((((((..(((((.(((((............)))))))))))))))).)))...))).....)))))).......((((.(((.((((((...((((((.((...((((((.....))))))...)).))))))...)))))).))).))))(((((((...((((((......))))))((((.((((((......)))))).))))..)))))))... (-78.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 182 147 195 162 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 355 120 71 210 161 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 351 168 127 79 31 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 346 226 187 207 173 NC_002967:TDE1939|5end_hypothetical_protein_1954627..1954857_POSITIVE 342 179 146 50 18 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 335 58 11 170 116 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 321 68 23 180 124 NC_002967:TDE1988|5end_hypothetical_protein_2002739..2002969_POSITIVE 314 111 71 120 89 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 313 147 102 220 172 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 312 173 133 209 170 NC_002967:TDE1369|5end_excinuclease_ABC_subunit_B_1411792..1412022_NEGATIVE 312 170 123 183 130 NC_002967:TDE0723|5end_hypothetical_protein_760304..760534_POSITIVE 308 150 102 173 133 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 305 168 125 178 111 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 302 168 121 218 178 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 300 60 14 145 97 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 300 167 126 159 120 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 300 58 11 223 163 NC_002967:TDE0844|5end_pyruvate_phosphate_dikinase,_putative_864886..865116_POSITIVE 299 156 111 209 166 NC_002967:TDE1218|5end_flagellum-specific_ATP_synthase_FliI_1250447..1250677_POSITIVE 296 169 121 170 126 NC_002967:TDE1014|5end_hypothetical_protein_1045544..1045774_NEGATIVE 295 167 125 175 121 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 137 91 87 40 NC_002967:TDE0570|3end_hypothetical_protein_600956..601106_POSITIVE 346 226 187 86 52 NC_002967:TDE1938|3end_hypothetical_protein_1954586..1954736_POSITIVE 339 52 12 66 20 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 332 180 134 114 66 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 317 50 2 133 83 NC_002967:TDE1232|3end_hypothetical_protein_1265353..1265503_NEGATIVE 302 149 102 79 26 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE 293 150 103 84 39 NC_002967:TDE2780|3end_hypothetical_protein_2830508..2830658_NEGATIVE 292 60 11 114 61 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 291 168 122 40 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 289 162 125 56 22 NC_002967:TDE2179|3end_voltage-gated_chloride_channel_2210614..2210764_POSITIVE 289 168 122 149 99 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 283 180 133 121 61 NC_002967:TDE2365|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2398930..2399080_NEGATIVE 282 149 101 78 18 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 282 135 93 50 7 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 280 145 102 61 21 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 280 58 11 56 5 NC_002967:TDE2064|3end_ferrous_iron_transport_protein_A_2091268..2091418_NEGATIVE 278 54 15 145 96 NC_002967:TDE1987|3end_hypothetical_protein_2002802..2002952_POSITIVE 278 139 94 76 29 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 277 112 78 96 61 NC_002967:TDE0865|3end_hypothetical_protein_887599..887749_POSITIVE 276 34 6 148 123 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE