Origin IGS: aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc .........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 ggggatgtgttcaattggtaatggataattacaaattacacattgccaattacaaattaaaaaaaaagcggctcgcaattttgataaattgctctccgcttaattaataatgtataattaataaagtataattaataattgttaatggagaattgataacctattatcaattaaaaatgaggaagctttt Mask Tandem Repeat Region ================================================ aaaagcttcctcatttttaattgataataggttatcaattctccattaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Find is-nt database================================================ Query_seq: TDE1932:TDE1933|TDE1932:TDE1933:hypothetical protein:hypothetical protein:<-<-:1949500..1949689 190 aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1932:TDE1933|TDE1932:TDE1933:hypothetical protein:hypothetical protein:<-<-:1949500..1949689 190 aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1932:TDE1933|TDE1932:TDE1933:hypothetical protein:hypothetical protein:<-<-:1949500..1949689 190 aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 87 End: 176 ...................................................................................... N L P S C N I L I A L R K K K L K Y N A I H L K Y N D M V M .............. aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc 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: 81 Start: 59 End: 88 ..........................................................ATTAATAATGTATAATTAATAAAGTATAAT...................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -5.8 Tail_Score: -6.28631 Start: 92 End: 123 Full_Region: TACATTATTAATTAA GCGGAGAGCAATTT ATCA AAATTGCGAGCCGC TTTTTTTTTAATTTG ...........................................................................................GCGGAGAGCAATTTATCAAAATTGCGAGCCGC................................................................... Find igs database================================================ Query_seq: TDE1932:TDE1933|TDE1932:TDE1933:hypothetical protein:hypothetical protein:<-<-:1949500..1949689 190 aaaagcttcctcatttttaattgataataggttatcaattctccattaacaattattaattatactttattaattatacattattaattaagcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_002967_TDE1932_TDE1933|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1949500,1949689]|190 HSP 1 e-value: 2.0E-33 bit: 143.0 Len: 99 Query Start:92 Query End:190 Subject Strand: POSITIVE Subject Start: 92 Subject End: 190 ...........................................................................................gcggagagcaatttatcaaaattgcgagccgcnnnnnnnnnaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc ...........................................................................................gcggagagcaatttatcaaaattgcgagccgctttttttttaatttgtaattggcaatgtgtaatttgtaattatccattaccaattgaacacatcccc HSP 2 e-value: 1.0E-16 bit: 87.7 Len: 44 Query Start:1 Query End:44 Subject Strand: POSITIVE Subject Start: 1 Subject End: 44 aaaagcttcctcatttttaattgataataggttatcaattctcc.................................................................................................................................................. aaaagcttcctcatttttaattgataataggttatcaattctcc.................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGCUUCCUCAUUUUUAAUUGAUAAUAGGUUAUCAAUUCUCCAUUAACAAUUAUUAAUUAUACUUUAUUAAUUAUACAUUAUUAAUUAAGCGGAGAGCAAUUUAUCAAAAUUGCGAGCCGCUUUUUUUUUAAUUUGUAAUUGGCAAUGUGUAAUUUGUAAUUAUCCAUUACCAAUUGAACACAUCCCC ...............((((((((.((((.((...........))......((((((.((((((((.((.(((((((((.((((..((..((((((...(((((((....)))))))...))))))..))..)))).))))))))).)).)))))))).))))))....)))).))))))))......... (-43.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGAUGUGUUCAAUUGGUAAUGGAUAAUUACAAAUUACACAUUGCCAAUUACAAAUUAAAAAAAAAGCGGCUCGCAAUUUUGAUAAAUUGCUCUCCGCUUAAUUAAUAAUGUAUAAUUAAUAAAGUAUAAUUAAUAAUUGUUAAUGGAGAAUUGAUAACCUAUUAUCAAUUAAAAAUGAGGAAGCUUUU ((.(((((((..((((.(((((.....))))).))))))))))).))..................((((((...(((((((....)))))))...)))))).(((((((((...((((((........))))))...)))))))))....(((((((((....)))))))))......(((....))).. (-44.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 806 140 91 231 182 NC_002967:TDE1932|5end_hypothetical_protein_1949409..1949639_NEGATIVE 365 133 92 50 12 NC_002967:TDE1751|5end_ribosomal_protein_L21_1804142..1804372_NEGATIVE 301 125 90 177 138 NC_002967:TDE2721|5end_helicase_domain_protein_2779605..2779835_NEGATIVE 297 129 90 130 80 NC_002967:TDE2182|5end_hypothetical_protein_2215035..2215265_NEGATIVE 292 178 131 152 92 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 285 140 91 194 132 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 276 157 117 177 141 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 274 122 92 160 133 NC_002967:TDE2383|5end_cobalamin_5'-phosphate_synthase_2412826..2413056_POSITIVE 268 134 92 78 30 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 262 102 64 160 124 NC_002967:TDE2088|5end_C4_zinc_finger_domain_protein,_DksA/TraR_family_2115744..2115974_POSITIVE 261 174 131 95 58 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 259 129 89 55 4 NC_002967:TDE0571|5end_hypothetical_protein_601135..601365_POSITIVE 257 139 91 203 154 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 257 147 119 119 95 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 253 190 153 161 112 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 252 145 113 129 94 NC_002967:TDE2050|5end_hypothetical_protein_2079940..2080170_NEGATIVE 252 147 116 160 124 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 240 123 89 107 79 NC_002967:TDE2604|5end_hypothetical_protein_2645774..2646004_NEGATIVE 237 118 91 75 41 NC_002967:TDE2529|5end_hypothetical_protein_2557238..2557468_NEGATIVE 235 128 94 111 79 NC_002967:TDE2464|5end_hypothetical_protein_2489143..2489373_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 125 90 116 77 NC_002967:TDE2722|3end_carhohydrate_kinase,_FGGY_family_2779666..2779816_NEGATIVE 292 178 131 81 21 NC_002967:TDE2003|3end_internalin-related_protein_2023631..2023781_POSITIVE 281 190 153 103 61 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 274 127 92 147 110 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 262 122 92 124 82 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 261 174 131 68 31 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 257 147 119 61 37 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 253 190 153 84 35 NC_002967:TDE0571|3end_hypothetical_protein_603497..603647_POSITIVE 252 145 113 79 44 NC_002967:TDE2051|3end_hypothetical_protein_2079990..2080140_NEGATIVE 252 147 116 59 23 NC_002967:TDE1292|3end_TldD/PmbA_family_protein_1329314..1329464_NEGATIVE 246 130 85 78 31 NC_002967:TDE2694|3end_hypothetical_protein_2734079..2734229_NEGATIVE 246 130 88 92 58 NC_002967:TDE0679|3end_aminotransferase,_class_V_717573..717723_POSITIVE 243 151 115 86 48 NC_002967:TDE1384|3end_cadmium-translocating_P-type_ATPase_1424776..1424926_POSITIVE 242 107 86 94 70 NC_002967:TDE0100|3end_hypothetical_protein_116974..117124_NEGATIVE 235 128 94 81 49 NC_002967:TDE2463|3end_hypothetical_protein_2489193..2489343_POSITIVE 233 128 94 44 4 NC_002967:TDE0340|3end_fructose-bisphosphate_aldolase_379606..379756_POSITIVE 228 45 6 138 99 NC_002967:TDE0593|3end_internalin-related_protein_632041..632191_NEGATIVE 226 68 28 99 57 NC_002967:TDE0294|3end_TrkA_domain_protein_323473..323623_NEGATIVE 224 132 91 81 41 NC_002967:TDE1045|3end_hypothetical_protein_1073739..1073889_POSITIVE 223 139 91 104 37 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE