Origin IGS: gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttctccaattttttgaattatatttgaaaaaagtagagttgtcaatagaatttgttttatgcctactattatgttatactgtttttatgagtactacaagaaaaacgcactattaaagattggctgattgataaataaaccgcagagagagttgagcttccgcacaac Mask Tandem Repeat Region ================================================ gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Find is-nt database================================================ Query_seq: TDE2160:TDE2161|TDE2160:TDE2161:hypothetical protein:acetyltransferase, GNAT family:<-->:2194059..2194229 171 gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2160:TDE2161|TDE2160:TDE2161:hypothetical protein:acetyltransferase, GNAT family:<-->:2194059..2194229 171 gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2160:TDE2161|TDE2160:TDE2161:hypothetical protein:acetyltransferase, GNAT family:<-->:2194059..2194229 171 gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 2 End: 97 . M C G S S T L S A V Y L S I S Q S L I V R F S C S T H K N S I T .......................................................................... Protein_Len: 30 Strand: - Start: 56 End: 145 ....................................................... Y H T K R T T S M F V T Y C L L L C L V F E I S L E V K K M .......................... Protein_Len: 36 Strand: - Start: 45 End: 152 ............................................ G I K L L A N K K Y Y E Y F C Y L M I T P M F C I R N V V R S K E F I M ................... gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt 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: 92 Start: 123 End: 152 ..........................................................................................................................ATTGACAACTCTACTTTTTTCAAATATAAT................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 89 End: 118 ........................................................................................TTTGTTTTATGCCTACTATTATGTTATACT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2160:TDE2161|TDE2160:TDE2161:hypothetical protein:acetyltransferase, GNAT family:<-->:2194059..2194229 171 gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_002967_TDE2160_TDE2161|hypothetical protein:acetyltransferase, GNAT family|NEGATIVE:POSITIVE|[2194059,2194229]|171 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt gttgtgcggaagctcaactctctctgcggtttatttatcaatcagccaatctttaatagtgcgtttttcttgtagtactcataaaaacagtataacataatagtaggcataaaacaaattctattgacaactctacttttttcaaatataattcaaaaaattggagaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUGCGGAAGCUCAACUCUCUCUGCGGUUUAUUUAUCAAUCAGCCAAUCUUUAAUAGUGCGUUUUUCUUGUAGUACUCAUAAAAACAGUAUAACAUAAUAGUAGGCAUAAAACAAAUUCUAUUGACAACUCUACUUUUUUCAAAUAUAAUUCAAAAAAUUGGAGAAAUU ((((.((....)).)))).........((((.(((....))).)))).....((((((((((.(......(((.(((((.........))))).))).......).)))...........)))))))...(((((.((((((.((......)).)))))).)))))..... (-27.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUCCAAUUUUUUGAAUUAUAUUUGAAAAAAGUAGAGUUGUCAAUAGAAUUUGUUUUAUGCCUACUAUUAUGUUAUACUGUUUUUAUGAGUACUACAAGAAAAACGCACUAUUAAAGAUUGGCUGAUUGAUAAAUAAACCGCAGAGAGAGUUGAGCUUCCGCACAAC ..((((((...(((((..(((...)))..))))).......((((((((((......((((((((......((.(((..((((.........))))..))).)).....)))....))))).....)).))))))))..........))))))((((.((....)).)))) (-23.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 924 50 1 141 92 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 310 30 5 184 154 NC_002967:TDE2054|5end_hypothetical_protein_2082524..2082754_NEGATIVE 294 31 1 112 75 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 294 31 1 112 75 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 274 47 2 61 6 NC_002967:TDE0120|5end_hypothetical_protein_137648..137878_POSITIVE 273 45 1 215 173 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 272 39 5 213 180 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 254 47 1 183 121 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 253 37 5 72 38 NC_002967:TDE0727|5end_iron-sulfur_cluster-binding_protein_766721..766951_POSITIVE 250 47 2 200 167 NC_002967:TDE2553|5end_lysyl-tRNA_synthetase_2580633..2580863_NEGATIVE 248 68 21 66 16 NC_002967:TDE2191|5end_pyrimidine-nucleoside_phosphorylase_2227651..2227881_NEGATIVE 245 29 1 48 19 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 245 28 2 147 114 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 242 60 22 173 138 NC_002967:TDE1518|5end_permease,_putative_1564284..1564514_POSITIVE 238 71 35 38 3 NC_002967:TDE1346|5end_RNA_polymerase_sigma_factor_1385219..1385449_POSITIVE 237 45 1 57 8 NC_002967:TDE0648|5end_protein-glutamate_methylesterase_682800..683030_POSITIVE 236 30 1 225 190 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 234 81 44 129 92 NC_002967:TDE2304|5end_hypothetical_protein_2343440..2343670_POSITIVE 234 52 11 86 41 NC_002967:TDE1798|5end_hypothetical_protein_1836676..1836906_NEGATIVE 233 63 22 57 18 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 47 6 41 4 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 310 30 5 150 120 NC_002967:TDE2055|3end_hemin-binding_protein_B_2082558..2082708_NEGATIVE 302 42 1 95 47 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 294 31 1 50 13 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 294 31 1 60 23 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 280 70 26 44 2 NC_002967:TDE1345|3end_DNA_primase_1385306..1385456_POSITIVE 253 37 5 82 48 NC_002967:TDE0726|3end_aldehyde_oxidase_and_xanthine_dehydrogenase_family_protein_766811..766961_POSITIVE 251 49 2 123 76 NC_002967:TDE0304|3end_hypothetical_protein_335492..335642_POSITIVE 245 29 1 76 47 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 245 49 5 126 83 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 245 28 2 54 21 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 238 29 1 148 109 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE 236 48 7 50 6 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 234 81 44 136 99 NC_002967:TDE2303|3end_hypothetical_protein_2343527..2343677_POSITIVE 234 52 11 73 28 NC_002967:TDE1799|3end_hypothetical_protein_1836689..1836839_NEGATIVE 232 30 2 147 120 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 225 47 6 100 62 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 224 56 11 52 1 NC_002967:TDE0737|3end_hypothetical_protein_775408..775558_NEGATIVE 224 54 11 106 58 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 223 66 25 133 84 NC_002967:TDE1478|3end_hypothetical_protein_1523475..1523625_NEGATIVE