Origin IGS: actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgaggtaatgccttaatactcaatttttatctcaatcttttacgcctacttgaagtctttttaaattgaatgtatagtaattattaatatattgagtatgttttccaataaatttttattttgagagagagt Mask Tandem Repeat Region ================================================ actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Find is-nt database================================================ Query_seq: TDE2518:TDE2519|TDE2518:TDE2519:nucleotide-binding protein:hypothetical protein:<-<-:2544796..2544928 133 actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2518:TDE2519|TDE2518:TDE2519:nucleotide-binding protein:hypothetical protein:<-<-:2544796..2544928 133 actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2518:TDE2519|TDE2518:TDE2519:nucleotide-binding protein:hypothetical protein:<-<-:2544796..2544928 133 actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Predict ORF larger than 30AA ================================================ actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat 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: 83 Start: 55 End: 84 ......................................................CTTGAAGTCTTTTTAAATTGAATGTATAGT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 66 End: 95 .................................................................TTTTACGCCTACTTGAAGTCTTTTTAAATT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2518:TDE2519|TDE2518:TDE2519:nucleotide-binding protein:hypothetical protein:<-<-:2544796..2544928 133 actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: NC_002967_TDE2518_TDE2519|nucleotide-binding protein:hypothetical protein|NEGATIVE:NEGATIVE|[2544796,2544928]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat actctctctcaaaataaaaatttattggaaaacatactcaatatattaataattactatacattcaatttaaaaagacttcaagtaggcgtaaaagattgagataaaaattgagtattaaggcattacctcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUCUCUCAAAAUAAAAAUUUAUUGGAAAACAUACUCAAUAUAUUAAUAAUUACUAUACAUUCAAUUUAAAAAGACUUCAAGUAGGCGUAAAAGAUUGAGAUAAAAAUUGAGUAUUAAGGCAUUACCUCAU .................................(((((((((......(((.....)))...((((((((.......((......)).......))))))))......)))))))))..(((.....)))... (-12.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAGGUAAUGCCUUAAUACUCAAUUUUUAUCUCAAUCUUUUACGCCUACUUGAAGUCUUUUUAAAUUGAAUGUAUAGUAAUUAUUAAUAUAUUGAGUAUGUUUUCCAAUAAAUUUUUAUUUUGAGAGAGAGU .(((((.....))))).......((((((.((((((....((((...(((....(((........)))....)))..)))).((..(((.(((((.(........)))))).)))..))..)))))))))))) (-15.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 786 130 81 221 172 NC_002967:TDE2518|5end_nucleotide-binding_protein_2544705..2544935_NEGATIVE 236 98 58 141 96 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 206 89 61 230 197 NC_002967:TDE1577|5end_lipoprotein,_putative_1624509..1624739_POSITIVE 195 130 82 53 12 NC_002967:TDE0003|5end_hypothetical_protein_3483..3713_POSITIVE 190 95 56 95 55 NC_002967:TDE2427|5end_preprotein_translocase,_SecE_subunit_2455982..2456212_NEGATIVE 188 130 83 80 39 NC_002967:TDE0116|5end_hypothetical_protein_134709..134939_POSITIVE 187 124 84 192 152 NC_002967:TDE2200|5end_methionine_gamma-lyase_2238455..2238685_NEGATIVE 187 129 86 106 61 NC_002967:TDE1446|5end_hypothetical_protein_1491970..1492200_POSITIVE 186 109 84 47 23 NC_002967:TDE2587|5end_endonuclease/exonuclease/phosphatase_family_protein_2622191..2622421_POSITIVE 186 116 72 71 38 NC_002967:TDE2287|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2325058..2325288_NEGATIVE 185 123 81 188 138 NC_002967:TDE1964|5end_Na/Pi_cotransporter_family_protein_1978780..1979010_NEGATIVE 183 125 87 36 4 NC_002967:TDE2388|5end_ATP-dependent_Clp_protease_proteolytic_subunit_2417737..2417967_POSITIVE 183 130 83 221 164 NC_002967:TDE2375|5end_hypothetical_protein_2406661..2406891_NEGATIVE 183 120 75 55 12 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 182 120 79 191 151 NC_002967:TDE2269|5end_hypothetical_protein_2305920..2306150_NEGATIVE 182 115 72 231 190 NC_002967:TDE0102|5end_cyclic_nucleotide-binding_protein_121175..121405_POSITIVE 181 90 56 52 16 NC_002967:TDE0863|5end_MgtC_family_protein_884526..884756_POSITIVE 179 66 21 90 50 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 178 129 81 218 177 NC_002967:TDE0477|5end_hypothetical_protein_534277..534507_NEGATIVE 177 109 82 64 37 NC_002967:TDE2694|5end_hypothetical_protein_2736301..2736531_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 211 129 83 105 46 NC_002967:TDE0175|3end_pyrrolidone-carboxylate_peptidase_208129..208279_NEGATIVE 210 115 74 56 12 NC_002967:TDE0315|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_348802..348952_POSITIVE 188 130 83 72 31 NC_002967:TDE0115|3end_hypothetical_protein_134781..134931_POSITIVE 187 100 59 44 1 NC_002967:TDE1896|3end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1915904..1916054_NEGATIVE 187 129 89 60 24 NC_002967:TDE0385|3end_ABC_transporter,_ATP-binding/permease_protein_437287..437437_POSITIVE 186 123 85 84 49 NC_002967:TDE0118|3end_hypothetical_protein_136574..136724_NEGATIVE 185 123 81 73 23 NC_002967:TDE1965|3end_sodium/hydrogen_exchanger_family_protein_1978895..1979045_NEGATIVE 183 120 75 55 12 NC_002967:TDE0409|3end_hypothetical_protein_462133..462283_POSITIVE 181 89 56 44 5 NC_002967:TDE2539|3end_hypothetical_protein_2564274..2564424_NEGATIVE 181 111 76 62 27 NC_002967:TDE0319|3end_hypothetical_protein_352547..352697_POSITIVE 177 100 63 104 72 NC_002967:TDE2045|3end_hypothetical_protein_2074613..2074763_NEGATIVE 177 129 81 64 18 NC_002967:TDE1494|3end_chemotaxis_protein_CheY_1539596..1539746_POSITIVE 177 114 79 85 47 NC_002967:TDE1302|3end_hemerythrin_family_protein_1339213..1339363_NEGATIVE 177 119 77 73 25 NC_002967:TDE1224|3end_zinc_ABC_transporter,_permease_protein_1257840..1257990_NEGATIVE 174 46 2 68 13 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 174 130 81 117 74 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 173 130 83 115 67 NC_002967:TDE0580|3end_hypothetical_protein_616716..616866_POSITIVE 171 103 63 70 27 NC_002967:TDE0335|3end_ribonucleotide-diphosphate_reductase_beta_subunit_374120..374270_NEGATIVE 170 97 54 62 17 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 166 34 1 142 106 NC_002967:TDE2655|3end_hypothetical_protein_2692963..2693113_NEGATIVE