Origin IGS: tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaactacctgcatctaaaaaaggagactttagaatttgcttatatcgaaatatcaacaccaatggcaccaaccctgactctaacgaaattttatacaaaaaagta Mask Tandem Repeat Region ================================================ tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Find is-nt database================================================ Query_seq: TDE0608:TDE0609|TDE0608:TDE0609:DNA-binding protein, putative:hypothetical protein:<-<-:645258..645365 108 tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0608:TDE0609|TDE0608:TDE0609:DNA-binding protein, putative:hypothetical protein:<-<-:645258..645365 108 tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0608:TDE0609|TDE0608:TDE0609:DNA-binding protein, putative:hypothetical protein:<-<-:645258..645365 108 tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 8 End: 106 ....... M Y K I S L E S G L V P L V L I F R Y K Q I L K S P F L D A G S L .. Protein_Len: 35 Strand: - Start: 3 End: 107 .. K K T Y F K T L T L T P A M P T S I E I Y A F E L T E K K L H L Y N M . tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt 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================================================ tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0608:TDE0609|TDE0608:TDE0609:DNA-binding protein, putative:hypothetical protein:<-<-:645258..645365 108 tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002967_TDE0608_TDE0609|DNA-binding protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[645258,645365]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt tacttttttgtataaaatttcgttagagtcagggttggtgccattggtgttgatatttcgatataagcaaattctaaagtctccttttttagatgcaggtagtttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUUUUUGUAUAAAAUUUCGUUAGAGUCAGGGUUGGUGCCAUUGGUGUUGAUAUUUCGAUAUAAGCAAAUUCUAAAGUCUCCUUUUUUAGAUGCAGGUAGUUUAUU .(((((..((..........))..))))).........((((....(((((((....)))))))..(((...(((((((.......)))))))))).))))....... (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAACUACCUGCAUCUAAAAAAGGAGACUUUAGAAUUUGCUUAUAUCGAAAUAUCAACACCAAUGGCACCAACCCUGACUCUAACGAAAUUUUAUACAAAAAAGUA .....(((....(((......((((....))))......))).......(((((...........((....))........((....)).))))).........))). ( -8.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 70 21 161 112 NC_002967:TDE0608|5end_DNA-binding_protein,_putative_645167..645397_NEGATIVE 291 50 3 161 126 NC_002967:TDE0059|5end_hypothetical_protein_67294..67524_POSITIVE 290 69 22 143 76 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 272 68 21 97 38 NC_002967:TDE1932|5end_hypothetical_protein_1949409..1949639_NEGATIVE 264 67 21 94 49 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 258 53 15 70 32 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 256 68 30 174 135 NC_002967:TDE2433|5end_treponemal_membrane_protein,_putative_2462484..2462714_POSITIVE 255 61 21 222 191 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 251 50 3 161 104 NC_002967:TDE2429|5end_hypothetical_protein_2458037..2458267_NEGATIVE 251 52 29 65 36 NC_002967:TDE0456|5end_pyridoxine_biosynthesis_protein_513384..513614_NEGATIVE 250 52 17 52 14 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 247 69 25 169 120 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 240 44 3 52 9 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 239 89 43 128 74 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 239 54 18 201 148 NC_002967:TDE0213|5end_TPR_domain_protein_249460..249690_NEGATIVE 237 88 43 195 150 NC_002967:TDE1860|5end_hypothetical_protein_1886152..1886382_POSITIVE 230 45 15 230 200 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 230 60 18 230 182 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 228 87 41 53 7 NC_002967:TDE0250|5end_sodium-dependent_transporter,_putative_284635..284865_NEGATIVE 223 56 20 55 13 NC_002967:TDE0349|5end_phosphoenolpyruvate_synthase,_putative_391093..391323_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 49 2 106 51 NC_002967:TDE2318|3end_LysM_domain/M23/M37_peptidase_domain_protein_2355868..2356018_POSITIVE 264 67 21 90 45 NC_002967:TDE0123|3end_hypothetical_protein_141543..141693_NEGATIVE 258 53 15 57 19 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 250 52 17 144 106 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 247 69 25 84 35 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 245 51 21 144 120 NC_002967:TDE1999|3end_DNA_polymerase_III_domain_protein_2017796..2017946_POSITIVE 240 46 1 67 11 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 235 62 31 126 97 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 232 79 40 55 19 NC_002967:TDE0117|3end_lipoprotein,_putative_136607..136757_POSITIVE 230 52 22 151 104 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 229 50 2 69 20 NC_002967:TDE0561|3end_hypothetical_protein_594723..594873_POSITIVE 229 65 21 101 59 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 224 52 20 32 3 NC_002967:TDE2143|3end_penicillin-binding_protein_2180484..2180634_POSITIVE 221 76 35 76 46 NC_002967:TDE0936|3end_hypothetical_protein_959872..960022_NEGATIVE 221 75 40 71 36 NC_002967:TDE0523|3end_hypothetical_protein_569238..569388_NEGATIVE 221 60 18 42 8 NC_002967:TDE0148|3end_histidine_kinase-related_ATPase,_putative_169920..170070_POSITIVE 221 60 18 142 99 NC_002967:TDE0042|3end_phosphate_acetyltransferase_49763..49913_POSITIVE 215 47 3 112 69 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 215 46 10 76 29 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 213 49 1 111 66 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE