Origin IGS: ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat .........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 attaaaaggaaaccgtaaagaacgctaaggaaaattcggaaatggagcataaattcaacgctttgtatctttgtggataaataataaataaaatttaattttttaaaattttactatttattgcaaactcttcatacaataattatgaaaggggaggatttttctcttttaaataattttattggagttttat Mask Tandem Repeat Region ================================================ ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Find is-nt database================================================ Query_seq: TDE0049:TDE0050|TDE0049:TDE0050:hypothetical protein:RNA methyltransferase, TrmH family:<-<-:59180..59372 193 ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0049:TDE0050|TDE0049:TDE0050:hypothetical protein:RNA methyltransferase, TrmH family:<-<-:59180..59372 193 ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0049:TDE0050|TDE0049:TDE0050:hypothetical protein:RNA methyltransferase, TrmH family:<-<-:59180..59372 193 ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 100 End: 189 ................................................................................................... M L F I I Y P Q R Y K A L N L C S I S E F S L A F F T V S F * .... Protein_Len: 35 Strand: - Start: 2 End: 106 . L V G I F N N L L S F D E G K M I I T H L T Q L L Y Y F K L F N F K M ....................................................................................... ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat 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================================================ ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0049:TDE0050|TDE0049:TDE0050:hypothetical protein:RNA methyltransferase, TrmH family:<-<-:59180..59372 193 ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagtaaaattttaaaaaattaaattttatttattatttatccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Intra-Species Hit: Count: 1 Min: 1 Max: 193 Len: 193 Subject: NC_002967_TDE0049_TDE0050|hypothetical protein:RNA methyltransferase, TrmH family|NEGATIVE:NEGATIVE|[59180,59372]|193 HSP 1 e-value: 1.0E-38 bit: 161.0 Len: 81 Query Start:1 Query End:81 Subject Strand: POSITIVE Subject Start: 1 Subject End: 81 ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagt................................................................................................................ ataaaactccaataaaattatttaaaagagaaaaatcctcccctttcataattattgtatgaagagtttgcaataaatagt................................................................................................................ HSP 2 e-value: 1.0E-35 bit: 151.0 Len: 76 Query Start:118 Query End:193 Subject Strand: POSITIVE Subject Start: 118 Subject End: 193 .....................................................................................................................ccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat .....................................................................................................................ccacaaagatacaaagcgttgaatttatgctccatttccgaattttccttagcgttctttacggtttccttttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAACUCCAAUAAAAUUAUUUAAAAGAGAAAAAUCCUCCCCUUUCAUAAUUAUUGUAUGAAGAGUUUGCAAUAAAUAGUAAAAUUUUAAAAAAUUAAAUUUUAUUUAUUAUUUAUCCACAAAGAUACAAAGCGUUGAAUUUAUGCUCCAUUUCCGAAUUUUCCUUAGCGUUCUUUACGGUUUCCUUUUAAU .....................(((((((.((((...((.......(((((.......)))))((((..(((.((((((((((((..(((((....))))).....)))))))))))).......((.....(((((.......))))).....)).............)))..))))..))))))))))))). (-23.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAAGGAAACCGUAAAGAACGCUAAGGAAAAUUCGGAAAUGGAGCAUAAAUUCAACGCUUUGUAUCUUUGUGGAUAAAUAAUAAAUAAAAUUUAAUUUUUUAAAAUUUUACUAUUUAUUGCAAACUCUUCAUACAAUAAUUAUGAAAGGGGAGGAUUUUUCUCUUUUAAAUAAUUUUAUUGGAGUUUUAU .(((((((.....(((.....)))...((((((((((.((.(..((((...........))))..).)).(((..(.((((((.((((.....(((((....)))))..)))).)))))))..))).(((((((((.......)))).)))))..)))))))))))))))))..................... (-30.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 737 80 31 171 122 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 655 89 41 181 133 NC_002967:TDE2136|5end_hypothetical_protein_2165659..2165889_NEGATIVE 555 90 41 184 134 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 531 88 41 185 137 NC_002967:TDE0403|5end_hypothetical_protein_454433..454663_POSITIVE 466 88 41 181 134 NC_002967:TDE2719|5end_hypothetical_protein_2776045..2776275_POSITIVE 441 88 42 184 138 NC_002967:TDE1976|5end_hypothetical_protein_1989115..1989345_POSITIVE 429 59 16 152 108 NC_002967:TDE1691|5end_hypothetical_protein_1748273..1748503_NEGATIVE 405 90 41 184 135 NC_002967:TDE0862|5end_hypothetical_protein_883192..883422_POSITIVE 405 59 14 154 107 NC_002967:TDE0007|5end_hypothetical_protein_9874..10104_POSITIVE 378 59 14 153 105 NC_002967:TDE2707|5end_hypothetical_protein_2753947..2754177_POSITIVE 345 66 25 157 118 NC_002967:TDE1344|5end_hypothetical_protein_1382392..1382622_POSITIVE 338 88 41 179 132 NC_002967:TDE0669|5end_hypothetical_protein_707827..708057_NEGATIVE 318 160 111 121 70 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 318 160 111 197 146 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 305 181 145 205 165 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 297 88 41 182 134 NC_002967:TDE0165|5end_hypothetical_protein_194122..194352_POSITIVE 293 189 149 65 27 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 282 189 148 129 83 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 272 174 131 148 109 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 269 186 141 138 87 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 88 44 45 1 NC_002967:TDE1975|3end_hypothetical_protein_1989056..1989206_POSITIVE 293 189 149 68 30 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 282 189 148 126 80 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 272 174 131 145 106 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 271 190 141 124 72 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 269 186 141 141 90 NC_002967:TDE0273|3end_ABC_transporter,_ATP-binding/permease_protein_302867..303017_NEGATIVE 260 185 147 123 79 NC_002967:TDE1690|3end_hypothetical_protein_1746583..1746733_NEGATIVE 259 119 76 100 54 NC_002967:TDE2237|3end_hypothetical_protein_2276298..2276448_NEGATIVE 256 189 144 108 56 NC_002967:TDE0896|3end_ABC_transporter,_ATP-binding/permease_protein_914193..914343_POSITIVE 253 180 140 132 89 NC_002967:TDE2177|3end_hypothetical_protein_2206300..2206450_NEGATIVE 250 178 131 109 56 NC_002967:TDE1041|3end_polyribonucleotide_nucleotidyltransferase_1070500..1070650_POSITIVE 249 178 131 125 79 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 248 180 133 59 11 NC_002967:TDE2767|3end_flagellar_protein-related_protein_2820896..2821046_NEGATIVE 248 185 152 35 6 NC_002967:TDE2537|3end_hypothetical_protein_2563858..2564008_POSITIVE 244 181 150 60 30 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE 242 190 161 149 117 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 237 190 146 64 10 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 237 181 143 143 102 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 234 190 149 51 8 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 229 181 152 37 11 NC_002967:TDE2731|3end_TIM-barrel_protein,_putative,_NifR3_family_2788453..2788603_POSITIVE