Origin IGS: atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctgtaattacagtagtatagaagagaatttattttaggagcgttcaaccgctcctcattttatctatcaatattgaataaatattcaatattatttggttttaaagataaacgaatatacatgcgcattatagatgtagaaaggagtagat Mask Tandem Repeat Region ================================================ atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Find is-nt database================================================ Query_seq: TDE0245:TDE0246|TDE0245:TDE0246:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:281034..281185 152 atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0245:TDE0246|TDE0245:TDE0246:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:281034..281185 152 atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0245:TDE0246|TDE0245:TDE0246:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:281034..281185 152 atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 2 End: 121 . R S R E V D I I R M Y I R K D K F G F L I S Y K N L I S L Y F S S R N F A G L M ............................... atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc 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================================================ atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -6.6 Tail_Score: -4.21465 Start: 62 End: 81 Full_Region: cattttatctatcaa tattgaat aaat attcaata ttatttggttttaaa .............................................................tattgaataaatattcaata....................................................................... Find igs database================================================ Query_seq: TDE0245:TDE0246|TDE0245:TDE0246:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:281034..281185 152 atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_002967_TDE0245_TDE0246|ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family|NEGATIVE:NEGATIVE|[281034,281185]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc atctactcctttctacatctataatgcgcatgtatattcgtttatctttaaaaccaaataatattgaatatttattcaatattgatagataaaatgaggagcggttgaacgctcctaaaataaattctcttctatactactgtaattacagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUACUCCUUUCUACAUCUAUAAUGCGCAUGUAUAUUCGUUUAUCUUUAAAACCAAAUAAUAUUGAAUAUUUAUUCAAUAUUGAUAGAUAAAAUGAGGAGCGGUUGAACGCUCCUAAAAUAAAUUCUCUUCUAUACUACUGUAAUUACAGC ..................((.((((..(((.(((((....(((((((...........(((((((((((....)))))))))))..)))))))...(((((((......)))))))................)))))...))).)))).)). (-29.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGUAAUUACAGUAGUAUAGAAGAGAAUUUAUUUUAGGAGCGUUCAACCGCUCCUCAUUUUAUCUAUCAAUAUUGAAUAAAUAUUCAAUAUUAUUUGGUUUUAAAGAUAAACGAAUAUACAUGCGCAUUAUAGAUGUAGAAAGGAGUAGAU .(((((((....((((((((................(((((((......)))))))...((((((((((((((((((((....)))))))))....)))).....)))))))....))))).)))..))))))).................. (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 830 140 91 231 182 NC_002967:TDE0245|5end_ABC_transporter,_ATP-binding/permease_protein_280943..281173_NEGATIVE 272 136 91 205 166 NC_002967:TDE2524|5end_ABC_transporter,_ATP-binding_protein_2550456..2550686_POSITIVE 248 41 6 60 17 NC_002967:TDE0035|5end_acetyltransferase,_GNAT_family_42020..42250_NEGATIVE 243 49 3 61 4 NC_002967:TDE1715|5end_phosphoglycerate_kinase_1770762..1770992_NEGATIVE 241 116 78 93 39 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 234 129 101 230 199 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 233 47 2 140 98 NC_002967:TDE1660|5end_leucine_Rich_Repeat_domain_protein_1715266..1715496_NEGATIVE 226 123 82 72 25 NC_002967:TDE0172|5end_undecaprenyl_pyrophosphate_phosphatase_203136..203366_POSITIVE 223 130 97 159 112 NC_002967:TDE0956|5end_hypothetical_protein_979456..979686_POSITIVE 222 117 82 66 38 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 222 117 82 141 113 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 218 105 75 166 139 NC_002967:TDE0254|5end_hypothetical_protein_288654..288884_POSITIVE 214 136 95 104 58 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 213 118 91 203 172 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 213 143 102 104 62 NC_002967:TDE0129|5end_PyrBI_protein_150299..150529_NEGATIVE 210 145 103 141 78 NC_002967:TDE2681|5end_hypothetical_protein_2721407..2721637_NEGATIVE 210 118 90 186 148 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 209 117 100 15 1 NC_002967:TDE2576|5end_RNA_pseudouridylate_synthase_family_protein_2601672..2601902_POSITIVE 209 140 93 147 106 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 209 148 101 221 178 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 114 77 64 27 NC_002967:TDE0427|3end_hypothetical_protein_484479..484629_POSITIVE 215 114 75 141 107 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 214 136 95 70 24 NC_002967:TDE1513|3end_hypothetical_protein_1560698..1560848_POSITIVE 211 113 97 121 106 NC_002967:TDE0955|3end_LemA_family_protein_979530..979680_POSITIVE 208 146 102 129 72 NC_002967:TDE1285|3end_flagellar_motor_switch_protein_FliG_,_putative_1322071..1322221_POSITIVE 207 130 97 40 6 NC_002967:TDE0679|3end_aminotransferase,_class_V_717573..717723_POSITIVE 207 139 91 76 22 NC_002967:TDE0208|3end_glycerate_kinase_244228..244378_POSITIVE 206 50 9 103 61 NC_002967:TDE1202|3end_cell_division_protein_FtsQ,_putative_1235120..1235270_POSITIVE 205 57 15 79 34 NC_002967:TDE1696|3end_hypothetical_protein_1754020..1754170_NEGATIVE 204 50 2 127 80 NC_002967:TDE1690|3end_hypothetical_protein_1746583..1746733_NEGATIVE 202 115 83 112 82 NC_002967:TDE2655|3end_hypothetical_protein_2692963..2693113_NEGATIVE 201 80 31 103 55 NC_002967:TDE2721|3end_helicase_domain_protein_2777833..2777983_NEGATIVE 199 41 15 67 37 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 199 48 6 49 2 NC_002967:TDE1553|3end_hypothetical_protein_1597098..1597248_POSITIVE 197 45 8 132 90 NC_002967:TDE0663|3end_hypothetical_protein_697840..697990_NEGATIVE 196 113 83 99 60 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 193 45 1 129 88 NC_002967:TDE2555|3end_precorrin-8X_methylmutase_2582316..2582466_POSITIVE 193 49 3 103 38 NC_002967:TDE2428|3end_ribosomal_protein_L33_2456122..2456272_NEGATIVE 193 147 101 78 12 NC_002967:TDE0543|3end_hypothetical_protein_583853..584003_POSITIVE 193 125 95 91 57 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE