Origin IGS: atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaaaaagtataattgataaaataaaaattatcaagtaatattgatataagacataattcatgctataattatttgtttaatttgttttattcaattatggtaattatacatttaattttgcggaggtaaggat Mask Tandem Repeat Region ================================================ atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Find is-nt database================================================ Query_seq: TDE0824:TDE0825|TDE0824:TDE0825:lipoprotein, putative:UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase, putative:<-->:845967..846101 135 atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0824:TDE0825|TDE0824:TDE0825:lipoprotein, putative:UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase, putative:<-->:845967..846101 135 atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0824:TDE0825|TDE0824:TDE0825:lipoprotein, putative:UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase, putative:<-->:845967..846101 135 atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Predict ORF larger than 30AA ================================================ atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat 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: 65 End: 94 ................................................................ATTGATATAAGACATAATTCATGCTATAAT......................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 99 End: 128 ..................................................................................................CTTGATAATTTTTATTTTATCAATTATACT....... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 93 End: 122 ............................................................................................ATTGATAAAATAAAAATTATCAAGTAATAT............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.8 Tail_Score: -3.91317 Start: 88 End: 105 Full_Region: ATGAATTATGTCTTA TATCAA TATTAC TTGATA ATTTTTATTTTATCA .......................................................................................TATCAATATTACTTGATA.............................. Find igs database================================================ Query_seq: TDE0824:TDE0825|TDE0824:TDE0825:lipoprotein, putative:UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase, putative:<-->:845967..846101 135 atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_002967_TDE0824_TDE0825|lipoprotein, putative:UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase, putative|NEGATIVE:POSITIVE|[845967,846101]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat atccttacctccgcaaaattaaatgtataattaccataattgaataaaacaaattaaacaaataattatagcatgaattatgtcttatatcaatattacttgataatttttattttatcaattatactttttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUUACCUCCGCAAAAUUAAAUGUAUAAUUACCAUAAUUGAAUAAAACAAAUUAAACAAAUAAUUAUAGCAUGAAUUAUGUCUUAUAUCAAUAUUACUUGAUAAUUUUUAUUUUAUCAAUUAUACUUUUUAAU .................((((((.((((((((..(((((((.(........(((((......)))))......).))))))).....((((((......))))))..............))))))))..)))))) (-13.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAAAGUAUAAUUGAUAAAAUAAAAAUUAUCAAGUAAUAUUGAUAUAAGACAUAAUUCAUGCUAUAAUUAUUUGUUUAAUUUGUUUUAUUCAAUUAUGGUAAUUAUACAUUUAAUUUUGCGGAGGUAAGGAU .......(.((((((((((((((((((...((((((......))))))..((((((((((........)))))..)))))..))))))))).))))))))).)..............((((((....)))))).. (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 712 50 1 141 92 NC_002967:TDE0824|5end_lipoprotein,_putative_845876..846106_NEGATIVE 225 42 1 170 106 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 189 44 2 145 97 NC_002967:TDE0809|5end_hypothetical_protein_830785..831015_NEGATIVE 183 46 1 100 44 NC_002967:TDE1587|5end_aspartyl-tRNA_synthetase_1634033..1634263_POSITIVE 175 60 11 78 24 NC_002967:TDE0139|5end_hypothetical_protein_162583..162813_NEGATIVE 174 92 52 201 153 NC_002967:TDE0375|5end_ABC_transporter,_ATP-binding_protein_430147..430377_NEGATIVE 172 43 1 152 99 NC_002967:TDE0378|5end_hypothetical_protein_432164..432394_POSITIVE 170 15 1 46 31 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 170 29 4 74 51 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 167 35 2 126 97 NC_002967:TDE2636|5end_hypothetical_protein_2676070..2676300_POSITIVE 165 15 4 227 216 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 163 20 8 112 100 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 163 109 65 211 172 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 163 125 83 73 35 NC_002967:TDE0482|5end_hypothetical_protein_538766..538996_NEGATIVE 159 45 9 138 98 NC_002967:TDE0280|5end_PIN_domain_protein_310296..310526_NEGATIVE 159 16 5 105 94 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 158 49 1 69 11 NC_002967:TDE2188|5end_hypothetical_protein_2223121..2223351_NEGATIVE 158 130 110 158 138 NC_002967:TDE1248|5end_hypothetical_protein_1282596..1282826_POSITIVE 154 25 7 125 101 NC_002967:TDE0168|5end_transcriptional_regulator,_GntR_family_197068..197298_NEGATIVE 153 43 2 144 95 NC_002967:TDE0128|5end_HAMP_domain/GGDEF_domain/EAL_domain_protein_146240..146470_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 189 44 2 118 70 NC_002967:TDE0810|3end_hypothetical_protein_830812..830962_NEGATIVE 175 110 62 52 3 NC_002967:TDE2016|3end_hypothetical_protein_2037824..2037974_NEGATIVE 170 15 1 144 129 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE 159 45 9 141 101 NC_002967:TDE0281|3end_hypothetical_protein_310293..310443_NEGATIVE 155 25 8 135 115 NC_002967:TDE1705|3end_hypothetical_protein_1762155..1762305_POSITIVE 154 25 7 59 35 NC_002967:TDE0169|3end_methyl-accepting_chemotaxis_domain_protein_197134..197284_NEGATIVE 153 110 65 92 52 NC_002967:TDE2215|3end_galactoside_ABC_transporter,_permease_protein,_putative_2253441..2253591_NEGATIVE 152 38 5 54 19 NC_002967:TDE2277|3end_transcriptional_regulator,_Sir2_family_2313515..2313665_POSITIVE 152 36 6 106 77 NC_002967:TDE0752|3end_hypothetical_protein_793262..793412_POSITIVE 150 15 5 115 105 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 150 15 1 75 64 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 148 24 8 57 40 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 148 42 1 107 60 NC_002967:TDE0058|3end_hypothetical_protein_67398..67548_POSITIVE 147 126 81 148 100 NC_002967:TDE2414|3end_hypothetical_protein_2441021..2441171_NEGATIVE 147 77 34 61 18 NC_002967:TDE0028|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_34056..34206_NEGATIVE 146 28 5 52 28 NC_002967:TDE1886|3end_MiaB-like_tRNA_modifying_enzyme_1907082..1907232_NEGATIVE 146 23 7 47 30 NC_002967:TDE1071|3end_peptide_ABC_transporter,_peptide-binding_protein_OppA_1098813..1098963_NEGATIVE 145 39 2 100 64 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 144 130 85 99 60 NC_002967:TDE1054|3end_methyl-accepting_chemotaxis_protein_1082998..1083148_POSITIVE 141 100 59 116 73 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE