Origin IGS: aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atccggatataagtattatgcaactttattgggattttcgttttaaattcattgacaagaacctgttttgcgtttaaaatggttatagatgtctagaagcaattattaaattttgaattttgcaggaggatatt Mask Tandem Repeat Region ================================================ aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Find is-nt database================================================ Query_seq: TDE2281:TDE2282|TDE2281:TDE2282:LysM domain protein:tRNA synthetase, class II family protein:<-<-:2318584..2318717 134 aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2281:TDE2282|TDE2281:TDE2282:LysM domain protein:tRNA synthetase, class II family protein:<-<-:2318584..2318717 134 aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2281:TDE2282|TDE2281:TDE2282:LysM domain protein:tRNA synthetase, class II family protein:<-<-:2318584..2318717 134 aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Predict ORF larger than 30AA ================================================ aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat 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: 90 Start: 55 End: 84 ......................................................ATTGACAAGAACCTGTTTTGCGTTTAAAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2281:TDE2282|TDE2281:TDE2282:LysM domain protein:tRNA synthetase, class II family protein:<-<-:2318584..2318717 134 aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_002967_TDE2281_TDE2282|LysM domain protein:tRNA synthetase, class II family protein|NEGATIVE:NEGATIVE|[2318584,2318717]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat aatatcctcctgcaaaattcaaaatttaataattgcttctagacatctataaccattttaaacgcaaaacaggttcttgtcaatgaatttaaaacgaaaatcccaataaagttgcataatacttatatccggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCCUCCUGCAAAAUUCAAAAUUUAAUAAUUGCUUCUAGACAUCUAUAACCAUUUUAAACGCAAAACAGGUUCUUGUCAAUGAAUUUAAAACGAAAAUCCCAAUAAAGUUGCAUAAUACUUAUAUCCGGAU ..............(((((((.((((....)))).......((((.....((((.((((......))))..))))..))))..))))))).........((((..(((((((........)))).)))..)))) (-13.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCGGAUAUAAGUAUUAUGCAACUUUAUUGGGAUUUUCGUUUUAAAUUCAUUGACAAGAACCUGUUUUGCGUUUAAAAUGGUUAUAGAUGUCUAGAAGCAAUUAUUAAAUUUUGAAUUUUGCAGGAGGAUAUU ((((.((((.((((........)))))))).))))..(((((((((((.((..((((......)))).)).))))))))))).....(((((((....((((..(((........))).))))....))))))) (-25.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 784 80 31 171 122 NC_002967:TDE2281|5end_LysM_domain_protein_2318493..2318723_NEGATIVE 234 106 70 160 124 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 218 45 7 133 97 NC_002967:TDE0117|5end_lipoprotein,_putative_135613..135843_POSITIVE 217 71 32 209 173 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 215 130 83 186 142 NC_002967:TDE1183|5end_ABC_transporter,_ATP-binding_protein_1210612..1210842_POSITIVE 214 114 71 46 1 NC_002967:TDE1425|5end_hypothetical_protein_1467548..1467778_POSITIVE 210 50 5 137 101 NC_002967:TDE2205|5end_enoate_reductase,_putative_2244755..2244985_NEGATIVE 209 109 61 159 112 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 205 74 33 49 11 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 201 118 71 230 179 NC_002967:TDE0874|5end_transcriptional_regulator,_putative_896939..897169_POSITIVE 197 95 54 122 73 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 197 73 33 64 18 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 193 76 33 146 96 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 190 73 36 139 103 NC_002967:TDE0514|5end_hypothetical_protein_562743..562973_NEGATIVE 187 80 31 158 118 NC_002967:TDE1526|5end_hypothetical_protein_1570565..1570795_POSITIVE 185 118 71 119 66 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 184 48 4 139 96 NC_002967:TDE2208|5end_conserved_hypothetical_protein_TIGR00486_2246733..2246963_POSITIVE 184 80 40 117 85 NC_002967:TDE1376|5end_hypothetical_protein_1418586..1418816_POSITIVE 183 48 5 201 166 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 183 80 32 54 15 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 78 32 136 77 NC_002967:TDE1140|3end_hypothetical_protein_1168730..1168880_NEGATIVE 220 86 63 122 102 NC_002967:TDE0330|3end_CRISPR-associated_SAG0897_family_protein_366998..367148_POSITIVE 218 45 7 110 74 NC_002967:TDE0116|3end_hypothetical_protein_135670..135820_POSITIVE 214 114 71 49 4 NC_002967:TDE1424|3end_hypothetical_protein_1467631..1467781_POSITIVE 197 95 54 122 73 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 193 76 33 149 99 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 190 73 36 112 76 NC_002967:TDE0515|3end_hypothetical_protein_562770..562920_NEGATIVE 184 80 40 94 62 NC_002967:TDE1375|3end_pantetheine-phosphate_adenylyltransferase_1418643..1418793_POSITIVE 183 48 5 130 95 NC_002967:TDE2003|3end_internalin-related_protein_2023631..2023781_POSITIVE 183 80 33 136 96 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 181 40 8 82 41 NC_002967:TDE1345|3end_DNA_primase_1385306..1385456_POSITIVE 181 79 32 141 100 NC_002967:TDE0411|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_465095..465245_POSITIVE 180 48 6 105 54 NC_002967:TDE2262|3end_peptidase,_U32_family_2298033..2298183_NEGATIVE 177 50 5 62 12 NC_002967:TDE2590|3end_hypothetical_protein_2626675..2626825_POSITIVE 177 84 41 58 14 NC_002967:TDE1972|3end_hypothetical_protein_1987102..1987252_NEGATIVE 177 80 33 136 96 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 177 38 5 130 97 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE 175 79 32 143 93 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE 175 116 73 62 10 NC_002967:TDE1694|3end_hypothetical_protein_1749223..1749373_NEGATIVE 173 77 31 138 81 NC_002967:TDE2770|3end_flagellar_hook-length_control_protein_FliK_2823044..2823194_NEGATIVE