Origin IGS: aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatgaacctgcaaaactttttccatttaattatcggcaaaaaagcggaatttattcactcttttcggatagaattataataaaaaacaaaaaaaattgcaaggtaataggcaaccttaaaccttttaaactgtctaaatagtt Mask Tandem Repeat Region ================================================ aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Find is-nt database================================================ Query_seq: TDE2317:TDE2318|TDE2317:TDE2318:hemolysin III:LysM domain/M23/M37 peptidase domain protein:<-->:2354862..2355004 143 aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2317:TDE2318|TDE2317:TDE2318:hemolysin III:LysM domain/M23/M37 peptidase domain protein:<-->:2354862..2355004 143 aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2317:TDE2318|TDE2317:TDE2318:hemolysin III:LysM domain/M23/M37 peptidase domain protein:<-->:2354862..2355004 143 aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 6 End: 95 ..... * K S L K F P K L N G I V K C N K K N K I I I R D S F L S Y M ................................................ aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata 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: 42 End: 71 .........................................CTTGCAATTTTTTTTGTTTTTTATTATAAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2317:TDE2318|TDE2317:TDE2318:hemolysin III:LysM domain/M23/M37 peptidase domain protein:<-->:2354862..2355004 143 aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaattttttttgttttttattataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: NC_002967_TDE2317_TDE2318|hemolysin III:LysM domain/M23/M37 peptidase domain protein|NEGATIVE:POSITIVE|[2354862,2355004]|143 HSP 1 e-value: 3.0E-38 bit: 159.0 Len: 80 Query Start:64 Query End:143 Subject Strand: POSITIVE Subject Start: 64 Subject End: 143 ...............................................................attataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata ...............................................................attataattctatccgaaaagagtgaataaattccgcttttttgccgataattaaatggaaaaagttttgcaggttcata HSP 2 e-value: 4.0E-19 bit: 95.6 Len: 48 Query Start:1 Query End:48 Subject Strand: POSITIVE Subject Start: 1 Subject End: 48 aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaa............................................................................................... aactatttagacagtttaaaaggtttaaggttgcctattaccttgcaa............................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAUUUAGACAGUUUAAAAGGUUUAAGGUUGCCUAUUACCUUGCAAUUUUUUUUGUUUUUUAUUAUAAUUCUAUCCGAAAAGAGUGAAUAAAUUCCGCUUUUUUGCCGAUAAUUAAAUGGAAAAAGUUUUGCAGGUUCAUA ((((....((((.....((((((((((((((........)))))).))))))))...(((((((((.((((..((((.((((((((((.........))))))))).).))))))))))))))))).))))....)))).... (-24.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAACCUGCAAAACUUUUUCCAUUUAAUUAUCGGCAAAAAAGCGGAAUUUAUUCACUCUUUUCGGAUAGAAUUAUAAUAAAAAACAAAAAAAAUUGCAAGGUAAUAGGCAACCUUAAACCUUUUAAACUGUCUAAAUAGUU .....((((((((...................((.((......)).)).(((((((.........))))))).......................)))).))))..((((((...((((.....))))..))))))....... (-19.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 766 140 91 231 182 NC_002967:TDE2317|5end_hemolysin_III_2354771..2355001_NEGATIVE 298 140 94 150 102 NC_002967:TDE0230|5end_DNA_replication_and_repair_protein_RecF_263881..264111_NEGATIVE 267 112 95 20 3 NC_002967:TDE0420|5end_hypothetical_protein_472218..472448_POSITIVE 256 111 71 46 9 NC_002967:TDE2478|5end_excinuclease_ABC,_C_subunit_2500873..2501103_POSITIVE 248 137 95 51 5 NC_002967:TDE2287|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2325058..2325288_NEGATIVE 247 57 11 165 113 NC_002967:TDE0391|5end_hypothetical_protein_441849..442079_NEGATIVE 243 105 61 50 6 NC_002967:TDE0374|5end_glycosyl_transferase,_group_1_family_protein_429200..429430_NEGATIVE 242 110 61 66 20 NC_002967:TDE1545|5end_phosphoribosyl_transferase_domain_protein_1588330..1588560_POSITIVE 237 139 96 222 170 NC_002967:TDE1195|5end_prolyl_endopeptidase_1229691..1229921_NEGATIVE 233 77 34 230 188 NC_002967:TDE0028|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_35930..36160_NEGATIVE 229 58 20 203 169 NC_002967:TDE2608|5end_hypothetical_protein_2649275..2649505_POSITIVE 228 130 83 190 138 NC_002967:TDE2573|5end_glucose-6-phosphate_isomerase_2598802..2599032_POSITIVE 227 139 91 143 94 NC_002967:TDE0110|5end_M23/M37_peptidase_domain_protein_130581..130811_POSITIVE 226 110 75 42 1 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 226 60 11 219 181 NC_002967:TDE2560|5end_hypothetical_protein_2587311..2587541_POSITIVE 225 123 81 198 146 NC_002967:TDE1239|5end_hypothetical_protein_1271363..1271593_NEGATIVE 224 80 34 157 101 NC_002967:TDE2654|5end_macrolide_efflux_protein,_putative_2691675..2691905_POSITIVE 224 107 69 56 18 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 223 109 61 69 24 NC_002967:TDE1413|5end_cytidylyltransferase/phosphoenolpyruvate_phosphomutase,_putative_1455510..1455740_POSITIVE 223 140 99 198 153 NC_002967:TDE0671|5end_PIN_domain_protein_710621..710851_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 140 94 141 93 NC_002967:TDE0231|3end_DNA_polymerase_III,_beta_subunit_263890..264040_NEGATIVE 285 114 78 39 1 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 256 111 71 42 5 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 252 139 97 67 19 NC_002967:TDE2513|3end_glucose-inhibited_division_protein_B_2539888..2540038_POSITIVE 243 105 61 53 9 NC_002967:TDE0375|3end_ABC_transporter,_ATP-binding_protein_429197..429347_NEGATIVE 237 139 96 122 70 NC_002967:TDE1196|3end_hypothetical_protein_1229791..1229941_NEGATIVE 233 47 21 130 104 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE 231 47 1 81 32 NC_002967:TDE1862|3end_hypothetical_protein_1887979..1888129_POSITIVE 230 63 26 146 104 NC_002967:TDE2706|3end_hypothetical_protein_2751916..2752066_NEGATIVE 224 80 34 146 90 NC_002967:TDE2653|3end_hypothetical_protein_2691744..2691894_POSITIVE 224 107 69 86 48 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 217 110 75 149 111 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 216 112 71 37 2 NC_002967:TDE0674|3end_hypothetical_protein_714077..714227_POSITIVE 214 67 21 58 13 NC_002967:TDE2686|3end_flagellar_biosynthetic_protein_FlhF_2725785..2725935_NEGATIVE 213 110 61 142 84 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 213 135 97 49 4 NC_002967:TDE0146|3end_amidohydrolase_family_protein_167435..167585_NEGATIVE 211 139 97 86 47 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 211 137 99 151 113 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 210 140 95 124 77 NC_002967:TDE0238|3end_thioredoxin,_selenocysteine-containing_271783..271933_POSITIVE 208 110 74 133 92 NC_002967:TDE1289|3end_hypothetical_protein_1327510..1327660_POSITIVE