Origin IGS: atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa .........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 tttaaactcctcttctgactataccataattaaataataaaaagtacagattaaaattccaaaaattaaaggtattgtcttttttttatcggctttttaaaccaaattatttagcacacaaccgacacaatattatacaataagtaagattttttgtaaagtgctaaaaaattatataatccgaattgtgtacaaagaattgaaaatgtgctataatcccttatctttttagatgaatttcggagtaaat Mask Tandem Repeat Region ================================================ atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Find is-nt database================================================ Query_seq: TDE0109:TDE0110|TDE0109:TDE0110:phenylalanyl-tRNA synthetase alpha subunit:M23/M37 peptidase domain protein:<-->:130471..130720 250 atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0109:TDE0110|TDE0109:TDE0110:phenylalanyl-tRNA synthetase alpha subunit:M23/M37 peptidase domain protein:<-->:130471..130720 250 atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0109:TDE0110|TDE0109:TDE0110:phenylalanyl-tRNA synthetase alpha subunit:M23/M37 peptidase domain protein:<-->:130471..130720 250 atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 27 End: 137 .......................... M R D Y S T F S I L C T Q F G L Y N F L A L Y K K S Y L L Y N I V S V V C ................................................................................................................. Protein_Len: 30 Strand: - Start: 22 End: 111 ..................... F S L P N Y C M K L E K Y V I R I I Y N K L V K C F I K S M ........................................................................................................................................... atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa 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: 90 End: 119 .........................................................................................CTTTACAAAAAATCTTACTTATTGTATAAT................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 188 End: 217 ...........................................................................................................................................................................................TTTGGAATTTTAATCTGTACTTTTTATTAT................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 34 End: 63 .................................GTGTACAAAGAATTGAAAATGTGCTATAAT........................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0109:TDE0110|TDE0109:TDE0110:phenylalanyl-tRNA synthetase alpha subunit:M23/M37 peptidase domain protein:<-->:130471..130720 250 atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: NC_002967_TDE0109_TDE0110|phenylalanyl-tRNA synthetase alpha subunit:M23/M37 peptidase domain protein|NEGATIVE:POSITIVE|[130471,130720]|250 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgatnnnnnnnngacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa atttactccgaaattcatctaaaaagataagggattatagcacattttcaattctttgtacacaattcggattatataattttttagcactttacaaaaaatcttacttattgtataatattgtgtcggttgtgtgctaaataatttggtttaaaaagccgataaaaaaaagacaatacctttaatttttggaattttaatctgtactttttattatttaattatggtatagtcagaagaggagtttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACUCCGAAAUUCAUCUAAAAAGAUAAGGGAUUAUAGCACAUUUUCAAUUCUUUGUACACAAUUCGGAUUAUAUAAUUUUUUAGCACUUUACAAAAAAUCUUACUUAUUGUAUAAUAUUGUGUCGGUUGUGUGCUAAAUAAUUUGGUUUAAAAAGCCGAUAAAAAAAAGACAAUACCUUUAAUUUUUGGAAUUUUAAUCUGUACUUUUUAUUAUUUAAUUAUGGUAUAGUCAGAAGAGGAGUUUAAA ....(((((........((((((((..((((((....((((((((..........(((.(((((((....((((((((((.....((...(((....)))..)).....))))))))))))))))))))..))))))))......((((((.....))))))................)))))).)))))))).......((((.(((...((((((......)))))).)))))))...)))))..... (-51.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAACUCCUCUUCUGACUAUACCAUAAUUAAAUAAUAAAAAGUACAGAUUAAAAUUCCAAAAAUUAAAGGUAUUGUCUUUUUUUUAUCGGCUUUUUAAACCAAAUUAUUUAGCACACAACCGACACAAUAUUAUACAAUAAGUAAGAUUUUUUGUAAAGUGCUAAAAAAUUAUAUAAUCCGAAUUGUGUACAAAGAAUUGAAAAUGUGCUAUAAUCCCUUAUCUUUUUAGAUGAAUUUCGGAGUAAAU .....(((((................................((((((..((((((..((..(((..(((((.....)))))..)))...))..))))))..(((....((((((((.......(((.((.(((.(((.....))).))).)).)))...))))))))....((((((((....)))))))).......)))....))))))........((((((....)))))).....))))).... (-38.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 70 21 161 112 NC_002967:TDE0109|5end_phenylalanyl-tRNA_synthetase_alpha_subunit_130380..130610_NEGATIVE 258 164 121 209 170 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 255 167 121 75 29 NC_002967:TDE0358|5end_cinnamoyl_ester_hydrolase_401638..401868_NEGATIVE 253 199 157 90 41 NC_002967:TDE0190|5end_hypothetical_protein_227366..227596_NEGATIVE 230 166 123 165 129 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 228 161 122 77 45 NC_002967:TDE0792|5end_ribosomal_protein_L17_818387..818617_POSITIVE 225 150 105 139 92 NC_002967:TDE0608|5end_DNA-binding_protein,_putative_645167..645397_NEGATIVE 223 161 128 144 117 NC_002967:TDE0959|5end_hypothetical_protein_981935..982165_POSITIVE 216 161 124 35 1 NC_002967:TDE0430|5end_TPR_domain_protein_486455..486685_NEGATIVE 214 70 26 167 130 NC_002967:TDE1542|5end_hypothetical_protein_1585857..1586087_POSITIVE 214 152 122 214 182 NC_002967:TDE1123|5end_sigma_factor_regulatory_protein,_putative_1155422..1155652_NEGATIVE 214 160 116 49 1 NC_002967:TDE1038|5end_hypothetical_protein_1066976..1067206_NEGATIVE 213 164 121 83 46 NC_002967:TDE2045|5end_hypothetical_protein_2074933..2075163_NEGATIVE 213 247 201 211 157 NC_002967:TDE0494|5end_hypothetical_protein_550515..550745_NEGATIVE 212 163 121 180 126 NC_002967:TDE0567|5end_hypothetical_protein_597853..598083_POSITIVE 210 160 111 78 19 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 209 141 103 208 172 NC_002967:TDE2003|5end_internalin-related_protein_2022277..2022507_POSITIVE 208 139 102 222 180 NC_002967:TDE2071|5end_hypothetical_protein_2098241..2098471_POSITIVE 207 50 6 129 97 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 204 133 97 37 6 NC_002967:TDE0529|5end_hypothetical_protein_573801..574031_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 199 157 78 29 NC_002967:TDE0191|3end_acetyltransferase,_GNAT_family_227378..227528_NEGATIVE 246 199 155 101 49 NC_002967:TDE1988|3end_hypothetical_protein_2005590..2005740_POSITIVE 234 149 106 150 105 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE 231 168 125 50 2 NC_002967:TDE0238|3end_thioredoxin,_selenocysteine-containing_271783..271933_POSITIVE 230 166 123 80 44 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 228 161 122 87 55 NC_002967:TDE0791|3end_DNA-directed_RNA_polymerase_alpha_subunit_818477..818627_POSITIVE 218 165 124 67 19 NC_002967:TDE0043|3end_TPR_domain_protein_51651..51801_POSITIVE 214 152 122 140 108 NC_002967:TDE1124|3end_hypothetical_protein_1155496..1155646_NEGATIVE 208 139 102 113 71 NC_002967:TDE2070|3end_hypothetical_protein_2098212..2098362_POSITIVE 204 205 169 139 103 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE 204 133 97 35 4 NC_002967:TDE0528|3end_hypothetical_protein_573879..574029_POSITIVE 204 50 1 128 73 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 203 159 117 74 31 NC_002967:TDE2565|3end_hypothetical_protein_2590392..2590542_NEGATIVE 194 130 82 87 29 NC_002967:TDE1033|3end_polyA_polymerase_family_protein_1062495..1062645_POSITIVE 193 136 101 118 86 NC_002967:TDE2764|3end_flagellar_protein_2818786..2818936_NEGATIVE 184 248 205 61 21 NC_002967:TDE2415|3end_hypothetical_protein_2441713..2441863_NEGATIVE 184 138 107 89 57 NC_002967:TDE2010|3end_hypothetical_protein_2031913..2032063_POSITIVE 184 70 23 58 3 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 183 137 120 147 128 NC_002967:TDE0881|3end_ribosomal_protein_S16_901492..901642_POSITIVE 183 137 100 82 41 NC_002967:TDE0290|3end_hypothetical_protein_320699..320849_NEGATIVE