Origin IGS: ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgaggttaatatgttttttgtaaatgatttatacttattgtctaattatgtgcagaaggttggatagataaacaatgaatttgtgcaaataaaatatagaaaataaattttatgtaataaggctcaaagataataaattattggtatataataaaataaaggaaaaagaaacggtgtatatatgtagaaataaaacttttttagacaatgtggtataaccccgagctattgctaatgattttgttatggatattttaagatttaaaaaacaagaatgagag Mask Tandem Repeat Region ================================================ ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Find is-nt database================================================ Query_seq: TDE2022:TDE2023|TDE2022:TDE2023:YD repeat protein:TPR domain protein:<-<-:2049313..2049594 282 ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2022:TDE2023|TDE2022:TDE2023:YD repeat protein:TPR domain protein:<-<-:2049313..2049594 282 ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2022:TDE2023|TDE2022:TDE2023:YD repeat protein:TPR domain protein:<-<-:2049313..2049594 282 ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 66 End: 155 ................................................................. M P H C L K K F Y F Y I Y T P F L F P L F Y Y I P I I Y Y L ............................................................................................................................... Protein_Len: 47 Strand: + Start: 29 End: 169 ............................ M S I T K S L A I A R G Y T T L S K K V L F L H I Y T V S F S F I L L Y T N N L L S L S L I T ................................................................................................................. Protein_Len: 30 Strand: + Start: 148 End: 237 ................................................................................................................................................... M I F E P Y Y I K F I F Y I L F A Q I H C L S I Q P S A H N ............................................. Protein_Len: 40 Strand: - Start: 67 End: 186 .................................................................. V V N D L F T K N R C I Y V T E K E K I K N Y V L L K N D K L R I V Y F K N E M ................................................................................................ ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa 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================================================ ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2022:TDE2023|TDE2022:TDE2023:YD repeat protein:TPR domain protein:<-<-:2049313..2049594 282 ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaagttttatttctacatatatacaccgtttctttttcctttattttattatataccaataatttattatctttgagccttattacataaaatttattttctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa Intra-Species Hit: Count: 1 Min: 1 Max: 282 Len: 282 Subject: NC_002967_TDE2022_TDE2023|YD repeat protein:TPR domain protein|NEGATIVE:NEGATIVE|[2049313,2049594]|282 HSP 1 e-value: 7.0E-50 bit: 198.0 Len: 100 Query Start:183 Query End:282 Subject Strand: POSITIVE Subject Start: 183 Subject End: 282 ......................................................................................................................................................................................ctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa ......................................................................................................................................................................................ctatattttatttgcacaaattcattgtttatctatccaaccttctgcacataattagacaataagtataaatcatttacaaaaaacatattaacctcaa HSP 2 e-value: 2.0E-41 bit: 170.0 Len: 86 Query Start:1 Query End:86 Subject Strand: POSITIVE Subject Start: 1 Subject End: 86 ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaag.................................................................................................................................................................................................... ctctcattcttgttttttaaatcttaaaatatccataacaaaatcattagcaatagctcggggttataccacattgtctaaaaaag.................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCAUUCUUGUUUUUUAAAUCUUAAAAUAUCCAUAACAAAAUCAUUAGCAAUAGCUCGGGGUUAUACCACAUUGUCUAAAAAAGUUUUAUUUCUACAUAUAUACACCGUUUCUUUUUCCUUUAUUUUAUUAUAUACCAAUAAUUUAUUAUCUUUGAGCCUUAUUACAUAAAAUUUAUUUUCUAUAUUUUAUUUGCACAAAUUCAUUGUUUAUCUAUCCAACCUUCUGCACAUAAUUAGACAAUAAGUAUAAAUCAUUUACAAAAAACAUAUUAACCUCAA ..........((((((((..............................(((....)))..(..((((((...(((((((((..(((((((((.......((((((..........................))))))..(((((....(((....)))...)))))..)))))))))............((((.((((.............................)))).)))))))))))))..))))))..)......))))))))............ (-24.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGGUUAAUAUGUUUUUUGUAAAUGAUUUAUACUUAUUGUCUAAUUAUGUGCAGAAGGUUGGAUAGAUAAACAAUGAAUUUGUGCAAAUAAAAUAUAGAAAAUAAAUUUUAUGUAAUAAGGCUCAAAGAUAAUAAAUUAUUGGUAUAUAAUAAAAUAAAGGAAAAAGAAACGGUGUAUAUAUGUAGAAAUAAAACUUUUUUAGACAAUGUGGUAUAACCCCGAGCUAUUGCUAAUGAUUUUGUUAUGGAUAUUUUAAGAUUUAAAAAACAAGAAUGAGAG ............(((((((((..((((((((((.(((...((((.....((..((((..((((..........))))...))))..))......((((((((......))))))))....))))...)))...))))))))))....(((((((((((...............(((((((((((.((((((.......))))))....)))).)))).)))...(((....)))....)))))))))))..............))))))))).......... (-41.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 80 31 171 122 NC_002967:TDE2022|5end_YD_repeat_protein_2049222..2049452_NEGATIVE 272 230 181 144 87 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 261 70 28 136 83 NC_002967:TDE2282|5end_tRNA_synthetase,_class_II_family_protein_2319665..2319895_NEGATIVE 234 88 50 80 45 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 227 198 152 118 77 NC_002967:TDE0060|5end_hypothetical_protein_67838..68068_NEGATIVE 226 97 51 90 54 NC_002967:TDE2315|5end_conserved_hypothetical_protein_TIGR00044_2352272..2352502_POSITIVE 223 146 112 79 49 NC_002967:TDE2780|5end_hypothetical_protein_2830621..2830851_NEGATIVE 222 125 84 201 161 NC_002967:TDE1860|5end_hypothetical_protein_1886152..1886382_POSITIVE 222 70 21 131 77 NC_002967:TDE0456|5end_pyridoxine_biosynthesis_protein_513384..513614_NEGATIVE 219 79 31 140 86 NC_002967:TDE1026|5end_acyl_carrier_protein_1057302..1057532_POSITIVE 216 229 185 104 53 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 215 249 201 104 37 NC_002967:TDE0513|5end_hypothetical_protein_562241..562471_NEGATIVE 214 232 202 121 86 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 209 239 192 63 26 NC_002967:TDE1670|5end_transcriptional_regulator,_MarR_family_1724461..1724691_NEGATIVE 207 146 108 168 125 NC_002967:TDE1952|5end_hypothetical_protein_1969046..1969276_NEGATIVE 206 197 158 70 41 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 204 100 56 193 137 NC_002967:TDE0176|5end_hypothetical_protein_209798..210028_NEGATIVE 203 95 56 216 169 NC_002967:TDE2601|5end_surface_antigen,_putative_2638490..2638720_POSITIVE 202 242 205 45 7 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 202 156 114 132 96 NC_002967:TDE1386|5end_methyl-accepting_chemotaxis_protein_1424941..1425171_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 70 28 122 69 NC_002967:TDE2283|3end_permease,_putative_2319679..2319829_NEGATIVE 256 160 113 121 77 NC_002967:TDE1156|3end_hypothetical_protein_1191621..1191771_NEGATIVE 243 98 55 75 31 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 228 124 84 136 97 NC_002967:TDE2474|3end_acetyltransferase,_GNAT_family_2496602..2496752_NEGATIVE 227 198 152 58 17 NC_002967:TDE0061|3end_fic_family_protein_67898..68048_NEGATIVE 226 97 51 117 81 NC_002967:TDE2314|3end_hypothetical_protein_2352379..2352529_POSITIVE 223 146 112 61 31 NC_002967:TDE2781|3end_ABC_transporter,_ATP-binding/permease_protein_2830639..2830789_NEGATIVE 219 79 31 127 73 NC_002967:TDE1025|3end_ribosomal_protein_L32_1057369..1057519_POSITIVE 218 99 51 151 96 NC_002967:TDE1753|3end_UDP-glucose_4-epimerase_1805521..1805671_NEGATIVE 214 232 202 128 93 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 206 197 158 61 32 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 205 71 44 114 87 NC_002967:TDE2519|3end_hypothetical_protein_2544839..2544989_NEGATIVE 200 162 122 101 64 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 200 80 32 150 108 NC_002967:TDE1511|3end_pathogen-specific_surface_antigen,_putative_1559194..1559344_POSITIVE 199 68 50 87 67 NC_002967:TDE0705|3end_SPFH_domain/Band_7_family_protein_739339..739489_NEGATIVE 198 228 203 107 82 NC_002967:TDE0771|3end_ribosomal_protein_S19_809153..809303_POSITIVE 196 79 33 126 78 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 195 75 47 117 86 NC_002967:TDE0213|3end_TPR_domain_protein_248318..248468_NEGATIVE 193 77 34 73 29 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 192 225 181 127 89 NC_002967:TDE2366|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399959..2400109_NEGATIVE