Origin IGS: tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt .........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 aaaaactcctaaatagtggtattttataatgcgcagcgagtttatcataatacaagattttttactagatggggtaaaataaaactcaataaaaaaaagtctattgacagtttttttattttttgatagaatcccttccaatatgtacggttgagtccgtatcttcatggaggggccaagatgatttattccttaattactagaagctgcaaattttgccaccctcgtttattttgataacatcggttttgccgatgttttttttttgcatttttgtttttaacaggagtttaaa Mask Tandem Repeat Region ================================================ tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Find is-nt database================================================ Query_seq: TDE0129:TDE0130|TDE0129:TDE0130:PyrBI protein:sodium/dicarboxylate symporter family protein:<-->:150390..150684 295 tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0129:TDE0130|TDE0129:TDE0130:PyrBI protein:sodium/dicarboxylate symporter family protein:<-->:150390..150684 295 tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0129:TDE0130|TDE0129:TDE0130:PyrBI protein:sodium/dicarboxylate symporter family protein:<-->:150390..150684 295 tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 107 End: 295 .......................................................................................................... M N H L G P S M K I R T Q P Y I L E G I L S K N K K T V N R L F F I E F Y F T P S S K K S C I M I N S L R I I K Y H Y L Protein_Len: 37 Strand: - Start: 173 End: 283 ............................................................................................................................................................................ F I F F S D I S K K K N L K I K G W R T F F R T N H Y V R Q A N Y F V V M ............ tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt 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: 164 End: 193 ...................................................................................................................................................................ATTGACAGTTTTTTTATTTTTTGATAGAAT...................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -8.7 Tail_Score: -6.40073 Start: 39 End: 55 Full_Region: cgtttattttgataa catcggt ttt gccgatg ttttttttttgcatt ......................................catcggttttgccgatg................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 48 HP_score: -2.4 Tail_Score: -3.63868 Start: 189 End: 210 Full_Region: AAAATAAAAAAACTG TCAATAGA CTTTTT TTTATTGA GTTTTATTTTACCCC ............................................................................................................................................................................................TCAATAGACTTTTTTTTATTGA..................................................................................... Find igs database================================================ Query_seq: TDE0129:TDE0130|TDE0129:TDE0130:PyrBI protein:sodium/dicarboxylate symporter family protein:<-->:150390..150684 295 tttaaactcctgttaaaaacaaaaatgcaaaaaaaaaacatcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatcaaaaaataaaaaaactgtcaatagacttttttttattgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Intra-Species Hit: Count: 1 Min: 39 Max: 295 Len: 257 Subject: NC_002967_TDE0129_TDE0130|PyrBI protein:sodium/dicarboxylate symporter family protein|NEGATIVE:POSITIVE|[150390,150684]|295 HSP 1 e-value: 2.0E-69 bit: 264.0 Len: 133 Query Start:39 Query End:171 Subject Strand: POSITIVE Subject Start: 39 Subject End: 171 ......................................catcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatc............................................................................................................................ ......................................catcggcaaaaccgatgttatcaaaataaacgagggtggcaaaatttgcagcttctagtaattaaggaataaatcatcttggcccctccatgaagatacggactcaaccgtacatattggaagggattctatc............................................................................................................................ HSP 2 e-value: 7.0E-44 bit: 178.0 Len: 90 Query Start:206 Query End:295 Subject Strand: POSITIVE Subject Start: 206 Subject End: 295 .............................................................................................................................................................................................................attgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt .............................................................................................................................................................................................................attgagttttattttaccccatctagtaaaaaatcttgtattatgataaactcgctgcgcattataaaataccactatttaggagttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCGGCAAAACCGAUGUUAUCAAAAUAAACGAGGGUGGCAAAAUUUGCAGCUUCUAGUAAUUAAGGAAUAAAUCAUCUUGGCCCCUCCAUGAAGAUACGGACUCAACCGUACAUAUUGGAAGGGAUUCUAUCAAAAAAUAAAAAAACUGUCAAUAGACUUUUUUUUAUUGAGUUUUAUUUUACCCCAUCUAGUAAAAAAUCUUGUAUUAUGAUAAACUCGCUGCGCAUUAUAAAAUACCACUAUUUAGGAGUUUUU ((((((.....))))))...((....((((..((((((....(((.((((((..((((.......((((((((...((....(((.((((......(((((......))))).....)))).)))............((((((((((..(((....))).))))))))))))..)))))))).......))))......(((.........)))......)))))).)))......)))).)).)))).))...... (-52.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACUCCUAAAUAGUGGUAUUUUAUAAUGCGCAGCGAGUUUAUCAUAAUACAAGAUUUUUUACUAGAUGGGGUAAAAUAAAACUCAAUAAAAAAAAGUCUAUUGACAGUUUUUUUAUUUUUUGAUAGAAUCCCUUCCAAUAUGUACGGUUGAGUCCGUAUCUUCAUGGAGGGGCCAAGAUGAUUUAUUCCUUAAUUACUAGAAGCUGCAAAUUUUGCCACCCUCGUUUAUUUUGAUAACAUCGGUUUUGCCGAUG ...............((((((......(((..(((((((((..(((((....(((((..(((((((......)))))))........((((((((((.(((....)))..))))))))))))))).......((((((((....((((((......)))))).....)))))))).....)))))..))))..............)))))..))).))))))..................((((((.....)))))) (-61.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 877 100 51 229 180 NC_002967:TDE0129|5end_PyrBI_protein_150299..150529_NEGATIVE 314 124 81 195 147 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 313 117 73 61 11 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 304 49 2 119 65 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 296 112 73 50 3 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 295 49 3 153 109 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 279 49 4 60 12 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 270 127 90 102 59 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 270 130 85 154 101 NC_002967:TDE0381|5end_hypothetical_protein_433932..434162_POSITIVE 265 128 84 148 99 NC_002967:TDE1251|5end_batB_protein,_putative_1285448..1285678_POSITIVE 265 111 74 131 88 NC_002967:TDE0490|5end_hypothetical_protein_546793..547023_NEGATIVE 262 119 76 177 121 NC_002967:TDE0601|5end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_639811..640041_NEGATIVE 256 120 74 227 179 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 255 135 93 189 145 NC_002967:TDE1689|5end_ABC_transporter,_ATP-binding_protein_1746565..1746795_NEGATIVE 255 50 1 65 11 NC_002967:TDE0818|5end_ABC_transporter,_ATP-binding/permease_protein_841647..841877_NEGATIVE 253 77 34 91 43 NC_002967:TDE2406|5end_TldD/PmbA_family_protein_2433513..2433743_NEGATIVE 253 128 83 140 102 NC_002967:TDE1229|5end_hypothetical_protein_1262413..1262643_POSITIVE 251 53 11 58 2 NC_002967:TDE2674|5end_hypothetical_protein_2713277..2713507_NEGATIVE 250 130 81 146 94 NC_002967:TDE0928|5end_phosphonate_ABC_transporter,_ATP-binding_protein,_putative_951640..951870_NEGATIVE 248 134 91 205 157 NC_002967:TDE2282|5end_tRNA_synthetase,_class_II_family_protein_2319665..2319895_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 124 81 84 36 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 286 67 23 117 67 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 272 125 83 45 6 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 270 130 85 124 71 NC_002967:TDE0380|3end_hypothetical_protein_433982..434132_POSITIVE 265 128 84 151 102 NC_002967:TDE1250|3end_batA_protein,_putative_1285531..1285681_POSITIVE 255 190 144 109 60 NC_002967:TDE0933|3end_acetate_kinase_959336..959486_POSITIVE 255 50 1 63 9 NC_002967:TDE0819|3end_ABC_transporter,_ATP-binding/permease_protein_841649..841799_NEGATIVE 253 128 83 143 105 NC_002967:TDE1228|3end_pentapeptide_repeat_family_protein_1262496..1262646_POSITIVE 250 130 81 67 15 NC_002967:TDE0929|3end_ornithine_carbamoyltransferase_951719..951869_NEGATIVE 247 110 77 109 70 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 239 130 81 66 3 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 237 190 146 62 20 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE 237 114 71 45 8 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 236 112 76 145 96 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 234 109 62 143 91 NC_002967:TDE2398|3end_conserved_hypothetical_protein_TIGR00278_2425586..2425736_NEGATIVE 234 128 84 85 42 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 231 104 61 76 30 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 230 120 80 149 110 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 230 241 201 57 22 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 230 58 31 42 18 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE