Origin IGS: ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa .........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 ttcattctccttttccgtaattttacggaataatttttttgagaaaattctcatttggttgtaaccataaataagcttttaattttattgacaagtttacacgatacaacacgtacataagtataagttattaaaaagaaaagtcaagccctcgctatttttttttaaaaatttatagacggctaaaatgattgactcttaattgacttatgataatgattatgttatacttttttttaaagaggtatacaa Mask Tandem Repeat Region ================================================ ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Find is-nt database================================================ Query_seq: TDE1716:TDE1717|TDE1716:TDE1717:glyoxalase family protein:hypothetical protein:<-->:1771319..1771570 252 ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1716:TDE1717|TDE1716:TDE1717:glyoxalase family protein:hypothetical protein:<-->:1771319..1771570 252 ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1716:TDE1717|TDE1716:TDE1717:glyoxalase family protein:hypothetical protein:<-->:1771319..1771570 252 ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 61 End: 153 ............................................................ M I L A V Y K F L K K N S E G L T F L F N N L Y L C T C C I V ................................................................................................... Protein_Len: 33 Strand: + Start: 129 End: 227 ................................................................................................................................ M L M Y V L Y R V N L S I K L K A Y L W L Q P N E N F L K K I I P ......................... ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa 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: 89 Start: 22 End: 51 .....................ATTGACTTATGATAATGATTATGTTATACT......................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 33 End: 62 ................................ATTGACTCTTAATTGACTTATGATAATGAT.............................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1716:TDE1717|TDE1716:TDE1717:glyoxalase family protein:hypothetical protein:<-->:1771319..1771570 252 ttgtatacctctttaaaaaaaagtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Intra-Species Hit: Count: 1 Min: 23 Max: 252 Len: 230 Subject: NC_002967_TDE1716_TDE1717|glyoxalase family protein:hypothetical protein|NEGATIVE:POSITIVE|[1771319,1771570]|252 HSP 1 e-value: 8.0E-99 bit: 361.0 Len: 230 Query Start:23 Query End:252 Subject Strand: POSITIVE Subject Start: 23 Subject End: 252 ......................gtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttnnnnnnnnntagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcnnnnnnnttattccgtaaaattacggaaaaggagaatgaa ......................gtataacataatcattatcataagtcaattaagagtcaatcattttagccgtctataaatttttaaaaaaaaatagcgagggcttgacttttctttttaataacttatacttatgtacgtgttgtatcgtgtaaacttgtcaataaaattaaaagcttatttatggttacaaccaaatgagaattttctcaaaaaaattattccgtaaaattacggaaaaggagaatgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAACAUAAUCAUUAUCAUAAGUCAAUUAAGAGUCAAUCAUUUUAGCCGUCUAUAAAUUUUUAAAAAAAAAUAGCGAGGGCUUGACUUUUCUUUUUAAUAACUUAUACUUAUGUACGUGUUGUAUCGUGUAAACUUGUCAAUAAAAUUAAAAGCUUAUUUAUGGUUACAACCAAAUGAGAAUUUUCUCAAAAAAAUUAUUCCGUAAAAUUACGGAAAAGGAGAAUGAA (((((((((...(((....((((((..(((((((((((........((((.((.....((((((....))))))...)).))))))))))......))))).))))))....)))...)))))))))............(((.............((((((..((((....))))))))))....(((((..........(((((((....)))))))...)))))))). (-40.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUUCUCCUUUUCCGUAAUUUUACGGAAUAAUUUUUUUGAGAAAAUUCUCAUUUGGUUGUAACCAUAAAUAAGCUUUUAAUUUUAUUGACAAGUUUACACGAUACAACACGUACAUAAGUAUAAGUUAUUAAAAAGAAAAGUCAAGCCCUCGCUAUUUUUUUUUAAAAAUUUAUAGACGGCUAAAAUGAUUGACUCUUAAUUGACUUAUGAUAAUGAUUAUGUUAUAC ............(((((((....))))))).........(((((....)))))....((((((........((((((((((((...))))).))))))).....))))))....((((((.(((((((((.....((((..(((((((((.((...((((((....)))))).....)).))))....)))))...))))...))))))))).......))))))..... (-42.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 753 90 41 203 154 NC_002967:TDE1716|5end_glyoxalase_family_protein_1771228..1771458_NEGATIVE 253 119 76 111 49 NC_002967:TDE0598|5end_3-oxoacyl-(acyl-carrier-protein)_reductase_638101..638331_NEGATIVE 235 86 41 140 89 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 225 98 52 149 102 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 225 127 88 137 96 NC_002967:TDE1521|5end_fumarate_hydratase_1567211..1567441_POSITIVE 224 227 191 80 50 NC_002967:TDE2598|5end_hypothetical_protein_2633330..2633560_NEGATIVE 223 94 51 136 97 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 218 119 73 177 129 NC_002967:TDE1913|5end_hypothetical_protein_1929810..1930040_POSITIVE 217 130 83 113 65 NC_002967:TDE0246|5end_transcriptional_regulator,_TetR_family_281665..281895_NEGATIVE 215 86 47 80 49 NC_002967:TDE2599|5end_thymidylate_kinase_2633963..2634193_NEGATIVE 215 97 51 150 106 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 213 119 73 61 10 NC_002967:TDE2274|5end_hypothetical_protein_2310201..2310431_POSITIVE 212 84 47 174 141 NC_002967:TDE1946|5end_hypothetical_protein_1962494..1962724_NEGATIVE 208 159 122 39 4 NC_002967:TDE0840|5end_hypothetical_protein_860894..861124_NEGATIVE 206 114 77 40 1 NC_002967:TDE1469|5end_conserved_hypothetical_protein_TIGR00150_1517764..1517994_NEGATIVE 206 157 114 173 131 NC_002967:TDE1213|5end_flagellar_basal_body_rod_protein_1245817..1246047_POSITIVE 205 144 103 138 96 NC_002967:TDE1959|5end_hypothetical_protein_1974197..1974427_NEGATIVE 203 56 22 106 72 NC_002967:TDE2506|5end_radical_SAM_domain_protein_2530581..2530811_POSITIVE 203 119 73 196 145 NC_002967:TDE1593|5end_Fe-hydrogenase_1642999..1643229_NEGATIVE 202 80 31 130 74 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 117 76 87 51 NC_002967:TDE1488|3end_glyceraldehyde-3-phosphate_dehydrogenase,_type_I_1531604..1531754_NEGATIVE 235 86 41 143 92 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE 225 127 88 122 81 NC_002967:TDE1520|3end_fumarate_hydratase_1567276..1567426_POSITIVE 224 227 191 76 46 NC_002967:TDE2599|3end_thymidylate_kinase_2633334..2633484_NEGATIVE 223 94 51 133 94 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 219 68 21 130 85 NC_002967:TDE0979|3end_penicillin_binding_protein_1002510..1002660_NEGATIVE 214 99 77 132 109 NC_002967:TDE2550|3end_hypothetical_protein_2575520..2575670_NEGATIVE 213 142 110 47 3 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 212 84 47 151 118 NC_002967:TDE1947|3end_ABC_transporter,_permease_protein_1962517..1962667_NEGATIVE 207 98 62 39 1 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE 206 157 114 149 107 NC_002967:TDE1212|3end_flagellar_basal-body_rod_protein_FlgB_1245873..1246023_POSITIVE 203 56 22 66 32 NC_002967:TDE2505|3end_hypothetical_protein_2530621..2530771_POSITIVE 202 80 31 63 7 NC_002967:TDE1952|3end_hypothetical_protein_1968396..1968546_NEGATIVE 202 141 113 31 6 NC_002967:TDE0773|3end_30S_ribosomal_protein_S3_810242..810392_POSITIVE 202 88 41 59 10 NC_002967:TDE0296|3end_formiminotransferase,_putative_326842..326992_NEGATIVE 200 66 33 65 27 NC_002967:TDE1006|3end_flagellar_basal-body_rod_protein_FlgG_1031319..1031469_POSITIVE 195 111 74 53 20 NC_002967:TDE1240|3end_PhoH_family_protein_1272362..1272512_POSITIVE 189 225 198 34 9 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 188 90 48 70 30 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 187 57 23 108 68 NC_002967:TDE0250|3end_sodium-dependent_transporter,_putative_283310..283460_NEGATIVE