Origin IGS: gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt .........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 aattatttctccaataaagataaacagtgaggcagaatttctgccgagctgtttatcgaaactccaataaaaactttttaaggcatttattgtacccattttgcttaaaaaaatctataggccggatttttttaaactgtacattaaaatgcacgaactctagcataaaatacaaaaaagtgatatactctgttgcttatgggccttgtttttgtttagatagcaataaggctgcttttaaaagctgatgtttttataagctgtttatataaattactaggagttttc Mask Tandem Repeat Region ================================================ gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Find is-nt database================================================ Query_seq: TDE2219:TDE2220|TDE2219:TDE2220:hypothetical protein:prolyl-tRNA synthetase:<-->:2260737..2261024 288 gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2219:TDE2220|TDE2219:TDE2220:hypothetical protein:prolyl-tRNA synthetase:<-->:2260737..2261024 288 gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2219:TDE2220|TDE2219:TDE2220:hypothetical protein:prolyl-tRNA synthetase:<-->:2260737..2261024 288 gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 105 End: 233 ........................................................................................................ M T F L Y F M L E F V H F N V Q F K K I R P I D F F K Q N G Y N K C L K K F L L E F R ....................................................... Protein_Len: 38 Strand: + Start: 175 End: 288 .............................................................................................................................................................................. M F L S K M G T I N A L K S F Y W S F D K Q L G R N S A S L F I F I G E I I Protein_Len: 60 Strand: - Start: 44 End: 262 ........................................... P G Y A V S Y I V K K Y K I S S N T C K L T C N L F I R G I S K K L C F P Y L L H R L F N K N S N R Y V A R C F N Q R M .......................... gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt 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================================================ gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.8 Tail_Score: -4.1552 Start: 232 End: 270 Full_Region: TTTTATTGGAGTTTC GATAAACAGCTCGGCAGA AAT TCTGCCTCACTGTTTATC TTTATTGGAGAAATA .......................................................................................................................................................................................................................................GATAAACAGCTCGGCAGAAATTCTGCCTCACTGTTTATC.................. Find igs database================================================ Query_seq: TDE2219:TDE2220|TDE2219:TDE2220:hypothetical protein:prolyl-tRNA synthetase:<-->:2260737..2261024 288 gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Intra-Species Hit: Count: 1 Min: 1 Max: 288 Len: 288 Subject: NC_002967_TDE2219_TDE2220|hypothetical protein:prolyl-tRNA synthetase|NEGATIVE:POSITIVE|[2260737,2261024]|288 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 288 Query Start:1 Query End:288 Subject Strand: POSITIVE Subject Start: 1 Subject End: 288 gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttnnnnnnntccggcctatagannnnnnnaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt gaaaactcctagtaatttatataaacagcttataaaaacatcagcttttaaaagcagccttattgctatctaaacaaaaacaaggcccataagcaacagagtatatcacttttttgtattttatgctagagttcgtgcattttaatgtacagtttaaaaaaatccggcctatagatttttttaagcaaaatgggtacaataaatgccttaaaaagtttttattggagtttcgataaacagctcggcagaaattctgcctcactgtttatctttattggagaaataatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAACUCCUAGUAAUUUAUAUAAACAGCUUAUAAAAACAUCAGCUUUUAAAAGCAGCCUUAUUGCUAUCUAAACAAAAACAAGGCCCAUAAGCAACAGAGUAUAUCACUUUUUUGUAUUUUAUGCUAGAGUUCGUGCAUUUUAAUGUACAGUUUAAAAAAAUCCGGCCUAUAGAUUUUUUUAAGCAAAAUGGGUACAAUAAAUGCCUUAAAAAGUUUUUAUUGGAGUUUCGAUAAACAGCUCGGCAGAAAUUCUGCCUCACUGUUUAUCUUUAUUGGAGAAAUAAUU .....((((.(((((...........(((((((((((((....((((....)))).((.((((((...................((((((.((((..((((((((.........)))))))).)))).......((((((....)))))).(((((((((((((.........)))))))))))))...)))))).))))))..))........))))))))..)))))..(((((((((...(((((.....)))))...))))))))).)))))))))........ (-70.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUUUCUCCAAUAAAGAUAAACAGUGAGGCAGAAUUUCUGCCGAGCUGUUUAUCGAAACUCCAAUAAAAACUUUUUAAGGCAUUUAUUGUACCCAUUUUGCUUAAAAAAAUCUAUAGGCCGGAUUUUUUUAAACUGUACAUUAAAAUGCACGAACUCUAGCAUAAAAUACAAAAAAGUGAUAUACUCUGUUGCUUAUGGGCCUUGUUUUUGUUUAGAUAGCAAUAAGGCUGCUUUUAAAAGCUGAUGUUUUUAUAAGCUGUUUAUAUAAAUUACUAGGAGUUUUC ..................((((((((((..(((((.....)))))..)))))))))).(((((((.................((((((..(((((.......(.((((((((((((.......)))))))))))).).)))))...))))))..((((...................(((..(((.....)))..)))...(((((((((.((((....)))).)))))))))((((.(((((((....))))))).)))).)))).............))))))).. (-76.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 100 51 191 142 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 630 270 224 70 24 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 594 270 223 68 21 NC_002967:TDE1583|5end_hypothetical_protein_1631808..1632038_POSITIVE 565 270 223 99 52 NC_002967:TDE2667|5end_hypothetical_protein_2704374..2704604_POSITIVE 548 270 224 221 175 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 477 270 231 146 107 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 461 270 222 180 137 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 443 268 223 148 108 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 412 270 230 128 88 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 401 270 222 140 97 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 392 270 221 146 97 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 382 270 231 151 112 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 379 270 231 151 112 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 377 270 223 164 123 NC_002967:TDE1625|5end_glycine_cleavage_system_P_protein,_subunit_1_1674823..1675053_NEGATIVE 367 270 231 194 155 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 361 270 222 189 145 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 361 270 222 167 123 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 361 270 222 190 146 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 361 270 222 89 45 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 361 270 222 65 21 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 599 270 224 60 14 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 458 270 222 61 18 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 443 268 223 72 32 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 412 270 230 52 12 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 401 270 222 72 29 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 392 270 221 79 30 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 382 270 231 139 100 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 377 270 223 76 35 NC_002967:TDE1626|3end_glycine_cleavage_system_H_protein_1674911..1675061_NEGATIVE 376 272 232 81 41 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 370 248 213 149 113 NC_002967:TDE1326|3end_hypothetical_protein_1361842..1361992_POSITIVE 367 270 231 78 39 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 361 270 222 78 34 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 361 270 222 69 25 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 361 270 222 50 6 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 361 270 222 72 28 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 351 270 225 76 30 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 351 270 230 82 41 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 348 270 232 73 35 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 342 270 222 75 32 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 340 270 222 82 26 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE