Origin IGS: ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta .........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 taggccgacctcccaaaaaatagtaataatagcttaccttataaagctattttgcataactgtcaatagtattaaggcataaaaagggcttttttttaatattttcaatccaaaaacaaaaaaacttaatatttttctatgatatatgtattgaatatatttcaattttatggtattataactattagaacatatattatccttgtgtattcggagtcgttcaagcggctccttttttgtatgcaaaaggtatcttgagaggaggttgaa Mask Tandem Repeat Region ================================================ ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Find is-nt database================================================ Query_seq: TDE1108:TDE1109|TDE1108:TDE1109:hypothetical protein:decarboxylase, pyridoxal-dependent family:<-->:1142950..1143219 270 ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1108:TDE1109|TDE1108:TDE1109:hypothetical protein:decarboxylase, pyridoxal-dependent family:<-->:1142950..1143219 270 ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1108:TDE1109|TDE1108:TDE1109:hypothetical protein:decarboxylase, pyridoxal-dependent family:<-->:1142950..1143219 270 ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 25 End: 234 ........................ M H T K K E P L E R L R I H K D N I C S N S Y N T I K L K Y I Q Y I Y H R K I L S F F V F G L K I L K K S P F Y A L I L .................................... Protein_Len: 42 Strand: - Start: 86 End: 211 ..................................................................................... Y N Y Y W L I S I Y E I C I D Y F F I L N K Q K Q I S F I L F F G K K H R L V I S M ........................................................... Protein_Len: 39 Strand: - Start: 16 End: 132 ............... S V K Q M C F L L R K F S E S Y V L I I Y T R I T I I G Y F Q F I N L V Y I M .......................................................................................................................................... ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta 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: 88 Start: 204 End: 233 ...........................................................................................................................................................................................................ATTGACAGTTATGCAAAATAGCTTTATAAG..................................... PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 92 End: 121 ...........................................................................................ATTGAATATATTTCAATTTTATGGTATTAT..................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.8 Tail_Score: -5.36441 Start: 39 End: 58 Full_Region: tatccttgtgtattc ggagtcgt tcaa gcggctcc ttttttgtatgcaaa ......................................ggagtcgttcaagcggctcc.................................................................................................................................................................................................................... TransTerm Strand: - Conf: 58 HP_score: -2.9 Tail_Score: -4.56629 Start: 106 End: 120 Full_Region: tctatgatatatgta ttgaa tatat ttcaa ttttatggtattata .........................................................................................................ttgaatatatttcaa...................................................................................................................................................... Find igs database================================================ Query_seq: TDE1108:TDE1109|TDE1108:TDE1109:hypothetical protein:decarboxylase, pyridoxal-dependent family:<-->:1142950..1143219 270 ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaaggataatatatgttctaatagttataataccataaaattgaaatatattcaatacatatatcatagaaaaatattaagtttttttgtttttggattgaaaatattaaaaaaaagccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: NC_002967_TDE1108_TDE1109|hypothetical protein:decarboxylase, pyridoxal-dependent family|NEGATIVE:POSITIVE|[1142950,1143219]|270 HSP 1 e-value: 3.0E-43 bit: 176.0 Len: 89 Query Start:182 Query End:270 Subject Strand: POSITIVE Subject Start: 182 Subject End: 270 .....................................................................................................................................................................................gccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta .....................................................................................................................................................................................gccctttttatgccttaatactattgacagttatgcaaaatagctttataaggtaagctattattactattttttgggaggtcggccta HSP 2 e-value: 6.0E-32 bit: 139.0 Len: 70 Query Start:1 Query End:70 Subject Strand: POSITIVE Subject Start: 1 Subject End: 70 ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaagg........................................................................................................................................................................................................ ttcaacctcctctcaagataccttttgcatacaaaaaaggagccgcttgaacgactccgaatacacaagg........................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAACCUCCUCUCAAGAUACCUUUUGCAUACAAAAAAGGAGCCGCUUGAACGACUCCGAAUACACAAGGAUAAUAUAUGUUCUAAUAGUUAUAAUACCAUAAAAUUGAAAUAUAUUCAAUACAUAUAUCAUAGAAAAAUAUUAAGUUUUUUUGUUUUUGGAUUGAAAAUAUUAAAAAAAAGCCCUUUUUAUGCCUUAAUACUAUUGACAGUUAUGCAAAAUAGCUUUAUAAGGUAAGCUAUUAUUACUAUUUUUUGGGAGGUCGGCCUA .....((.((((((((((......(((((((.......((((.((......)).))))....................((((..((((((........(((((((((..(((((.((((((.((......((((((((((.....))))))))))...)).)))))).)))))..)).........))))))).......))))))))))..)))))))((((((((........)))))))).........))))))))))..)).... (-53.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGCCGACCUCCCAAAAAAUAGUAAUAAUAGCUUACCUUAUAAAGCUAUUUUGCAUAACUGUCAAUAGUAUUAAGGCAUAAAAAGGGCUUUUUUUUAAUAUUUUCAAUCCAAAAACAAAAAAACUUAAUAUUUUUCUAUGAUAUAUGUAUUGAAUAUAUUUCAAUUUUAUGGUAUUAUAACUAUUAGAACAUAUAUUAUCCUUGUGUAUUCGGAGUCGUUCAAGCGGCUCCUUUUUUGUAUGCAAAAGGUAUCUUGAGAGGAGGUUGAA .....((((((((.........((((.((((((((........)))))))))))).......((((.(((((((((...(((((((.....)))))))...((((......)))).........))))))))).....(((((((((((.(((((.....)))))....(((((......)))))....)))))))))))((((.(((((.(((((((((....))))))))......).))))).))))....))))..)))))))).. (-60.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 929 70 21 161 112 NC_002967:TDE1108|5end_hypothetical_protein_1142859..1143089_NEGATIVE 317 60 25 70 36 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 317 60 25 227 193 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 310 78 39 56 14 NC_002967:TDE2369|5end_hypothetical_protein_2402292..2402522_POSITIVE 297 59 16 126 77 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 281 49 4 72 37 NC_002967:TDE1582|5end_glycogen_synthase_1631759..1631989_NEGATIVE 275 48 6 215 177 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 270 46 9 139 99 NC_002967:TDE0067|5end_cyclic_nucleotide-binding_protein_75188..75418_NEGATIVE 269 60 22 61 22 NC_002967:TDE2327|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2364627..2364857_NEGATIVE 269 60 23 57 16 NC_002967:TDE2302|5end_HD_domain_protein_2341790..2342020_POSITIVE 269 59 16 157 116 NC_002967:TDE1887|5end_TPR_domain_protein_1909133..1909363_NEGATIVE 265 80 31 65 15 NC_002967:TDE1664|5end_hypothetical_protein_1717862..1718092_POSITIVE 261 59 20 225 189 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 261 65 22 71 31 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 260 48 2 62 3 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 259 60 11 149 105 NC_002967:TDE2623|5end_hypothetical_protein_2664324..2664554_NEGATIVE 255 267 224 212 173 NC_002967:TDE0636|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_671500..671730_NEGATIVE 254 59 21 163 112 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 254 69 37 173 140 NC_002967:TDE0654|5end_peptidase,_M20/M25/M40_family_689606..689836_POSITIVE 252 49 6 149 106 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 60 25 49 15 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 279 48 6 72 44 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 276 50 5 141 85 NC_002967:TDE0761|3end_protease_complex-associated_polypeptide_801968..802118_POSITIVE 275 268 223 117 69 NC_002967:TDE2087|3end_translation_initiation_factor_IF-1_2115468..2115618_NEGATIVE 265 75 39 51 18 NC_002967:TDE0005|3end_L-threonine_aldolase,_low-specificity_4985..5135_NEGATIVE 261 65 22 48 8 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 260 69 25 49 9 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 255 230 181 66 12 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 255 60 25 38 5 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 252 71 38 55 12 NC_002967:TDE2664|3end_hypothetical_protein_2702113..2702263_POSITIVE 252 49 6 143 100 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 250 48 5 88 38 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 246 60 28 39 4 NC_002967:TDE2301|3end_FlhB_domain_protein_2341852..2342002_POSITIVE 246 48 9 148 108 NC_002967:TDE0050|3end_RNA_methyltransferase,_TrmH_family_59283..59433_NEGATIVE 245 59 12 119 83 NC_002967:TDE1079|3end_DNA-binding_protein/PTS_system,_IIA_component_1111805..1111955_POSITIVE 243 59 11 151 108 NC_002967:TDE2624|3end_hypothetical_protein_2664321..2664471_NEGATIVE 243 269 223 140 103 NC_002967:TDE2589|3end_putative_aminopeptidase_1_2625000..2625150_NEGATIVE 240 269 221 64 6 NC_002967:TDE2405|3end_hypothetical_protein_2430716..2430866_NEGATIVE 240 48 6 121 87 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE 238 269 223 137 96 NC_002967:TDE0731|3end_hypothetical_protein_770691..770841_NEGATIVE