Origin IGS: acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agacaaatactatccttttttttgatgagggtcaagtcttctttatgaattccgatagcggcggatgtaagcaacacaatctaattgaaattgtttatgcattttgatattcggtgttacatattaatgttgtaacttttttcatttatgccttgattaaaataaaaaaatgatgt Mask Tandem Repeat Region ================================================ acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Find is-nt database================================================ Query_seq: TDE2065:TDE2066|TDE2065:TDE2066:FeoA family protein:exodeoxyribonuclease VII, small subunit:<-->:2091870..2092045 176 acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2065:TDE2066|TDE2065:TDE2066:FeoA family protein:exodeoxyribonuclease VII, small subunit:<-->:2091870..2092045 176 acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2065:TDE2066|TDE2065:TDE2066:FeoA family protein:exodeoxyribonuclease VII, small subunit:<-->:2091870..2092045 176 acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 73 End: 165 ........................................................................ F A Y V I E I L N H Q K C G G S D S N M F F V Q G E D F F L M ........... acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct 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: 81 Start: 141 End: 170 ............................................................................................................................................CTTGACCCTCATCAAAAAAAAGGATAGTAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2065:TDE2066|TDE2065:TDE2066:FeoA family protein:exodeoxyribonuclease VII, small subunit:<-->:2091870..2092045 176 acatcatttttttattttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatcaaaaaaaaggatagtatttgtct Intra-Species Hit: Count: 1 Min: 14 Max: 153 Len: 140 Subject: NC_002967_TDE2065_TDE2066|FeoA family protein:exodeoxyribonuclease VII, small subunit|NEGATIVE:POSITIVE|[2091870,2092045]|176 HSP 1 e-value: 6.0E-74 bit: 278.0 Len: 140 Query Start:14 Query End:153 Subject Strand: POSITIVE Subject Start: 14 Subject End: 153 .............attttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatc....................... .............attttaatcaaggcataaatgaaaaaagttacaacattaatatgtaacaccgaatatcaaaatgcataaacaatttcaattagattgtgttgcttacatccgccgctatcggaattcataaagaagacttgaccctcatc....................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAAUCAAGGCAUAAAUGAAAAAAGUUACAACAUUAAUAUGUAACACCGAAUAUCAAAAUGCAUAAACAAUUUCAAUUAGAUUGUGUUGCUUACAUCCGCCGCUAUCGGAAUUCAUAAAGAAGACUUGACCCUCAUC .......(((((...............((((((.........))))))...((((........(((...(((((((.....)))))))..))).....((((.......))))))))..........)))))........ (-21.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAGGGUCAAGUCUUCUUUAUGAAUUCCGAUAGCGGCGGAUGUAAGCAACACAAUCUAAUUGAAAUUGUUUAUGCAUUUUGAUAUUCGGUGUUACAUAUUAAUGUUGUAACUUUUUUCAUUUAUGCCUUGAUUAAAAU ......(((((((.(......(((((..((((.......((((((((((((..((((...))))...)))))..)))))))......)))).((((((.........))))))....)))))....).)))))))..... (-24.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 856 120 71 224 175 NC_002967:TDE2065|5end_FeoA_family_protein_2091779..2092009_NEGATIVE 313 136 91 81 25 NC_002967:TDE1397|5end_flagellar_synthesis_regulator_FleN,_putative_1436014..1436244_POSITIVE 273 119 74 231 194 NC_002967:TDE2592|5end_DbpA_RNA_binding_domain_protein_2627026..2627256_POSITIVE 266 140 91 146 105 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 258 112 84 126 90 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 247 136 97 42 6 NC_002967:TDE0744|5end_thioredoxin_779844..780074_POSITIVE 246 117 71 61 1 NC_002967:TDE0424|5end_bacteriocin-type_signal_domain_protein_477870..478100_POSITIVE 244 140 92 188 159 NC_002967:TDE1714|5end_N-acetylmuramoyl-L-alanine_amidase,_family_3_1769496..1769726_NEGATIVE 242 109 72 76 38 NC_002967:TDE0685|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_722620..722850_NEGATIVE 241 111 85 68 37 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 241 140 100 52 10 NC_002967:TDE1341|5end_hypothetical_protein_1377063..1377293_POSITIVE 240 119 88 200 155 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 238 137 98 155 111 NC_002967:TDE1631|5end_citrate_lyase,_alpha_subunit_1681556..1681786_NEGATIVE 236 117 80 184 127 NC_002967:TDE0260|5end_iron-sulfur_cluster-binding_protein_293734..293964_POSITIVE 235 140 95 77 25 NC_002967:TDE1875|5end_hypothetical_protein_1896906..1897136_NEGATIVE 235 135 91 231 190 NC_002967:TDE0869|5end_hypothetical_protein_891470..891700_POSITIVE 233 113 79 68 36 NC_002967:TDE0953|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_976863..977093_POSITIVE 232 130 81 127 67 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 229 135 92 190 141 NC_002967:TDE1969|5end_sigma-54_dependent_transcriptional_regulator/response_regulator_1984500..1984730_NEGATIVE 229 140 91 111 58 NC_002967:TDE1459|5end_hypothetical_protein_1508707..1508937_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 136 91 114 58 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 273 118 74 136 97 NC_002967:TDE2591|3end_rhodanese-like_domain_protein_2627009..2627159_POSITIVE 266 140 91 136 95 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 266 130 83 105 52 NC_002967:TDE0903|3end_ATP-dependent_DNA_helicase_PcrA_922296..922446_POSITIVE 262 140 100 136 101 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 251 133 97 52 20 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 248 130 84 125 83 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 247 118 92 72 41 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 239 113 101 120 108 NC_002967:TDE0206|3end_surface_antigen,_putative_239671..239821_NEGATIVE 238 137 98 142 98 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 237 132 98 43 6 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 233 113 79 71 39 NC_002967:TDE0952|3end_ABC_transporter,_ATP-binding_protein_976946..977096_POSITIVE 232 130 81 134 74 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 229 140 91 111 58 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE 225 138 100 31 6 NC_002967:TDE2047|3end_hypothetical_protein_2076058..2076208_NEGATIVE 225 114 85 52 22 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 221 136 92 79 40 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 218 140 91 100 56 NC_002967:TDE1364|3end_valyl-tRNA_synthetase_1407572..1407722_POSITIVE 218 137 91 64 26 NC_002967:TDE1101|3end_acetyltransferase,_GNAT_family_1134663..1134813_NEGATIVE 216 112 89 77 52 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE