Origin IGS: agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttttccttaaaagcttataaattcccataaaatttgacaataaatgccttttttcattctatcattattgcaaaaaaaagtaaagaagtagtataatggcgagct Mask Tandem Repeat Region ================================================ agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Find is-nt database================================================ Query_seq: TDE0001:TDE0002|TDE0001:TDE0002:chromosomal replication initiator protein DnaA:DNA gyrase, B subunit:<-->:1576..1683 108 agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0001:TDE0002|TDE0001:TDE0002:chromosomal replication initiator protein DnaA:DNA gyrase, B subunit:<-->:1576..1683 108 agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0001:TDE0002|TDE0001:TDE0002:chromosomal replication initiator protein DnaA:DNA gyrase, B subunit:<-->:1576..1683 108 agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Predict ORF larger than 30AA ================================================ agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa 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: 83 Start: 21 End: 50 ....................CTTTACTTTTTTTTGCAATAATGATAGAAT.......................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 44 End: 73 ...........................................TTTGACAATAAATGCCTTTTTTCATTCTAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0001:TDE0002|TDE0001:TDE0002:chromosomal replication initiator protein DnaA:DNA gyrase, B subunit:<-->:1576..1683 108 agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaaggaaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002967_TDE0001_TDE0002|chromosomal replication initiator protein DnaA:DNA gyrase, B subunit|NEGATIVE:POSITIVE|[1576,1683]|108 HSP 1 e-value: 1.0E-36 bit: 153.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 agctcgccattatactacttctttacnnnnnnnngcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaagg....... agctcgccattatactacttctttacttttttttgcaataatgatagaatgaaaaaaggcatttattgtcaaattttatgggaatttataagcttttaagg....... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCGCCAUUAUACUACUUCUUUACUUUUUUUUGCAAUAAUGAUAGAAUGAAAAAAGGCAUUUAUUGUCAAAUUUUAUGGGAAUUUAUAAGCUUUUAAGG ((((...((((((........................)))))).....((((((...((((.....))))...))))))...........))))....... ( -8.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUAAAAGCUUAUAAAUUCCCAUAAAAUUUGACAAUAAAUGCCUUUUUUCAUUCUAUCAUUAUUGCAAAAAAAAGUAAAGAAGUAGUAUAAUGGCGAGCU .......((((..((((((.......)))))).........(((..........((((..((.((((........)))).)).))))......))).)))) ( -7.99) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 50 1 141 92 NC_002967:TDE0001|5end_chromosomal_replication_initiator_protein_DnaA_1485..1715_NEGATIVE 244 69 22 225 177 NC_002967:TDE0381|5end_hypothetical_protein_433932..434162_POSITIVE 219 39 2 125 81 NC_002967:TDE0348|5end_transcriptional_regulator,_TetR_family_390457..390687_POSITIVE 208 37 1 106 65 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 206 37 1 161 121 NC_002967:TDE1056|5end_hypothetical_protein_1085210..1085440_POSITIVE 200 38 1 53 14 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 200 82 56 158 128 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 200 71 35 206 176 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 197 48 2 118 62 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 195 46 1 168 121 NC_002967:TDE0782|5end_50S_ribosomal_protein_L6_812970..813200_POSITIVE 188 36 4 117 84 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 185 26 3 39 14 NC_002967:TDE2176|5end_site-specific_recombinase,_putative_2206239..2206469_NEGATIVE 184 47 4 40 7 NC_002967:TDE1180|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1209833..1210063_NEGATIVE 184 60 21 152 111 NC_002967:TDE0704|5end_SPFH_domain/Band_7_family_protein_739346..739576_NEGATIVE 184 96 55 85 41 NC_002967:TDE0364|5end_ABC_transporter,_ATP-binding_protein_411605..411835_NEGATIVE 183 47 1 133 75 NC_002967:TDE1641|5end_ribose_5-phosphate_isomerase_A_1691877..1692107_POSITIVE 183 94 57 210 169 NC_002967:TDE1398|5end_hypothetical_protein_1437192..1437422_POSITIVE 183 41 1 93 47 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 182 96 62 98 66 NC_002967:TDE2187|5end_ParB-like_nuclease_domain_protein_2221548..2221778_NEGATIVE 182 46 1 45 3 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 214 70 45 147 117 NC_002967:TDE0272|3end_hypothetical_protein_302256..302406_NEGATIVE 200 82 56 131 101 NC_002967:TDE1226|3end_zinc_ABC_transporter,_periplasmic_zinc-binding_protein_1259545..1259695_NEGATIVE 197 48 2 106 50 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 192 43 1 66 23 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 188 36 4 117 84 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 187 70 24 148 94 NC_002967:TDE1674|3end_hypothetical_protein_1728232..1728382_NEGATIVE 183 47 1 133 75 NC_002967:TDE1640|3end_3-dehydroquinate_dehydratase,_type_1,_putative/shikimate_5-dehydrogenase,_putative_1691957..1692107_POSITIVE 183 41 1 70 24 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 182 96 62 72 40 NC_002967:TDE2188|3end_hypothetical_protein_2221574..2221724_NEGATIVE 182 40 1 118 80 NC_002967:TDE1711|3end_RelA/SpoT_domain_protein_1765552..1765702_NEGATIVE 179 45 2 138 96 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE 177 36 1 135 93 NC_002967:TDE2517|3end_DNA_repair_protein_RadA_2542454..2542604_NEGATIVE 177 96 57 144 106 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 177 83 43 70 25 NC_002967:TDE1172|3end_hypothetical_protein_1201280..1201430_POSITIVE 174 48 1 125 80 NC_002967:TDE1318|3end_hypothetical_protein_1356681..1356831_POSITIVE 173 46 3 148 105 NC_002967:TDE0705|3end_SPFH_domain/Band_7_family_protein_739339..739489_NEGATIVE 172 35 1 138 102 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 170 38 8 107 76 NC_002967:TDE1049|3end_elongation_factor_EF-2_1077454..1077604_POSITIVE 170 29 1 82 56 NC_002967:TDE0887|3end_PIN_domain_protein_904333..904483_NEGATIVE 169 48 1 118 63 NC_002967:TDE1440|3end_glucose-1-phosphate_thymidylyltransferase_1486308..1486458_POSITIVE