Origin IGS: ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattgatacctccataaactaaaagctgcggattaaaaccaatccgcagcttaaatattatcataagaaacgcatttgctcaagagaaccaagactgttgtcataaattttataatagacactttttttacctcag Mask Tandem Repeat Region ================================================ ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Find is-nt database================================================ Query_seq: TDE1077:TDE1078|TDE1077:TDE1078:hypothetical protein:metallo-beta-lactamase family protein:->->:1109741..1109878 138 ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1077:TDE1078|TDE1077:TDE1078:hypothetical protein:metallo-beta-lactamase family protein:->->:1109741..1109878 138 ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1077:TDE1078|TDE1077:TDE1078:hypothetical protein:metallo-beta-lactamase family protein:->->:1109741..1109878 138 ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 3 End: 95 .. L Y F F H R N Y F K H C C D Q N E Q A F A N R I I I N L S R M ........................................... ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt 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: 53 End: 82 ....................................................CTTGAGCAAATGCGTTTCTTATGATAATAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -4.61873 Start: 87 End: 112 Full_Region: TATGATAATATTTAA GCTGCGGATTG GTTT TAATCCGCAGC TTTTAGTTTATGGAG ......................................................................................GCTGCGGATTGGTTTTAATCCGCAGC.......................... Find igs database================================================ Query_seq: TDE1077:TDE1078|TDE1077:TDE1078:hypothetical protein:metallo-beta-lactamase family protein:->->:1109741..1109878 138 ctgaggtaaaaaaagtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Intra-Species Hit: Count: 1 Min: 15 Max: 138 Len: 124 Subject: NC_002967_TDE1077_TDE1078|hypothetical protein:metallo-beta-lactamase family protein|POSITIVE:POSITIVE|[1109741,1109878]|138 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 124 Query Start:15 Query End:138 Subject Strand: POSITIVE Subject Start: 15 Subject End: 138 ..............gtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt ..............gtgtctattataaaatttatgacaacagtcttggttctcttgagcaaatgcgtttcttatgataatatttaagctgcggattggttttaatccgcagcttttagtttatggaggtatcaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCUAUUAUAAAAUUUAUGACAACAGUCUUGGUUCUCUUGAGCAAAUGCGUUUCUUAUGAUAAUAUUUAAGCUGCGGAUUGGUUUUAAUCCGCAGCUUUUAGUUUAUGGAGGUAUCAAUUUU .((((...............))))......(((((((((((((((.....(((.....))).........(((((((((((((....)))))))))))))...))))).))))).))))).... (-32.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUGAUACCUCCAUAAACUAAAAGCUGCGGAUUAAAACCAAUCCGCAGCUUAAAUAUUAUCAUAAGAAACGCAUUUGCUCAAGAGAACCAAGACUGUUGUCAUAAAUUUUAUAAUAGACAC ((((((.....(((..........((((((((((((......))))))))))))...................((....))....)))......(((....)))...))))))........... (-26.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 114 72 163 110 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 288 115 71 170 120 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 276 115 71 213 155 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 265 115 71 204 176 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 251 115 72 165 130 NC_002967:TDE1486|5end_hypothetical_protein_1530299..1530529_POSITIVE 249 120 71 222 166 NC_002967:TDE2657|5end_precorrin-2_C20-methyltransferase,_putative_2693822..2694052_POSITIVE 249 116 75 176 129 NC_002967:TDE2167|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2200847..2201077_NEGATIVE 249 117 72 64 17 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 248 98 71 62 34 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 247 100 54 42 1 NC_002967:TDE0388|5end_hypothetical_protein_439173..439403_POSITIVE 247 63 22 175 123 NC_002967:TDE0368|5end_type_I_restriction-modification_system,_S_subunit,_putative_418245..418475_NEGATIVE 245 105 63 154 116 NC_002967:TDE1498|5end_hypothetical_protein_1543669..1543899_POSITIVE 245 56 31 75 47 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 244 107 71 66 31 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 243 58 27 151 120 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 243 116 80 166 130 NC_002967:TDE1222|5end_iron-dependent_transcriptional_regulator_1256709..1256939_NEGATIVE 243 114 75 159 117 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 242 57 19 65 15 NC_002967:TDE1886|5end_MiaB-like_tRNA_modifying_enzyme_1908488..1908718_NEGATIVE 241 119 73 205 149 NC_002967:TDE2245|5end_DNA_topoisomerase_IV_subunit_B_2284240..2284470_POSITIVE 240 116 74 54 12 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 120 73 107 62 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 276 102 71 83 49 NC_002967:TDE0755|3end_Na+/H+_antiporter_family_protein_794533..794683_NEGATIVE 266 114 71 55 2 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 262 113 72 54 11 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 261 100 72 103 76 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 258 117 75 105 56 NC_002967:TDE1666|3end_hypothetical_protein_1720021..1720171_POSITIVE 256 118 72 129 70 NC_002967:TDE0903|3end_ATP-dependent_DNA_helicase_PcrA_922296..922446_POSITIVE 250 114 72 49 10 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 249 116 75 148 101 NC_002967:TDE2168|3end_hypothetical_protein_2200875..2201025_NEGATIVE 249 117 72 52 5 NC_002967:TDE0780|3end_ribosomal_protein_S14_812629..812779_POSITIVE 249 119 72 67 23 NC_002967:TDE0536|3end_hypothetical_protein_578064..578214_NEGATIVE 247 100 54 45 4 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE 247 63 22 64 12 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 246 80 36 142 110 NC_002967:TDE1037|3end_hypothetical_protein_1065461..1065611_POSITIVE 245 120 71 119 57 NC_002967:TDE1931|3end_cytidine_deaminase_1949020..1949170_POSITIVE 245 105 63 109 71 NC_002967:TDE1497|3end_hypothetical_protein_1543704..1543854_POSITIVE 245 56 31 58 30 NC_002967:TDE1137|3end_hypothetical_protein_1166066..1166216_NEGATIVE 243 115 73 58 16 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 243 58 27 134 103 NC_002967:TDE1491|3end_chemotaxis_protein_CheA_1537294..1537444_POSITIVE 243 116 80 140 104 NC_002967:TDE1223|3end_zinc_ABC_transporter,_permease_protein_1256735..1256885_NEGATIVE