Origin IGS: taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacaatcctcccaaaaaattaaaaacctttcagttaagctaaggctttgcattgtaccatgtttttacggattgtacaagggaagaattgaagggattgattgatggtgctaggctgaatttaaaaatcggta Mask Tandem Repeat Region ================================================ taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Find is-nt database================================================ Query_seq: TDE2334:TDE2335|TDE2334:TDE2335:hypothetical protein:ATP-dependent DNA helicase, UvrD/Rep family:->->:2369648..2369780 133 taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2334:TDE2335|TDE2334:TDE2335:hypothetical protein:ATP-dependent DNA helicase, UvrD/Rep family:->->:2369648..2369780 133 taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2334:TDE2335|TDE2334:TDE2335:hypothetical protein:ATP-dependent DNA helicase, UvrD/Rep family:->->:2369648..2369780 133 taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Predict ORF larger than 30AA ================================================ taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt 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: 54 End: 83 .....................................................CTTGTACAATCCGTAAAAACATGGTACAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2334:TDE2335|TDE2334:TDE2335:hypothetical protein:ATP-dependent DNA helicase, UvrD/Rep family:->->:2369648..2369780 133 taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaaggtttttaattttttgggaggattgtt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002967_TDE2334_TDE2335|hypothetical protein:ATP-dependent DNA helicase, UvrD/Rep family|POSITIVE:POSITIVE|[2369648,2369780]|133 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaagg......................... taccgatttttaaattcagcctagcaccatcaatcaatcccttcaattcttcccttgtacaatccgtaaaaacatggtacaatgcaaagccttagcttaactgaaagg......................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCGAUUUUUAAAUUCAGCCUAGCACCAUCAAUCAAUCCCUUCAAUUCUUCCCUUGUACAAUCCGUAAAAACAUGGUACAAUGCAAAGCCUUAGCUUAACUGAAAGG ..............(((((...(((.............................((((((.....((....))...)))))).((...))....)))...)))))... (-11.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUCAGUUAAGCUAAGGCUUUGCAUUGUACCAUGUUUUUACGGAUUGUACAAGGGAAGAAUUGAAGGGAUUGAUUGAUGGUGCUAGGCUGAAUUUAAAAAUCGGUA ((((((((((.........((((.(.((((((..(((....)))....))))))).))))))))))))))..................(((((.........))))). (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 66 26 127 87 NC_002967:TDE1593|5end_Fe-hydrogenase_1642999..1643229_NEGATIVE 258 57 15 181 141 NC_002967:TDE1304|5end_hypothetical_protein_1339716..1339946_POSITIVE 255 59 18 118 81 NC_002967:TDE2682|5end_hypothetical_protein_2723358..2723588_NEGATIVE 251 49 3 64 20 NC_002967:TDE1995|5end_magnesium_chelatase_family_protein_2012464..2012694_POSITIVE 249 96 63 64 23 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 249 60 13 144 98 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 246 58 13 108 41 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 244 54 18 89 52 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 243 82 44 56 19 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 239 96 53 40 1 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 235 93 51 51 6 NC_002967:TDE0980|5end_asparaginyl-tRNA_synthetase_1005400..1005630_NEGATIVE 234 98 71 36 11 NC_002967:TDE1290|5end_hypothetical_protein_1327399..1327629_POSITIVE 230 53 17 102 64 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 228 90 42 184 143 NC_002967:TDE1494|5end_chemotaxis_protein_CheY_1539076..1539306_POSITIVE 227 47 1 104 61 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 227 66 21 179 127 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 222 100 51 212 167 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 222 97 51 222 173 NC_002967:TDE0600|5end_hypothetical_protein_638777..639007_NEGATIVE 222 66 24 225 186 NC_002967:TDE0355|5end_hypothetical_protein_399005..399235_POSITIVE 222 59 16 76 24 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 56 17 149 108 NC_002967:TDE2165|3end_hydrogenase_accessory_protein_HypB_2197053..2197203_NEGATIVE 262 66 26 133 93 NC_002967:TDE1594|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1642993..1643143_NEGATIVE 255 59 18 109 72 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 254 97 61 48 12 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 249 60 13 144 98 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 244 54 18 89 52 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE 235 41 4 111 49 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 234 98 71 67 42 NC_002967:TDE1289|3end_hypothetical_protein_1327510..1327660_POSITIVE 222 66 24 141 102 NC_002967:TDE0354|3end_general_stress_protein_14_399001..399151_POSITIVE 221 59 37 116 93 NC_002967:TDE1280|3end_hypothetical_protein_1315750..1315900_NEGATIVE 221 98 51 134 95 NC_002967:TDE1173|3end_site-specific_recombinase,_phage_integrase_family_1201257..1201407_NEGATIVE 221 49 3 63 7 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 219 60 16 149 104 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 218 97 52 45 7 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE 213 60 14 146 93 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 209 55 18 42 8 NC_002967:TDE1504|3end_ribosomal_protein_L31_1553633..1553783_POSITIVE 208 71 32 53 15 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 208 66 22 98 59 NC_002967:TDE0193|3end_hypothetical_protein_228613..228763_NEGATIVE 207 98 52 52 4 NC_002967:TDE1909|3end_conserved_hypothetical_protein_TIGR00159_1926048..1926198_NEGATIVE 207 41 18 76 56 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE