Origin IGS: cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttcccccgaccaaaaaaaaacggctgagccgtttttaggcttccaaccgtgctttagtataacttatttttgacttatccgcaagggggcagtttgaatttaattatacgaactgcaatttagcaggtaaaatttgtgagtctatctagg Mask Tandem Repeat Region ================================================ cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Find is-nt database================================================ Query_seq: TDE2691:TDE2692|TDE2691:TDE2692:hypothetical protein:CTP synthetase:->->:2729407..2729560 154 cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2691:TDE2692|TDE2691:TDE2692:hypothetical protein:CTP synthetase:->->:2729407..2729560 154 cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2691:TDE2692|TDE2691:TDE2692:hypothetical protein:CTP synthetase:->->:2729407..2729560 154 cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Predict ORF larger than 30AA ================================================ cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt 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: 19 End: 48 ..................TTTTACCTGCTAAATTGCAGTTCGTATAAT.......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.2 Tail_Score: -6.15828 Start: 120 End: 130 Full_Region: TTGGAAGCCTAAAAA CGGC TCA GCCG TTTTTTTTTGGTCGG .......................................................................................................................CGGCTCAGCCG........................ Find igs database================================================ Query_seq: TDE2691:TDE2692|TDE2691:TDE2692:hypothetical protein:CTP synthetase:->->:2729407..2729560 154 cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccgtttttttttggtcgggggaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE2691_TDE2692|hypothetical protein:CTP synthetase|POSITIVE:POSITIVE|[2729407,2729560]|154 HSP 1 e-value: 5.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccg........................ cctagatagactcacaaattttacctgctaaattgcagttcgtataattaaattcaaactgcccccttgcggataagtcaaaaataagttatactaaagcacggttggaagcctaaaaacggctcagccg........................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUAGAUAGACUCACAAAUUUUACCUGCUAAAUUGCAGUUCGUAUAAUUAAAUUCAAACUGCCCCCUUGCGGAUAAGUCAAAAAUAAGUUAUACUAAAGCACGGUUGGAAGCCUAAAAACGGCUCAGCCG ........((((....((((.(((((((......))))...))).)))).........((((......))))...))))......................((((((..((((.......)))))))))) (-26.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGCUGAGCCGUUUUUAGGCUUCCAACCGUGCUUUAGUAUAACUUAUUUUUGACUUAUCCGCAAGGGGGCAGUUUGAAUUUAAUUAUACGAACUGCAAUUUAGCAGGUAAAAUUUGUGAGUCUAUCUAGG ((((...))))....((((((..(((((.((((........................(((....))).((((((((.((......)).)))))))).....)))))))......))..))))))...... (-33.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 130 94 213 173 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 281 129 84 67 25 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 275 129 99 89 47 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 269 130 99 185 144 NC_002967:TDE0845|5end_conserved_hypothetical_protein_TIGR00266_867795..868025_POSITIVE 267 44 20 228 199 NC_002967:TDE0679|5end_aminotransferase,_class_V_716345..716575_POSITIVE 262 130 86 226 185 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 261 123 87 135 104 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 261 91 55 68 22 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 256 130 104 36 6 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 254 129 100 120 89 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 249 128 96 219 168 NC_002967:TDE0491|5end_hypothetical_protein_546716..546946_POSITIVE 247 73 33 37 3 NC_002967:TDE2571|5end_hypothetical_protein_2598152..2598382_NEGATIVE 247 108 61 67 1 NC_002967:TDE1402|5end_hypothetical_protein_1443158..1443388_POSITIVE 244 130 94 208 155 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 243 125 85 200 154 NC_002967:TDE1597|5end_transporter,_putative_1647402..1647632_NEGATIVE 243 129 102 191 163 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 242 130 96 184 147 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 242 130 81 99 43 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 239 129 95 206 177 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 235 130 101 184 155 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 130 100 118 92 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 269 130 99 83 42 NC_002967:TDE0844|3end_pyruvate_phosphate_dikinase,_putative_867773..867923_POSITIVE 261 123 87 54 23 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 261 91 55 55 9 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 247 73 33 44 10 NC_002967:TDE2572|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598145..2598295_NEGATIVE 246 130 97 51 12 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 246 130 110 97 77 NC_002967:TDE2517|3end_DNA_repair_protein_RadA_2542454..2542604_NEGATIVE 244 90 52 129 89 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 243 129 102 133 105 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 241 130 96 71 41 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 241 130 93 83 41 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 236 127 99 71 32 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 234 130 99 73 46 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 233 130 91 82 43 NC_002967:TDE0251|3end_tryptophanase_284717..284867_NEGATIVE 232 73 53 141 118 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 232 79 33 58 6 NC_002967:TDE0795|3end_hypothetical_protein_819588..819738_NEGATIVE 230 130 92 48 8 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 228 130 97 69 32 NC_002967:TDE2712|3end_hypothetical_protein_2769615..2769765_POSITIVE 227 129 97 138 102 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 224 116 72 94 44 NC_002967:TDE1262|3end_hypothetical_protein_1297213..1297363_NEGATIVE