Origin IGS: ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttatctccttatttgtttcaatatacttaatcctttcagccgatcttcttcatcaactatattttttatatcctaattatatcatttttcattattgtttttaagggggaaagatgaaaagctgacagtagaaaaaataccttaaaaaggatataatggtatcaaatatgtaatgcaatgagaattgtgaacggagagatgataa Mask Tandem Repeat Region ================================================ ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Find is-nt database================================================ Query_seq: TDE0536:TDE0537|TDE0536:TDE0537:hypothetical protein:hypothetical protein:<-->:578955..579163 209 ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0536:TDE0537|TDE0536:TDE0537:hypothetical protein:hypothetical protein:<-->:578955..579163 209 ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0536:TDE0537|TDE0536:TDE0537:hypothetical protein:hypothetical protein:<-->:578955..579163 209 ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 105 End: 209 ........................................................................................................ F C Y H F I I Y N P Y L F Y L Q H L L D A S L I L Y I S V F L S I F M ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat 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: 84 Start: 49 End: 78 ................................................GTAGAAAAAATACCTTAAAAAGGATATAAT................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 101 End: 130 ....................................................................................................CTTAAAAACAATAATGAAAAATGATATAAT............................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0536:TDE0537|TDE0536:TDE0537:hypothetical protein:hypothetical protein:<-->:578955..579163 209 ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttcccccttaaaaacaataatgaaaaatgatataattaggatataaaaaatatagttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_002967_TDE0536_TDE0537|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[578955,579163]|209 HSP 1 e-value: 3.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttccccct........................................................................................................... ttatcatctctccgttcacaattctcattgcattacatatttgataccattatatcctttttaaggtattttttctactgtcagcttttcatctttccccct........................................................................................................... HSP 2 e-value: 1.0E-26 bit: 121.0 Len: 61 Query Start:149 Query End:209 Subject Strand: POSITIVE Subject Start: 149 Subject End: 209 ....................................................................................................................................................gttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat ....................................................................................................................................................gttgatgaagaagatcggctgaaaggattaagtatattgaaacaaataaggagataaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCAUCUCUCCGUUCACAAUUCUCAUUGCAUUACAUAUUUGAUACCAUUAUAUCCUUUUUAAGGUAUUUUUUCUACUGUCAGCUUUUCAUCUUUCCCCCUUAAAAACAAUAAUGAAAAAUGAUAUAAUUAGGAUAUAAAAAAUAUAGUUGAUGAAGAAGAUCGGCUGAAAGGAUUAAGUAUAUUGAAACAAAUAAGGAGAUAAAAAU ........(((((.....((((....))))......(((((((((.((.(((((((((..(((.((((.......))))((((..(((((((..((.............))..))))))).)))).)))..)))))))))......((((((((.......))))))))...)))))))))))..............)))))....... (-37.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAUCUCCUUAUUUGUUUCAAUAUACUUAAUCCUUUCAGCCGAUCUUCUUCAUCAACUAUAUUUUUUAUAUCCUAAUUAUAUCAUUUUUCAUUAUUGUUUUUAAGGGGGAAAGAUGAAAAGCUGACAGUAGAAAAAAUACCUUAAAAAGGAUAUAAUGGUAUCAAAUAUGUAAUGCAAUGAGAAUUGUGAACGGAGAGAUGAUAA .......(((((.((((((..(((.((((.....((((((((((.((......))..............................(((((((((....(((....)))....)))))))))...)))))..(((.......)))......))))))))).)))...))))))......(((((....)))))....)))))........ (-34.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 797 50 1 141 92 NC_002967:TDE0536|5end_hypothetical_protein_578864..579094_NEGATIVE 299 103 62 50 1 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 270 99 51 106 53 NC_002967:TDE2774|5end_hypothetical_protein_2825994..2826224_POSITIVE 260 46 9 122 81 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 248 104 64 107 52 NC_002967:TDE1329|5end_ATPase,_AAA_family_1363503..1363733_POSITIVE 240 193 158 36 3 NC_002967:TDE2300|5end_trypsin_domain/PDZ_domain_protein_2341434..2341664_NEGATIVE 239 175 148 28 1 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 237 100 57 100 63 NC_002967:TDE1752|5end_ISTde2,_transposase_1805398..1805628_NEGATIVE 237 100 57 100 63 NC_002967:TDE1022|5end_ISTde2,_transposase_1054988..1055218_NEGATIVE 237 100 57 100 63 NC_002967:TDE0140|5end_ISTde2,_transposase_162731..162961_POSITIVE 233 188 144 161 118 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 231 102 64 196 160 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 229 100 55 208 160 NC_002967:TDE2155|5end_50S_ribosomal_protein_L35_2190165..2190395_NEGATIVE 229 180 132 225 179 NC_002967:TDE1992|5end_OmpA_family_protein_2009464..2009694_POSITIVE 228 103 65 56 4 NC_002967:TDE2187|5end_ParB-like_nuclease_domain_protein_2221548..2221778_NEGATIVE 228 104 64 126 94 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 228 100 54 102 62 NC_002967:TDE0532|5end_TPR_domain_protein_575570..575800_POSITIVE 227 59 13 103 52 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 222 40 3 56 17 NC_002967:TDE2453|5end_hypothetical_protein_2481437..2481667_POSITIVE 221 90 49 214 174 NC_002967:TDE0499|5end_hypothetical_protein_553497..553727_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 34 1 56 24 NC_002967:TDE0501|3end_hypothetical_protein_554185..554335_NEGATIVE 278 99 57 148 98 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 264 181 149 33 5 NC_002967:TDE0008|3end_copper-translocating_P-type_ATPase_13646..13796_POSITIVE 260 46 9 110 69 NC_002967:TDE1301|3end_DNA_repair_protein_RecN_1337431..1337581_NEGATIVE 242 199 158 69 25 NC_002967:TDE0668|3end_FeS_assembly_protein_SufD_706966..707116_POSITIVE 233 188 144 99 56 NC_002967:TDE0070|3end_RNA_polymerase_sigma-70_factor,_region_2_family_78620..78770_POSITIVE 231 105 69 126 85 NC_002967:TDE0475|3end_ABC_transporter,_ATP-binding_protein_531153..531303_NEGATIVE 228 104 64 45 13 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 228 104 64 133 101 NC_002967:TDE0611|3end_hypothetical_protein_647279..647429_NEGATIVE 228 100 54 74 34 NC_002967:TDE0531|3end_hypothetical_protein_575622..575772_POSITIVE 227 100 55 111 56 NC_002967:TDE0759|3end_hypothetical_protein_799128..799278_NEGATIVE 224 172 147 149 126 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 221 100 54 88 37 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 221 90 49 147 107 NC_002967:TDE0500|3end_hypothetical_protein_553564..553714_NEGATIVE 220 58 11 100 44 NC_002967:TDE2363|3end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2397472..2397622_NEGATIVE 217 96 54 151 111 NC_002967:TDE1712|3end_flagellar_filament_outer_layer_protein_1766866..1767016_NEGATIVE 217 169 130 113 81 NC_002967:TDE0031|3end_hypothetical_protein_38835..38985_NEGATIVE 215 98 55 88 44 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 212 100 51 87 35 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 211 101 68 113 85 NC_002967:TDE1953|3end_transcriptional_regulator,_TetR_family_1969030..1969180_NEGATIVE