Origin IGS: tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttattacaactccttattatactgttgtctatgttttttgcagtatcatgcactgttacagacagtttaatgttgtttcaaatgctattgatacaattagccgttatttgtttgaacgaccttatatca Mask Tandem Repeat Region ================================================ tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Find is-nt database================================================ Query_seq: TDE2452:TDE2453|TDE2452:TDE2453:hypothetical protein:hypothetical protein:->->:2481447..2481576 130 tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2452:TDE2453|TDE2452:TDE2453:hypothetical protein:hypothetical protein:->->:2481447..2481576 130 tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2452:TDE2453|TDE2452:TDE2453:hypothetical protein:hypothetical protein:->->:2481447..2481576 130 tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 2 End: 127 . I Y P R E F L Y R S I T D I A N S V V N F Q R Y C H M I S C F V Y V V T Y Y P T T M ... Protein_Len: 38 Strand: - Start: 1 End: 114 S I L D N L C I V A L Q I L L M Q F L M L S D T V T C S V A F F M S L L I M ................ tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2452:TDE2453|TDE2452:TDE2453:hypothetical protein:hypothetical protein:->->:2481447..2481576 130 tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE2452_TDE2453|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2481447,2481576]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa tgatataaggtcgttcaaacaaataacggctaattgtatcaatagcatttgaaacaacattaaactgtctgtaacagtgcatgatactgcaaaaaacatagacaacagtataataaggagttgtaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUAAGGUCGUUCAAACAAAUAACGGCUAAUUGUAUCAAUAGCAUUUGAAACAACAUUAAACUGUCUGUAACAGUGCAUGAUACUGCAAAAAACAUAGACAACAGUAUAAUAAGGAGUUGUAAUAAA (((((((((((((((.........)))))))..))))))))............(((((((((.(((((((((.....((((......))))......))))))...))).)))).....)))))...... (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUACAACUCCUUAUUAUACUGUUGUCUAUGUUUUUUGCAGUAUCAUGCACUGUUACAGACAGUUUAAUGUUGUUUCAAAUGCUAUUGAUACAAUUAGCCGUUAUUUGUUUGAACGACCUUAUAUCA ..................((((..(((((..........((((......))))......(((((((..(((((((((.((((......)))).)))).....))))).))))))).)))))..))))... (-20.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 123 86 223 188 NC_002967:TDE2546|5end_hypothetical_protein_2572761..2572991_NEGATIVE 264 47 7 213 174 NC_002967:TDE2627|5end_transcriptional_regulator,_TetR_family_2669140..2669370_NEGATIVE 241 80 31 138 70 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 237 90 66 228 198 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 236 92 59 228 184 NC_002967:TDE2178|5end_hypothetical_protein_2208758..2208988_NEGATIVE 235 119 76 212 167 NC_002967:TDE1049|5end_elongation_factor_EF-2_1075287..1075517_POSITIVE 220 110 64 150 114 NC_002967:TDE0241|5end_hypothetical_protein_275303..275533_NEGATIVE 213 48 8 108 62 NC_002967:TDE0220|5end_hypothetical_protein_254005..254235_NEGATIVE 212 49 1 85 41 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 209 90 65 207 181 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 209 109 62 43 3 NC_002967:TDE0324|5end_hypothetical_protein_357444..357674_POSITIVE 208 127 85 55 2 NC_002967:TDE0583|5end_hypothetical_protein_622199..622429_NEGATIVE 207 90 41 195 141 NC_002967:TDE1231|5end_hypothetical_protein_1265203..1265433_NEGATIVE 202 30 3 35 7 NC_002967:TDE1399|5end_prolipoprotein_diacylglyceryl_transferase_1439393..1439623_POSITIVE 197 127 83 225 175 NC_002967:TDE1960|5end_hypothetical_protein_1974298..1974528_POSITIVE 197 73 32 77 26 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 196 119 81 103 74 NC_002967:TDE2780|5end_hypothetical_protein_2830621..2830851_NEGATIVE 194 89 64 204 173 NC_002967:TDE2750|5end_GTP-binding_protein_HflX,_truncation_2806033..2806263_POSITIVE 194 108 61 73 17 NC_002967:TDE1698|5end_serine/threonine_protein_phosphatase_family_protein_1757184..1757414_NEGATIVE 192 92 56 196 157 NC_002967:TDE1947|5end_ABC_transporter,_permease_protein_1963449..1963679_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 80 31 120 52 NC_002967:TDE1548|3end_conserved_hypothetical_protein_TIGR00103_1592202..1592352_POSITIVE 220 110 64 139 103 NC_002967:TDE0242|3end_hypothetical_protein_275314..275464_NEGATIVE 213 48 8 67 21 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 212 49 1 78 34 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 208 75 37 149 108 NC_002967:TDE1343|3end_trypsin_domain/PDZ_domain_protein_1382236..1382386_POSITIVE 208 127 85 58 5 NC_002967:TDE0584|3end_permease,_putative_622196..622346_NEGATIVE 197 73 32 53 2 NC_002967:TDE1095|3end_alanine_racemase_1131045..1131195_POSITIVE 196 119 81 85 56 NC_002967:TDE2781|3end_ABC_transporter,_ATP-binding/permease_protein_2830639..2830789_NEGATIVE 195 70 26 147 113 NC_002967:TDE1018|3end_hypothetical_protein_1049735..1049885_POSITIVE 194 89 64 147 116 NC_002967:TDE2749|3end_hypothetical_protein_2806056..2806206_POSITIVE 194 108 61 71 15 NC_002967:TDE1699|3end_hypothetical_protein_1757186..1757336_NEGATIVE 187 110 69 51 9 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 185 48 5 69 27 NC_002967:TDE0815|3end_hypothetical_protein_835977..836127_NEGATIVE 183 77 36 68 16 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 182 46 1 52 6 NC_002967:TDE0799|3end_glycerophosphoryl_diester_phosphodiesterase,_putative_823468..823618_POSITIVE 181 94 56 53 13 NC_002967:TDE1824|3end_hypothetical_protein_1857198..1857348_POSITIVE 180 110 66 84 37 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 180 60 20 60 13 NC_002967:TDE1436|3end_inner_membrane_protein_1482290..1482440_POSITIVE 178 90 41 50 4 NC_002967:TDE1566|3end_hypothetical_protein_1618984..1619134_POSITIVE 177 40 4 74 27 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE