Origin IGS: aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca .........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 tgactttttaaaaaactctaattagataagctaaaaccgaaacaacacatttaacttcggccttcggaatttccgtaccgaagttaaatgtgcaattctaaaagaaaaagaaatcgaagacttcataagaataaatttttcaaataaataggataaaaatatttaatacaaattattgacagaaagtaattaattattatataatagtatgagtaaggaaagtaaggaggcgtttt Mask Tandem Repeat Region ================================================ aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Find is-nt database================================================ Query_seq: TDE0037:TDE0038|TDE0037:TDE0038:transcriptional regulator, AbrB family:3-oxoacyl-(acyl-carrier-protein) synthase II:<-<-:42890..43125 236 aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0037:TDE0038|TDE0037:TDE0038:transcriptional regulator, AbrB family:3-oxoacyl-(acyl-carrier-protein) synthase II:<-<-:42890..43125 236 aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0037:TDE0038|TDE0037:TDE0038:transcriptional regulator, AbrB family:3-oxoacyl-(acyl-carrier-protein) synthase II:<-<-:42890..43125 236 aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 75 End: 203 .......................................................................... M F L S Y L F E K F I L M K S S I S F S F R I A H L T S V R K F R R P K L N V L F R F ................................. aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca 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================================================ aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -5.0 Tail_Score: -5.46706 Start: 113 End: 127 Full_Region: AAAATTTATTCTTAT GAAGTC TTC GATTTC TTTTTCTTTTAGAAT ................................................................................................................GAAGTCTTCGATTTC............................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -4.08307 Start: 145 End: 191 Full_Region: TTTCTTTTAGAATTG CACATTTAACTTCGGTACGGA AAT TCCGAAGGCCGAAGTTAAATGTG TTGTTTCGGTTTTAG ................................................................................................................................................CACATTTAACTTCGGTACGGAAATTCCGAAGGCCGAAGTTAAATGTG............................................. Find igs database================================================ Query_seq: TDE0037:TDE0038|TDE0037:TDE0038:transcriptional regulator, AbrB family:3-oxoacyl-(acyl-carrier-protein) synthase II:<-<-:42890..43125 236 aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaatatttttatcctatttatttgaaaaatttattcttatgaagtcttcgatttctttttcttttagaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002967_TDE0037_TDE0038|transcriptional regulator, AbrB family:3-oxoacyl-(acyl-carrier-protein) synthase II|NEGATIVE:NEGATIVE|[42890,43125]|236 HSP 1 e-value: 9.0E-49 bit: 194.0 Len: 98 Query Start:139 Query End:236 Subject Strand: POSITIVE Subject Start: 139 Subject End: 236 ..........................................................................................................................................gaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca ..........................................................................................................................................gaattgcacatttaacttcggtacggaaattccgaaggccgaagttaaatgtgttgtttcggttttagcttatctaattagagttttttaaaaagtca HSP 2 e-value: 5.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaa................................................................................................................................................................. aaaacgcctccttactttccttactcatactattatataataattaattactttctgtcaataatttgtattaaa................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACGCCUCCUUACUUUCCUUACUCAUACUAUUAUAUAAUAAUUAAUUACUUUCUGUCAAUAAUUUGUAUUAAAUAUUUUUAUCCUAUUUAUUUGAAAAAUUUAUUCUUAUGAAGUCUUCGAUUUCUUUUUCUUUUAGAAUUGCACAUUUAACUUCGGUACGGAAAUUCCGAAGGCCGAAGUUAAAUGUGUUGUUUCGGUUUUAGCUUAUCUAAUUAGAGUUUUUUAAAAAGUCA .............(((((....((((...............(((..(..(((((.((..(((((.((...(((((((.............)))))))..)).)))))..)).)))))..)..))).............(((..(((((((((((((((((.(((.....)))...)))))))))))))))))...)))....................)))).......))))).. (-44.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUUUUUAAAAAACUCUAAUUAGAUAAGCUAAAACCGAAACAACACAUUUAACUUCGGCCUUCGGAAUUUCCGUACCGAAGUUAAAUGUGCAAUUCUAAAAGAAAAAGAAAUCGAAGACUUCAUAAGAAUAAAUUUUUCAAAUAAAUAGGAUAAAAAUAUUUAAUACAAAUUAUUGACAGAAAGUAAUUAAUUAUUAUAUAAUAGUAUGAGUAAGGAAAGUAAGGAGGCGUUUU ...(((((((....((((..((((((((.................(((((((((((((((....(((.....)))..)))))))))))))))..((((((.........(((.((...)).)))....(((.......))).......)))))).....))))))))...(((((((.......)))))))...................))))........)))))))....... (-43.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 706 50 1 141 92 NC_002967:TDE0037|5end_transcriptional_regulator,_AbrB_family_42799..43029_NEGATIVE 302 200 151 230 176 NC_002967:TDE2422|5end_ribosomal_protein_L7/L12_2453300..2453530_NEGATIVE 291 207 161 58 12 NC_002967:TDE0046|5end_formiminotransferase-cyclodeaminase_family_protein_55849..56079_NEGATIVE 280 200 157 62 22 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 276 209 168 200 159 NC_002967:TDE1579|5end_fibronectin/fibrinogen-binding_protein,_internal_deletion_1627489..1627719_NEGATIVE 275 194 154 231 188 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 272 185 153 229 190 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 271 209 167 75 30 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 270 178 140 216 170 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 269 194 156 65 26 NC_002967:TDE1195|5end_prolyl_endopeptidase_1229691..1229921_NEGATIVE 267 200 152 180 136 NC_002967:TDE1783|5end_hypothetical_protein_1823605..1823835_NEGATIVE 267 198 156 124 75 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 265 180 131 45 2 NC_002967:TDE1428|5end_hypothetical_protein_1471107..1471337_POSITIVE 264 184 144 213 170 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 264 200 154 217 167 NC_002967:TDE1355|5end_hypothetical_protein_1395109..1395339_POSITIVE 262 145 109 51 12 NC_002967:TDE2353|5end_flagellar_hook-associated_protein_2389129..2389359_POSITIVE 261 198 154 52 7 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 259 180 134 179 131 NC_002967:TDE1094|5end_hypothetical_protein_1128065..1128295_POSITIVE 258 230 186 105 66 NC_002967:TDE1941|5end_hypothetical_protein_1959285..1959515_NEGATIVE 258 200 154 207 160 NC_002967:TDE1609|5end_hypothetical_protein_1658326..1658556_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 200 151 113 59 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 290 200 155 88 29 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 285 179 145 134 92 NC_002967:TDE1054|3end_methyl-accepting_chemotaxis_protein_1082998..1083148_POSITIVE 272 207 161 52 3 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 265 180 131 48 5 NC_002967:TDE1427|3end_glycosyl_transferase,_group_1_family_protein_1471190..1471340_POSITIVE 258 179 147 67 26 NC_002967:TDE0766|3end_30S_ribosomal_protein_S10_806372..806522_POSITIVE 258 196 157 89 47 NC_002967:TDE0493|3end_hypothetical_protein_548581..548731_NEGATIVE 258 179 132 135 87 NC_002967:TDE0244|3end_ABC_transporter,_ATP-binding/permease_protein_277489..277639_NEGATIVE 258 208 161 92 42 NC_002967:TDE0044|3end_ABC_transporter,_ATP-binding_protein_51660..51810_NEGATIVE 252 184 154 81 51 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 252 213 172 90 49 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 252 210 170 86 47 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 250 198 157 131 86 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 250 176 131 74 24 NC_002967:TDE2073|3end_TPR_domain_protein_2100504..2100654_POSITIVE 250 198 154 151 108 NC_002967:TDE0941|3end_NLP/P60_family_protein_963623..963773_NEGATIVE 248 209 163 59 14 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 247 203 161 140 93 NC_002967:TDE2737|3end_hypothetical_protein_2792690..2792840_POSITIVE 247 190 154 137 108 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 247 199 156 64 2 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 243 200 156 151 113 NC_002967:TDE0857|3end_lipoprotein,_putative_879598..879748_POSITIVE