Origin IGS: aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttaggaggtacgataaacagctcggcaggaattcagcctcactgtttatcttcgagtttgccgtaaacggcaaacatcgtttatcgtatgcggtttgtaaacaaaccgcttgaaaaaacttttttcggaaactaatgtttcctgcaaaaagtttttagagaggtaggtt Mask Tandem Repeat Region ================================================ aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Find is-nt database================================================ Query_seq: TDE1915:TDE1916|TDE1915:TDE1916:alcohol dehydrogenase, iron-containing:glycerol kinase:<-<-:1933194..1933366 173 aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1915:TDE1916|TDE1915:TDE1916:alcohol dehydrogenase, iron-containing:glycerol kinase:<-<-:1933194..1933366 173 aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1915:TDE1916|TDE1915:TDE1916:alcohol dehydrogenase, iron-containing:glycerol kinase:<-<-:1933194..1933366 173 aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 23 End: 121 ...................... M Q E T L V S E K S F F K R F V Y K P H T I N D V C R L R Q T R R .................................................... Protein_Len: 46 Strand: + Start: 34 End: 171 ................................. M S F R K K F F Q A V C L Q T A Y D K R C L P F T A N S K I N S E A E F L P S C L S Y L L K .. aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt 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================================================ aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -7.2 Tail_Score: -4.57569 Start: 19 End: 51 Full_Region: aaccgcttgaaaaaa cttttttcggaaac taat gtttcctgcaaaaag tttttagagaggtag ..................cttttttcggaaactaatgtttcctgcaaaaag.......................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -7.7 Tail_Score: -3.85698 Start: 77 End: 109 Full_Region: ttatcttcgagtttg ccgtaaacggcaaac atc gtttatcgtatgcgg tttgtaaacaaaccg ............................................................................ccgtaaacggcaaacatcgtttatcgtatgcgg................................................................ TransTerm Strand: - Conf: 91 HP_score: -11.7 Tail_Score: -4.01888 Start: 91 End: 117 Full_Region: ctcactgtttatctt cgagtttgccg taaa cggcaaacatcg tttatcgtatgcggt ..........................................................................................cgagtttgccgtaaacggcaaacatcg........................................................ Find igs database================================================ Query_seq: TDE1915:TDE1916|TDE1915:TDE1916:alcohol dehydrogenase, iron-containing:glycerol kinase:<-<-:1933194..1933366 173 aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Intra-Species Hit: Count: 6 Min: 1 Max: 173 Len: 173 Subject: NC_002967_TDE1915_TDE1916|alcohol dehydrogenase, iron-containing:glycerol kinase|NEGATIVE:NEGATIVE|[1933194,1933366]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt aacctacctctctaaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaacgatgtttgccgtttacggcaaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaaatt Subject: NC_002967_TDE0743_TDE0744|thioredoxin reductase:thioredoxin|POSITIVE:POSITIVE|[779812, 779983]|172 HSP 1 e-value: 1.0E-25 bit: 117.0 Len: 71 Query Start:13 Query End:83 Subject Strand: NEGATIVE Subject Start: 89 Subject End: 159 ............taaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcata.......................................................................................... ............taaagactttttgcaggaaacctcagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcata.......................................................................................... HSP 2 e-value: 2.0E-12 bit: 73.8 Len: 56 Query Start:111 Query End:166 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 57 ..............................................................................................................aaactcga-agataaacagtgaggctgaattcctgccgagctgtttatcgtacctcc....... ..............................................................................................................aaactcgatagataaacagtgaggctgaattcctgccgaaccgtttatcgtatctcc....... Subject: NC_002967_TDE0064_TDE0065|diphosphate--fructose-6-phosphate 1-phosphotransferase:hypothetical protein|NEGATIVE:NEGATIVE|[72742,72911]|170 HSP 1 e-value: 3.0E-17 bit: 89.7 Len: 57 Query Start:111 Query End:167 Subject Strand: POSITIVE Subject Start: 112 Subject End: 168 ..............................................................................................................aaactcgaagataaacagtgaggctgaattcctgccgagctgtttatcgtacctcct...... ..............................................................................................................aaactcgaagataaacagtgaggctgaatttctgccgaactgtttatcttacctcct...... HSP 2 e-value: 7.0E-15 bit: 81.8 Len: 77 Query Start:13 Query End:89 Subject Strand: POSITIVE Subject Start: 12 Subject End: 88 ............taaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataa.................................................................................... ............taaaaactttttgcagcaaatatcaatttgcgaaaaaagttttttcaagcagtttgttcacaaactgcatacaataa.................................................................................... Subject: NC_002967_TDE0641_TDE0642|UDP-N-acetylglucosamine 1-carboxyvinyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[678373,678549]|177 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 125 Query Start:44 Query End:168 Subject Strand: POSITIVE Subject Start: 45 Subject End: 169 ...........................................gaaaaaagttttttcaagcggtttgtttacaaaccgcatacgataaa-cgatgtttgccgtttacggcaaactcga-agataaacagtgaggctgaattcctgccgagctgtttatcgtacctccta..... ...........................................gaaaaaagttttttcacgcagtttgtttacaaactgcatacaataatgcgacgtttgccga--aaggcaaacttggcagataaacagtgaggctgaattccttccgaactgtttatcatatctccta..... Subject: NC_002967_TDE2497_TDE2498|hypothetical protein:metallo-beta-lactamase family protein|NEGATIVE:NEGATIVE|[2522174,2522283]|110 HSP 1 e-value: 4.0E-13 bit: 75.8 Len: 107 Query Start:64 Query End:170 Subject Strand: POSITIVE Subject Start: 4 Subject End: 110 ...............................................................gtttgtttacaaaccgcatacgataaa-cgatgtttgccgtttacggcaaactcga-agataaacagtgaggctgaattcctgccgagctgtttatcgtacctcctaaa... ...............................................................gtttgtttacaaactgcatacaataatgcgacgtttgccga--aaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcacacctcctaaa... Subject: NC_002967_TDE0521_TDE0522|carboxylesterase family protein:hypothetical protein|NEGATIVE:POSITIVE|[568343,568638]|296 HSP 1 e-value: 1.0E-7 bit: 58.0 Len: 49 Query Start:119 Query End:167 Subject Strand: NEGATIVE Subject Start: 124 Subject End: 172 ......................................................................................................................agataaacagtgaggctgaattcctgccgagctgtttatcgtacctcct...... ......................................................................................................................agataaacagtggggctgaatttctgccgaactgtttatcatatctcct...... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 49 Query Start:13 Query End:61 Subject Strand: NEGATIVE Subject Start: 235 Subject End: 283 ............taaaaactttttgcaggaaacattagtttccgaaaaaagttttttcaag................................................................................................................ ............taaaaactttttgcagcaaatatcaatttgcgaaaaaagttttttcaag................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUACCUCUCUAAAAACUUUUUGCAGGAAACAUUAGUUUCCGAAAAAAGUUUUUUCAAGCGGUUUGUUUACAAACCGCAUACGAUAAACGAUGUUUGCCGUUUACGGCAAACUCGAAGAUAAACAGUGAGGCUGAAUUCCUGCCGAGCUGUUUAUCGUACCUCCUAAAAUU .............(((((((((((...((((((....))))))..)))))))))))....((((((((....))))))))..........(((.((((((((....)))))))))))..((((((((((..(((.........)))..))))))))))............... (-65.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAGGAGGUACGAUAAACAGCUCGGCAGGAAUUCAGCCUCACUGUUUAUCUUCGAGUUUGCCGUAAACGGCAAACAUCGUUUAUCGUAUGCGGUUUGUAAACAAACCGCUUGAAAAAACUUUUUUCGGAAACUAAUGUUUCCUGCAAAAAGUUUUUAGAGAGGUAGGUU ...............(((((((((...(((.........)))...)))))))))..(((((((((((....)))))))).))).(((((....((((((((....))))))))....(((((((((((.(((((((....)))))).).))))))))))).....)))))... (-60.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 922 110 61 201 152 NC_002967:TDE1915|5end_alcohol_dehydrogenase,_iron-containing_1933103..1933333_NEGATIVE 881 159 111 179 131 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 881 159 111 69 21 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 854 168 121 138 91 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 812 170 121 179 130 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 795 170 121 201 152 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 793 160 111 142 93 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 778 168 121 75 28 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 777 168 121 200 153 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 777 168 121 99 52 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 755 159 111 182 134 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 745 159 111 178 129 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 742 166 121 159 114 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 740 100 51 191 141 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 720 80 31 172 123 NC_002967:TDE0744|5end_thioredoxin_779844..780074_POSITIVE 712 168 121 156 109 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 709 158 111 180 133 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 702 100 51 210 159 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 696 139 91 231 184 NC_002967:TDE1903|5end_hypothetical_protein_1922417..1922647_POSITIVE 685 160 111 91 41 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 854 168 121 62 15 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 853 160 111 84 34 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 834 160 111 63 14 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 795 170 121 90 41 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 793 160 111 74 25 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 779 170 124 47 1 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 778 168 121 60 13 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 777 168 121 79 32 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 772 158 111 79 32 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 766 167 121 81 35 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 755 159 111 80 32 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 745 159 111 74 25 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 712 168 121 89 42 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 711 158 111 82 34 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 710 168 121 82 35 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 705 89 43 145 99 NC_002967:TDE1513|3end_hypothetical_protein_1560698..1560848_POSITIVE 702 100 51 136 85 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 681 89 43 145 99 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE 659 160 111 69 20 NC_002967:TDE2398|3end_conserved_hypothetical_protein_TIGR00278_2425586..2425736_NEGATIVE 657 69 21 150 102 NC_002967:TDE1325|3end_hypothetical_protein_1361620..1361770_NEGATIVE