Origin IGS: aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg .........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 catgactcctataatctcctgtataatataacaatttgaaaattaatattcaataagaaagacgtataaactttgcactcatttttcatttttcataatgtgacttagtctcttgaaaaaatataaaatttatggtaagcttgtttatcgggactgttcatttccattatacgcagtatgcttctaaaatcatattttctttttgtaatagacttgaataatccctaatacttttataaggacggttttt Mask Tandem Repeat Region ================================================ aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Find is-nt database================================================ Query_seq: TDE0665:TDE0666|TDE0665:TDE0666:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:FeS assembly ATPase SufC:<-->:703443..703692 250 aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0665:TDE0666|TDE0665:TDE0666:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:FeS assembly ATPase SufC:<-->:703443..703692 250 aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0665:TDE0666|TDE0665:TDE0666:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:FeS assembly ATPase SufC:<-->:703443..703692 250 aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 42 End: 143 ......................................... M T K R K Y D F R S I L R I M E M N S P D K Q A Y H K F Y I F S R D ........................................................................................................... Protein_Len: 32 Strand: - Start: 33 End: 128 ................................ E L R N C F S F I I K S A Y Q T Y H F H V T G I F L S V M F K M .......................................................................................................................... aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg 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: 197 End: 226 ....................................................................................................................................................................................................ATTGAATATTAATTTTCAAATTGTTATATT........................ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 110 End: 139 .............................................................................................................CTTGAAAAAATATAAAATTTATGGTAAGCT............................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0665:TDE0666|TDE0665:TDE0666:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:FeS assembly ATPase SufC:<-->:703443..703692 250 aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: NC_002967_TDE0665_TDE0666|pyruvate ferredoxin/flavodoxin oxidoreductase family protein:FeS assembly ATPase SufC|NEGATIVE:POSITIVE|[703443,703692]|250 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg aaaaaccgtccttataaaagtattagggattattcaagtctattacaaaaagaaaatatgattttagaagcatactgcgtataatggaaatgaacagtcccgataaacaagcttaccataaattttatattttttcaagagactaagtcacattatgaaaaatgaaaaatgagtgcaaagtttatacgtctttcttattgaatattaattttcaaattgttatattatacaggagattataggagtcatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCGUCCUUAUAAAAGUAUUAGGGAUUAUUCAAGUCUAUUACAAAAAGAAAAUAUGAUUUUAGAAGCAUACUGCGUAUAAUGGAAAUGAACAGUCCCGAUAAACAAGCUUACCAUAAAUUUUAUAUUUUUUCAAGAGACUAAGUCACAUUAUGAAAAAUGAAAAAUGAGUGCAAAGUUUAUACGUCUUUCUUAUUGAAUAUUAAUUUUCAAAUUGUUAUAUUAUACAGGAGAUUAUAGGAGUCAUG ........(((((((((..(((...((((((.((((..(((((((......((((......))))....((.....))...)))))))..)))).)))))).......((((((..(((..(((((.((((((((...(.(((...))).).....)))))))).)))))..)))..)))))).)))..........(((((........))))).........))))).))))((((.....))))... (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGACUCCUAUAAUCUCCUGUAUAAUAUAACAAUUUGAAAAUUAAUAUUCAAUAAGAAAGACGUAUAAACUUUGCACUCAUUUUUCAUUUUUCAUAAUGUGACUUAGUCUCUUGAAAAAAUAUAAAAUUUAUGGUAAGCUUGUUUAUCGGGACUGUUCAUUUCCAUUAUACGCAGUAUGCUUCUAAAAUCAUAUUUUCUUUUUGUAAUAGACUUGAAUAAUCCCUAAUACUUUUAUAAGGACGGUUUUU ............((((((((...............(((((........)))))...(((((....(((((((((((....(((((...(((((((....(.(((...))).).)))))))....))))).....)))))...)))))).((((.((((((..((.((((((...((((((.((....)).)))))).......)))))).))..)))))).)))).....)))))...)))).))))... (-36.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 857 120 71 211 162 NC_002967:TDE0665|5end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_703352..703582_NEGATIVE 233 113 81 163 132 NC_002967:TDE2540|5end_lipoprotein,_putative_2567981..2568211_NEGATIVE 226 113 71 69 28 NC_002967:TDE0746|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_782109..782339_NEGATIVE 224 49 6 52 6 NC_002967:TDE1557|5end_hypothetical_protein_1599986..1600216_POSITIVE 223 102 73 205 176 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 222 107 69 84 31 NC_002967:TDE2530|5end_radical_SAM_domain_protein_2557362..2557592_POSITIVE 222 110 61 126 65 NC_002967:TDE2526|5end_hypothetical_protein_2555034..2555264_NEGATIVE 222 96 59 86 49 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 219 119 76 218 172 NC_002967:TDE0753|5end_hypothetical_protein_793200..793430_POSITIVE 215 189 141 81 19 NC_002967:TDE1053|5end_lipoprotein,_putative_1080726..1080956_NEGATIVE 214 250 207 202 151 NC_002967:TDE2481|5end_hypothetical_protein_2505477..2505707_NEGATIVE 209 118 95 42 16 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 208 187 144 62 11 NC_002967:TDE2471|5end_hypothetical_protein_2494946..2495176_NEGATIVE 208 117 75 162 116 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 208 120 71 171 125 NC_002967:TDE1251|5end_batB_protein,_putative_1285448..1285678_POSITIVE 206 114 74 207 168 NC_002967:TDE0641|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_678282..678512_NEGATIVE 205 112 76 53 21 NC_002967:TDE2396|5end_putative_inner_membrane_protein_translocase_component_YidC_2425398..2425628_NEGATIVE 205 117 74 50 13 NC_002967:TDE2332|5end_hypothetical_protein_2367774..2368004_NEGATIVE 204 104 73 229 200 NC_002967:TDE1386|5end_methyl-accepting_chemotaxis_protein_1424941..1425171_POSITIVE 201 91 52 170 139 NC_002967:TDE2599|5end_thymidylate_kinase_2633963..2634193_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 110 66 59 2 NC_002967:TDE1037|3end_hypothetical_protein_1065461..1065611_POSITIVE 226 113 71 82 41 NC_002967:TDE0747|3end_iron_compound_ABC_transporter,_permease_protein,_putative_782096..782246_NEGATIVE 224 49 6 55 9 NC_002967:TDE1556|3end_hypothetical_protein_1600069..1600219_POSITIVE 222 96 59 74 37 NC_002967:TDE0780|3end_ribosomal_protein_S14_812629..812779_POSITIVE 219 118 75 135 96 NC_002967:TDE0350|3end_MATE_efflux_family_protein_395019..395169_POSITIVE 209 118 95 32 6 NC_002967:TDE0295|3end_DNA_gyrase,_A_subunit_324220..324370_NEGATIVE 204 117 72 52 6 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 198 44 6 95 54 NC_002967:TDE0849|3end_hypothetical_protein_872329..872479_POSITIVE 196 105 70 143 107 NC_002967:TDE1674|3end_hypothetical_protein_1728232..1728382_NEGATIVE 195 83 47 36 3 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 194 100 66 86 49 NC_002967:TDE2456|3end_hypothetical_protein_2484136..2484286_NEGATIVE 193 107 70 117 75 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 190 200 166 84 46 NC_002967:TDE1745|3end_hypothetical_protein_1799115..1799265_NEGATIVE 190 102 70 35 4 NC_002967:TDE1405|3end_phosphoribosylformylglycinamidine_synthetase_I_1447862..1448012_NEGATIVE 190 110 73 43 5 NC_002967:TDE0584|3end_permease,_putative_622196..622346_NEGATIVE 188 52 25 30 3 NC_002967:TDE2404|3end_RNA_polymerase_sigma-54_factor,_putative_2429313..2429463_NEGATIVE 187 169 130 46 4 NC_002967:TDE1717|3end_hypothetical_protein_1772161..1772311_POSITIVE 186 113 74 149 111 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 184 128 83 79 32 NC_002967:TDE1027|3end_ribonuclease_III_1058382..1058532_POSITIVE 183 120 75 103 58 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE