Origin IGS: ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttcccccaatcaatattatcgtattcagagcattttagcataactaagggattaggggaagtgggagatgatttgtgcgtgtacttgacaagccgttttttttgtattacacttgtaatacggaggttgcc Mask Tandem Repeat Region ================================================ ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Find is-nt database================================================ Query_seq: TDE1962:TDE1963|TDE1962:TDE1963:hypothetical protein:selenocysteine-specific translation elongation factor:<-->:1975295..1975428 134 ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1962:TDE1963|TDE1962:TDE1963:hypothetical protein:selenocysteine-specific translation elongation factor:<-->:1975295..1975428 134 ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1962:TDE1963|TDE1962:TDE1963:hypothetical protein:selenocysteine-specific translation elongation factor:<-->:1975295..1975428 134 ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 13 End: 132 ............ M T S V I Q K K R L V K Y T H K S S P T S P N P L V M L K C S E Y D N I D W G K .. Protein_Len: 39 Strand: - Start: 3 End: 119 .. L R R I V L T I C F F R S T L Y V C L D D G V E G L G K T I S F H E S Y S L M ............... ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga 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: 85 Start: 19 End: 48 ..................CTTGACAAGCCGTTTTTTTTGTATTACACT...................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 71 End: 100 ......................................................................CTTCCCCTAATCCCTTAGTTATGCTAAAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1962:TDE1963|TDE1962:TDE1963:hypothetical protein:selenocysteine-specific translation elongation factor:<-->:1975295..1975428 134 ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_002967_TDE1962_TDE1963|hypothetical protein:selenocysteine-specific translation elongation factor|NEGATIVE:POSITIVE|[1975295,1975428]|134 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 ggcaacctccgtattacaagtgtaatacnnnnnnnncggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga ggcaacctccgtattacaagtgtaatacaaaaaaaacggcttgtcaagtacacgcacaaatcatctcccacttcccctaatcccttagttatgctaaaatgctctgaatacgataatattgattgggggaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAACCUCCGUAUUACAAGUGUAAUACAAAAAAAACGGCUUGUCAAGUACACGCACAAAUCAUCUCCCACUUCCCCUAAUCCCUUAGUUAUGCUAAAAUGCUCUGAAUACGAUAAUAUUGAUUGGGGGAAAGA ((........(((((((....)))))))..........((.(((.....))).))............))..(((((((((((..((((....((......)).)))).............)))))))))))... (-27.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCCCCCAAUCAAUAUUAUCGUAUUCAGAGCAUUUUAGCAUAACUAAGGGAUUAGGGGAAGUGGGAGAUGAUUUGUGCGUGUACUUGACAAGCCGUUUUUUUUGUAUUACACUUGUAAUACGGAGGUUGCC ..(((((((.((((.......((.......))....(((((.....))))).)))).)))))))...((((((..((((.((......))))))..))))))(((((((((((....)))))))))))...... (-30.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 922 90 41 181 132 NC_002967:TDE1962|5end_hypothetical_protein_1975204..1975434_NEGATIVE 291 86 52 199 153 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 275 56 14 59 18 NC_002967:TDE2313|5end_hypothetical_protein_2352010..2352240_NEGATIVE 273 106 66 206 166 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 268 78 37 101 53 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 261 103 61 140 101 NC_002967:TDE1207|5end_DNA_processing_protein_DprA,_putative_1239236..1239466_POSITIVE 260 78 36 215 169 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 255 103 63 129 96 NC_002967:TDE1254|5end_Smr_domain_protein_1288411..1288641_POSITIVE 247 80 33 228 189 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 242 127 81 205 149 NC_002967:TDE2777|5end_hypothetical_protein_2828312..2828542_POSITIVE 241 75 36 161 116 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 241 103 64 202 159 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 240 48 5 154 106 NC_002967:TDE0296|5end_formiminotransferase,_putative_327741..327971_NEGATIVE 239 66 28 103 73 NC_002967:TDE0649|5end_hypothetical_protein_684363..684593_NEGATIVE 236 109 67 137 98 NC_002967:TDE2181|5end_PAP2_family_protein_2213035..2213265_NEGATIVE 234 50 1 220 160 NC_002967:TDE1397|5end_flagellar_synthesis_regulator_FleN,_putative_1436014..1436244_POSITIVE 232 49 8 175 131 NC_002967:TDE1754|5end_desulfoferrodoxin/neelaredoxin_1807023..1807253_NEGATIVE 231 79 34 102 40 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 229 104 66 123 76 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 229 106 61 130 88 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 86 52 122 76 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 261 103 61 136 97 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE 260 78 36 128 82 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 255 103 63 111 78 NC_002967:TDE1253|3end_hypothetical_protein_1288473..1288623_POSITIVE 241 103 64 70 27 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 240 48 5 99 51 NC_002967:TDE0297|3end_hypothetical_protein_327796..327946_NEGATIVE 238 112 71 134 77 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 238 76 36 39 5 NC_002967:TDE1386|3end_methyl-accepting_chemotaxis_protein_1426856..1427006_POSITIVE 236 109 67 137 98 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 234 94 51 96 63 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 231 65 36 150 116 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 231 43 3 141 105 NC_002967:TDE0019|3end_formate--tetrahydrofolate_ligase_23665..23815_NEGATIVE 229 106 61 133 91 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 226 75 36 72 42 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 222 106 61 151 91 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 222 103 65 119 74 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 221 100 59 134 89 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 220 80 37 89 48 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 219 90 46 110 70 NC_002967:TDE1291|3end_HD_domain_protein_1328638..1328788_NEGATIVE 218 108 63 135 99 NC_002967:TDE1594|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1642993..1643143_NEGATIVE