Origin IGS: ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaacccgtgatgatagcatttatctaggtgccttgtctagtgtaaattaaaaattaaaaattaaaaataaaggatttttttagtctgtcgcttgacaataattctctcttattttagagtataggcggaggagatttttgtaa Mask Tandem Repeat Region ================================================ ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttnnnnnnnnnnnnnnnnnnnnnnnnnacactagacaaggcacctagataaatgctatcatcacgggttct Find is-nt database================================================ Query_seq: TDE1731:TDE1732|TDE1731:TDE1732:hypothetical protein:hypothetical protein:<-->:1787026..1787169 144 ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1731:TDE1732|TDE1731:TDE1732:hypothetical protein:hypothetical protein:<-->:1787026..1787169 144 ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1731:TDE1732|TDE1731:TDE1732:hypothetical protein:hypothetical protein:<-->:1787026..1787169 144 ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct Predict ORF larger than 30AA ================================================ ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct 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: 87 Start: 24 End: 53 .......................CTTGACAATAATTCTCTCTTATTTTAGAGT........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1731:TDE1732|TDE1731:TDE1732:hypothetical protein:hypothetical protein:<-->:1787026..1787169 144 ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagactaaaaaaatcctttatttttaatttttaatttttaatttacactagacaaggcacctagataaatgctatcatcacgggttct Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_002967_TDE1731_TDE1732|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1787026,1787169]|144 HSP 1 e-value: 2.0E-27 bit: 123.0 Len: 62 Query Start:1 Query End:62 Subject Strand: POSITIVE Subject Start: 1 Subject End: 62 ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagact.................................................................................. ttacaaaaatctcctccgcctatactctaaaataagagagaattattgtcaagcgacagact.................................................................................. HSP 2 e-value: 4.0E-16 bit: 85.7 Len: 43 Query Start:102 Query End:144 Subject Strand: POSITIVE Subject Start: 102 Subject End: 144 .....................................................................................................cactagacaaggcacctagataaatgctatcatcacgggttct .....................................................................................................cactagacaaggcacctagataaatgctatcatcacgggttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAAAAAUCUCCUCCGCCUAUACUCUAAAAUAAGAGAGAAUUAUUGUCAAGCGACAGACUAAAAAAAUCCUUUAUUUUUAAUUUUUAAUUUUUAAUUUACACUAGACAAGGCACCUAGAUAAAUGCUAUCAUCACGGGUUCU ...........(((...((((...((((......)))).((((((.((((....))))......((((((.....)))))).............))))))..........)))).....((((.....)))).....))).... (-17.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAACCCGUGAUGAUAGCAUUUAUCUAGGUGCCUUGUCUAGUGUAAAUUAAAAAUUAAAAAUUAAAAAUAAAGGAUUUUUUUAGUCUGUCGCUUGACAAUAAUUCUCUCUUAUUUUAGAGUAUAGGCGGAGGAGAUUUUUGUAA ...(((...(((((......)))))..)))...(((((.((((((.((((((((.......................)))))))).)).)))).)))))...(((((((((((........))))).))))))........... (-25.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 885 60 11 151 102 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 268 56 11 218 175 NC_002967:TDE1062|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1088430..1088660_POSITIVE 267 140 99 221 188 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 257 137 106 40 3 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 256 60 14 111 72 NC_002967:TDE1881|5end_methyltransferase,_putative_1903000..1903230_POSITIVE 252 56 15 111 56 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 248 54 11 230 189 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 229 60 13 95 30 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 229 24 11 32 19 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 228 58 13 60 1 NC_002967:TDE0666|5end_FeS_assembly_ATPase_SufC_703553..703783_POSITIVE 222 55 16 183 137 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 221 40 7 119 94 NC_002967:TDE2483|5end_hypothetical_protein_2506659..2506889_NEGATIVE 221 59 11 158 104 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 221 136 93 152 110 NC_002967:TDE1857|5end_hypothetical_protein_1884450..1884680_NEGATIVE 220 60 13 151 97 NC_002967:TDE1962|5end_hypothetical_protein_1975204..1975434_NEGATIVE 211 58 12 71 24 NC_002967:TDE1712|5end_flagellar_filament_outer_layer_protein_1767915..1768145_NEGATIVE 210 60 16 56 3 NC_002967:TDE0753|5end_hypothetical_protein_793200..793430_POSITIVE 210 50 3 182 145 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 209 54 12 142 98 NC_002967:TDE1025|5end_ribosomal_protein_L32_1057101..1057331_POSITIVE 206 24 7 29 6 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 60 14 89 50 NC_002967:TDE1880|3end_hypothetical_protein_1903058..1903208_POSITIVE 245 140 104 55 14 NC_002967:TDE0271|3end_hypothetical_protein_302199..302349_POSITIVE 229 60 13 95 30 NC_002967:TDE1744|3end_chromate_transport_protein_1798503..1798653_NEGATIVE 221 40 7 125 100 NC_002967:TDE2484|3end_hypothetical_protein_2506653..2506803_NEGATIVE 220 37 8 135 97 NC_002967:TDE2009|3end_hypothetical_protein_2031247..2031397_POSITIVE 216 59 26 110 73 NC_002967:TDE2318|3end_LysM_domain/M23/M37_peptidase_domain_protein_2355868..2356018_POSITIVE 210 50 3 147 110 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 206 24 7 32 9 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 205 52 13 44 13 NC_002967:TDE0100|3end_hypothetical_protein_116974..117124_NEGATIVE 201 138 109 141 118 NC_002967:TDE2705|3end_ISTde3,_transposase_2751127..2751277_NEGATIVE 198 40 12 125 95 NC_002967:TDE1215|3end_flagellar_M-ring_protein_1248519..1248669_POSITIVE 196 57 15 145 98 NC_002967:TDE0614|3end_precorrin-4_C11-methyltransferase_648816..648966_POSITIVE 195 51 15 85 41 NC_002967:TDE0499|3end_hypothetical_protein_552517..552667_NEGATIVE 192 58 11 151 98 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 192 135 106 98 65 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 190 33 8 83 47 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 189 137 105 83 37 NC_002967:TDE1568|3end_hypothetical_protein_1619827..1619977_POSITIVE 188 20 1 28 7 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 188 39 6 40 3 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 186 44 5 76 39 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE