Origin IGS: aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaactaatatatcacagtatccgtaaattgtaaagaacggaaaaaagcttgttttttcattattgaaacttttatcaaaaaatgatagagtataagttaggagatatgataaacaggagaaattt Mask Tandem Repeat Region ================================================ aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Find is-nt database================================================ Query_seq: TDE2090:TDE2091|TDE2090:TDE2091:NAD(P)H-dependent glycerol-3-phosphate dehydrogenase:amino acid ABC transporter, amino acid-binding protein, putative:<-->:2118727..2118852 126 aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2090:TDE2091|TDE2090:TDE2091:NAD(P)H-dependent glycerol-3-phosphate dehydrogenase:amino acid ABC transporter, amino acid-binding protein, putative:<-->:2118727..2118852 126 aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2090:TDE2091|TDE2090:TDE2091:NAD(P)H-dependent glycerol-3-phosphate dehydrogenase:amino acid ABC transporter, amino acid-binding protein, putative:<-->:2118727..2118852 126 aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Predict ORF larger than 30AA ================================================ aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct 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: 91 End: 120 ..........................................................................................CTTTACAATTTACGGATACTGTGATATATT...... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 35 End: 64 ..................................ATTGAAACTTTTATCAAAAAATGATAGAGT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2090:TDE2091|TDE2090:TDE2091:NAD(P)H-dependent glycerol-3-phosphate dehydrogenase:amino acid ABC transporter, amino acid-binding protein, putative:<-->:2118727..2118852 126 aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002967_TDE2090_TDE2091|NAD(P)H-dependent glycerol-3-phosphate dehydrogenase:amino acid ABC transporter, amino acid-binding protein, putative|NEGATIVE:POSITIVE|[2118727,2118852]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct aaatttctcctgtttatcatatctcctaacttatactctatcattttttgataaaagtttcaataatgaaaaaacaagcttttttccgttctttacaatttacggatactgtgatatattagttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUCUCCUGUUUAUCAUAUCUCCUAACUUAUACUCUAUCAUUUUUUGAUAAAAGUUUCAAUAAUGAAAAAACAAGCUUUUUUCCGUUCUUUACAAUUUACGGAUACUGUGAUAUAUUAGUUCU .........(((..(((((((...................(((((..((((........)))).)))))...............(((((............)))))...)))))))...))).... (-16.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAACUAAUAUAUCACAGUAUCCGUAAAUUGUAAAGAACGGAAAAAAGCUUGUUUUUUCAUUAUUGAAACUUUUAUCAAAAAAUGAUAGAGUAUAAGUUAGGAGAUAUGAUAAACAGGAGAAAUUU ........((((((......(((((............)))))....(((((((..(((((....))))).((((((((.....)))))))).)))))))....))))))................. (-19.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 734 120 71 211 162 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 280 41 2 215 169 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 280 41 2 114 68 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 274 29 2 200 168 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 268 28 2 99 68 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 265 28 2 150 119 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 263 50 2 125 68 NC_002967:TDE1131|5end_hypothetical_protein_1163182..1163412_POSITIVE 263 47 2 202 159 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 261 32 2 84 44 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 245 112 76 133 98 NC_002967:TDE1380|5end_hypothetical_protein_1421284..1421514_NEGATIVE 235 42 2 208 156 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 234 50 7 115 67 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 229 27 1 123 92 NC_002967:TDE0932|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_957944..958174_NEGATIVE 228 95 66 118 90 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 222 27 10 98 81 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 222 27 10 119 102 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 222 66 21 141 97 NC_002967:TDE1455|5end_prevent-host-death_family_protein_1502865..1503095_POSITIVE 221 118 77 70 26 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 221 111 77 60 23 NC_002967:TDE0948|5end_hypothetical_protein_971837..972067_NEGATIVE 221 107 75 190 162 NC_002967:TDE0411|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_462931..463161_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 41 2 94 48 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 274 29 2 89 57 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 270 32 2 91 51 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 268 28 2 35 4 NC_002967:TDE0691|3end_ABC_transporter,_ATP-binding/permease_protein_729728..729878_POSITIVE 265 28 2 82 51 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 263 50 2 103 46 NC_002967:TDE1130|3end_methyltransferase,_putative_1163240..1163390_POSITIVE 263 47 2 50 7 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 261 32 2 69 29 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 254 27 2 81 51 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 246 40 2 103 61 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 245 112 76 129 94 NC_002967:TDE1381|3end_V-type_ATP_synthase_subunit_E_1421288..1421438_NEGATIVE 235 42 2 104 52 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 234 50 7 81 33 NC_002967:TDE1513|3end_hypothetical_protein_1560698..1560848_POSITIVE 229 90 50 92 42 NC_002967:TDE2473|3end_30S_ribosomal_protein_S21_2496587..2496737_POSITIVE 228 95 66 112 84 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 227 113 74 143 96 NC_002967:TDE0019|3end_formate--tetrahydrofolate_ligase_23665..23815_NEGATIVE 222 27 10 83 66 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 222 66 21 78 34 NC_002967:TDE1454|3end_sugar_transporter_1502882..1503032_POSITIVE 221 118 77 58 14 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE 220 31 2 76 40 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE