Origin IGS: tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagccgagcctgtttgcttaggaaacaaaggtaaactaaaaagaagcagcagaggctatgccggagagcgaactctcgcgacatagcctcacgatgctttcagtgaaaaaaaacgtacaata Mask Tandem Repeat Region ================================================ tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Find is-nt database================================================ Query_seq: PG1417:PG1418|PG1417:PG1418:fumarate hydratase class I, anaerobic:DNA polymerase III, gamma and tau subunits:->->:1503082..1503203 122 tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1417:PG1418|PG1417:PG1418:fumarate hydratase class I, anaerobic:DNA polymerase III, gamma and tau subunits:->->:1503082..1503203 122 tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1417:PG1418|PG1417:PG1418:fumarate hydratase class I, anaerobic:DNA polymerase III, gamma and tau subunits:->->:1503082..1503203 122 tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Predict ORF larger than 30AA ================================================ tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc 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================================================ tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.4 Tail_Score: -5.01042 Start: 23 End: 80 Full_Region: CGTTTTTTTTCACTG AAAGCATCGTGAGGCTATGTCGCGAGAG TTCG CTCTCCGGCATAGCCTCTGCTGCTTC TTTTTAGTTTACCTT ......................AAAGCATCGTGAGGCTATGTCGCGAGAGTTCGCTCTCCGGCATAGCCTCTGCTGCTTC.......................................... TransTerm Strand: + Conf: 100 HP_score: -16.1 Tail_Score: -4.58698 Start: 26 End: 77 Full_Region: TTTTTTTCACTGAAA GCATCGTGAGGCTATGTCGCGAGAG TTCG CTCTCCGGCATAGCCTCTGCTGC TTCTTTTTAGTTTAC .........................GCATCGTGAGGCTATGTCGCGAGAGTTCGCTCTCCGGCATAGCCTCTGCTGC............................................. TransTerm Strand: - Conf: 89 HP_score: -11.7 Tail_Score: -3.64703 Start: 26 End: 77 Full_Region: gtaaactaaaaagaa gcagcagaggctatgccggagag cgaa ctctcgcgacatagcctcacgatgc tttcagtgaaaaaaa .........................gcagcagaggctatgccggagagcgaactctcgcgacatagcctcacgatgc............................................. Find igs database================================================ Query_seq: PG1417:PG1418|PG1417:PG1418:fumarate hydratase class I, anaerobic:DNA polymerase III, gamma and tau subunits:->->:1503082..1503203 122 tattgtacgttttttttcactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Intra-Species Hit: Count: 1 Min: 18 Max: 122 Len: 105 Subject: NC_002950_PG1417_PG1418|fumarate hydratase class I, anaerobic:DNA polymerase III, gamma and tau subunits|POSITIVE:POSITIVE|[1503082,1503203]|122 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:18 Query End:122 Subject Strand: POSITIVE Subject Start: 18 Subject End: 122 .................cactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc .................cactgaaagcatcgtgaggctatgtcgcgagagttcgctctccggcatagcctctgctgcttctttttagtttacctttgtttcctaagcaaacaggctcggctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUGAAAGCAUCGUGAGGCUAUGUCGCGAGAGUUCGCUCUCCGGCAUAGCCUCUGCUGCUUCUUUUUAGUUUACCUUUGUUUCCUAAGCAAACAGGCUCGGCUC .((((((((((.((.((((((((((((.(((((....))))))))))))))))))).))))....))))))...((((((((.....)))))..)))........ (-41.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCCGAGCCUGUUUGCUUAGGAAACAAAGGUAAACUAAAAAGAAGCAGCAGAGGCUAUGCCGGAGAGCGAACUCUCGCGACAUAGCCUCACGAUGCUUUCAGUG ...........((((((((.(....)..))))))))......((((((...(((((((((.(((((((....))))).)).)))))))))....))))))..... (-39.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 65 23 170 114 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 408 65 25 230 176 NC_002950:PG1352|5end_hypothetical_protein_1433150..1433380_NEGATIVE 404 57 12 163 122 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 385 60 11 74 14 NC_002950:PG0672|5end_iron_compound_ABC_transporter,_ATP-binding_protein_723002..723232_POSITIVE 385 60 11 139 87 NC_002950:PG0604|5end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_660262..660492_POSITIVE 383 64 25 69 25 NC_002950:PG1463|5end_hypothetical_protein_1541110..1541340_POSITIVE 382 59 18 56 3 NC_002950:PG2110|5end_thiamine_biosynthesis_protein_ThiC_2221212..2221442_NEGATIVE 382 60 13 82 36 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 381 60 11 151 81 NC_002950:PG1485|5end_conjugative_transposon_protein_TraC_1560370..1560600_NEGATIVE 381 60 15 124 65 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 378 86 41 198 150 NC_002950:PG0571|5end_aspartate-semialdehyde_dehydrogenase_626399..626629_POSITIVE 378 64 26 62 12 NC_002950:PG0195|5end_rubrerythrin_232046..232276_POSITIVE 376 59 12 60 2 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 375 58 13 193 156 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 370 59 18 107 57 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 369 54 18 215 177 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 369 60 16 49 4 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 368 60 11 124 56 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 367 49 3 226 164 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 362 47 9 77 30 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 611 58 16 66 20 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 434 60 16 72 24 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 429 57 18 79 35 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 416 60 11 149 100 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 403 61 24 112 68 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 402 70 23 72 22 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 401 60 13 122 75 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 400 58 16 42 7 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 388 54 11 63 18 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 385 60 11 142 90 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 383 64 25 46 2 NC_002950:PG1462|3end_hypothetical_protein_1541167..1541317_POSITIVE 382 60 13 77 31 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 371 60 16 144 104 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 370 60 20 78 26 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 369 54 18 68 30 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 368 60 11 110 42 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 366 58 18 67 30 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 362 60 12 78 26 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 361 60 13 122 66 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 352 58 13 55 10 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE