Origin IGS: taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattctcttcccttctcacgctaaagtgcggtcggaaattcatttgtttttttgaccgcactttttctgattttccaccttctttaatatgaattaagccctta Mask Tandem Repeat Region ================================================ taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Find is-nt database================================================ Query_seq: AA02992:AA02993|AA02992:AA02993:RNA methyltransferase:6-phosphofructokinase:->->:2091801..2091905 105 taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02992:AA02993|AA02992:AA02993:RNA methyltransferase:6-phosphofructokinase:->->:2091801..2091905 105 taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02992:AA02993|AA02992:AA02993:RNA methyltransferase:6-phosphofructokinase:->->:2091801..2091905 105 taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 11 End: 103 .......... M H I K E G G K S E K V R S K K Q M N F R P H F S V R R E E N .. taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta 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================================================ taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.0 Tail_Score: -5.09245 Start: 44 End: 79 Full_Region: ccttctcacgctaaa gtgcggtcggaaattc attt gtttttttgaccgcac tttttctgattttcc ...........................................gtgcggtcggaaattcatttgtttttttgaccgcac.......................... Find igs database================================================ Query_seq: AA02992:AA02993|AA02992:AA02993:RNA methyltransferase:6-phosphofructokinase:->->:2091801..2091905 105 taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: aact_AA02992_AA02993|RNA methyltransferase:6- phosphofructokinase|POSITIVE:POSITIVE|[2091801, 2091905]|105 HSP 1 e-value: 9.0E-41 bit: 167.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcnnnnnnncaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta taagggcttaattcatattaaagaaggtggaaaatcagaaaaagtgcggtcaaaaaaacaaatgaatttccgaccgcactttagcgtgagaagggaagagaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGGCUUAAUUCAUAUUAAAGAAGGUGGAAAAUCAGAAAAAGUGCGGUCAAAAAAACAAAUGAAUUUCCGACCGCACUUUAGCGUGAGAAGGGAAGAGAAUUA ........((((((...........(((.....))).(..(((((((((((....................)))))))))))..)..............)))))) (-21.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCUCUUCCCUUCUCACGCUAAAGUGCGGUCGGAAAUUCAUUUGUUUUUUUGACCGCACUUUUUCUGAUUUUCCACCUUCUUUAAUAUGAAUUAAGCCCUUA ((((((..............(..((((((((((((((((..(....)..))))))))))))))))..).((..........))........))))))........ (-25.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 80 31 186 135 aact:AA02893|5end_oligopeptide_transport_system_permease_protein,_N-terminal_2027201..2027431_POSITIVE 504 90 41 161 110 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 504 90 41 220 172 aact:AA01145|5end_glycyl-tRNA_synthetase_alpha_subunit_783478..783708_POSITIVE 498 89 41 90 41 aact:AA02378|5end_hypothetical_protein_1627753..1627983_POSITIVE 473 80 38 139 98 aact:AA00126|5end_conserved_hypothetical_protein_91053..91283_POSITIVE 467 85 41 188 144 aact:AA02722|5end_cytidine_deaminase_1905379..1905609_POSITIVE 433 87 41 220 172 aact:AA01625|5end_riboflavin_synthase,_beta_chain_1099964..1100194_POSITIVE 432 80 36 192 148 aact:AA02902|5end_aerobic_respiration_control_protein_2031171..2031401_POSITIVE 432 86 41 60 13 aact:AA00697|5end_hypothetical_protein_476999..477229_POSITIVE 428 88 45 192 147 aact:AA01251|5end_hypothetical_protein_851825..852055_POSITIVE 420 80 35 167 116 aact:AA00721|5end_probable_beta-N-acetylhexosaminidase_(lacto-N-biosidase);_dispersin_B_494739..494969_POSITIVE 420 80 35 55 4 aact:AA00719|5end_hypothetical_protein_494627..494857_POSITIVE 412 80 36 140 96 aact:AA00497|5end_hexose_phosphate_transport_system_regulatory_protein;_regulator_of_uhpT_expression_345077..345307_POSITIVE 402 82 41 205 165 aact:AA02754|5end_conserved_hypothetical_protein_1928949..1929179_POSITIVE 392 80 39 149 104 aact:AA01648|5end_alpha-amylase_protein;_1,4-alpha-D-glucan_glucanohydrolase_1115170..1115400_POSITIVE 392 80 39 48 3 aact:AA01646|5end_hypothetical_protein_1115069..1115299_POSITIVE 391 80 39 160 119 aact:AA02128|5end_DNA_topoisomerase_I_1451395..1451625_POSITIVE 387 87 41 172 124 aact:AA00899|5end_possible_quaternary_ammonium_compound_resistance_protein_623214..623444_POSITIVE 383 87 41 124 79 aact:AA02362|5end_conserved_hypothetical_protein_1619905..1620135_POSITIVE 382 80 31 160 110 aact:AA01871|5end_conserved_hypothetical_protein_1258223..1258453_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 80 31 82 31 aact:AA02892|3end_oligopeptide_ABC_transporter,_periplasmic-binding_protein_2027177..2027327_POSITIVE 504 90 41 86 35 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 467 85 41 63 19 aact:AA02721|3end_spermidine/putrescine_ABC_transporter,_periplasmic-binding_protein_1905334..1905484_POSITIVE 433 87 41 77 29 aact:AA01624|3end_glucose-6-phosphate_isomerase_1099901..1100051_POSITIVE 432 80 36 79 35 aact:AA02899|3end_oligopeptide_ABC_transporter,_ATP-binding_protein_2031138..2031288_POSITIVE 432 86 41 87 40 aact:AA00696|3end_iron(III)_ABC_transporter,_periplasmic_iron-compound-binding_protein_477106..477256_POSITIVE 428 88 45 67 22 aact:AA01250|3end_nadAB_transcriptional_regulator_851780..851930_POSITIVE 420 80 35 71 20 aact:AA00718|3end_ABC-related_ATP-binding_protein;_MRP_protein_494723..494873_POSITIVE 415 82 41 57 17 aact:AA00010|3end_transposase_orfB_fragment_6297..6447_POSITIVE 412 80 36 122 78 aact:AA00495|3end_hypothetical_protein_345139..345289_POSITIVE 402 82 41 44 4 aact:AA02751|3end_L-lactate_permease_1928868..1929018_POSITIVE 398 89 41 86 30 aact:AA00629|3end_inosine_5'_monophosphate_dehydrogenase_(IMP_dehydrogenase)_433469..433619_POSITIVE 392 80 39 83 38 aact:AA01645|3end_ferric_transport_ABC-related_ATP-binding_protein_1115184..1115334_POSITIVE 391 80 39 69 28 aact:AA02126|3end_conserved_hypothetical_protein_1451384..1451534_POSITIVE 387 87 41 84 36 aact:AA00896|3end_prolyl-tRNA_synthetase_(proline-tRNA_ligase)_623206..623356_POSITIVE 383 87 41 86 41 aact:AA02360|3end_threonine_synthase_1619947..1620097_POSITIVE 381 87 41 85 36 aact:AA00218|3end_argininosuccinate_lyase_152211..152361_POSITIVE 380 87 42 116 68 aact:AA00909|3end_molybdopterin-guanine_dinucleotide_biosynthesis_protein_B_627183..627333_POSITIVE 370 85 42 92 43 aact:AA02105|3end_killing_protein_1433290..1433440_POSITIVE 369 80 33 65 13 aact:AA02035|3end_translation_initiation_factor_IF-3_1386905..1387055_POSITIVE