Origin IGS: taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatctcctttttgcgtattatttttcttatcttagcactttcacaataaaaaagtgcggtcgaaattttacatgaattttcaaccgcactttagcttctcttttttgtgttggaactaatta Mask Tandem Repeat Region ================================================ taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Find is-nt database================================================ Query_seq: AA02721:AA02722|AA02721:AA02722:spermidine/putrescine ABC transporter, periplasmic-binding protein:cytidine deaminase:->->:1905395..1905518 124 taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02721:AA02722|AA02721:AA02722:spermidine/putrescine ABC transporter, periplasmic-binding protein:cytidine deaminase:->->:1905395..1905518 124 taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02721:AA02722|AA02721:AA02722:spermidine/putrescine ABC transporter, periplasmic-binding protein:cytidine deaminase:->->:1905395..1905518 124 taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Predict ORF larger than 30AA ================================================ taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt 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================================================ taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.3 Tail_Score: -5.55769 Start: 34 End: 69 Full_Region: AAAAGAGAAGCTAAA GTGCGGTTGAAAATT CATGTA AAATTTCGACCGCAC TTTTTTATTGTGAAA .................................GTGCGGTTGAAAATTCATGTAAAATTTCGACCGCAC....................................................... TransTerm Strand: - Conf: 83 HP_score: -9.8 Tail_Score: -3.8802 Start: 34 End: 69 Full_Region: tttcacaataaaaaa gtgcggtcgaaatttt acat gaattttcaaccgcac tttagcttctctttt .................................gtgcggtcgaaattttacatgaattttcaaccgcac....................................................... Find igs database================================================ Query_seq: AA02721:AA02722|AA02721:AA02722:spermidine/putrescine ABC transporter, periplasmic-binding protein:cytidine deaminase:->->:1905395..1905518 124 taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: aact_AA02721_AA02722|spermidine/putrescine ABC transporter, periplasmic-binding protein:cytidine deaminase|POSITIVE:POSITIVE|[1905395,1905518]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt taattagttccaacacaaaaaagagaagctaaagtgcggttgaaaattcatgtaaaatttcgaccgcacttttttattgtgaaagtgctaagataagaaaaataatacgcaaaaaggagatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAGUUCCAACACAAAAAAGAGAAGCUAAAGUGCGGUUGAAAAUUCAUGUAAAAUUUCGACCGCACUUUUUUAUUGUGAAAGUGCUAAGAUAAGAAAAAUAAUACGCAAAAAGGAGAUUUU .......((((..(((((.(((((........(((((((((((((.((......)).)))))))))))))))))).)))))....(((....................)))....))))..... (-28.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCCUUUUUGCGUAUUAUUUUUCUUAUCUUAGCACUUUCACAAUAAAAAAGUGCGGUCGAAAUUUUACAUGAAUUUUCAACCGCACUUUAGCUUCUCUUUUUUGUGUUGGAACUAAUUA .................................((((..((..(((((.(((((((((((((.((((.(((....))).)))).))))))))))........))).)))))..))..))))... (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 505 75 31 161 118 aact:AA00759|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_I_520603..520833_POSITIVE 496 75 32 43 1 aact:AA00758|5end_hypothetical_protein_520485..520715_POSITIVE 488 80 31 149 101 aact:AA00497|5end_hexose_phosphate_transport_system_regulatory_protein;_regulator_of_uhpT_expression_345077..345307_POSITIVE 480 70 21 210 162 aact:AA01625|5end_riboflavin_synthase,_beta_chain_1099964..1100194_POSITIVE 479 80 31 166 117 aact:AA02757|5end_histidinol-phosphate_aminotransferase_2_1930634..1930864_POSITIVE 471 70 24 160 117 aact:AA02340|5end_hypothetical_protein_1598887..1599117_POSITIVE 453 75 31 168 124 aact:AA00899|5end_possible_quaternary_ammonium_compound_resistance_protein_623214..623444_POSITIVE 450 79 31 81 33 aact:AA02002|5end_hypothetical_protein_1360196..1360426_POSITIVE 449 70 28 154 112 aact:AA02993|5end_6-phosphofructokinase_2091766..2091996_POSITIVE 444 75 31 150 106 aact:AA00825|5end_P-protein_(chorismate_mutase/prephenate_dehydratase)_567020..567250_POSITIVE 444 75 31 50 6 aact:AA00824|5end_hypothetical_protein_566920..567150_POSITIVE 443 70 27 166 124 aact:AA01544|5end_conserved_hypothetical_protein_1034265..1034495_POSITIVE 443 70 27 76 34 aact:AA01543|5end_hypothetical_protein_1034175..1034405_POSITIVE 431 73 31 189 146 aact:AA02893|5end_oligopeptide_transport_system_permease_protein,_N-terminal_2027201..2027431_POSITIVE 407 70 22 148 105 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 405 70 26 173 132 aact:AA01584|5end_host_factor-I_protein_1065589..1065819_POSITIVE 402 74 31 207 165 aact:AA02754|5end_conserved_hypothetical_protein_1928949..1929179_POSITIVE 402 74 31 163 121 aact:AA00194|5end_oxygen-independent_coproporphyrinogen_III_oxidase_135545..135775_POSITIVE 402 78 31 158 112 aact:AA00124|5end_conserved_hypothetical_protein_(possible_cytoplasmic_protein)_90270..90500_POSITIVE 402 78 31 109 63 aact:AA00123|5end_hypothetical_protein_90221..90451_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 488 80 31 131 83 aact:AA00495|3end_hypothetical_protein_345139..345289_POSITIVE 480 70 21 67 19 aact:AA01624|3end_glucose-6-phosphate_isomerase_1099901..1100051_POSITIVE 479 80 31 88 39 aact:AA02756|3end_phosphoserine_aminotransferase_1930636..1930786_POSITIVE 471 70 24 78 35 aact:AA02338|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1598885..1599035_POSITIVE 457 79 31 93 46 aact:AA02280|3end_conserved_hypothetical_protein_1552767..1552917_POSITIVE 453 75 31 80 36 aact:AA00896|3end_prolyl-tRNA_synthetase_(proline-tRNA_ligase)_623206..623356_POSITIVE 449 70 28 48 6 aact:AA02992|3end_RNA_methyltransferase_2091740..2091890_POSITIVE 431 73 31 85 42 aact:AA02892|3end_oligopeptide_ABC_transporter,_periplasmic-binding_protein_2027177..2027327_POSITIVE 430 79 31 86 38 aact:AA02781|3end_protein-export_membrane_protein_1945981..1946131_POSITIVE 427 72 31 60 19 aact:AA02721|3end_spermidine/putrescine_ABC_transporter,_periplasmic-binding_protein_1905334..1905484_POSITIVE 407 70 22 73 30 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 402 74 31 46 4 aact:AA02751|3end_L-lactate_permease_1928868..1929018_POSITIVE 402 74 31 83 41 aact:AA00191|3end_conserved_hypothetical_protein_(possible_acetyltransferase,_GNAT_family)_135545..135695_POSITIVE 402 78 31 89 43 aact:AA00120|3end_ATP-dependent_Clp_protease_ATP-binding_subunit_90281..90431_POSITIVE 401 73 31 69 28 aact:AA01963|3end_dnaK_suppressor_protein_1329438..1329588_POSITIVE 387 78 31 88 39 aact:AA00799|3end_iron(III)_dicitrate_transport_ATP-binding_protein_548502..548652_POSITIVE 387 70 24 61 14 aact:AA00471|3end_3,4-dihydroxy-2-butanone_4-phosphate_synthase;_GTP_cyclohydrase_II_328983..329133_POSITIVE 383 76 31 90 46 aact:AA02243|3end_conserved_hypothetical_protein_1526411..1526561_POSITIVE 382 75 31 85 42 aact:AA02474|3end_transmembrane_protein_1711548..1711698_POSITIVE 381 79 31 93 37 aact:AA02777|3end_tRNA-guanine_transglycosylase_1942527..1942677_POSITIVE