Origin IGS: gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataattccttcatttttatcccgtaaaattgcgttctattgtactgccaaatttcgtttctgtcagtttgcgtgctaaaatggcgcgattttttattgcttaacgaggaatttttc Mask Tandem Repeat Region ================================================ gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Find is-nt database================================================ Query_seq: AA01062:AA01063|AA01062:AA01063:ribonuclease PH (RNase PH):conserved hypothetical protein:->->:736560..736676 117 gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01062:AA01063|AA01062:AA01063:ribonuclease PH (RNase PH):conserved hypothetical protein:->->:736560..736676 117 gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01062:AA01063|AA01062:AA01063:ribonuclease PH (RNase PH):conserved hypothetical protein:->->:736560..736676 117 gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Predict ORF larger than 30AA ================================================ gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt 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: 83 Start: 50 End: 79 .................................................ACTGACAGAAACGAAATTTGGCAGTACAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -3.0 Tail_Score: -5.5604 Start: 29 End: 47 Full_Region: cgtttctgtcagttt gcgtgcta aaa tggcgcga ttttttattgcttaa ............................gcgtgctaaaatggcgcga...................................................................... Find igs database================================================ Query_seq: AA01062:AA01063|AA01062:AA01063:ribonuclease PH (RNase PH):conserved hypothetical protein:->->:736560..736676 117 gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: aact_AA01062_AA01063|ribonuclease PH (RNase PH):conserved hypothetical protein|POSITIVE:POSITIVE|[736560,736676]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt gaaaaattcctcgttaagcaataaaaaatcgcgccattttagcacgcaaactgacagaaacgaaatttggcagtacaatagaacgcaattttacgggataaaaatgaaggaattatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAUUCCUCGUUAAGCAAUAAAAAAUCGCGCCAUUUUAGCACGCAAACUGACAGAAACGAAAUUUGGCAGUACAAUAGAACGCAAUUUUACGGGAUAAAAAUGAAGGAAUUAUU ....(((((((((((..((...........(((...........)))..((((.((((.......)))).))))..........)).((((....))))...)))).)))))))... (-17.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUCCUUCAUUUUUAUCCCGUAAAAUUGCGUUCUAUUGUACUGCCAAAUUUCGUUUCUGUCAGUUUGCGUGCUAAAAUGGCGCGAUUUUUUAUUGCUUAACGAGGAAUUUUUC ...((((((((..............(((((((((((.....((((.((.(((((.((....))..)))))))))))......)))))))))))............)))))))).... (-22.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 80 32 54 4 aact:AA01875|5end_PTS_system,_glucose-specific_enzyme_II,_A_component_1262563..1262793_POSITIVE 309 87 41 60 9 aact:AA01843|5end_sensor_protein;_probable_two-component_system_sensor_histidine_kinase_1238377..1238607_POSITIVE 307 60 11 160 109 aact:AA02419|5end_hypothetical_protein_1661731..1661961_POSITIVE 307 77 31 146 103 aact:AA01628|5end_thiamin-monophosphate_kinase_1100888..1101118_POSITIVE 305 70 27 165 123 aact:AA02091|5end_hypothetical_protein_1424441..1424671_POSITIVE 285 47 10 140 98 aact:AA02082|5end_glutaminyl-tRNA_synthetase_1416101..1416331_POSITIVE 280 69 24 200 142 aact:AA02715|5end_paraquat-inducible_protein_pqiB_homolog_1897053..1897283_POSITIVE 278 86 41 79 47 aact:AA01610|5end_hypothetical_protein_1088811..1089041_POSITIVE 277 109 61 168 114 aact:AA01092|5end_hypothetical_protein_756114..756344_POSITIVE 273 83 46 42 3 aact:AA00116|5end_conserved_hypothetical_protein_86529..86759_POSITIVE 256 63 30 183 141 aact:AA01270|5end_hydrolase_(possible_2-haloalkanoic_acid_dehalogenase_I)_863317..863547_POSITIVE 251 48 7 48 2 aact:AA01081|5end_hypothetical_protein_747804..748034_POSITIVE 250 109 61 77 24 aact:AA01154|5end_sec-independent_protein_translocase_protein_790832..791062_POSITIVE 249 49 1 117 74 aact:AA01792|5end_conserved_hypothetical_protein_1208058..1208288_POSITIVE 245 75 31 139 85 aact:AA02933|5end_conserved_hypothetical_protein_(HesA/MoeB/ThiF_family_protein)_2053467..2053697_POSITIVE 245 97 52 172 112 aact:AA00396|5end_conserved_hypothetical_protein_265591..265821_POSITIVE 243 71 31 146 98 aact:AA02002|5end_hypothetical_protein_1360196..1360426_POSITIVE 241 62 29 214 173 aact:AA01859|5end_hypothetical_protein_1251718..1251948_POSITIVE 238 72 31 222 167 aact:AA00013|5end_hypothetical_protein_6695..6925_POSITIVE 237 66 28 172 132 aact:AA01473|5end_type_I_restriction-modification_system_S_(specificity_subunit)_989025..989255_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 87 41 70 19 aact:AA01842|3end_conserved_hypothetical_protein_1238467..1238617_POSITIVE 307 77 31 124 81 aact:AA01626|3end_N_utilization_substance_protein_B_1100946..1101096_POSITIVE 297 50 7 145 108 aact:AA02418|3end_peptidyl-tRNA_hydrolase_1661811..1661961_POSITIVE 255 97 53 124 71 aact:AA00112|3end_uracil_permease_81239..81389_POSITIVE 251 44 11 108 73 aact:AA02260|3end_pseudouridylate_synthase_I_1537962..1538112_POSITIVE 251 48 7 48 2 aact:AA01080|3end_hypothetical_protein_747884..748034_POSITIVE 250 109 61 70 17 aact:AA01153|3end_sec-independent_protein_translocase_790905..791055_POSITIVE 249 49 1 114 71 aact:AA01790|3end_riboflavin_bifunctional_biosynthesis_protein_1208135..1208285_POSITIVE 245 75 31 136 82 aact:AA02932|3end_lytic_murein_transglycosylase_A_2053544..2053694_POSITIVE 243 71 31 109 61 aact:AA02001|3end_conserved_hypothetical_protein_1360239..1360389_POSITIVE 237 66 28 69 29 aact:AA01471|3end_type_I_restriction_enzyme_M_(modification_chain)_989002..989152_POSITIVE 234 75 33 144 103 aact:AA01550|3end_hypothetical_protein_1038292..1038442_POSITIVE 233 104 62 123 76 aact:AA01546|3end_deoxyribose_operon_repressor_1036320..1036470_POSITIVE 232 47 16 70 45 aact:AA00980|3end_hypothetical_protein_685409..685559_POSITIVE 228 43 5 83 41 aact:AA02205|3end_short_chain_dehydrogenase/reductase_1501984..1502134_POSITIVE 226 79 31 88 41 aact:AA01431|3end_conserved_hypothetical_protein_(possible_hydrolase)_960751..960901_POSITIVE 225 70 27 146 103 aact:AA01997|3end_probable_translation_factor_1356864..1357014_POSITIVE 225 50 16 136 95 aact:AA00363|3end_50S_ribosomal_protein_L22_245980..246130_POSITIVE 225 77 31 67 8 aact:AA00252|3end_conserved_hypothetical_protein_177526..177676_POSITIVE 223 34 7 148 118 aact:AA01696|3end_conserved_hypothetical_protein_1153730..1153880_POSITIVE