Origin IGS: taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatggtgagcatggcttaaccgataacatgtggtaagacgtaaaacggcgcacattgtgattaacctgaaagcactttattgagctttcctttatataattcgagtattttta Mask Tandem Repeat Region ================================================ taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Find is-nt database================================================ Query_seq: AA00148:AA00150|AA00148:AA00150:ATP-dependent RNA helicase:conserved hypothetical protein (possible TPR domain protein):->->:107904..108017 114 taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00148:AA00150|AA00148:AA00150:ATP-dependent RNA helicase:conserved hypothetical protein (possible TPR domain protein):->->:107904..108017 114 taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00148:AA00150|AA00148:AA00150:ATP-dependent RNA helicase:conserved hypothetical protein (possible TPR domain protein):->->:107904..108017 114 taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 19 End: 114 .................. M K E S S I K C F Q V N H N V R R F T S Y H M L S V K P C S P L taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta 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================================================ taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -4.4 Tail_Score: -3.076 Start: 25 End: 46 Full_Region: cattgtgattaacct gaaagcac tttatt gagctttc ctttatataattcga ........................gaaagcactttattgagctttc.................................................................... Find igs database================================================ Query_seq: AA00148:AA00150|AA00148:AA00150:ATP-dependent RNA helicase:conserved hypothetical protein (possible TPR domain protein):->->:107904..108017 114 taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: aact_AA00148_AA00150|ATP-dependent RNA helicase:conserved hypothetical protein (possible TPR domain protein)|POSITIVE:POSITIVE|[107904,108017]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta taaaaatactcgaattatataaaggaaagctcaataaagtgctttcaggttaatcacaatgtgcgccgttttacgtcttaccacatgttatcggttaagccatgctcaccatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUACUCGAAUUAUAUAAAGGAAAGCUCAAUAAAGUGCUUUCAGGUUAAUCACAAUGUGCGCCGUUUUACGUCUUACCACAUGUUAUCGGUUAAGCCAUGCUCACCAUUA ........................((((((.(......).)))))).(((........(((.((((((....((((........))))...))))...)))))....))).... (-18.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGUGAGCAUGGCUUAACCGAUAACAUGUGGUAAGACGUAAAACGGCGCACAUUGUGAUUAACCUGAAAGCACUUUAUUGAGCUUUCCUUUAUAUAAUUCGAGUAUUUUUA ...((((((((...)))).))))...(((((((((....((.....)))).)))).))).........((((((.(......).))))))........................ (-17.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 104 62 92 44 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 339 109 64 184 142 aact:AA01347|5end_conserved_hypothetical_protein_913209..913439_POSITIVE 327 110 63 61 3 aact:AA02035|5end_translation_initiation_factor_IF-3_1386349..1386579_POSITIVE 317 100 57 131 79 aact:AA02933|5end_conserved_hypothetical_protein_(HesA/MoeB/ThiF_family_protein)_2053467..2053697_POSITIVE 315 89 45 160 116 aact:AA03013|5end_ribonuclease_P_protein_component_2104434..2104664_POSITIVE 308 105 61 178 141 aact:AA01355|5end_large_subunit_pseudouridylate_synthase_D_917228..917458_POSITIVE 307 105 63 81 36 aact:AA00369|5end_50S_ribosomal_protein_L3_247974..248204_POSITIVE 304 110 61 218 159 aact:AA01998|5end_16S_rRNA_pseudouridine_synthase_1356842..1357072_POSITIVE 300 110 64 129 82 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 295 99 57 88 40 aact:AA02964|5end_opacity_associated_protein_A_2072738..2072968_POSITIVE 295 110 62 112 51 aact:AA00734|5end_citrate_lyase,_gamma_chain_(acyl_carrier_protein)_502528..502758_POSITIVE 293 105 61 82 18 aact:AA02961|5end_pyrroline-5-carboxylate_reductase_2070785..2071015_POSITIVE 289 110 61 194 144 aact:AA01255|5end_hypothetical_protein_852656..852886_POSITIVE 288 110 63 228 182 aact:AA01247|5end_hypothetical_protein_849664..849894_POSITIVE 287 104 63 65 33 aact:AA02697|5end_hydrogenase_3_maturation_protease_1879870..1880100_POSITIVE 284 98 56 154 109 aact:AA02316|5end_exodeoxyribonuclease_VII_large_subunit_1581682..1581912_POSITIVE 284 100 51 156 112 aact:AA00003|5end_DNA_replication_and_repair_protein_2337..2567_POSITIVE 282 110 61 231 180 aact:AA02947|5end_riboflavin_biosynthesis_protein_2060871..2061101_POSITIVE 282 96 53 201 154 aact:AA02196|5end_oxaloacetate_decarboxylase_beta_chain_1496308..1496538_POSITIVE 280 110 62 148 102 aact:AA01628|5end_thiamin-monophosphate_kinase_1100888..1101118_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 100 53 145 104 aact:AA01345|3end_conserved_hypothetical_protein_(possible_membrane_protein)_913261..913411_POSITIVE 317 100 57 128 76 aact:AA02932|3end_lytic_murein_transglycosylase_A_2053544..2053694_POSITIVE 307 105 63 62 17 aact:AA00368|3end_50S_ribosomal_protein_L4_248035..248185_POSITIVE 287 104 63 72 40 aact:AA02696|3end_formate_hydrogenlyase_maturation_protein_1879957..1880107_POSITIVE 284 98 56 144 99 aact:AA02315|3end_conserved_hypothetical_protein_1581752..1581902_POSITIVE 284 100 51 149 105 aact:AA00002|3end_DNA_polymerase_III,_beta_subunit_2410..2560_POSITIVE 282 110 61 150 99 aact:AA02946|3end_virulence_factor_protein_2060870..2061020_POSITIVE 280 110 62 126 80 aact:AA01626|3end_N_utilization_substance_protein_B_1100946..1101096_POSITIVE 279 105 65 136 91 aact:AA01619|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthase)_1095578..1095728_POSITIVE 279 68 22 147 112 aact:AA00837|3end_cell_division_protein_W_577584..577734_POSITIVE 273 78 32 122 86 aact:AA02153|3end_iron(III)_ABC_transporter,_permease_protein_1473620..1473770_POSITIVE 273 105 61 67 9 aact:AA00523|3end_conserved_hypothetical_protein_358929..359079_POSITIVE 267 101 61 114 71 aact:AA02973|3end_tyrosine-specific_transport_protein_2078998..2079148_POSITIVE 267 110 64 56 13 aact:AA02171|3end_polysialic_acid_capsule_expression_protein_1486096..1486246_POSITIVE 265 105 61 118 75 aact:AA02543|3end_conserved_hypothetical_protein_1773434..1773584_POSITIVE 265 106 62 56 26 aact:AA00363|3end_50S_ribosomal_protein_L22_245980..246130_POSITIVE 261 83 41 146 104 aact:AA00709|3end_metallocluster_assembly_(NifU_protein)_487838..487988_POSITIVE 261 105 61 119 75 aact:AA00093|3end_L-serine_dehydratase_(L-serine_deaminase)_71173..71323_POSITIVE 260 79 33 127 70 aact:AA00062|3end_bicyclomycin_resistance_protein_(Sulfonamide_resistance_protein)_48030..48180_POSITIVE 258 110 61 61 19 aact:AA01417|3end_probable_4-diphosphocytidyl-2C-methyl-D-erthyritol_synthase_(MEP_cytidyltransferase)_(MCT)_954028..954178_POSITIVE