Origin IGS: ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattttttactaactaacttttcataacggcacttctaagtgtcgttttttatatgtatttttggcataatgctcacacatttatctaaaggagaaacaa Mask Tandem Repeat Region ================================================ ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Find is-nt database================================================ Query_seq: AA02526:AA02527|AA02526:AA02527:conserved hypothetical protein:integration host factor,beta-subunit:->->:1755659..1755759 101 ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02526:AA02527|AA02526:AA02527:conserved hypothetical protein:integration host factor,beta-subunit:->->:1755659..1755759 101 ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02526:AA02527|AA02526:AA02527:conserved hypothetical protein:integration host factor,beta-subunit:->->:1755659..1755759 101 ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Predict ORF larger than 30AA ================================================ ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta 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================================================ ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02526:AA02527|AA02526:AA02527:conserved hypothetical protein:integration host factor,beta-subunit:->->:1755659..1755759 101 ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: aact_AA02526_AA02527|conserved hypothetical protein:integration host factor,beta-subunit|POSITIVE:POSITIVE|[1755659, 1755759]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta ttgtttctcctttagataaatgtgtgagcattatgccaaaaatacatataaaaaacgacacttagaagtgccgttatgaaaagttagttagtaaaaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUCUCCUUUAGAUAAAUGUGUGAGCAUUAUGCCAAAAAUACAUAUAAAAAACGACACUUAGAAGUGCCGUUAUGAAAAGUUAGUUAGUAAAAAAUUA ...((((............((((((..((.....)).....))))))......((((.((((....)))).))))..)))).................... (-12.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUUUACUAACUAACUUUUCAUAACGGCACUUCUAAGUGUCGUUUUUUAUAUGUAUUUUUGGCAUAAUGCUCACACAUUUAUCUAAAGGAGAAACAA ...................(((((..(((((((((....))))))))).............(((((...((((......))))...))))).))))).... (-16.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 90 41 153 101 aact:AA01436|5end_fructose-bisphosphate_aldolase_class_II_962981..963211_POSITIVE 217 73 46 149 124 aact:AA02687|5end_hydrogenase-4_component_D_1872521..1872751_POSITIVE 207 39 21 23 5 aact:AA01173|5end_VapD-homolog_803850..804080_POSITIVE 204 85 65 78 54 aact:AA02031|5end_type_III_site-specific_deoxyribonuclease_1384338..1384568_POSITIVE 202 80 31 71 17 aact:AA01517|5end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1020989..1021219_POSITIVE 200 40 2 230 197 aact:AA01685|5end_molybdenum_ABC_transporter,_ATP-binding_protein_1136979..1137209_POSITIVE 200 70 22 152 107 aact:AA00130|5end_mercuric_transport_protein_(periplasmic_mercury_ion_binding_protein)_(mercury_scavenger_protein)_94217..94447_POSITIVE 200 70 22 57 12 aact:AA00129|5end_hypothetical_protein_94122..94352_POSITIVE 199 89 55 120 79 aact:AA01776|5end_conserved_hypothetical_protein_1196074..1196304_POSITIVE 199 89 55 47 6 aact:AA01775|5end_hypothetical_protein_1196001..1196231_POSITIVE 197 96 64 130 94 aact:AA01569|5end_dipeptide_transport_ATP-binding_protein_1056859..1057089_POSITIVE 197 59 18 173 127 aact:AA01251|5end_hypothetical_protein_851825..852055_POSITIVE 197 76 34 57 23 aact:AA00876|5end_tight_adherence_protein_C_607761..607991_POSITIVE 196 94 56 61 26 aact:AA01304|5end_penicillin-binding_protein_1A_882936..883166_POSITIVE 195 62 21 180 138 aact:AA01886|5end_UDP-glucose-4-epimerase_1271464..1271694_POSITIVE 189 45 2 130 91 aact:AA00807|5end_fumarate_reductase_13_kD_hydrophobic_protein_552767..552997_POSITIVE 188 89 52 200 167 aact:AA01803|5end_arginine_repressor_1214546..1214776_POSITIVE 188 89 52 86 53 aact:AA01802|5end_hypothetical_protein_1214432..1214662_POSITIVE 187 70 21 144 104 aact:AA02929|5end_hypothetical_protein_2049189..2049419_POSITIVE 186 75 45 153 123 aact:AA02077|5end_probable_outer_membrane_protein_1411294..1411524_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 90 41 113 61 aact:AA01434|3end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_963021..963171_POSITIVE 217 73 46 133 108 aact:AA02686|3end_hydrogenase_4_component_C_1872585..1872735_POSITIVE 207 79 38 94 57 aact:AA00172|3end_conserved_hypothetical_protein_(possible_regulator_protein_/_nitrogen_fixation_protein)_122904..123054_POSITIVE 200 79 33 114 64 aact:AA01598|3end_conserved_hypothetical_protein_1079966..1080116_POSITIVE 200 70 22 62 17 aact:AA00128|3end_cation-transporting_ATPase_(probable_potassium/copper_transporter)_94207..94357_POSITIVE 199 89 55 148 107 aact:AA01775|3end_hypothetical_protein_1196182..1196332_POSITIVE 197 96 64 123 87 aact:AA01568|3end_dipeptide_transport_system_ATP-binding_protein_1056932..1057082_POSITIVE 197 59 18 48 2 aact:AA01250|3end_nadAB_transcriptional_regulator_851780..851930_POSITIVE 197 76 34 57 23 aact:AA00875|3end_tight_adherence_protein_B_607841..607991_POSITIVE 189 45 2 117 78 aact:AA00806|3end_fumarate_reductase_15_kD_hydrophobic_protein_552834..552984_POSITIVE 187 70 21 119 79 aact:AA02928|3end_conserved_hypothetical_protein_2049244..2049394_POSITIVE 185 36 4 54 14 aact:AA02334|3end_outer_membrane_protein_P1_1596814..1596964_POSITIVE 184 41 2 110 73 aact:AA02106|3end_hypothetical_protein_1433455..1433605_POSITIVE 184 46 18 123 96 aact:AA01143|3end_hypothetical_protein_783535..783685_POSITIVE 183 37 22 72 57 aact:AA01155|3end_hypothetical_protein_791411..791561_POSITIVE 183 38 3 125 97 aact:AA00935|3end_ribose_ABC_transporter,_permease_protein,_N-terminal_646328..646478_POSITIVE 183 45 5 138 84 aact:AA00017|3end_hypothetical_protein_10271..10421_POSITIVE 180 77 33 55 1 aact:AA00786|3end_possible_protein-export_membrane_protein_540402..540552_POSITIVE 179 38 5 61 29 aact:AA02554|3end_conserved_hypothetical_protein_1780486..1780636_POSITIVE 179 70 22 72 23 aact:AA01303|3end_competence_protein_A_882882..883032_POSITIVE