Origin IGS: ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaacctctttatatgaactttaagtacattataaagaggaactgaaagtacttcaagttttatttataattgaaccattagttcaaaggtaagaaaa Mask Tandem Repeat Region ================================================ ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Find is-nt database================================================ Query_seq: AA01906:AA01908|AA01906:AA01908:repressor protein CI:conserved hypothetical protein:->->:1287108..1287207 100 ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01906:AA01908|AA01906:AA01908:repressor protein CI:conserved hypothetical protein:->->:1287108..1287207 100 ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01906:AA01908|AA01906:AA01908:repressor protein CI:conserved hypothetical protein:->->:1287108..1287207 100 ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Predict ORF larger than 30AA ================================================ ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat 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: 88 Start: 41 End: 70 ........................................CTTGAAGTACTTTCAGTTCCTCTTTATAAT.............................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 28 End: 57 ...........................ACTGAAAGTACTTCAAGTTTTATTTATAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01906:AA01908|AA01906:AA01908:repressor protein CI:conserved hypothetical protein:->->:1287108..1287207 100 ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: aact_AA01906_AA01908|repressor protein CI:conserved hypothetical protein|POSITIVE:POSITIVE|[1287108,1287207]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat ttttcttacctttgaactaatggttcaattataaataaaacttgaagtactttcagttcctctttataatgtacttaaagttcatataaagaggttttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUACCUUUGAACUAAUGGUUCAAUUAUAAAUAAAACUUGAAGUACUUUCAGUUCCUCUUUAUAAUGUACUUAAAGUUCAUAUAAAGAGGUUUUAU ...........((((((.....))))))..........((((.(((....))).))))((((((((((.((.((.....)).))))))))))))...... (-18.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAACCUCUUUAUAUGAACUUUAAGUACAUUAUAAAGAGGAACUGAAAGUACUUCAAGUUUUAUUUAUAAUUGAACCAUUAGUUCAAAGGUAAGAAAA ......((((((((((((.((.....)).)).))))))))))...((((.....)))).......(((((..((((((.....))))))..))))).... (-21.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 90 47 216 172 aact:AA00174|5end_ribosomal_protein_L11_methyltransferase_123072..123302_POSITIVE 241 90 47 112 68 aact:AA00173|5end_hypothetical_protein_122968..123198_POSITIVE 214 67 21 109 49 aact:AA00605|5end_CDP-diglyceride_pyrophosphorylase_410930..411160_POSITIVE 186 44 5 201 171 aact:AA01981|5end_4-alpha-glucanotransferase_1337202..1337432_POSITIVE 186 44 5 54 24 aact:AA01978|5end_hypothetical_protein_1337055..1337285_POSITIVE 185 73 39 114 72 aact:AA01904|5end_hypothetical_protein_1284448..1284678_POSITIVE 185 88 41 222 172 aact:AA00412|5end_conserved_hypothetical_protein_279174..279404_POSITIVE 179 60 11 204 163 aact:AA01308|5end_cyclic_AMP_receptor_protein_888044..888274_POSITIVE 177 95 60 208 177 aact:AA02409|5end_DNA_ligase_1653315..1653545_POSITIVE 165 94 51 127 91 aact:AA02779|5end_conserved_hypothetical_protein_1942742..1942972_POSITIVE 162 77 51 226 206 aact:AA00226|5end_hypothetical_protein_156276..156506_POSITIVE 161 48 5 185 135 aact:AA02869|5end_hypothetical_protein_2013788..2014018_POSITIVE 160 73 33 189 149 aact:AA01893|5end_acetyl-coenzyme-A_carboxylase_subunit_A_1276842..1277072_POSITIVE 158 83 42 133 93 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 158 73 43 35 4 aact:AA01892|5end_hypothetical_protein_1276688..1276918_POSITIVE 156 86 48 199 149 aact:AA02920|5end_hypothetical_protein_2045394..2045624_POSITIVE 154 81 41 108 60 aact:AA01499|5end_fructose_1,6-bisphosphatase_protein_1008357..1008587_POSITIVE 153 67 39 61 28 aact:AA01566|5end_conserved_hypothetical_protein_1051811..1052041_POSITIVE 153 67 39 61 28 aact:AA01261|5end_conserved_hypothetical_protein_856443..856673_POSITIVE 152 96 56 188 151 aact:AA02466|5end_N-acetylneuraminate_lyase_1704963..1705193_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 214 67 21 91 31 aact:AA00603|3end_undecaprenyl_pyrophosphate_synthetase_(UPPS)_410992..411142_POSITIVE 186 44 5 51 21 aact:AA01976|3end_colicin_V_production_protein_1337132..1337282_POSITIVE 179 60 11 65 24 aact:AA01306|3end_glutathione_reductase_887985..888135_POSITIVE 177 95 60 53 22 aact:AA02407|3end_thymidine_kinase_1653240..1653390_POSITIVE 172 78 41 40 7 aact:AA02419|3end_hypothetical_protein_1661954..1662104_POSITIVE 165 94 51 107 71 aact:AA02778|3end_hypothetical_protein_1942802..1942952_POSITIVE 163 60 21 58 17 aact:AA00933|3end_ribose_ABC_transporter,_ATP-binding_protein_645197..645347_POSITIVE 160 73 33 51 11 aact:AA01891|3end_pyridoxine_kinase_1276784..1276934_POSITIVE 152 65 36 141 107 aact:AA02731|3end_outer_membrane_lipoprotein_carrier_precursor_1912192..1912342_POSITIVE 151 24 1 44 22 aact:AA02632|3end_rhamnosyltransferase_1832694..1832844_POSITIVE 149 97 51 133 100 aact:AA01108|3end_hypothetical_protein_763983..764133_POSITIVE 148 94 63 32 1 aact:AA01906|3end_repressor_protein_CI_1287047..1287197_POSITIVE 148 84 53 134 108 aact:AA00231|3end_long-chain-fatty-acid--CoA_ligase_162399..162549_POSITIVE 147 69 45 28 2 aact:AA02416|3end_conserved_hypothetical_protein_1659578..1659728_POSITIVE 144 63 39 109 88 aact:AA00323|3end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_220222..220372_POSITIVE 142 75 31 86 39 aact:AA01226|3end_IS200-like_transposase_ISAa1_838511..838661_POSITIVE 141 79 43 47 16 aact:AA00356|3end_DNA-directed_RNA_polymerase,_beta'_chain_243282..243432_POSITIVE 140 47 1 93 39 aact:AA01895|3end_hypothetical_protein_1280601..1280751_POSITIVE 139 72 41 145 96 aact:AA01718|3end_DNA_polymerase_III,_chi_subunit_1163316..1163466_POSITIVE 139 70 39 77 40 aact:AA00148|3end_ATP-dependent_RNA_helicase_107843..107993_POSITIVE