Origin IGS: aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcctttacgatcgtggcactgacattgatgaaaatgcgagcatttaaaaaagtgtggtcgttttttcgattattttttaaaagcaaaaaaatatcgaaaaatacttgcttttgtgcgtgatctcttgctattaattaagcctttacacaacatcttttcaatctcatctagaaggacaaactt Mask Tandem Repeat Region ================================================ aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Find is-nt database================================================ Query_seq: AA01215:AA01216|AA01215:AA01216:aspartate-semialdehyde dehydrogenase:conserved hypothetical protein:->->:831774..831959 186 aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01215:AA01216|AA01215:AA01216:aspartate-semialdehyde dehydrogenase:conserved hypothetical protein:->->:831774..831959 186 aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01215:AA01216|AA01215:AA01216:aspartate-semialdehyde dehydrogenase:conserved hypothetical protein:->->:831774..831959 186 aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 22 End: 111 ..................... M E K M L C K G L I N S K R S R T K A S I F R Y F F A F K K ........................................................................... Protein_Len: 44 Strand: + Start: 53 End: 184 .................................................... M A R D H A Q K Q V F F D I F L L L K N N R K N D H T F L N A R I F I N V S A T I V K A .. Protein_Len: 36 Strand: - Start: 67 End: 174 .................................................................. A C F C T N K S I K K S K F F L R F F S W V K K F A R M K M L T L A V M ............ aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta 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================================================ PromScan Matrix: RpoN Strand: - Score: 82 Start: 155 End: 171 ..........................................................................................................................................................GTGGCACTGACATTGAT............... aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -3.4 Tail_Score: -3.76186 Start: 80 End: 124 Full_Region: taaaaaagtgtggtc gttttttcgattatttttt aaaagca aaaaaatatcgaaaaatac ttgcttttgtgcgtg ...............................................................................gttttttcgattattttttaaaagcaaaaaaatatcgaaaaatac.............................................................. TransTerm Strand: - Conf: 59 HP_score: -6.2 Tail_Score: -2.9652 Start: 83 End: 122 Full_Region: aaaaagtgtggtcgt tttttcgattatttttt aaaagca aaaaaatatcgaaaaa tacttgcttttgtgc ..................................................................................tttttcgattattttttaaaagcaaaaaaatatcgaaaaa................................................................ Find igs database================================================ Query_seq: AA01215:AA01216|AA01215:AA01216:aspartate-semialdehyde dehydrogenase:conserved hypothetical protein:->->:831774..831959 186 aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgatatttttttgcttttaaaaaataatcgaaaaaacgaccacacttttttaaatgctcgcattttcatcaatgtcagtgccacgatcgtaaaggctta Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: aact_AA01215_AA01216|aspartate-semialdehyde dehydrogenase:conserved hypothetical protein|POSITIVE:POSITIVE|[831774,831959]|186 HSP 1 e-value: 3.0E-45 bit: 182.0 Len: 92 Query Start:1 Query End:92 Subject Strand: POSITIVE Subject Start: 1 Subject End: 92 aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgata.............................................................................................. aagtttgtccttctagatgagattgaaaagatgttgtgtaaaggcttaattaatagcaagagatcacgcacaaaagcaagtatttttcgata.............................................................................................. HSP 2 e-value: 4.0E-10 bit: 65.9 Len: 33 Query Start:154 Query End:186 Subject Strand: POSITIVE Subject Start: 154 Subject End: 186 .........................................................................................................................................................catcaatgtcagtgccacgatcgtaaaggctta .........................................................................................................................................................catcaatgtcagtgccacgatcgtaaaggctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUUUGUCCUUCUAGAUGAGAUUGAAAAGAUGUUGUGUAAAGGCUUAAUUAAUAGCAAGAGAUCACGCACAAAAGCAAGUAUUUUUCGAUAUUUUUUUGCUUUUAAAAAAUAAUCGAAAAAACGACCACACUUUUUUAAAUGCUCGCAUUUUCAUCAAUGUCAGUGCCACGAUCGUAAAGGCUUA .((((...((((.((.(..(.(((.....))).)..).))))))...))))...(((....((((..((((...........((((((((((((((((.......))))))).)))))))))..(((...........(((((....)))))........))).))))...))))......))).. (-33.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCUUUACGAUCGUGGCACUGACAUUGAUGAAAAUGCGAGCAUUUAAAAAAGUGUGGUCGUUUUUUCGAUUAUUUUUUAAAAGCAAAAAAAUAUCGAAAAAUACUUGCUUUUGUGCGUGAUCUCUUGCUAUUAAUUAAGCCUUUACACAACAUCUUUUCAAUCUCAUCUAGAAGGACAAACUU ...((((((..(((.(.((...(((....((((.(((((....)))))......((((((((..(((((((((.(((((((.......)))))))))))))))).....((......))..))))....(((........)))....))))..))))...))).)).))))..))))).)...... (-32.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 148 101 170 119 aact:AA02409|5end_DNA_ligase_1653315..1653545_POSITIVE 291 157 114 80 39 aact:AA02091|5end_hypothetical_protein_1424441..1424671_POSITIVE 289 179 137 57 9 aact:AA00870|5end_rough_colony_protein_C_601735..601965_POSITIVE 280 137 95 124 82 aact:AA02937|5end_conserved_hypothetical_protein_2056379..2056609_POSITIVE 276 168 121 140 107 aact:AA01936|5end_tyrosyl-tRNA_synthetase_1307043..1307273_POSITIVE 274 176 143 198 159 aact:AA01203|5end_diaminopimelate_epimerase_824140..824370_POSITIVE 271 158 116 101 52 aact:AA02965|5end_hypothetical_protein_2074069..2074299_POSITIVE 267 178 132 193 146 aact:AA00170|5end_hypothetical_protein_121238..121468_POSITIVE 266 168 122 132 68 aact:AA00908|5end_probable_sigma-E_factor_regulatory_protein_626076..626306_POSITIVE 264 168 121 162 123 aact:AA02410|5end_cell_division_protein_1655429..1655659_POSITIVE 263 172 143 167 139 aact:AA02196|5end_oxaloacetate_decarboxylase_beta_chain_1496308..1496538_POSITIVE 260 160 114 139 98 aact:AA02106|5end_hypothetical_protein_1433241..1433471_POSITIVE 260 146 106 177 133 aact:AA00239|5end_hypothetical_protein_171213..171443_POSITIVE 258 148 106 228 186 aact:AA00084|5end_aminotransferase_60814..61044_POSITIVE 258 148 106 78 36 aact:AA00083|5end_hypothetical_protein_60664..60894_POSITIVE 255 173 144 228 200 aact:AA02142|5end_outer_membrane_protein_OprM_precursor_1466037..1466267_POSITIVE 252 178 140 90 47 aact:AA02402|5end_O-sialoglycoprotein_endopeptidase_1651337..1651567_POSITIVE 252 154 119 197 160 aact:AA00212|5end_ribokinase_146056..146286_POSITIVE 252 154 119 96 59 aact:AA00211|5end_hypothetical_protein_145955..146185_POSITIVE 251 176 140 192 161 aact:AA02605|5end_hypothetical_protein_1816555..1816785_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 157 114 108 67 aact:AA02090|3end_glucose-1-phosphate_adenylyltransferase_1424549..1424699_POSITIVE 271 158 116 80 31 aact:AA02964|3end_opacity_associated_protein_A_2074128..2074278_POSITIVE 266 168 122 119 55 aact:AA00906|3end_sigma-E_factor_regulatory_protein_626143..626293_POSITIVE 264 168 121 57 18 aact:AA02409|3end_DNA_ligase_1655404..1655554_POSITIVE 261 177 142 92 50 aact:AA01573|3end_peptide_transport_periplasmic_protein_1061454..1061604_POSITIVE 260 160 114 108 67 aact:AA02105|3end_killing_protein_1433290..1433440_POSITIVE 260 146 106 53 9 aact:AA00237|3end_hypothetical_protein_171169..171319_POSITIVE 258 148 106 101 59 aact:AA00081|3end_fatty_acid_metabolism_regulator_protein_60767..60917_POSITIVE 252 178 140 64 21 aact:AA02400|3end_hypothetical_protein_1651391..1651541_POSITIVE 252 154 119 93 56 aact:AA00209|3end_D-ribose_ABC_transporter,_periplasmic-binding_protein_146032..146182_POSITIVE 251 176 140 139 108 aact:AA02604|3end_thioredoxin_reductase_1816582..1816732_POSITIVE 248 169 130 115 81 aact:AA01342|3end_conserved_hypotheticl_protein_(possible_ribosomal_RNA_adenine_dimethylase)_911085..911235_POSITIVE 248 169 121 138 75 aact:AA00384|3end_conserved_hypothetical_protein_(possible_nitrogen_fixation_protein)_261168..261318_POSITIVE 247 179 135 138 91 aact:AA01590|3end_hypothetical_protein_1070971..1071121_POSITIVE 247 100 54 81 36 aact:AA01048|3end_iron_binding_protein_afuA,_periplasmic_protein_730497..730647_POSITIVE 246 172 131 51 14 aact:AA01471|3end_type_I_restriction_enzyme_M_(modification_chain)_989002..989152_POSITIVE 243 146 101 48 7 aact:AA01006|3end_conserved_hypothetical_protein_(possible_cytosine_deaminas)_703446..703596_POSITIVE 242 144 102 64 18 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 241 180 133 109 70 aact:AA02280|3end_conserved_hypothetical_protein_1552767..1552917_POSITIVE 239 168 124 99 58 aact:AA01624|3end_glucose-6-phosphate_isomerase_1099901..1100051_POSITIVE