Origin IGS: tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt .........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 aatgacacctcaaatagtgatagtgaatgaattgaaagggtgttagagaagcgacttatattactctgaacgtagttttatcactccgtttcaaagaaacgcaattatcagatcttccgagcctattacgttttttctcttttgtgacccagtccacaataaacaataatcttaaatccaatgcgaaataacgtaattgatcgtcaaagggcttttatcaagaatagtgccaaattaaccctgtcccggaggctaca Mask Tandem Repeat Region ================================================ tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Find is-nt database================================================ Query_seq: AA01453:AA01455|AA01453:AA01455:D-xylose isomerase:D-xylose ABC transporter, periplasmic-binding protein:->->:974914..975170 257 tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01453:AA01455|AA01453:AA01455:D-xylose isomerase:D-xylose ABC transporter, periplasmic-binding protein:->->:974914..975170 257 tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01453:AA01455|AA01453:AA01455:D-xylose isomerase:D-xylose ABC transporter, periplasmic-binding protein:->->:974914..975170 257 tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 77 End: 199 ............................................................................ M D L R L L F I V D W V T K E K K R N R L G R S D N C V S L K R S D K T T F R V I .......................................................... Protein_Len: 43 Strand: - Start: 70 End: 198 ..................................................................... K A N S K L N N N I T S Q T V F S F F R L L S P L D S L Q T E K F R L S L V V N L T M ........................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. L R R S L T L K A S N K I F A R Q R D I V N N R M P N L I M ..................................................................................................................................................................... tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt 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: 83 Start: 25 End: 41 ........................TTGGCACTATTCTTGAT........................................................................................................................................................................................................................ tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.1 Tail_Score: -2.65112 Start: 162 End: 194 Full_Region: CTGATAATTGCGTTT CTTTGAAACGGAGT GATAAA ACTACGTTCAGAG TAATATAAGTCGCTT .................................................................................................................................................................CTTTGAAACGGAGTGATAAAACTACGTTCAGAG............................................................... Find igs database================================================ Query_seq: AA01453:AA01455|AA01453:AA01455:D-xylose isomerase:D-xylose ABC transporter, periplasmic-binding protein:->->:974914..975170 257 tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Intra-Species Hit: Count: 1 Min: 1 Max: 257 Len: 257 Subject: aact_AA01453_AA01455|D-xylose isomerase:D-xylose ABC transporter, periplasmic-binding protein|POSITIVE:POSITIVE|[974914,975170]|257 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 257 Query Start:1 Query End:257 Subject Strand: POSITIVE Subject Start: 1 Subject End: 257 tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt tgtagcctccgggacagggttaatttggcactattcttgataaaagccctttgacgatcaattacgttatttcgcattggatttaagattattgtttattgtggactgggtcacaaaagagaaaaaacgtaataggctcggaagatctgataattgcgtttctttgaaacggagtgataaaactacgttcagagtaatataagtcgcttctctaacaccctttcaattcattcactatcactatttgaggtgtcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAGCCUCCGGGACAGGGUUAAUUUGGCACUAUUCUUGAUAAAAGCCCUUUGACGAUCAAUUACGUUAUUUCGCAUUGGAUUUAAGAUUAUUGUUUAUUGUGGACUGGGUCACAAAAGAGAAAAAACGUAAUAGGCUCGGAAGAUCUGAUAAUUGCGUUUCUUUGAAACGGAGUGAUAAAACUACGUUCAGAGUAAUAUAAGUCGCUUCUCUAACACCCUUUCAAUUCAUUCACUAUCACUAUUUGAGGUGUCAUU ..((((((........))))))...(((((((.....(((((...((((..(((((........))))).((((((.(((((...........))))).))))))..))))......((((((.(((((((((.((.((....)).))....)))))))))(((((((.((.(((......))).))))))))).............))))))......................)))))........))))))).. (-56.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGACACCUCAAAUAGUGAUAGUGAAUGAAUUGAAAGGGUGUUAGAGAAGCGACUUAUAUUACUCUGAACGUAGUUUUAUCACUCCGUUUCAAAGAAACGCAAUUAUCAGAUCUUCCGAGCCUAUUACGUUUUUUCUCUUUUGUGACCCAGUCCACAAUAAACAAUAAUCUUAAAUCCAAUGCGAAAUAACGUAAUUGAUCGUCAAAGGGCUUUUAUCAAGAAUAGUGCCAAAUUAACCCUGUCCCGGAGGCUACA .......((((.....(.(((((.(....((((.....((..(((.((((((..(((.......(((((....(((......))).((((((...))))))......))))).....(((....((((((((.((((.(..(((((........))))).......................).)))).))))))))...)))...))).))))))........)))..)).))))...)))))).).))))..... (-43.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 55 13 169 130 aact:AA02002|5end_hypothetical_protein_1360196..1360426_POSITIVE 321 80 38 137 101 aact:AA02970|5end_tyrosine_phenol-lyase_2076373..2076603_POSITIVE 291 161 121 99 62 aact:AA01883|5end_recycling_protein;_permease_1269821..1270051_POSITIVE 287 176 137 183 134 aact:AA01305|5end_conserved_hypothetical_protein_885598..885828_POSITIVE 286 189 147 154 110 aact:AA00374|5end_short-chain_fatty_acids_transporter_251681..251911_POSITIVE 281 57 11 78 27 aact:AA01458|5end_aminotransferase_978820..979050_POSITIVE 278 166 127 221 180 aact:AA00899|5end_possible_quaternary_ammonium_compound_resistance_protein_623214..623444_POSITIVE 278 47 1 97 58 aact:AA00846|5end_cell_division_protein_L_584643..584873_POSITIVE 277 59 17 127 85 aact:AA02337|5end_DNA_mismatch_repair_protein_1597350..1597580_POSITIVE 269 250 205 65 7 aact:AA01054|5end_conserved_hypothetical_protein_733678..733908_POSITIVE 268 50 1 181 123 aact:AA01477|5end_type_I_restriction_enzyme_R_protein_992249..992479_POSITIVE 265 49 8 118 81 aact:AA01011|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_705149..705379_POSITIVE 265 49 1 65 18 aact:AA00142|5end_glycerate_kinase_101309..101539_POSITIVE 262 49 5 186 135 aact:AA02823|5end_exodeoxyribonuclease_V_gamma_chain_1982703..1982933_POSITIVE 262 176 133 91 30 aact:AA00855|5end_arginine_ABC_transporter,_permease_protein_589584..589814_POSITIVE 260 137 92 75 28 aact:AA02605|5end_hypothetical_protein_1816555..1816785_POSITIVE 258 49 1 70 19 aact:AA02123|5end_hypothetical_protein_1448244..1448474_POSITIVE 255 176 135 111 54 aact:AA00386|5end_aspartate--ammonia_ligase_(asparagine_synthetase_A)_261150..261380_POSITIVE 254 176 132 194 156 aact:AA02494|5end_conserved_hypothetical_protein_1730747..1730977_POSITIVE 253 160 117 72 35 aact:AA02889|5end_hypothetical_protein_2025045..2025275_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 55 13 132 93 aact:AA02001|3end_conserved_hypothetical_protein_1360239..1360389_POSITIVE 321 80 38 101 65 aact:AA02969|3end_beta_tyrosinase_(tyrosine_phenol-lyase)_2076417..2076567_POSITIVE 304 50 1 148 103 aact:AA01069|3end_translation_elongation_factor_(EF-Ts)_740700..740850_POSITIVE 287 176 137 85 36 aact:AA01304|3end_penicillin-binding_protein_1A_885580..885730_POSITIVE 286 189 147 148 104 aact:AA00373|3end_CoA-transferase_(beta)_251755..251905_POSITIVE 278 166 127 133 92 aact:AA00896|3end_prolyl-tRNA_synthetase_(proline-tRNA_ligase)_623206..623356_POSITIVE 278 47 1 104 65 aact:AA00845|3end_hypothetical_protein_584730..584880_POSITIVE 277 59 17 127 85 aact:AA02335|3end_6-O-methylguanine-DNA_methyltransferase_1597430..1597580_POSITIVE 268 50 1 113 55 aact:AA01476|3end_hypothetical_protein_992261..992411_POSITIVE 265 49 8 142 105 aact:AA01010|3end_hypothetical_protein_705253..705403_POSITIVE 262 176 133 85 24 aact:AA00854|3end_arginine_transport_system_permease_protein_589658..589808_POSITIVE 254 89 44 87 31 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE 253 241 201 111 54 aact:AA01690|3end_penicillin-binding_protein_1C_1149142..1149292_POSITIVE 253 88 46 150 111 aact:AA00698|3end_iron(III)_ABC_transporter,_periplasmic_iron-compound-binding_protein_478311..478461_POSITIVE 252 48 3 87 39 aact:AA01066|3end_conserved_hypothetical_protein_738900..739050_POSITIVE 251 172 135 113 68 aact:AA02395|3end_ATP-dependent_proteinase_1647107..1647257_POSITIVE 250 179 135 151 93 aact:AA02461|3end_ferrochelatase_1702132..1702282_POSITIVE 247 138 100 120 80 aact:AA01227|3end_hypothetical_protein_838845..838995_POSITIVE 244 227 183 123 88 aact:AA01923|3end_type_III_restriction-modification_system_methylation_subunit_1299936..1300086_POSITIVE 237 150 101 65 26 aact:AA02246|3end_peptidase_E_1528355..1528505_POSITIVE