Origin IGS: taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaaatttcggttcgaaagtttagcggtatttaggcggggtgtaaacggaagaattttcggaaatagcaaataaaaaaccctgttttgataaacagggttaagttcattaaagataggggctaatta Mask Tandem Repeat Region ================================================ taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Find is-nt database================================================ Query_seq: AA00972:AA00973|AA00972:AA00973:DNA-binding protein HU-ALPHA:transcriptional regulator, DeoR family:->->:678375..678502 128 taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00972:AA00973|AA00972:AA00973:DNA-binding protein HU-ALPHA:transcriptional regulator, DeoR family:->->:678375..678502 128 taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00972:AA00973|AA00972:AA00973:DNA-binding protein HU-ALPHA:transcriptional regulator, DeoR family:->->:678375..678502 128 taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 13 End: 126 ............ M F N E L N P V Y Q N R V F Y L L F P K I L P F T P R L N T A K L S N R N L .. taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat 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: 82 Start: 81 End: 110 ................................................................................GTTTACACCCCGCCTAAATACCGCTAAACT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -10.8 Tail_Score: -3.23899 Start: 30 End: 49 Full_Region: atagcaaataaaaaa ccctgttt tgat aaacaggg ttaagttcattaaag .............................ccctgttttgataaacaggg............................................................................... Find igs database================================================ Query_seq: AA00972:AA00973|AA00972:AA00973:DNA-binding protein HU-ALPHA:transcriptional regulator, DeoR family:->->:678375..678502 128 taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: aact_AA00972_AA00973|DNA-binding protein HU-ALPHA:transcriptional regulator, DeoR family|POSITIVE:POSITIVE|[678375,678502]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat taattagcccctatctttaatgaacttaaccctgtttatcaaaacagggttttttatttgctatttccgaaaattcttccgtttacaccccgcctaaataccgctaaactttcgaaccgaaatttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAGCCCCUAUCUUUAAUGAACUUAACCCUGUUUAUCAAAACAGGGUUUUUUAUUUGCUAUUUCCGAAAAUUCUUCCGUUUACACCCCGCCUAAAUACCGCUAAACUUUCGAACCGAAAUUUAAU ...(((((..........((((((...((((((((((....)))))))))).))))))..........(((.....))).......................)))))..(((((...)))))...... (-19.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAUUUCGGUUCGAAAGUUUAGCGGUAUUUAGGCGGGGUGUAAACGGAAGAAUUUUCGGAAAUAGCAAAUAAAAAACCCUGUUUUGAUAAACAGGGUUAAGUUCAUUAAAGAUAGGGGCUAAUUA ............(((((((((((..(.((..(((.((...)).))))).)..)))))))))))..((((........((((((((((....))))))))))....((......)).....)))).... (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 120 78 60 21 aact:AA01861|5end_phosphomethylpyrimidine_kinase_1251806..1252036_POSITIVE 327 118 77 89 37 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 318 119 72 60 9 aact:AA01755|5end_cobalt_membrane_transport_protein_1185825..1186055_POSITIVE 314 106 64 120 80 aact:AA01829|5end_hypothetical_protein_1231403..1231633_POSITIVE 287 120 75 230 179 aact:AA01450|5end_hypothetical_protein_971860..972090_POSITIVE 285 69 28 206 159 aact:AA02265|5end_exodeoxyribonuclease_V,_alpha_chain_1539701..1539931_POSITIVE 283 118 74 49 2 aact:AA02367|5end_conserved_hypothetical_protein_1623174..1623404_POSITIVE 281 119 76 210 161 aact:AA02538|5end_conserved_hypothetical_protein_1765187..1765417_POSITIVE 281 118 72 157 103 aact:AA01957|5end_conserved_hypothetical_protein_1323211..1323441_POSITIVE 280 109 71 86 54 aact:AA01569|5end_dipeptide_transport_ATP-binding_protein_1056859..1057089_POSITIVE 278 61 28 209 174 aact:AA01217|5end_hypothetical_protein_832656..832886_POSITIVE 278 93 57 184 139 aact:AA01188|5end_conserved_hypothetical_protein_813912..814142_POSITIVE 278 94 54 203 160 aact:AA00416|5end_D-methionine_transport_system_permease_protein_(ABC_transport_system)_282677..282907_POSITIVE 275 119 90 45 19 aact:AA01517|5end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1020989..1021219_POSITIVE 268 104 68 52 8 aact:AA01476|5end_hypothetical_protein_991402..991632_POSITIVE 266 94 53 151 110 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 266 120 79 57 12 aact:AA00323|5end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_219387..219617_POSITIVE 265 105 61 196 149 aact:AA01400|5end_phosphopantetheine_adenylyltransferase_945679..945909_POSITIVE 262 106 64 90 45 aact:AA02076|5end_conserved_hypothetical_protein_1409926..1410156_POSITIVE 262 119 72 100 53 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 96 64 41 3 aact:AA01962|3end_recombination_protein_rec2_1328706..1328856_POSITIVE 338 120 78 64 25 aact:AA01859|3end_hypothetical_protein_1251890..1252040_POSITIVE 318 119 72 57 6 aact:AA01753|3end_conserved_hypothetical_protein_1185902..1186052_POSITIVE 314 106 64 44 4 aact:AA01827|3end_iron(III)_ABC_transporter,_periplasmic_binding_protein_1231407..1231557_POSITIVE 294 119 80 126 85 aact:AA00977|3end_transcriptional_regulator_(LysR_family)_683334..683484_POSITIVE 291 119 78 147 99 aact:AA01603|3end_oligopeptidase_A_1085014..1085164_POSITIVE 280 109 71 79 47 aact:AA01568|3end_dipeptide_transport_system_ATP-binding_protein_1056932..1057082_POSITIVE 276 118 79 47 5 aact:AA02366|3end_hypothetical_protein_1623252..1623402_POSITIVE 272 119 74 136 78 aact:AA00221|3end_NADP-specific_glutamate_dehydrogenase_153865..154015_POSITIVE 272 120 88 31 5 aact:AA00166|3end_conserved_hypothetical_protein_(possible_acetyltransferase)_117919..118069_POSITIVE 267 119 72 113 59 aact:AA01021|3end_hypothetical_protein_714276..714426_POSITIVE 266 94 53 151 110 aact:AA00992|3end_ribonuclease_BN_694568..694718_POSITIVE 265 105 61 128 81 aact:AA01398|3end_KDO_kinase_945691..945841_POSITIVE 262 106 64 63 18 aact:AA02075|3end_conserved_hypothetical_protein_1409979..1410129_POSITIVE 259 94 51 57 15 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE 256 117 74 115 69 aact:AA01890|3end_cell-cycle_protein_1275967..1276117_POSITIVE 253 119 71 119 65 aact:AA02228|3end_regulatory_protein,_sorC_family_1516011..1516161_POSITIVE 252 119 84 38 2 aact:AA00937|3end_L-xylulokinase_647525..647675_POSITIVE 249 120 77 137 96 aact:AA01284|3end_heat_shock_protein_(hsp60)_870294..870444_POSITIVE 249 104 65 36 3 aact:AA01260|3end_hypothetical_protein_855758..855908_POSITIVE