Origin IGS: caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtagcaagttgtaagactggctgcttttttatttatagaaccaaaccactagaatctacggataagccttgaaaataaaatacgaaagtagtatactagaatcacaattatgaaaacgtttgcgtaaaattggaattaaaactttaggagacaaattg Mask Tandem Repeat Region ================================================ caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Find is-nt database================================================ Query_seq: SMT_1434:SMT_1435|SMT_1434:SMT_1435:neopullulanase:phosphoribosylanthranilate isomerase:<-<-:1419736..1419896 161 caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1434:SMT_1435|SMT_1434:SMT_1435:neopullulanase:phosphoribosylanthranilate isomerase:<-<-:1419736..1419896 161 caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1434:SMT_1435|SMT_1434:SMT_1435:neopullulanase:phosphoribosylanthranilate isomerase:<-<-:1419736..1419896 161 caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 5 End: 100 .... M S P K V L I P I L R K R F H N C D S S I L L S Y F I F K A Y P ............................................................. caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt 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: 85 Start: 62 End: 91 .............................................................CTTGAAAATAAAATACGAAAGTAGTATACT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1434:SMT_1435|SMT_1434:SMT_1435:neopullulanase:phosphoribosylanthranilate isomerase:<-<-:1419736..1419896 161 caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: smit_SMT_1434_SMT_1435|neopullulanase:phosphoribosylanthranilate isomerase|NEGATIVE:NEGATIVE|[1419736,1419896]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt caatttgtctcctaaagttttaattccaattttacgcaaacgttttcataattgtgattctagtatactactttcgtattttattttcaaggcttatccgtagattctagtggtttggttctataaataaaaaagcagccagtcttacaacttgctacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUUUGUCUCCUAAAGUUUUAAUUCCAAUUUUACGCAAACGUUUUCAUAAUUGUGAUUCUAGUAUACUACUUUCGUAUUUUAUUUUCAAGGCUUAUCCGUAGAUUCUAGUGGUUUGGUUCUAUAAAUAAAAAAGCAGCCAGUCUUACAACUUGCUACUUU ..............(((((((...(((((((..(((....)))......))))).))...(((.((((.......)))).))).....)))))))....(((((..((((....)))).))))).......((((.(((.(((......))).))).)))) (-18.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUAGCAAGUUGUAAGACUGGCUGCUUUUUUAUUUAUAGAACCAAACCACUAGAAUCUACGGAUAAGCCUUGAAAAUAAAAUACGAAAGUAGUAUACUAGAAUCACAAUUAUGAAAACGUUUGCGUAAAAUUGGAAUUAAAACUUUAGGAGACAAAUUG ((((((((.((((....)))).)))))))).............((((....((((.(((....))).................(((....))).....))))................(((....)))....)))).............(....)...... (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 847 140 91 231 182 smit:SMT_1434|5end_neopullulanase_1419645..1419875_NEGATIVE 283 76 34 174 134 smit:SMT_1142|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1085546..1085776_POSITIVE 260 116 74 157 119 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 244 100 53 186 136 smit:SMT_2030|5end_chromosomal_replication_initiator_protein_DnaA_1945167..1945397_NEGATIVE 243 100 51 126 72 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 240 114 71 134 95 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 239 100 58 165 122 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 239 100 58 126 83 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 239 100 58 209 166 smit:SMT_1927|5end_cell_division_protein_FtsH_1868779..1869009_NEGATIVE 239 100 58 166 123 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 239 100 58 147 104 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 239 100 58 212 169 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 239 100 58 194 151 smit:SMT_1672|5end_hypothetical_protein_1660051..1660281_NEGATIVE 239 100 58 227 184 smit:SMT_714|5end_hypothetical_protein_predicted_by_Glimmer/Critica_620979..621209_NEGATIVE 237 123 97 72 41 smit:SMT_463|5end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_401926..402156_POSITIVE 232 113 71 227 183 smit:SMT_83|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_15295..15525_NEGATIVE 231 119 71 78 32 smit:SMT_1418|5end_lysine_decarboxylase_1403147..1403377_NEGATIVE 230 115 71 78 31 smit:SMT_992|5end_hypothetical_protein_934882..935112_NEGATIVE 228 40 3 167 128 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 228 40 3 167 128 smit:SMT_1818|5end_tryptophan_synthase,_alpha_subunit_1792190..1792420_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 118 71 146 102 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 256 108 74 151 117 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 252 118 71 134 96 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 240 114 71 144 105 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 239 100 58 46 3 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE 239 100 58 77 34 smit:SMT_955|3end_acyltransferase_family_protein_904703..904853_POSITIVE 234 139 97 139 97 smit:SMT_1789|3end_hypothetical_protein_1765511..1765661_POSITIVE 230 115 71 77 30 smit:SMT_993|3end_hypothetical_protein_934883..935033_NEGATIVE 226 140 93 62 3 smit:SMT_1260|3end_hypothetical_protein_1226664..1226814_POSITIVE 225 129 83 147 84 smit:SMT_737|3end_hypothetical_protein_642270..642420_NEGATIVE 225 118 71 44 6 smit:SMT_492|3end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_427217..427367_POSITIVE 223 118 90 147 115 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 222 109 61 93 52 smit:SMT_1204|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164595..1164745_NEGATIVE 221 101 64 129 92 smit:SMT_705|3end_hypothetical_protein_614674..614824_NEGATIVE 217 119 71 146 81 smit:SMT_2078|3end_acetyl_xylan_esterase,_putative_1979839..1979989_POSITIVE 213 156 111 149 96 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 212 42 3 144 97 smit:SMT_1011|3end_xanthine_phosphoribosyltransferase_949234..949384_POSITIVE 211 160 111 91 39 smit:SMT_122|3end_hypothetical_protein_75396..75546_POSITIVE 210 139 91 48 2 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 209 146 104 80 21 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE