Origin IGS: agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaggtacctccattcatctattttaccacactttcaaaaaagcttctttcttatatcatgaaactgggaatatttttttctttatgatagaataaacttact Mask Tandem Repeat Region ================================================ agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Find is-nt database================================================ Query_seq: SMT_559:SMT_560|SMT_559:SMT_560:D-alanyl-D-alanine carboxypeptidase:predicted permease:<-->:478133..478234 102 agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_559:SMT_560|SMT_559:SMT_560:D-alanyl-D-alanine carboxypeptidase:predicted permease:<-->:478133..478234 102 agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_559:SMT_560|SMT_559:SMT_560:D-alanyl-D-alanine carboxypeptidase:predicted permease:<-->:478133..478234 102 agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Predict ORF larger than 30AA ================================================ agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc 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================================================ agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_559:SMT_560|SMT_559:SMT_560:D-alanyl-D-alanine carboxypeptidase:predicted permease:<-->:478133..478234 102 agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: smit_SMT_559_SMT_560|D-alanyl-D-alanine carboxypeptidase:predicted permease|NEGATIVE:POSITIVE|[478133,478234]|102 HSP 1 e-value: 5.0E-39 bit: 161.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 agtaagtttattctatcataaagnnnnnnntattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc agtaagtttattctatcataaagaaaaaaatattcccagtttcatgatataagaaagaagcttttttgaaagtgtggtaaaatagatgaatggaggtacctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAGUUUAUUCUAUCAUAAAGAAAAAAAUAUUCCCAGUUUCAUGAUAUAAGAAAGAAGCUUUUUUGAAAGUGUGGUAAAAUAGAUGAAUGGAGGUACCUC .....(((((((.(((((((.....(((((.......((((((.............))))))))))).....))))))).))))))).....(((....))) (-15.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGUACCUCCAUUCAUCUAUUUUACCACACUUUCAAAAAAGCUUCUUUCUUAUAUCAUGAAACUGGGAAUAUUUUUUUCUUUAUGAUAGAAUAAACUUACU (((....))).............................(((.((..((((...((((((((...(..((.....))..)))))))))))))..)))))... (-11.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 795 100 51 191 142 smit:SMT_559|5end_D-alanyl-D-alanine_carboxypeptidase_478042..478272_NEGATIVE 287 76 32 222 178 smit:SMT_1899|5end_hypothetical_protein_1850018..1850248_POSITIVE 223 96 51 226 169 smit:SMT_1802|5end_tyrosyl-tRNA_synthetase_1776712..1776942_NEGATIVE 216 97 53 225 187 smit:SMT_128|5end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_79868..80098_NEGATIVE 211 80 31 57 3 smit:SMT_1242|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1203383..1203613_NEGATIVE 210 78 35 156 108 smit:SMT_1286|5end_hypothetical_protein_1248388..1248618_POSITIVE 207 68 35 172 131 smit:SMT_1365|5end_translation_initiation_factor_IF-3_1344485..1344715_NEGATIVE 204 77 35 167 132 smit:SMT_1013|5end_galactose-1-phosphate_uridylyltransferase_950626..950856_NEGATIVE 201 95 67 126 98 smit:SMT_996|5end_K03309_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter,_DAACS_family_936859..937089_POSITIVE 199 97 59 215 177 smit:SMT_571|5end_putative_transposase,_ISSmu1_489261..489491_POSITIVE 198 99 60 45 2 smit:SMT_845|5end_hypothetical_protein_791868..792098_NEGATIVE 196 90 41 183 140 smit:SMT_1519|5end_DNA-binding_response_regulator_VncR_1499662..1499892_NEGATIVE 194 99 60 141 94 smit:SMT_374|5end_hypothetical_protein_309788..310018_POSITIVE 192 69 31 144 105 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 189 66 22 78 24 smit:SMT_1522|5end_K02004_1503177..1503407_NEGATIVE 188 69 32 39 8 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 185 99 51 63 7 smit:SMT_1937|5end_glycosyl_transferase,_family_2_1874428..1874658_POSITIVE 185 98 52 194 151 smit:SMT_1037|5end_alpha-galactosidase_979609..979839_NEGATIVE 185 98 52 194 151 smit:SMT_1030|5end_alpha-galactosidase_967829..968059_NEGATIVE 183 100 58 43 1 smit:SMT_582|5end_ATP_synthase_F0,_B_subunit_499003..499233_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 213 71 33 151 114 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 210 78 31 151 92 smit:SMT_702|3end_hypothetical_protein_611946..612096_NEGATIVE 204 77 35 148 113 smit:SMT_1014|3end_galactokinase_950645..950795_NEGATIVE 199 97 59 53 15 smit:SMT_570|3end_hypothetical_protein_489179..489329_POSITIVE 198 99 60 58 15 smit:SMT_846|3end_hypothetical_protein_791855..792005_NEGATIVE 195 96 58 132 78 smit:SMT_473|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409634..409784_NEGATIVE 194 99 60 62 15 smit:SMT_373|3end_cytosine_specific_DNA_methyltransferase_309789..309939_POSITIVE 190 100 51 49 7 smit:SMT_1520|3end_K02004_1499805..1499955_NEGATIVE 188 69 32 37 6 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 183 95 60 73 37 smit:SMT_89|3end_chromosomal_replication_initiator_protein_21298..21448_POSITIVE 182 100 61 141 100 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 181 74 38 43 1 smit:SMT_1987|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1915972..1916122_NEGATIVE 181 74 38 43 1 smit:SMT_1207|3end_choline_binding_protein_A_1167242..1167392_NEGATIVE 179 72 37 54 15 smit:SMT_1931|3end_23S_rRNA_methyltransferase_1870796..1870946_NEGATIVE 177 49 22 98 77 smit:SMT_838|3end_cation_efflux_family_protein_784203..784353_POSITIVE 177 65 31 77 45 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 175 36 5 121 93 smit:SMT_449|3end_hypothetical_protein_388219..388369_POSITIVE 174 86 51 55 30 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE 173 99 55 47 9 smit:SMT_950|3end_UDP-glucose_4-epimerase_897677..897827_NEGATIVE 168 54 11 85 31 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE