Origin IGS: agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttattctcctgtctgatttttctcccctcattatagcaaaaagccaggtctaattgaactctttttcctattatataaagtagagagaagattttataaaaatagtgaacaaatgtgct Mask Tandem Repeat Region ================================================ agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Find is-nt database================================================ Query_seq: SMT_460:SMT_461|SMT_460:SMT_461:6-phospho-beta-glucosidase:mannose-6-phosphate isomerase:->->:399399..399518 120 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_460:SMT_461|SMT_460:SMT_461:6-phospho-beta-glucosidase:mannose-6-phosphate isomerase:->->:399399..399518 120 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_460:SMT_461|SMT_460:SMT_461:6-phospho-beta-glucosidase:mannose-6-phosphate isomerase:->->:399399..399518 120 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 28 End: 120 ........................... M F S L L Y I I G K R V Q L D L A F C Y N E G R K I R Q E N K agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag 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: 84 Start: 61 End: 90 ............................................................GTTCAATTAGACCTGGCTTTTTGCTATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_460:SMT_461|SMT_460:SMT_461:6-phospho-beta-glucosidase:mannose-6-phosphate isomerase:->->:399399..399518 120 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: smit_SMT_460_SMT_461|6-phospho-beta-glucosidase:mannose-6-phosphate isomerase|POSITIVE:POSITIVE|[399399,399518]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag Inter-species Hit: Count: 3 Min: 1 Max: 120 Len: 120 Subject: NC_003028_SP_0734_SP_0736|hypothetical protein:mannose-6-phosphate isomerase|NEGATIVE:POSITIVE|[698459,698939]|481 HSP 1 e-value: 3.0E-28 bit: 125.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 362 Subject End: 476 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggaga..... agcacatttgtttactatttttataaaatcttctccctgctttataagatgtaaaaaagagttcaattcgaactctttttttgctataatgaggggagaaaaatcagacaggaga..... Subject: NC_008533_SPD_0639_SPD_0641|hypothetical protein:mannose-6-phosphate isomerase, class I|NEGATIVE:POSITIVE|[660215,661063]|849 HSP 1 e-value: 2.0E-26 bit: 119.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 730 Subject End: 849 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag agcacatttgtttactatttttataaaatcttctccctgctttataagatgtaaaaaagagttcaaatggaactctttttttgctataatgaggggagaaaaatcagacaggagattaag Subject: NC_003098_spr0646_spr0647|Phospho-beta-gluco or galactosidase, truncation:Mannose-6-phosphate isomerase|POSITIVE:POSITIVE|[653413,653532]|120 HSP 1 e-value: 2.0E-26 bit: 119.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 agcacatttgttcactatttttataaaatcttctctctactttatataataggaaaaagagttcaattagacctggctttttgctataatgaggggagaaaaatcagacaggagaataag agcacatttgtttactatttttataaaatcttctccctgctttataagatgtaaaaaagagttcaaatggaactctttttttgctataatgaggggagaaaaatcagacaggagattaag Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCACAUUUGUUCACUAUUUUUAUAAAAUCUUCUCUCUACUUUAUAUAAUAGGAAAAAGAGUUCAAUUAGACCUGGCUUUUUGCUAUAAUGAGGGGAGAAAAAUCAGACAGGAGAAUAAG .......((((((.((............(((((((((........((.((((.((((((.(((......)))....)))))).)))).)))))))))))...........)).)))))). (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUCUCCUGUCUGAUUUUUCUCCCCUCAUUAUAGCAAAAAGCCAGGUCUAAUUGAACUCUUUUUCCUAUUAUAUAAAGUAGAGAGAAGAUUUUAUAAAAAUAGUGAACAAAUGUGCU ............................(((((((.((.....))..........((((.((((((..(((((......)))))..)))))).)))).....)))))))........... (-15.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 100 58 197 150 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 291 98 51 120 63 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 264 120 71 208 154 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 259 97 58 231 198 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 258 99 52 207 149 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 254 120 71 215 148 smit:SMT_947|5end_ferredoxin_896405..896635_POSITIVE 251 103 69 186 146 smit:SMT_702|5end_hypothetical_protein_612311..612541_NEGATIVE 247 118 72 53 9 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 242 118 91 183 153 smit:SMT_2142|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2019999..2020229_POSITIVE 239 100 51 224 188 smit:SMT_1930|5end_peptide_chain_release_factor_1_1870765..1870995_NEGATIVE 239 108 65 214 158 smit:SMT_709|5end_hypothetical_protein_618919..619149_NEGATIVE 232 43 1 179 138 smit:SMT_365|5end_hypothetical_protein_301485..301715_POSITIVE 223 100 57 213 153 smit:SMT_1630|5end_hypothetical_protein_1617291..1617521_POSITIVE 223 100 57 213 153 smit:SMT_1241|5end_hypothetical_protein_1201040..1201270_POSITIVE 220 98 58 39 1 smit:SMT_1784|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1760755..1760985_POSITIVE 220 115 71 36 2 smit:SMT_1520|5end_K02004_1501184..1501414_NEGATIVE 220 111 72 70 22 smit:SMT_107|5end_ribose-phosphate_pyrophosphokinase_52402..52632_POSITIVE 218 98 51 193 137 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 218 85 66 112 94 smit:SMT_771|5end_spermidine/putrescine_transport_system_permease_protein_PotB_682183..682413_NEGATIVE 217 95 60 144 101 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 119 80 70 24 smit:SMT_1875|3end_hypothetical_protein_1833422..1833572_POSITIVE 291 98 51 150 93 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 264 120 71 129 75 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 240 88 48 95 60 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 234 87 50 87 43 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 218 80 33 74 23 smit:SMT_857|3end_endo-beta-N-acetylglucosaminidase_800881..801031_NEGATIVE 216 111 74 39 1 smit:SMT_114|3end_alpha-mannosidase_65529..65679_POSITIVE 215 117 72 71 25 smit:SMT_1346|3end_tellurite_resistance_protein_TehB_1323843..1323993_NEGATIVE 215 46 6 95 54 smit:SMT_786|3end_hypothetical_protein_697239..697389_NEGATIVE 214 85 49 90 50 smit:SMT_142|3end_hypothetical_protein_93409..93559_NEGATIVE 213 112 71 128 77 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 212 87 42 91 46 smit:SMT_1778|3end_ATP-dependent_RNA_helicase_1753611..1753761_NEGATIVE 212 48 1 131 72 smit:SMT_589|3end_hypothetical_protein_506827..506977_POSITIVE 211 95 51 82 43 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 211 99 51 89 36 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 209 115 71 54 6 smit:SMT_1585|3end_phosphopantetheine_adenylyltransferase_1575810..1575960_POSITIVE 208 100 51 112 66 smit:SMT_1125|3end_K08987_putative_membrane_protein_1060975..1061125_NEGATIVE 208 113 74 107 56 smit:SMT_1090|3end_K07485_transposase_1026425..1026575_POSITIVE 207 115 74 112 66 smit:SMT_1679|3end_hypothetical_protein_1663590..1663740_POSITIVE 206 108 73 44 3 smit:SMT_881|3end_peptidoglycan_branched_peptide_synthesis_protein,_alanine_adding_enzyme_828305..828455_NEGATIVE