Origin IGS: gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttttgctttcacaaaaaatttctatcagtgcaatttaaaatatatatnnnnnttaattaattaannnnntcgcttggaaaagaatatccatgatatttatcagttagagcttagtcaaaaagatgccaatatgcgggc Mask Tandem Repeat Region ================================================ gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Find is-nt database================================================ Query_seq: SMT_1527:SMT_1528|SMT_1527:SMT_1528:two-component sensor kinase:K03310 alanine or glycine:cation symporter, AGCS family:<-<-:1511274..1511413 140 gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1527:SMT_1528|SMT_1527:SMT_1528:two-component sensor kinase:K03310 alanine or glycine:cation symporter, AGCS family:<-<-:1511274..1511413 140 gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1527:SMT_1528|SMT_1527:SMT_1528:two-component sensor kinase:K03310 alanine or glycine:cation symporter, AGCS family:<-<-:1511274..1511413 140 gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Predict ORF larger than 30AA ================================================ gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa 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: 20 End: 49 ...................TTTGACTAAGCTCTAACTGATAAATATCAT........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1527:SMT_1528|SMT_1527:SMT_1528:two-component sensor kinase:K03310 alanine or glycine:cation symporter, AGCS family:<-<-:1511274..1511413 140 gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: smit_SMT_1527_SMT_1528|two-component sensor kinase:K03310 alanine or glycine:cation symporter, AGCS family|NEGATIVE:NEGATIVE|[1511274,1511413]|140 HSP 1 e-value: 4.0E-56 bit: 218.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa gcccgcatattggcatctttttgactaagctctaactgataaatatcatggatattcttttccaagcgannnnnttaattaattaannnnnatatatattttaaattgcactgatagaaattttttgtgaaagcaaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCCGCAUAUUGGCAUCUUUUUGACUAAGCUCUAACUGAUAAAUAUCAUGGAUAUUCUUUUCCAAGCGANNNNNUUAAUUAAUUAANNNNNAUAUAUAUUUUAAAUUGCACUGAUAGAAAUUUUUUGUGAAAGCAAAAAA (((........))).............................(((((.(((........)))..((((.....((((......................)))).))))..)))))....((((((((....)))))))) (-16.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUGCUUUCACAAAAAAUUUCUAUCAGUGCAAUUUAAAAUAUAUAUNNNNNUUAAUUAAUUAANNNNNUCGCUUGGAAAAGAAUAUCCAUGAUAUUUAUCAGUUAGAGCUUAGUCAAAAAGAUGCCAAUAUGCGGGC ......(((((.((......((((((..((((....((((......................))))......)))))))))).(((((((...)))))))....)).)))))..............(((........))) (-14.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 859 50 1 141 92 smit:SMT_1527|5end_two-component_sensor_kinase_1511183..1511413_NEGATIVE 282 48 1 166 115 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 272 48 1 50 3 smit:SMT_784|5end_hypothetical_protein_696298..696528_NEGATIVE 243 38 1 199 160 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 242 69 46 227 199 smit:SMT_1147|5end_hypothetical_protein_1092144..1092374_NEGATIVE 236 48 2 56 6 smit:SMT_1829|5end_hypothetical_protein_1798156..1798386_POSITIVE 222 49 1 58 17 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 221 68 29 177 132 smit:SMT_849|5end_hypothetical_protein_796127..796357_NEGATIVE 212 59 11 184 139 smit:SMT_1729|5end_exodeoxyribonuclease_VII_small_subunit_1714566..1714796_POSITIVE 206 50 3 136 94 smit:SMT_1473|5end_hypothetical_protein_1454320..1454550_POSITIVE 206 59 12 172 117 smit:SMT_309|5end_acyl-carrier-protein_S-malonyltransferase_250406..250636_POSITIVE 203 60 28 43 9 smit:SMT_1132|5end_glutamate--cysteine_ligase,_putative,_truncated_1068108..1068338_NEGATIVE 203 35 9 85 55 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 202 58 13 100 52 smit:SMT_322|5end_hypothetical_protein_260193..260423_POSITIVE 201 67 25 45 7 smit:SMT_796|5end_K03734_thiamine_biosynthesis_lipoprotein_704211..704441_POSITIVE 200 37 11 144 115 smit:SMT_2090|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1985971..1986201_NEGATIVE 200 49 5 51 6 smit:SMT_325|5end_K02029_polar_amino_acid_transport_system_permease_protein_263023..263253_NEGATIVE 199 48 2 155 109 smit:SMT_276|5end_exopolysaccharide_biosynthesis_protein_218821..219051_POSITIVE 198 38 2 69 32 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 198 38 2 69 32 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 40 1 69 25 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 230 48 8 41 3 smit:SMT_785|3end_hypothetical_protein_696307..696457_NEGATIVE 222 49 1 77 36 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 208 68 23 150 101 smit:SMT_1623|3end_K03498_trk_system_potassium_uptake_protein_TrkH_1611115..1611265_POSITIVE 204 67 24 147 106 smit:SMT_368|3end_hypothetical_protein_303996..304146_POSITIVE 203 35 9 64 34 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 202 58 13 97 49 smit:SMT_321|3end_hypothetical_protein_260270..260420_POSITIVE 200 69 26 146 99 smit:SMT_1440|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1423867..1424017_NEGATIVE 199 48 2 148 102 smit:SMT_275|3end_transcriptional_activator-exopolysaccharide_biosynthesis_218894..219044_POSITIVE 198 38 2 59 22 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 198 50 3 54 14 smit:SMT_549|3end_hypothetical_cytosolic_protein_467367..467517_POSITIVE 195 50 3 132 82 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 195 38 6 122 92 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 195 60 14 109 43 smit:SMT_628|3end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_534050..534200_POSITIVE 192 67 21 69 24 smit:SMT_1607|3end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1597699..1597849_POSITIVE 191 69 25 151 105 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 188 33 3 37 1 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 187 50 1 76 36 smit:SMT_623|3end_50S_ribosomal_protein_L21_529812..529962_POSITIVE 186 42 1 48 9 smit:SMT_2131|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2012731..2012881_POSITIVE 186 69 28 55 10 smit:SMT_1082|3end_Cof_family_protein_1020877..1021027_POSITIVE