Origin IGS: tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtagttacctgctttctagaaatgttagttatattagtagtattttgataatttgcaaataattgtattttatctttttattggatataaaaagatctatttgtacccatatttttacttgctcctatggatttatcaacaatttcctatctttattaatttcctgttatacaattatgtactttcatca Mask Tandem Repeat Region ================================================ tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Find is-nt database================================================ Query_seq: SMT_375:SMT_376|SMT_375:SMT_376:hypothetical protein predicted by Glimmer/Critica:DNA (cytosine-5-)-methyltransferase:->->:312850..313039 190 tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_375:SMT_376|SMT_375:SMT_376:hypothetical protein predicted by Glimmer/Critica:DNA (cytosine-5-)-methyltransferase:->->:312850..313039 190 tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_375:SMT_376|SMT_375:SMT_376:hypothetical protein predicted by Glimmer/Critica:DNA (cytosine-5-)-methyltransferase:->->:312850..313039 190 tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 3 End: 128 .. H F Y M I T Y C S I L L S L F N N I F G Y S C T F I H T C I S R K I D L L F I F Y M .............................................................. Protein_Len: 46 Strand: - Start: 1 End: 138 S S L V Y N Y L L F N I F I P F Q Q Y I W L L L Y F Y P Y L Y I K K Y G I F L Y F V I I Q M .................................................... tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac 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: 51 End: 80 ..................................................GTTGATAAATCCATAGGAGCAAGTAAAAAT.............................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 110 End: 139 .............................................................................................................TTTGCAAATAATTGTATTTTATCTTTTTAT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -3.9 Tail_Score: -3.53174 Start: 94 End: 120 Full_Region: caaataattgtattt tatctttttat tggat ataaaaagatc tatttgtacccatat .............................................................................................tatctttttattggatataaaaagatc...................................................................... Find igs database================================================ Query_seq: SMT_375:SMT_376|SMT_375:SMT_376:hypothetical protein predicted by Glimmer/Critica:DNA (cytosine-5-)-methyltransferase:->->:312850..313039 190 tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: smit_SMT_375_SMT_376|hypothetical protein predicted by Glimmer/Critica:DNA (cytosine-5-)- methyltransferase|POSITIVE:POSITIVE|[312850,313039]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac tgatgaaagtacataattgtataacaggaaattaataaagataggaaattgttgataaatccataggagcaagtaaaaatatgggtacaaatagatctttttatatccaataaaaagataaaatacaattatttgcaaattatcaaaatactactaatataactaacatttctagaaagcaggtaactac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGAAAGUACAUAAUUGUAUAACAGGAAAUUAAUAAAGAUAGGAAAUUGUUGAUAAAUCCAUAGGAGCAAGUAAAAAUAUGGGUACAAAUAGAUCUUUUUAUAUCCAAUAAAAAGAUAAAAUACAAUUAUUUGCAAAUUAUCAAAAUACUACUAAUAUAACUAACAUUUCUAGAAAGCAGGUAACUAC ((((((..(((.((((((((((........((((((((..........))))))))..(((((((..............)))))))........((((((((((.....))))))))))...)))))))))).)))...))))))......((((.......(((.......)))......))))..... (-28.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGUUACCUGCUUUCUAGAAAUGUUAGUUAUAUUAGUAGUAUUUUGAUAAUUUGCAAAUAAUUGUAUUUUAUCUUUUUAUUGGAUAUAAAAAGAUCUAUUUGUACCCAUAUUUUUACUUGCUCCUAUGGAUUUAUCAACAAUUUCCUAUCUUUAUUAAUUUCCUGUUAUACAAUUAUGUACUUUCAUCA ((((....))))......((((.(..(((((....(((((.((((((((((..((((((((..........((((((((((.....)))))))))).)))))))).(((((..............)))))..))))))).)))...))).))....)))))..).....((((....)))).)))).... (-24.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 73 40 59 22 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 251 73 40 59 22 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 243 49 2 195 145 smit:SMT_582|5end_ATP_synthase_F0,_B_subunit_499003..499233_POSITIVE 242 70 25 99 65 smit:SMT_1923|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1866021..1866251_POSITIVE 240 83 44 174 138 smit:SMT_1684|5end_acetyltransferase,_GNAT_family_1667757..1667987_NEGATIVE 238 73 36 65 22 smit:SMT_1450|5end_K02057_simple_sugar_transport_system_permease_protein_1433622..1433852_NEGATIVE 237 86 43 202 163 smit:SMT_1864|5end_integral_membrane_protein_1826517..1826747_POSITIVE 232 76 38 205 170 smit:SMT_1596|5end_oligopeptide_transport_ATP-binding_protein_OppD_1585903..1586133_POSITIVE 210 179 131 67 23 smit:SMT_939|5end_phosphomethylpyrimidine_kinase_892025..892255_NEGATIVE 203 72 44 51 20 smit:SMT_597|5end_K08974_putative_membrane_protein_513917..514147_NEGATIVE 202 186 145 58 21 smit:SMT_445|5end_hypothetical_protein_384309..384539_POSITIVE 201 70 22 37 2 smit:SMT_255|5end_K02026_multiple_sugar_transport_system_permease_protein_191731..191961_POSITIVE 196 102 61 48 12 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 195 73 40 50 12 smit:SMT_1856|5end_polypeptide_deformylase_1820650..1820880_POSITIVE 195 181 162 204 184 smit:SMT_1086|5end_K01992_ABC-2_type_transport_system_permease_protein_1023279..1023509_NEGATIVE 193 101 83 80 62 smit:SMT_2131|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2011665..2011895_POSITIVE 189 78 39 81 43 smit:SMT_1614|5end_K08998_hypothetical_protein_1601330..1601560_POSITIVE 186 95 60 59 20 smit:SMT_1579|5end_ABC-type_sugar_transport_system,_periplasmic_component_1571890..1572120_POSITIVE 186 183 147 64 25 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 184 185 142 221 179 smit:SMT_2057|5end_cell_division_protein_FtsH_1967283..1967513_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 73 36 62 19 smit:SMT_1451|3end_K02057_simple_sugar_transport_system_permease_protein_1433625..1433775_NEGATIVE 210 179 131 77 33 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 200 73 43 151 122 smit:SMT_1863|3end_glutamyl_aminopeptidase_1826556..1826706_POSITIVE 196 102 61 61 25 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 191 69 25 89 35 smit:SMT_1656|3end_glutamine_ABC_transporter_ATP-binding_protein_1645172..1645322_NEGATIVE 190 68 22 145 106 smit:SMT_129|3end_putative_glycosyltransferase_80883..81033_POSITIVE 189 78 39 81 43 smit:SMT_1613|3end_ribosomal_large_subunit_pseudouridine_synthase_B_1601410..1601560_POSITIVE 184 108 61 91 42 smit:SMT_139|3end_hypothetical_protein_91058..91208_POSITIVE 182 98 66 54 22 smit:SMT_1322|3end_K02075_zinc/manganese_transport_system_permease_protein_1292257..1292407_POSITIVE 180 73 43 56 22 smit:SMT_1729|3end_exodeoxyribonuclease_VII_small_subunit_1714858..1715008_POSITIVE 174 88 58 150 118 smit:SMT_1754|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1732363..1732513_NEGATIVE 172 94 69 72 50 smit:SMT_989|3end_hypothetical_protein_932949..933099_NEGATIVE 171 74 38 35 1 smit:SMT_1810|3end_hypothetical_protein_1785598..1785748_POSITIVE 171 180 140 61 32 smit:SMT_1556|3end_phosphoglycerate_mutase_1541966..1542116_POSITIVE 171 85 41 83 39 smit:SMT_672|3end_hypothetical_protein_580899..581049_POSITIVE 170 110 61 50 5 smit:SMT_1906|3end_peptidyl-tRNA_hydrolase_1853723..1853873_NEGATIVE 170 90 41 58 5 smit:SMT_941|3end_hypothetical_protein_892863..893013_NEGATIVE 167 94 60 68 26 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 167 90 42 82 36 smit:SMT_939|3end_phosphomethylpyrimidine_kinase_891252..891402_NEGATIVE 163 100 53 112 59 smit:SMT_1126|3end_K08987_putative_membrane_protein_1061157..1061307_NEGATIVE