Origin IGS: aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt .........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 acatttatatttatttctattaaataaattttaacttctgtagtaactatagagtcaaataaaaaataaaattaacattatttttttaaagaatacagaaaatataaaaaatagtgaaaaaattattaaaaaataaaaaattgactctatagttacagtatagaatatactaaataaataagattagctgaaatacataagcaaaaaacaaaaaaaattttatttattgagataggaggatataatt Mask Tandem Repeat Region ================================================ aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Find is-nt database================================================ Query_seq: FN1745:FN1746|FN1745:FN1746:Cystathionine gamma-synthase:Cystathionine beta-lyase:<-->:244234..244480 247 aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1745:FN1746|FN1745:FN1746:Cystathionine gamma-synthase:Cystathionine beta-lyase:<-->:244234..244480 247 aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1745:FN1746|FN1745:FN1746:Cystathionine gamma-synthase:Cystathionine beta-lyase:<-->:244234..244480 247 aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 80 End: 190 ............................................................................... M F Y T V T I E S I F Y F L I I F S L F F I F S V F F K K I M L I L F F I ......................................................... aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt 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: 118 End: 147 .....................................................................................................................TTTAATAATTTTTTCACTATTTTTTATATT.................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 129 End: 158 ................................................................................................................................TTTCACTATTTTTTATATTTTCTGTATTCT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1745:FN1746|FN1745:FN1746:Cystathionine gamma-synthase:Cystathionine beta-lyase:<-->:244234..244480 247 aattatatcctcctatctcaataaataaaattttttttgttttttgcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaattttttattttttaataattttttcactattttttatattttctgtattctttaaaaaaataatgttaattttattttttatttgactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt Intra-Species Hit: Count: 1 Min: 1 Max: 247 Len: 247 Subject: NC_003454_FN1745_FN1746|Cystathionine gamma-synthase:Cystathionine beta-lyase|NEGATIVE:POSITIVE|[244234,244480]|247 HSP 1 e-value: 3.0E-27 bit: 123.0 Len: 62 Query Start:46 Query End:107 Subject Strand: POSITIVE Subject Start: 46 Subject End: 107 .............................................gcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaa............................................................................................................................................ .............................................gcttatgtatttcagctaatcttatttatttagtatattctatactgtaactatagagtcaa............................................................................................................................................ HSP 2 e-value: 1.0E-23 bit: 111.0 Len: 56 Query Start:192 Query End:247 Subject Strand: POSITIVE Subject Start: 192 Subject End: 247 ...............................................................................................................................................................................................gactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt ...............................................................................................................................................................................................gactctatagttactacagaagttaaaatttatttaatagaaataaatataaatgt HSP 3 e-value: 4.0E-8 bit: 60.0 Len: 30 Query Start:1 Query End:30 Subject Strand: POSITIVE Subject Start: 1 Subject End: 30 aattatatcctcctatctcaataaataaaa......................................................................................................................................................................................................................... aattatatcctcctatctcaataaataaaa......................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUAUCCUCCUAUCUCAAUAAAUAAAAUUUUUUUUGUUUUUUGCUUAUGUAUUUCAGCUAAUCUUAUUUAUUUAGUAUAUUCUAUACUGUAACUAUAGAGUCAAUUUUUUAUUUUUUAAUAAUUUUUUCACUAUUUUUUAUAUUUUCUGUAUUCUUUAAAAAAAUAAUGUUAAUUUUAUUUUUUAUUUGACUCUAUAGUUACUACAGAAGUUAAAAUUUAUUUAAUAGAAAUAAAUAUAAAUGU ..((((((..........(((.((((((((....)))))))).)))......((((((.(((((..........)))))...((((.....((((((((((((((((....(((((....)))))....................................(((((((((........)))))))))..))))))))))))))))...))))..................)))))).)))))).... (-40.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUAUAUUUAUUUCUAUUAAAUAAAUUUUAACUUCUGUAGUAACUAUAGAGUCAAAUAAAAAAUAAAAUUAACAUUAUUUUUUUAAAGAAUACAGAAAAUAUAAAAAAUAGUGAAAAAAUUAUUAAAAAAUAAAAAAUUGACUCUAUAGUUACAGUAUAGAAUAUACUAAAUAAAUAAGAUUAGCUGAAAUACAUAAGCAAAAAACAAAAAAAAUUUUAUUUAUUGAGAUAGGAGGAUAUAAUU ....(((((((..((((((((..............(((((((((((((((((((((((.................(((((((((((...................)))))))))))......(((((....)))))....))))))))))))))))..))))))).......(((((((((((((.(((..........))).............)))))))))))))..))))))))))))))).. (-49.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 670 100 51 191 142 NC_003454:FN1745|5end_Cystathionine_gamma-synthase_244143..244373_NEGATIVE 215 240 191 109 63 NC_003454:FN0184|5end_hypothetical_protein_809087..809317_NEGATIVE 213 71 31 193 158 NC_003454:FN1923|5end_Adenine-specific_methyltransferase_421097..421327_NEGATIVE 211 48 5 135 96 NC_003454:FN1635|5end_LSU_ribosomal_protein_L14P_136572..136802_NEGATIVE 208 77 34 135 91 NC_003454:FN0207|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_833618..833848_POSITIVE 206 108 81 92 61 NC_003454:FN0335|5end_Outer_membrane_porin_F_969675..969905_NEGATIVE 205 220 177 162 113 NC_003454:FN1009|5end_hypothetical_protein_1663950..1664180_NEGATIVE 202 143 107 100 62 NC_003454:FN1467|5end_hypothetical_protein_2149207..2149437_POSITIVE 201 115 77 78 38 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 201 41 8 165 134 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 201 86 41 166 126 NC_003454:FN0577|5end_hypothetical_protein_1227237..1227467_POSITIVE 197 138 94 135 86 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 196 89 47 148 102 NC_003454:FN1202|5end_NAD(+)_synthetase_1862298..1862528_NEGATIVE 196 48 5 138 93 NC_003454:FN1757|5end_thiamine_biosynthesis_protein_ThiC_253249..253479_NEGATIVE 194 44 9 132 99 NC_003454:FN1037|5end_flavodoxin_1689447..1689677_POSITIVE 194 64 27 168 124 NC_003454:FN0927|5end_hypothetical_protein_1582352..1582582_NEGATIVE 194 48 3 182 139 NC_003454:FN2101|5end_Transporter_610246..610476_POSITIVE 193 48 1 136 86 NC_003454:FN0219|5end_Autolysin_response_regulator_843316..843546_NEGATIVE 193 57 13 216 178 NC_003454:FN0009|5end_L-aspartate_oxidase_648908..649138_POSITIVE 191 100 64 44 5 NC_003454:FN1176|5end_Hypothetical_cytosolic_protein_1837826..1838056_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 217 100 54 81 33 NC_003454:FN1177|3end_hypothetical_protein_1837789..1837939_NEGATIVE 211 48 5 106 67 NC_003454:FN1636|3end_SSU_ribosomal_protein_S17P_136601..136751_NEGATIVE 208 77 34 72 28 NC_003454:FN0206|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_833635..833785_POSITIVE 207 158 133 106 77 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 202 143 107 39 1 NC_003454:FN1466|3end_hypothetical_protein_2149226..2149376_POSITIVE 201 115 77 48 8 NC_003454:FN1414|3end_NA+/H+_antiporter_NHAC_2074300..2074450_NEGATIVE 201 86 41 151 111 NC_003454:FN0576|3end_D-amino_acid_dehydrogenase_large_subunit_1227302..1227452_POSITIVE 197 138 94 118 69 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 196 89 47 135 89 NC_003454:FN1203|3end_GTP-binding_protein_1862311..1862461_NEGATIVE 196 48 5 121 76 NC_003454:FN1758|3end_Thiamin-phosphate_pyrophosphorylase_253266..253416_NEGATIVE 194 44 9 83 50 NC_003454:FN1036|3end_hypothetical_protein_1689478..1689628_POSITIVE 194 64 27 138 94 NC_003454:FN0928|3end_O-sialoglycoprotein_endopeptidase_1582382..1582532_NEGATIVE 193 158 115 126 87 NC_003454:FN1098|3end_hypothetical_protein_1743898..1744048_POSITIVE 193 48 1 143 93 NC_003454:FN0220|3end_Autolysin_sensor_kinase_843309..843459_NEGATIVE 189 67 30 44 2 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 186 91 55 145 108 NC_003454:FN1422|3end_NA+/H+_antiporter_NHAC_2087005..2087155_NEGATIVE 186 160 113 108 65 NC_003454:FN0710|3end_hypothetical_protein_1369632..1369782_POSITIVE 186 190 141 89 49 NC_003454:FN1727|3end_Chloride_channel_protein_226062..226212_NEGATIVE 185 151 111 112 75 NC_003454:FN0815|3end_Propionate_permease_1475813..1475963_POSITIVE 184 139 93 86 40 NC_003454:FN2124|3end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633251..633401_NEGATIVE