Origin IGS: taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaattgccactttttagctttacgattctttttcataatgaaactcctttttgatttaaagtacttaacaatattatacaaaaattacaaaatataaacaataacagttcagaacgaaataatgacatttcaggattcacttattgttcggaatttatttttattatcattgtactagttatataatacactttatttttcttttttgcaagccttttctttaattttttttaacgtagcagatttttgcaatcacatcaaaaaaaagatagaatatgactatcaaaaaatgacactctactatttaaaagagtacaaaggagttttta Mask Tandem Repeat Region ================================================ taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Find is-nt database================================================ Query_seq: SMT_520:SMT_521|SMT_520:SMT_521:glutathione reductase:K02005 HlyD family secretion protein:<-->:445376..445705 330 taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_520:SMT_521|SMT_520:SMT_521:glutathione reductase:K02005 HlyD family secretion protein:<-->:445376..445705 330 taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_520:SMT_521|SMT_520:SMT_521:glutathione reductase:K02005 HlyD family secretion protein:<-->:445376..445705 330 taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 190 End: 294 ............................................................................................................................................................................................. M N P E M S L F R S E L L L F I F C N F C I I L L S T L N Q K G V S L .................................... Protein_Len: 37 Strand: - Start: 147 End: 257 .................................................................................................................................................. I V L V I I I F I F E S C Y T F G S I D N N R E S S N N N I N Q L K Q I M ......................................................................... Protein_Len: 41 Strand: - Start: 2 End: 124 . F V G K Y E K L Y Y L T M K Q Y D Y E I K K K I H N C F D A V N F F I L S F A Q M .............................................................................................................................................................................................................. taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt 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: 85 Start: 118 End: 147 .....................................................................................................................CTTGCAAAAAAGAAAAATAAAGTGTATTAT....................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 228 End: 257 ...................................................................................................................................................................................................................................ATTGTTTATATTTTGTAATTTTTGTATAAT......................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 55 End: 84 ......................................................TTTGCAATCACATCAAAAAAAAGATAGAAT...................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -2.3 Tail_Score: -5.90981 Start: 46 End: 62 Full_Region: AGAGTGTCATTTTTT GATAG TCATATT CTATC TTTTTTTTGATGTGA .............................................GATAGTCATATTCTATC............................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SMT_520:SMT_521|SMT_520:SMT_521:glutathione reductase:K02005 HlyD family secretion protein:<-->:445376..445705 330 taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatcttttttttgatgtgattgcaaaaatctgctacgttaaaaaaaattaaagaaaaggcttgcaaaaaagaaaaataaagtgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt Intra-Species Hit: Count: 1 Min: 1 Max: 330 Len: 330 Subject: smit_SMT_520_SMT_521|glutathione reductase:K02005 HlyD family secretion protein|NEGATIVE:POSITIVE|[445376,445705]|330 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 191 Query Start:140 Query End:330 Subject Strand: POSITIVE Subject Start: 140 Subject End: 330 ...........................................................................................................................................tgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt ...........................................................................................................................................tgtattatataactagtacaatgataataaaaataaattccgaacaataagtgaatcctgaaatgtcattatttcgttctgaactgttattgtttatattttgtaatttttgtataatattgttaagtactttaaatcaaaaaggagtttcattatgaaaaagaatcgtaaagctaaaaagtggcaattgt HSP 2 e-value: 4.0E-27 bit: 123.0 Len: 62 Query Start:1 Query End:62 Subject Strand: POSITIVE Subject Start: 1 Subject End: 62 taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatc............................................................................................................................................................................................................................................................................ taaaaactcctttgtactcttttaaatagtagagtgtcattttttgatagtcatattctatc............................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACUCCUUUGUACUCUUUUAAAUAGUAGAGUGUCAUUUUUUGAUAGUCAUAUUCUAUCUUUUUUUUGAUGUGAUUGCAAAAAUCUGCUACGUUAAAAAAAAUUAAAGAAAAGGCUUGCAAAAAAGAAAAAUAAAGUGUAUUAUAUAACUAGUACAAUGAUAAUAAAAAUAAAUUCCGAACAAUAAGUGAAUCCUGAAAUGUCAUUAUUUCGUUCUGAACUGUUAUUGUUUAUAUUUUGUAAUUUUUGUAUAAUAUUGUUAAGUACUUUAAAUCAAAAAGGAGUUUCAUUAUGAAAAAGAAUCGUAAAGCUAAAAAGUGGCAAUUGU ...((((((((((.((((((..........))))))...(((((((..((((...((((...((((((((((((((...(((......)))))))))))))))))....))))..))))..)))))))......(((((((((((((((((....(((((..((((....(((((.(((.((((((..(((((...........)))))..)).)))).)))...)))))..))))...)))))....)))))))))))........))))))......))))))))))..((((((.......)))))).((((.....))))...... (-65.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUUGCCACUUUUUAGCUUUACGAUUCUUUUUCAUAAUGAAACUCCUUUUUGAUUUAAAGUACUUAACAAUAUUAUACAAAAAUUACAAAAUAUAAACAAUAACAGUUCAGAACGAAAUAAUGACAUUUCAGGAUUCACUUAUUGUUCGGAAUUUAUUUUUAUUAUCAUUGUACUAGUUAUAUAAUACACUUUAUUUUUCUUUUUUGCAAGCCUUUUCUUUAAUUUUUUUUAACGUAGCAGAUUUUUGCAAUCACAUCAAAAAAAAGAUAGAAUAUGACUAUCAAAAAAUGACACUCUACUAUUUAAAAGAGUACAAAGGAGUUUUUA ........................................(((((((((((..........((((((.....(((((((.((....(((((...(((((.(((((..((((.(((((((((..(((....)))..)))......)))))).)))))))))))))).....)))))....)).)))))))....((((((((.....(((((((..(((.((((((......))))...)).)))..)))))))...............(((((.......))))).)))))))).................))))))))))))))))).. (-44.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 724 120 71 211 162 smit:SMT_520|5end_glutathione_reductase_445285..445515_NEGATIVE 271 224 190 106 76 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 255 67 28 106 64 smit:SMT_1360|5end_lactoylglutathione_lyase_1338632..1338862_NEGATIVE 255 68 36 106 73 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 226 50 6 158 97 smit:SMT_1396|5end_uracil-DNA_glycosylase_1372064..1372294_POSITIVE 220 239 202 183 145 smit:SMT_654|5end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_566058..566288_NEGATIVE 219 218 175 77 35 smit:SMT_379|5end_acetyltransferase,_GNAT_family_316095..316325_POSITIVE 217 219 181 102 67 smit:SMT_1551|5end_K02221_YggT_family_protein_1534859..1535089_POSITIVE 212 119 75 157 104 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 212 308 264 152 111 smit:SMT_947|5end_ferredoxin_896405..896635_POSITIVE 209 69 26 106 56 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 208 238 194 166 114 smit:SMT_1475|5end_K02004_1455873..1456103_POSITIVE 207 231 191 143 92 smit:SMT_179|5end_ribosomal_protein_S17_119392..119622_POSITIVE 206 100 51 61 3 smit:SMT_1335|5end_RNA_polymerase_sigma_factor_RpoD_1310201..1310431_NEGATIVE 204 81 59 193 171 smit:SMT_1795|5end_DNA_polymerase_III,_delta_subunit_1769847..1770077_NEGATIVE 203 74 35 120 86 smit:SMT_874|5end_dipeptidase_822765..822995_NEGATIVE 201 97 54 136 94 smit:SMT_1072|5end_Cof_family_protein_1011193..1011423_NEGATIVE 200 99 51 152 105 smit:SMT_2085|5end_K01207_beta-N-acetylhexosaminidase_1983039..1983269_POSITIVE 199 259 214 91 36 smit:SMT_1140|5end_glycogen_phosphorylase_1083574..1083804_NEGATIVE 199 320 285 208 171 smit:SMT_818|5end_cystathionine_gamma-synthase_729801..730031_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 224 190 97 67 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 228 225 184 75 36 smit:SMT_1450|3end_K02057_simple_sugar_transport_system_permease_protein_1432666..1432816_NEGATIVE 228 244 209 123 94 smit:SMT_1290|3end_autolysin_1253753..1253903_POSITIVE 226 50 6 96 35 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE 217 219 181 102 67 smit:SMT_1550|3end_hypothetical_protein_1534939..1535089_POSITIVE 215 83 41 140 99 smit:SMT_406|3end_hypothetical_protein_351260..351410_POSITIVE 212 80 33 52 1 smit:SMT_240|3end_glutamate_synthase_small_subunit,_putative_178200..178350_POSITIVE 209 69 26 122 72 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 207 231 191 118 67 smit:SMT_178|3end_50S_ribosomal_protein_L29_119447..119597_POSITIVE 206 219 176 143 96 smit:SMT_1474|3end_K02003_1455951..1456101_POSITIVE 205 255 213 70 32 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 204 100 61 58 10 smit:SMT_1336|3end_DNA_primase_1310204..1310354_NEGATIVE 204 97 61 133 89 smit:SMT_788|3end_hypothetical_protein_699153..699303_NEGATIVE 203 74 35 106 72 smit:SMT_875|3end_nitroreductase_family_protein_822779..822929_NEGATIVE 199 259 214 65 10 smit:SMT_1141|3end_4-alpha-glucanotransferase_1083600..1083750_NEGATIVE 199 320 285 43 6 smit:SMT_819|3end_hypothetical_protein_predicted_by_Glimmer/Critica_729966..730116_NEGATIVE 198 80 45 50 11 smit:SMT_1031|3end_MSM_(multiple_sugar_metabolism)_operon_regulatory_protein_968827..968977_POSITIVE 198 89 43 104 36 smit:SMT_104|3end_DNA_repair_protein_50926..51076_POSITIVE 194 81 45 91 55 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 194 81 45 91 55 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE