Origin IGS: tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact .........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 agtactccttccaaaatggggaatgttcagagcacgcaaaaagctcccttgagggagctaaaaaataccaagtagaggttttttttagcgatggcatgtcccaaacatcgtaatattctactaacagtctagcatattttttgaaaaatggcaaagggcaagaaaaaagagaccaaagcaagtacttggtctctcgtttga Mask Tandem Repeat Region ================================================ tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Find is-nt database================================================ Query_seq: SMT_1004:SMT_1005|SMT_1004:SMT_1005:thioredoxin:possible aluminum resistance protein:->->:945885..946085 201 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1004:SMT_1005|SMT_1004:SMT_1005:thioredoxin:possible aluminum resistance protein:->->:945885..946085 201 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1004:SMT_1005|SMT_1004:SMT_1005:thioredoxin:possible aluminum resistance protein:->->:945885..946085 201 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 21 End: 200 .................... M L W S L F S C P L P F F K K Y A R L L V E Y Y D V W D M P S L K K T S T W Y F L A P S R E L F A C S E H S P F W K E Y . tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact 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: 47 End: 76 ..............................................TTTGCCATTTTTCAAAAAATATGCTAGACT............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -10.4 Tail_Score: -4.69664 Start: 144 End: 159 Full_Region: ACTTGGTATTTTTTA GCTCCC TCAA GGGAGC TTTTTGCGTGCTCTG ...............................................................................................................................................GCTCCCTCAAGGGAGC.......................................... Find igs database================================================ Query_seq: SMT_1004:SMT_1005|SMT_1004:SMT_1005:thioredoxin:possible aluminum resistance protein:->->:945885..946085 201 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: smit_SMT_1004_SMT_1005|thioredoxin:possible aluminum resistance protein|POSITIVE:POSITIVE|[945885,946085]|201 HSP 1 e-value: 6.0E-96 bit: 351.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctnnnnnnnncctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagactgttagtagaatattacgatgtttgggacatgccatcgctaaaaaaaacctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact Inter-species Hit: Count: 3 Min: 1 Max: 201 Len: 201 Subject: NC_008533_SPD_1567_SPD_1568|thioredoxin:GTP cyclohydrolase, putative|POSITIVE:POSITIVE|[1586063,1586555]|493 HSP 1 e-value: 3.0E-33 bit: 143.0 Len: 76 Query Start:1 Query End:76 Subject Strand: POSITIVE Subject Start: 1 Subject End: 76 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagact............................................................................................................................. tcaaacgagagaccaagtactttctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagact............................................................................................................................. HSP 2 e-value: 1.0E-29 bit: 131.0 Len: 122 Query Start:80 Query End:201 Subject Strand: POSITIVE Subject Start: 185 Subject End: 304 ...............................................................................agtagaatattacgatgtttgggacatgccatcgctnnnnnnnncctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact ...............................................................................agtagaatattacgatgtttgggatatgccatcgctaaaaaaa--ctcgatttggtattttttagctccctaatgggagctttttgcgtgctctgaacatttcccattttggaaggagtact Subject: NC_003098_spr1602_spr1603|Thioredoxin reductase:hypothetical protein|POSITIVE:POSITIVE|[1578532,1578796]|265 HSP 1 e-value: 3.0E-33 bit: 143.0 Len: 76 Query Start:1 Query End:76 Subject Strand: POSITIVE Subject Start: 1 Subject End: 76 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagact............................................................................................................................. tcaaacgagagaccaagtactttctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagact............................................................................................................................. HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 36 Query Start:80 Query End:115 Subject Strand: POSITIVE Subject Start: 185 Subject End: 220 ...............................................................................agtagaatattacgatgtttgggacatgccatcgct...................................................................................... ...............................................................................agtagaatattacgatgtttgggatatgccatcgct...................................................................................... Subject: NC_003028_SP_1776_SP_1777|thioredoxin:hypothetical protein|POSITIVE:POSITIVE|[1694828,1695200]|373 HSP 1 e-value: 3.0E-33 bit: 143.0 Len: 76 Query Start:1 Query End:76 Subject Strand: POSITIVE Subject Start: 1 Subject End: 76 tcaaacgagagaccaagtacttgctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagact............................................................................................................................. tcaaacgagagaccaagtactttctttggtctcttttttcttgccctttgccatttttcaaaaaatatgctagact............................................................................................................................. HSP 2 e-value: 2.0E-31 bit: 137.0 Len: 122 Query Start:80 Query End:201 Subject Strand: POSITIVE Subject Start: 185 Subject End: 305 ...............................................................................agtagaatattacgatgtttgggacatgccatcgctnnnnnnnncctctacttggtattttttagctccctcaagggagctttttgcgtgctctgaacattccccattttggaaggagtact ...............................................................................agtagaatattacgatgtttgggatatgccatcgctaaaaaaa-cctcgatttggtattttttagctccctaatgggagctttttgcgtgctctgaacatttcccattttggaaggagtact Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAACGAGAGACCAAGUACUUGCUUUGGUCUCUUUUUUCUUGCCCUUUGCCAUUUUUCAAAAAAUAUGCUAGACUGUUAGUAGAAUAUUACGAUGUUUGGGACAUGCCAUCGCUAAAAAAAACCUCUACUUGGUAUUUUUUAGCUCCCUCAAGGGAGCUUUUUGCGUGCUCUGAACAUUCCCCAUUUUGGAAGGAGUACU ..(((.((((((((((((....)).)))))))))).)))..((((((...(((..............((((((....)))))).........((((((..(..(((((......(((((((.(((.......))).)))))))((((((....)))))).....)))))..)..))))))........))).))).))).. (-58.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUACUCCUUCCAAAAUGGGGAAUGUUCAGAGCACGCAAAAAGCUCCCUUGAGGGAGCUAAAAAAUACCAAGUAGAGGUUUUUUUUAGCGAUGGCAUGUCCCAAACAUCGUAAUAUUCUACUAACAGUCUAGCAUAUUUUUUGAAAAAUGGCAAAGGGCAAGAAAAAAGAGACCAAAGCAAGUACUUGGUCUCUCGUUUGA .....((((((((...((((..((((.((..((........(((((((....)))))))((((((.(((.......))).)))))).))..))))))..))))....(((.(((((.(((.........))).)))))...)))....)))..)))))....(((..(((((((((.........)))))))))..))).. (-53.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 187 152 190 152 smit:SMT_1964|5end_sodium/hydrogen_exchanger_family_protein_1896718..1896948_NEGATIVE 327 54 22 91 62 smit:SMT_1347|5end_SsrA-binding_protein_1325185..1325415_NEGATIVE 297 166 130 221 178 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 296 174 131 147 84 smit:SMT_309|5end_acyl-carrier-protein_S-malonyltransferase_250406..250636_POSITIVE 294 112 76 76 29 smit:SMT_1363|5end_50S_ribosomal_protein_L20_1343613..1343843_NEGATIVE 293 188 141 231 190 smit:SMT_1562|5end_hypothetical_protein_1554992..1555222_NEGATIVE 292 170 129 89 30 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 278 53 12 57 12 smit:SMT_1613|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1600608..1600838_POSITIVE 278 137 92 48 8 smit:SMT_1607|5end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1596648..1596878_POSITIVE 276 172 131 108 50 smit:SMT_1083|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1020829..1021059_POSITIVE 273 185 144 187 138 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 272 195 151 54 2 smit:SMT_1652|5end_Cof_family_protein_1640534..1640764_POSITIVE 270 168 123 160 97 smit:SMT_1832|5end_tagatose-6-phosphate_kinase_1800438..1800668_POSITIVE 270 185 143 55 17 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 266 36 5 55 12 smit:SMT_1713|5end_K03284_metal_ion_transporter,_MIT_family_1700400..1700630_POSITIVE 265 166 128 118 82 smit:SMT_1079|5end_dihydropteroate_synthase_1017659..1017889_NEGATIVE 264 174 140 230 191 smit:SMT_916|5end_3-hydroxy-3-methylglutaryl-CoA_reductase_870004..870234_NEGATIVE 263 158 113 124 87 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 261 185 142 62 13 smit:SMT_1704|5end_D-alanine-D-alanine_ligase_1687431..1687661_POSITIVE 260 135 95 230 191 smit:SMT_1497|5end_acetyltransferase,_GNAT_family_1481432..1481662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 54 22 128 99 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 278 53 12 70 25 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 278 137 92 51 11 smit:SMT_1606|3end_glutamate_racemase_1596731..1596881_POSITIVE 276 172 131 76 18 smit:SMT_1082|3end_Cof_family_protein_1020877..1021027_POSITIVE 272 195 151 57 5 smit:SMT_1651|3end_chromosome_segregation_SMC_protein_1640617..1640767_POSITIVE 270 168 123 149 86 smit:SMT_1831|3end_galactose-6-phosphate_isomerase_1800507..1800657_POSITIVE 267 185 144 116 87 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 260 199 154 83 47 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE 257 113 72 69 29 smit:SMT_1752|3end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1730451..1730601_POSITIVE 255 51 13 114 62 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 251 136 92 78 38 smit:SMT_2031|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1945633..1945783_NEGATIVE 251 170 123 145 83 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 251 182 143 38 3 smit:SMT_547|3end_branched-chain_amino_acid_aminotransferase_465049..465199_POSITIVE 251 156 113 103 67 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 250 103 63 79 27 smit:SMT_1911|3end_hypothetical_protein_1857840..1857990_POSITIVE 250 103 63 79 27 smit:SMT_867|3end_hypothetical_protein_816542..816692_POSITIVE 249 59 11 71 23 smit:SMT_567|3end_conserved_hypothetical_protein_485752..485902_POSITIVE 248 165 126 148 100 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 247 166 124 90 29 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 245 66 22 112 66 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE