Origin IGS: tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc .........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 gactggcctagcctcgcttctggaaatgggcaagcgcaggcaagatgctagctgaacttgacagataaaggaagtagccaaggctgggctattttccatctcatatcataaacattagaaagaggagcgagttgcaattcagatttgagttctgcttcgctgctcttttttaggtaagaaa Mask Tandem Repeat Region ================================================ tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Find is-nt database================================================ Query_seq: SSA_2237:SSA_2239|SSA_2237:SSA_2239:Dihydrofolate:folylpolyglutamate synthetase, putative:Conserved uncharacterized cytosolic protein:<-<-:2236831..2237011 181 tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2237:SSA_2239|SSA_2237:SSA_2239:Dihydrofolate:folylpolyglutamate synthetase, putative:Conserved uncharacterized cytosolic protein:<-<-:2236831..2237011 181 tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2237:SSA_2239|SSA_2237:SSA_2239:Dihydrofolate:folylpolyglutamate synthetase, putative:Conserved uncharacterized cytosolic protein:<-<-:2236831..2237011 181 tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 83 End: 181 .................................................................................. M E N S P A L A T S F I C Q V Q L A S C L R L P I S R S E A R P V tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -2.4 Tail_Score: -5.08824 Start: 17 End: 60 Full_Region: cataaacattagaaa gaggagcgagttgcaattca gatt tgagttctgcttcgctgctc ttttttaggtaagaa ................gaggagcgagttgcaattcagatttgagttctgcttcgctgctc......................................................................................................................... Find igs database================================================ Query_seq: SSA_2237:SSA_2239|SSA_2237:SSA_2239:Dihydrofolate:folylpolyglutamate synthetase, putative:Conserved uncharacterized cytosolic protein:<-<-:2236831..2237011 181 tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_009009_SSA_2237_SSA_2239|Dihydrofolate:folylpolyglutamate synthetase, putative:Conserved uncharacterized cytosolic protein|NEGATIVE:NEGATIVE|[2236831,2237011]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc tttcttacctaaaaaagagcagcgaagcagaactcaaatctgaattgcaactcgctcctctttctaatgtttatgatatgagatggaaaatagcccagccttggctacttcctttatctgtcaagttcagctagcatcttgcctgcgcttgcccatttccagaagcgaggctaggccagtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUACCUAAAAAAGAGCAGCGAAGCAGAACUCAAAUCUGAAUUGCAACUCGCUCCUCUUUCUAAUGUUUAUGAUAUGAGAUGGAAAAUAGCCCAGCCUUGGCUACUUCCUUUAUCUGUCAAGUUCAGCUAGCAUCUUGCCUGCGCUUGCCCAUUUCCAGAAGCGAGGCUAGGCCAGUC .............((((((.(((((.((((...(((....))).))))...))))).))))))(((.((..(.(((((.((...((((..(((((.......))))).))))....))))))).)..))..)))...((.((((((.(((((............))))))).)))).)).. (-45.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUGGCCUAGCCUCGCUUCUGGAAAUGGGCAAGCGCAGGCAAGAUGCUAGCUGAACUUGACAGAUAAAGGAAGUAGCCAAGGCUGGGCUAUUUUCCAUCUCAUAUCAUAAACAUUAGAAAGAGGAGCGAGUUGCAAUUCAGAUUUGAGUUCUGCUUCGCUGCUCUUUUUUAGGUAAGAAA ...(((((((((((.((((((.....((..((((.((.(((.....))).))....)))).))......)))))).....)))))))))))....................((...((((((((.(((((((.(.(((((......)))))).)).))))).))))))))...))...... (-57.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 964 140 91 231 182 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 415 160 114 225 185 NC_009009:SSA_0999|5end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_999716..999946_NEGATIVE 407 177 131 112 64 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 399 150 102 142 91 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 392 170 122 65 2 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 380 176 139 186 150 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 379 179 131 62 18 NC_009009:SSA_1454|5end_hypothetical_protein_1461100..1461330_NEGATIVE 378 178 133 227 174 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 377 140 91 202 138 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 374 179 131 134 78 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 370 179 131 219 165 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 365 180 131 187 127 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 364 180 133 77 24 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 362 180 131 221 161 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 357 180 136 223 177 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 355 176 142 60 27 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 354 140 94 144 87 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 349 177 134 63 14 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 347 179 131 169 110 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 346 170 129 218 168 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 446 180 132 147 92 NC_009009:SSA_1725|3end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1710993..1711143_NEGATIVE 409 179 131 149 99 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 407 177 131 83 35 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 388 178 131 151 95 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 374 179 131 134 78 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 365 180 131 145 85 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 354 140 94 140 83 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 349 177 134 51 2 NC_009009:SSA_0420|3end_Hydrolase,_HAD_superfamily,_putative_419632..419782_POSITIVE 341 179 136 49 2 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 340 180 138 36 3 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 332 179 137 52 3 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 329 179 145 138 100 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 325 140 92 132 79 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 325 169 123 60 8 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 325 145 109 130 81 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 322 130 81 99 46 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 322 139 95 91 33 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 322 180 134 127 86 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 320 178 131 136 86 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 319 150 101 89 32 NC_009009:SSA_1711|3end_Endonuclease_III,_putative_1699007..1699157_NEGATIVE