Origin IGS: ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctaggtcgctagactgatttttagcactcttgtaaaaagagtgctaattttttgagtttttgtcttgactttggagtagaagagtgtataatagaatcatgagttagcactcgaggtgattgagtgctaatcgacagcagaatcttgaatggaggtgatgcc Mask Tandem Repeat Region ================================================ ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Find is-nt database================================================ Query_seq: SSA_2009:SSA_2010|SSA_2009:SSA_2010:Heat shock transcription repressor HrcA, putative:ABC-type multidrug transport system, permease component, putative:<-<-:2011223..2011385 163 ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2009:SSA_2010|SSA_2009:SSA_2010:Heat shock transcription repressor HrcA, putative:ABC-type multidrug transport system, permease component, putative:<-<-:2011223..2011385 163 ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2009:SSA_2010|SSA_2009:SSA_2010:Heat shock transcription repressor HrcA, putative:ABC-type multidrug transport system, permease component, putative:<-<-:2011223..2011385 163 ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 20 End: 139 ................... M L L S I S T Q S P R V L T H D S I I H S S T P K S R Q K L K K L A L F L Q E C ........................ ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga 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================================================ ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2009:SSA_2010|SSA_2009:SSA_2010:Heat shock transcription repressor HrcA, putative:ABC-type multidrug transport system, permease component, putative:<-<-:2011223..2011385 163 ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_2009_SSA_2010|Heat shock transcription repressor HrcA, putative:ABC-type multidrug transport system, permease component, putative|NEGATIVE:NEGATIVE|[2011223,2011385]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga ggcatcacctccattcaagattctgctgtcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga Inter-species Hit: Count: 1 Min: 29 Max: 163 Len: 135 Subject: smit_SMT_337_SMT_338|hypothetical protein:heat-inducible transcription repressor HrcA|POSITIVE:POSITIVE|[276258,276964]|707 HSP 1 e-value: 5.0E-28 bit: 125.0 Len: 135 Query Start:29 Query End:163 Subject Strand: NEGATIVE Subject Start: 551 Subject End: 685 ............................tcgattagcactcaatcacctcgagtgctaactcatgattctattatacactcttctactccaaagtcaagacaaaaactcaaaaaattagcactctttttacaagagtgctaaaaatcagtctagcgacctaga ............................tcgattagcactcgatacactcaagtgctaacttatgattctattatacacccttaaaagagaatgtcaagacaaaaactcaaaaaattagcactcttttgccaagagtgctaaaaatcagtctaaagacctaga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAUUAGCACUCAAUCACCUCGAGUGCUAACUCAUGAUUCUAUUAUACACUCUUCUACUCCAAAGUCAAGACAAAAACUCAAAAAAUUAGCACUCUUUUUACAAGAGUGCUAAAAAUCAGUCUAGCGACCUAGA ..(((((((((((.........))))))))).)).(((((...........((((..(((....))).))))...............(((((((((((.....))))))))))).))))).(((((....))))) (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGGUCGCUAGACUGAUUUUUAGCACUCUUGUAAAAAGAGUGCUAAUUUUUUGAGUUUUUGUCUUGACUUUGGAGUAGAAGAGUGUAUAAUAGAAUCAUGAGUUAGCACUCGAGGUGAUUGAGUGCUAAUCGA (((((((((..((((.((((((((((((((((.....)))))))))))......)))))...)))))))).)))))........................(((.(((((((((((.....)))))))))))))). (-42.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 871 50 1 169 120 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 312 58 12 106 54 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 272 43 3 204 168 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 256 63 22 163 120 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 247 33 5 145 116 NC_009009:SSA_0225|5end_10_kDa_chaperonin_218642..218872_POSITIVE 246 29 1 81 52 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 246 58 16 147 96 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 239 60 11 75 23 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 238 29 2 35 15 NC_009009:SSA_1819|5end_Valyl-tRNA_synthetase,_putative_1808867..1809097_NEGATIVE 236 70 22 122 53 NC_009009:SSA_1321|5end_Ferrochelatase,_putative_1338343..1338573_NEGATIVE 236 68 23 224 163 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 226 46 3 93 34 NC_009009:SSA_2240|5end_Holliday_junction_resolvase,_putative_2237677..2237907_NEGATIVE 226 95 53 198 156 NC_009009:SSA_0644|5end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630170..630400_POSITIVE 226 37 1 178 142 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 225 48 1 67 5 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 222 127 83 124 80 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 221 100 51 203 160 NC_009009:SSA_1817|5end_Conserved_uncharacterized_protein_1805595..1805825_NEGATIVE 220 130 87 160 124 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 220 72 39 150 111 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 215 130 90 64 32 NC_009009:SSA_0610|5end_LemA-like_protein,_putative_598968..599198_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 58 12 93 41 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 272 78 40 62 15 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 246 29 1 84 55 NC_009009:SSA_2276|3end_hypothetical_protein_2275587..2275737_NEGATIVE 246 58 16 101 50 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 238 29 2 33 13 NC_009009:SSA_1820|3end_hypothetical_protein_1808869..1809019_NEGATIVE 238 75 32 134 76 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 226 46 3 93 34 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 224 124 81 78 24 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 221 100 51 143 100 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 220 130 87 126 90 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 214 60 11 149 106 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 209 72 42 116 85 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 207 58 12 104 67 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 206 64 21 103 64 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 206 53 13 59 22 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 203 129 90 127 81 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 203 129 94 129 85 NC_009009:SSA_1386|3end_NADPH-dependent_FMN_reductase,_putative_1403428..1403578_POSITIVE 202 33 8 68 43 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 202 45 1 119 78 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 201 49 2 79 37 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE