Origin IGS: gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga .........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 tcaatattttctaaaatttaaagaaaggaacatgggtgttcgcaactgaacacgggttccaaaaattctgactcaatataaaagaaaggaactgaacccgacctaaattctcggaaaagagagaaatctgtctaggggcatcgctccgtcgcctgatttcctatttttcagtcgaattttacggtcttggtatcttac Mask Tandem Repeat Region ================================================ gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Find is-nt database================================================ Query_seq: SSA_2005:SSA_2006|SSA_2005:SSA_2006:Chaperone protein dnaJ, putative:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:<-<-:2006475..2006672 198 gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2005:SSA_2006|SSA_2005:SSA_2006:Chaperone protein dnaJ, putative:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:<-<-:2006475..2006672 198 gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2005:SSA_2006|SSA_2005:SSA_2006:Chaperone protein dnaJ, putative:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:<-<-:2006475..2006672 198 gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 42 End: 185 ......................................... M R R R S D A P R Q I S L F S E N L G R V Q F L S F I L S Q N F W N P C S V A N T H V P F F K F ............. Protein_Len: 30 Strand: - Start: 3 End: 92 .. L Y W S R L I R S F F L F D P S P A I G R S L N R E K G L M .......................................................................................................... gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga 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================================================ gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2005:SSA_2006|SSA_2005:SSA_2006:Chaperone protein dnaJ, putative:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:<-<-:2006475..2006672 198 gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: NC_009009_SSA_2005_SSA_2006|Chaperone protein dnaJ, putative:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative|NEGATIVE:NEGATIVE|[2006475,2006672]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga gtaagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttcagttgcgaacacccatgttcctttctttaaattttagaaaatattga Inter-species Hit: Count: 1 Min: 3 Max: 152 Len: 150 Subject: smit_SMT_341_SMT_342|ThiJ/PfpI family protein:chaperone protein DnaJ|POSITIVE:POSITIVE|[281742,281939]|198 HSP 1 e-value: 8.0E-49 bit: 194.0 Len: 150 Query Start:3 Query End:152 Subject Strand: NEGATIVE Subject Start: 47 Subject End: 196 ..aagataccaagaccgtaaaattcgactgaaaaataggaaatcaggcgacggagcgatgcccctagacagatttctctcttttccgagaatttaggtcgggttcagttcctttcttttatattgagtcagaatttttggaacccgtgttca.............................................. ..aagataccaagaccgtaaaattcgactgaaaaataggaaatctgacgctggagcgatgctcctaggcagatttatcttttttccgagaatttaggtcgggttcaattcctttcttttatattgagtaataaatttgggaacccgtgttca.............................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUACCAAGACCGUAAAAUUCGACUGAAAAAUAGGAAAUCAGGCGACGGAGCGAUGCCCCUAGACAGAUUUCUCUCUUUUCCGAGAAUUUAGGUCGGGUUCAGUUCCUUUCUUUUAUAUUGAGUCAGAAUUUUUGGAACCCGUGUUCA ..(((((.....(((.(((((((((((.((....((((((.........(((((...((((...(((....(((((........))))).....)))))))...))))))))))).....)).)))).)))))))))).....))))).. (-37.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACACGGGUUCCAAAAAUUCUGACUCAAUAUAAAAGAAAGGAACUGAACCCGACCUAAAUUCUCGGAAAAGAGAGAAAUCUGUCUAGGGGCAUCGCUCCGUCGCCUGAUUUCCUAUUUUUCAGUCGAAUUUUACGGUCUUGGUAUCUU ........((((((.....((((.............)))).))))))..(((.((((.((((((...((((((((.((((((.((...(((((...)))))...))..)))))))).))))))....))))))...))))..)))..... (-37.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1024 90 41 183 134 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 409 50 1 145 93 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 408 116 73 211 166 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 374 116 73 137 91 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 346 59 13 152 106 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 338 79 39 218 172 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 336 86 43 159 100 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 327 90 42 230 182 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 323 119 74 87 30 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 316 87 41 58 7 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 313 70 24 61 4 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 309 88 42 212 144 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 308 85 43 221 178 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 304 88 43 67 24 NC_009009:SSA_0453|5end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_452212..452442_POSITIVE 293 75 36 59 7 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 292 89 41 218 158 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 290 90 42 45 3 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 290 99 51 168 109 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 281 88 45 119 62 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 279 87 43 69 13 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 90 42 108 60 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 316 87 41 65 14 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 313 130 81 99 44 NC_009009:SSA_1521|3end_Phosphoenolpyruvate_carboxylase,_putative_1527837..1527987_NEGATIVE 309 88 42 127 59 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 306 86 41 70 14 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 301 60 22 74 30 NC_009009:SSA_2109|3end_Elongation_factor_G,_putative_2112787..2112937_NEGATIVE 298 109 67 136 99 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 294 116 84 78 46 NC_009009:SSA_0913|3end_Acetyltransferase,_putative_924784..924934_POSITIVE 293 75 36 58 6 NC_009009:SSA_0924|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_934828..934978_POSITIVE 291 87 41 149 101 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 290 90 42 48 6 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 281 99 59 135 100 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 281 88 45 87 30 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 281 88 44 116 54 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 279 87 43 109 53 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 276 79 32 84 33 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 275 87 51 148 100 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 273 100 51 65 20 NC_009009:SSA_0260|3end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_253656..253806_NEGATIVE 271 86 44 121 66 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 270 84 41 109 38 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE