Origin IGS: gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgatcgttgacnnnnnttaattaattaannnnnaaaatctctagtcaagcgctttatttttttgtataatagaagtagcaaagtatagataagaagagaaaagc Mask Tandem Repeat Region ================================================ gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Find is-nt database================================================ Query_seq: SMT_984:SMT_985|SMT_984:SMT_985:transcriptional regulator Spx:guanylate kinase:<-->:930989..931093 105 gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_984:SMT_985|SMT_984:SMT_985:transcriptional regulator Spx:guanylate kinase:<-->:930989..931093 105 gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_984:SMT_985|SMT_984:SMT_985:transcriptional regulator Spx:guanylate kinase:<-->:930989..931093 105 gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Predict ORF larger than 30AA ================================================ gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag 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: 35 End: 64 ..................................CTAGTCAAGCGCTTTATTTTTTTGTATAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_984:SMT_985|SMT_984:SMT_985:transcriptional regulator Spx:guanylate kinase:<-->:930989..931093 105 gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: smit_SMT_984_SMT_985|transcriptional regulator Spx:guanylate kinase|NEGATIVE:POSITIVE|[930989,931093]|105 HSP 1 e-value: 7.0E-23 bit: 107.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 gcttttctcttcttatctatactttgctacttctattatacnnnnnnntaaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag gcttttctcttcttatctatactttgctacttctattatacaaaaaaataaagcgcttgactagagattttnnnnnttaattaattaannnnngtcaacgatcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUUCUCUUCUUAUCUAUACUUUGCUACUUCUAUUAUACAAAAAAAUAAAGCGCUUGACUAGAGAUUUUNNNNNUUAAUUAAUUAANNNNNGUCAACGAUCAG .....(((((..(((......(((((......................)))))....)))..)))))...................................... ( -4.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAUCGUUGACNNNNNUUAAUUAAUUAANNNNNAAAAUCUCUAGUCAAGCGCUUUAUUUUUUUGUAUAAUAGAAGUAGCAAAGUAUAGAUAAGAAGAGAAAAGC ......................................(((((.(((.(..(((((...(((((((...)))))))....))))).).)))....)))))..... ( -8.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 747 70 21 161 112 smit:SMT_984|5end_transcriptional_regulator_Spx_930898..931128_NEGATIVE 259 58 22 163 130 smit:SMT_1305|5end_glycerol_kinase_1268217..1268447_POSITIVE 222 41 2 130 92 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 208 34 2 133 104 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 203 70 23 158 112 smit:SMT_875|5end_nitroreductase_family_protein_823384..823614_NEGATIVE 202 35 1 67 37 smit:SMT_1818|5end_tryptophan_synthase,_alpha_subunit_1792190..1792420_POSITIVE 202 68 23 159 109 smit:SMT_311|5end_3-oxoacyl-_252123..252353_POSITIVE 201 42 1 132 81 smit:SMT_1693|5end_dimethyladenosine_transferase_1675800..1676030_POSITIVE 200 62 23 120 91 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 194 32 2 121 82 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 192 42 4 130 94 smit:SMT_1387|5end_hypothetical_protein_1364663..1364893_POSITIVE 191 28 1 63 37 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 191 35 3 166 139 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 185 70 21 130 84 smit:SMT_1283|5end_K02240_competence_protein_ComFA_1245667..1245897_POSITIVE 185 30 1 112 81 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 184 54 13 117 72 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 184 54 13 117 72 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 182 34 1 136 96 smit:SMT_2029|5end_acetyltransferase,_GNAT_family_1943749..1943979_POSITIVE 182 34 1 136 96 smit:SMT_1755|5end_acetyltransferase,_GNAT_family_1733042..1733272_POSITIVE 182 40 1 129 92 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 67 23 60 17 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 208 34 2 151 122 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 203 42 10 125 88 smit:SMT_1506|3end_Cl-channel,_voltage-gated_family_protein_1488916..1489066_NEGATIVE 202 35 1 131 101 smit:SMT_1753|3end_tryptophan_synthase_beta_chain_1731652..1731802_POSITIVE 202 68 23 137 87 smit:SMT_310|3end_3-oxoacyl-_252181..252331_POSITIVE 201 42 1 67 16 smit:SMT_1692|3end_hypothetical_protein_1675815..1675965_POSITIVE 200 62 23 127 98 smit:SMT_167|3end_acetyltransferase,_GNAT_family_113757..113907_POSITIVE 196 59 15 53 7 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 194 32 2 119 80 smit:SMT_109|3end_beta-galactosidase_57523..57673_POSITIVE 188 68 48 66 47 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 185 32 1 62 34 smit:SMT_1069|3end_acetyl_xylan_esterase,_putative_1009595..1009745_POSITIVE 182 40 1 40 3 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 180 33 9 119 95 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 179 27 1 77 52 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 175 58 11 84 29 smit:SMT_494|3end_K04767_acetoin_utilization_protein_AcuB_428891..429041_POSITIVE 172 27 7 42 17 smit:SMT_1118|3end_hypothetical_protein_1054779..1054929_NEGATIVE 172 55 17 70 40 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 172 55 17 70 40 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 172 55 17 70 40 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 172 55 17 70 40 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE