Origin IGS: gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttaatcctttctttgggttcggttggtcttttcttcaagtgttctaagtagaagtcaagctcgtttaaattttgaagtgtcaaaaccaaaaaagcaaaattgcgagaatcttgc Mask Tandem Repeat Region ================================================ gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Find is-nt database================================================ Query_seq: SSA_1214:SSA_1215|SSA_1214:SSA_1215:Conserved uncharacterized Lactobacillales protein:hypothetical protein:->->:1237970..1238085 116 gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1214:SSA_1215|SSA_1214:SSA_1215:Conserved uncharacterized Lactobacillales protein:hypothetical protein:->->:1237970..1238085 116 gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1214:SSA_1215|SSA_1214:SSA_1215:Conserved uncharacterized Lactobacillales protein:hypothetical protein:->->:1237970..1238085 116 gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 26 End: 115 ......................... M V L T L Q N L N E L D F Y L E H L K K R P T E P K E R I N . Protein_Len: 30 Strand: - Start: 3 End: 92 .. L N E C N Q K K P K S V E F N L R A Q S R S L V S S S F V M ........................ gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca 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================================================ gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1214:SSA_1215|SSA_1214:SSA_1215:Conserved uncharacterized Lactobacillales protein:hypothetical protein:->->:1237970..1238085 116 gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_009009_SSA_1214_SSA_1215|Conserved uncharacterized Lactobacillales protein:hypothetical protein|POSITIVE:POSITIVE|[1237970,1238085]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca gcaagattctcgcaattttgcttttttggttttgacacttcaaaatttaaacgagcttgacttctacttagaacacttgaagaaaagaccaaccgaacccaaagaaaggattaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAGAUUCUCGCAAUUUUGCUUUUUUGGUUUUGACACUUCAAAAUUUAAACGAGCUUGACUUCUACUUAGAACACUUGAAGAAAAGACCAACCGAACCCAAAGAAAGGAUUAACA ((((((((.....))))))))....((((((((....((((((...((((......)))).((((....))))...))))))..))))))))......((.......))....... (-18.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUAAUCCUUUCUUUGGGUUCGGUUGGUCUUUUCUUCAAGUGUUCUAAGUAGAAGUCAAGCUCGUUUAAAUUUUGAAGUGUCAAAACCAAAAAAGCAAAAUUGCGAGAAUCUUGC .........(((((...((..((.((((........)))).))..))....))))).(((((((((...(((((((...((.......))......))))))))))))...)))). (-17.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 96 52 173 133 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 279 99 54 147 93 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 240 36 3 85 54 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 235 44 1 48 14 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 230 94 53 158 120 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 228 56 11 57 17 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 226 95 55 179 130 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 226 100 56 224 169 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 225 60 12 50 7 NC_009009:SSA_1641|5end_MutT/nudix_family_protein,_putative_1643094..1643324_NEGATIVE 223 36 1 178 145 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 223 71 33 51 6 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 219 95 53 164 122 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 218 83 46 228 194 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 217 110 63 51 3 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 216 95 54 61 14 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 216 100 55 212 157 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 215 85 55 143 114 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 215 68 25 202 156 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 214 60 16 154 107 NC_009009:SSA_0926|5end_Histone_acetyltransferase_HPA2,_putative_935465..935695_POSITIVE 213 98 54 57 8 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 99 54 147 93 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 240 36 3 39 8 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 234 99 53 66 19 NC_009009:SSA_1326|3end_Peptidase_T,_putative_1343735..1343885_POSITIVE 230 94 53 143 105 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 227 95 52 37 4 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 223 71 33 79 34 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 215 85 55 109 80 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 214 60 16 103 56 NC_009009:SSA_0925|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_935494..935644_POSITIVE 213 98 54 64 15 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 202 35 1 151 116 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 192 60 11 125 63 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 191 110 81 36 7 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 190 45 1 69 28 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 189 59 12 118 81 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 189 46 8 122 90 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 189 70 21 150 105 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 188 78 31 79 25 NC_009009:SSA_2365|3end_Cobalt_transport_protein_cbiQ,_putative_2367243..2367393_NEGATIVE 187 46 2 73 24 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 186 91 69 44 21 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 185 107 66 61 15 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE