Origin IGS: agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcattttgactcctcttttatttctatcatctcgtctaggtcttgtactctgcctgtcagaacaccaatttatcctcttgcgtccatttattcgaaaccgcttattgagtctcaaatcatacctcggtaagagttttaaggagcaagaattgtcgtcaaaaaaggtggaattttctactttaagagtataccacaattcttaaaaaattctataaatttaaccaaaaacttttttgttaaatttattcagtccagtcttacaacatagctctaaaaagtcattgcctaatgctgtccagcact Mask Tandem Repeat Region ================================================ agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Find is-nt database================================================ Query_seq: SSA_0168:SSA_0169|SSA_0168:SSA_0169:hypothetical protein:hypothetical protein:->->:167578..167880 303 agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0168:SSA_0169|SSA_0168:SSA_0169:hypothetical protein:hypothetical protein:->->:167578..167880 303 agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0168:SSA_0169|SSA_0168:SSA_0169:hypothetical protein:hypothetical protein:->->:167578..167880 303 agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 108 End: 302 ........................................................................................................... M W Y T L K V E N S T F F D D N S C S L K L L P R Y D L R L N K R F R I N G R K R I N W C S D R Q S T R P R R D D R N K . Protein_Len: 36 Strand: - Start: 177 End: 284 ................................................................................................................................................................................ R P I I Q S E I L P K S Y I S A L P Y I P T R V P L T C S R S S I I S M ................... Protein_Len: 60 Strand: - Start: 104 End: 301 ....................................................................................................... L T S F E V K K S S L E Q E K F S K G L Y S K L S L L R N R I F P R L L I F Q H E S L C L V L G L R S S L F L L P T L M .. Protein_Len: 39 Strand: - Start: 39 End: 155 ...................................... T T L S S Q I F K V F F N K T L N I S N K L F Q P I S K F Y F I G G K K V V M .................................................................................................................................................... agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga 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================================================ agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -9.5 Tail_Score: -3.0792 Start: 59 End: 91 Full_Region: tcttaaaaaattcta taaatttaaccaaaa act tttttgttaaattta ttcagtccagtctta ..........................................................taaatttaaccaaaaacttttttgttaaattta.................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0168:SSA_0169|SSA_0168:SSA_0169:hypothetical protein:hypothetical protein:->->:167578..167880 303 agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: NC_009009_SSA_0168_SSA_0169|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[167578,167880]|303 HSP 1 e-value: 1.0E-171 bit: 601.0 Len: 303 Query Start:1 Query End:303 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga agtgctggacagcattaggcaatgactttttagagctatgttgtaagactggactgaataaatttaacaaaaaagtttttggttaaatttatagaattttttaagaattgtggtatactcttaaagtagaaaattccaccttttttgacgacaattcttgctccttaaaactcttaccgaggtatgatttgagactcaataagcggtttcgaataaatggacgcaagaggataaattggtgttctgacaggcagagtacaagacctagacgagatgatagaaataaaagaggagtcaaaatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGCUGGACAGCAUUAGGCAAUGACUUUUUAGAGCUAUGUUGUAAGACUGGACUGAAUAAAUUUAACAAAAAAGUUUUUGGUUAAAUUUAUAGAAUUUUUUAAGAAUUGUGGUAUACUCUUAAAGUAGAAAAUUCCACCUUUUUUGACGACAAUUCUUGCUCCUUAAAACUCUUACCGAGGUAUGAUUUGAGACUCAAUAAGCGGUUUCGAAUAAAUGGACGCAAGAGGAUAAAUUGGUGUUCUGACAGGCAGAGUACAAGACCUAGACGAGAUGAUAGAAAUAAAAGAGGAGUCAAAAUGA ((((((....))))))......(((((((((.......((((((((((..((.....(((((((((((((((....)))).))))))))))).((((((((((......(.(.....).)......))))))))))..))..)))).)))))).((((((((((......(((.....))).....((((((((((........))))))))))....))).))))))).........((((((((.....)))))))).............................)))))))))...... (-67.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUUUGACUCCUCUUUUAUUUCUAUCAUCUCGUCUAGGUCUUGUACUCUGCCUGUCAGAACACCAAUUUAUCCUCUUGCGUCCAUUUAUUCGAAACCGCUUAUUGAGUCUCAAAUCAUACCUCGGUAAGAGUUUUAAGGAGCAAGAAUUGUCGUCAAAAAAGGUGGAAUUUUCUACUUUAAGAGUAUACCACAAUUCUUAAAAAAUUCUAUAAAUUUAACCAAAAACUUUUUUGUUAAAUUUAUUCAGUCCAGUCUUACAACAUAGCUCUAAAAAGUCAUUGCCUAAUGCUGUCCAGCACU ......(((((....(((((...((((......(.((.((.((((((((((....((.((((((((.........((((((.(((....((((...((((.....(((........))).....))))..)))).....))))))))).(((....)))....)))).....))))))....)))))))).....................(((((((((((.((((....)))))))))))))))..)).)))).).......))))...))))))))))........((((....)))).. (-55.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 214 172 199 152 NC_009009:SSA_1214|5end_Conserved_uncharacterized_Lactobacillales_protein_1237482..1237712_POSITIVE 310 240 192 212 159 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 302 254 211 225 171 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 296 286 242 189 151 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 291 250 203 210 150 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 289 197 152 192 146 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 288 56 11 206 160 NC_009009:SSA_1865|5end_Thioredoxin_reductase,_putative_1861892..1862122_NEGATIVE 287 280 238 48 13 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 278 42 1 81 42 NC_009009:SSA_1038|5end_Lipoprotein,_putative_1052579..1052809_POSITIVE 275 49 1 166 100 NC_009009:SSA_1199|5end_Phosphinothricin_acetyltransferase,_putative_1223958..1224188_NEGATIVE 274 245 203 84 42 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 269 279 235 74 20 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 266 45 2 55 2 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 266 274 235 63 8 NC_009009:SSA_0260|5end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_254585..254815_NEGATIVE 262 182 150 120 87 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 261 279 236 231 185 NC_009009:SSA_2152|5end_ABC-type_transporter_(uncharacterized),_ATPase_component,_putative_2153801..2154031_NEGATIVE 260 250 201 178 118 NC_009009:SSA_2303|5end_hypothetical_protein_2305177..2305407_NEGATIVE 259 247 202 226 171 NC_009009:SSA_1631|5end_Sortase-like_protein,_putative_1632538..1632768_NEGATIVE 258 266 228 168 126 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 256 44 4 96 45 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 56 11 140 94 NC_009009:SSA_1866|3end_hypothetical_protein_1861958..1862108_NEGATIVE 279 280 244 36 1 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE 276 46 7 96 60 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 269 279 235 74 20 NC_009009:SSA_1516|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522129..1522279_NEGATIVE 267 49 1 74 26 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 266 45 2 65 12 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 265 229 181 74 20 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 265 38 4 146 108 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 262 182 150 148 115 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 260 274 237 62 11 NC_009009:SSA_1984|3end_Cell_surface_SD_repeat_antigen_precursor,_putative_1976048..1976198_NEGATIVE 260 270 225 143 96 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 254 265 223 55 4 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 249 263 224 151 106 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 249 283 242 56 1 NC_009009:SSA_0261|3end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_254605..254755_NEGATIVE 248 42 4 150 98 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 247 269 223 67 30 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 247 264 223 81 36 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 245 167 133 143 104 NC_009009:SSA_0155|3end_hypothetical_protein_151406..151556_POSITIVE 242 245 202 82 46 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 241 269 221 65 16 NC_009009:SSA_1107|3end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1133784..1133934_POSITIVE