Origin IGS: acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg .........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 cgaaagtctcccctgctttatatttcttgtcaattttattcatgtattgattgtaacaaaaaagagtcggaaagtctgcttttttctttgcaaacaaaatctaatttttgaatagatctgctatataaatagaaactgttatttgcttcatttttctttgttctaaaaaactatcaatgtccagttctgttcaagattttctacgagcgatagaacaaaaagagctggacagattccaactcttctttgt Mask Tandem Repeat Region ================================================ acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Find is-nt database================================================ Query_seq: SSA_0718:SSA_0720|SSA_0718:SSA_0720:Conserved uncharacterized protein:hypothetical protein:->->:704996..705245 250 acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0718:SSA_0720|SSA_0718:SSA_0720:Conserved uncharacterized protein:hypothetical protein:->->:704996..705245 250 acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0718:SSA_0720|SSA_0718:SSA_0720:Conserved uncharacterized protein:hypothetical protein:->->:704996..705245 250 acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 151 End: 249 ...................................................................................................................................................... M L F A K K K A D F P T L F C Y N Q Y M N K I D K K Y K A G E T F . Protein_Len: 32 Strand: - Start: 143 End: 238 .............................................................................................................................................. F N S K T Q L S F L L S E S E K K N C D I C S Y F Q C S I Y L M ............ Protein_Len: 31 Strand: - Start: 139 End: 231 .......................................................................................................................................... E F I L N Q K C L F F C V K R S K K T V I L V H I F N V L F M ................... Protein_Len: 40 Strand: - Start: 3 End: 122 .. F F L Q F R D L E K Q E I A R L F D Q V S S S M S L K K S C L F I F C I V T E M ................................................................................................................................ acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg 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================================================ acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0718:SSA_0720|SSA_0718:SSA_0720:Conserved uncharacterized protein:hypothetical protein:->->:704996..705245 250 acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: NC_009009_SSA_0718_SSA_0720|Conserved uncharacterized protein:hypothetical protein|POSITIVE:POSITIVE|[704996,705245]|250 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg acaaagaagagttggaatctgtccagctctttttgttctatcgctcgtagaaaatcttgaacagaactggacattgatagttttttagaacaaagaaaaatgaagcaaataacagtttctatttatatagcagatctattcaaaaattagattttgtttgcaaagaaaaaagcagactttccgactcttttttgttacaatcaatacatgaataaaattgacaagaaatataaagcaggggagactttcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAGAAGAGUUGGAAUCUGUCCAGCUCUUUUUGUUCUAUCGCUCGUAGAAAAUCUUGAACAGAACUGGACAUUGAUAGUUUUUUAGAACAAAGAAAAAUGAAGCAAAUAACAGUUUCUAUUUAUAUAGCAGAUCUAUUCAAAAAUUAGAUUUUGUUUGCAAAGAAAAAAGCAGACUUUCCGACUCUUUUUUGUUACAAUCAAUACAUGAAUAAAAUUGACAAGAAAUAUAAAGCAGGGGAGACUUUCG (((((((((((((((((...(((..(((.(((((((((((....(((.((.....)))))..(((((((........))))))).)))))))))))........((((((((......((((....))))..((((((.........)))))))))))))).........))).))).))))))))))))))))).....(((((...........))))).............(.((((....))))). (-57.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAAGUCUCCCCUGCUUUAUAUUUCUUGUCAAUUUUAUUCAUGUAUUGAUUGUAACAAAAAAGAGUCGGAAAGUCUGCUUUUUUCUUUGCAAACAAAAUCUAAUUUUUGAAUAGAUCUGCUAUAUAAAUAGAAACUGUUAUUUGCUUCAUUUUUCUUUGUUCUAAAAAACUAUCAAUGUCCAGUUCUGUUCAAGAUUUUCUACGAGCGAUAGAACAAAAAGAGCUGGACAGAUUCCAACUCUUCUUUGU ..(((((.......))))).........((((((...........))))))....(((((.((((((.((((.((((((((((((((((((....(((((((......((((((((.(((((((....)))).....(((.((((...((........))...)))).)))..........))).)))))))))))))))......)))).)))....))))))).))))...)))).)))))).))))) (-47.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 45 1 189 151 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 321 47 1 222 165 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 313 59 11 225 163 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 312 48 10 60 23 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 297 45 8 116 69 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 294 48 12 121 85 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 293 50 3 164 113 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 288 46 9 137 92 NC_009009:SSA_1212|5end_Ribose-phosphate_pyrophosphokinase_2,_putative_1235401..1235631_POSITIVE 283 32 1 227 195 NC_009009:SSA_1080|5end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1097538..1097768_POSITIVE 281 50 8 42 8 NC_009009:SSA_2208|5end_Preprotein_translocase_secE_component,_putative_2207913..2208143_NEGATIVE 280 50 12 196 164 NC_009009:SSA_1392|5end_hypothetical_protein_1408423..1408653_NEGATIVE 280 49 5 228 171 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 270 57 17 100 57 NC_009009:SSA_1738|5end_Polysaccharide_biosynthesis_protein,_putative_1725503..1725733_NEGATIVE 270 48 2 187 113 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 269 58 11 99 46 NC_009009:SSA_1186|5end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1215219..1215449_NEGATIVE 265 45 1 157 101 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 263 56 12 214 175 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 263 69 24 155 118 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 258 51 11 152 110 NC_009009:SSA_2041|5end_Leucine-rich_protein,_putative_2046682..2046912_NEGATIVE 257 43 2 169 128 NC_009009:SSA_0668|5end_hypothetical_protein_650737..650967_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 45 1 118 80 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 340 45 4 88 44 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 323 37 5 91 61 NC_009009:SSA_1373|3end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1391313..1391463_POSITIVE 312 39 4 51 18 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 312 48 10 48 11 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 309 48 1 108 55 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 297 45 8 103 56 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 294 48 12 120 84 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE 293 50 3 100 49 NC_009009:SSA_0329|3end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_323815..323965_POSITIVE 283 49 1 95 34 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 283 32 1 57 25 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 280 34 5 66 30 NC_009009:SSA_2345|3end_hypothetical_protein_2347502..2347652_POSITIVE 274 50 16 144 105 NC_009009:SSA_0936|3end_FAD_synthase,_putative_946151..946301_POSITIVE 269 58 11 123 70 NC_009009:SSA_1187|3end_Transcriptional_antiterminator,_BglG_family,_putative_1215195..1215345_NEGATIVE 265 45 1 61 5 NC_009009:SSA_1671|3end_hypothetical_protein_1670337..1670487_POSITIVE 265 50 5 89 46 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 263 50 1 107 65 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 258 50 1 119 53 NC_009009:SSA_1616|3end_PhoH-like_protein,_putative_1619356..1619506_NEGATIVE 257 43 2 109 68 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 253 59 12 150 108 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE