Origin IGS: tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaagagtctttgaggaaatactccttgaagactttattattaggaaagaattctacttaaaataagagcgttttaagtggaattccgtcttaacaagcttgcatggcacatttcccttgcattctgggacttgtcgtgctataatactagta Mask Tandem Repeat Region ================================================ tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Find is-nt database================================================ Query_seq: SSA_1901:SSA_1902|SSA_1901:SSA_1902:Conserved uncharacterized protein:tRNA (guanine-N(7)-)-methyltransferase, putative:<-<-:1896690..1896842 153 tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1901:SSA_1902|SSA_1901:SSA_1902:Conserved uncharacterized protein:tRNA (guanine-N(7)-)-methyltransferase, putative:<-<-:1896690..1896842 153 tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1901:SSA_1902|SSA_1901:SSA_1902:Conserved uncharacterized protein:tRNA (guanine-N(7)-)-methyltransferase, putative:<-<-:1896690..1896842 153 tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M I A R Q V P E C K G N V P C K L V K T E F H L K R S Y F K ........................................................ tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc 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: 8 End: 37 .......CTTGCATTCTGGGACTTGTCGTGCTATAAT.................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 69 HP_score: -7.3 Tail_Score: -3.80573 Start: 68 End: 105 Full_Region: AAGCTTGTTAAGACG GAATTCCACTTAAAA CGCTCTTA TTTTAAGTAGAATTC TTTCCTAATAATAAA ...................................................................GAATTCCACTTAAAACGCTCTTATTTTAAGTAGAATTC................................................ TransTerm Strand: + Conf: 57 HP_score: -3.2 Tail_Score: -4.03141 Start: 71 End: 102 Full_Region: CTTGTTAAGACGGAA TTCCACTTAAAA CGCTCTTA TTTTAAGTAGAA TTCTTTCCTAATAAT ......................................................................TTCCACTTAAAACGCTCTTATTTTAAGTAGAA................................................... TransTerm Strand: - Conf: 58 HP_score: -6.1 Tail_Score: -3.1855 Start: 71 End: 102 Full_Region: attattaggaaagaa ttctacttaaaat aagagc gttttaagtggaa ttccgtcttaacaag ......................................................................ttctacttaaaataagagcgttttaagtggaa................................................... Find igs database================================================ Query_seq: SSA_1901:SSA_1902|SSA_1901:SSA_1902:Conserved uncharacterized protein:tRNA (guanine-N(7)-)-methyltransferase, putative:<-<-:1896690..1896842 153 tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_009009_SSA_1901_SSA_1902|Conserved uncharacterized protein:tRNA (guanine-N(7)-)-methyltransferase, putative|NEGATIVE:NEGATIVE|[1896690,1896842]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc tactagtattatagcacgacaagtcccagaatgcaagggaaatgtgccatgcaagcttgttaagacggaattccacttaaaacgctcttattttaagtagaattctttcctaataataaagtcttcaaggagtatttcctcaaagactctttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUAGUAUUAUAGCACGACAAGUCCCAGAAUGCAAGGGAAAUGUGCCAUGCAAGCUUGUUAAGACGGAAUUCCACUUAAAACGCUCUUAUUUUAAGUAGAAUUCUUUCCUAAUAAUAAAGUCUUCAAGGAGUAUUUCCUCAAAGACUCUUUC .....((((....(((((.....((((.........))))..))))).))))....((((((.((.(((((((.((((((((........)))))))).))))))).)).))))))...((((((..(((((...)))))..))))))..... (-39.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAGAGUCUUUGAGGAAAUACUCCUUGAAGACUUUAUUAUUAGGAAAGAAUUCUACUUAAAAUAAGAGCGUUUUAAGUGGAAUUCCGUCUUAACAAGCUUGCAUGGCACAUUUCCCUUGCAUUCUGGGACUUGUCGUGCUAUAAUACUAGUA ...((((((((..((((.....))))..))))))))....((((((..((((((((((((((((......))))))))))))))))..)))))).......((((((((....((((.........))))..))))))))............. (-56.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 978 60 11 151 102 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 334 42 7 199 164 NC_009009:SSA_0437|5end_30S_ribosomal_protein_S6,_putative_440313..440543_POSITIVE 321 66 28 224 177 NC_009009:SSA_1214|5end_Conserved_uncharacterized_Lactobacillales_protein_1237482..1237712_POSITIVE 309 64 24 74 31 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 309 49 13 44 3 NC_009009:SSA_0684|5end_Fibril-like_structure_subunit_FibA,_putative_664992..665222_POSITIVE 306 58 14 223 150 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 306 49 2 60 21 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 300 77 32 205 164 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 281 68 21 205 147 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 277 60 13 74 11 NC_009009:SSA_1499|5end_50S_ribosomal_protein_L35,_putative_1504357..1504587_NEGATIVE 275 56 14 71 30 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 273 90 46 47 1 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 269 58 18 76 26 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 268 146 107 106 64 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 265 88 49 149 109 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 265 59 11 210 166 NC_009009:SSA_1850|5end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1846024..1846254_NEGATIVE 265 67 24 58 2 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 265 57 13 58 17 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 263 98 62 85 44 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 263 98 62 220 179 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 109 62 151 99 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 275 59 13 47 3 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 266 60 12 150 108 NC_009009:SSA_1135|3end_Na+-driven_multidrug_efflux_pump,_putative_1161775..1161925_POSITIVE 265 88 49 133 93 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 263 98 62 85 44 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 260 88 43 134 78 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 258 60 12 150 96 NC_009009:SSA_1631|3end_Sortase-like_protein,_putative_1631651..1631801_NEGATIVE 258 68 23 62 13 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 258 58 11 51 10 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 254 57 11 107 52 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 253 111 71 44 5 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 250 59 18 71 29 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 250 68 23 61 13 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 249 50 5 101 57 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 248 60 12 79 13 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 244 59 14 43 13 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 242 60 13 60 13 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 242 56 14 73 31 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 241 74 32 54 14 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 240 75 32 68 27 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE