Origin IGS: gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcgctttcgcacttctcaaaactactttgagcagactgctcctgcttagtttattcatgaatttcattgaatataagtctactcaaaaatcctcggctgacccgaggattttttatatttc Mask Tandem Repeat Region ================================================ gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Find is-nt database================================================ Query_seq: SSA_0035:SSA_0036|SSA_0035:SSA_0036:Bifunctional purine biosynthesis protein purH, putative:Secreted protein, possible function in cell-wall metabolism (amidase), putative:-><-:42018..42139 122 gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0035:SSA_0036|SSA_0035:SSA_0036:Bifunctional purine biosynthesis protein purH, putative:Secreted protein, possible function in cell-wall metabolism (amidase), putative:-><-:42018..42139 122 gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0035:SSA_0036|SSA_0035:SSA_0036:Bifunctional purine biosynthesis protein purH, putative:Secreted protein, possible function in cell-wall metabolism (amidase), putative:-><-:42018..42139 122 gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 3 End: 95 .. I Y F I R P D A S S K Q T S K Y E I F N M F L S L L L L R S M ........................... gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac 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================================================ gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0035:SSA_0036|SSA_0035:SSA_0036:Bifunctional purine biosynthesis protein purH, putative:Secreted protein, possible function in cell-wall metabolism (amidase), putative:-><-:42018..42139 122 gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_009009_SSA_0035_SSA_0036|Bifunctional purine biosynthesis protein purH, putative:Secreted protein, possible function in cell-wall metabolism (amidase), putative|POSITIVE:NEGATIVE|[42018,42139]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac gaaatataaaaaatcctcgggtcagccgaggatttttgagtagacttatattcaatgaaattcatgaataaactaagcaggagcagtctgctcaaagtagttttgagaagtgcgaaagcgac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUAUAAAAAAUCCUCGGGUCAGCCGAGGAUUUUUGAGUAGACUUAUAUUCAAUGAAAUUCAUGAAUAAACUAAGCAGGAGCAGUCUGCUCAAAGUAGUUUUGAGAAGUGCGAAAGCGAC (((((...((((((((((((.....))))))))))))((((((((...((((((.((.....))))))))......((....)).))))))))......)))))......(((....))).. (-40.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCGCUUUCGCACUUCUCAAAACUACUUUGAGCAGACUGCUCCUGCUUAGUUUAUUCAUGAAUUUCAUUGAAUAUAAGUCUACUCAAAAAUCCUCGGCUGACCCGAGGAUUUUUUAUAUUUC ...((....))................(((((.(((((((....))......((((((((.....)).))))))..))))).)))))((((((((((.....)))))))))).......... (-29.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 107 77 231 197 NC_009009:SSA_1944|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1936611..1936841_NEGATIVE 287 119 72 66 8 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 273 58 14 138 95 NC_009009:SSA_1321|5end_Ferrochelatase,_putative_1338343..1338573_NEGATIVE 272 116 78 225 172 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 269 115 73 179 137 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 267 119 76 89 35 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 267 114 73 76 35 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 267 120 72 227 185 NC_009009:SSA_2007|5end_Chaperone_protein_dnaK/HSP70,_putative_2009272..2009502_NEGATIVE 265 49 17 184 149 NC_009009:SSA_1214|5end_Conserved_uncharacterized_Lactobacillales_protein_1237482..1237712_POSITIVE 264 116 82 75 30 NC_009009:SSA_1776|5end_Potassium_uptake_protein,_Trk_family,_putative_1762639..1762869_POSITIVE 264 119 72 192 143 NC_009009:SSA_1324|5end_Ceramide_glucosyltransferase,_putative_1341618..1341848_NEGATIVE 262 109 70 77 31 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 261 102 61 214 174 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 260 120 77 46 1 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 257 120 82 119 75 NC_009009:SSA_0786|5end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_768737..768967_POSITIVE 254 116 76 63 17 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 254 104 76 176 150 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 253 113 71 100 60 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 252 115 72 219 177 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 251 59 16 47 2 NC_009009:SSA_1347|5end_PhnA_protein,_putative_1365141..1365371_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 45 14 41 4 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 305 37 9 82 54 NC_009009:SSA_0035|3end_Bifunctional_purine_biosynthesis_protein_purH,_putative_41957..42107_POSITIVE 292 105 66 151 94 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 289 114 71 58 18 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 287 119 72 76 18 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 264 116 82 69 24 NC_009009:SSA_1775|3end_Potassium_uptake_protein,_Trk_family,_putative_1762713..1762863_POSITIVE 262 90 41 80 34 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 262 109 70 90 44 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 260 117 76 67 17 NC_009009:SSA_2330|3end_Acetyltransferase,_putative_2333170..2333320_NEGATIVE 259 119 75 139 96 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 253 120 83 128 74 NC_009009:SSA_2041|3end_Leucine-rich_protein,_putative_2045807..2045957_NEGATIVE 253 113 71 62 22 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 249 92 54 70 35 NC_009009:SSA_1854|3end_Conserved_uncharacterized_protein_1849433..1849583_NEGATIVE 247 117 77 47 11 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 247 120 75 76 34 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 240 99 56 143 100 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 238 47 11 145 101 NC_009009:SSA_1628|3end_MutT/nudix_family_protein,_putative_1630363..1630513_POSITIVE 238 119 73 151 103 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 237 54 17 50 13 NC_009009:SSA_1619|3end_Ribosome_recycling_factor,_putative_1621679..1621829_NEGATIVE 236 119 73 40 1 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE