Origin IGS: gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactcattagaaaacaataaaacccgagcaattagctcgggttttattgttttctacctacagatagaaacttctttaactaattatgttagcaagttcaatc Mask Tandem Repeat Region ================================================ gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Find is-nt database================================================ Query_seq: SSA_1570:SSA_1571|SSA_1570:SSA_1571:hypothetical protein:Threonyl-tRNA synthetase, putative:-><-:1573198..1573300 103 gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1570:SSA_1571|SSA_1570:SSA_1571:hypothetical protein:Threonyl-tRNA synthetase, putative:-><-:1573198..1573300 103 gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1570:SSA_1571|SSA_1570:SSA_1571:hypothetical protein:Threonyl-tRNA synthetase, putative:-><-:1573198..1573300 103 gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Predict ORF larger than 30AA ================================================ gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt 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================================================ gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.2 Tail_Score: -4.35042 Start: 58 End: 86 Full_Region: GTAGGTAGAAAACAA TAAAACCCGAGC TAATT GCTCGGGTTTTA TTGTTTTCTAATGAG .........................................................TAAAACCCGAGCTAATTGCTCGGGTTTTA................. TransTerm Strand: + Conf: 100 HP_score: -11.7 Tail_Score: -5.12916 Start: 63 End: 81 Full_Region: TAGAAAACAATAAAA CCCGAGC TAATT GCTCGGG TTTTATTGTTTTCTA ..............................................................CCCGAGCTAATTGCTCGGG...................... Find igs database================================================ Query_seq: SSA_1570:SSA_1571|SSA_1570:SSA_1571:hypothetical protein:Threonyl-tRNA synthetase, putative:-><-:1573198..1573300 103 gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_009009_SSA_1570_SSA_1571|hypothetical protein:Threonyl-tRNA synthetase, putative|POSITIVE:NEGATIVE|[1573198,1573300]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt gattgaacttgctaacataattagttaaagaagtttctatctgtaggtagaaaacaataaaacccgagctaattgctcgggttttattgttttctaatgagtt HSP 2 e-value: 9.0E-13 bit: 73.8 Len: 49 Query Start:48 Query End:96 Subject Strand: NEGATIVE Subject Start: 48 Subject End: 96 ...............................................tagaaaacaataaaacccgagctaattgctcgggttttattgttttcta....... ...............................................tagaaaacaataaaacccgagcaattagctcgggttttattgttttcta....... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGAACUUGCUAACAUAAUUAGUUAAAGAAGUUUCUAUCUGUAGGUAGAAAACAAUAAAACCCGAGCUAAUUGCUCGGGUUUUAUUGUUUUCUAAUGAGUU (((.(((((((((((.....))))).....))))))..)))......((((((((((((((((((((((.....))))))))))))))))))))))....... (-40.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCAUUAGAAAACAAUAAAACCCGAGCAAUUAGCUCGGGUUUUAUUGUUUUCUACCUACAGAUAGAAACUUCUUUAACUAAUUAUGUUAGCAAGUUCAAUC .......((((((((((((((((((((((.....))))))))))))))))))))))......(((.(((.(((..(((((.......))))).)))))).))) (-38.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 87 41 223 182 NC_009009:SSA_2328|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2331483..2331713_POSITIVE 272 90 64 195 156 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 252 96 63 194 150 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 244 50 5 169 129 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 242 57 11 82 42 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 242 80 33 70 21 NC_009009:SSA_0815|5end_hypothetical_protein_796975..797205_POSITIVE 234 85 42 50 5 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 227 95 64 224 182 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 217 98 59 199 146 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 217 78 31 180 129 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 217 76 42 229 197 NC_009009:SSA_0333|5end_Mevalonate_kinase,_putative_326995..327225_POSITIVE 217 77 43 221 195 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 215 90 41 182 120 NC_009009:SSA_1647|5end_hypothetical_protein_1647169..1647399_NEGATIVE 210 80 41 53 15 NC_009009:SSA_0004|5end_Lipoprotein,_putative_3704..3934_NEGATIVE 207 90 41 166 117 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 206 98 75 162 142 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 205 83 42 228 197 NC_009009:SSA_2313|5end_hypothetical_protein_2315848..2316078_NEGATIVE 204 80 37 40 1 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 203 100 63 56 16 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 203 82 64 230 213 NC_009009:SSA_0725|5end_hypothetical_protein_710247..710477_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 586 96 54 43 1 NC_009009:SSA_1570|3end_hypothetical_protein_1573137..1573287_POSITIVE 286 87 41 60 19 NC_009009:SSA_2327|3end_hypothetical_protein_2331400..2331550_POSITIVE 283 85 42 90 46 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 252 96 63 100 56 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 243 84 41 75 14 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 242 57 11 89 49 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 242 79 35 127 89 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 240 85 41 91 44 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 239 84 42 109 60 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 234 85 42 148 103 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 229 70 32 69 34 NC_009009:SSA_1890|3end_Acetyltransferase,_putative_1887693..1887843_NEGATIVE 220 86 49 64 16 NC_009009:SSA_1387|3end_hypothetical_protein_1403497..1403647_NEGATIVE 217 98 59 103 50 NC_009009:SSA_1671|3end_hypothetical_protein_1670337..1670487_POSITIVE 215 90 45 80 35 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE 210 96 57 93 40 NC_009009:SSA_1702|3end_hypothetical_protein_1692197..1692347_NEGATIVE 210 93 64 87 56 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 207 93 55 78 37 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 206 100 65 119 67 NC_009009:SSA_2109|3end_Elongation_factor_G,_putative_2112787..2112937_NEGATIVE 205 100 64 97 49 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 203 89 51 103 60 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE