Origin IGS: gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat .........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 attgctctccttttttccattgtccccttatcttagcacaaaagttcactcaaccacaagtagttagaaggtttacgtctttttaccccagcaagctcctttcgtttaggaacctagcgctcacgtcactccgctcctcagcatcaatgtctctaagctcggcttcgaccagaggtcttgcctcgctaagatacatagaaaaatcccccaccaaagggcaggggatgaccgacaaactgtcttatttttaattgaggaagctattccc Mask Tandem Repeat Region ================================================ gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Find is-nt database================================================ Query_seq: SSA_0068:SSA_0069|SSA_0068:SSA_0069:Alcohol-acetaldehyde dehydrogenase, putative:Hypothetical protein, possibly membrane-associated:->->:72909..73176 268 gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0068:SSA_0069|SSA_0068:SSA_0069:Alcohol-acetaldehyde dehydrogenase, putative:Hypothetical protein, possibly membrane-associated:->->:72909..73176 268 gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0068:SSA_0069|SSA_0068:SSA_0069:Alcohol-acetaldehyde dehydrogenase, putative:Hypothetical protein, possibly membrane-associated:->->:72909..73176 268 gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 5 End: 145 .... M A S S I K N K T V C R S S P A L W W G I F L C I L A R Q D L W S K P S L E T L M L R S G V T ........................................................................................................................... Protein_Len: 50 Strand: + Start: 34 End: 183 ................................. M S V I P C P L V G D F S M Y L S E A R P L V E A E L R D I D A E E R S D V S A R F L N E R S L L G ..................................................................................... Protein_Len: 60 Strand: - Start: 21 End: 239 .................... P S K E I Y R L S A L G R T S A S S L S M S A S S R L S T L A L N R F S L L K S P Y F S T F R R V V Q P Q T F K Q A L M ............................. Protein_Len: 42 Strand: - Start: 1 End: 126 P I A E E I L F L V T Q R D D G A R Q H P I K R H I K A L C S R Q D F G L K S V N M .............................................................................................................................................. gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat 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================================================ gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -5.4 Tail_Score: -4.53777 Start: 28 End: 38 Full_Region: gggcaggggatgacc gaca aac tgtc ttatttttaattgag ...........................gacaaactgtc...................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -10.1 Tail_Score: -5.08178 Start: 44 End: 65 Full_Region: ACAGTTTGTCGGTCA TCCCCTGCC CTTT GGTGGGGGA TTTTTCTATGTATCT ...........................................TCCCCTGCCCTTTGGTGGGGGA........................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0068:SSA_0069|SSA_0068:SSA_0069:Alcohol-acetaldehyde dehydrogenase, putative:Hypothetical protein, possibly membrane-associated:->->:72909..73176 268 gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Intra-Species Hit: Count: 1 Min: 1 Max: 268 Len: 268 Subject: NC_009009_SSA_0068_SSA_0069|Alcohol-acetaldehyde dehydrogenase, putative:Hypothetical protein, possibly membrane-associated|POSITIVE:POSITIVE|[72909,73176]|268 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat gggaatagcttcctcaattaaaaataagacagtttgtcggtcatcccctgccctttggtgggggatttttctatgtatcttagcgaggcaagacctctggtcgaagccgagcttagagacattgatgctgaggagcggagtgacgtgagcgctaggttcctaaacgaaaggagcttgctggggtaaaaagacgtaaaccttctaactacttgtggttgagtgaacttttgtgctaagataaggggacaatggaaaaaaggagagcaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAUAGCUUCCUCAAUUAAAAAUAAGACAGUUUGUCGGUCAUCCCCUGCCCUUUGGUGGGGGAUUUUUCUAUGUAUCUUAGCGAGGCAAGACCUCUGGUCGAAGCCGAGCUUAGAGACAUUGAUGCUGAGGAGCGGAGUGACGUGAGCGCUAGGUUCCUAAACGAAAGGAGCUUGCUGGGGUAAAAAGACGUAAACCUUCUAACUACUUGUGGUUGAGUGAACUUUUGUGCUAAGAUAAGGGGACAAUGGAAAAAAGGAGAGCAAU .......(((((((.............(((.....)))....((((((..((....))..))))))((((((((.(((((((((..(((..((((...))))...))).(((...((....))...))).((((((..((((.(....)))))..))))))..(((((((..((((...(((((............)))))..(((((....)))))))))...)))))))))))))))).(....).)))))))).)))).)))... (-83.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGCUCUCCUUUUUUCCAUUGUCCCCUUAUCUUAGCACAAAAGUUCACUCAACCACAAGUAGUUAGAAGGUUUACGUCUUUUUACCCCAGCAAGCUCCUUUCGUUUAGGAACCUAGCGCUCACGUCACUCCGCUCCUCAGCAUCAAUGUCUCUAAGCUCGGCUUCGACCAGAGGUCUUGCCUCGCUAAGAUACAUAGAAAAAUCCCCCACCAAAGGGCAGGGGAUGACCGACAAACUGUCUUAUUUUUAAUUGAGGAAGCUAUUCCC ...(((.(((((..((...(..(((((((((((((((......................((((..(((.(.....).)))..))))....(((((..(((((.(((..(((.((.(((....((((......(((....)))....))))......))).)).)))))).))))).)))))...))))))))).............(((......))).))))))..)..(((.....)))........))..))))))))....... (-64.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 501 140 91 186 128 NC_009009:SSA_0637|5end_Tryptophan_synthase_beta_chain,_putative_625719..625949_POSITIVE 392 160 118 100 56 NC_009009:SSA_1353|5end_hypothetical_protein_1368519..1368749_NEGATIVE 389 144 101 67 22 NC_009009:SSA_0181|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_184902..185132_POSITIVE 358 128 86 56 7 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 357 179 132 178 130 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 351 110 78 150 105 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 349 150 104 173 124 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 344 180 140 160 113 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 340 179 131 77 18 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 339 149 105 94 33 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 339 179 131 170 105 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 338 65 30 186 136 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 336 160 115 191 127 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 334 186 144 59 19 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 331 170 124 63 14 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 330 138 96 189 145 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 327 112 79 203 161 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 326 139 94 158 101 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 325 138 92 64 19 NC_009009:SSA_1848|5end_Methionyl-tRNA_formyltransferase,_putative_1843178..1843408_NEGATIVE 324 79 31 124 72 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 160 118 64 20 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 389 144 101 74 29 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 351 110 78 143 98 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 334 186 144 83 43 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 331 160 111 148 100 NC_009009:SSA_2087|3end_Conserved_uncharacterized_protein_2091674..2091824_NEGATIVE 330 138 96 148 104 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 329 180 140 146 112 NC_009009:SSA_1301|3end_Conserved_uncharacterized_protein,_possible_surface_protein_1319010..1319160_NEGATIVE 325 180 134 57 6 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 324 79 31 112 60 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 322 64 30 151 102 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 322 138 95 86 39 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 319 88 51 73 39 NC_009009:SSA_1878|3end_Conserved_uncharacterized_protein_1871943..1872093_NEGATIVE 315 168 124 52 2 NC_009009:SSA_1122|3end_Thioredoxin_family_protein,_putative_1148526..1148676_POSITIVE 310 156 116 148 103 NC_009009:SSA_0592|3end_hypothetical_protein_584248..584398_POSITIVE 309 139 94 47 3 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 308 88 43 105 50 NC_009009:SSA_1062|3end_50S_ribosomal_protein_L27,_putative_1078657..1078807_POSITIVE 307 122 86 49 15 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 304 160 111 57 15 NC_009009:SSA_2214|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215113..2215263_NEGATIVE 304 75 33 66 25 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 303 218 175 49 6 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE