Origin IGS: acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaagaagacctagattcattctaggtctttattttgtaaaatgaaaacctaacaataatttgacaataatctaatttattgttatgatttgttaaacaaaaatctaacaagagtaaaggagatgtcgt Mask Tandem Repeat Region ================================================ acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Find is-nt database================================================ Query_seq: SSA_2128:SSA_2129|SSA_2128:SSA_2129:hypothetical protein:Arsenical resistance operon transcription repressor (ArsR), putative:<-<-:2132183..2132312 130 acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2128:SSA_2129|SSA_2128:SSA_2129:hypothetical protein:Arsenical resistance operon transcription repressor (ArsR), putative:<-<-:2132183..2132312 130 acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2128:SSA_2129|SSA_2128:SSA_2129:hypothetical protein:Arsenical resistance operon transcription repressor (ArsR), putative:<-<-:2132183..2132312 130 acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Predict ORF larger than 30AA ================================================ acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa 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: 92 Start: 41 End: 70 ........................................TTTGACAATAATCTAATTTATTGTTATGAT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -3.3 Tail_Score: -3.10244 Start: 45 End: 68 Full_Region: aacctaacaataatt tgacaataa tctaat ttattgtta tgatttgttaaacaa ............................................tgacaataatctaatttattgtta.............................................................. TransTerm Strand: - Conf: 47 HP_score: -2.8 Tail_Score: -3.68962 Start: 48 End: 65 Full_Region: ctaacaataatttga caataa tctaat ttattg ttatgatttgttaaa ...............................................caataatctaatttattg................................................................. Find igs database================================================ Query_seq: SSA_2128:SSA_2129|SSA_2128:SSA_2129:hypothetical protein:Arsenical resistance operon transcription repressor (ArsR), putative:<-<-:2132183..2132312 130 acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_009009_SSA_2128_SSA_2129|hypothetical protein:Arsenical resistance operon transcription repressor (ArsR), putative|NEGATIVE:NEGATIVE|[2132183,2132312]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa acgacatctcctttactcttgttagatttttgtttaacaaatcataacaataaattagattattgtcaaattattgttaggttttcattttacaaaataaagacctagaatgaatctaggtcttcttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGACAUCUCCUUUACUCUUGUUAGAUUUUUGUUUAACAAAUCAUAACAAUAAAUUAGAUUAUUGUCAAAUUAUUGUUAGGUUUUCAUUUUACAAAAUAAAGACCUAGAAUGAAUCUAGGUCUUCUUAAA ..(((.............(((((((((....)))))))))....(((((((((.((.(((....))))).))))))))).)))................((((((((((.....))))))))))...... (-28.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGAAGACCUAGAUUCAUUCUAGGUCUUUAUUUUGUAAAAUGAAAACCUAACAAUAAUUUGACAAUAAUCUAAUUUAUUGUUAUGAUUUGUUAAACAAAAAUCUAACAAGAGUAAAGGAGAUGUCGU .....(((((((((((.....))))))))))).((((((............((((((.....(((((((((......)))))))))....))))))............))))))................ (-29.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 731 50 1 141 92 NC_009009:SSA_2128|5end_hypothetical_protein_2132092..2132322_NEGATIVE 274 126 82 123 85 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 220 110 83 222 195 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 213 43 7 130 98 NC_009009:SSA_2052|5end_Thioredoxin,_putative_2057507..2057737_NEGATIVE 213 50 7 227 187 NC_009009:SSA_0362|5end_Thioredoxin,_putative_353290..353520_POSITIVE 208 87 59 155 128 NC_009009:SSA_2313|5end_hypothetical_protein_2315848..2316078_NEGATIVE 208 44 7 128 92 NC_009009:SSA_0429|5end_Histidine_ammonia-lyase,_putative_431251..431481_NEGATIVE 207 35 4 207 173 NC_009009:SSA_1357|5end_hypothetical_protein_1373024..1373254_NEGATIVE 205 36 1 162 127 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 199 46 3 148 97 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 198 44 2 128 79 NC_009009:SSA_2305|5end_hypothetical_protein_2308059..2308289_NEGATIVE 198 124 83 222 179 NC_009009:SSA_1314|5end_Fe-S-cluster_oxidoreductase,_putative_1331240..1331470_NEGATIVE 197 129 102 105 75 NC_009009:SSA_1578|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1581803..1582033_POSITIVE 196 127 95 169 138 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 194 35 2 66 37 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 189 106 67 60 20 NC_009009:SSA_0932|5end_hypothetical_protein_941453..941683_POSITIVE 187 31 2 163 133 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 187 44 1 216 178 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 185 125 82 73 19 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 184 121 84 219 173 NC_009009:SSA_1703|5end_Methionyl-tRNA_synthetase,_putative_1695640..1695870_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 126 82 121 83 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 226 127 82 86 39 NC_009009:SSA_1544|3end_Conserved_uncharacterized_protein_1548314..1548464_NEGATIVE 213 43 7 111 79 NC_009009:SSA_2053|3end_hypothetical_protein_2057526..2057676_NEGATIVE 213 50 7 48 8 NC_009009:SSA_0360|3end_Conserved_uncharacterized_protein_353191..353341_POSITIVE 208 87 59 117 90 NC_009009:SSA_2314|3end_hypothetical_protein_2315886..2316036_NEGATIVE 208 44 7 131 95 NC_009009:SSA_0430|3end_Cationic_amino_acid_transporter,_putative_431248..431398_NEGATIVE 207 35 4 127 93 NC_009009:SSA_1358|3end_hypothetical_protein_1373104..1373254_NEGATIVE 207 120 73 83 41 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 199 46 3 112 61 NC_009009:SSA_0782|3end_Proton-translocating_ATPase,_F0_sector,_subunit_c,_putative_766859..767009_POSITIVE 198 124 83 54 11 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 191 109 61 118 67 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 185 125 82 76 22 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 184 121 84 90 44 NC_009009:SSA_1704|3end_Conserved_uncharacterized_protein_1695769..1695919_NEGATIVE 184 86 42 147 99 NC_009009:SSA_0402|3end_Histidine_kinase,_putative_400099..400249_POSITIVE 183 44 2 131 77 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 182 105 62 35 2 NC_009009:SSA_2375|3end_Tryptophanyl-tRNA_synthetase,_putative_2377221..2377371_NEGATIVE 181 127 107 104 81 NC_009009:SSA_1876|3end_hypothetical_protein_1871742..1871892_POSITIVE 181 124 82 84 46 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 180 21 2 145 126 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 178 50 6 113 75 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE