Origin IGS: aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctttcaattcgataacactgttatcgcctttcttcttttattataaattctgacaatttaactgtcaaggaaaaacaaaagagaccgagaaatattttcatcagtccatatctcttacttttgtaaacatgacaaaaggagcttattgacaagctcctctaaaatt Mask Tandem Repeat Region ================================================ aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Find is-nt database================================================ Query_seq: SSA_0926:SSA_0927|SSA_0926:SSA_0927:Histone acetyltransferase HPA2, putative:Transcriptional regulator, TetR/AcrR family, putative:->->:936022..936188 167 aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0926:SSA_0927|SSA_0926:SSA_0927:Histone acetyltransferase HPA2, putative:Transcriptional regulator, TetR/AcrR family, putative:->->:936022..936188 167 aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0926:SSA_0927|SSA_0926:SSA_0927:Histone acetyltransferase HPA2, putative:Transcriptional regulator, TetR/AcrR family, putative:->->:936022..936188 167 aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 15 End: 143 .............. M S I S S F C H V Y K S K R Y G L M K I F L G L F C F S L T V K L S E F I I K E E R R ........................ Protein_Len: 35 Strand: - Start: 1 End: 105 I K S S S T L L S R K D H K C F Y S I H V S S F I E R D R K N K R S M .............................................................. aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc 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: 90 Start: 98 End: 127 .................................................................................................CTTGACAGTTAAATTGTCAGAATTTATAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0926:SSA_0927|SSA_0926:SSA_0927:Histone acetyltransferase HPA2, putative:Transcriptional regulator, TetR/AcrR family, putative:->->:936022..936188 167 aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_009009_SSA_0926_SSA_0927|Histone acetyltransferase HPA2, putative:Transcriptional regulator, TetR/AcrR family, putative|POSITIVE:POSITIVE|[936022,936188]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc aattttagaggagcttgtcaataagctccttttgtcatgtttacaaaagtaagagatatggactgatgaaaatatttctcggtctcttttgtttttccttgacagttaaattgtcagaatttataataaaagaagaaaggcgataacagtgttatcgaattgaaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAGAGGAGCUUGUCAAUAAGCUCCUUUUGUCAUGUUUACAAAAGUAAGAGAUAUGGACUGAUGAAAAUAUUUCUCGGUCUCUUUUGUUUUUCCUUGACAGUUAAAUUGUCAGAAUUUAUAAUAAAAGAAGAAAGGCGAUAACAGUGUUAUCGAAUUGAAAGC ......(((((((((((....)))))))))))((((...(((((....))))).)))).(((((((.(((.....))))))))))((((((((.....((((((((...)))))))).......))))))))....((..(((((((...)))))))..))...... (-42.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUCAAUUCGAUAACACUGUUAUCGCCUUUCUUCUUUUAUUAUAAAUUCUGACAAUUUAACUGUCAAGGAAAAACAAAAGAGACCGAGAAAUAUUUUCAUCAGUCCAUAUCUCUUACUUUUGUAAACAUGACAAAAGGAGCUUAUUGACAAGCUCCUCUAAAAUU (((((((((.(((((((...))))))).....((((((((.((((...((((((((.......)))).))))...(((((((.(((.(((((.....))).)).)))...........)))))))....)))).))))))))...))))).))))............ (-31.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 105 63 66 26 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 275 108 64 227 181 NC_009009:SSA_0164|5end_hypothetical_protein_162478..162708_POSITIVE 261 115 79 87 51 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 258 44 2 51 3 NC_009009:SSA_0118|5end_50S_ribosomal_protein_L24,_putative_113363..113593_POSITIVE 253 40 3 229 185 NC_009009:SSA_1504|5end_hypothetical_protein_1506947..1507177_NEGATIVE 253 93 53 197 162 NC_009009:SSA_0454|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_457015..457245_NEGATIVE 252 117 75 133 94 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 245 56 13 216 165 NC_009009:SSA_1505|5end_hypothetical_protein_1509555..1509785_NEGATIVE 244 108 63 174 122 NC_009009:SSA_1473|5end_hypothetical_protein_1478920..1479150_NEGATIVE 237 48 10 164 125 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 236 153 112 135 91 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 236 100 52 212 172 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 234 60 12 92 33 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 233 63 21 76 29 NC_009009:SSA_2012|5end_hypothetical_protein_2013470..2013700_NEGATIVE 232 42 6 219 181 NC_009009:SSA_0716|5end_Competence_protein,_putative_701390..701620_POSITIVE 231 50 9 224 175 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 231 42 5 41 7 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 229 48 6 56 4 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 229 99 53 115 63 NC_009009:SSA_1129|5end_Periplasmic_iron_transport_lipoprotein,_putative_1154925..1155155_POSITIVE 228 103 61 63 15 NC_009009:SSA_0866|5end_Cation-transporting_ATPase,_E1-E_2_family,_putative_856983..857213_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 32 7 84 59 NC_009009:SSA_0926|3end_Histone_acetyltransferase_HPA2,_putative_935961..936111_POSITIVE 292 100 51 89 42 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 261 115 79 75 39 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 253 40 3 149 105 NC_009009:SSA_1505|3end_hypothetical_protein_1507027..1507177_NEGATIVE 249 100 52 104 49 NC_009009:SSA_0505|3end_Conserved_protein/domain_typically_associated_with_flavoprotein_oxygenases,_DIM6/NTAB_family,_putative_504427..504577_POSITIVE 245 149 103 55 8 NC_009009:SSA_0350|3end_Helicase,_putative_341852..342002_NEGATIVE 233 63 21 76 29 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 231 42 5 44 10 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 226 99 51 125 62 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 226 63 27 68 28 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 224 44 8 113 78 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 224 107 76 83 54 NC_009009:SSA_0515|3end_Propanediol_utilization_protein_PduU,_putative_514540..514690_POSITIVE 224 140 91 57 10 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 222 96 51 49 3 NC_009009:SSA_1544|3end_Conserved_uncharacterized_protein_1548314..1548464_NEGATIVE 222 98 56 127 78 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 222 50 7 120 77 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 221 38 6 94 64 NC_009009:SSA_1614|3end_Acetyltransferase,_GNAT_family,_putative_1617476..1617626_NEGATIVE 221 41 1 44 9 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 221 50 2 114 55 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 219 157 111 65 26 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE