Origin IGS: ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag .........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 cttacccctccttctagtataatattaaacaaatatttcatttgaagcaatgaaaaactggattgatacataaataacatactctgttaataaaaatgttacaaactatatgcaagacaattagacaaaaaatagattttatgagcttttccacgattttttggctgtttacatcgtaatctttttgtaacaaataacgagtctatgagtaggagaaaaataacatttttgcaacatttcttttcctctgtaa Mask Tandem Repeat Region ================================================ ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Find is-nt database================================================ Query_seq: SSA_2325:SSA_2327|SSA_2325:SSA_2327:3-methyladenine DNA glycosylase, putative:hypothetical protein:<-->:2330812..2331064 253 ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2325:SSA_2327|SSA_2325:SSA_2327:3-methyladenine DNA glycosylase, putative:hypothetical protein:<-->:2330812..2331064 253 ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2325:SSA_2327|SSA_2325:SSA_2327:3-methyladenine DNA glycosylase, putative:hypothetical protein:<-->:2330812..2331064 253 ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 33 End: 152 ................................ M F L L L I D S L F V T K R L R C K Q P K N R G K A H K I Y F L S N C L A Y S L ..................................................................................................... Protein_Len: 51 Strand: + Start: 61 End: 213 ............................................................ M L Q K D Y D V N S Q K I V E K L I K S I F C L I V L H I V C N I F I N R V C Y L C I N P V F H C F K ........................................ Protein_Len: 31 Strand: - Start: 78 End: 170 ............................................................................. S T F L W F I T S F S M F D I K Q R I T K C I T Q L M K I L M ................................................................................... ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag 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================================================ ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -2.9 Tail_Score: -4.1399 Start: 165 End: 179 Full_Region: TTGTAACATTTTTAT TAACA GAGTA TGTTA TTTATGTATCAATCC ....................................................................................................................................................................TAACAGAGTATGTTA.......................................................................... Find igs database================================================ Query_seq: SSA_2325:SSA_2327|SSA_2325:SSA_2327:3-methyladenine DNA glycosylase, putative:hypothetical protein:<-->:2330812..2331064 253 ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Intra-Species Hit: Count: 1 Min: 1 Max: 253 Len: 253 Subject: NC_009009_SSA_2325_SSA_2327|3-methyladenine DNA glycosylase, putative:hypothetical protein|NEGATIVE:POSITIVE|[2330812,2331064]|253 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 253 Query Start:1 Query End:253 Subject Strand: POSITIVE Subject Start: 1 Subject End: 253 ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag ttacagaggaaaagaaatgttgcaaaaatgttatttttctcctactcatagactcgttatttgttacaaaaagattacgatgtaaacagccaaaaaatcgtggaaaagctcataaaatctattttttgtctaattgtcttgcatatagtttgtaacatttttattaacagagtatgttatttatgtatcaatccagtttttcattgcttcaaatgaaatatttgtttaatattatactagaaggaggggtaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAGAGGAAAAGAAAUGUUGCAAAAAUGUUAUUUUUCUCCUACUCAUAGACUCGUUAUUUGUUACAAAAAGAUUACGAUGUAAACAGCCAAAAAAUCGUGGAAAAGCUCAUAAAAUCUAUUUUUUGUCUAAUUGUCUUGCAUAUAGUUUGUAACAUUUUUAUUAACAGAGUAUGUUAUUUAUGUAUCAAUCCAGUUUUUCAUUGCUUCAAAUGAAAUAUUUGUUUAAUAUUAUACUAGAAGGAGGGGUAAG ((((.((((((((..((((((.....)))))).))))))))...(((.(((..((((.((((.........)))).))))..(((((((...........((((......((((((...(((.((((((.(((..((.(((((.......))))).))..)))...)))))).)))...))))))......))))...(((((((......)))))))...)))))))........)))....)))..)))). (-41.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACCCCUCCUUCUAGUAUAAUAUUAAACAAAUAUUUCAUUUGAAGCAAUGAAAAACUGGAUUGAUACAUAAAUAACAUACUCUGUUAAUAAAAAUGUUACAAACUAUAUGCAAGACAAUUAGACAAAAAAUAGAUUUUAUGAGCUUUUCCACGAUUUUUUGGCUGUUUACAUCGUAAUCUUUUUGUAACAAAUAACGAGUCUAUGAGUAGGAGAAAAAUAACAUUUUUGCAACAUUUCUUUUCCUCUGUAA ........((..((((((...(((((.....)))))((((((......))))))..))))))..))(((...........((((.((((.......(((((((((.....(((........(((.((((((((.((.............))....)))))))).)))........))).....)))))))))..))))))))....(((.((((((((.....((....)).....)))))))).))).))). (-33.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 797 90 41 181 132 NC_009009:SSA_2325|5end_3-methyladenine_DNA_glycosylase,_putative_2330721..2330951_NEGATIVE 296 57 24 117 81 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 253 47 4 107 58 NC_009009:SSA_0851|5end_Cation_efflux_family_protein,_putative_838900..839130_NEGATIVE 246 58 16 120 80 NC_009009:SSA_1589|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1592608..1592838_NEGATIVE 240 130 89 114 78 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 230 47 4 213 166 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 227 146 101 109 60 NC_009009:SSA_0868|5end_hypothetical_protein_861535..861765_NEGATIVE 226 129 87 109 64 NC_009009:SSA_1642|5end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1644482..1644712_NEGATIVE 224 90 46 137 88 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 222 49 3 91 52 NC_009009:SSA_0384|5end_hypothetical_protein_376240..376470_POSITIVE 221 130 87 89 45 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 220 65 30 206 175 NC_009009:SSA_0892|5end_ATP-binding_cassette_lipoprotein,_putative_884226..884456_POSITIVE 218 132 101 109 79 NC_009009:SSA_1305|5end_hypothetical_protein_1324079..1324309_NEGATIVE 215 111 85 152 124 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 212 150 101 216 161 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 209 248 207 147 100 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 207 109 61 80 29 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 207 108 71 48 9 NC_009009:SSA_0960|5end_Sensor_protein_ciaH,_putative_968506..968736_POSITIVE 206 128 88 68 21 NC_009009:SSA_2076|5end_Conserved_uncharacterized_protein_2080481..2080711_NEGATIVE 206 84 54 187 158 NC_009009:SSA_0612|5end_Rgg_protein,_putative_600896..601126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 57 24 98 62 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 221 130 87 87 43 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 218 79 40 151 109 NC_009009:SSA_0299|3end_hypothetical_protein_293342..293492_POSITIVE 207 250 204 60 11 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 207 64 34 128 96 NC_009009:SSA_1231|3end_hypothetical_protein_1253649..1253799_NEGATIVE 207 108 71 58 19 NC_009009:SSA_0959|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_968596..968746_POSITIVE 204 100 52 119 65 NC_009009:SSA_1936|3end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923104..1923254_NEGATIVE 201 121 86 43 5 NC_009009:SSA_1857|3end_Conserved_DivIVA-like_protein,_putative_1852725..1852875_NEGATIVE 201 142 106 144 105 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 201 248 206 55 10 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 200 190 141 118 69 NC_009009:SSA_0291|3end_Oxidoreductase,_putative_286269..286419_POSITIVE 199 138 101 64 22 NC_009009:SSA_1468|3end_3-dehydroquinate_synthase,_putative_1474385..1474535_NEGATIVE 199 55 27 126 93 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 197 66 34 118 83 NC_009009:SSA_2288|3end_Cadmium_resistance_transporter,_putative_2291155..2291305_POSITIVE 197 66 34 118 83 NC_009009:SSA_2026|3end_Cadmium_resistance_transporter,_putative_2032195..2032345_NEGATIVE 197 46 4 95 46 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 194 210 169 65 33 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 192 156 118 122 79 NC_009009:SSA_0909|3end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_921158..921308_POSITIVE 191 206 161 145 101 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 191 109 67 62 25 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE