Origin IGS: ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatatttctccgtttttctataatagtagtatagcatatctagatatatttttcaagaaaattatagtttttcggaaagatgatagagtaatcgaaatggatttattttcttatatttatgttataatatcattgtgctttattaaataatattatatagtttaggagtaaaacaa Mask Tandem Repeat Region ================================================ ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Find is-nt database================================================ Query_seq: SSA_1170:SSA_1171|SSA_1170:SSA_1171:hypothetical protein:Tyrosine recombinase xerC:<-->:1198052..1198227 176 ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1170:SSA_1171|SSA_1170:SSA_1171:hypothetical protein:Tyrosine recombinase xerC:<-->:1198052..1198227 176 ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1170:SSA_1171|SSA_1170:SSA_1171:hypothetical protein:Tyrosine recombinase xerC:<-->:1198052..1198227 176 ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 30 End: 173 ............................. K I F C L S I I V Y I Y S F L D M E I V R D D K R F V I I K K F F I D L Y A I S S N Y F F P S M ... ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata 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: 87 Start: 120 End: 149 .......................................................................................................................CTTGAAAAATATATCTAGATATGCTATACT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1170:SSA_1171|SSA_1170:SSA_1171:hypothetical protein:Tyrosine recombinase xerC:<-->:1198052..1198227 176 ttgttttactcctaaactatataatattatttaataaagcacaatgatattataacataaatataagaaaataaatccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Intra-Species Hit: Count: 1 Min: 77 Max: 176 Len: 100 Subject: NC_009009_SSA_1170_SSA_1171|hypothetical protein:Tyrosine recombinase xerC|NEGATIVE:POSITIVE|[1198052,1198227]|176 HSP 1 e-value: 4.0E-50 bit: 198.0 Len: 100 Query Start:77 Query End:176 Subject Strand: POSITIVE Subject Start: 77 Subject End: 176 ............................................................................ccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata ............................................................................ccatttcgattactctatcatctttccgaaaaactataattttcttgaaaaatatatctagatatgctatactactattatagaaaaacggagaaatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAUUUCGAUUACUCUAUCAUCUUUCCGAAAAACUAUAAUUUUCUUGAAAAAUAUAUCUAGAUAUGCUAUACUACUAUUAUAGAAAAACGGAGAAAUAUA .......(((......)))...((((((.....(((((((...........((((......))))...........))))))).....))))))...... (-12.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUUCUCCGUUUUUCUAUAAUAGUAGUAUAGCAUAUCUAGAUAUAUUUUUCAAGAAAAUUAUAGUUUUUCGGAAAGAUGAUAGAGUAAUCGAAAUGG ..((((((...(((...((((....))))...)))...((((....((((((((..((((((....))))))..)))))))).))))......)))))). (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 730 50 1 217 168 NC_009009:SSA_1170|5end_hypothetical_protein_1197961..1198191_NEGATIVE 237 100 57 149 108 NC_009009:SSA_0349|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341110..341340_POSITIVE 216 94 59 198 161 NC_009009:SSA_1318|5end_GTP-binding_protein_lepA,_putative_1335821..1336051_NEGATIVE 214 86 41 227 174 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 213 49 2 128 74 NC_009009:SSA_1589|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1592608..1592838_NEGATIVE 211 74 40 131 96 NC_009009:SSA_0232|5end_hypothetical_protein_227012..227242_POSITIVE 205 46 1 174 126 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 195 87 56 165 125 NC_009009:SSA_2258|5end_hypothetical_protein_2254699..2254929_NEGATIVE 191 84 54 212 184 NC_009009:SSA_0056|5end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_59926..60156_POSITIVE 190 70 21 204 152 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 186 47 7 55 13 NC_009009:SSA_0983|5end_Conserved_uncharacterized_protein_986086..986316_POSITIVE 183 47 5 224 182 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 182 59 12 178 134 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 181 46 7 174 129 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 176 47 2 108 71 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 176 50 1 160 113 NC_009009:SSA_1352|5end_hypothetical_protein_1367941..1368171_NEGATIVE 173 59 14 136 85 NC_009009:SSA_1460|5end_Transcriptional_attenuator_LytR,_putative_1468915..1469145_NEGATIVE 172 94 59 202 166 NC_009009:SSA_0763|5end_Transcription_repressor,_putative_744980..745210_POSITIVE 170 43 1 200 150 NC_009009:SSA_1288|5end_hypothetical_protein_1307578..1307808_NEGATIVE 168 79 42 171 128 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 100 57 73 32 NC_009009:SSA_0348|3end_CAAX_amino_terminal_protease_family,_putative_341114..341264_POSITIVE 236 45 2 104 50 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 211 74 40 121 86 NC_009009:SSA_0231|3end_Conserved_uncharacterized_protein_227082..227232_POSITIVE 210 48 1 89 32 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE 195 87 56 137 97 NC_009009:SSA_2259|3end_hypothetical_protein_2254727..2254877_NEGATIVE 185 94 68 52 18 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 182 59 12 145 101 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 176 47 2 56 19 NC_009009:SSA_1987|3end_hypothetical_protein_1982583..1982733_NEGATIVE 176 50 1 127 80 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 173 59 14 117 66 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 170 37 1 146 107 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 168 26 2 88 61 NC_009009:SSA_0541|3end_Acetate_kinase,_putative_537082..537232_POSITIVE 168 79 42 83 40 NC_009009:SSA_0199|3end_GTP_cyclohydrolase_I,_putative_198910..199060_POSITIVE 167 29 1 146 113 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 165 68 21 110 66 NC_009009:SSA_0046|3end_Adenylosuccinate_lyase,_putative_52269..52419_POSITIVE 164 28 3 106 79 NC_009009:SSA_1860|3end_Penicillin-binding_protein_1A,_putative_1856520..1856670_POSITIVE 164 27 1 135 110 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 164 45 14 151 116 NC_009009:SSA_0008|3end_Transcription-repair_coupling_factor,_putative_9154..9304_POSITIVE 162 29 7 114 88 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 161 91 56 65 33 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE