Origin IGS: gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcatttttctttgaattggaaaggtgagcggtctattattgaatgctggtaaatgatgtaaaaaaggagaataaaaccagaaagaaactgtttttctttctggttttttgtgtatagttaagtacagttgc Mask Tandem Repeat Region ================================================ gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Find is-nt database================================================ Query_seq: SSA_2132:SSA_2133|SSA_2132:SSA_2133:Ure cluster protein, putative:3-methyladenine DNA glycosylase, putative:-><-:2135726..2135856 131 gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2132:SSA_2133|SSA_2132:SSA_2133:Ure cluster protein, putative:3-methyladenine DNA glycosylase, putative:-><-:2135726..2135856 131 gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2132:SSA_2133|SSA_2132:SSA_2133:Ure cluster protein, putative:3-methyladenine DNA glycosylase, putative:-><-:2135726..2135856 131 gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 5 End: 130 .... M Y L T I H K K P E R K T V S F W F Y S P F L H H L P A F N N R P L T F P I Q R K M . gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga 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: 81 Start: 93 End: 122 ............................................................................................TTTGAATTGGAAAGGTGAGCGGTCTATTAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -2.3 Tail_Score: -5.13521 Start: 19 End: 66 Full_Region: ACTGTACTTAACTAT ACACAAAAAACCAGAAAGAAA AACAG TTTCTTTCTGGTTTTATTCTCC TTTTTTACATCATTT ..................ACACAAAAAACCAGAAAGAAAAACAGTTTCTTTCTGGTTTTATTCTCC................................................................. TransTerm Strand: + Conf: 100 HP_score: -12.6 Tail_Score: -3.81575 Start: 24 End: 60 Full_Region: ACTTAACTATACACA AAAAACCAGAAAGAAA AACAG TTTCTTTCTGGTTTTA TTCTCCTTTTTTACA .......................AAAAACCAGAAAGAAAAACAGTTTCTTTCTGGTTTTA....................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.5 Tail_Score: -5.43414 Start: 29 End: 55 Full_Region: aaaaggagaataaaa ccagaaagaaa ctgtt tttctttctgg ttttttgtgtatagt ............................ccagaaagaaactgtttttctttctgg............................................................................ Find igs database================================================ Query_seq: SSA_2132:SSA_2133|SSA_2132:SSA_2133:Ure cluster protein, putative:3-methyladenine DNA glycosylase, putative:-><-:2135726..2135856 131 gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_009009_SSA_2132_SSA_2133|Ure cluster protein, putative:3-methyladenine DNA glycosylase, putative|POSITIVE:NEGATIVE|[2135726,2135856]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga gcaactgtacttaactatacacaaaaaaccagaaagaaaaacagtttctttctggttttattctccttttttacatcatttaccagcattcaataatagaccgctcacctttccaattcaaagaaaaatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAACUGUACUUAACUAUACACAAAAAACCAGAAAGAAAAACAGUUUCUUUCUGGUUUUAUUCUCCUUUUUUACAUCAUUUACCAGCAUUCAAUAAUAGACCGCUCACCUUUCCAAUUCAAAGAAAAAUGA .....((((........))))...(((((((((((((((.....)))))))))))))))................((((((...(((..((.......))..)))...((((.......))))..)))))) (-22.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUUUUCUUUGAAUUGGAAAGGUGAGCGGUCUAUUAUUGAAUGCUGGUAAAUGAUGUAAAAAAGGAGAAUAAAACCAGAAAGAAACUGUUUUUCUUUCUGGUUUUUUGUGUAUAGUUAAGUACAGUUGC ((((((((((.......))))))))))(((.((.......)).)))..((((....((((............(((((((((((((((.....)))))))))))))))...............)))).)))) (-30.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 89 42 199 146 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 268 105 61 143 96 NC_009009:SSA_1418|5end_Conserved_uncharacterized_protein_1428927..1429157_NEGATIVE 260 86 47 125 81 NC_009009:SSA_1244|5end_hypothetical_protein_1268704..1268934_NEGATIVE 259 89 43 133 93 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 248 90 44 167 118 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 245 107 62 186 139 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 245 107 62 121 73 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 244 112 78 215 181 NC_009009:SSA_0191|5end_Adenine-specific_DNA_methylase,_putative_191907..192137_POSITIVE 242 87 52 127 97 NC_009009:SSA_0108|5end_50S_ribosomal_protein_L4,_putative_108816..109046_POSITIVE 239 109 61 214 159 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 236 115 83 217 188 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 236 120 74 227 181 NC_009009:SSA_1482|5end_Pullulanase,_putative_1489246..1489476_NEGATIVE 236 87 49 203 160 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 236 116 83 83 44 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 234 84 42 153 121 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 233 110 62 160 103 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 233 109 65 222 172 NC_009009:SSA_0462|5end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_464815..465045_POSITIVE 232 109 77 228 202 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 231 86 41 124 69 NC_009009:SSA_1849|5end_Primosomal_protein_N',_putative_1845649..1845879_NEGATIVE 231 115 81 102 49 NC_009009:SSA_0786|5end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_768737..768967_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 59 25 66 32 NC_009009:SSA_2132|3end_Ure_cluster_protein,_putative_2135665..2135815_POSITIVE 268 105 61 75 28 NC_009009:SSA_1419|3end_hypothetical_protein_1428995..1429145_NEGATIVE 246 110 61 142 84 NC_009009:SSA_2154|3end_Conserved_uncharacterized_protein_2154762..2154912_NEGATIVE 245 107 62 124 76 NC_009009:SSA_0063|3end_Holliday_junction_DNA_helicase_ruvB,_putative_66413..66563_POSITIVE 244 112 78 133 99 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 242 87 52 102 72 NC_009009:SSA_0107|3end_50S_ribosomal_protein_L3,_putative_108871..109021_POSITIVE 236 87 49 150 107 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 236 116 83 81 42 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 234 84 42 144 112 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 231 86 41 63 8 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE 230 126 82 77 26 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 228 107 63 127 82 NC_009009:SSA_1087|3end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1106472..1106622_POSITIVE 225 88 46 54 6 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 225 87 43 107 61 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 222 87 42 121 83 NC_009009:SSA_0692|3end_D-Ala-D-Ala_adding_enzyme,_putative_677820..677970_POSITIVE 221 124 82 101 47 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 220 110 63 127 83 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 217 70 29 51 14 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 217 60 21 80 48 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 214 74 51 113 90 NC_009009:SSA_0465|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469963..470113_POSITIVE