Origin IGS: tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggatctcctttttatttatttatgattataagattaatagtaatagtagtttgtgtgaattatgtggaaaaatagctttatccttattctaacaagttttgagacttgttcacaaagtgtggataagttttgaaaaaattctgtagttttccacaaa Mask Tandem Repeat Region ================================================ tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Find is-nt database================================================ Query_seq: SSA_0001:SSA_0002|SSA_0001:SSA_0002:Chromosomal replication initiator protein dnaA, putative:DNA polymerase III, beta chain, putative:->->:1567..1724 158 tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0001:SSA_0002|SSA_0001:SSA_0002:Chromosomal replication initiator protein dnaA, putative:DNA polymerase III, beta chain, putative:->->:1567..1724 158 tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0001:SSA_0002|SSA_0001:SSA_0002:Chromosomal replication initiator protein dnaA, putative:DNA polymerase III, beta chain, putative:->->:1567..1724 158 tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 2 End: 121 . M W K T T E F F Q N L S T L C E Q V S K L V R I R I K L F F H I I H T N Y Y Y Y ..................................... tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc 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================================================ tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -7.8 Tail_Score: -4.10007 Start: 31 End: 53 Full_Region: taacaagttttgaga cttgttcaca aag tgtggataag ttttgaaaaaattct ..............................cttgttcacaaagtgtggataag......................................................................................................... Find igs database================================================ Query_seq: SSA_0001:SSA_0002|SSA_0001:SSA_0002:Chromosomal replication initiator protein dnaA, putative:DNA polymerase III, beta chain, putative:->->:1567..1724 158 tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_009009_SSA_0001_SSA_0002|Chromosomal replication initiator protein dnaA, putative:DNA polymerase III, beta chain, putative|POSITIVE:POSITIVE|[1567,1724]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc tttgtggaaaactacagaattttttcaaaacttatccacactttgtgaacaagtctcaaaacttgttagaataaggataaagctatttttccacataattcacacaaactactattactattaatcttataatcataaataaataaaaaggagatccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUGGAAAACUACAGAAUUUUUUCAAAACUUAUCCACACUUUGUGAACAAGUCUCAAAACUUGUUAGAAUAAGGAUAAAGCUAUUUUUCCACAUAAUUCACACAAACUACUAUUACUAUUAAUCUUAUAAUCAUAAAUAAAUAAAAAGGAGAUCCC ..(((((((((.....(((....))).....((((((....(((...(((((((......))))))).)))...))))))......)))))))))......................................................((....)). (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAUCUCCUUUUUAUUUAUUUAUGAUUAUAAGAUUAAUAGUAAUAGUAGUUUGUGUGAAUUAUGUGGAAAAAUAGCUUUAUCCUUAUUCUAACAAGUUUUGAGACUUGUUCACAAAGUGUGGAUAAGUUUUGAAAAAAUUCUGUAGUUUUCCACAAA (((....)))................(((((((((((.((....)).)))))).)))))....(((((((((((((.......(((........)))(((..((((((((((((.....))))))))))))..))).....))))..))))))))).. (-33.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 70 21 74 24 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 234 69 21 187 125 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 228 106 61 113 60 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 224 88 46 47 1 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 221 78 35 137 97 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 214 113 74 178 136 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 213 92 54 230 188 NC_009009:SSA_1782|5end_hypothetical_protein_1768123..1768353_NEGATIVE 210 68 22 223 173 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 207 39 3 91 49 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 201 77 35 205 166 NC_009009:SSA_2381|5end_DegP_protein,_putative_2386298..2386528_POSITIVE 198 128 81 141 86 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 198 90 41 226 169 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 195 90 41 133 84 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 193 84 48 49 9 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 188 109 62 195 150 NC_009009:SSA_1140|5end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1167868..1168098_POSITIVE 188 113 93 86 65 NC_009009:SSA_1022|5end_Glycosyl_transferase,_group_1,_putative_1037283..1037513_POSITIVE 186 86 50 169 132 NC_009009:SSA_0394|5end_hypothetical_protein_390573..390803_POSITIVE 185 76 33 181 140 NC_009009:SSA_1988|5end_ABC-type_transport_system_(uncharacterized),_permease_component,_putative_1984188..1984418_NEGATIVE 185 77 40 66 30 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 185 102 71 165 136 NC_009009:SSA_0381|5end_hypothetical_protein_372763..372993_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 70 21 84 34 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 228 106 61 103 50 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 221 78 35 47 7 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 193 84 48 56 16 NC_009009:SSA_1924|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1912691..1912841_NEGATIVE 193 108 65 79 31 NC_009009:SSA_0133|3end_50S_ribosomal_protein_L17,_putative_122562..122712_POSITIVE 191 97 66 105 75 NC_009009:SSA_2021|3end_hypothetical_protein_2022500..2022650_NEGATIVE 188 56 18 75 37 NC_009009:SSA_0859|3end_Triosephosphate_isomerase,_putative_847485..847635_POSITIVE 185 76 34 127 82 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 175 85 41 55 13 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 172 88 46 54 13 NC_009009:SSA_0387|3end_Transcriptional_regulator,_GntR_family,_putative_381702..381852_NEGATIVE 171 68 32 121 72 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 171 95 51 54 8 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 170 70 22 56 20 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 170 67 26 84 49 NC_009009:SSA_0875|3end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_870240..870390_POSITIVE 169 44 13 38 10 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 168 86 61 30 10 NC_009009:SSA_2311|3end_Nitric_oxide_reductase_NorD_/_Von_Willebrand_factor_type_A_(vWA)_domain_protein,_putative_2313431..2313581_NEGATIVE 168 93 54 102 55 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE 167 85 45 110 68 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 167 67 31 73 33 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 166 58 12 146 100 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE