Origin IGS: ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagattattttaccacaaaaaattcaaaaaagaagataaaattccttgcatttaacaaagtttagtgtataatagaaaggtatgcgaaaagcatacttgtgggaggtaaaaatctttatttaccgccaaaaccacaaaggaggatttaaaa Mask Tandem Repeat Region ================================================ ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Find is-nt database================================================ Query_seq: SSA_1623:SSA_1624|SSA_1623:SSA_1624:50S ribosomal protein L11, putative:hypothetical protein:<-->:1626059..1626209 151 ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1623:SSA_1624|SSA_1623:SSA_1624:50S ribosomal protein L11, putative:hypothetical protein:<-->:1626059..1626209 151 ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1623:SSA_1624|SSA_1623:SSA_1624:50S ribosomal protein L11, putative:hypothetical protein:<-->:1626059..1626209 151 ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 33 End: 125 ................................ M K I F T S H K Y A F R I P F Y Y T L N F V K C K E F Y L L F .......................... ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt 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: 82 Start: 79 End: 108 ..............................................................................CCTTGCATTTAACAAAGTTTAGTGTATAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1623:SSA_1624|SSA_1623:SSA_1624:50S ribosomal protein L11, putative:hypothetical protein:<-->:1626059..1626209 151 ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttcttttttgaattttttgtggtaaaataatctt Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_009009_SSA_1623_SSA_1624|50S ribosomal protein L11, putative:hypothetical protein|NEGATIVE:POSITIVE|[1626059,1626209]|151 HSP 1 e-value: 4.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttc............................... ttttaaatcctcctttgtggttttggcggtaaataaagatttttacctcccacaagtatgcttttcgcatacctttctattatacactaaactttgttaaatgcaaggaattttatcttc............................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAAUCCUCCUUUGUGGUUUUGGCGGUAAAUAAAGAUUUUUACCUCCCACAAGUAUGCUUUUCGCAUACCUUUCUAUUAUACACUAAACUUUGUUAAAUGCAAGGAAUUUUAUCUUC ................(((.....((.((((((........)))))).)).....((((((.....))))))............)))....((((((.....))))))............ (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGAUAAAAUUCCUUGCAUUUAACAAAGUUUAGUGUAUAAUAGAAAGGUAUGCGAAAAGCAUACUUGUGGGAGGUAAAAAUCUUUAUUUACCGCCAAAACCACAAAGGAGGAUUUAAAA .....((((.(((((((((((.(((...))).))))))........((((((((.....))))))))((((..((((((........)))))).......))))..)))))..))))... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 60 11 151 102 NC_009009:SSA_1623|5end_50S_ribosomal_protein_L11,_putative_1625968..1626198_NEGATIVE 275 48 8 143 98 NC_009009:SSA_2329|5end_hypothetical_protein_2332262..2332492_POSITIVE 255 78 46 205 176 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 249 49 3 147 91 NC_009009:SSA_2012|5end_hypothetical_protein_2013470..2013700_NEGATIVE 249 73 36 189 144 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 249 32 7 124 96 NC_009009:SSA_1630|5end_hypothetical_protein_1631192..1631422_POSITIVE 242 50 8 146 96 NC_009009:SSA_1862|5end_hypothetical_protein_1858541..1858771_NEGATIVE 239 85 41 96 46 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 235 68 40 213 185 NC_009009:SSA_1652|5end_Acetyltransferases,_putative_1650329..1650559_NEGATIVE 233 76 34 103 53 NC_009009:SSA_1562|5end_hypothetical_protein_1566364..1566594_NEGATIVE 232 47 8 139 98 NC_009009:SSA_1312|5end_RADC-like_protein,_putative_1329663..1329893_NEGATIVE 225 81 45 119 81 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 224 47 10 141 99 NC_009009:SSA_1716|5end_Restriction_endonuclease_SsuRB,_putative_1703616..1703846_NEGATIVE 224 98 59 165 124 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 223 68 27 57 19 NC_009009:SSA_2146|5end_Metallo-beta-lactamase,_putative_2148399..2148629_NEGATIVE 223 57 12 110 67 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 223 31 8 116 98 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 222 90 48 146 99 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 220 68 36 52 19 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 218 53 16 189 132 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 48 8 110 65 NC_009009:SSA_2328|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2332309..2332459_POSITIVE 273 54 12 64 16 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 249 49 3 147 91 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 249 73 36 129 84 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 249 32 7 88 60 NC_009009:SSA_1629|3end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1631236..1631386_POSITIVE 242 50 8 98 48 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 235 68 40 133 105 NC_009009:SSA_1653|3end_hypothetical_protein_1650409..1650559_NEGATIVE 232 47 8 87 46 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 228 49 6 97 51 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 225 41 9 123 90 NC_009009:SSA_1120|3end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1147005..1147155_POSITIVE 223 57 12 113 70 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 223 31 8 119 101 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 218 38 10 59 35 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 218 97 52 105 60 NC_009009:SSA_1497|3end_DCMP_deaminase,_putative_1503068..1503218_NEGATIVE 214 49 8 92 46 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 213 76 48 138 106 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 211 80 40 104 61 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 211 50 10 115 73 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 210 47 9 35 1 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 209 82 42 148 112 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE