Origin IGS: tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttctccttgcagcttatttattattttcattataacaaagttaagggctttctgctgattttttaaatgaattaaaagtggatattataaaatttcattagagaggaaagtaaacgagaaaatcaatgaatttacaactttgtaaatattctttacagttgataattctagttgaatttctgatttgttttcctaggcctttcatgctataataggccttgctcaagcgaccttcaatcgttgaaagcacagcacgaccttcaatcgtgaaataacgaaaagatgggagaacaca Mask Tandem Repeat Region ================================================ tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Find is-nt database================================================ Query_seq: SSA_2360:SSA_2361|SSA_2360:SSA_2361:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, putative:L-serine dehydratase beta subunit:<-->:2363870..2364167 298 tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2360:SSA_2361|SSA_2360:SSA_2361:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, putative:L-serine dehydratase beta subunit:<-->:2363870..2364167 298 tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2360:SSA_2361|SSA_2360:SSA_2361:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, putative:L-serine dehydratase beta subunit:<-->:2363870..2364167 298 tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 31 End: 195 .............................. M E G R A V L S T I E G R L S K A Y Y S M K G L G K Q I R N S T R I I N C K E Y L Q S C K F I D F L V Y F P L ....................................................................................................... Protein_Len: 30 Strand: + Start: 119 End: 208 ...................................................................................................................... M Q L E L S T V K N I Y K V V N S L I F S F T F L S N E I L .......................................................................................... tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc 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: 85 Start: 83 End: 112 ..................................................................................TTTGTTTTCCTAGGCCTTTCATGCTATAAT.......................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 137 End: 166 ........................................................................................................................................ATTTACAACTTTGTAAATATTCTTTACAGT.................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 58 End: 87 .........................................................ATTGAAGGTCGCTTGAGCAAGGCCTATTAT................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -2.5 Tail_Score: -3.31589 Start: 138 End: 156 Full_Region: aatgaatttacaact ttgtaaa tattc tttacag ttgataattctagtt .........................................................................................................................................ttgtaaatattctttacag.............................................................................................................................................. TransTerm Strand: - Conf: 45 HP_score: -3.8 Tail_Score: -2.58231 Start: 139 End: 155 Full_Region: atgaatttacaactt tgtaaa tattc tttaca gttgataattctagt ..........................................................................................................................................tgtaaatattctttaca............................................................................................................................................... Find igs database================================================ Query_seq: SSA_2360:SSA_2361|SSA_2360:SSA_2361:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, putative:L-serine dehydratase beta subunit:<-->:2363870..2364167 298 tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 298 Len: 298 Subject: NC_009009_SSA_2360_SSA_2361|tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, putative:L-serine dehydratase beta subunit|NEGATIVE:POSITIVE|[2363870,2364167]|298 HSP 1 e-value: 1.0E-168 bit: 591.0 Len: 298 Query Start:1 Query End:298 Subject Strand: POSITIVE Subject Start: 1 Subject End: 298 tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc tgtgttctcccatcttttcgttatttcacgattgaaggtcgtgctgtgctttcaacgattgaaggtcgcttgagcaaggcctattatagcatgaaaggcctaggaaaacaaatcagaaattcaactagaattatcaactgtaaagaatatttacaaagttgtaaattcattgattttctcgtttactttcctctctaatgaaattttataatatccacttttaattcatttaaaaaatcagcagaaagcccttaactttgttataatgaaaataataaataagctgcaaggagaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGUUCUCCCAUCUUUUCGUUAUUUCACGAUUGAAGGUCGUGCUGUGCUUUCAACGAUUGAAGGUCGCUUGAGCAAGGCCUAUUAUAGCAUGAAAGGCCUAGGAAAACAAAUCAGAAAUUCAACUAGAAUUAUCAACUGUAAAGAAUAUUUACAAAGUUGUAAAUUCAUUGAUUUUCUCGUUUACUUUCCUCUCUAAUGAAAUUUUAUAAUAUCCACUUUUAAUUCAUUUAAAAAAUCAGCAGAAAGCCCUUAACUUUGUUAUAAUGAAAAUAAUAAAUAAGCUGCAAGGAGAAAUC ....((((((.....((((((((...((((((.....))))))..(((((((((.....)))))).)))..(((..((((((.((((...)))).)))))).(((((..((((.(((((.((((...(((((..((((((((((.....)))))..)))))..))))).)))).))))).))))..))))).)))))))))))...............((((((.....)))))).....((((......((((..((((((((.......))))))))))))))))..))))))... (-67.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCUCCUUGCAGCUUAUUUAUUAUUUUCAUUAUAACAAAGUUAAGGGCUUUCUGCUGAUUUUUUAAAUGAAUUAAAAGUGGAUAUUAUAAAAUUUCAUUAGAGAGGAAAGUAAACGAGAAAAUCAAUGAAUUUACAACUUUGUAAAUAUUCUUUACAGUUGAUAAUUCUAGUUGAAUUUCUGAUUUGUUUUCCUAGGCCUUUCAUGCUAUAAUAGGCCUUGCUCAAGCGACCUUCAAUCGUUGAAAGCACAGCACGACCUUCAAUCGUGAAAUAACGAAAAGAUGGGAGAACACA ...((((((((((.(((((((..((((.......))))...(((.(((((((.((((.(((..(((((((((.((.....))...)))).)))))..))).)))).(((((((((((..(((((.((((((((((..(((((..(((((.....))))))))))..)))))..))))).)))))..))))))))))).)))))))...)))..)))))))..((((..(((((.......)))))...))))..)))..........((((......))))......))))))).... (-65.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 987 80 31 171 122 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 363 80 32 139 80 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 343 80 37 42 3 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 327 80 35 70 32 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 324 79 33 160 110 NC_009009:SSA_0047|5end_NAD(P)H_dehydrogenase_(Quinone),_putative_52850..53080_NEGATIVE 315 119 77 129 92 NC_009009:SSA_0100|5end_DNA_polymerase_I_-_3'-5'_exonuclease_and_polymerase_domains,_putative_100680..100910_POSITIVE 309 101 64 57 2 NC_009009:SSA_2020|5end_hypothetical_protein_2019284..2019514_POSITIVE 308 80 36 43 4 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 305 100 52 121 72 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 303 99 56 156 110 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 303 90 43 218 161 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 302 90 42 172 124 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 298 195 155 219 172 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 295 49 4 88 41 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 294 90 43 217 168 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 291 80 31 187 137 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 291 98 57 112 72 NC_009009:SSA_1297|5end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1314976..1315206_NEGATIVE 291 90 43 230 165 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 290 69 25 221 152 NC_009009:SSA_2357|5end_50S_ribosomal_protein_L9,_putative_2358437..2358667_NEGATIVE 290 90 44 187 135 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 116 74 71 25 NC_009009:SSA_0604|3end_hypothetical_protein_592992..593142_POSITIVE 305 100 52 124 75 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 302 90 42 151 103 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 294 45 3 104 64 NC_009009:SSA_1907|3end_hypothetical_protein_1900813..1900963_POSITIVE 289 85 41 58 23 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 289 100 53 62 1 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 287 55 11 149 105 NC_009009:SSA_1490|3end_Ribonuclease_BN,_putative_1495821..1495971_NEGATIVE 284 94 56 141 101 NC_009009:SSA_2364|3end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2366442..2366592_NEGATIVE 284 55 13 79 40 NC_009009:SSA_0771|3end_Glutaredoxin-like_protein,_putative_751572..751722_NEGATIVE 283 59 11 113 76 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 283 77 33 45 8 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 281 50 2 123 72 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 279 46 1 139 77 NC_009009:SSA_2281|3end_hypothetical_protein_2281912..2282062_NEGATIVE 277 80 37 77 22 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 276 49 1 135 87 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 276 108 65 83 41 NC_009009:SSA_0997|3end_DNA-directed_DNA_polymerase_III_chain,_putative_998529..998679_POSITIVE 273 70 27 148 102 NC_009009:SSA_1434|3end_Conserved_uncharacterized_Firmicutes_protein_1441100..1441250_POSITIVE 272 80 31 96 47 NC_009009:SSA_0996|3end_cGMP-specific_phosphodiesterase,_putative_996859..997009_POSITIVE 272 69 28 150 110 NC_009009:SSA_0035|3end_Bifunctional_purine_biosynthesis_protein_purH,_putative_41957..42107_POSITIVE 271 80 35 86 51 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE