Origin IGS: cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataagaaaaatagggtgtacagaaccaaaagaggttttgtacaccctgtataatttttcaaaatatgaaaagagctggaacccattgggttccagcaacttcttacagcattttcaaaagaaattctg Mask Tandem Repeat Region ================================================ cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Find is-nt database================================================ Query_seq: SSA_2345:SSA_2346|SSA_2345:SSA_2346:hypothetical protein:3-oxoacyl-[acyl-carrier-protein] synthase III, putative:-><-:2347563..2347691 129 cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2345:SSA_2346|SSA_2345:SSA_2346:hypothetical protein:3-oxoacyl-[acyl-carrier-protein] synthase III, putative:-><-:2347563..2347691 129 cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2345:SSA_2346|SSA_2345:SSA_2346:hypothetical protein:3-oxoacyl-[acyl-carrier-protein] synthase III, putative:-><-:2347563..2347691 129 cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 5 End: 127 .... M S F E N A V R S C W N P M G S S S F H I L K N Y T G C T K P L L V L Y T L F F L .. Protein_Len: 33 Strand: + Start: 31 End: 129 .............................. M L E P N G F Q L F S Y F E K L Y R V Y K T S F G S V H P I F L I Protein_Len: 42 Strand: - Start: 3 End: 128 .. F K K Q F H Q L F N S S G L P N W S K E Y K S F N Y L T Y L V E K P E T C G I K R M . cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata 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================================================ cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -9.0 Tail_Score: -4.12198 Start: 22 End: 65 Full_Region: TTCTTTTGAAAATGC TGTAAGAAGTTGCTGGAACCC AAT GGGTTCCAGCTCTTTTCATA TTTTGAAAAATTATA .....................TGTAAGAAGTTGCTGGAACCCAATGGGTTCCAGCTCTTTTCATA................................................................ TransTerm Strand: + Conf: 81 HP_score: -9.4 Tail_Score: -3.6543 Start: 24 End: 63 Full_Region: CTTTTGAAAATGCTG TAAGAAGTTGCTGGAACCC AAT GGGTTCCAGCTCTTTTCA TATTTTGAAAAATTA .......................TAAGAAGTTGCTGGAACCCAATGGGTTCCAGCTCTTTTCA.................................................................. TransTerm Strand: - Conf: 86 HP_score: -10.6 Tail_Score: -3.64685 Start: 30 End: 57 Full_Region: ttcaaaatatgaaaa gagctggaaccc att gggttccagcaac ttcttacagcatttt .............................gagctggaacccattgggttccagcaac........................................................................ TransTerm Strand: - Conf: 79 HP_score: -10.8 Tail_Score: -2.78088 Start: 31 End: 57 Full_Region: ttcaaaatatgaaaa gagctggaaccc att gggttccagcaa cttcttacagcattt ..............................gagctggaacccattgggttccagcaa........................................................................ Find igs database================================================ Query_seq: SSA_2345:SSA_2346|SSA_2345:SSA_2346:hypothetical protein:3-oxoacyl-[acyl-carrier-protein] synthase III, putative:-><-:2347563..2347691 129 cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_009009_SSA_2345_SSA_2346|hypothetical protein:3-oxoacyl-[acyl-carrier-protein] synthase III, putative|POSITIVE:NEGATIVE|[2347563,2347691]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata cagaatttcttttgaaaatgctgtaagaagttgctggaacccaatgggttccagctcttttcatattttgaaaaattatacagggtgtacaaaacctcttttggttctgtacaccctatttttcttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAAUUUCUUUUGAAAAUGCUGUAAGAAGUUGCUGGAACCCAAUGGGUUCCAGCUCUUUUCAUAUUUUGAAAAAUUAUACAGGGUGUACAAAACCUCUUUUGGUUCUGUACACCCUAUUUUUCUUAUA .....((((....))))....(((((((((..((((((((((...))))))))))..((((((.....)))))).......((((((((((.((((......)))).))))))))))...))))))))) (-50.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAGAAAAAUAGGGUGUACAGAACCAAAAGAGGUUUUGUACACCCUGUAUAAUUUUUCAAAAUAUGAAAAGAGCUGGAACCCAUUGGGUUCCAGCAACUUCUUACAGCAUUUUCAAAAGAAAUUCUG ..((((((..(((((((((((((((((......)))))))))))))))))....(((((((.....))))))).((((((((((...))))))))))...))))))(((...((((....))))..))) (-55.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 59 18 181 139 NC_009009:SSA_1860|5end_Penicillin-binding_protein_1A,_putative_1854299..1854529_POSITIVE 324 58 18 149 109 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 304 63 29 61 32 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 287 68 21 93 35 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 283 54 16 218 164 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 280 57 20 73 39 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 280 57 20 230 196 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 278 50 5 137 97 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 273 58 26 184 152 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 267 60 11 202 141 NC_009009:SSA_1339|5end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1355424..1355654_NEGATIVE 266 60 11 231 174 NC_009009:SSA_1927|5end_Exfoliative_toxin,_putative_1915873..1916103_NEGATIVE 263 63 23 186 151 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 259 59 20 46 1 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 258 60 20 63 19 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 257 57 19 49 9 NC_009009:SSA_2348|5end_Metal_dependent_hydrolase,_putative_2350720..2350950_NEGATIVE 257 63 31 177 143 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 255 59 20 46 3 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 254 57 19 193 152 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 252 55 14 72 28 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 252 56 11 70 27 NC_009009:SSA_1689|5end_hypothetical_protein_1682505..1682735_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 441 61 26 65 30 NC_009009:SSA_2345|3end_hypothetical_protein_2347502..2347652_POSITIVE 324 58 18 133 93 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 311 55 19 69 32 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 304 63 29 64 35 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 287 68 21 139 81 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 283 49 4 82 36 NC_009009:SSA_2349|3end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2350677..2350827_NEGATIVE 277 59 20 53 5 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 276 63 21 70 27 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 264 70 22 142 101 NC_009009:SSA_2164|3end_Glutamine_amidotransferase,_putative_2160866..2161016_NEGATIVE 263 63 23 131 96 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 261 47 5 151 113 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 260 61 25 86 60 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 259 59 19 70 24 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 258 60 20 76 32 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 254 57 19 137 96 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 252 55 14 75 31 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 252 59 19 136 84 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 251 58 20 146 111 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 250 61 23 100 67 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 248 55 19 137 105 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE