Origin IGS: tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaccatctgctgtttttattttggaaaatacatcttaagcctgatttagctgagattagatgtttttgtaagagttttattcctaagtatggtaaaatagttttcggaatatactagaataaaaggatttaaagaggtcttata Mask Tandem Repeat Region ================================================ tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Find is-nt database================================================ Query_seq: SSA_0338:SSA_0339|SSA_0338:SSA_0339:Hydroxymethylglutaryl-CoA synthase, putative:hypothetical protein:<-<-:333429..333572 144 tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0338:SSA_0339|SSA_0338:SSA_0339:Hydroxymethylglutaryl-CoA synthase, putative:hypothetical protein:<-<-:333429..333572 144 tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0338:SSA_0339|SSA_0338:SSA_0339:Hydroxymethylglutaryl-CoA synthase, putative:hypothetical protein:<-<-:333429..333572 144 tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 35 End: 142 .................................. M P K T I L P Y L G I K L L Q K H L I S A K S G L R C I F Q N K N S R W .. Protein_Len: 36 Strand: - Start: 31 End: 138 .............................. Y I G F V I K G Y K P I F S K C F C R I E A L D P K L H I K W F L F L M ...... tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt 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================================================ tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0338:SSA_0339|SSA_0338:SSA_0339:Hydroxymethylglutaryl-CoA synthase, putative:hypothetical protein:<-<-:333429..333572 144 tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_009009_SSA_0338_SSA_0339|Hydroxymethylglutaryl-CoA synthase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[333429,333572]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt tataagacctctttaaatccttttattctagtatattccgaaaactattttaccatacttaggaataaaactcttacaaaaacatctaatctcagctaaatcaggcttaagatgtattttccaaaataaaaacagcagatggtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAGACCUCUUUAAAUCCUUUUAUUCUAGUAUAUUCCGAAAACUAUUUUACCAUACUUAGGAAUAAAACUCUUACAAAAACAUCUAAUCUCAGCUAAAUCAGGCUUAAGAUGUAUUUUCCAAAAUAAAAACAGCAGAUGGUU .....(((((((........((((((((((((((.....((((....))))...)))))..)))))))))...........((((((......((((......))))..)))))).....................))).)))) (-18.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCAUCUGCUGUUUUUAUUUUGGAAAAUACAUCUUAAGCCUGAUUUAGCUGAGAUUAGAUGUUUUUGUAAGAGUUUUAUUCCUAAGUAUGGUAAAAUAGUUUUCGGAAUAUACUAGAAUAAAAGGAUUUAAAGAGGUCUUAUA .(((.(((..(.((((((((((((.(((.((((((..(((........)))......)))))).)))..........((((((.((.(((......))).))...))))))..)))))))))))).).....))))))...... (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 787 140 91 231 182 NC_009009:SSA_0338|5end_Hydroxymethylglutaryl-CoA_synthase,_putative_333338..333568_NEGATIVE 271 65 26 156 107 NC_009009:SSA_0094|5end_Cell_wall_metabolism,_LysM_type_protein,_putative_95345..95575_POSITIVE 249 65 34 61 31 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 240 123 83 192 154 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 230 108 71 134 105 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 226 139 91 51 11 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 221 57 11 137 94 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 214 114 90 143 119 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 213 114 76 73 34 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 212 120 83 54 13 NC_009009:SSA_2376|5end_ABC_transporter_with_duplicated_ATPase_domains,_putative_2378744..2378974_POSITIVE 210 116 89 197 159 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 207 140 91 108 45 NC_009009:SSA_2263|5end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2261176..2261406_NEGATIVE 205 119 75 133 91 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 205 39 5 122 95 NC_009009:SSA_0322|5end_Transcriptional_activator,_TipA_family,_putative_314717..314947_POSITIVE 204 137 91 68 26 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 200 140 110 26 2 NC_009009:SSA_1603|5end_hypothetical_protein_1610034..1610264_NEGATIVE 200 123 84 132 95 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 200 113 77 63 22 NC_009009:SSA_0634|5end_Anthranilate_phosphoribosyltransferase,_putative_623387..623617_POSITIVE 200 107 70 126 92 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 196 122 84 44 9 NC_009009:SSA_0046|5end_Adenylosuccinate_lyase,_putative_50894..51124_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 136 94 71 22 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 259 107 62 144 98 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 242 139 92 81 36 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 205 119 75 112 70 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 200 123 84 113 76 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 200 113 77 52 11 NC_009009:SSA_0633|3end_Anthranilate_synthase_component_II,_putative_623456..623606_POSITIVE 200 107 70 51 17 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 196 29 5 105 85 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 196 100 53 47 7 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 193 41 7 131 86 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 192 42 4 81 33 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 188 122 83 45 2 NC_009009:SSA_2036|3end_Conserved_hypothetical_cytosolic_protein_2040278..2040428_NEGATIVE 188 111 74 81 45 NC_009009:SSA_0856|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_844216..844366_POSITIVE 188 81 50 151 123 NC_009009:SSA_0206|3end_hypothetical_protein_204500..204650_POSITIVE 187 130 83 128 87 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 187 140 91 74 22 NC_009009:SSA_0525|3end_Microcompartment_protein,_putative_523842..523992_POSITIVE 185 123 83 139 92 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 185 107 84 130 104 NC_009009:SSA_1906|3end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900516..1900666_POSITIVE 185 106 71 121 88 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 184 118 83 85 55 NC_009009:SSA_1393|3end_hypothetical_protein_1408414..1408564_NEGATIVE