Origin IGS: tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt .........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 aaggaaacctcttttcgtttgatagcttattataccatccagaaaacactttcacaagaatttgaaactgctggctttcgaaagaccagaaaagcagtttggtatttaaactccattccacaaaaaaacacttctgccgttagactttactgcctaactttagaagtgctgtcttatatttcgtttttcta Mask Tandem Repeat Region ================================================ tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Find is-nt database================================================ Query_seq: SSA_0766:SSA_0767|SSA_0766:SSA_0767:hypothetical protein:Diacylglycerol kinase catalytic domain protein, putative:->->:747036..747226 191 tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0766:SSA_0767|SSA_0766:SSA_0767:hypothetical protein:Diacylglycerol kinase catalytic domain protein, putative:->->:747036..747226 191 tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0766:SSA_0767|SSA_0766:SSA_0767:hypothetical protein:Diacylglycerol kinase catalytic domain protein, putative:->->:747036..747226 191 tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 61 End: 159 ............................................................ M F F C G M E F K Y Q T A F L V F R K P A V S N S C E S V F W M V ................................ Protein_Len: 40 Strand: + Start: 71 End: 190 ...................................................................... M E W S L N T K L L F W S F E S Q Q F Q I L V K V F S G W Y N K L S N E K R F P . Protein_Len: 57 Strand: - Start: 3 End: 173 .. F F S I Y S L V E L T L C Y L R V A S T N K Q P I S N L Y W V A K R T K R F G A T E F E Q S L T K Q I T Y Y A I M .................. tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt 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: 86 Start: 134 End: 163 .....................................................................................................................................CTTGTGAAAGTGTTTTCTGGATGGTATAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -4.3 Tail_Score: -5.626 Start: 24 End: 63 Full_Region: CGAAATATAAGACAG CACTTCTAAAGTTAGGC AGTAAA GTCTAACGGCAGAAGTG TTTTTTTGTGGAATG .......................CACTTCTAAAGTTAGGCAGTAAAGTCTAACGGCAGAAGTG................................................................................................................................ TransTerm Strand: - Conf: 47 HP_score: -4.3 Tail_Score: -2.58134 Start: 24 End: 63 Full_Region: cattccacaaaaaaa cacttctgccgttagac tttact gcctaactttagaagtg ctgtcttatatttcg .......................cacttctgccgttagactttactgcctaactttagaagtg................................................................................................................................ TransTerm Strand: - Conf: 47 HP_score: -2.1 Tail_Score: -3.5882 Start: 34 End: 53 Full_Region: aaaaacacttctgcc gttagac tttact gcctaac tttagaagtgctgtc .................................gttagactttactgcctaac.......................................................................................................................................... Find igs database================================================ Query_seq: SSA_0766:SSA_0767|SSA_0766:SSA_0767:hypothetical protein:Diacylglycerol kinase catalytic domain protein, putative:->->:747036..747226 191 tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: NC_009009_SSA_0766_SSA_0767|hypothetical protein:Diacylglycerol kinase catalytic domain protein, putative|POSITIVE:POSITIVE|[747036,747226]|191 HSP 1 e-value: 8.0E-92 bit: 337.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgnnnnnnngtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt tagaaaaacgaaatataagacagcacttctaaagttaggcagtaaagtctaacggcagaagtgtttttttgtggaatggagtttaaataccaaactgcttttctggtctttcgaaagccagcagtttcaaattcttgtgaaagtgttttctggatggtataataagctatcaaacgaaaagaggtttcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAACGAAAUAUAAGACAGCACUUCUAAAGUUAGGCAGUAAAGUCUAACGGCAGAAGUGUUUUUUUGUGGAAUGGAGUUUAAAUACCAAACUGCUUUUCUGGUCUUUCGAAAGCCAGCAGUUUCAAAUUCUUGUGAAAGUGUUUUCUGGAUGGUAUAAUAAGCUAUCAAACGAAAAGAGGUUUCCUU ..((((.((.....((((((.(((((((((...(((((((......)))))))...))))))))).))))))((((.(.(((((.......))))).).))))..)).))))..(((((.(((.(((((........))))).)))((((..((((((.......))))))....))))...))))).... (-48.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAAACCUCUUUUCGUUUGAUAGCUUAUUAUACCAUCCAGAAAACACUUUCACAAGAAUUUGAAACUGCUGGCUUUCGAAAGACCAGAAAAGCAGUUUGGUAUUUAAACUCCAUUCCACAAAAAAACACUUCUGCCGUUAGACUUUACUGCCUAACUUUAGAAGUGCUGUCUUAUAUUUCGUUUUUCUA ..(((((.........((..((((((.....(((((.....((((....))))...........((((((((..((.((....))..))...)))))))))))))........................(((((((..(((((.(......).)))))..)))))))))))))..))........))))). (-40.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 65 25 171 123 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 328 135 91 191 137 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 320 136 97 54 25 NC_009009:SSA_2126|5end_hypothetical_protein_2130755..2130985_NEGATIVE 303 140 91 65 10 NC_009009:SSA_0569|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563613..563843_POSITIVE 299 137 95 64 14 NC_009009:SSA_0083|5end_hypothetical_protein_85437..85667_POSITIVE 298 159 112 190 140 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 295 155 117 58 21 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 295 158 111 156 113 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 290 140 98 231 191 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 290 62 23 61 16 NC_009009:SSA_0937|5end_Arsenate_reductase,_glutaredoxin_family,_putative_946183..946413_POSITIVE 286 122 90 52 18 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 284 138 95 212 170 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 277 138 93 207 156 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 276 140 96 62 12 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 276 124 81 48 9 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 274 129 95 44 2 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 272 147 101 60 9 NC_009009:SSA_0345|5end_hypothetical_protein_338803..339033_POSITIVE 267 138 94 83 35 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 266 147 101 203 147 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 264 152 113 44 10 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 136 97 57 28 NC_009009:SSA_2127|3end_hypothetical_protein_2130752..2130902_NEGATIVE 304 65 22 69 26 NC_009009:SSA_0766|3end_hypothetical_protein_746975..747125_POSITIVE 289 128 89 137 101 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 286 122 90 76 42 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 285 75 32 65 17 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 276 124 81 63 24 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 267 138 94 81 33 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 267 54 21 61 27 NC_009009:SSA_2391|3end_30S_ribosomal_protein_S14,_putative_114517..114667_POSITIVE 264 152 113 47 13 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 263 136 102 88 49 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 263 129 84 145 107 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 261 128 93 67 26 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 259 137 94 143 102 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 258 60 17 57 4 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 257 136 93 99 54 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 256 73 31 45 1 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 253 147 103 139 95 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 253 57 21 79 27 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 252 110 65 92 40 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 248 138 91 49 8 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE