Origin IGS: tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac .........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 gtgtcgctgtttttttgcgaacagcacaataaaaaattgatgcacttaaagagtcctttccgatagcaatctccacctgataccggaatttgtcttttccggatacaggtttacagaatgagagcaaaaacctaagagccattcgagttagtttgtctatcgttttttctcttgggttttggaatttttgtttggatgctttgcagtgcttccggattttgttgtaaactaaatgcgga Mask Tandem Repeat Region ================================================ tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Find is-nt database================================================ Query_seq: PG1859:PG1860|PG1859:PG1860:glycerate kinase family protein:hypothetical protein:<-<-:1958425..1958663 239 tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1859:PG1860|PG1859:PG1860:glycerate kinase family protein:hypothetical protein:<-<-:1958425..1958663 239 tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1859:PG1860|PG1859:PG1860:glycerate kinase family protein:hypothetical protein:<-<-:1958425..1958663 239 tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 136 End: 237 ....................................................................................................................................... M R K R Q I P V S G G D C Y R K G L F K C I N F L L C C S Q K N S D .. Protein_Len: 60 Strand: + Start: 23 End: 238 ...................... M R K H C K A S K Q K F Q N P R E K T I D K L T R M A L R F L L S F C K P V S G K D K F R Y Q V E I A I G K D S L S A S . Protein_Len: 45 Strand: - Start: 16 End: 150 ............... L L I R F C Q L A D L C F N W F G L S F V I S L S V R I A R L N K S E N Q L G T D P F S M ......................................................................................... tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac 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================================================ tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -2.6 Tail_Score: -3.55444 Start: 131 End: 164 Full_Region: cgatagcaatctcca cctgataccggaa tttgtctt ttccggatacagg tttacagaatgagag ..................................................................................................................................cctgataccggaatttgtcttttccggatacagg........................................................................... Find igs database================================================ Query_seq: PG1859:PG1860|PG1859:PG1860:glycerate kinase family protein:hypothetical protein:<-<-:1958425..1958663 239 tccgcatttagtttacaacaaaatccggaagcactgcaaagcatccaaacaaaaattccaaaacccaagagaaaaaacgatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgcaaaaaaacagcgacac Intra-Species Hit: Count: 1 Min: 79 Max: 223 Len: 145 Subject: NC_002950_PG1859_PG1860|glycerate kinase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[1958425,1958663]|239 HSP 1 e-value: 9.0E-77 bit: 287.0 Len: 145 Query Start:79 Query End:223 Subject Strand: POSITIVE Subject Start: 79 Subject End: 223 ..............................................................................gatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgc................ ..............................................................................gatagacaaactaactcgaatggctcttaggtttttgctctcattctgtaaacctgtatccggaaaagacaaattccggtatcaggtggagattgctatcggaaaggactctttaagtgcatcaattttttattgtgctgttcgc................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGACAAACUAACUCGAAUGGCUCUUAGGUUUUUGCUCUCAUUCUGUAAACCUGUAUCCGGAAAAGACAAAUUCCGGUAUCAGGUGGAGAUUGCUAUCGGAAAGGACUCUUUAAGUGCAUCAAUUUUUUAUUGUGCUGUUCGC (((((.(((.((.....(((((((............))...))))).....(((((...((((((........))))))...)))))..)).)))))))).....((((.........(((.((((.....))))))).)))).. (-34.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAACAGCACAAUAAAAAAUUGAUGCACUUAAAGAGUCCUUUCCGAUAGCAAUCUCCACCUGAUACCGGAAUUUGUCUUUUCCGGAUACAGGUUUACAGAAUGAGAGCAAAAACCUAAGAGCCAUUCGAGUUAGUUUGUCUAUC ((((((.(((((((.....)))).))).((..((..(..(((.......((..((((.(((((((.((((((........)))))))).))))).........))))))........)))..)..))..))...))))))..... (-31.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 870 60 11 229 180 NC_002950:PG1859|5end_glycerate_kinase_family_protein_1958334..1958564_NEGATIVE 371 120 75 74 32 NC_002950:PG1155|5end_ADP-heptose--LPS_heptosyltransferase,_putative_1235861..1236091_POSITIVE 338 89 41 178 122 NC_002950:PG1372|5end_hypothetical_protein_1454722..1454952_NEGATIVE 326 117 77 201 165 NC_002950:PG0867|5end_hypothetical_protein_930933..931163_NEGATIVE 320 97 52 229 180 NC_002950:PG0209|5end_formate/nitrite_transporter_243231..243461_POSITIVE 312 94 54 205 165 NC_002950:PG2042|5end_thioredoxin_family_protein_2141109..2141339_NEGATIVE 309 116 76 173 134 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 301 96 53 194 153 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 299 89 55 175 126 NC_002950:PG1483|5end_conjugative_transposon_protein_TraE_1559085..1559315_NEGATIVE 297 115 72 107 57 NC_002950:PG0162|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_185086..185316_NEGATIVE 294 120 76 207 148 NC_002950:PG0876|5end_tRNA_modification_GTPase_940806..941036_NEGATIVE 288 110 73 40 3 NC_002950:PG1790|5end_hypothetical_protein_1880954..1881184_NEGATIVE 286 117 75 56 15 NC_002950:PG0074|5end_peptide_chain_release_factor_1_89172..89402_NEGATIVE 284 97 53 214 171 NC_002950:PG1767|5end_lipoprotein,_putative_1853995..1854225_POSITIVE 281 90 53 75 32 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 280 119 75 220 173 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 280 56 11 190 152 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 279 96 52 193 153 NC_002950:PG1362|5end_hypothetical_protein_1443594..1443824_NEGATIVE 276 118 76 54 11 NC_002950:PG1088|5end_acetyltransferase,_GNAT_family_1155426..1155656_NEGATIVE 276 63 21 183 142 NC_002950:PG0700|5end_hypothetical_protein_756595..756825_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 120 75 61 12 NC_002950:PG0963|3end_hypothetical_protein_1024087..1024237_NEGATIVE 324 96 52 61 23 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 288 110 73 43 6 NC_002950:PG1791|3end_hypothetical_protein_1880951..1881101_NEGATIVE 281 97 53 108 66 NC_002950:PG1745|3end_phosphoribulokinase_family_protein_1829435..1829585_NEGATIVE 281 90 53 73 30 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 280 110 61 124 73 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 275 113 76 150 117 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 274 90 42 57 18 NC_002950:PG1961|3end_hypothetical_protein_2048886..2049036_NEGATIVE 274 70 21 149 99 NC_002950:PG1544|3end_hypothetical_protein_1623442..1623592_POSITIVE 271 103 61 50 3 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 268 108 61 81 25 NC_002950:PG1566|3end_glutamyl-tRNA_synthetase_1645884..1646034_NEGATIVE 267 102 62 62 29 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 266 57 12 82 32 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 266 123 86 36 2 NC_002950:PG0075|3end_phosphoribosylformylglycinamidine_cyclo-ligase,_putative_89197..89347_NEGATIVE 265 109 61 60 12 NC_002950:PG0302|3end_hypothetical_protein_338721..338871_POSITIVE 265 88 43 85 35 NC_002950:PG0218|3end_hypothetical_protein_254334..254484_POSITIVE 264 90 41 63 11 NC_002950:PG0659|3end_hypothetical_protein_708336..708486_NEGATIVE 263 91 54 57 17 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 263 57 17 151 113 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 263 104 76 117 83 NC_002950:PG0935|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_994297..994447_NEGATIVE