Origin IGS: tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca .........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 tgcaggaaccggatggatccatatattcagcagactcggatcctttgctccgatatcaccctgtccgcttgataccggatccgacaaaaaataaagagggcagacttcatccggcccaatccatcgagtaaatacctgcctacagaaaataaaaagatttgcccacttccatttggcaatccgcactccgtttcaaggggttttctgccgtgatattactacctttgccaaactgaaaaatatctgaatagaaggacatagatactatcattgaaaaa Mask Tandem Repeat Region ================================================ tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Find is-nt database================================================ Query_seq: PG0962:PG0963|PG0962:PG0963:prolyl-tRNA synthetase:hypothetical protein:<-<-:1023899..1024176 278 tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0962:PG0963|PG0962:PG0963:prolyl-tRNA synthetase:hypothetical protein:<-<-:1023899..1024176 278 tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0962:PG0963|PG0962:PG0963:prolyl-tRNA synthetase:hypothetical protein:<-<-:1023899..1024176 278 tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 8 End: 136 ....... M I V S M S F Y S D I F Q F G K G S N I T A E N P L K R S A D C Q M E V G K S F Y F L .............................................................................................................................................. Protein_Len: 50 Strand: + Start: 100 End: 249 ................................................................................................... M P N G S G Q I F L F S V G R Y L L D G L G R M K S A L F I F C R I R Y Q A D R V I S E Q R I R V C ............................. Protein_Len: 60 Strand: + Start: 93 End: 278 ............................................................................................ M R I A K W K W A N L F I F C R Q V F T R W I G P D E V C P L Y F L S D P V S S G Q G D I G A K D P S L L N I W I H P V Protein_Len: 36 Strand: - Start: 151 End: 258 ...................................................................................................................................................... E I S Q A P H L R G E K N K T P D P I L R V P H Y R L L P D S D A S Y M .................... Protein_Len: 44 Strand: - Start: 69 End: 200 .................................................................... P L F G R S V S H P N G F P L P C I K K N E T P L Y K S S P N P R I F D A R K I K Q R M .............................................................................. Protein_Len: 42 Strand: - Start: 35 End: 160 .................................. I N K L K A F T T I D R C F V G Q F P T R I A L H F H A F R K I K Q L C T N V R H M ...................................................................................................................... tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca 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================================================ tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0962:PG0963|PG0962:PG0963:prolyl-tRNA synthetase:hypothetical protein:<-<-:1023899..1024176 278 tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Intra-Species Hit: Count: 1 Min: 1 Max: 278 Len: 278 Subject: NC_002950_PG0962_PG0963|prolyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1023899,1024176]|278 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 278 Query Start:1 Query End:278 Subject Strand: POSITIVE Subject Start: 1 Subject End: 278 tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca tttttcaatgatagtatctatgtccttctattcagatatttttcagtttggcaaaggtagtaatatcacggcagaaaaccccttgaaacggagtgcggattgccaaatggaagtgggcaaatctttttattttctgtaggcaggtatttactcgatggattgggccggatgaagtctgccctctttattttttgtcggatccggtatcaagcggacagggtgatatcggagcaaaggatccgagtctgctgaatatatggatccatccggttcctgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCAAUGAUAGUAUCUAUGUCCUUCUAUUCAGAUAUUUUUCAGUUUGGCAAAGGUAGUAAUAUCACGGCAGAAAACCCCUUGAAACGGAGUGCGGAUUGCCAAAUGGAAGUGGGCAAAUCUUUUUAUUUUCUGUAGGCAGGUAUUUACUCGAUGGAUUGGGCCGGAUGAAGUCUGCCCUCUUUAUUUUUUGUCGGAUCCGGUAUCAAGCGGACAGGGUGAUAUCGGAGCAAAGGAUCCGAGUCUGCUGAAUAUAUGGAUCCAUCCGGUUCCUGCA .(((((..(((.(((((((..((......))..)))))))..))).....((...((((....))))...)).))))).(((((((.((.(((((.(..(((((....(((((((((........)))))))))....)))))...).)))))...(((((.(((.((((((((........))))))))...))).))))).)).))))).)).(((((....((((((.....(((((((..((....)).....))))))).))))))))))).. (-74.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGGAACCGGAUGGAUCCAUAUAUUCAGCAGACUCGGAUCCUUUGCUCCGAUAUCACCCUGUCCGCUUGAUACCGGAUCCGACAAAAAAUAAAGAGGGCAGACUUCAUCCGGCCCAAUCCAUCGAGUAAAUACCUGCCUACAGAAAAUAAAAAGAUUUGCCCACUUCCAUUUGGCAAUCCGCACUCCGUUUCAAGGGGUUUUCUGCCGUGAUAUUACUACCUUUGCCAAACUGAAAAAUAUCUGAAUAGAAGGACAUAGAUACUAUCAUUGAAAAA .(((((..(((((.((((((...((((.(((.((((((((........))))).........))).))).))))..)))))).............((((.....)))).))))).....((....)).......)))))...((((((.......(..(((((...........)))))..)..(((((.......)))))))))))..((((((.((((((((((........((......))......)))))...))).)).))))))....... (-64.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1000 120 71 211 162 NC_002950:PG0962|5end_prolyl-tRNA_synthetase_1023808..1024038_NEGATIVE 492 250 202 228 157 NC_002950:PG1156|5end_S4_domain_protein_1236735..1236965_POSITIVE 417 250 203 205 150 NC_002950:PG1296|5end_hypothetical_protein_1374794..1375024_POSITIVE 391 239 192 81 34 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 385 244 204 80 33 NC_002950:PG1044|5end_iron_dependent_repressor,_putative_1113818..1114048_NEGATIVE 383 180 131 229 174 NC_002950:PG1348|5end_conserved_hypothetical_protein_TIGR00147_1428608..1428838_POSITIVE 381 249 202 224 173 NC_002950:PG1876|5end_hypothetical_protein_1971460..1971690_NEGATIVE 376 250 201 83 27 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 368 207 161 179 128 NC_002950:PG0705|5end_glutamate_racemase_759529..759759_POSITIVE 365 270 223 98 45 NC_002950:PG0604|5end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_660262..660492_POSITIVE 357 239 193 82 43 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 357 249 203 107 52 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 356 219 177 230 186 NC_002950:PG0409|5end_hypothetical_protein_441449..441679_POSITIVE 356 247 202 228 190 NC_002950:PG0155|5end_riboflavin_biosynthesis_protein_RibD_178853..179083_NEGATIVE 354 196 151 120 73 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 353 139 104 84 50 NC_002950:PG0816|5end_hypothetical_protein_876859..877089_NEGATIVE 353 237 194 77 36 NC_002950:PG0285|5end_hypothetical_protein_318459..318689_POSITIVE 348 228 188 159 119 NC_002950:PG1638|5end_thioredoxin_family_protein_1719650..1719880_NEGATIVE 348 250 202 198 129 NC_002950:PG0647|5end_iron_compound_ABC_transporter,_permease_protein_700113..700343_NEGATIVE 347 220 176 222 172 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 247 201 151 102 NC_002950:PG1402|3end_AP_endonuclease_domain_protein_1485031..1485181_NEGATIVE 368 207 161 117 66 NC_002950:PG0704|3end_phosphoglycerate_mutase_family_protein_759547..759697_POSITIVE 367 251 211 103 65 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 365 270 223 101 48 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 359 171 136 140 100 NC_002950:PG1022|3end_hypothetical_protein_1085098..1085248_POSITIVE 357 249 203 107 52 NC_002950:PG0927|3end_conserved_hypothetical_protein_TIGR00150_984634..984784_NEGATIVE 356 250 201 126 72 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 352 249 201 78 28 NC_002950:PG2070|3end_hypothetical_protein_2166547..2166697_POSITIVE 351 196 151 102 54 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 350 219 174 83 39 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 349 199 151 95 37 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 348 220 173 88 42 NC_002950:PG0951|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010828..1010978_POSITIVE 347 229 181 73 18 NC_002950:PG0647|3end_iron_compound_ABC_transporter,_permease_protein_699079..699229_NEGATIVE 336 233 197 76 42 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 335 249 209 63 27 NC_002950:PG1636|3end_FtsK/SpoIIIE_family_protein_1715875..1716025_NEGATIVE 333 183 155 148 115 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 333 199 151 69 2 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 331 240 194 81 15 NC_002950:PG1602|3end_hypothetical_protein_1681764..1681914_NEGATIVE 330 198 151 128 77 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 329 250 202 72 28 NC_002950:PG2123|3end_hypothetical_protein_2230243..2230393_POSITIVE