Origin IGS: cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag .........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 ctctattcatcgttttgtggatacattgcaatgcttatacgaggcattccgccctctatcgtaattccattcttattgaattgaaaaagcattgcagtgctataaaatcttccacatttatcacttgggaaacaagacctatccttgctccattcttctatcaatatgcgaaaatacaaaaaaaaagccttatagtcgaaaaaaatcagtaattttgcacaaaattttgatttaagcaatggcagaaagaaaagtaagagtacgctttgcgcccagtcctactgggccg Mask Tandem Repeat Region ================================================ cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Find is-nt database================================================ Query_seq: PI0410:PI0411|PI0410:PI0411:glutamyl-tRNA synthetase (glutamate--tRNA ligase):conserved hypothetial protein; possible hydrolase:->->:377551..377839 289 cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0410:PI0411|PI0410:PI0411:glutamyl-tRNA synthetase (glutamate--tRNA ligase):conserved hypothetial protein; possible hydrolase:->->:377551..377839 289 cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0410:PI0411|PI0410:PI0411:glutamyl-tRNA synthetase (glutamate--tRNA ligase):conserved hypothetial protein; possible hydrolase:->->:377551..377839 289 cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 45 End: 284 ............................................ M P L L K S K F C A K L L I F F D Y K A F F L Y F R I L I E E W S K D R S C F P S D K C G R F Y S T A M L F Q F N K N G ..... Protein_Len: 60 Strand: - Start: 81 End: 281 ................................................................................ S K K Q I K A Y Q Y F F P A L I P R T E W T I F T S S K I A S C H K K L E I L I S N R Y L A S H R T Y A N C H I W L V M ........ Protein_Len: 51 Strand: - Start: 58 End: 210 ......................................................... I L I K H L I V S K K R S Y P K K K T N E C I S L L I S C P Y T K N G L H Y I H F I K Y C Q L A K E M ............................................................................... cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag 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================================================ cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.1 Tail_Score: -3.56092 Start: 143 End: 157 Full_Region: GATAGAAGAATGGAG CAAGG ATAGG TCTTG TTTCCCAAGTGATAA ..............................................................................................................................................CAAGGATAGGTCTTG.................................................................................................................................... Find igs database================================================ Query_seq: PI0410:PI0411|PI0410:PI0411:glutamyl-tRNA synthetase (glutamate--tRNA ligase):conserved hypothetial protein; possible hydrolase:->->:377551..377839 289 cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: pint_PI0410_PI0411|glutamyl-tRNA synthetase (glutamate--tRNA ligase):conserved hypothetial protein; possible hydrolase|POSITIVE:POSITIVE|[377551,377839]|289 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 289 Query Start:1 Query End:289 Subject Strand: POSITIVE Subject Start: 1 Subject End: 289 cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggcnnnnnnnnngtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag cggcccagtaggactgggcgcaaagcgtactcttacttttctttctgccattgcttaaatcaaaattttgtgcaaaattactgatttttttcgactataaggctttttttttgtattttcgcatattgatagaagaatggagcaaggataggtcttgtttcccaagtgataaatgtggaagattttatagcactgcaatgctttttcaattcaataagaatggaattacgatagagggcggaatgcctcgtataagcattgcaatgtatccacaaaacgatgaatagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGCCCAGUAGGACUGGGCGCAAAGCGUACUCUUACUUUUCUUUCUGCCAUUGCUUAAAUCAAAAUUUUGUGCAAAAUUACUGAUUUUUUUCGACUAUAAGGCUUUUUUUUUGUAUUUUCGCAUAUUGAUAGAAGAAUGGAGCAAGGAUAGGUCUUGUUUCCCAAGUGAUAAAUGUGGAAGAUUUUAUAGCACUGCAAUGCUUUUUCAAUUCAAUAAGAAUGGAAUUACGAUAGAGGGCGGAAUGCCUCGUAUAAGCAUUGCAAUGUAUCCACAAAACGAUGAAUAGAG ..((((((.....))))))......(((....(((((((((((.(((.((.(((..(((((((((......((........(((......)))........)).....))))).))))..)))...)).)))))))).(((((((((.....)))))))))..))))))....((((((..........(((.((((((((((.(((.((((.....)))).))).(((((.....(((.....)))))))).)))))))))).))).))))))..))).......... (-70.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUAUUCAUCGUUUUGUGGAUACAUUGCAAUGCUUAUACGAGGCAUUCCGCCCUCUAUCGUAAUUCCAUUCUUAUUGAAUUGAAAAAGCAUUGCAGUGCUAUAAAAUCUUCCACAUUUAUCACUUGGGAAACAAGACCUAUCCUUGCUCCAUUCUUCUAUCAAUAUGCGAAAAUACAAAAAAAAAGCCUUAUAGUCGAAAAAAAUCAGUAAUUUUGCACAAAAUUUUGAUUUAAGCAAUGGCAGAAAGAAAAGUAAGAGUACGCUUUGCGCCCAGUCCUACUGGGCCG ((((.......(((((((..((((((((((((((((.((((((((.....))).....))))).(((.((((.....)))).))).))))))))))))).))).......(((.((.........))))).))))))).....(((.((((((((((..(((((..(((((((.(((.........((......)).((......)).))).))))))).......)))))..))).))))).)).))).......))))........(.((((((.....))))))). (-70.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 262 221 40 3 pint:PI2018|5end_50S_ribosomal_protein_L34_1975757..1975987_POSITIVE 326 280 231 120 59 pint:PI0018|5end_hypothetical_protein_23022..23252_POSITIVE 321 50 1 63 5 pint:PI1513|5end_conserved_hypothetical_protein_1430152..1430382_POSITIVE 319 267 221 195 160 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 316 280 236 219 156 pint:PI0275|5end_hypothetical_protein_263138..263368_POSITIVE 300 266 221 231 185 pint:PI2143|5end_DNA_mismatch_repair_protein_2089123..2089353_POSITIVE 295 190 141 178 129 pint:PI0717|5end_conserved_hypothetical_protein_652558..652788_POSITIVE 291 271 233 55 15 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 289 29 1 116 82 pint:PI0123|5end_outer_membrane_protein,_ompH_family_113906..114136_POSITIVE 288 55 16 197 156 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 287 54 11 84 37 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 287 50 1 201 141 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 284 50 1 90 29 pint:PI0446|5end_DNA-directed_RNA_polymerase,_beta_subunit_413478..413708_POSITIVE 281 43 1 118 64 pint:PI2029|5end_DNA_topoisomerase_I_1982775..1983005_POSITIVE 279 270 223 177 124 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 279 49 1 72 9 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 278 240 192 59 13 pint:PI0787|5end_glycosyltransferase_724136..724366_POSITIVE 278 257 213 155 110 pint:PI0101|5end_lauroyl/myristoyl_acyltransferase_96729..96959_POSITIVE 276 190 144 71 20 pint:PI1734|5end_possible_carboxyl-terminal_protease-related_protein_1652409..1652639_POSITIVE 276 247 201 94 47 pint:PI1525|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1446758..1446988_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 36 2 25 1 pint:PI0825|3end_hypothetical_protein_764196..764346_POSITIVE 300 34 3 151 121 pint:PI0767|3end_possible_TonB-dependent_receptor_704025..704175_POSITIVE 295 190 141 145 96 pint:PI0716|3end_conserved_hypothetical_protein_652605..652755_POSITIVE 293 268 221 146 92 pint:PI1029|3end_seryl-tRNA_synthetase_947205..947355_POSITIVE 291 271 233 52 12 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 290 49 3 130 72 pint:PI0410|3end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_377490..377640_POSITIVE 288 50 1 147 89 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 288 50 1 56 15 pint:PI0783|3end_hypothetical_protein_723397..723547_POSITIVE 285 270 221 97 35 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 281 43 1 65 11 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 278 257 213 72 27 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 277 49 1 126 75 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 276 168 121 150 81 pint:PI1198|3end_acetyltransferase_1115219..1115369_POSITIVE 274 49 1 83 27 pint:PI0073|3end_dihydropteroate_synthase_71785..71935_POSITIVE 272 74 31 147 104 pint:PI0121|3end_outer_membrane_protein,_ompH_family_113208..113358_POSITIVE 268 48 1 98 31 pint:PI0300|3end_transposase_285761..285911_POSITIVE 266 280 236 100 45 pint:PI2113|3end_hypothetical_protein_2064278..2064428_POSITIVE 265 49 3 144 112 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 264 54 17 140 107 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 263 272 235 44 7 pint:PI2050|3end_hypothetical_protein_2007628..2007778_POSITIVE