Origin IGS: taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta .........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 taaagtaatgtttattgttggttctctaactttatcttcactttattgaagactacaaatgcaaacctactctattttctcgaaacgaacaatctttttcagggaaatatgcgaaaagcaagaactatttaacattttgacccaaattccacccaatagttatttatactaaatttgtaatagaaagcgaattttagagaataaaaagaaagcagaaagactttgtatcgataaattatcagtgattatcagaaaatatcaataacagcgtaaggtattaaaaacaatactttacgctgttctcttttccatcaatagcaattgatggaaatactttctattccacactttcgtccta Mask Tandem Repeat Region ================================================ taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Find is-nt database================================================ Query_seq: PI1021:PI1022|PI1021:PI1022:conserved hypothetical protein; possible methyltransferase:hypothetical protein:->->:939695..940052 358 taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1021:PI1022|PI1021:PI1022:conserved hypothetical protein; possible methyltransferase:hypothetical protein:->->:939695..940052 358 taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1021:PI1022|PI1021:PI1022:conserved hypothetical protein; possible methyltransferase:hypothetical protein:->->:939695..940052 358 taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 117 End: 227 .................................................................................................................... M I I Y R Y K V F L L S F Y S L K F A F Y Y K F S I N N Y W V E F G S K C ................................................................................................................................... Protein_Len: 32 Strand: - Start: 230 End: 325 ..................................................................................................................................................................................................................................... I T R A K R M N G Q F L N N T E L F Y L L N A N T T K L L T F M ................................. Protein_Len: 31 Strand: - Start: 222 End: 314 ............................................................................................................................................................................................................................. F T L Y N K S K A Y K G S F S Q E N R S F L T P K C K Y D E M ............................................ Protein_Len: 37 Strand: - Start: 190 End: 300 ............................................................................................................................................................................................. Y L Y S N P P I Q T L I N F L E Q K E C I E R F F I T R K S F I S Y T Q M .......................................................... Protein_Len: 30 Strand: - Start: 97 End: 186 ................................................................................................ Q Y K R I I V S L K D I C L R E A K K K N E L I R K R N C M ............................................................................................................................................................................ taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta 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================================================ taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -12.1 Tail_Score: -3.11182 Start: 28 End: 53 Full_Region: tttacgctgttctct tttccatcaat agca attgatggaaa tactttctattccac ...........................tttccatcaatagcaattgatggaaa................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 89 HP_score: -9.1 Tail_Score: -4.19817 Start: 55 End: 98 Full_Region: ttatcagaaaatatc aataacagcgtaaggtatt aaaaac aatactttacgctgttctc ttttccatcaatagc ......................................................aataacagcgtaaggtattaaaaacaatactttacgctgttctc.................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -11.9 Tail_Score: -3.90315 Start: 60 End: 93 Full_Region: TGATGGAAAAGAGAA CAGCGTAAAGTATTG TTTT TAATACCTTACGCTG TTATTGATATTTTCT ...........................................................CAGCGTAAAGTATTGTTTTTAATACCTTACGCTG......................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.4 Tail_Score: -3.97622 Start: 60 End: 93 Full_Region: agaaaatatcaataa cagcgtaaggtatt aaaaac aatactttacgctg ttctcttttccatca ...........................................................cagcgtaaggtattaaaaacaatactttacgctg......................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1021:PI1022|PI1021:PI1022:conserved hypothetical protein; possible methyltransferase:hypothetical protein:->->:939695..940052 358 taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Intra-Species Hit: Count: 1 Min: 1 Max: 358 Len: 358 Subject: pint_PI1021_PI1022|conserved hypothetical protein; possible methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[939695,940052]|358 HSP 1 e-value: 0.0 bit: 710.0 Len: 358 Query Start:1 Query End:358 Subject Strand: POSITIVE Subject Start: 1 Subject End: 358 taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta taggacgaaagtgtggaatagaaagtatttccatcaattgctattgatggaaaagagaacagcgtaaagtattgtttttaataccttacgctgttattgatattttctgataatcactgataatttatcgatacaaagtctttctgctttctttttattctctaaaattcgctttctattacaaatttagtataaataactattgggtggaatttgggtcaaaatgttaaatagttcttgcttttcgcatatttccctgaaaaagattgttcgtttcgagaaaatagagtaggtttgcatttgtagtcttcaataaagtgaagataaagttagagaaccaacaataaacattacttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGACGAAAGUGUGGAAUAGAAAGUAUUUCCAUCAAUUGCUAUUGAUGGAAAAGAGAACAGCGUAAAGUAUUGUUUUUAAUACCUUACGCUGUUAUUGAUAUUUUCUGAUAAUCACUGAUAAUUUAUCGAUACAAAGUCUUUCUGCUUUCUUUUUAUUCUCUAAAAUUCGCUUUCUAUUACAAAUUUAGUAUAAAUAACUAUUGGGUGGAAUUUGGGUCAAAAUGUUAAAUAGUUCUUGCUUUUCGCAUAUUUCCCUGAAAAAGAUUGUUCGUUUCGAGAAAAUAGAGUAGGUUUGCAUUUGUAGUCUUCAAUAAAGUGAAGAUAAAGUUAGAGAACCAACAAUAAACAUUACUUUA ....((....)).(((..((((((((((((((((((((....)))))))))......((((((((((.((((((....)))))).))))))))))...)))))))))))....((.(((((..........((((((((...((((((((.(((....((((.(((....((..(((.((((.....((((.......))))....))))..((..((..((.((((.(((.(((....)))))).)))).))..))..))..)))..))...))).))))))).))))))))...)).))))))(((((((......)))))))...))))).)).))).................. (-84.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUAAUGUUUAUUGUUGGUUCUCUAACUUUAUCUUCACUUUAUUGAAGACUACAAAUGCAAACCUACUCUAUUUUCUCGAAACGAACAAUCUUUUUCAGGGAAAUAUGCGAAAAGCAAGAACUAUUUAACAUUUUGACCCAAAUUCCACCCAAUAGUUAUUUAUACUAAAUUUGUAAUAGAAAGCGAAUUUUAGAGAAUAAAAAGAAAGCAGAAAGACUUUGUAUCGAUAAAUUAUCAGUGAUUAUCAGAAAAUAUCAAUAACAGCGUAAGGUAUUAAAAACAAUACUUUACGCUGUUCUCUUUUCCAUCAAUAGCAAUUGAUGGAAAUACUUUCUAUUCCACACUUUCGUCCUA ......((((((......(((((((....((((.((((((......)))))).......((((.........(((((((..((((.((....))..))))..))))))))))).))))..)))))))...))))))..(((...............((((.......))))....((.(((((((((........(((((.......((..(((((.....)))))...(((((.(((....))))))))........))....(((((((((((((((......))))))))))))))))))))(((((((((((....)))))))))))..))))))))).)).......)))... (-75.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 280 232 155 102 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 311 279 233 75 24 pint:PI0424|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_388429..388659_POSITIVE 285 250 205 91 48 pint:PI1353|5end_conserved_hypothetical_protein_1269710..1269940_POSITIVE 274 69 27 40 7 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 270 49 2 206 161 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 269 79 31 159 120 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 266 248 204 213 161 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 265 57 12 55 17 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 261 300 256 84 29 pint:PI1565|5end_conserved_hypothetical_protein;_possible_surface_antigen_1485460..1485690_POSITIVE 260 248 205 178 134 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 260 248 205 63 19 pint:PI1649|5end_hypothetical_protein_1563080..1563310_POSITIVE 259 326 288 200 158 pint:PI0156|5end_conserved_hypothetical_protein_148716..148946_POSITIVE 256 109 61 172 128 pint:PI0999|5end_hypothetical_protein_922376..922606_POSITIVE 254 75 31 51 9 pint:PI1420|5end_probable_membrane_protein_1340123..1340353_POSITIVE 253 250 206 85 41 pint:PI0241|5end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_239627..239857_POSITIVE 252 289 245 185 146 pint:PI1150|5end_30S_ribosomal_protein_S6_1075683..1075913_POSITIVE 250 50 2 182 134 pint:PI0587|5end_conserved_hypothetical_protein_534416..534646_POSITIVE 249 257 215 136 95 pint:PI1241|5end_probable_phosphoesterase_1166365..1166595_POSITIVE 245 277 240 56 23 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 242 74 40 55 24 pint:PI2169|5end_hypothetical_protein_2111706..2111936_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 280 232 142 89 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 285 250 205 88 45 pint:PI1352|3end_conserved_hypothetical_protein_1269787..1269937_POSITIVE 270 49 2 93 48 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 266 69 29 131 74 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 265 57 12 119 81 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 260 79 31 40 3 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE 259 326 288 91 49 pint:PI0155|3end_conserved_hypothetical_protein_148687..148837_POSITIVE 256 89 41 128 83 pint:PI1565|3end_conserved_hypothetical_protein;_possible_surface_antigen_1487357..1487507_POSITIVE 251 280 235 138 97 pint:PI0378|3end_conserved_hypothetical_protein;_possible_helicase_349539..349689_POSITIVE 250 50 2 50 2 pint:PI0586|3end_hypothetical_protein_534364..534514_POSITIVE 244 53 28 63 38 pint:PI1021|3end_conserved_hypothetical_protein;_possible_methyltransferase_939634..939784_POSITIVE 241 259 214 91 42 pint:PI0343|3end_hypothetical_protein_317920..318070_POSITIVE 240 330 288 53 7 pint:PI0875|3end_conserved_hypothetical_protein_811437..811587_POSITIVE 238 279 234 44 4 pint:PI0858|3end_carbamyl_phosphate_synthase,_large_subunit_793394..793544_POSITIVE 238 99 56 74 25 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 238 250 203 119 57 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 229 63 26 89 51 pint:PI1883|3end_conserved_hypothetical_protein;_possible_surface_protein_1826174..1826324_POSITIVE 229 309 265 115 73 pint:PI0547|3end_fructose-bisphosphate_aldolase_499466..499616_POSITIVE 222 68 31 48 3 pint:PI1082|3end_polypeptide_deformylase_1001922..1002072_POSITIVE 219 47 3 52 12 pint:PI0607|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_555548..555698_POSITIVE