Origin IGS: tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatagataacttgttagatgatagatattctttggaagaatctttacattatttgtgctcttttccgataggcatatacagatgtgctttaggttttaacgaaccaccaataatctgtgttcaatgtttgcaatgcctccgcaaccttggtgtagatacatcttttttgcttctgtttgctcgcctttttagggcaaaaccttggcttttatggtattgtatagtagaaaatatacattccttgcagcgaatagtgcgtaaagaaagaatgtttttgtatctttgcaaaagttttcatttataatccgcaaaacgaaatgttgcgaaagaacaaaacgaagtgtttggttacgtaaaacgaaatgtactttttaaagctcccctcatacataaaaaaacgcctcaaaaatcttttattttgagacgtttttctatgataaatatttgtatatctcgcaaaaaaatactacctttgtatagtataaattgggggcttatactctca Mask Tandem Repeat Region ================================================ tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Find is-nt database================================================ Query_seq: PI1665:PI1666|PI1665:PI1666:thymidylate synthase:conserved hypothetical protein:->->:1578865..1579370 506 tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1665:PI1666|PI1665:PI1666:thymidylate synthase:conserved hypothetical protein:->->:1578865..1579370 506 tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1665:PI1666|PI1665:PI1666:thymidylate synthase:conserved hypothetical protein:->->:1578865..1579370 506 tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 8 End: 100 ....... M S P Q F I L Y K G S I F L R D I Q I F I I E K R L K I K D F ...................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 47 Strand: + Start: 64 End: 204 ............................................................... M Y H R K T S Q N K R F L R R F F M Y E G S F K K Y I S F Y V T K H F V L F F R N I S F C G L .............................................................................................................................................................................................................................................................................................................. Protein_Len: 40 Strand: + Start: 195 End: 314 .................................................................................................................................................................................................. M R I I N E N F C K D T K T F F L Y A L F A A R N V Y F L L Y N T I K A K V L P ................................................................................................................................................................................................ Protein_Len: 55 Strand: + Start: 218 End: 382 ......................................................................................................................................................................................................................... M Q R Y K N I L S L R T I R C K E C I F S T I Q Y H K S Q G F A L K R R A N R S K K D V S T P R L R R H C K H ............................................................................................................................ Protein_Len: 60 Strand: - Start: 205 End: 504 ............................................................................................................................................................................................................ A F L L L F S T D V G L N R L C Q L C Q V C I I P P E N F G L A C R Y I G I P F S C L Y H L S E E L S Y R D D L L N D M .. Protein_Len: 30 Strand: - Start: 134 End: 223 ..................................................................................................................................... F T C K T K R L W V S R K T R E C C K T K R I I F S F K Q M ........................................................................................................................................................................................................................................................................................... Protein_Len: 55 Strand: - Start: 1 End: 165 S L I L G W N I S Y L P L I K K R S I C I N I M S F R R L I F S K Q P T K K H I L P A K F L V N R K V Y G F M ..................................................................................................................................................................................................................................................................................................................................................... tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca 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================================================ tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -6.4 Tail_Score: -5.76633 Start: 80 End: 107 Full_Region: TTTATCATAGAAAAA CGTCTCAAAA TAAAAGAT TTTTGAGGCG TTTTTTTATGTATGA ...............................................................................CGTCTCAAAATAAAAGATTTTTGAGGCG............................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -4.2 Tail_Score: -5.00895 Start: 80 End: 107 Full_Region: tcatacataaaaaaa cgcctcaaaa atctttta ttttgagacg tttttctatgataaa ...............................................................................cgcctcaaaaatcttttattttgagacg............................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 74 HP_score: -3.1 Tail_Score: -5.3671 Start: 344 End: 357 Full_Region: tgcctccgcaacctt ggtgt agat acatc ttttttgcttctgtt .......................................................................................................................................................................................................................................................................................................................................................ggtgtagatacatc..................................................................................................................................................... Find igs database================================================ Query_seq: PI1665:PI1666|PI1665:PI1666:thymidylate synthase:conserved hypothetical protein:->->:1578865..1579370 506 tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Intra-Species Hit: Count: 1 Min: 1 Max: 506 Len: 506 Subject: pint_PI1665_PI1666|thymidylate synthase:conserved hypothetical protein|POSITIVE:POSITIVE|[1578865,1579370]|506 HSP 1 e-value: 0.0 bit: 920.0 Len: 506 Query Start:1 Query End:506 Subject Strand: POSITIVE Subject Start: 1 Subject End: 506 tgagagtataagcccccaatttatactatacaaaggtagtannnnnnngcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgnnnnnnnatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca tgagagtataagcccccaatttatactatacaaaggtagtatttttttgcgagatatacaaatatttatcatagaaaaacgtctcaaaataaaagatttttgaggcgtttttttatgtatgaggggagctttaaaaagtacatttcgttttacgtaaccaaacacttcgttttgttctttcgcaacatttcgttttgcggattataaatgaaaacttttgcaaagatacaaaaacattctttctttacgcactattcgctgcaaggaatgtatattttctactatacaataccataaaagccaaggttttgccctaaaaaggcgagcaaacagaagcaaaaaagatgtatctacaccaaggttgcggaggcattgcaaacattgaacacagattattggtggttcgttaaaacctaaagcacatctgtatatgcctatcggaaaagagcacaaataatgtaaagattcttccaaagaatatctatcatctaacaagttatctatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAGUAUAAGCCCCCAAUUUAUACUAUACAAAGGUAGUAUUUUUUUGCGAGAUAUACAAAUAUUUAUCAUAGAAAAACGUCUCAAAAUAAAAGAUUUUUGAGGCGUUUUUUUAUGUAUGAGGGGAGCUUUAAAAAGUACAUUUCGUUUUACGUAACCAAACACUUCGUUUUGUUCUUUCGCAACAUUUCGUUUUGCGGAUUAUAAAUGAAAACUUUUGCAAAGAUACAAAAACAUUCUUUCUUUACGCACUAUUCGCUGCAAGGAAUGUAUAUUUUCUACUAUACAAUACCAUAAAAGCCAAGGUUUUGCCCUAAAAAGGCGAGCAAACAGAAGCAAAAAAGAUGUAUCUACACCAAGGUUGCGGAGGCAUUGCAAACAUUGAACACAGAUUAUUGGUGGUUCGUUAAAACCUAAAGCACAUCUGUAUAUGCCUAUCGGAAAAGAGCACAAAUAAUGUAAAGAUUCUUCCAAAGAAUAUCUAUCAUCUAACAAGUUAUCUAUCA ....((((((((.......)))))))).......((((((((((((..(((((((.(((..........((((((((((((((((((((........))))))))))))))))))))..(((((....)))))....))).))))))).....((((((......(((((((......(((((((.........)))))))....)))))))...........(((((((.........(((((....((.....(((((...(((..((((((........))))))........(((((....)))))..))).....)))))))....))))).........))))))).......))))))(((((.(((....((((((...((((((.......((((......))))........))))))...(((((........)).)))....))))))...))).))))).))))))).))))).................... (-111.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAGAUAACUUGUUAGAUGAUAGAUAUUCUUUGGAAGAAUCUUUACAUUAUUUGUGCUCUUUUCCGAUAGGCAUAUACAGAUGUGCUUUAGGUUUUAACGAACCACCAAUAAUCUGUGUUCAAUGUUUGCAAUGCCUCCGCAACCUUGGUGUAGAUACAUCUUUUUUGCUUCUGUUUGCUCGCCUUUUUAGGGCAAAACCUUGGCUUUUAUGGUAUUGUAUAGUAGAAAAUAUACAUUCCUUGCAGCGAAUAGUGCGUAAAGAAAGAAUGUUUUUGUAUCUUUGCAAAAGUUUUCAUUUAUAAUCCGCAAAACGAAAUGUUGCGAAAGAACAAAACGAAGUGUUUGGUUACGUAAAACGAAAUGUACUUUUUAAAGCUCCCCUCAUACAUAAAAAAACGCCUCAAAAAUCUUUUAUUUUGAGACGUUUUUCUAUGAUAAAUAUUUGUAUAUCUCGCAAAAAAAUACUACCUUUGUAUAGUAUAAAUUGGGGGCUUAUACUCUCA .((.((...........((((.((((.(((((.....))))).))))))))....((((...((((....((((((((....))))))))...((((((.(((((((.((........(((((..((....)).......((((((.(((.((..(((...(((((..(((..(((((((((.(((.....(((......))).)))......((...((((((........))))))..))....))))))))).))).)))))..(((..((((((((....))))))))..))).......)))..))...)))...))))))...)))))........))..))))).)))))))))))).))))......((((((((......((((.(((((((.(((((((........))))))).))))))).)))).......(((((.......)))))...((((((........)))))).....))))))))...)).)). (-120.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 117 75 138 96 pint:PI0372|5end_conserved_hypothetical_protein;_possible_ATPase_342011..342241_POSITIVE 331 400 355 188 139 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 312 406 361 45 4 pint:PI1755|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1681930..1682160_POSITIVE 300 336 298 101 49 pint:PI0169|5end_hypothetical_protein_163645..163875_POSITIVE 300 377 331 64 2 pint:PI0152|5end_DNA_mismatch_endonuclease_vsr_145314..145544_POSITIVE 300 199 152 208 151 pint:PI0148|5end_mannose-1-phosphate_guanylyltransferase_141423..141653_POSITIVE 296 368 321 133 87 pint:PI1790|5end_hypothetical_protein_1722179..1722409_POSITIVE 295 399 351 160 112 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 291 51 11 201 157 pint:PI1328|5end_conserved_hypothetical_protein_1246197..1246427_POSITIVE 291 370 321 41 4 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 289 150 105 182 131 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 286 377 332 140 87 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 285 400 354 184 135 pint:PI0273|5end_hypothetical_protein_262956..263186_POSITIVE 285 400 354 84 35 pint:PI0274|5end_conserved_hypothetical_protein_262856..263086_POSITIVE 284 391 353 83 42 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 283 190 145 59 14 pint:PI0819|5end_hypothetical_protein_759414..759644_POSITIVE 282 188 141 81 35 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 281 327 285 120 82 pint:PI1948|5end_hypothetical_protein_1903084..1903314_POSITIVE 281 183 141 62 22 pint:PI1945|5end_ribonuclease_HII_1901932..1902162_POSITIVE 280 403 361 217 185 pint:PI0170|5end_hypothetical_protein_163305..163535_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 475 431 142 91 pint:PI1962|3end_conserved_hypothetical_protein_1920706..1920856_POSITIVE 312 406 361 45 4 pint:PI1754|3end_conserved_hypothetical_protein_1682010..1682160_POSITIVE 301 490 441 62 6 pint:PI0815|3end_hypothetical_protein_754677..754827_POSITIVE 300 336 298 75 23 pint:PI0167|3end_hypothetical_protein_163699..163849_POSITIVE 299 226 181 73 29 pint:PI2040|3end_conserved_hypothetical_protein;_possible_transporter_1994065..1994215_POSITIVE 289 150 105 147 96 pint:PI0705|3end_conserved_hypothetical_protein;_possible_lipoprotein_642271..642421_POSITIVE 285 400 354 91 42 pint:PI0272|3end_conserved_hypothetical_protein_262943..263093_POSITIVE 284 391 353 75 34 pint:PI0120|3end_glutamate_racemase_112697..112847_POSITIVE 282 188 141 121 75 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 280 410 361 91 44 pint:PI1069|3end_hypothetical_protein_988458..988608_POSITIVE 280 403 361 111 79 pint:PI0168|3end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_163279..163429_POSITIVE 279 377 333 61 15 pint:PI1267|3end_probable_integrase_1186475..1186625_POSITIVE 277 383 343 151 113 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 277 409 362 127 91 pint:PI0043|3end_thiamine_phosphate_pyrophosphorylase_43156..43306_POSITIVE 269 405 362 117 61 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 269 382 344 83 50 pint:PI0424|3end_methylated-DNA--[protein]-cysteine_S-methyltransferase_388976..389126_POSITIVE 265 200 165 124 82 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 263 329 285 137 89 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 260 394 351 68 25 pint:PI0673|3end_hypothetical_protein_612705..612855_POSITIVE 260 452 413 138 102 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE