Multiple sequence alignment - TraesCS5D01G183600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G183600 chr5D 100.000 1721 0 0 400 2120 285252671 285250951 0.000000e+00 3179.0
1 TraesCS5D01G183600 chr5D 100.000 200 0 0 1 200 285253070 285252871 9.240000e-99 370.0
2 TraesCS5D01G183600 chr5B 95.502 1645 70 4 478 2120 322864037 322862395 0.000000e+00 2625.0
3 TraesCS5D01G183600 chr5B 96.500 200 7 0 1 200 322864289 322864090 4.360000e-87 331.0
4 TraesCS5D01G183600 chr5A 94.939 1640 73 10 488 2118 377124755 377123117 0.000000e+00 2560.0
5 TraesCS5D01G183600 chr5A 97.000 200 6 0 1 200 377125013 377124814 9.370000e-89 337.0
6 TraesCS5D01G183600 chr7D 91.549 71 5 1 400 470 550891997 550891928 1.730000e-16 97.1
7 TraesCS5D01G183600 chr1D 96.078 51 2 0 1054 1104 453288109 453288159 1.350000e-12 84.2
8 TraesCS5D01G183600 chr1D 94.340 53 2 1 1053 1104 453266325 453266377 1.740000e-11 80.5
9 TraesCS5D01G183600 chr1D 93.750 48 3 0 1054 1101 452898583 452898630 2.920000e-09 73.1
10 TraesCS5D01G183600 chr1A 96.078 51 2 0 1054 1104 547959127 547959177 1.350000e-12 84.2
11 TraesCS5D01G183600 chr1A 96.078 51 2 0 1054 1104 547978064 547978114 1.350000e-12 84.2
12 TraesCS5D01G183600 chr1B 94.340 53 2 1 1053 1104 623737594 623737646 1.740000e-11 80.5
13 TraesCS5D01G183600 chr3A 85.507 69 9 1 1053 1120 34580240 34580172 1.050000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G183600 chr5D 285250951 285253070 2119 True 1774.5 3179 100.0000 1 2120 2 chr5D.!!$R1 2119
1 TraesCS5D01G183600 chr5B 322862395 322864289 1894 True 1478.0 2625 96.0010 1 2120 2 chr5B.!!$R1 2119
2 TraesCS5D01G183600 chr5A 377123117 377125013 1896 True 1448.5 2560 95.9695 1 2118 2 chr5A.!!$R1 2117

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
702 703 0.933097 CGTGCAGTGCAGATGATACC 59.067 55.0 20.42 2.75 40.08 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1940 0.308993 GGCTCGCATTTCACTATGGC 59.691 55.0 0.0 0.0 0.0 4.4 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 4.546829 TTGTGATACCCCTGTACAAGTC 57.453 45.455 0.00 0.00 0.00 3.01
425 426 4.715534 TTACCACTCAAATGGAAGGTCA 57.284 40.909 0.00 0.00 43.02 4.02
426 427 3.146104 ACCACTCAAATGGAAGGTCAG 57.854 47.619 0.00 0.00 43.02 3.51
427 428 2.711009 ACCACTCAAATGGAAGGTCAGA 59.289 45.455 0.00 0.00 43.02 3.27
428 429 3.244700 ACCACTCAAATGGAAGGTCAGAG 60.245 47.826 0.00 0.00 43.02 3.35
429 430 3.008375 CCACTCAAATGGAAGGTCAGAGA 59.992 47.826 0.00 0.00 43.02 3.10
430 431 4.505566 CCACTCAAATGGAAGGTCAGAGAA 60.506 45.833 0.00 0.00 43.02 2.87
431 432 5.251764 CACTCAAATGGAAGGTCAGAGAAT 58.748 41.667 0.00 0.00 0.00 2.40
432 433 5.709164 CACTCAAATGGAAGGTCAGAGAATT 59.291 40.000 0.00 0.00 0.00 2.17
433 434 6.881065 CACTCAAATGGAAGGTCAGAGAATTA 59.119 38.462 0.00 0.00 0.00 1.40
434 435 6.881602 ACTCAAATGGAAGGTCAGAGAATTAC 59.118 38.462 0.00 0.00 0.00 1.89
435 436 6.778821 TCAAATGGAAGGTCAGAGAATTACA 58.221 36.000 0.00 0.00 0.00 2.41
436 437 6.881065 TCAAATGGAAGGTCAGAGAATTACAG 59.119 38.462 0.00 0.00 0.00 2.74
437 438 4.207891 TGGAAGGTCAGAGAATTACAGC 57.792 45.455 0.00 0.00 0.00 4.40
438 439 3.582647 TGGAAGGTCAGAGAATTACAGCA 59.417 43.478 0.00 0.00 0.00 4.41
439 440 4.187694 GGAAGGTCAGAGAATTACAGCAG 58.812 47.826 0.00 0.00 0.00 4.24
440 441 4.081420 GGAAGGTCAGAGAATTACAGCAGA 60.081 45.833 0.00 0.00 0.00 4.26
441 442 4.734398 AGGTCAGAGAATTACAGCAGAG 57.266 45.455 0.00 0.00 0.00 3.35
442 443 3.450457 AGGTCAGAGAATTACAGCAGAGG 59.550 47.826 0.00 0.00 0.00 3.69
443 444 3.196685 GGTCAGAGAATTACAGCAGAGGT 59.803 47.826 0.00 0.00 0.00 3.85
444 445 4.323104 GGTCAGAGAATTACAGCAGAGGTT 60.323 45.833 0.00 0.00 0.00 3.50
445 446 4.867608 GTCAGAGAATTACAGCAGAGGTTC 59.132 45.833 0.00 0.00 0.00 3.62
446 447 4.774726 TCAGAGAATTACAGCAGAGGTTCT 59.225 41.667 0.00 0.00 0.00 3.01
447 448 4.869297 CAGAGAATTACAGCAGAGGTTCTG 59.131 45.833 1.75 1.75 46.90 3.02
448 449 4.081198 AGAGAATTACAGCAGAGGTTCTGG 60.081 45.833 8.06 0.00 44.43 3.86
457 458 4.686839 GCAGAGGTTCTGGTACAAATTC 57.313 45.455 8.06 0.00 44.43 2.17
458 459 4.072131 GCAGAGGTTCTGGTACAAATTCA 58.928 43.478 8.06 0.00 44.43 2.57
459 460 4.154918 GCAGAGGTTCTGGTACAAATTCAG 59.845 45.833 8.06 0.00 44.43 3.02
460 461 4.154918 CAGAGGTTCTGGTACAAATTCAGC 59.845 45.833 0.00 0.00 40.71 4.26
461 462 4.042187 AGAGGTTCTGGTACAAATTCAGCT 59.958 41.667 0.00 0.00 38.70 4.24
462 463 5.248477 AGAGGTTCTGGTACAAATTCAGCTA 59.752 40.000 0.00 0.00 38.70 3.32
463 464 5.491982 AGGTTCTGGTACAAATTCAGCTAG 58.508 41.667 0.00 0.00 38.70 3.42
464 465 5.248477 AGGTTCTGGTACAAATTCAGCTAGA 59.752 40.000 0.00 0.00 38.70 2.43
465 466 5.938125 GGTTCTGGTACAAATTCAGCTAGAA 59.062 40.000 0.00 0.00 38.70 2.10
466 467 6.092807 GGTTCTGGTACAAATTCAGCTAGAAG 59.907 42.308 0.00 0.00 37.56 2.85
467 468 5.734720 TCTGGTACAAATTCAGCTAGAAGG 58.265 41.667 0.00 0.00 37.56 3.46
468 469 4.843728 TGGTACAAATTCAGCTAGAAGGG 58.156 43.478 0.00 0.00 35.48 3.95
469 470 4.534500 TGGTACAAATTCAGCTAGAAGGGA 59.466 41.667 0.00 0.00 35.48 4.20
470 471 5.013704 TGGTACAAATTCAGCTAGAAGGGAA 59.986 40.000 0.00 0.00 35.48 3.97
471 472 6.122964 GGTACAAATTCAGCTAGAAGGGAAT 58.877 40.000 0.00 0.00 40.15 3.01
472 473 6.603599 GGTACAAATTCAGCTAGAAGGGAATT 59.396 38.462 0.00 2.49 40.59 2.17
473 474 6.765915 ACAAATTCAGCTAGAAGGGAATTC 57.234 37.500 7.63 0.00 38.60 2.17
490 491 6.715264 AGGGAATTCTGGTACTTAGTTTTGTG 59.285 38.462 5.23 0.00 0.00 3.33
495 496 6.243216 TCTGGTACTTAGTTTTGTGAACCT 57.757 37.500 0.00 0.00 0.00 3.50
518 519 1.490490 TGGTGGACAGATAGGAATGGC 59.510 52.381 0.00 0.00 0.00 4.40
522 523 2.846206 TGGACAGATAGGAATGGCTTGT 59.154 45.455 0.00 0.00 0.00 3.16
538 539 2.423538 GCTTGTGCCGGTGATATCTTTT 59.576 45.455 1.90 0.00 0.00 2.27
546 547 4.024809 GCCGGTGATATCTTTTAGCTGTTC 60.025 45.833 1.90 0.00 0.00 3.18
666 667 7.604545 GGAGCTTAGTCATCCTTATCATAAACC 59.395 40.741 0.00 0.00 0.00 3.27
688 689 6.119536 ACCTCTTTTATTTATCCATCGTGCA 58.880 36.000 0.00 0.00 0.00 4.57
702 703 0.933097 CGTGCAGTGCAGATGATACC 59.067 55.000 20.42 2.75 40.08 2.73
709 710 1.942657 GTGCAGATGATACCGCAATGT 59.057 47.619 0.00 0.00 35.87 2.71
849 850 9.072294 GTTAGTTTATGGAAATATGTGCACAAC 57.928 33.333 25.72 12.54 0.00 3.32
854 855 4.085009 TGGAAATATGTGCACAACCATGA 58.915 39.130 25.72 5.53 0.00 3.07
897 898 1.510480 GACACAGCCCACACAGAAGC 61.510 60.000 0.00 0.00 0.00 3.86
943 945 3.885724 AACTCCAAAAACCCAACACAG 57.114 42.857 0.00 0.00 0.00 3.66
1107 1109 0.100682 GCGTCGTGATGCTCCTAAGA 59.899 55.000 6.81 0.00 40.09 2.10
1116 1118 3.329814 TGATGCTCCTAAGATGGCATGAT 59.670 43.478 3.81 0.00 44.06 2.45
1336 1338 2.956333 ACCCTTTTGTCCCTTTTCTTCG 59.044 45.455 0.00 0.00 0.00 3.79
1623 1632 6.701340 AGTGTGATATCTCAGCAGTTTACAA 58.299 36.000 7.71 0.00 30.18 2.41
1686 1695 2.356673 GGGGTTTTCGACGCGACT 60.357 61.111 15.93 0.00 41.82 4.18
1759 1768 2.916052 AAGAGACGCGTCCGAGCAA 61.916 57.895 34.08 0.00 38.29 3.91
1902 1912 1.594331 AAACAGTGCCTTCCTCGTTC 58.406 50.000 0.00 0.00 0.00 3.95
1930 1940 6.461110 AATAAAGCCTGATGGTGAAATGAG 57.539 37.500 0.00 0.00 35.27 2.90
2018 2028 2.528564 TGGCTCTTCTTTTGGGGATTG 58.471 47.619 0.00 0.00 0.00 2.67
2050 2060 7.912056 TCTAGATCTTTCTTCACATGTTTGG 57.088 36.000 0.00 0.00 33.17 3.28
2053 2063 4.305989 TCTTTCTTCACATGTTTGGTGC 57.694 40.909 0.00 0.00 36.22 5.01
2071 2082 3.520569 GTGCTGGTTTTGCTTTTCTTGA 58.479 40.909 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.865706 ATCACAATAACTTCCATAGTCAACC 57.134 36.000 0.00 0.00 35.54 3.77
76 77 2.749621 GGTAGGAAAGTCAGCACCAATG 59.250 50.000 0.00 0.00 0.00 2.82
399 400 8.723365 TGACCTTCCATTTGAGTGGTAATATAT 58.277 33.333 0.00 0.00 40.27 0.86
400 401 8.096621 TGACCTTCCATTTGAGTGGTAATATA 57.903 34.615 0.00 0.00 40.27 0.86
401 402 6.969043 TGACCTTCCATTTGAGTGGTAATAT 58.031 36.000 0.00 0.00 40.27 1.28
402 403 6.214615 TCTGACCTTCCATTTGAGTGGTAATA 59.785 38.462 0.00 0.00 40.27 0.98
403 404 5.014123 TCTGACCTTCCATTTGAGTGGTAAT 59.986 40.000 0.00 0.00 40.27 1.89
404 405 4.349636 TCTGACCTTCCATTTGAGTGGTAA 59.650 41.667 0.00 0.00 40.27 2.85
405 406 3.907474 TCTGACCTTCCATTTGAGTGGTA 59.093 43.478 0.00 0.00 40.27 3.25
406 407 2.711009 TCTGACCTTCCATTTGAGTGGT 59.289 45.455 0.00 0.00 40.27 4.16
407 408 3.008375 TCTCTGACCTTCCATTTGAGTGG 59.992 47.826 0.00 0.00 40.76 4.00
408 409 4.277515 TCTCTGACCTTCCATTTGAGTG 57.722 45.455 0.00 0.00 0.00 3.51
409 410 4.982241 TTCTCTGACCTTCCATTTGAGT 57.018 40.909 0.00 0.00 0.00 3.41
410 411 6.881065 TGTAATTCTCTGACCTTCCATTTGAG 59.119 38.462 0.00 0.00 0.00 3.02
411 412 6.778821 TGTAATTCTCTGACCTTCCATTTGA 58.221 36.000 0.00 0.00 0.00 2.69
412 413 6.404074 GCTGTAATTCTCTGACCTTCCATTTG 60.404 42.308 0.00 0.00 0.00 2.32
413 414 5.649831 GCTGTAATTCTCTGACCTTCCATTT 59.350 40.000 0.00 0.00 0.00 2.32
414 415 5.189180 GCTGTAATTCTCTGACCTTCCATT 58.811 41.667 0.00 0.00 0.00 3.16
415 416 4.225942 TGCTGTAATTCTCTGACCTTCCAT 59.774 41.667 0.00 0.00 0.00 3.41
416 417 3.582647 TGCTGTAATTCTCTGACCTTCCA 59.417 43.478 0.00 0.00 0.00 3.53
417 418 4.081420 TCTGCTGTAATTCTCTGACCTTCC 60.081 45.833 0.00 0.00 0.00 3.46
418 419 5.078411 TCTGCTGTAATTCTCTGACCTTC 57.922 43.478 0.00 0.00 0.00 3.46
419 420 4.081198 CCTCTGCTGTAATTCTCTGACCTT 60.081 45.833 0.00 0.00 0.00 3.50
420 421 3.450457 CCTCTGCTGTAATTCTCTGACCT 59.550 47.826 0.00 0.00 0.00 3.85
421 422 3.196685 ACCTCTGCTGTAATTCTCTGACC 59.803 47.826 0.00 0.00 0.00 4.02
422 423 4.464069 ACCTCTGCTGTAATTCTCTGAC 57.536 45.455 0.00 0.00 0.00 3.51
423 424 4.774726 AGAACCTCTGCTGTAATTCTCTGA 59.225 41.667 0.00 0.00 0.00 3.27
424 425 4.869297 CAGAACCTCTGCTGTAATTCTCTG 59.131 45.833 0.00 0.00 37.72 3.35
425 426 4.081198 CCAGAACCTCTGCTGTAATTCTCT 60.081 45.833 0.00 0.00 42.98 3.10
426 427 4.187694 CCAGAACCTCTGCTGTAATTCTC 58.812 47.826 0.00 0.00 42.98 2.87
427 428 3.584848 ACCAGAACCTCTGCTGTAATTCT 59.415 43.478 0.00 0.00 42.98 2.40
428 429 3.944087 ACCAGAACCTCTGCTGTAATTC 58.056 45.455 0.00 0.00 42.98 2.17
429 430 4.286032 TGTACCAGAACCTCTGCTGTAATT 59.714 41.667 0.00 0.00 42.98 1.40
430 431 3.838317 TGTACCAGAACCTCTGCTGTAAT 59.162 43.478 0.00 0.00 42.98 1.89
431 432 3.236047 TGTACCAGAACCTCTGCTGTAA 58.764 45.455 0.00 0.00 42.98 2.41
432 433 2.884320 TGTACCAGAACCTCTGCTGTA 58.116 47.619 0.00 0.00 42.98 2.74
433 434 1.717032 TGTACCAGAACCTCTGCTGT 58.283 50.000 0.00 0.00 42.98 4.40
434 435 2.839486 TTGTACCAGAACCTCTGCTG 57.161 50.000 0.00 0.00 42.98 4.41
435 436 4.202461 TGAATTTGTACCAGAACCTCTGCT 60.202 41.667 0.00 0.00 42.98 4.24
436 437 4.072131 TGAATTTGTACCAGAACCTCTGC 58.928 43.478 0.00 0.00 42.98 4.26
437 438 4.154918 GCTGAATTTGTACCAGAACCTCTG 59.845 45.833 0.00 0.00 43.91 3.35
438 439 4.042187 AGCTGAATTTGTACCAGAACCTCT 59.958 41.667 0.00 0.00 0.00 3.69
439 440 4.327680 AGCTGAATTTGTACCAGAACCTC 58.672 43.478 0.00 0.00 0.00 3.85
440 441 4.373156 AGCTGAATTTGTACCAGAACCT 57.627 40.909 0.00 0.00 0.00 3.50
441 442 5.488341 TCTAGCTGAATTTGTACCAGAACC 58.512 41.667 0.00 0.00 0.00 3.62
442 443 6.092807 CCTTCTAGCTGAATTTGTACCAGAAC 59.907 42.308 0.00 0.00 33.71 3.01
443 444 6.173339 CCTTCTAGCTGAATTTGTACCAGAA 58.827 40.000 0.00 0.00 33.71 3.02
444 445 5.338381 CCCTTCTAGCTGAATTTGTACCAGA 60.338 44.000 0.00 0.00 33.71 3.86
445 446 4.878397 CCCTTCTAGCTGAATTTGTACCAG 59.122 45.833 0.00 0.00 33.71 4.00
446 447 4.534500 TCCCTTCTAGCTGAATTTGTACCA 59.466 41.667 0.00 0.00 33.71 3.25
447 448 5.099042 TCCCTTCTAGCTGAATTTGTACC 57.901 43.478 0.00 0.00 33.71 3.34
448 449 7.554476 AGAATTCCCTTCTAGCTGAATTTGTAC 59.446 37.037 0.65 0.00 42.56 2.90
449 450 7.554118 CAGAATTCCCTTCTAGCTGAATTTGTA 59.446 37.037 0.65 0.00 42.48 2.41
450 451 6.376581 CAGAATTCCCTTCTAGCTGAATTTGT 59.623 38.462 0.65 0.00 42.48 2.83
451 452 6.183360 CCAGAATTCCCTTCTAGCTGAATTTG 60.183 42.308 0.65 8.44 42.48 2.32
452 453 5.890419 CCAGAATTCCCTTCTAGCTGAATTT 59.110 40.000 0.65 0.00 42.48 1.82
453 454 5.044550 ACCAGAATTCCCTTCTAGCTGAATT 60.045 40.000 0.65 7.05 42.48 2.17
454 455 4.476479 ACCAGAATTCCCTTCTAGCTGAAT 59.524 41.667 0.65 0.00 42.48 2.57
455 456 3.846588 ACCAGAATTCCCTTCTAGCTGAA 59.153 43.478 0.65 0.00 42.48 3.02
456 457 3.454858 ACCAGAATTCCCTTCTAGCTGA 58.545 45.455 0.65 0.00 42.48 4.26
457 458 3.922171 ACCAGAATTCCCTTCTAGCTG 57.078 47.619 0.65 0.00 42.48 4.24
458 459 4.625963 AGTACCAGAATTCCCTTCTAGCT 58.374 43.478 0.65 0.00 42.48 3.32
459 460 5.360649 AAGTACCAGAATTCCCTTCTAGC 57.639 43.478 0.65 0.00 42.48 3.42
460 461 7.663043 ACTAAGTACCAGAATTCCCTTCTAG 57.337 40.000 0.65 0.00 42.48 2.43
461 462 8.445361 AAACTAAGTACCAGAATTCCCTTCTA 57.555 34.615 0.65 0.00 42.48 2.10
462 463 6.954352 AACTAAGTACCAGAATTCCCTTCT 57.046 37.500 0.65 0.00 45.34 2.85
463 464 7.447545 ACAAAACTAAGTACCAGAATTCCCTTC 59.552 37.037 0.65 0.00 0.00 3.46
464 465 7.230712 CACAAAACTAAGTACCAGAATTCCCTT 59.769 37.037 0.65 0.20 0.00 3.95
465 466 6.715264 CACAAAACTAAGTACCAGAATTCCCT 59.285 38.462 0.65 0.00 0.00 4.20
466 467 6.713450 TCACAAAACTAAGTACCAGAATTCCC 59.287 38.462 0.65 0.00 0.00 3.97
467 468 7.739498 TCACAAAACTAAGTACCAGAATTCC 57.261 36.000 0.65 0.00 0.00 3.01
468 469 8.074370 GGTTCACAAAACTAAGTACCAGAATTC 58.926 37.037 0.00 0.00 0.00 2.17
469 470 7.778382 AGGTTCACAAAACTAAGTACCAGAATT 59.222 33.333 0.00 0.00 27.86 2.17
470 471 7.287810 AGGTTCACAAAACTAAGTACCAGAAT 58.712 34.615 0.00 0.00 27.86 2.40
471 472 6.655930 AGGTTCACAAAACTAAGTACCAGAA 58.344 36.000 0.00 0.00 27.86 3.02
472 473 6.243216 AGGTTCACAAAACTAAGTACCAGA 57.757 37.500 0.00 0.00 27.86 3.86
473 474 6.937436 AAGGTTCACAAAACTAAGTACCAG 57.063 37.500 0.00 0.00 30.19 4.00
474 475 7.363094 CCAAAAGGTTCACAAAACTAAGTACCA 60.363 37.037 0.00 0.00 30.19 3.25
475 476 6.976349 CCAAAAGGTTCACAAAACTAAGTACC 59.024 38.462 0.00 0.00 30.19 3.34
476 477 7.486870 CACCAAAAGGTTCACAAAACTAAGTAC 59.513 37.037 0.00 0.00 30.19 2.73
477 478 7.363094 CCACCAAAAGGTTCACAAAACTAAGTA 60.363 37.037 0.00 0.00 30.19 2.24
478 479 6.394809 CACCAAAAGGTTCACAAAACTAAGT 58.605 36.000 0.00 0.00 30.19 2.24
479 480 5.810074 CCACCAAAAGGTTCACAAAACTAAG 59.190 40.000 0.00 0.00 30.19 2.18
480 481 5.480772 TCCACCAAAAGGTTCACAAAACTAA 59.519 36.000 0.00 0.00 30.19 2.24
481 482 5.017490 TCCACCAAAAGGTTCACAAAACTA 58.983 37.500 0.00 0.00 30.19 2.24
482 483 3.835395 TCCACCAAAAGGTTCACAAAACT 59.165 39.130 0.00 0.00 32.29 2.66
483 484 3.930229 GTCCACCAAAAGGTTCACAAAAC 59.070 43.478 0.00 0.00 0.00 2.43
490 491 4.010349 CCTATCTGTCCACCAAAAGGTTC 58.990 47.826 0.00 0.00 0.00 3.62
495 496 4.599041 CCATTCCTATCTGTCCACCAAAA 58.401 43.478 0.00 0.00 0.00 2.44
518 519 4.260784 GCTAAAAGATATCACCGGCACAAG 60.261 45.833 0.00 0.00 0.00 3.16
522 523 3.118408 ACAGCTAAAAGATATCACCGGCA 60.118 43.478 0.00 0.00 0.00 5.69
666 667 7.128331 CACTGCACGATGGATAAATAAAAGAG 58.872 38.462 0.00 0.00 0.00 2.85
702 703 9.988350 GATAAATAATAGGGTAATCACATTGCG 57.012 33.333 0.00 0.00 0.00 4.85
709 710 9.053472 ACCCGATGATAAATAATAGGGTAATCA 57.947 33.333 8.93 0.00 46.53 2.57
849 850 3.760151 TGAGGCTTCTTTCAATGTCATGG 59.240 43.478 0.00 0.00 0.00 3.66
854 855 3.442977 GCTGATGAGGCTTCTTTCAATGT 59.557 43.478 0.00 0.00 0.00 2.71
891 892 2.993899 CGGTTTATATAGGCGGCTTCTG 59.006 50.000 19.76 1.09 0.00 3.02
897 898 5.886960 AGTAGTACGGTTTATATAGGCGG 57.113 43.478 0.00 0.00 0.00 6.13
943 945 2.879103 TGGAATCCCAAACTCTGGTC 57.121 50.000 0.00 0.00 44.76 4.02
1116 1118 5.787953 TTCACTCCAAATTGCTTGATCAA 57.212 34.783 8.12 8.12 37.17 2.57
1310 1312 7.361799 CGAAGAAAAGGGACAAAAGGGTATAAG 60.362 40.741 0.00 0.00 0.00 1.73
1336 1338 7.872163 TCAAAATGCATGTCATGTTTTAGAC 57.128 32.000 14.26 0.00 35.13 2.59
1623 1632 1.053424 TTAAACTCGGGCCACTGTCT 58.947 50.000 4.39 0.00 0.00 3.41
1686 1695 1.522092 CTAGGGCAAGCCGATCACA 59.478 57.895 4.80 0.00 36.85 3.58
1759 1768 4.398988 TCAAGCAAAGAAATGTGTGTCTGT 59.601 37.500 0.00 0.00 0.00 3.41
1902 1912 5.902613 TCACCATCAGGCTTTATTTCAAG 57.097 39.130 0.00 0.00 39.06 3.02
1930 1940 0.308993 GGCTCGCATTTCACTATGGC 59.691 55.000 0.00 0.00 0.00 4.40
2018 2028 6.815641 TGTGAAGAAAGATCTAGAAGATGTGC 59.184 38.462 0.00 0.00 34.53 4.57
2050 2060 3.520569 TCAAGAAAAGCAAAACCAGCAC 58.479 40.909 0.00 0.00 0.00 4.40
2053 2063 6.982724 AGAGAAATCAAGAAAAGCAAAACCAG 59.017 34.615 0.00 0.00 0.00 4.00
2071 2082 6.933514 AGGAGAAGAGTTTCTGAGAGAAAT 57.066 37.500 2.26 0.00 44.94 2.17


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.