Multiple sequence alignment - TraesCS2D01G084100

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 TraesCS2D01G084100 chr2D 100.000 2432 0 0 1 2432 36490459 36488028 0.000000e+00 4492.0
1 TraesCS2D01G084100 chr2B 90.239 2008 116 38 439 2432 59104602 59106543 0.000000e+00 2549.0
2 TraesCS2D01G084100 chr2A 93.750 848 42 4 834 1674 40492422 40491579 0.000000e+00 1262.0
3 TraesCS2D01G084100 chr2A 88.947 760 73 5 922 1678 40374133 40373382 0.000000e+00 928.0
4 TraesCS2D01G084100 chr2A 92.067 479 18 6 1876 2351 40373230 40372769 0.000000e+00 656.0
5 TraesCS2D01G084100 chr2A 85.714 245 22 7 458 701 40494238 40494006 1.870000e-61 246.0
6 TraesCS2D01G084100 chr2A 90.667 75 6 1 704 777 40493977 40493903 5.530000e-17 99.0
7 TraesCS2D01G084100 chr6D 79.365 126 20 2 2146 2266 98218636 98218760 1.550000e-12 84.2
8 TraesCS2D01G084100 chr7D 100.000 29 0 0 97 125 538867697 538867669 1.000000e-03 54.7
9 TraesCS2D01G084100 chr6B 100.000 28 0 0 2157 2184 182745379 182745352 4.000000e-03 52.8


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 TraesCS2D01G084100 chr2D 36488028 36490459 2431 True 4492.000000 4492 100.000000 1 2432 1 chr2D.!!$R1 2431
1 TraesCS2D01G084100 chr2B 59104602 59106543 1941 False 2549.000000 2549 90.239000 439 2432 1 chr2B.!!$F1 1993
2 TraesCS2D01G084100 chr2A 40372769 40374133 1364 True 792.000000 928 90.507000 922 2351 2 chr2A.!!$R1 1429
3 TraesCS2D01G084100 chr2A 40491579 40494238 2659 True 535.666667 1262 90.043667 458 1674 3 chr2A.!!$R2 1216

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
414 415 0.036022 GAGGAGCAGAACTGGCTGTT 59.964 55.0 9.68 9.68 42.78 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 3111 0.174389 ATCGCACTCGCATCTTGACT 59.826 50.0 0.0 0.0 38.4 3.41 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
31 32 6.751514 TTTTCTTTTTCCTTTTTCCTTGGC 57.248 33.333 0.00 0.00 0.00 4.52
32 33 5.428184 TTCTTTTTCCTTTTTCCTTGGCA 57.572 34.783 0.00 0.00 0.00 4.92
33 34 5.428184 TCTTTTTCCTTTTTCCTTGGCAA 57.572 34.783 0.00 0.00 0.00 4.52
34 35 5.427378 TCTTTTTCCTTTTTCCTTGGCAAG 58.573 37.500 20.31 20.31 0.00 4.01
35 36 4.835284 TTTTCCTTTTTCCTTGGCAAGT 57.165 36.364 24.57 0.00 0.00 3.16
36 37 4.835284 TTTCCTTTTTCCTTGGCAAGTT 57.165 36.364 24.57 0.00 0.00 2.66
37 38 4.835284 TTCCTTTTTCCTTGGCAAGTTT 57.165 36.364 24.57 0.00 0.00 2.66
38 39 4.835284 TCCTTTTTCCTTGGCAAGTTTT 57.165 36.364 24.57 0.00 0.00 2.43
39 40 4.765273 TCCTTTTTCCTTGGCAAGTTTTC 58.235 39.130 24.57 0.00 0.00 2.29
40 41 4.223923 TCCTTTTTCCTTGGCAAGTTTTCA 59.776 37.500 24.57 6.07 0.00 2.69
41 42 4.940654 CCTTTTTCCTTGGCAAGTTTTCAA 59.059 37.500 24.57 10.35 0.00 2.69
42 43 5.065090 CCTTTTTCCTTGGCAAGTTTTCAAG 59.935 40.000 24.57 17.60 38.01 3.02
43 44 4.817318 TTTCCTTGGCAAGTTTTCAAGT 57.183 36.364 24.57 0.00 36.94 3.16
44 45 4.817318 TTCCTTGGCAAGTTTTCAAGTT 57.183 36.364 24.57 0.00 36.94 2.66
45 46 4.817318 TCCTTGGCAAGTTTTCAAGTTT 57.183 36.364 24.57 0.00 36.94 2.66
46 47 5.159273 TCCTTGGCAAGTTTTCAAGTTTT 57.841 34.783 24.57 0.00 36.94 2.43
47 48 5.555966 TCCTTGGCAAGTTTTCAAGTTTTT 58.444 33.333 24.57 0.00 36.94 1.94
336 337 6.625873 ACTCTTGAACAATCTTTGGAAGAC 57.374 37.500 0.00 0.00 41.01 3.01
337 338 6.122277 ACTCTTGAACAATCTTTGGAAGACA 58.878 36.000 0.00 0.00 41.01 3.41
338 339 6.774656 ACTCTTGAACAATCTTTGGAAGACAT 59.225 34.615 0.00 0.00 41.01 3.06
339 340 7.939039 ACTCTTGAACAATCTTTGGAAGACATA 59.061 33.333 0.00 0.00 41.01 2.29
340 341 8.868522 TCTTGAACAATCTTTGGAAGACATAT 57.131 30.769 0.00 0.00 41.01 1.78
341 342 9.300681 TCTTGAACAATCTTTGGAAGACATATT 57.699 29.630 0.00 0.00 41.01 1.28
342 343 9.565213 CTTGAACAATCTTTGGAAGACATATTC 57.435 33.333 0.00 0.00 41.01 1.75
343 344 8.868522 TGAACAATCTTTGGAAGACATATTCT 57.131 30.769 0.00 0.00 41.01 2.40
345 346 9.565213 GAACAATCTTTGGAAGACATATTCTTG 57.435 33.333 5.29 0.00 45.24 3.02
346 347 8.868522 ACAATCTTTGGAAGACATATTCTTGA 57.131 30.769 5.29 0.00 45.24 3.02
347 348 9.300681 ACAATCTTTGGAAGACATATTCTTGAA 57.699 29.630 5.29 0.00 45.24 2.69
348 349 9.565213 CAATCTTTGGAAGACATATTCTTGAAC 57.435 33.333 5.29 0.00 45.24 3.18
349 350 8.868522 ATCTTTGGAAGACATATTCTTGAACA 57.131 30.769 5.29 0.00 45.24 3.18
350 351 8.690203 TCTTTGGAAGACATATTCTTGAACAA 57.310 30.769 5.29 0.00 45.24 2.83
351 352 9.300681 TCTTTGGAAGACATATTCTTGAACAAT 57.699 29.630 5.29 0.00 45.24 2.71
352 353 9.565213 CTTTGGAAGACATATTCTTGAACAATC 57.435 33.333 5.29 0.00 45.24 2.67
353 354 8.868522 TTGGAAGACATATTCTTGAACAATCT 57.131 30.769 5.29 0.00 45.24 2.40
354 355 8.868522 TGGAAGACATATTCTTGAACAATCTT 57.131 30.769 5.29 0.00 45.24 2.40
355 356 9.958180 TGGAAGACATATTCTTGAACAATCTTA 57.042 29.630 5.29 0.00 45.24 2.10
359 360 9.911788 AGACATATTCTTGAACAATCTTATGGT 57.088 29.630 0.00 0.00 0.00 3.55
361 362 9.125026 ACATATTCTTGAACAATCTTATGGTCC 57.875 33.333 0.00 0.00 36.14 4.46
362 363 6.683974 ATTCTTGAACAATCTTATGGTCCG 57.316 37.500 0.00 0.00 36.14 4.79
363 364 4.513442 TCTTGAACAATCTTATGGTCCGG 58.487 43.478 0.00 0.00 36.14 5.14
364 365 4.224147 TCTTGAACAATCTTATGGTCCGGA 59.776 41.667 0.00 0.00 36.14 5.14
365 366 4.137116 TGAACAATCTTATGGTCCGGAG 57.863 45.455 3.06 0.00 36.14 4.63
378 379 2.590007 CGGAGGTATGCCAGCAGC 60.590 66.667 1.54 0.00 44.14 5.25
387 388 3.510846 GCCAGCAGCAGAGGATTG 58.489 61.111 0.00 0.00 42.97 2.67
388 389 2.119655 GCCAGCAGCAGAGGATTGG 61.120 63.158 0.00 0.00 42.97 3.16
389 390 2.119655 CCAGCAGCAGAGGATTGGC 61.120 63.158 0.00 0.00 0.00 4.52
390 391 2.124819 AGCAGCAGAGGATTGGCG 60.125 61.111 0.00 0.00 0.00 5.69
391 392 2.124983 GCAGCAGAGGATTGGCGA 60.125 61.111 0.00 0.00 0.00 5.54
392 393 1.746615 GCAGCAGAGGATTGGCGAA 60.747 57.895 0.00 0.00 0.00 4.70
393 394 1.099879 GCAGCAGAGGATTGGCGAAT 61.100 55.000 0.00 0.00 0.00 3.34
394 395 1.811558 GCAGCAGAGGATTGGCGAATA 60.812 52.381 0.00 0.00 0.00 1.75
395 396 2.141517 CAGCAGAGGATTGGCGAATAG 58.858 52.381 0.00 0.00 0.00 1.73
396 397 2.042464 AGCAGAGGATTGGCGAATAGA 58.958 47.619 0.00 0.00 0.00 1.98
397 398 2.036992 AGCAGAGGATTGGCGAATAGAG 59.963 50.000 0.00 0.00 0.00 2.43
398 399 2.869636 GCAGAGGATTGGCGAATAGAGG 60.870 54.545 0.00 0.00 0.00 3.69
399 400 2.630098 CAGAGGATTGGCGAATAGAGGA 59.370 50.000 0.00 0.00 0.00 3.71
400 401 2.896685 AGAGGATTGGCGAATAGAGGAG 59.103 50.000 0.00 0.00 0.00 3.69
401 402 1.346068 AGGATTGGCGAATAGAGGAGC 59.654 52.381 0.00 0.00 0.00 4.70
402 403 1.070758 GGATTGGCGAATAGAGGAGCA 59.929 52.381 0.00 0.00 0.00 4.26
403 404 2.411904 GATTGGCGAATAGAGGAGCAG 58.588 52.381 0.00 0.00 0.00 4.24
404 405 1.485124 TTGGCGAATAGAGGAGCAGA 58.515 50.000 0.00 0.00 0.00 4.26
405 406 1.485124 TGGCGAATAGAGGAGCAGAA 58.515 50.000 0.00 0.00 0.00 3.02
406 407 1.137086 TGGCGAATAGAGGAGCAGAAC 59.863 52.381 0.00 0.00 0.00 3.01
407 408 1.410882 GGCGAATAGAGGAGCAGAACT 59.589 52.381 0.00 0.00 0.00 3.01
408 409 2.468831 GCGAATAGAGGAGCAGAACTG 58.531 52.381 0.00 0.00 0.00 3.16
409 410 2.801342 GCGAATAGAGGAGCAGAACTGG 60.801 54.545 3.99 0.00 0.00 4.00
410 411 2.801342 CGAATAGAGGAGCAGAACTGGC 60.801 54.545 3.99 0.00 0.00 4.85
411 412 2.173126 ATAGAGGAGCAGAACTGGCT 57.827 50.000 3.99 0.00 46.07 4.75
412 413 1.189752 TAGAGGAGCAGAACTGGCTG 58.810 55.000 3.99 0.00 42.78 4.85
413 414 0.835543 AGAGGAGCAGAACTGGCTGT 60.836 55.000 3.99 0.00 42.78 4.40
414 415 0.036022 GAGGAGCAGAACTGGCTGTT 59.964 55.000 9.68 9.68 42.78 3.16
415 416 0.475906 AGGAGCAGAACTGGCTGTTT 59.524 50.000 11.21 0.00 42.78 2.83
416 417 0.877743 GGAGCAGAACTGGCTGTTTC 59.122 55.000 11.21 4.88 42.78 2.78
417 418 0.877743 GAGCAGAACTGGCTGTTTCC 59.122 55.000 11.21 0.00 42.78 3.13
418 419 0.183492 AGCAGAACTGGCTGTTTCCA 59.817 50.000 11.21 0.00 40.80 3.53
419 420 1.032014 GCAGAACTGGCTGTTTCCAA 58.968 50.000 11.21 0.00 39.30 3.53
420 421 1.408702 GCAGAACTGGCTGTTTCCAAA 59.591 47.619 11.21 0.00 39.30 3.28
421 422 2.159114 GCAGAACTGGCTGTTTCCAAAA 60.159 45.455 11.21 0.00 39.30 2.44
422 423 3.678529 GCAGAACTGGCTGTTTCCAAAAA 60.679 43.478 11.21 0.00 39.30 1.94
451 452 2.294512 GAGAACTGGCTGTTTCCAAAGG 59.705 50.000 11.21 0.00 39.30 3.11
452 453 2.091885 AGAACTGGCTGTTTCCAAAGGA 60.092 45.455 11.21 0.00 39.30 3.36
480 481 1.981256 ACCTGCTTTTCGTGTGGAAT 58.019 45.000 0.00 0.00 33.85 3.01
531 532 0.175302 CTCGAGAGCTCAATGTGCCT 59.825 55.000 17.77 1.22 0.00 4.75
547 548 5.365403 TGTGCCTGTCCGTAAATTTTAAG 57.635 39.130 0.00 0.00 0.00 1.85
709 738 0.610174 TGATGTGGAGGTGAGCACTC 59.390 55.000 0.16 0.00 0.00 3.51
726 755 0.095935 CTCAGCAGCGACCGATTTTG 59.904 55.000 0.00 0.00 0.00 2.44
775 804 2.203070 GCTGGCCCATCTACACCG 60.203 66.667 0.00 0.00 0.00 4.94
776 805 3.031417 GCTGGCCCATCTACACCGT 62.031 63.158 0.00 0.00 0.00 4.83
777 806 1.682451 GCTGGCCCATCTACACCGTA 61.682 60.000 0.00 0.00 0.00 4.02
779 808 1.332144 TGGCCCATCTACACCGTACC 61.332 60.000 0.00 0.00 0.00 3.34
781 810 1.047034 GCCCATCTACACCGTACCCT 61.047 60.000 0.00 0.00 0.00 4.34
782 811 1.755265 GCCCATCTACACCGTACCCTA 60.755 57.143 0.00 0.00 0.00 3.53
788 1444 3.098377 TCTACACCGTACCCTATGCAAA 58.902 45.455 0.00 0.00 0.00 3.68
795 1451 3.181514 CCGTACCCTATGCAAACTTTTCG 60.182 47.826 0.00 0.00 0.00 3.46
796 1452 3.434299 CGTACCCTATGCAAACTTTTCGT 59.566 43.478 0.00 0.00 0.00 3.85
797 1453 4.435121 CGTACCCTATGCAAACTTTTCGTC 60.435 45.833 0.00 0.00 0.00 4.20
798 1454 3.751518 ACCCTATGCAAACTTTTCGTCT 58.248 40.909 0.00 0.00 0.00 4.18
824 1480 3.414549 AACTAAGGTGTGCAAACGTTG 57.585 42.857 22.24 14.91 31.15 4.10
896 2350 3.625764 TGACTGCCAACTTGTAACTCAAC 59.374 43.478 0.00 0.00 32.18 3.18
1134 2597 3.953775 CGCAACTCCCCCACAGGT 61.954 66.667 0.00 0.00 0.00 4.00
1280 2746 4.122046 CGCTTCAACACCATGATCTCATA 58.878 43.478 0.00 0.00 34.26 2.15
1370 2836 4.052229 CGTCTTCGGTGGGCTCGT 62.052 66.667 0.00 0.00 0.00 4.18
1463 2929 2.600470 AGGGTTTTTCCGGCTGCC 60.600 61.111 9.11 9.11 37.00 4.85
1604 3077 4.214332 GGATCGTTCTTTGTTTCTTGAGCT 59.786 41.667 0.00 0.00 0.00 4.09
1619 3092 1.021968 GAGCTGTTGTTCCCGTTGTT 58.978 50.000 0.00 0.00 0.00 2.83
1620 3093 1.002792 GAGCTGTTGTTCCCGTTGTTC 60.003 52.381 0.00 0.00 0.00 3.18
1621 3094 1.021968 GCTGTTGTTCCCGTTGTTCT 58.978 50.000 0.00 0.00 0.00 3.01
1622 3095 2.158871 AGCTGTTGTTCCCGTTGTTCTA 60.159 45.455 0.00 0.00 0.00 2.10
1623 3096 2.032290 GCTGTTGTTCCCGTTGTTCTAC 60.032 50.000 0.00 0.00 0.00 2.59
1624 3097 3.463944 CTGTTGTTCCCGTTGTTCTACT 58.536 45.455 0.00 0.00 0.00 2.57
1625 3098 3.460103 TGTTGTTCCCGTTGTTCTACTC 58.540 45.455 0.00 0.00 0.00 2.59
1626 3099 2.427232 TGTTCCCGTTGTTCTACTCG 57.573 50.000 0.00 0.00 0.00 4.18
1627 3100 1.682854 TGTTCCCGTTGTTCTACTCGT 59.317 47.619 0.00 0.00 0.00 4.18
1628 3101 2.056577 GTTCCCGTTGTTCTACTCGTG 58.943 52.381 0.00 0.00 0.00 4.35
1629 3102 1.608055 TCCCGTTGTTCTACTCGTGA 58.392 50.000 0.00 0.00 0.00 4.35
1630 3103 1.267806 TCCCGTTGTTCTACTCGTGAC 59.732 52.381 0.00 0.00 0.00 3.67
1631 3104 1.268899 CCCGTTGTTCTACTCGTGACT 59.731 52.381 0.00 0.00 0.00 3.41
1632 3105 2.582687 CCGTTGTTCTACTCGTGACTC 58.417 52.381 0.00 0.00 0.00 3.36
1633 3106 2.225963 CCGTTGTTCTACTCGTGACTCT 59.774 50.000 0.00 0.00 0.00 3.24
1634 3107 3.480894 CGTTGTTCTACTCGTGACTCTC 58.519 50.000 0.00 0.00 0.00 3.20
1635 3108 3.059120 CGTTGTTCTACTCGTGACTCTCA 60.059 47.826 0.00 0.00 0.00 3.27
1636 3109 4.378563 CGTTGTTCTACTCGTGACTCTCAT 60.379 45.833 0.00 0.00 0.00 2.90
1637 3110 4.948608 TGTTCTACTCGTGACTCTCATC 57.051 45.455 0.00 0.00 0.00 2.92
1638 3111 4.324267 TGTTCTACTCGTGACTCTCATCA 58.676 43.478 0.00 0.00 0.00 3.07
1639 3112 4.393371 TGTTCTACTCGTGACTCTCATCAG 59.607 45.833 0.00 0.00 0.00 2.90
1740 3281 0.324368 TCCACCGTACTCCTCAGCAT 60.324 55.000 0.00 0.00 0.00 3.79
1854 3395 3.032017 AGTTCACGTCCAGATCAGTTG 57.968 47.619 0.00 0.00 0.00 3.16
1869 3410 3.937814 TCAGTTGTCGTTCTTGGCATAT 58.062 40.909 0.00 0.00 0.00 1.78
1870 3411 5.079689 TCAGTTGTCGTTCTTGGCATATA 57.920 39.130 0.00 0.00 0.00 0.86
1871 3412 5.670485 TCAGTTGTCGTTCTTGGCATATAT 58.330 37.500 0.00 0.00 0.00 0.86
1990 3535 0.456142 GCATCAGCATGTGCACACAG 60.456 55.000 24.37 18.82 45.48 3.66
1994 3539 2.049802 GCATGTGCACACAGCCAC 60.050 61.111 27.15 9.98 45.48 5.01
2007 3552 1.340697 ACAGCCACACATGCATGATCT 60.341 47.619 32.75 16.92 0.00 2.75
2132 3677 3.067106 CAGTCGTGCCAATGTTTCTACT 58.933 45.455 0.00 0.00 0.00 2.57
2389 3937 0.620556 GGTGGGATTCTGGCTCTTCA 59.379 55.000 0.00 0.00 0.00 3.02
2399 3947 3.882444 TCTGGCTCTTCATGAGATTTGG 58.118 45.455 0.00 0.00 45.39 3.28
2403 3951 3.376546 GGCTCTTCATGAGATTTGGTCAC 59.623 47.826 0.00 0.00 45.39 3.67
2414 3962 4.504858 AGATTTGGTCACGAGGTTACATC 58.495 43.478 0.00 0.00 0.00 3.06
2426 3974 4.694339 GAGGTTACATCAAGGCGTATTCT 58.306 43.478 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.898761 GCCAAGGAAAAAGGAAAAAGAAAATAA 58.101 29.630 0.00 0.00 0.00 1.40
6 7 8.049721 TGCCAAGGAAAAAGGAAAAAGAAAATA 58.950 29.630 0.00 0.00 0.00 1.40
7 8 6.889177 TGCCAAGGAAAAAGGAAAAAGAAAAT 59.111 30.769 0.00 0.00 0.00 1.82
8 9 6.241645 TGCCAAGGAAAAAGGAAAAAGAAAA 58.758 32.000 0.00 0.00 0.00 2.29
9 10 5.810095 TGCCAAGGAAAAAGGAAAAAGAAA 58.190 33.333 0.00 0.00 0.00 2.52
10 11 5.428184 TGCCAAGGAAAAAGGAAAAAGAA 57.572 34.783 0.00 0.00 0.00 2.52
11 12 5.045942 ACTTGCCAAGGAAAAAGGAAAAAGA 60.046 36.000 9.64 0.00 0.00 2.52
12 13 5.185454 ACTTGCCAAGGAAAAAGGAAAAAG 58.815 37.500 9.64 0.00 0.00 2.27
13 14 5.172687 ACTTGCCAAGGAAAAAGGAAAAA 57.827 34.783 9.64 0.00 0.00 1.94
14 15 4.835284 ACTTGCCAAGGAAAAAGGAAAA 57.165 36.364 9.64 0.00 0.00 2.29
15 16 4.835284 AACTTGCCAAGGAAAAAGGAAA 57.165 36.364 9.64 0.00 0.00 3.13
16 17 4.835284 AAACTTGCCAAGGAAAAAGGAA 57.165 36.364 9.64 0.00 0.00 3.36
17 18 4.223923 TGAAAACTTGCCAAGGAAAAAGGA 59.776 37.500 9.64 0.00 0.00 3.36
18 19 4.512484 TGAAAACTTGCCAAGGAAAAAGG 58.488 39.130 9.64 0.00 0.00 3.11
19 20 5.643348 ACTTGAAAACTTGCCAAGGAAAAAG 59.357 36.000 9.64 8.18 40.99 2.27
20 21 5.555966 ACTTGAAAACTTGCCAAGGAAAAA 58.444 33.333 9.64 0.00 40.99 1.94
21 22 5.159273 ACTTGAAAACTTGCCAAGGAAAA 57.841 34.783 9.64 0.00 40.99 2.29
22 23 4.817318 ACTTGAAAACTTGCCAAGGAAA 57.183 36.364 9.64 0.00 40.99 3.13
23 24 4.817318 AACTTGAAAACTTGCCAAGGAA 57.183 36.364 9.64 0.00 40.99 3.36
24 25 4.817318 AAACTTGAAAACTTGCCAAGGA 57.183 36.364 9.64 0.00 40.99 3.36
25 26 5.878332 AAAAACTTGAAAACTTGCCAAGG 57.122 34.783 9.64 0.00 40.99 3.61
310 311 9.436957 GTCTTCCAAAGATTGTTCAAGAGTATA 57.563 33.333 0.00 0.00 40.18 1.47
311 312 7.939039 TGTCTTCCAAAGATTGTTCAAGAGTAT 59.061 33.333 0.00 0.00 40.18 2.12
312 313 7.279615 TGTCTTCCAAAGATTGTTCAAGAGTA 58.720 34.615 0.00 0.00 40.18 2.59
313 314 6.122277 TGTCTTCCAAAGATTGTTCAAGAGT 58.878 36.000 0.00 0.00 40.18 3.24
314 315 6.624352 TGTCTTCCAAAGATTGTTCAAGAG 57.376 37.500 0.00 0.00 40.18 2.85
315 316 8.868522 ATATGTCTTCCAAAGATTGTTCAAGA 57.131 30.769 0.00 0.00 40.18 3.02
316 317 9.565213 GAATATGTCTTCCAAAGATTGTTCAAG 57.435 33.333 0.00 0.00 40.18 3.02
317 318 9.300681 AGAATATGTCTTCCAAAGATTGTTCAA 57.699 29.630 11.17 0.00 40.18 2.69
318 319 8.868522 AGAATATGTCTTCCAAAGATTGTTCA 57.131 30.769 11.17 0.12 40.18 3.18
319 320 9.565213 CAAGAATATGTCTTCCAAAGATTGTTC 57.435 33.333 0.00 0.14 45.25 3.18
320 321 9.300681 TCAAGAATATGTCTTCCAAAGATTGTT 57.699 29.630 0.00 0.00 45.25 2.83
321 322 8.868522 TCAAGAATATGTCTTCCAAAGATTGT 57.131 30.769 0.00 0.00 45.25 2.71
322 323 9.565213 GTTCAAGAATATGTCTTCCAAAGATTG 57.435 33.333 0.00 0.00 45.25 2.67
323 324 9.300681 TGTTCAAGAATATGTCTTCCAAAGATT 57.699 29.630 0.00 0.00 45.25 2.40
324 325 8.868522 TGTTCAAGAATATGTCTTCCAAAGAT 57.131 30.769 0.00 0.00 45.25 2.40
325 326 8.690203 TTGTTCAAGAATATGTCTTCCAAAGA 57.310 30.769 0.00 0.00 45.25 2.52
326 327 9.565213 GATTGTTCAAGAATATGTCTTCCAAAG 57.435 33.333 0.00 0.00 45.25 2.77
327 328 9.300681 AGATTGTTCAAGAATATGTCTTCCAAA 57.699 29.630 0.00 0.00 45.25 3.28
328 329 8.868522 AGATTGTTCAAGAATATGTCTTCCAA 57.131 30.769 0.00 0.00 45.25 3.53
329 330 8.868522 AAGATTGTTCAAGAATATGTCTTCCA 57.131 30.769 0.00 0.00 45.25 3.53
333 334 9.911788 ACCATAAGATTGTTCAAGAATATGTCT 57.088 29.630 10.39 0.00 38.69 3.41
335 336 9.125026 GGACCATAAGATTGTTCAAGAATATGT 57.875 33.333 0.00 0.00 0.00 2.29
336 337 8.285394 CGGACCATAAGATTGTTCAAGAATATG 58.715 37.037 0.00 0.00 0.00 1.78
337 338 7.445402 CCGGACCATAAGATTGTTCAAGAATAT 59.555 37.037 0.00 0.00 0.00 1.28
338 339 6.765989 CCGGACCATAAGATTGTTCAAGAATA 59.234 38.462 0.00 0.00 0.00 1.75
339 340 5.590259 CCGGACCATAAGATTGTTCAAGAAT 59.410 40.000 0.00 0.00 0.00 2.40
340 341 4.941263 CCGGACCATAAGATTGTTCAAGAA 59.059 41.667 0.00 0.00 0.00 2.52
341 342 4.224147 TCCGGACCATAAGATTGTTCAAGA 59.776 41.667 0.00 0.00 0.00 3.02
342 343 4.513442 TCCGGACCATAAGATTGTTCAAG 58.487 43.478 0.00 0.00 0.00 3.02
343 344 4.513442 CTCCGGACCATAAGATTGTTCAA 58.487 43.478 0.00 0.00 0.00 2.69
344 345 3.118408 CCTCCGGACCATAAGATTGTTCA 60.118 47.826 0.00 0.00 0.00 3.18
345 346 3.118371 ACCTCCGGACCATAAGATTGTTC 60.118 47.826 0.00 0.00 0.00 3.18
346 347 2.844348 ACCTCCGGACCATAAGATTGTT 59.156 45.455 0.00 0.00 0.00 2.83
347 348 2.478292 ACCTCCGGACCATAAGATTGT 58.522 47.619 0.00 0.00 0.00 2.71
348 349 4.569943 CATACCTCCGGACCATAAGATTG 58.430 47.826 0.00 0.00 0.00 2.67
349 350 3.008049 GCATACCTCCGGACCATAAGATT 59.992 47.826 0.00 0.00 0.00 2.40
350 351 2.567615 GCATACCTCCGGACCATAAGAT 59.432 50.000 0.00 0.00 0.00 2.40
351 352 1.968493 GCATACCTCCGGACCATAAGA 59.032 52.381 0.00 0.00 0.00 2.10
352 353 1.002087 GGCATACCTCCGGACCATAAG 59.998 57.143 0.00 0.00 0.00 1.73
353 354 1.053424 GGCATACCTCCGGACCATAA 58.947 55.000 0.00 0.00 0.00 1.90
354 355 0.105401 TGGCATACCTCCGGACCATA 60.105 55.000 0.00 0.00 36.63 2.74
355 356 1.383943 TGGCATACCTCCGGACCAT 60.384 57.895 0.00 0.00 36.63 3.55
356 357 2.039787 TGGCATACCTCCGGACCA 59.960 61.111 0.00 1.66 36.63 4.02
357 358 2.822399 CTGGCATACCTCCGGACC 59.178 66.667 0.00 0.00 36.63 4.46
358 359 2.109181 GCTGGCATACCTCCGGAC 59.891 66.667 0.00 0.00 36.63 4.79
359 360 2.364973 TGCTGGCATACCTCCGGA 60.365 61.111 2.93 2.93 36.63 5.14
360 361 2.109799 CTGCTGGCATACCTCCGG 59.890 66.667 0.00 0.00 36.63 5.14
361 362 2.590007 GCTGCTGGCATACCTCCG 60.590 66.667 0.00 0.00 41.35 4.63
370 371 2.119655 CCAATCCTCTGCTGCTGGC 61.120 63.158 6.69 0.00 42.22 4.85
371 372 2.119655 GCCAATCCTCTGCTGCTGG 61.120 63.158 6.69 2.19 0.00 4.85
372 373 2.470362 CGCCAATCCTCTGCTGCTG 61.470 63.158 0.00 0.00 0.00 4.41
373 374 2.124819 CGCCAATCCTCTGCTGCT 60.125 61.111 0.00 0.00 0.00 4.24
374 375 1.099879 ATTCGCCAATCCTCTGCTGC 61.100 55.000 0.00 0.00 0.00 5.25
375 376 2.141517 CTATTCGCCAATCCTCTGCTG 58.858 52.381 0.00 0.00 0.00 4.41
376 377 2.036992 CTCTATTCGCCAATCCTCTGCT 59.963 50.000 0.00 0.00 0.00 4.24
377 378 2.411904 CTCTATTCGCCAATCCTCTGC 58.588 52.381 0.00 0.00 0.00 4.26
378 379 2.630098 TCCTCTATTCGCCAATCCTCTG 59.370 50.000 0.00 0.00 0.00 3.35
379 380 2.896685 CTCCTCTATTCGCCAATCCTCT 59.103 50.000 0.00 0.00 0.00 3.69
380 381 2.611722 GCTCCTCTATTCGCCAATCCTC 60.612 54.545 0.00 0.00 0.00 3.71
381 382 1.346068 GCTCCTCTATTCGCCAATCCT 59.654 52.381 0.00 0.00 0.00 3.24
382 383 1.070758 TGCTCCTCTATTCGCCAATCC 59.929 52.381 0.00 0.00 0.00 3.01
383 384 2.036475 TCTGCTCCTCTATTCGCCAATC 59.964 50.000 0.00 0.00 0.00 2.67
384 385 2.042464 TCTGCTCCTCTATTCGCCAAT 58.958 47.619 0.00 0.00 0.00 3.16
385 386 1.485124 TCTGCTCCTCTATTCGCCAA 58.515 50.000 0.00 0.00 0.00 4.52
386 387 1.137086 GTTCTGCTCCTCTATTCGCCA 59.863 52.381 0.00 0.00 0.00 5.69
387 388 1.410882 AGTTCTGCTCCTCTATTCGCC 59.589 52.381 0.00 0.00 0.00 5.54
388 389 2.468831 CAGTTCTGCTCCTCTATTCGC 58.531 52.381 0.00 0.00 0.00 4.70
389 390 2.801342 GCCAGTTCTGCTCCTCTATTCG 60.801 54.545 0.00 0.00 0.00 3.34
390 391 2.433970 AGCCAGTTCTGCTCCTCTATTC 59.566 50.000 0.00 0.00 32.41 1.75
391 392 2.170187 CAGCCAGTTCTGCTCCTCTATT 59.830 50.000 0.00 0.00 36.81 1.73
392 393 1.761784 CAGCCAGTTCTGCTCCTCTAT 59.238 52.381 0.00 0.00 36.81 1.98
393 394 1.189752 CAGCCAGTTCTGCTCCTCTA 58.810 55.000 0.00 0.00 36.81 2.43
394 395 0.835543 ACAGCCAGTTCTGCTCCTCT 60.836 55.000 0.00 0.00 36.81 3.69
395 396 0.036022 AACAGCCAGTTCTGCTCCTC 59.964 55.000 0.00 0.00 36.81 3.71
396 397 0.475906 AAACAGCCAGTTCTGCTCCT 59.524 50.000 0.00 0.00 40.26 3.69
397 398 0.877743 GAAACAGCCAGTTCTGCTCC 59.122 55.000 0.00 0.00 40.26 4.70
398 399 0.877743 GGAAACAGCCAGTTCTGCTC 59.122 55.000 0.00 0.00 40.26 4.26
399 400 0.183492 TGGAAACAGCCAGTTCTGCT 59.817 50.000 0.00 0.00 40.26 4.24
400 401 1.032014 TTGGAAACAGCCAGTTCTGC 58.968 50.000 0.00 0.00 44.54 4.26
401 402 3.799281 TTTTGGAAACAGCCAGTTCTG 57.201 42.857 0.00 0.00 44.54 3.02
421 422 7.147742 TGGAAACAGCCAGTTCTCTAAATTTTT 60.148 33.333 0.00 0.00 40.26 1.94
422 423 6.323739 TGGAAACAGCCAGTTCTCTAAATTTT 59.676 34.615 0.00 0.00 40.26 1.82
423 424 5.833131 TGGAAACAGCCAGTTCTCTAAATTT 59.167 36.000 0.00 0.00 40.26 1.82
424 425 5.385198 TGGAAACAGCCAGTTCTCTAAATT 58.615 37.500 0.00 0.00 40.26 1.82
425 426 4.985538 TGGAAACAGCCAGTTCTCTAAAT 58.014 39.130 0.00 0.00 40.26 1.40
426 427 4.431416 TGGAAACAGCCAGTTCTCTAAA 57.569 40.909 0.00 0.00 40.26 1.85
427 428 4.431416 TTGGAAACAGCCAGTTCTCTAA 57.569 40.909 0.00 0.00 44.54 2.10
428 429 4.389374 CTTTGGAAACAGCCAGTTCTCTA 58.611 43.478 0.00 0.00 44.54 2.43
429 430 3.217626 CTTTGGAAACAGCCAGTTCTCT 58.782 45.455 0.00 0.00 44.54 3.10
430 431 2.294512 CCTTTGGAAACAGCCAGTTCTC 59.705 50.000 0.00 0.00 44.54 2.87
431 432 2.091885 TCCTTTGGAAACAGCCAGTTCT 60.092 45.455 0.00 0.00 44.54 3.01
432 433 2.306847 TCCTTTGGAAACAGCCAGTTC 58.693 47.619 0.00 0.00 44.54 3.01
433 434 2.452600 TCCTTTGGAAACAGCCAGTT 57.547 45.000 0.00 0.00 44.54 3.16
434 435 2.310538 CTTCCTTTGGAAACAGCCAGT 58.689 47.619 0.53 0.00 41.54 4.00
435 436 1.000171 GCTTCCTTTGGAAACAGCCAG 60.000 52.381 0.53 0.00 41.54 4.85
436 437 1.039856 GCTTCCTTTGGAAACAGCCA 58.960 50.000 0.53 0.00 41.54 4.75
437 438 1.000171 CTGCTTCCTTTGGAAACAGCC 60.000 52.381 14.30 0.00 45.03 4.85
480 481 3.394674 TGGTCGCTATTGAGTGTTCAA 57.605 42.857 0.00 0.00 46.67 2.69
531 532 5.295950 TCACGGACTTAAAATTTACGGACA 58.704 37.500 0.00 0.00 0.00 4.02
709 738 1.512734 GCAAAATCGGTCGCTGCTG 60.513 57.895 0.00 0.00 0.00 4.41
741 770 0.179000 AGCCCATTTAGCTCTCACGG 59.821 55.000 0.00 0.00 34.91 4.94
772 801 3.428413 AAAGTTTGCATAGGGTACGGT 57.572 42.857 0.00 0.00 0.00 4.83
773 802 3.181514 CGAAAAGTTTGCATAGGGTACGG 60.182 47.826 0.00 0.00 0.00 4.02
775 804 4.694037 AGACGAAAAGTTTGCATAGGGTAC 59.306 41.667 0.00 0.00 0.00 3.34
776 805 4.901868 AGACGAAAAGTTTGCATAGGGTA 58.098 39.130 0.00 0.00 0.00 3.69
777 806 3.751518 AGACGAAAAGTTTGCATAGGGT 58.248 40.909 0.00 0.00 0.00 4.34
806 1462 1.944024 TCCAACGTTTGCACACCTTAG 59.056 47.619 0.00 0.00 0.00 2.18
808 1464 0.738389 CTCCAACGTTTGCACACCTT 59.262 50.000 0.00 0.00 0.00 3.50
821 1477 2.076863 CCAAGACACCGATTCTCCAAC 58.923 52.381 0.00 0.00 0.00 3.77
824 1480 1.740718 GCTCCAAGACACCGATTCTCC 60.741 57.143 0.00 0.00 0.00 3.71
896 2350 4.560108 CGGGAGTATTATAACTCGGTTGGG 60.560 50.000 0.00 0.00 45.69 4.12
1091 2554 1.646189 CTTGAGGAAGTAGAAGGCGC 58.354 55.000 0.00 0.00 0.00 6.53
1333 2799 2.731571 CGCCCTTGATCCCGGAGAA 61.732 63.158 0.73 0.00 0.00 2.87
1463 2929 0.460987 AGGCAAGCTCGATCGGAAAG 60.461 55.000 16.41 6.61 0.00 2.62
1535 3001 6.385537 ACAAAAATTACGTACAGCGACTAG 57.614 37.500 0.00 0.00 44.77 2.57
1539 3005 6.768029 ACTAACAAAAATTACGTACAGCGA 57.232 33.333 0.00 0.00 44.77 4.93
1604 3077 3.460103 GAGTAGAACAACGGGAACAACA 58.540 45.455 0.00 0.00 0.00 3.33
1619 3092 4.185394 GACTGATGAGAGTCACGAGTAGA 58.815 47.826 0.00 0.00 41.84 2.59
1620 3093 3.935828 TGACTGATGAGAGTCACGAGTAG 59.064 47.826 0.00 0.00 45.96 2.57
1621 3094 3.939066 TGACTGATGAGAGTCACGAGTA 58.061 45.455 0.00 0.00 45.96 2.59
1622 3095 2.784347 TGACTGATGAGAGTCACGAGT 58.216 47.619 0.00 0.00 45.96 4.18
1628 3101 3.114809 CGCATCTTGACTGATGAGAGTC 58.885 50.000 8.46 0.00 44.71 3.36
1629 3102 2.757314 TCGCATCTTGACTGATGAGAGT 59.243 45.455 8.46 0.00 44.24 3.24
1630 3103 3.433513 TCGCATCTTGACTGATGAGAG 57.566 47.619 8.46 0.33 44.24 3.20
1631 3104 2.757314 ACTCGCATCTTGACTGATGAGA 59.243 45.455 8.46 9.15 45.90 3.27
1632 3105 2.858941 CACTCGCATCTTGACTGATGAG 59.141 50.000 8.46 5.46 44.71 2.90
1633 3106 2.884827 CACTCGCATCTTGACTGATGA 58.115 47.619 8.46 0.00 44.71 2.92
1634 3107 1.326852 GCACTCGCATCTTGACTGATG 59.673 52.381 0.00 0.00 44.72 3.07
1635 3108 1.649664 GCACTCGCATCTTGACTGAT 58.350 50.000 0.00 0.00 38.36 2.90
1636 3109 0.733909 CGCACTCGCATCTTGACTGA 60.734 55.000 0.00 0.00 38.40 3.41
1637 3110 0.733909 TCGCACTCGCATCTTGACTG 60.734 55.000 0.00 0.00 38.40 3.51
1638 3111 0.174389 ATCGCACTCGCATCTTGACT 59.826 50.000 0.00 0.00 38.40 3.41
1639 3112 0.574454 GATCGCACTCGCATCTTGAC 59.426 55.000 0.00 0.00 38.40 3.18
1740 3281 3.139077 GGAAGTTCAAAGAAGGCTTCGA 58.861 45.455 20.78 10.12 37.14 3.71
1774 3315 4.371786 TCAGTGATCCGCATAGTCAATTC 58.628 43.478 0.00 0.00 0.00 2.17
1846 3387 2.143122 TGCCAAGAACGACAACTGATC 58.857 47.619 0.00 0.00 0.00 2.92
1854 3395 9.850628 TGTATAACTATATATGCCAAGAACGAC 57.149 33.333 0.00 0.00 0.00 4.34
1869 3410 5.181811 CCGGTGTGGATCGTGTATAACTATA 59.818 44.000 0.00 0.00 42.00 1.31
1870 3411 4.022589 CCGGTGTGGATCGTGTATAACTAT 60.023 45.833 0.00 0.00 42.00 2.12
1871 3412 3.316029 CCGGTGTGGATCGTGTATAACTA 59.684 47.826 0.00 0.00 42.00 2.24
1990 3535 2.032550 GTGTAGATCATGCATGTGTGGC 59.967 50.000 25.43 14.53 0.00 5.01
1994 3539 2.286025 CGGTGTGTAGATCATGCATGTG 59.714 50.000 25.43 3.46 0.00 3.21
2007 3552 4.270392 CCGATTGTGCGGTGTGTA 57.730 55.556 0.00 0.00 46.07 2.90
2111 3656 3.067106 AGTAGAAACATTGGCACGACTG 58.933 45.455 0.00 0.00 0.00 3.51
2132 3677 8.193438 CAGATGTGACATGTTAAGAGTCTCATA 58.807 37.037 1.23 0.00 42.85 2.15
2365 3913 1.142688 AGCCAGAATCCCACCAGGTT 61.143 55.000 0.00 0.00 36.75 3.50
2366 3914 1.542375 AGCCAGAATCCCACCAGGT 60.542 57.895 0.00 0.00 36.75 4.00
2367 3915 1.225704 GAGCCAGAATCCCACCAGG 59.774 63.158 0.00 0.00 0.00 4.45
2368 3916 0.622665 AAGAGCCAGAATCCCACCAG 59.377 55.000 0.00 0.00 0.00 4.00
2389 3937 3.703001 AACCTCGTGACCAAATCTCAT 57.297 42.857 0.00 0.00 0.00 2.90
2399 3947 2.000447 GCCTTGATGTAACCTCGTGAC 59.000 52.381 0.00 0.00 0.00 3.67
2403 3951 2.572191 TACGCCTTGATGTAACCTCG 57.428 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.