Multiple sequence alignment - TraesCS1B01G018600

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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 TraesCS1B01G018600 chr1B 100.000 4511 0 0 1 4511 8868230 8863720 0.000000e+00 8331.0
1 TraesCS1B01G018600 chr1B 93.593 4292 202 19 128 4380 9160898 9165155 0.000000e+00 6335.0
2 TraesCS1B01G018600 chr1B 82.849 2682 349 49 930 3552 548199967 548197338 0.000000e+00 2302.0
3 TraesCS1B01G018600 chr1B 81.659 2677 383 63 993 3607 10007492 10004862 0.000000e+00 2124.0
4 TraesCS1B01G018600 chr1B 79.920 503 82 10 1013 1503 8855868 8855373 7.180000e-93 351.0
5 TraesCS1B01G018600 chr1B 83.256 215 30 3 557 766 9280744 9280957 4.610000e-45 193.0
6 TraesCS1B01G018600 chr1D 92.475 4518 254 26 1 4473 6722593 6718117 0.000000e+00 6381.0
7 TraesCS1B01G018600 chr1D 82.251 2710 376 52 988 3641 407672556 407669896 0.000000e+00 2242.0
8 TraesCS1B01G018600 chr1D 81.403 2737 434 42 933 3625 6714676 6711971 0.000000e+00 2165.0
9 TraesCS1B01G018600 chr1D 80.930 2753 412 63 952 3641 6913119 6915821 0.000000e+00 2071.0
10 TraesCS1B01G018600 chr1D 91.684 469 25 2 471 936 6692395 6691938 4.920000e-179 638.0
11 TraesCS1B01G018600 chr1D 93.333 150 10 0 938 1087 6691906 6691757 5.870000e-54 222.0
12 TraesCS1B01G018600 chr1D 84.360 211 31 2 557 766 6897834 6898043 5.920000e-49 206.0
13 TraesCS1B01G018600 chr1D 93.617 47 2 1 521 567 6692435 6692390 8.100000e-08 69.4
14 TraesCS1B01G018600 chr1A 92.367 4035 212 30 474 4472 8160377 8156403 0.000000e+00 5657.0
15 TraesCS1B01G018600 chr1A 82.431 2641 378 46 938 3529 8331893 8334496 0.000000e+00 2228.0
16 TraesCS1B01G018600 chr1A 81.273 2734 435 42 938 3625 8144563 8141861 0.000000e+00 2141.0
17 TraesCS1B01G018600 chr1A 87.852 675 53 14 637 1288 8089150 8088482 0.000000e+00 765.0
18 TraesCS1B01G018600 chr1A 87.048 664 79 3 983 1646 8337974 8338630 0.000000e+00 743.0
19 TraesCS1B01G018600 chr1A 83.015 524 49 14 44 548 8089933 8089431 5.360000e-119 438.0
20 TraesCS1B01G018600 chr1A 91.667 288 22 2 70 355 8169980 8169693 9.090000e-107 398.0
21 TraesCS1B01G018600 chr1A 79.101 378 47 12 557 933 8326529 8326875 9.760000e-57 231.0
22 TraesCS1B01G018600 chr1A 85.854 205 22 7 3528 3727 7831016 7831218 1.270000e-50 211.0
23 TraesCS1B01G018600 chr4B 84.209 3464 438 60 223 3623 36636640 36633223 0.000000e+00 3265.0
24 TraesCS1B01G018600 chr4B 88.444 225 17 2 1 220 36639374 36639154 3.460000e-66 263.0
25 TraesCS1B01G018600 chr2B 82.088 2758 395 56 938 3642 548623928 548626639 0.000000e+00 2265.0
26 TraesCS1B01G018600 chr2B 81.640 2647 386 55 937 3536 729766537 729769130 0.000000e+00 2104.0
27 TraesCS1B01G018600 chr2B 77.568 477 81 14 3900 4359 548627195 548627662 9.620000e-67 265.0
28 TraesCS1B01G018600 chr2D 81.447 2765 406 58 938 3642 469990525 469993242 0.000000e+00 2165.0
29 TraesCS1B01G018600 chr2D 81.856 2640 383 53 937 3531 599926367 599928955 0.000000e+00 2134.0
30 TraesCS1B01G018600 chr2D 79.470 453 65 15 3926 4359 469993683 469994126 3.410000e-76 296.0
31 TraesCS1B01G018600 chr2D 95.312 64 2 1 3746 3809 469993477 469993539 2.870000e-17 100.0
32 TraesCS1B01G018600 chr2A 81.815 2645 387 48 937 3536 733628845 733631440 0.000000e+00 2134.0
33 TraesCS1B01G018600 chr5B 90.000 60 6 0 870 929 549547824 549547883 1.350000e-10 78.7
34 TraesCS1B01G018600 chr6D 94.872 39 1 1 4470 4508 468653748 468653711 4.870000e-05 60.2


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 TraesCS1B01G018600 chr1B 8863720 8868230 4510 True 8331.000000 8331 100.000000 1 4511 1 chr1B.!!$R2 4510
1 TraesCS1B01G018600 chr1B 9160898 9165155 4257 False 6335.000000 6335 93.593000 128 4380 1 chr1B.!!$F1 4252
2 TraesCS1B01G018600 chr1B 548197338 548199967 2629 True 2302.000000 2302 82.849000 930 3552 1 chr1B.!!$R4 2622
3 TraesCS1B01G018600 chr1B 10004862 10007492 2630 True 2124.000000 2124 81.659000 993 3607 1 chr1B.!!$R3 2614
4 TraesCS1B01G018600 chr1D 6711971 6722593 10622 True 4273.000000 6381 86.939000 1 4473 2 chr1D.!!$R3 4472
5 TraesCS1B01G018600 chr1D 407669896 407672556 2660 True 2242.000000 2242 82.251000 988 3641 1 chr1D.!!$R1 2653
6 TraesCS1B01G018600 chr1D 6913119 6915821 2702 False 2071.000000 2071 80.930000 952 3641 1 chr1D.!!$F2 2689
7 TraesCS1B01G018600 chr1D 6691757 6692435 678 True 309.800000 638 92.878000 471 1087 3 chr1D.!!$R2 616
8 TraesCS1B01G018600 chr1A 8156403 8160377 3974 True 5657.000000 5657 92.367000 474 4472 1 chr1A.!!$R2 3998
9 TraesCS1B01G018600 chr1A 8141861 8144563 2702 True 2141.000000 2141 81.273000 938 3625 1 chr1A.!!$R1 2687
10 TraesCS1B01G018600 chr1A 8331893 8338630 6737 False 1485.500000 2228 84.739500 938 3529 2 chr1A.!!$F3 2591
11 TraesCS1B01G018600 chr1A 8088482 8089933 1451 True 601.500000 765 85.433500 44 1288 2 chr1A.!!$R4 1244
12 TraesCS1B01G018600 chr4B 36633223 36639374 6151 True 1764.000000 3265 86.326500 1 3623 2 chr4B.!!$R1 3622
13 TraesCS1B01G018600 chr2B 729766537 729769130 2593 False 2104.000000 2104 81.640000 937 3536 1 chr2B.!!$F1 2599
14 TraesCS1B01G018600 chr2B 548623928 548627662 3734 False 1265.000000 2265 79.828000 938 4359 2 chr2B.!!$F2 3421
15 TraesCS1B01G018600 chr2D 599926367 599928955 2588 False 2134.000000 2134 81.856000 937 3531 1 chr2D.!!$F1 2594
16 TraesCS1B01G018600 chr2D 469990525 469994126 3601 False 853.666667 2165 85.409667 938 4359 3 chr2D.!!$F2 3421
17 TraesCS1B01G018600 chr2A 733628845 733631440 2595 False 2134.000000 2134 81.815000 937 3536 1 chr2A.!!$F1 2599

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
48 49 0.179029 AGTTGGTTTGTCCCTCACGG 60.179 55.0 0.0 0.0 34.77 4.94 F
663 3424 1.039856 ACGGCAGCTTTTGTGGAAAT 58.960 45.0 0.0 0.0 0.00 2.17 F
1431 4404 0.601057 GCATAAACACCACCACCACC 59.399 55.0 0.0 0.0 0.00 4.61 F
2742 5748 0.615850 AGCAGTTTAGGGCTGAGGTC 59.384 55.0 0.0 0.0 39.30 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 3898 1.075536 GGGAAAGAGGAGAAGCCCAAA 59.924 52.381 0.0 0.0 37.37 3.28 R
2259 5256 6.064060 AGCATTATAGGAATAAGCTGTGCAA 58.936 36.000 0.0 0.0 34.47 4.08 R
3276 13292 0.886563 GAAGCTTGCTGATGGCTTGT 59.113 50.000 2.1 0.0 44.81 3.16 R
3918 14512 0.105964 TGGCAGCAGTAACAAGACGT 59.894 50.000 0.0 0.0 0.00 4.34 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
46 47 5.528870 CATTTAAGTTGGTTTGTCCCTCAC 58.471 41.667 0.00 0.00 34.77 3.51
48 49 0.179029 AGTTGGTTTGTCCCTCACGG 60.179 55.000 0.00 0.00 34.77 4.94
74 80 3.555324 TTCCAGCCGACACAGCCA 61.555 61.111 0.00 0.00 0.00 4.75
140 153 2.818751 TATCCAATTCCGCCAACCTT 57.181 45.000 0.00 0.00 0.00 3.50
232 2757 3.492756 CCACGCCTTTTGGTTATTTTGTG 59.507 43.478 0.00 0.00 42.99 3.33
235 2760 5.064071 CACGCCTTTTGGTTATTTTGTGTTT 59.936 36.000 0.00 0.00 42.99 2.83
330 2855 4.927425 GTCTGTGGTCGCATTTTCTTAGTA 59.073 41.667 0.00 0.00 0.00 1.82
346 2871 8.710749 TTTCTTAGTACTGGTCTTAGGTGTTA 57.289 34.615 5.39 0.00 0.00 2.41
360 2895 7.220108 GTCTTAGGTGTTACTTTTGCTTTTGTG 59.780 37.037 0.00 0.00 0.00 3.33
411 2946 8.801882 TCTGGGTTGGTTAGTAAAATGATTAG 57.198 34.615 0.00 0.00 0.00 1.73
639 3397 2.621998 CCCCATGATTGACTTGAGCATC 59.378 50.000 0.00 0.00 0.00 3.91
663 3424 1.039856 ACGGCAGCTTTTGTGGAAAT 58.960 45.000 0.00 0.00 0.00 2.17
734 3518 1.837439 ACTGACTTGGACACTTGGTGA 59.163 47.619 4.62 0.00 36.96 4.02
780 3564 1.801178 GTGTGCTGGAGAGCTTGTAAC 59.199 52.381 0.00 0.00 46.39 2.50
818 3609 7.041372 AGCACGTAGTTTTCATGAAAATAGTGT 60.041 33.333 32.01 26.09 41.61 3.55
827 3618 4.156556 TCATGAAAATAGTGTCAGCCTTGC 59.843 41.667 0.00 0.00 0.00 4.01
878 3669 3.801997 CCTGCTCGGAATGGGGCT 61.802 66.667 0.00 0.00 33.16 5.19
1024 3898 5.603750 TGCATCCCCTCTACATATTATCCT 58.396 41.667 0.00 0.00 0.00 3.24
1041 3918 2.065799 TCCTTTGGGCTTCTCCTCTTT 58.934 47.619 0.00 0.00 34.39 2.52
1063 3943 1.449246 ACATCTTGCTGCTCCTCGC 60.449 57.895 0.00 0.00 39.77 5.03
1319 4277 3.070734 ACACAGCTCAAGATCTCAAGTGT 59.929 43.478 0.00 3.32 33.33 3.55
1349 4307 6.852858 TCTTGTCATTGTCGTAAAACATGA 57.147 33.333 0.00 0.00 0.00 3.07
1430 4403 1.269448 CAGCATAAACACCACCACCAC 59.731 52.381 0.00 0.00 0.00 4.16
1431 4404 0.601057 GCATAAACACCACCACCACC 59.399 55.000 0.00 0.00 0.00 4.61
1432 4405 1.988293 CATAAACACCACCACCACCA 58.012 50.000 0.00 0.00 0.00 4.17
1444 4417 2.146724 ACCACCACTAGTGCTGCCA 61.147 57.895 17.86 0.00 45.83 4.92
1503 4482 2.834549 AGATAGCCCATTATCGGACCTG 59.165 50.000 0.00 0.00 35.63 4.00
1659 4638 2.047061 AGCCTTGGACTAGACACAACA 58.953 47.619 0.00 0.00 0.00 3.33
1989 4971 1.596934 CCTTCCGCCTGCTACTTGA 59.403 57.895 0.00 0.00 0.00 3.02
2042 5024 1.381928 CCATCCTGTGACTGCATGCC 61.382 60.000 16.68 0.00 0.00 4.40
2106 5088 1.134580 CGAACAGGAGGATGCATCAGT 60.135 52.381 27.25 14.40 0.00 3.41
2259 5256 2.697654 GCTTGTCTCAGAACATGCTCT 58.302 47.619 0.00 0.00 43.34 4.09
2445 5445 2.068837 ATGTTGGAATTGTTGCTGCG 57.931 45.000 0.00 0.00 0.00 5.18
2484 5487 5.957842 TTGGGTTACTCATGTTCATGTTC 57.042 39.130 11.73 0.00 0.00 3.18
2742 5748 0.615850 AGCAGTTTAGGGCTGAGGTC 59.384 55.000 0.00 0.00 39.30 3.85
3013 13017 4.227300 AGCCAGGAAACATACTATTGGACA 59.773 41.667 0.00 0.00 0.00 4.02
3253 13269 1.344438 ACACTAGCAGCAGCAGTAACA 59.656 47.619 3.17 0.00 45.49 2.41
3264 13280 3.665323 GCAGCAGTAACAACAATGTCGAG 60.665 47.826 0.00 0.00 39.40 4.04
3276 13292 5.670792 ACAATGTCGAGTATTTCCCTGTA 57.329 39.130 0.00 0.00 0.00 2.74
3439 13455 0.252330 TATGGGTGAAGTGGTCCGGA 60.252 55.000 0.00 0.00 0.00 5.14
3685 13995 5.993055 AGCATTTTTAGCAAAATATGGCCT 58.007 33.333 3.32 0.00 40.09 5.19
3688 13998 6.458615 GCATTTTTAGCAAAATATGGCCTTGG 60.459 38.462 3.32 0.00 40.09 3.61
3840 14328 5.006746 GCACTACATTCTGAGGTAAATTCCG 59.993 44.000 0.00 0.00 0.00 4.30
3899 14493 7.148407 CGTATTACATTTCTTCAGGTCTTGCTT 60.148 37.037 0.00 0.00 0.00 3.91
3905 14499 6.959639 TTTCTTCAGGTCTTGCTTTACATT 57.040 33.333 0.00 0.00 0.00 2.71
3906 14500 6.959639 TTCTTCAGGTCTTGCTTTACATTT 57.040 33.333 0.00 0.00 0.00 2.32
3908 14502 6.299141 TCTTCAGGTCTTGCTTTACATTTCT 58.701 36.000 0.00 0.00 0.00 2.52
3909 14503 6.772716 TCTTCAGGTCTTGCTTTACATTTCTT 59.227 34.615 0.00 0.00 0.00 2.52
3911 14505 6.061441 TCAGGTCTTGCTTTACATTTCTTCA 58.939 36.000 0.00 0.00 0.00 3.02
3913 14507 6.860023 CAGGTCTTGCTTTACATTTCTTCAAG 59.140 38.462 0.00 0.00 0.00 3.02
3914 14508 5.631096 GGTCTTGCTTTACATTTCTTCAAGC 59.369 40.000 0.00 0.00 40.29 4.01
3915 14509 6.442112 GTCTTGCTTTACATTTCTTCAAGCT 58.558 36.000 4.03 0.00 40.48 3.74
3916 14510 6.920210 GTCTTGCTTTACATTTCTTCAAGCTT 59.080 34.615 0.00 0.00 40.48 3.74
3918 14512 6.389830 TGCTTTACATTTCTTCAAGCTTCA 57.610 33.333 0.00 0.00 40.48 3.02
3919 14513 6.208644 TGCTTTACATTTCTTCAAGCTTCAC 58.791 36.000 0.00 0.00 40.48 3.18
3920 14514 5.340667 GCTTTACATTTCTTCAAGCTTCACG 59.659 40.000 0.00 0.00 37.47 4.35
3921 14515 6.371809 TTTACATTTCTTCAAGCTTCACGT 57.628 33.333 0.00 0.00 0.00 4.49
3923 14517 4.130118 ACATTTCTTCAAGCTTCACGTCT 58.870 39.130 0.00 0.00 0.00 4.18
3924 14518 4.576463 ACATTTCTTCAAGCTTCACGTCTT 59.424 37.500 0.00 0.00 0.00 3.01
3925 14519 4.536364 TTTCTTCAAGCTTCACGTCTTG 57.464 40.909 8.10 8.10 40.62 3.02
3973 14578 4.351054 CCCAGAACCAAGCCGGCT 62.351 66.667 27.08 27.08 39.03 5.52
4149 14788 2.029369 GCCAACGTACACGGTCCA 59.971 61.111 6.72 0.00 44.95 4.02
4153 14792 1.874872 CCAACGTACACGGTCCATTTT 59.125 47.619 6.72 0.00 44.95 1.82
4292 16302 4.475944 CCAGAATGCTCAAACTTAAACGG 58.524 43.478 0.00 0.00 31.97 4.44
4318 16328 3.191162 TGAAGCTGTGCAAATGTATGTCC 59.809 43.478 0.00 0.00 0.00 4.02
4347 16359 4.398549 TGCAACTATAACGTTTCTGTGC 57.601 40.909 5.91 11.02 0.00 4.57
4368 16380 0.607489 AGCATGGACTGTGGCTGAAC 60.607 55.000 0.00 0.00 34.83 3.18
4407 16419 4.408378 GCTTTTGCCCCGGTCTAA 57.592 55.556 0.00 0.00 40.15 2.10
4434 17894 2.210116 AGCACCAACAAACAGAGTACG 58.790 47.619 0.00 0.00 0.00 3.67
4436 17896 1.070843 CACCAACAAACAGAGTACGCG 60.071 52.381 3.53 3.53 0.00 6.01
4448 17908 1.370900 GTACGCGCCCGAACGATAT 60.371 57.895 5.73 0.00 38.29 1.63
4458 17918 3.869246 GCCCGAACGATATAATATGGTGG 59.131 47.826 0.00 0.00 0.00 4.61
4460 17920 4.160814 CCCGAACGATATAATATGGTGGGA 59.839 45.833 0.00 0.00 33.52 4.37
4477 17937 2.845363 GGAAGACCCACTTACCGAAA 57.155 50.000 0.00 0.00 39.13 3.46
4478 17938 3.130280 GGAAGACCCACTTACCGAAAA 57.870 47.619 0.00 0.00 39.13 2.29
4479 17939 3.479489 GGAAGACCCACTTACCGAAAAA 58.521 45.455 0.00 0.00 39.13 1.94
4480 17940 3.501062 GGAAGACCCACTTACCGAAAAAG 59.499 47.826 0.00 0.00 39.13 2.27
4481 17941 3.136009 AGACCCACTTACCGAAAAAGG 57.864 47.619 0.00 0.00 37.30 3.11
4482 17942 2.156917 GACCCACTTACCGAAAAAGGG 58.843 52.381 0.00 0.00 37.30 3.95
4483 17943 1.496001 ACCCACTTACCGAAAAAGGGT 59.504 47.619 0.00 0.00 38.84 4.34
4484 17944 2.091720 ACCCACTTACCGAAAAAGGGTT 60.092 45.455 0.00 0.00 40.04 4.11
4485 17945 2.960384 CCCACTTACCGAAAAAGGGTTT 59.040 45.455 0.00 0.00 38.99 3.27
4486 17946 3.243602 CCCACTTACCGAAAAAGGGTTTG 60.244 47.826 0.00 0.00 38.99 2.93
4487 17947 3.377439 CACTTACCGAAAAAGGGTTTGC 58.623 45.455 0.00 0.00 38.99 3.68
4488 17948 2.363038 ACTTACCGAAAAAGGGTTTGCC 59.637 45.455 0.00 0.00 38.99 4.52
4498 17958 3.230990 GGTTTGCCCCCGCTTTGT 61.231 61.111 0.00 0.00 35.36 2.83
4499 17959 1.904378 GGTTTGCCCCCGCTTTGTA 60.904 57.895 0.00 0.00 35.36 2.41
4500 17960 1.254975 GGTTTGCCCCCGCTTTGTAT 61.255 55.000 0.00 0.00 35.36 2.29
4501 17961 0.606096 GTTTGCCCCCGCTTTGTATT 59.394 50.000 0.00 0.00 35.36 1.89
4502 17962 0.892063 TTTGCCCCCGCTTTGTATTC 59.108 50.000 0.00 0.00 35.36 1.75
4505 17965 0.968393 GCCCCCGCTTTGTATTCCAA 60.968 55.000 0.00 0.00 0.00 3.53
4506 17966 1.551452 CCCCCGCTTTGTATTCCAAA 58.449 50.000 0.00 0.00 40.71 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 74 4.954970 CAACCCACCGCTGGCTGT 62.955 66.667 0.00 0.00 36.00 4.40
74 80 2.847234 TGTCCTCAACCCACCGCT 60.847 61.111 0.00 0.00 0.00 5.52
100 113 3.568000 TGGCAACACACAGAACAGT 57.432 47.368 0.00 0.00 46.17 3.55
140 153 1.708993 GCCTGCTATGGGACCATCCA 61.709 60.000 7.19 5.86 38.64 3.41
299 2824 3.610040 TGCGACCACAGACAGAAATAT 57.390 42.857 0.00 0.00 0.00 1.28
330 2855 4.820173 GCAAAAGTAACACCTAAGACCAGT 59.180 41.667 0.00 0.00 0.00 4.00
346 2871 5.278604 GTCGAATACCACAAAAGCAAAAGT 58.721 37.500 0.00 0.00 0.00 2.66
427 2962 5.070047 CCACACGTATCCTAGGGTTATCTTT 59.930 44.000 9.46 0.00 0.00 2.52
441 2976 3.930848 CCAGAAAAGGTACCACACGTATC 59.069 47.826 15.94 2.44 0.00 2.24
445 2980 2.140717 GACCAGAAAAGGTACCACACG 58.859 52.381 15.94 0.00 43.38 4.49
663 3424 1.687563 TGGTCAAGTCAGTCGTGAGA 58.312 50.000 0.00 0.00 35.45 3.27
734 3518 5.082425 AGGAGGACTTTCAATGATGCTTTT 58.918 37.500 0.00 0.00 0.00 2.27
780 3564 4.514577 CGTGCTAGTCGGCAGGGG 62.515 72.222 0.00 0.00 43.25 4.79
818 3609 2.698274 TCTCCGTATAATGCAAGGCTGA 59.302 45.455 0.00 0.00 0.00 4.26
827 3618 6.657966 TGGTACCACTATCTCTCCGTATAATG 59.342 42.308 11.60 0.00 0.00 1.90
878 3669 9.739276 AATCAAATTCAGATTAGGACAACAGTA 57.261 29.630 4.72 0.00 34.14 2.74
1024 3898 1.075536 GGGAAAGAGGAGAAGCCCAAA 59.924 52.381 0.00 0.00 37.37 3.28
1041 3918 1.203441 AGGAGCAGCAAGATGTGGGA 61.203 55.000 0.00 0.00 0.00 4.37
1319 4277 2.884012 ACGACAATGACAAGATTGCCAA 59.116 40.909 0.00 0.00 36.89 4.52
1349 4307 1.688772 GGATTCAGTGCTGGCATCAT 58.311 50.000 0.00 0.00 0.00 2.45
1430 4403 1.209019 AGAGAATGGCAGCACTAGTGG 59.791 52.381 23.95 9.71 0.00 4.00
1431 4404 2.676839 CAAGAGAATGGCAGCACTAGTG 59.323 50.000 18.93 18.93 0.00 2.74
1432 4405 2.568956 TCAAGAGAATGGCAGCACTAGT 59.431 45.455 0.00 0.00 0.00 2.57
1444 4417 5.053978 AGGTTTCCAGTGTTCAAGAGAAT 57.946 39.130 0.00 0.00 35.92 2.40
2259 5256 6.064060 AGCATTATAGGAATAAGCTGTGCAA 58.936 36.000 0.00 0.00 34.47 4.08
2484 5487 7.452880 TTTGATCCTCCAAATCAGTAACAAG 57.547 36.000 0.00 0.00 34.76 3.16
3013 13017 4.060205 GCAACTTTTGGAGCAAATGATGT 58.940 39.130 0.00 0.00 35.43 3.06
3120 13124 1.946283 GCAACTCCACTAAGCCACTCC 60.946 57.143 0.00 0.00 0.00 3.85
3253 13269 4.906618 ACAGGGAAATACTCGACATTGTT 58.093 39.130 0.00 0.00 0.00 2.83
3264 13280 4.523083 TGATGGCTTGTACAGGGAAATAC 58.477 43.478 7.15 0.00 0.00 1.89
3276 13292 0.886563 GAAGCTTGCTGATGGCTTGT 59.113 50.000 2.10 0.00 44.81 3.16
3328 13344 7.526608 TCCAAATTGAAGTCGTCATGTAATTC 58.473 34.615 0.00 0.00 35.70 2.17
3338 13354 2.814336 GCCTCTTCCAAATTGAAGTCGT 59.186 45.455 0.00 0.00 41.96 4.34
3405 13421 1.474320 CCCATAGTCGGCCGATCAAAA 60.474 52.381 33.58 15.32 0.00 2.44
3439 13455 2.909006 TCTTCTGCAGACCCTCAAGAAT 59.091 45.455 18.03 0.00 0.00 2.40
3658 13968 6.403418 GCCATATTTTGCTAAAAATGCTTGCA 60.403 34.615 6.67 0.00 44.04 4.08
3668 13978 6.191315 TCTACCAAGGCCATATTTTGCTAAA 58.809 36.000 5.01 0.00 0.00 1.85
3669 13979 5.761205 TCTACCAAGGCCATATTTTGCTAA 58.239 37.500 5.01 0.00 0.00 3.09
3685 13995 8.006298 ACACATCAACAGAAAATTTCTACCAA 57.994 30.769 8.03 0.00 38.11 3.67
3688 13998 8.345565 AGTGACACATCAACAGAAAATTTCTAC 58.654 33.333 8.03 0.00 35.46 2.59
3742 14102 8.192110 GGTGGTTGTGAAAACTTATTTACTTGA 58.808 33.333 0.00 0.00 0.00 3.02
3899 14493 5.758296 AGACGTGAAGCTTGAAGAAATGTAA 59.242 36.000 2.10 0.00 0.00 2.41
3905 14499 3.531538 ACAAGACGTGAAGCTTGAAGAA 58.468 40.909 18.43 0.00 43.11 2.52
3906 14500 3.179443 ACAAGACGTGAAGCTTGAAGA 57.821 42.857 18.43 0.00 43.11 2.87
3908 14502 4.270084 CAGTAACAAGACGTGAAGCTTGAA 59.730 41.667 18.43 6.21 43.11 2.69
3909 14503 3.802139 CAGTAACAAGACGTGAAGCTTGA 59.198 43.478 18.43 0.00 43.11 3.02
3911 14505 2.544267 GCAGTAACAAGACGTGAAGCTT 59.456 45.455 0.00 0.00 0.00 3.74
3913 14507 2.096713 CAGCAGTAACAAGACGTGAAGC 60.097 50.000 0.00 0.00 0.00 3.86
3914 14508 2.096713 GCAGCAGTAACAAGACGTGAAG 60.097 50.000 0.00 0.00 0.00 3.02
3915 14509 1.864711 GCAGCAGTAACAAGACGTGAA 59.135 47.619 0.00 0.00 0.00 3.18
3916 14510 1.497991 GCAGCAGTAACAAGACGTGA 58.502 50.000 0.00 0.00 0.00 4.35
3918 14512 0.105964 TGGCAGCAGTAACAAGACGT 59.894 50.000 0.00 0.00 0.00 4.34
3919 14513 1.442769 ATGGCAGCAGTAACAAGACG 58.557 50.000 0.00 0.00 0.00 4.18
3920 14514 2.813754 TGAATGGCAGCAGTAACAAGAC 59.186 45.455 0.00 0.00 0.00 3.01
3921 14515 3.138884 TGAATGGCAGCAGTAACAAGA 57.861 42.857 0.00 0.00 0.00 3.02
3923 14517 3.441222 CAGATGAATGGCAGCAGTAACAA 59.559 43.478 0.00 0.00 34.69 2.83
3924 14518 3.011818 CAGATGAATGGCAGCAGTAACA 58.988 45.455 0.00 0.00 34.69 2.41
3925 14519 3.273434 TCAGATGAATGGCAGCAGTAAC 58.727 45.455 0.00 0.00 34.69 2.50
3973 14578 1.883638 GCAATGGACTGCAGGTTCAGA 60.884 52.381 19.93 0.00 42.17 3.27
4149 14788 2.945668 GGTATCTCGAAGCTGGCAAAAT 59.054 45.455 0.00 0.00 0.00 1.82
4153 14792 0.175760 GTGGTATCTCGAAGCTGGCA 59.824 55.000 0.00 0.00 0.00 4.92
4292 16302 1.269936 ACATTTGCACAGCTTCAAGGC 60.270 47.619 0.00 0.00 0.00 4.35
4318 16328 3.184541 ACGTTATAGTTGCAACTAGGCG 58.815 45.455 35.23 34.27 44.06 5.52
4347 16359 0.538584 TCAGCCACAGTCCATGCTAG 59.461 55.000 0.00 0.00 31.69 3.42
4368 16380 5.474876 AGCCTGTTTAGAGATTGTTTTCCAG 59.525 40.000 0.00 0.00 0.00 3.86
4401 16413 8.301002 TGTTTGTTGGTGCTTTATATTTAGACC 58.699 33.333 0.00 0.00 0.00 3.85
4402 16414 9.341899 CTGTTTGTTGGTGCTTTATATTTAGAC 57.658 33.333 0.00 0.00 0.00 2.59
4404 16416 9.559958 CTCTGTTTGTTGGTGCTTTATATTTAG 57.440 33.333 0.00 0.00 0.00 1.85
4407 16419 7.524717 ACTCTGTTTGTTGGTGCTTTATATT 57.475 32.000 0.00 0.00 0.00 1.28
4434 17894 2.538449 CCATATTATATCGTTCGGGCGC 59.462 50.000 0.00 0.00 0.00 6.53
4436 17896 3.869246 CCACCATATTATATCGTTCGGGC 59.131 47.826 0.00 0.00 0.00 6.13
4458 17918 2.845363 TTTCGGTAAGTGGGTCTTCC 57.155 50.000 0.00 0.00 37.56 3.46
4460 17920 3.483421 CCTTTTTCGGTAAGTGGGTCTT 58.517 45.455 0.00 0.00 39.89 3.01
4481 17941 1.254975 ATACAAAGCGGGGGCAAACC 61.255 55.000 0.00 0.00 39.11 3.27
4482 17942 0.606096 AATACAAAGCGGGGGCAAAC 59.394 50.000 0.00 0.00 0.00 2.93
4483 17943 0.892063 GAATACAAAGCGGGGGCAAA 59.108 50.000 0.00 0.00 0.00 3.68
4484 17944 0.968393 GGAATACAAAGCGGGGGCAA 60.968 55.000 0.00 0.00 0.00 4.52
4485 17945 1.379309 GGAATACAAAGCGGGGGCA 60.379 57.895 0.00 0.00 0.00 5.36
4486 17946 0.968393 TTGGAATACAAAGCGGGGGC 60.968 55.000 0.00 0.00 35.79 5.80
4487 17947 1.551452 TTTGGAATACAAAGCGGGGG 58.449 50.000 0.00 0.00 43.81 5.40


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

AutoCloner maintained by Alex Coulton.