Multiple sequence alignment - TraesCS3A01G049900

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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 TraesCS3A01G049900 chr3A 100.000 2594 0 0 1 2594 26261229 26263822 0.000000e+00 4791.0
1 TraesCS3A01G049900 chr3A 90.232 1464 133 8 314 1770 26481456 26482916 0.000000e+00 1903.0
2 TraesCS3A01G049900 chr3A 85.978 271 30 7 1 265 26481188 26481456 1.520000e-72 283.0
3 TraesCS3A01G049900 chr3A 88.034 117 9 2 2198 2314 26429683 26429794 1.620000e-27 134.0
4 TraesCS3A01G049900 chr3A 86.735 98 13 0 2042 2139 26429482 26429579 2.730000e-20 110.0
5 TraesCS3A01G049900 chr3A 91.228 57 5 0 1788 1844 26429104 26429160 7.700000e-11 78.7
6 TraesCS3A01G049900 chr3A 100.000 40 0 0 2320 2359 26429836 26429875 9.960000e-10 75.0
7 TraesCS3A01G049900 chr3B 92.949 1787 112 12 1 1776 30517011 30518794 0.000000e+00 2590.0
8 TraesCS3A01G049900 chr3B 91.343 1779 129 8 1 1770 30504003 30505765 0.000000e+00 2409.0
9 TraesCS3A01G049900 chr3B 90.950 1779 147 7 1 1766 30207002 30208779 0.000000e+00 2381.0
10 TraesCS3A01G049900 chr3B 90.899 1780 149 8 1 1767 29781613 29783392 0.000000e+00 2377.0
11 TraesCS3A01G049900 chr3B 90.903 1539 124 14 235 1770 29853880 29855405 0.000000e+00 2052.0
12 TraesCS3A01G049900 chr3B 82.118 576 53 16 1768 2317 29629947 29630498 5.090000e-122 448.0
13 TraesCS3A01G049900 chr3B 86.364 374 36 11 1768 2139 29783422 29783782 6.730000e-106 394.0
14 TraesCS3A01G049900 chr3B 85.662 272 28 6 1 265 30532985 30533252 2.540000e-70 276.0
15 TraesCS3A01G049900 chr3B 86.900 229 18 6 1787 2008 30208914 30209137 1.990000e-61 246.0
16 TraesCS3A01G049900 chr3B 87.981 208 22 2 1931 2138 30535577 30535781 2.580000e-60 243.0
17 TraesCS3A01G049900 chr3B 85.167 209 19 7 2165 2365 30247079 30247283 1.220000e-48 204.0
18 TraesCS3A01G049900 chr3B 92.632 95 7 0 1770 1864 29855434 29855528 1.250000e-28 137.0
19 TraesCS3A01G049900 chr3B 88.136 118 9 2 2198 2315 29736544 29736656 4.500000e-28 135.0
20 TraesCS3A01G049900 chr3B 84.000 100 12 3 2042 2139 29736343 29736440 2.750000e-15 93.5
21 TraesCS3A01G049900 chr3B 91.228 57 5 0 1788 1844 29735965 29736021 7.700000e-11 78.7
22 TraesCS3A01G049900 chr3D 90.150 1868 150 17 276 2133 18908624 18910467 0.000000e+00 2399.0
23 TraesCS3A01G049900 chr3D 90.179 112 7 1 2204 2315 18954653 18954760 2.690000e-30 143.0
24 TraesCS3A01G049900 chr3D 84.848 99 11 3 2042 2138 18954454 18954550 2.120000e-16 97.1
25 TraesCS3A01G049900 chr3D 89.333 75 8 0 1770 1844 18954058 18954132 7.640000e-16 95.3
26 TraesCS3A01G049900 chr3D 88.312 77 8 1 1768 1844 18802759 18802834 9.890000e-15 91.6
27 TraesCS3A01G049900 chr3D 95.652 46 2 0 2320 2365 18954803 18954848 9.960000e-10 75.0
28 TraesCS3A01G049900 chr7B 90.621 1546 125 9 235 1770 64321531 64323066 0.000000e+00 2034.0
29 TraesCS3A01G049900 chr7B 87.554 233 19 6 1911 2139 64323206 64323432 7.120000e-66 261.0
30 TraesCS3A01G049900 chr7D 90.635 1495 129 6 280 1772 105686153 105687638 0.000000e+00 1975.0


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 TraesCS3A01G049900 chr3A 26261229 26263822 2593 False 4791.0 4791 100.0000 1 2594 1 chr3A.!!$F1 2593
1 TraesCS3A01G049900 chr3A 26481188 26482916 1728 False 1093.0 1903 88.1050 1 1770 2 chr3A.!!$F3 1769
2 TraesCS3A01G049900 chr3B 30517011 30518794 1783 False 2590.0 2590 92.9490 1 1776 1 chr3B.!!$F4 1775
3 TraesCS3A01G049900 chr3B 30504003 30505765 1762 False 2409.0 2409 91.3430 1 1770 1 chr3B.!!$F3 1769
4 TraesCS3A01G049900 chr3B 29781613 29783782 2169 False 1385.5 2377 88.6315 1 2139 2 chr3B.!!$F6 2138
5 TraesCS3A01G049900 chr3B 30207002 30209137 2135 False 1313.5 2381 88.9250 1 2008 2 chr3B.!!$F8 2007
6 TraesCS3A01G049900 chr3B 29853880 29855528 1648 False 1094.5 2052 91.7675 235 1864 2 chr3B.!!$F7 1629
7 TraesCS3A01G049900 chr3B 29629947 29630498 551 False 448.0 448 82.1180 1768 2317 1 chr3B.!!$F1 549
8 TraesCS3A01G049900 chr3B 30532985 30535781 2796 False 259.5 276 86.8215 1 2138 2 chr3B.!!$F9 2137
9 TraesCS3A01G049900 chr3D 18908624 18910467 1843 False 2399.0 2399 90.1500 276 2133 1 chr3D.!!$F2 1857
10 TraesCS3A01G049900 chr7B 64321531 64323432 1901 False 1147.5 2034 89.0875 235 2139 2 chr7B.!!$F1 1904
11 TraesCS3A01G049900 chr7D 105686153 105687638 1485 False 1975.0 1975 90.6350 280 1772 1 chr7D.!!$F1 1492

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
55 58 1.622725 CCAGGTAGCAAGGGGACTAGT 60.623 57.143 0.0 0.0 42.68 2.57 F
1073 1091 1.722034 AGCTTTGGAGTGGTCTCAGA 58.278 50.000 0.0 0.0 42.05 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1113 0.179065 TCTCCAGCAGCATCATTCCG 60.179 55.0 0.00 0.00 0.00 4.30 R
2094 3119 0.042621 GGAGAGTAGTACGTACGCGC 60.043 60.0 19.49 16.95 42.83 6.86 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
55 58 1.622725 CCAGGTAGCAAGGGGACTAGT 60.623 57.143 0.00 0.00 42.68 2.57
103 106 5.294060 GCTCAAACTTTTGCCATTTTCTCAA 59.706 36.000 0.00 0.00 38.05 3.02
380 397 8.046708 TGCTCTTTACATGTATTTATGTCCTGT 58.953 33.333 6.36 0.00 41.31 4.00
508 525 7.251704 AGCTCCAAAAAGATACATGTATTCG 57.748 36.000 19.19 5.29 0.00 3.34
567 584 2.066592 TGGGAAAGGTGGTTATGGTGA 58.933 47.619 0.00 0.00 0.00 4.02
573 590 3.434940 AGGTGGTTATGGTGAGGTTTC 57.565 47.619 0.00 0.00 0.00 2.78
583 600 2.239400 GGTGAGGTTTCCAAAGGAAGG 58.761 52.381 0.00 0.00 43.06 3.46
656 673 2.178912 TGGGGACGAGTTTGTGAATC 57.821 50.000 0.00 0.00 0.00 2.52
673 690 4.037208 GTGAATCAGGTTATGAGCATTGGG 59.963 45.833 0.00 0.00 42.53 4.12
900 918 3.944422 ATACGCATCGTCCATTTTGAC 57.056 42.857 0.00 0.00 41.54 3.18
903 921 2.487762 ACGCATCGTCCATTTTGACATT 59.512 40.909 0.00 0.00 33.69 2.71
1072 1090 2.421619 GAAGCTTTGGAGTGGTCTCAG 58.578 52.381 0.00 0.00 42.05 3.35
1073 1091 1.722034 AGCTTTGGAGTGGTCTCAGA 58.278 50.000 0.00 0.00 42.05 3.27
1148 1166 7.178983 AGGCAGGAGAAATGTAAAATCAATTGA 59.821 33.333 11.26 11.26 0.00 2.57
1246 1264 6.791887 GTGAAGTCACATCAGAAATTGAGA 57.208 37.500 6.57 0.00 45.75 3.27
1478 1504 4.737855 ACTTGACCTACACGCATATCTT 57.262 40.909 0.00 0.00 0.00 2.40
1484 1510 6.811954 TGACCTACACGCATATCTTTCATTA 58.188 36.000 0.00 0.00 0.00 1.90
1585 1611 6.155827 TCAAAAATCCTACAAAAATCGCCAG 58.844 36.000 0.00 0.00 0.00 4.85
1628 1654 9.109393 GCTATGTGAATCAAAGAACCTACATTA 57.891 33.333 0.00 0.00 0.00 1.90
1827 2753 0.543749 GGAGGCAGACAGCTACCAAT 59.456 55.000 0.00 0.00 44.79 3.16
1888 2900 4.250464 CACGATTTGGGCTCTAACTACAA 58.750 43.478 0.00 0.00 0.00 2.41
1903 2915 8.625786 TCTAACTACAACCCCTAAAATTTCAC 57.374 34.615 0.00 0.00 0.00 3.18
1910 2922 4.668636 ACCCCTAAAATTTCACAATCCGA 58.331 39.130 0.00 0.00 0.00 4.55
1918 2930 9.467258 CTAAAATTTCACAATCCGAATGCATAT 57.533 29.630 0.00 0.00 0.00 1.78
1920 2932 8.801715 AAATTTCACAATCCGAATGCATATAC 57.198 30.769 0.00 0.00 0.00 1.47
2008 3031 0.928229 GCGCATACTTACTTGGTCCG 59.072 55.000 0.30 0.00 0.00 4.79
2056 3080 2.126850 GCGCCGTGCTTTTCCTTC 60.127 61.111 0.00 0.00 41.73 3.46
2094 3119 3.977244 GCAACCACCGCCCAACTG 61.977 66.667 0.00 0.00 0.00 3.16
2151 3191 1.574428 GTTTGCACATCGCTTCCGT 59.426 52.632 0.00 0.00 43.06 4.69
2204 3253 4.973055 CCGCAACGGTTGGTCGGA 62.973 66.667 25.88 0.00 42.73 4.55
2210 3259 1.189524 AACGGTTGGTCGGAGATCCA 61.190 55.000 0.00 0.00 36.35 3.41
2211 3260 1.153628 CGGTTGGTCGGAGATCCAC 60.154 63.158 0.00 0.00 36.35 4.02
2212 3261 1.153628 GGTTGGTCGGAGATCCACG 60.154 63.158 0.00 0.55 36.35 4.94
2213 3262 1.810030 GTTGGTCGGAGATCCACGC 60.810 63.158 0.00 0.00 36.35 5.34
2219 3268 3.838271 GGAGATCCACGCGCCAGA 61.838 66.667 5.73 0.00 35.64 3.86
2256 3305 2.884685 CAGGCTCTTCTCTGCGCG 60.885 66.667 0.00 0.00 0.00 6.86
2259 3308 4.443266 GCTCTTCTCTGCGCGGGT 62.443 66.667 17.88 0.00 0.00 5.28
2346 3395 3.849953 GCAACGCCGATCCACGTC 61.850 66.667 7.99 0.00 42.68 4.34
2356 3405 4.762825 TCCACGTCGGAGGTTTTG 57.237 55.556 0.00 0.00 39.64 2.44
2357 3406 1.070105 TCCACGTCGGAGGTTTTGG 59.930 57.895 0.00 0.31 39.64 3.28
2358 3407 1.964373 CCACGTCGGAGGTTTTGGG 60.964 63.158 0.00 0.00 36.56 4.12
2359 3408 1.227734 CACGTCGGAGGTTTTGGGT 60.228 57.895 0.00 0.00 0.00 4.51
2360 3409 0.816421 CACGTCGGAGGTTTTGGGTT 60.816 55.000 0.00 0.00 0.00 4.11
2361 3410 0.758123 ACGTCGGAGGTTTTGGGTTA 59.242 50.000 0.00 0.00 0.00 2.85
2362 3411 1.348696 ACGTCGGAGGTTTTGGGTTAT 59.651 47.619 0.00 0.00 0.00 1.89
2363 3412 2.566724 ACGTCGGAGGTTTTGGGTTATA 59.433 45.455 0.00 0.00 0.00 0.98
2364 3413 3.192466 CGTCGGAGGTTTTGGGTTATAG 58.808 50.000 0.00 0.00 0.00 1.31
2365 3414 3.119029 CGTCGGAGGTTTTGGGTTATAGA 60.119 47.826 0.00 0.00 0.00 1.98
2366 3415 4.186926 GTCGGAGGTTTTGGGTTATAGAC 58.813 47.826 0.00 0.00 0.00 2.59
2367 3416 4.081254 GTCGGAGGTTTTGGGTTATAGACT 60.081 45.833 0.00 0.00 0.00 3.24
2368 3417 5.127682 GTCGGAGGTTTTGGGTTATAGACTA 59.872 44.000 0.00 0.00 0.00 2.59
2369 3418 5.127682 TCGGAGGTTTTGGGTTATAGACTAC 59.872 44.000 0.00 0.00 0.00 2.73
2370 3419 5.678583 GGAGGTTTTGGGTTATAGACTACC 58.321 45.833 0.00 0.00 0.00 3.18
2371 3420 5.427806 GGAGGTTTTGGGTTATAGACTACCT 59.572 44.000 0.00 0.00 36.26 3.08
2372 3421 6.612863 GGAGGTTTTGGGTTATAGACTACCTA 59.387 42.308 0.00 0.00 33.85 3.08
2373 3422 7.291885 GGAGGTTTTGGGTTATAGACTACCTAT 59.708 40.741 0.00 0.00 40.92 2.57
2374 3423 8.634188 AGGTTTTGGGTTATAGACTACCTATT 57.366 34.615 0.00 0.00 38.87 1.73
2375 3424 9.065722 AGGTTTTGGGTTATAGACTACCTATTT 57.934 33.333 0.00 0.00 38.87 1.40
2376 3425 9.690913 GGTTTTGGGTTATAGACTACCTATTTT 57.309 33.333 0.00 0.00 38.87 1.82
2401 3450 6.698359 TTGCGAAATAAAACAAACCATAGC 57.302 33.333 0.00 0.00 0.00 2.97
2402 3451 4.854291 TGCGAAATAAAACAAACCATAGCG 59.146 37.500 0.00 0.00 0.00 4.26
2403 3452 4.854839 GCGAAATAAAACAAACCATAGCGT 59.145 37.500 0.00 0.00 0.00 5.07
2404 3453 5.003121 GCGAAATAAAACAAACCATAGCGTC 59.997 40.000 0.00 0.00 0.00 5.19
2405 3454 6.311723 CGAAATAAAACAAACCATAGCGTCT 58.688 36.000 0.00 0.00 0.00 4.18
2406 3455 6.799925 CGAAATAAAACAAACCATAGCGTCTT 59.200 34.615 0.00 0.00 0.00 3.01
2407 3456 7.958567 CGAAATAAAACAAACCATAGCGTCTTA 59.041 33.333 0.00 0.00 0.00 2.10
2408 3457 9.274065 GAAATAAAACAAACCATAGCGTCTTAG 57.726 33.333 0.00 0.00 0.00 2.18
2409 3458 8.556213 AATAAAACAAACCATAGCGTCTTAGA 57.444 30.769 0.00 0.00 0.00 2.10
2410 3459 6.870971 AAAACAAACCATAGCGTCTTAGAA 57.129 33.333 0.00 0.00 0.00 2.10
2411 3460 6.481954 AAACAAACCATAGCGTCTTAGAAG 57.518 37.500 0.00 0.00 0.00 2.85
2412 3461 3.933332 ACAAACCATAGCGTCTTAGAAGC 59.067 43.478 12.02 12.02 37.32 3.86
2413 3462 3.887621 AACCATAGCGTCTTAGAAGCA 57.112 42.857 20.87 8.48 39.36 3.91
2414 3463 3.444703 ACCATAGCGTCTTAGAAGCAG 57.555 47.619 20.87 10.65 39.36 4.24
2415 3464 2.101582 ACCATAGCGTCTTAGAAGCAGG 59.898 50.000 20.87 19.45 39.36 4.85
2416 3465 2.362397 CCATAGCGTCTTAGAAGCAGGA 59.638 50.000 20.87 7.29 39.36 3.86
2417 3466 3.181475 CCATAGCGTCTTAGAAGCAGGAA 60.181 47.826 20.87 5.20 39.36 3.36
2418 3467 2.663826 AGCGTCTTAGAAGCAGGAAG 57.336 50.000 20.87 0.00 39.36 3.46
2419 3468 1.003108 GCGTCTTAGAAGCAGGAAGC 58.997 55.000 14.79 0.00 46.19 3.86
2429 3478 2.044452 GCAGGAAGCATAATGGGCC 58.956 57.895 0.00 0.00 44.79 5.80
2430 3479 1.799258 GCAGGAAGCATAATGGGCCG 61.799 60.000 0.00 0.00 44.79 6.13
2431 3480 1.151450 AGGAAGCATAATGGGCCGG 59.849 57.895 0.00 0.00 0.00 6.13
2432 3481 2.564721 GGAAGCATAATGGGCCGGC 61.565 63.158 21.18 21.18 0.00 6.13
2433 3482 2.521708 AAGCATAATGGGCCGGCC 60.522 61.111 38.57 38.57 0.00 6.13
2434 3483 3.372422 AAGCATAATGGGCCGGCCA 62.372 57.895 44.46 30.82 37.98 5.36
2435 3484 3.605664 GCATAATGGGCCGGCCAC 61.606 66.667 44.46 32.87 37.98 5.01
2436 3485 2.123939 CATAATGGGCCGGCCACA 60.124 61.111 44.46 36.91 37.98 4.17
2437 3486 2.123897 ATAATGGGCCGGCCACAC 60.124 61.111 44.46 28.85 37.98 3.82
2438 3487 2.990083 ATAATGGGCCGGCCACACA 61.990 57.895 44.46 33.39 37.98 3.72
2439 3488 2.506884 ATAATGGGCCGGCCACACAA 62.507 55.000 44.46 28.39 37.98 3.33
2445 3494 2.353189 CCGGCCACACAACCCATA 59.647 61.111 2.24 0.00 0.00 2.74
2446 3495 2.043980 CCGGCCACACAACCCATAC 61.044 63.158 2.24 0.00 0.00 2.39
2447 3496 1.002624 CGGCCACACAACCCATACT 60.003 57.895 2.24 0.00 0.00 2.12
2448 3497 0.608035 CGGCCACACAACCCATACTT 60.608 55.000 2.24 0.00 0.00 2.24
2449 3498 1.627864 GGCCACACAACCCATACTTT 58.372 50.000 0.00 0.00 0.00 2.66
2450 3499 2.797786 GGCCACACAACCCATACTTTA 58.202 47.619 0.00 0.00 0.00 1.85
2451 3500 3.361786 GGCCACACAACCCATACTTTAT 58.638 45.455 0.00 0.00 0.00 1.40
2452 3501 4.528920 GGCCACACAACCCATACTTTATA 58.471 43.478 0.00 0.00 0.00 0.98
2453 3502 5.137551 GGCCACACAACCCATACTTTATAT 58.862 41.667 0.00 0.00 0.00 0.86
2454 3503 5.596772 GGCCACACAACCCATACTTTATATT 59.403 40.000 0.00 0.00 0.00 1.28
2455 3504 6.097696 GGCCACACAACCCATACTTTATATTT 59.902 38.462 0.00 0.00 0.00 1.40
2456 3505 7.364320 GGCCACACAACCCATACTTTATATTTT 60.364 37.037 0.00 0.00 0.00 1.82
2457 3506 7.704899 GCCACACAACCCATACTTTATATTTTC 59.295 37.037 0.00 0.00 0.00 2.29
2458 3507 8.966868 CCACACAACCCATACTTTATATTTTCT 58.033 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.689649 CCTTGCTACCTGGAACATAACAC 59.310 47.826 0.00 0.00 38.20 3.32
32 35 0.035343 GTCCCCTTGCTACCTGGAAC 60.035 60.000 0.00 0.00 0.00 3.62
55 58 9.480861 AGCATACCTATTAGCATACTCATCTTA 57.519 33.333 0.00 0.00 0.00 2.10
123 126 8.693625 ACATAGAAATAACTGTAGTGGACTACC 58.306 37.037 13.22 0.00 46.22 3.18
380 397 5.891551 GTCTTTTCCCCTTTCTATGCCATAA 59.108 40.000 0.00 0.00 0.00 1.90
567 584 2.445525 TGTAGCCTTCCTTTGGAAACCT 59.554 45.455 0.53 2.94 41.54 3.50
573 590 2.009774 CATCGTGTAGCCTTCCTTTGG 58.990 52.381 0.00 0.00 0.00 3.28
656 673 2.173356 TCCTCCCAATGCTCATAACCTG 59.827 50.000 0.00 0.00 0.00 4.00
673 690 9.482627 CTAACAATATTAACATGAGAGGTCCTC 57.517 37.037 11.31 11.31 42.30 3.71
716 733 1.065854 AGCTCGTTTTGATCCCTCCAG 60.066 52.381 0.00 0.00 0.00 3.86
858 876 6.808008 ATATTACAGCCATGATGCAAGTAC 57.192 37.500 0.00 0.00 0.00 2.73
900 918 6.983906 AGAAGGATATTTTGGGGCTTAATG 57.016 37.500 0.00 0.00 0.00 1.90
903 921 6.388689 TGTCTAGAAGGATATTTTGGGGCTTA 59.611 38.462 0.00 0.00 0.00 3.09
1072 1090 9.362539 TCCGTAACTATAAACATCTGACTTTTC 57.637 33.333 0.00 0.00 0.00 2.29
1073 1091 9.715121 TTCCGTAACTATAAACATCTGACTTTT 57.285 29.630 0.00 0.00 0.00 2.27
1095 1113 0.179065 TCTCCAGCAGCATCATTCCG 60.179 55.000 0.00 0.00 0.00 4.30
1148 1166 3.665745 ACTTTTCGCTGGATTTTGCAT 57.334 38.095 0.00 0.00 0.00 3.96
1246 1264 9.783081 AATTAAGGTCATCTTTCTTGCAATTTT 57.217 25.926 0.00 0.00 36.93 1.82
1371 1389 4.343239 AGCAATCCTGAGAAGTTTTGCTTT 59.657 37.500 3.43 0.00 45.32 3.51
1478 1504 6.017934 GTGAGCTGAACTTTCACTGTAATGAA 60.018 38.462 0.00 0.00 38.49 2.57
1484 1510 3.266510 TGTGAGCTGAACTTTCACTGT 57.733 42.857 0.00 0.00 41.30 3.55
1601 1627 6.472016 TGTAGGTTCTTTGATTCACATAGCA 58.528 36.000 0.00 0.00 0.00 3.49
1628 1654 5.242393 CCATCTTCTCACAGTGTTGGAAATT 59.758 40.000 0.00 0.00 0.00 1.82
1671 1704 1.981533 GCTGCGCTTGTTCAATTTCTC 59.018 47.619 9.73 0.00 0.00 2.87
1827 2753 5.300792 GGGGAAAATTACAGTCAACAAGTCA 59.699 40.000 0.00 0.00 0.00 3.41
1888 2900 4.668636 TCGGATTGTGAAATTTTAGGGGT 58.331 39.130 0.00 0.00 0.00 4.95
1903 2915 5.240891 AGACTGGTATATGCATTCGGATTG 58.759 41.667 3.54 0.00 0.00 2.67
1910 2922 8.623903 CACAATGTTTAGACTGGTATATGCATT 58.376 33.333 3.54 0.00 0.00 3.56
1941 2960 8.578448 TGCTTGCTATGAATTGGCATATATAA 57.422 30.769 0.00 0.00 35.84 0.98
1942 2961 8.048514 TCTGCTTGCTATGAATTGGCATATATA 58.951 33.333 0.00 0.00 35.84 0.86
1943 2962 6.888088 TCTGCTTGCTATGAATTGGCATATAT 59.112 34.615 0.00 0.00 35.84 0.86
2094 3119 0.042621 GGAGAGTAGTACGTACGCGC 60.043 60.000 19.49 16.95 42.83 6.86
2099 3124 1.202580 GCGGAGGGAGAGTAGTACGTA 60.203 57.143 0.00 0.00 0.00 3.57
2190 3239 0.739813 GGATCTCCGACCAACCGTTG 60.740 60.000 4.12 4.12 0.00 4.10
2192 3241 1.608336 TGGATCTCCGACCAACCGT 60.608 57.895 0.00 0.00 39.43 4.83
2204 3253 2.185350 CTTCTGGCGCGTGGATCT 59.815 61.111 8.43 0.00 0.00 2.75
2232 3281 0.687427 AGAGAAGAGCCTGGCCTCTC 60.687 60.000 24.75 24.75 41.19 3.20
2329 3378 3.849953 GACGTGGATCGGCGTTGC 61.850 66.667 6.85 4.31 44.69 4.17
2340 3389 1.964373 CCCAAAACCTCCGACGTGG 60.964 63.158 0.00 0.00 40.09 4.94
2341 3390 0.816421 AACCCAAAACCTCCGACGTG 60.816 55.000 0.00 0.00 0.00 4.49
2342 3391 0.758123 TAACCCAAAACCTCCGACGT 59.242 50.000 0.00 0.00 0.00 4.34
2343 3392 2.103537 ATAACCCAAAACCTCCGACG 57.896 50.000 0.00 0.00 0.00 5.12
2344 3393 4.081254 AGTCTATAACCCAAAACCTCCGAC 60.081 45.833 0.00 0.00 0.00 4.79
2345 3394 4.098894 AGTCTATAACCCAAAACCTCCGA 58.901 43.478 0.00 0.00 0.00 4.55
2346 3395 4.482952 AGTCTATAACCCAAAACCTCCG 57.517 45.455 0.00 0.00 0.00 4.63
2347 3396 5.427806 AGGTAGTCTATAACCCAAAACCTCC 59.572 44.000 0.00 0.00 36.34 4.30
2348 3397 6.556974 AGGTAGTCTATAACCCAAAACCTC 57.443 41.667 0.00 0.00 36.34 3.85
2349 3398 8.634188 AATAGGTAGTCTATAACCCAAAACCT 57.366 34.615 0.00 0.00 37.69 3.50
2350 3399 9.690913 AAAATAGGTAGTCTATAACCCAAAACC 57.309 33.333 0.00 0.00 37.69 3.27
2375 3424 8.064814 GCTATGGTTTGTTTTATTTCGCAAAAA 58.935 29.630 0.00 0.00 33.43 1.94
2376 3425 7.567771 CGCTATGGTTTGTTTTATTTCGCAAAA 60.568 33.333 0.00 0.00 33.43 2.44
2377 3426 6.129062 CGCTATGGTTTGTTTTATTTCGCAAA 60.129 34.615 0.00 0.00 0.00 3.68
2378 3427 5.343593 CGCTATGGTTTGTTTTATTTCGCAA 59.656 36.000 0.00 0.00 0.00 4.85
2379 3428 4.854291 CGCTATGGTTTGTTTTATTTCGCA 59.146 37.500 0.00 0.00 0.00 5.10
2380 3429 4.854839 ACGCTATGGTTTGTTTTATTTCGC 59.145 37.500 0.00 0.00 0.00 4.70
2381 3430 6.311723 AGACGCTATGGTTTGTTTTATTTCG 58.688 36.000 0.00 0.00 0.00 3.46
2382 3431 9.274065 CTAAGACGCTATGGTTTGTTTTATTTC 57.726 33.333 0.00 0.00 0.00 2.17
2383 3432 9.005777 TCTAAGACGCTATGGTTTGTTTTATTT 57.994 29.630 0.00 0.00 0.00 1.40
2384 3433 8.556213 TCTAAGACGCTATGGTTTGTTTTATT 57.444 30.769 0.00 0.00 0.00 1.40
2385 3434 8.556213 TTCTAAGACGCTATGGTTTGTTTTAT 57.444 30.769 0.00 0.00 0.00 1.40
2386 3435 7.360607 GCTTCTAAGACGCTATGGTTTGTTTTA 60.361 37.037 0.00 0.00 0.00 1.52
2387 3436 6.567891 GCTTCTAAGACGCTATGGTTTGTTTT 60.568 38.462 0.00 0.00 0.00 2.43
2388 3437 5.106673 GCTTCTAAGACGCTATGGTTTGTTT 60.107 40.000 0.00 0.00 0.00 2.83
2389 3438 4.392138 GCTTCTAAGACGCTATGGTTTGTT 59.608 41.667 0.00 0.00 0.00 2.83
2390 3439 3.933332 GCTTCTAAGACGCTATGGTTTGT 59.067 43.478 0.00 0.00 0.00 2.83
2391 3440 3.932710 TGCTTCTAAGACGCTATGGTTTG 59.067 43.478 0.00 0.00 0.00 2.93
2392 3441 4.184629 CTGCTTCTAAGACGCTATGGTTT 58.815 43.478 0.00 0.00 0.00 3.27
2393 3442 3.430929 CCTGCTTCTAAGACGCTATGGTT 60.431 47.826 0.00 0.00 0.00 3.67
2394 3443 2.101582 CCTGCTTCTAAGACGCTATGGT 59.898 50.000 0.00 0.00 0.00 3.55
2395 3444 2.362397 TCCTGCTTCTAAGACGCTATGG 59.638 50.000 0.00 0.00 0.00 2.74
2396 3445 3.717400 TCCTGCTTCTAAGACGCTATG 57.283 47.619 0.00 0.00 0.00 2.23
2397 3446 3.491792 GCTTCCTGCTTCTAAGACGCTAT 60.492 47.826 0.00 0.00 38.95 2.97
2398 3447 2.159226 GCTTCCTGCTTCTAAGACGCTA 60.159 50.000 0.00 0.00 38.95 4.26
2399 3448 1.404851 GCTTCCTGCTTCTAAGACGCT 60.405 52.381 0.00 0.00 38.95 5.07
2400 3449 1.003108 GCTTCCTGCTTCTAAGACGC 58.997 55.000 0.00 0.00 38.95 5.19
2401 3450 2.370281 TGCTTCCTGCTTCTAAGACG 57.630 50.000 0.00 0.00 43.37 4.18
2402 3451 5.238214 CCATTATGCTTCCTGCTTCTAAGAC 59.762 44.000 0.00 0.00 43.37 3.01
2403 3452 5.371526 CCATTATGCTTCCTGCTTCTAAGA 58.628 41.667 0.00 0.00 43.37 2.10
2404 3453 4.518211 CCCATTATGCTTCCTGCTTCTAAG 59.482 45.833 0.00 0.00 43.37 2.18
2405 3454 4.464008 CCCATTATGCTTCCTGCTTCTAA 58.536 43.478 0.00 0.00 43.37 2.10
2406 3455 3.748668 GCCCATTATGCTTCCTGCTTCTA 60.749 47.826 0.00 0.00 43.37 2.10
2407 3456 2.941480 CCCATTATGCTTCCTGCTTCT 58.059 47.619 0.00 0.00 43.37 2.85
2408 3457 1.339291 GCCCATTATGCTTCCTGCTTC 59.661 52.381 0.00 0.00 43.37 3.86
2409 3458 1.406903 GCCCATTATGCTTCCTGCTT 58.593 50.000 0.00 0.00 43.37 3.91
2410 3459 0.468771 GGCCCATTATGCTTCCTGCT 60.469 55.000 0.00 0.00 43.37 4.24
2411 3460 1.799258 CGGCCCATTATGCTTCCTGC 61.799 60.000 0.00 0.00 43.25 4.85
2412 3461 1.174712 CCGGCCCATTATGCTTCCTG 61.175 60.000 0.00 0.00 0.00 3.86
2413 3462 1.151450 CCGGCCCATTATGCTTCCT 59.849 57.895 0.00 0.00 0.00 3.36
2414 3463 2.564721 GCCGGCCCATTATGCTTCC 61.565 63.158 18.11 0.00 0.00 3.46
2415 3464 2.564721 GGCCGGCCCATTATGCTTC 61.565 63.158 36.64 4.38 0.00 3.86
2416 3465 2.521708 GGCCGGCCCATTATGCTT 60.522 61.111 36.64 0.00 0.00 3.91
2417 3466 3.819652 TGGCCGGCCCATTATGCT 61.820 61.111 41.75 0.00 39.18 3.79
2427 3476 3.929334 TATGGGTTGTGTGGCCGGC 62.929 63.158 21.18 21.18 0.00 6.13
2428 3477 2.043980 GTATGGGTTGTGTGGCCGG 61.044 63.158 0.00 0.00 0.00 6.13
2429 3478 0.608035 AAGTATGGGTTGTGTGGCCG 60.608 55.000 0.00 0.00 0.00 6.13
2430 3479 1.627864 AAAGTATGGGTTGTGTGGCC 58.372 50.000 0.00 0.00 0.00 5.36
2431 3480 6.709018 AATATAAAGTATGGGTTGTGTGGC 57.291 37.500 0.00 0.00 0.00 5.01
2432 3481 8.966868 AGAAAATATAAAGTATGGGTTGTGTGG 58.033 33.333 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.