Multiple sequence alignment - TraesCS5D01G568400

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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 TraesCS5D01G568400 chr5D 100.000 2835 0 0 1 2835 565660737 565657903 0.000000e+00 5236.0
1 TraesCS5D01G568400 chr5D 90.798 489 33 6 1018 1497 565703097 565702612 0.000000e+00 643.0
2 TraesCS5D01G568400 chr5D 87.815 238 28 1 1635 1871 565702601 565702364 7.740000e-71 278.0
3 TraesCS5D01G568400 chr5B 90.898 1648 104 27 282 1889 707475221 707476862 0.000000e+00 2170.0
4 TraesCS5D01G568400 chr5B 85.762 892 58 36 1890 2751 707476908 707477760 0.000000e+00 880.0
5 TraesCS5D01G568400 chr5B 89.775 489 38 8 1018 1494 707439994 707440482 1.440000e-172 616.0
6 TraesCS5D01G568400 chr5B 95.109 184 9 0 63 246 707475046 707475229 9.940000e-75 291.0
7 TraesCS5D01G568400 chr5B 87.037 162 20 1 1339 1499 529988183 529988344 6.240000e-42 182.0
8 TraesCS5D01G568400 chr5B 85.185 162 23 1 1339 1499 529609311 529609472 6.280000e-37 165.0
9 TraesCS5D01G568400 chr5B 94.118 51 3 0 13 63 707472499 707472549 8.420000e-11 78.7
10 TraesCS5D01G568400 chr5B 86.154 65 5 3 2685 2748 252299635 252299696 1.820000e-07 67.6
11 TraesCS5D01G568400 chr4A 90.920 1630 82 27 594 2195 607178712 607177121 0.000000e+00 2130.0
12 TraesCS5D01G568400 chr4A 90.593 489 34 7 1018 1497 607262047 607261562 3.080000e-179 638.0
13 TraesCS5D01G568400 chr4A 86.219 566 37 13 63 607 607180133 607179588 2.450000e-160 575.0
14 TraesCS5D01G568400 chr4A 90.625 416 26 7 2211 2620 607177005 607176597 8.940000e-150 540.0
15 TraesCS5D01G568400 chr4A 84.861 251 37 1 1622 1871 607261564 607261314 4.690000e-63 252.0
16 TraesCS5D01G568400 chr4A 85.556 90 13 0 2746 2835 186735767 186735678 8.360000e-16 95.3
17 TraesCS5D01G568400 chr4A 97.222 36 1 0 835 870 607263046 607263011 8.480000e-06 62.1
18 TraesCS5D01G568400 chr7D 81.333 225 24 10 113 332 626379771 626379560 1.750000e-37 167.0
19 TraesCS5D01G568400 chr7D 85.870 92 9 3 2746 2835 310372499 310372410 8.360000e-16 95.3
20 TraesCS5D01G568400 chr6D 90.123 81 8 0 270 350 412532004 412532084 3.860000e-19 106.0
21 TraesCS5D01G568400 chr6D 84.783 92 14 0 2744 2835 432354385 432354294 3.010000e-15 93.5
22 TraesCS5D01G568400 chr3D 84.906 106 14 2 270 374 555196221 555196325 3.860000e-19 106.0
23 TraesCS5D01G568400 chr3D 82.569 109 17 2 270 377 550608791 550608684 8.360000e-16 95.3
24 TraesCS5D01G568400 chr1D 87.778 90 9 2 262 350 264356465 264356553 1.390000e-18 104.0
25 TraesCS5D01G568400 chr1D 83.505 97 16 0 2739 2835 327626456 327626552 1.080000e-14 91.6
26 TraesCS5D01G568400 chr1B 86.022 93 13 0 2743 2835 609415319 609415411 1.800000e-17 100.0
27 TraesCS5D01G568400 chr1B 82.569 109 17 2 270 377 313991864 313991757 8.360000e-16 95.3
28 TraesCS5D01G568400 chr1B 79.787 94 9 5 2656 2748 575228656 575228572 3.050000e-05 60.2
29 TraesCS5D01G568400 chr4D 85.714 91 13 0 2745 2835 207783403 207783493 2.320000e-16 97.1
30 TraesCS5D01G568400 chr4D 85.714 91 12 1 2746 2835 275519692 275519602 8.360000e-16 95.3
31 TraesCS5D01G568400 chr4D 82.692 104 16 2 275 377 154756027 154755925 1.080000e-14 91.6
32 TraesCS5D01G568400 chr2D 85.556 90 13 0 2746 2835 394570981 394570892 8.360000e-16 95.3
33 TraesCS5D01G568400 chr2D 85.556 90 13 0 2746 2835 418555180 418555269 8.360000e-16 95.3
34 TraesCS5D01G568400 chr3A 81.731 104 17 2 275 377 439566823 439566721 5.030000e-13 86.1
35 TraesCS5D01G568400 chr3B 82.716 81 10 3 2668 2748 440512642 440512718 5.070000e-08 69.4
36 TraesCS5D01G568400 chr2A 81.111 90 10 4 2656 2745 712060467 712060549 6.560000e-07 65.8
37 TraesCS5D01G568400 chr6B 80.435 92 9 4 2656 2746 637877284 637877367 8.480000e-06 62.1
38 TraesCS5D01G568400 chr5A 89.362 47 3 2 2704 2749 699319315 699319360 1.100000e-04 58.4
39 TraesCS5D01G568400 chr1A 76.515 132 15 12 2626 2748 520873025 520872901 1.100000e-04 58.4
40 TraesCS5D01G568400 chr1A 75.940 133 18 9 2623 2745 5170864 5170736 3.950000e-04 56.5


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 TraesCS5D01G568400 chr5D 565657903 565660737 2834 True 5236.000000 5236 100.000000 1 2835 1 chr5D.!!$R1 2834
1 TraesCS5D01G568400 chr5D 565702364 565703097 733 True 460.500000 643 89.306500 1018 1871 2 chr5D.!!$R2 853
2 TraesCS5D01G568400 chr5B 707472499 707477760 5261 False 854.925000 2170 91.471750 13 2751 4 chr5B.!!$F5 2738
3 TraesCS5D01G568400 chr4A 607176597 607180133 3536 True 1081.666667 2130 89.254667 63 2620 3 chr4A.!!$R2 2557
4 TraesCS5D01G568400 chr4A 607261314 607263046 1732 True 317.366667 638 90.892000 835 1871 3 chr4A.!!$R3 1036

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
19 20 0.107654 GGTTTCGAGGTGGCTATGCT 60.108 55.0 0.0 0.0 0.0 3.79 F
530 3049 0.320334 TCATGCGCGAAAAGGACTGA 60.320 50.0 12.1 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 5941 0.240945 CGTAGTACCCGTCCACGTTT 59.759 55.0 0.00 0.00 37.74 3.60 R
1895 6251 0.972883 GCAGGTAGCTCCATCCTAGG 59.027 60.0 0.82 0.82 41.15 3.02 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
18 19 2.394604 GGTTTCGAGGTGGCTATGC 58.605 57.895 0.00 0.00 0.00 3.14
19 20 0.107654 GGTTTCGAGGTGGCTATGCT 60.108 55.000 0.00 0.00 0.00 3.79
20 21 1.138266 GGTTTCGAGGTGGCTATGCTA 59.862 52.381 0.00 0.00 0.00 3.49
21 22 2.224305 GGTTTCGAGGTGGCTATGCTAT 60.224 50.000 0.00 0.00 0.00 2.97
22 23 3.060602 GTTTCGAGGTGGCTATGCTATC 58.939 50.000 0.00 0.00 0.00 2.08
23 24 2.294449 TCGAGGTGGCTATGCTATCT 57.706 50.000 0.00 0.00 31.88 1.98
24 25 2.598565 TCGAGGTGGCTATGCTATCTT 58.401 47.619 0.00 0.00 28.59 2.40
25 26 3.763057 TCGAGGTGGCTATGCTATCTTA 58.237 45.455 0.00 0.00 28.59 2.10
226 2724 1.402456 CCACGTCCGGTACAGAAGAAG 60.402 57.143 0.00 0.00 0.00 2.85
228 2726 2.163815 CACGTCCGGTACAGAAGAAGAT 59.836 50.000 0.00 0.00 0.00 2.40
232 2730 3.444388 GTCCGGTACAGAAGAAGATGAGT 59.556 47.826 0.00 0.00 0.00 3.41
244 2742 2.515523 ATGAGTGAGCGCATGGGC 60.516 61.111 26.04 26.04 33.89 5.36
246 2744 4.479993 GAGTGAGCGCATGGGCCT 62.480 66.667 29.03 19.67 36.38 5.19
247 2745 4.479993 AGTGAGCGCATGGGCCTC 62.480 66.667 29.03 23.70 37.65 4.70
248 2746 4.783621 GTGAGCGCATGGGCCTCA 62.784 66.667 29.03 25.63 41.74 3.86
249 2747 4.032452 TGAGCGCATGGGCCTCAA 62.032 61.111 29.03 11.15 41.34 3.02
272 2770 2.292267 CCCTATCTGTTTGCATCGCTT 58.708 47.619 0.00 0.00 0.00 4.68
274 2772 2.938451 CCTATCTGTTTGCATCGCTTGA 59.062 45.455 0.00 0.00 0.00 3.02
340 2838 2.664081 CCTCACTGCCCTGGACCTC 61.664 68.421 0.00 0.00 0.00 3.85
364 2883 2.836154 GCCACACCTGACTCCCAA 59.164 61.111 0.00 0.00 0.00 4.12
382 2901 1.822990 CAATGCAGCCCATCTCAAACT 59.177 47.619 0.00 0.00 31.43 2.66
417 2936 5.276461 TCTCAGCACACAACTCTTTCTAA 57.724 39.130 0.00 0.00 0.00 2.10
427 2946 9.956720 CACACAACTCTTTCTAAAATCTCAAAT 57.043 29.630 0.00 0.00 0.00 2.32
456 2975 2.811431 TCAAAAATGAACTCGACGGCAT 59.189 40.909 0.00 0.00 0.00 4.40
459 2978 5.123186 TCAAAAATGAACTCGACGGCATATT 59.877 36.000 0.00 0.00 0.00 1.28
465 2984 1.887198 ACTCGACGGCATATTCTAGGG 59.113 52.381 0.00 0.00 0.00 3.53
525 3044 2.351418 TGTAGAATCATGCGCGAAAAGG 59.649 45.455 12.10 0.00 0.00 3.11
530 3049 0.320334 TCATGCGCGAAAAGGACTGA 60.320 50.000 12.10 0.00 0.00 3.41
570 3089 4.081087 ACAAACACGCTTGGATAGGTAGAT 60.081 41.667 0.00 0.00 0.00 1.98
573 3092 5.392767 ACACGCTTGGATAGGTAGATATG 57.607 43.478 0.00 0.00 0.00 1.78
683 4096 6.853872 CGTACTAATTCTGAACTAGCTAGCTG 59.146 42.308 27.68 18.34 0.00 4.24
816 4237 0.409484 ATTAAGTTGGGCTGGCAGGT 59.591 50.000 17.64 0.00 0.00 4.00
820 4241 4.047125 TTGGGCTGGCAGGTAGGC 62.047 66.667 17.64 2.71 44.50 3.93
1023 5307 2.544721 GATAGAGATCCCATGGAGGCA 58.455 52.381 15.22 0.00 34.05 4.75
1452 5748 3.317571 ACGCTGGAGGAGCTGCTT 61.318 61.111 9.91 0.00 46.64 3.91
1539 5842 7.591057 TGAACTCGCAAAGAACATATTTTTCTG 59.409 33.333 0.00 0.00 33.46 3.02
1579 5883 6.790285 ATTGTGATGATTTTGTTGGCTTTC 57.210 33.333 0.00 0.00 0.00 2.62
1633 5941 4.348461 TGTGAACTGTAGGTGGGATTGTTA 59.652 41.667 0.00 0.00 0.00 2.41
1841 6150 0.250901 GTGGACACCATGACCTGCTT 60.251 55.000 0.00 0.00 35.28 3.91
1854 6163 0.753111 CCTGCTTACCATCCAAGCCC 60.753 60.000 4.75 0.00 46.32 5.19
1857 6166 0.179018 GCTTACCATCCAAGCCCGAT 60.179 55.000 0.00 0.00 42.08 4.18
1863 6172 1.905215 CCATCCAAGCCCGATATCTCT 59.095 52.381 0.34 0.00 0.00 3.10
1886 6196 4.453093 GCTAGCTAGCCTGGCTTG 57.547 61.111 31.67 25.55 43.98 4.01
1887 6197 1.524482 GCTAGCTAGCCTGGCTTGT 59.476 57.895 31.67 16.68 43.98 3.16
1888 6198 0.753262 GCTAGCTAGCCTGGCTTGTA 59.247 55.000 31.67 16.89 43.98 2.41
1895 6251 3.615351 GCTAGCCTGGCTTGTATACTAGC 60.615 52.174 28.55 25.35 42.83 3.42
1905 6261 5.017490 GCTTGTATACTAGCCTAGGATGGA 58.983 45.833 23.64 0.22 38.48 3.41
1906 6262 5.126384 GCTTGTATACTAGCCTAGGATGGAG 59.874 48.000 23.64 6.31 38.48 3.86
1907 6263 4.601084 TGTATACTAGCCTAGGATGGAGC 58.399 47.826 18.24 4.61 30.32 4.70
1908 6264 4.292571 TGTATACTAGCCTAGGATGGAGCT 59.707 45.833 18.24 5.77 39.37 4.09
1909 6265 5.491439 TGTATACTAGCCTAGGATGGAGCTA 59.509 44.000 18.24 6.68 36.79 3.32
1913 6271 0.972883 GCCTAGGATGGAGCTACCTG 59.027 60.000 14.75 0.00 39.86 4.00
2152 6526 1.135094 TCTGGGGGAGATGCTGATTC 58.865 55.000 0.00 0.00 0.00 2.52
2335 6810 4.691216 AGTAGCTACAACTTGCAGCTTTAC 59.309 41.667 25.28 13.33 44.21 2.01
2343 6818 1.169661 TTGCAGCTTTACCCGTGTGG 61.170 55.000 0.00 0.00 41.37 4.17
2499 6979 1.140652 TGTTCATGTGCTGTCCAGTCA 59.859 47.619 0.00 0.00 0.00 3.41
2536 7023 1.173913 GTATCCAACCAACACAGGCC 58.826 55.000 0.00 0.00 0.00 5.19
2562 7049 3.735746 CGTGGAAAGAAACCAAAGAATGC 59.264 43.478 0.00 0.00 39.22 3.56
2563 7050 4.692228 GTGGAAAGAAACCAAAGAATGCA 58.308 39.130 0.00 0.00 39.22 3.96
2617 7104 5.046231 ACCCTCACAATTCTTCTTAGACTCC 60.046 44.000 0.00 0.00 0.00 3.85
2633 7120 7.836685 TCTTAGACTCCTCACAATGAGAAGTAT 59.163 37.037 7.41 2.61 42.34 2.12
2637 7124 7.782168 AGACTCCTCACAATGAGAAGTATCATA 59.218 37.037 7.41 0.00 42.34 2.15
2638 7125 8.311395 ACTCCTCACAATGAGAAGTATCATAA 57.689 34.615 7.41 0.00 40.43 1.90
2671 7166 6.286240 TCATGCATATGATACTACCTCCAC 57.714 41.667 6.97 0.00 38.37 4.02
2673 7168 6.269769 TCATGCATATGATACTACCTCCACAA 59.730 38.462 6.97 0.00 38.37 3.33
2683 7184 8.094548 TGATACTACCTCCACAATATAATGCAC 58.905 37.037 0.00 0.00 0.00 4.57
2685 7186 6.658849 ACTACCTCCACAATATAATGCACAA 58.341 36.000 0.00 0.00 0.00 3.33
2722 7223 7.983484 TCGTAGCATCATATCTGCATCATTTAT 59.017 33.333 8.97 0.00 42.15 1.40
2750 7251 7.154656 TCATGCATGACACATATTAGTACTCC 58.845 38.462 25.42 0.00 0.00 3.85
2751 7252 5.853936 TGCATGACACATATTAGTACTCCC 58.146 41.667 0.00 0.00 0.00 4.30
2752 7253 5.602561 TGCATGACACATATTAGTACTCCCT 59.397 40.000 0.00 0.00 0.00 4.20
2753 7254 6.159988 GCATGACACATATTAGTACTCCCTC 58.840 44.000 0.00 0.00 0.00 4.30
2754 7255 6.692486 CATGACACATATTAGTACTCCCTCC 58.308 44.000 0.00 0.00 0.00 4.30
2755 7256 5.773091 TGACACATATTAGTACTCCCTCCA 58.227 41.667 0.00 0.00 0.00 3.86
2756 7257 6.382087 TGACACATATTAGTACTCCCTCCAT 58.618 40.000 0.00 0.00 0.00 3.41
2757 7258 7.532199 TGACACATATTAGTACTCCCTCCATA 58.468 38.462 0.00 0.00 0.00 2.74
2758 7259 8.177456 TGACACATATTAGTACTCCCTCCATAT 58.823 37.037 0.00 0.00 0.00 1.78
2759 7260 8.596781 ACACATATTAGTACTCCCTCCATATC 57.403 38.462 0.00 0.00 0.00 1.63
2760 7261 7.339721 ACACATATTAGTACTCCCTCCATATCG 59.660 40.741 0.00 0.00 0.00 2.92
2761 7262 7.556635 CACATATTAGTACTCCCTCCATATCGA 59.443 40.741 0.00 0.00 0.00 3.59
2762 7263 8.282982 ACATATTAGTACTCCCTCCATATCGAT 58.717 37.037 2.16 2.16 0.00 3.59
2763 7264 8.572185 CATATTAGTACTCCCTCCATATCGATG 58.428 40.741 8.54 0.00 0.00 3.84
2777 7278 6.115450 CATATCGATGGATTAGGCACATTG 57.885 41.667 8.54 0.00 34.00 2.82
2778 7279 2.221169 TCGATGGATTAGGCACATTGC 58.779 47.619 0.00 0.00 44.08 3.56
2779 7280 4.504689 TATCGATGGATTAGGCACATTGCA 60.505 41.667 8.54 0.00 38.44 4.08
2780 7281 5.976379 TATCGATGGATTAGGCACATTGCAA 60.976 40.000 8.54 0.00 38.44 4.08
2781 7282 7.411930 TATCGATGGATTAGGCACATTGCAAA 61.412 38.462 8.54 0.00 38.44 3.68
2782 7283 8.815343 TATCGATGGATTAGGCACATTGCAAAA 61.815 37.037 8.54 0.00 38.44 2.44
2794 7295 7.958112 GCACATTGCAAAAATGAAATAATCC 57.042 32.000 1.71 0.00 44.26 3.01
2795 7296 6.968335 GCACATTGCAAAAATGAAATAATCCC 59.032 34.615 1.71 0.00 44.26 3.85
2796 7297 7.361885 GCACATTGCAAAAATGAAATAATCCCA 60.362 33.333 1.71 0.00 44.26 4.37
2797 7298 8.512956 CACATTGCAAAAATGAAATAATCCCAA 58.487 29.630 1.71 0.00 0.00 4.12
2798 7299 9.075678 ACATTGCAAAAATGAAATAATCCCAAA 57.924 25.926 1.71 0.00 0.00 3.28
2799 7300 9.909644 CATTGCAAAAATGAAATAATCCCAAAA 57.090 25.926 1.71 0.00 0.00 2.44
2800 7301 9.911138 ATTGCAAAAATGAAATAATCCCAAAAC 57.089 25.926 1.71 0.00 0.00 2.43
2801 7302 8.455903 TGCAAAAATGAAATAATCCCAAAACA 57.544 26.923 0.00 0.00 0.00 2.83
2802 7303 8.348507 TGCAAAAATGAAATAATCCCAAAACAC 58.651 29.630 0.00 0.00 0.00 3.32
2803 7304 8.567104 GCAAAAATGAAATAATCCCAAAACACT 58.433 29.630 0.00 0.00 0.00 3.55
2807 7308 9.942850 AAATGAAATAATCCCAAAACACTTAGG 57.057 29.630 0.00 0.00 0.00 2.69
2808 7309 6.930731 TGAAATAATCCCAAAACACTTAGGC 58.069 36.000 0.00 0.00 0.00 3.93
2809 7310 5.576447 AATAATCCCAAAACACTTAGGCG 57.424 39.130 0.00 0.00 0.00 5.52
2810 7311 1.173913 ATCCCAAAACACTTAGGCGC 58.826 50.000 0.00 0.00 0.00 6.53
2811 7312 1.209127 CCCAAAACACTTAGGCGCG 59.791 57.895 0.00 0.00 0.00 6.86
2812 7313 1.209127 CCAAAACACTTAGGCGCGG 59.791 57.895 8.83 0.00 0.00 6.46
2813 7314 1.512156 CCAAAACACTTAGGCGCGGT 61.512 55.000 8.83 0.00 0.00 5.68
2814 7315 0.385473 CAAAACACTTAGGCGCGGTG 60.385 55.000 8.83 9.75 37.05 4.94
2815 7316 2.125202 AAAACACTTAGGCGCGGTGC 62.125 55.000 8.83 4.64 45.38 5.01
2824 7325 3.486263 GCGCGGTGCATTAACTCT 58.514 55.556 8.83 0.00 45.45 3.24
2825 7326 1.348594 GCGCGGTGCATTAACTCTC 59.651 57.895 8.83 0.00 45.45 3.20
2826 7327 1.358725 GCGCGGTGCATTAACTCTCA 61.359 55.000 8.83 0.00 45.45 3.27
2827 7328 0.370273 CGCGGTGCATTAACTCTCAC 59.630 55.000 0.00 0.00 0.00 3.51
2828 7329 1.438651 GCGGTGCATTAACTCTCACA 58.561 50.000 0.00 0.00 0.00 3.58
2829 7330 2.009774 GCGGTGCATTAACTCTCACAT 58.990 47.619 0.00 0.00 0.00 3.21
2830 7331 2.030946 GCGGTGCATTAACTCTCACATC 59.969 50.000 0.00 0.00 0.00 3.06
2831 7332 2.282555 CGGTGCATTAACTCTCACATCG 59.717 50.000 0.00 0.00 0.00 3.84
2832 7333 3.262420 GGTGCATTAACTCTCACATCGT 58.738 45.455 0.00 0.00 0.00 3.73
2833 7334 3.684788 GGTGCATTAACTCTCACATCGTT 59.315 43.478 0.00 0.00 0.00 3.85
2834 7335 4.154195 GGTGCATTAACTCTCACATCGTTT 59.846 41.667 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.596904 TAGCATAGCCACCTCGAAAC 57.403 50.000 0.00 0.00 0.00 2.78
3 4 2.598565 AGATAGCATAGCCACCTCGAA 58.401 47.619 0.00 0.00 0.00 3.71
6 7 5.930837 AGATAAGATAGCATAGCCACCTC 57.069 43.478 0.00 0.00 0.00 3.85
7 8 6.326064 CCATAGATAAGATAGCATAGCCACCT 59.674 42.308 0.00 0.00 0.00 4.00
8 9 6.098982 ACCATAGATAAGATAGCATAGCCACC 59.901 42.308 0.00 0.00 0.00 4.61
9 10 6.983307 CACCATAGATAAGATAGCATAGCCAC 59.017 42.308 0.00 0.00 0.00 5.01
10 11 6.669591 ACACCATAGATAAGATAGCATAGCCA 59.330 38.462 0.00 0.00 0.00 4.75
11 12 7.118496 ACACCATAGATAAGATAGCATAGCC 57.882 40.000 0.00 0.00 0.00 3.93
12 13 8.253810 TCAACACCATAGATAAGATAGCATAGC 58.746 37.037 0.00 0.00 0.00 2.97
15 16 8.600668 ACATCAACACCATAGATAAGATAGCAT 58.399 33.333 0.00 0.00 0.00 3.79
16 17 7.966812 ACATCAACACCATAGATAAGATAGCA 58.033 34.615 0.00 0.00 0.00 3.49
17 18 8.715998 CAACATCAACACCATAGATAAGATAGC 58.284 37.037 0.00 0.00 0.00 2.97
18 19 9.212641 CCAACATCAACACCATAGATAAGATAG 57.787 37.037 0.00 0.00 0.00 2.08
19 20 7.661437 GCCAACATCAACACCATAGATAAGATA 59.339 37.037 0.00 0.00 0.00 1.98
20 21 6.488006 GCCAACATCAACACCATAGATAAGAT 59.512 38.462 0.00 0.00 0.00 2.40
21 22 5.822519 GCCAACATCAACACCATAGATAAGA 59.177 40.000 0.00 0.00 0.00 2.10
22 23 5.589855 TGCCAACATCAACACCATAGATAAG 59.410 40.000 0.00 0.00 0.00 1.73
23 24 5.504853 TGCCAACATCAACACCATAGATAA 58.495 37.500 0.00 0.00 0.00 1.75
24 25 5.109500 TGCCAACATCAACACCATAGATA 57.891 39.130 0.00 0.00 0.00 1.98
25 26 3.966979 TGCCAACATCAACACCATAGAT 58.033 40.909 0.00 0.00 0.00 1.98
101 2599 5.732331 ACCCAAAATCCTGAGATTATGGA 57.268 39.130 0.00 0.00 42.03 3.41
226 2724 2.541120 GCCCATGCGCTCACTCATC 61.541 63.158 9.73 0.00 0.00 2.92
228 2726 4.783621 GGCCCATGCGCTCACTCA 62.784 66.667 9.73 0.00 38.85 3.41
232 2730 3.348554 ATTGAGGCCCATGCGCTCA 62.349 57.895 9.73 0.00 40.63 4.26
244 2742 2.360165 GCAAACAGATAGGGCATTGAGG 59.640 50.000 0.00 0.00 0.00 3.86
246 2744 3.084536 TGCAAACAGATAGGGCATTGA 57.915 42.857 0.00 0.00 0.00 2.57
247 2745 3.549423 CGATGCAAACAGATAGGGCATTG 60.549 47.826 0.00 0.00 44.52 2.82
248 2746 2.620115 CGATGCAAACAGATAGGGCATT 59.380 45.455 0.00 0.00 44.52 3.56
249 2747 2.224606 CGATGCAAACAGATAGGGCAT 58.775 47.619 0.00 0.00 46.91 4.40
272 2770 2.922503 TGGCCCTGCTCGAGTTCA 60.923 61.111 15.13 3.28 0.00 3.18
274 2772 4.400961 GCTGGCCCTGCTCGAGTT 62.401 66.667 15.13 0.00 0.00 3.01
351 2870 1.310933 GCTGCATTGGGAGTCAGGTG 61.311 60.000 0.00 0.00 34.49 4.00
352 2871 1.001641 GCTGCATTGGGAGTCAGGT 60.002 57.895 0.00 0.00 34.49 4.00
355 2874 1.866483 ATGGGCTGCATTGGGAGTCA 61.866 55.000 0.50 0.00 39.09 3.41
364 2883 1.471119 CAGTTTGAGATGGGCTGCAT 58.529 50.000 0.50 0.00 0.00 3.96
382 2901 4.081185 TGAGAATCTGCCGCCGCA 62.081 61.111 0.00 0.00 44.78 5.69
427 2946 8.172484 CCGTCGAGTTCATTTTTGATATTACAA 58.828 33.333 0.00 0.00 0.00 2.41
434 2953 2.811431 TGCCGTCGAGTTCATTTTTGAT 59.189 40.909 0.00 0.00 0.00 2.57
456 2975 8.019537 TCCCAGAATATACTTCCCCTAGAATA 57.980 38.462 0.00 0.00 32.82 1.75
459 2978 5.755365 GCTCCCAGAATATACTTCCCCTAGA 60.755 48.000 0.00 0.00 0.00 2.43
465 2984 6.515696 GCAAAATGCTCCCAGAATATACTTCC 60.516 42.308 0.00 0.00 40.96 3.46
506 3025 2.607635 GTCCTTTTCGCGCATGATTCTA 59.392 45.455 8.75 0.00 0.00 2.10
513 3032 1.639298 GCTCAGTCCTTTTCGCGCAT 61.639 55.000 8.75 0.00 0.00 4.73
525 3044 4.093556 GTGTAGTGCAATTAAGGCTCAGTC 59.906 45.833 0.00 0.00 0.00 3.51
530 3049 4.582656 TGTTTGTGTAGTGCAATTAAGGCT 59.417 37.500 0.00 0.00 0.00 4.58
570 3089 6.749923 TGCACAATAACATACTGTTGCATA 57.250 33.333 2.85 0.00 41.30 3.14
573 3092 6.949578 AAATGCACAATAACATACTGTTGC 57.050 33.333 2.85 0.00 41.30 4.17
643 4052 9.610705 AGAATTAGTACGACAGACTACTTGATA 57.389 33.333 0.00 0.00 0.00 2.15
658 4068 6.853872 CAGCTAGCTAGTTCAGAATTAGTACG 59.146 42.308 18.86 0.00 0.00 3.67
816 4237 6.940298 GCTTGGATGTTGGTATAATAAGCCTA 59.060 38.462 0.00 0.00 33.75 3.93
820 4241 6.488006 AGCTGCTTGGATGTTGGTATAATAAG 59.512 38.462 0.00 0.00 0.00 1.73
889 4332 1.079405 GTAGCTAAGGTGCGGTGCA 60.079 57.895 0.00 0.00 38.13 4.57
1072 5362 2.348605 TTCTTGCCGCTGTTGTTGCC 62.349 55.000 0.00 0.00 0.00 4.52
1313 5609 2.440247 TCTCGCCGATCAGCTCCA 60.440 61.111 0.00 0.00 0.00 3.86
1539 5842 7.748683 TCATCACAATTTTGCACGAAACTATAC 59.251 33.333 0.00 0.00 0.00 1.47
1556 5859 5.406175 CGAAAGCCAACAAAATCATCACAAT 59.594 36.000 0.00 0.00 0.00 2.71
1575 5879 4.032217 CCTCGATCAAACTCATCACGAAAG 59.968 45.833 0.00 0.00 0.00 2.62
1579 5883 2.600420 CACCTCGATCAAACTCATCACG 59.400 50.000 0.00 0.00 0.00 4.35
1633 5941 0.240945 CGTAGTACCCGTCCACGTTT 59.759 55.000 0.00 0.00 37.74 3.60
1841 6150 2.832129 GAGATATCGGGCTTGGATGGTA 59.168 50.000 0.00 0.00 0.00 3.25
1854 6163 3.585748 GCTAGCTAGCGAGAGATATCG 57.414 52.381 28.89 0.75 45.48 2.92
1884 6194 5.017490 GCTCCATCCTAGGCTAGTATACAA 58.983 45.833 19.68 0.98 0.00 2.41
1886 6196 4.862371 AGCTCCATCCTAGGCTAGTATAC 58.138 47.826 19.68 0.00 32.94 1.47
1887 6197 5.104024 GGTAGCTCCATCCTAGGCTAGTATA 60.104 48.000 19.68 5.93 37.85 1.47
1888 6198 4.325501 GGTAGCTCCATCCTAGGCTAGTAT 60.326 50.000 19.68 7.31 37.85 2.12
1895 6251 0.972883 GCAGGTAGCTCCATCCTAGG 59.027 60.000 0.82 0.82 41.15 3.02
1906 6262 2.743636 TGTGTAGTTGAGCAGGTAGC 57.256 50.000 0.00 0.00 46.19 3.58
1907 6263 7.097192 TCTTAATTGTGTAGTTGAGCAGGTAG 58.903 38.462 0.00 0.00 0.00 3.18
1908 6264 6.999950 TCTTAATTGTGTAGTTGAGCAGGTA 58.000 36.000 0.00 0.00 0.00 3.08
1909 6265 5.865085 TCTTAATTGTGTAGTTGAGCAGGT 58.135 37.500 0.00 0.00 0.00 4.00
1913 6271 7.806690 TGTCAATCTTAATTGTGTAGTTGAGC 58.193 34.615 0.00 0.00 42.46 4.26
2098 6466 4.950050 AGATACCACATACTAGCACAAGC 58.050 43.478 0.00 0.00 42.56 4.01
2099 6467 7.334421 ACAAAAGATACCACATACTAGCACAAG 59.666 37.037 0.00 0.00 0.00 3.16
2158 6532 2.989253 GGTTGCCAAGAACCCCCG 60.989 66.667 0.00 0.00 39.74 5.73
2225 6699 3.257393 GCCACATCCATCATCGATCTAC 58.743 50.000 0.00 0.00 0.00 2.59
2354 6829 1.348696 TGACCTCTCACACACATGCAT 59.651 47.619 0.00 0.00 0.00 3.96
2499 6979 6.914665 TGGATACTTGGATTGGATCAGATTT 58.085 36.000 0.00 0.00 37.61 2.17
2536 7023 3.625764 TCTTTGGTTTCTTTCCACGTCTG 59.374 43.478 0.00 0.00 34.45 3.51
2562 7049 1.400846 GAGTGAGCATTGTGAGCCATG 59.599 52.381 0.00 0.00 0.00 3.66
2563 7050 1.281287 AGAGTGAGCATTGTGAGCCAT 59.719 47.619 0.00 0.00 0.00 4.40
2658 7153 8.094548 TGTGCATTATATTGTGGAGGTAGTATC 58.905 37.037 0.00 0.00 0.00 2.24
2659 7154 7.973402 TGTGCATTATATTGTGGAGGTAGTAT 58.027 34.615 0.00 0.00 0.00 2.12
2665 7160 8.339344 TGATATTGTGCATTATATTGTGGAGG 57.661 34.615 0.00 0.00 0.00 4.30
2694 7195 5.727434 TGATGCAGATATGATGCTACGAAT 58.273 37.500 10.09 0.00 44.17 3.34
2697 7198 6.418585 AAATGATGCAGATATGATGCTACG 57.581 37.500 10.09 0.00 44.17 3.51
2698 7199 9.717892 CAATAAATGATGCAGATATGATGCTAC 57.282 33.333 10.09 5.70 44.17 3.58
2710 7211 6.212955 TCATGCATGACAATAAATGATGCAG 58.787 36.000 25.42 0.00 46.33 4.41
2737 7238 8.572185 CATCGATATGGAGGGAGTACTAATATG 58.428 40.741 0.00 0.00 0.00 1.78
2753 7254 8.326453 GCAATGTGCCTAATCCATCGATATGG 62.326 46.154 0.00 0.00 45.03 2.74
2754 7255 5.448225 GCAATGTGCCTAATCCATCGATATG 60.448 44.000 0.00 0.00 37.42 1.78
2755 7256 4.637534 GCAATGTGCCTAATCCATCGATAT 59.362 41.667 0.00 0.00 37.42 1.63
2756 7257 4.002982 GCAATGTGCCTAATCCATCGATA 58.997 43.478 0.00 0.00 37.42 2.92
2757 7258 2.816087 GCAATGTGCCTAATCCATCGAT 59.184 45.455 0.00 0.00 37.42 3.59
2758 7259 2.221169 GCAATGTGCCTAATCCATCGA 58.779 47.619 0.00 0.00 37.42 3.59
2759 7260 1.948834 TGCAATGTGCCTAATCCATCG 59.051 47.619 0.00 0.00 44.23 3.84
2760 7261 4.389890 TTTGCAATGTGCCTAATCCATC 57.610 40.909 0.00 0.00 44.23 3.51
2761 7262 4.822685 TTTTGCAATGTGCCTAATCCAT 57.177 36.364 0.00 0.00 44.23 3.41
2762 7263 4.613925 TTTTTGCAATGTGCCTAATCCA 57.386 36.364 0.00 0.00 44.23 3.41
2763 7264 5.177326 TCATTTTTGCAATGTGCCTAATCC 58.823 37.500 0.00 0.00 44.23 3.01
2764 7265 6.724694 TTCATTTTTGCAATGTGCCTAATC 57.275 33.333 0.00 0.00 44.23 1.75
2765 7266 7.690952 ATTTCATTTTTGCAATGTGCCTAAT 57.309 28.000 0.00 0.00 44.23 1.73
2766 7267 8.613060 TTATTTCATTTTTGCAATGTGCCTAA 57.387 26.923 0.00 0.00 44.23 2.69
2767 7268 8.789825 ATTATTTCATTTTTGCAATGTGCCTA 57.210 26.923 0.00 0.00 44.23 3.93
2768 7269 7.148205 GGATTATTTCATTTTTGCAATGTGCCT 60.148 33.333 0.00 0.00 44.23 4.75
2769 7270 6.968335 GGATTATTTCATTTTTGCAATGTGCC 59.032 34.615 0.00 0.00 44.23 5.01
2770 7271 6.968335 GGGATTATTTCATTTTTGCAATGTGC 59.032 34.615 0.00 0.00 45.29 4.57
2771 7272 8.041829 TGGGATTATTTCATTTTTGCAATGTG 57.958 30.769 0.00 0.00 0.00 3.21
2772 7273 8.632906 TTGGGATTATTTCATTTTTGCAATGT 57.367 26.923 0.00 0.00 0.00 2.71
2773 7274 9.909644 TTTTGGGATTATTTCATTTTTGCAATG 57.090 25.926 0.00 0.00 0.00 2.82
2774 7275 9.911138 GTTTTGGGATTATTTCATTTTTGCAAT 57.089 25.926 0.00 0.00 0.00 3.56
2775 7276 8.906867 TGTTTTGGGATTATTTCATTTTTGCAA 58.093 25.926 0.00 0.00 0.00 4.08
2776 7277 8.348507 GTGTTTTGGGATTATTTCATTTTTGCA 58.651 29.630 0.00 0.00 0.00 4.08
2777 7278 8.567104 AGTGTTTTGGGATTATTTCATTTTTGC 58.433 29.630 0.00 0.00 0.00 3.68
2781 7282 9.942850 CCTAAGTGTTTTGGGATTATTTCATTT 57.057 29.630 0.00 0.00 0.00 2.32
2782 7283 8.040727 GCCTAAGTGTTTTGGGATTATTTCATT 58.959 33.333 0.00 0.00 30.91 2.57
2783 7284 7.555965 GCCTAAGTGTTTTGGGATTATTTCAT 58.444 34.615 0.00 0.00 30.91 2.57
2784 7285 6.349777 CGCCTAAGTGTTTTGGGATTATTTCA 60.350 38.462 0.00 0.00 30.91 2.69
2785 7286 6.033966 CGCCTAAGTGTTTTGGGATTATTTC 58.966 40.000 0.00 0.00 30.91 2.17
2786 7287 5.623596 GCGCCTAAGTGTTTTGGGATTATTT 60.624 40.000 0.00 0.00 30.91 1.40
2787 7288 4.142249 GCGCCTAAGTGTTTTGGGATTATT 60.142 41.667 0.00 0.00 30.91 1.40
2788 7289 3.380320 GCGCCTAAGTGTTTTGGGATTAT 59.620 43.478 0.00 0.00 30.91 1.28
2789 7290 2.750712 GCGCCTAAGTGTTTTGGGATTA 59.249 45.455 0.00 0.00 30.91 1.75
2790 7291 1.544246 GCGCCTAAGTGTTTTGGGATT 59.456 47.619 0.00 0.00 30.91 3.01
2791 7292 1.173913 GCGCCTAAGTGTTTTGGGAT 58.826 50.000 0.00 0.00 30.91 3.85
2792 7293 1.231958 CGCGCCTAAGTGTTTTGGGA 61.232 55.000 0.00 0.00 30.91 4.37
2793 7294 1.209127 CGCGCCTAAGTGTTTTGGG 59.791 57.895 0.00 0.00 30.91 4.12
2794 7295 1.209127 CCGCGCCTAAGTGTTTTGG 59.791 57.895 0.00 0.00 33.04 3.28
2795 7296 0.385473 CACCGCGCCTAAGTGTTTTG 60.385 55.000 0.00 0.00 0.00 2.44
2796 7297 1.946267 CACCGCGCCTAAGTGTTTT 59.054 52.632 0.00 0.00 0.00 2.43
2797 7298 2.613506 GCACCGCGCCTAAGTGTTT 61.614 57.895 12.83 0.00 33.96 2.83
2798 7299 3.047877 GCACCGCGCCTAAGTGTT 61.048 61.111 12.83 0.00 33.96 3.32
2799 7300 3.605749 ATGCACCGCGCCTAAGTGT 62.606 57.895 12.83 0.00 41.33 3.55
2800 7301 1.087202 TAATGCACCGCGCCTAAGTG 61.087 55.000 0.00 4.02 41.33 3.16
2801 7302 0.391927 TTAATGCACCGCGCCTAAGT 60.392 50.000 0.00 0.00 41.33 2.24
2802 7303 0.027586 GTTAATGCACCGCGCCTAAG 59.972 55.000 0.00 0.00 41.33 2.18
2803 7304 0.391927 AGTTAATGCACCGCGCCTAA 60.392 50.000 0.00 0.00 41.33 2.69
2804 7305 0.808453 GAGTTAATGCACCGCGCCTA 60.808 55.000 0.00 0.00 41.33 3.93
2805 7306 2.046314 AGTTAATGCACCGCGCCT 60.046 55.556 0.00 0.00 41.33 5.52
2806 7307 2.036764 GAGAGTTAATGCACCGCGCC 62.037 60.000 0.00 0.00 41.33 6.53
2807 7308 1.348594 GAGAGTTAATGCACCGCGC 59.651 57.895 0.00 0.00 42.89 6.86
2808 7309 0.370273 GTGAGAGTTAATGCACCGCG 59.630 55.000 0.00 0.00 0.00 6.46
2809 7310 1.438651 TGTGAGAGTTAATGCACCGC 58.561 50.000 0.00 0.00 0.00 5.68
2810 7311 2.282555 CGATGTGAGAGTTAATGCACCG 59.717 50.000 0.00 0.00 0.00 4.94
2811 7312 3.262420 ACGATGTGAGAGTTAATGCACC 58.738 45.455 0.00 0.00 0.00 5.01
2812 7313 4.928661 AACGATGTGAGAGTTAATGCAC 57.071 40.909 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.