Multiple sequence alignment - TraesCS7A01G274700

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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 TraesCS7A01G274700 chr7A 100.000 3176 0 0 1 3176 287612013 287615188 0.000000e+00 5866
1 TraesCS7A01G274700 chr7A 94.064 1196 27 12 306 1488 660200560 660199396 0.000000e+00 1775
2 TraesCS7A01G274700 chr7A 91.226 1003 61 14 1 990 207882507 207883495 0.000000e+00 1339
3 TraesCS7A01G274700 chr7A 98.858 438 5 0 2739 3176 195711710 195712147 0.000000e+00 782
4 TraesCS7A01G274700 chr7A 98.858 438 5 0 2739 3176 490956223 490955786 0.000000e+00 782
5 TraesCS7A01G274700 chr7A 87.231 603 66 10 894 1492 207883433 207884028 0.000000e+00 676
6 TraesCS7A01G274700 chr7A 85.981 107 12 3 1449 1554 287613399 287613503 9.310000e-21 111
7 TraesCS7A01G274700 chr2B 98.979 2743 26 1 1 2743 457193552 457196292 0.000000e+00 4909
8 TraesCS7A01G274700 chr2B 98.903 1367 15 0 1376 2742 25339762 25338396 0.000000e+00 2442
9 TraesCS7A01G274700 chr2B 95.866 1258 38 12 306 1554 25340899 25339647 0.000000e+00 2023
10 TraesCS7A01G274700 chr3B 96.974 2743 65 8 1 2742 465044250 465041525 0.000000e+00 4590
11 TraesCS7A01G274700 chr3B 89.340 1379 116 18 1387 2743 656603251 656601882 0.000000e+00 1703
12 TraesCS7A01G274700 chr3B 85.950 1452 117 41 221 1641 656604409 656603014 0.000000e+00 1471
13 TraesCS7A01G274700 chr1B 98.963 1350 14 0 1390 2739 573062360 573063709 0.000000e+00 2416
14 TraesCS7A01G274700 chr1B 98.963 1350 14 0 1390 2739 573066996 573068345 0.000000e+00 2416
15 TraesCS7A01G274700 chr4B 96.795 1373 41 3 1376 2745 649665226 649663854 0.000000e+00 2289
16 TraesCS7A01G274700 chr4B 89.827 462 41 5 894 1352 498932899 498933357 3.530000e-164 588
17 TraesCS7A01G274700 chr5A 87.967 1687 133 40 1 1637 634172131 634170465 0.000000e+00 1927
18 TraesCS7A01G274700 chr5A 89.759 1328 109 19 1416 2739 634170545 634169241 0.000000e+00 1674
19 TraesCS7A01G274700 chr5A 90.936 1004 63 14 1 990 452242195 452243184 0.000000e+00 1325
20 TraesCS7A01G274700 chr5A 98.858 438 5 0 2739 3176 169872553 169872116 0.000000e+00 782
21 TraesCS7A01G274700 chr5A 98.194 443 8 0 2734 3176 554952214 554951772 0.000000e+00 774
22 TraesCS7A01G274700 chr5A 91.391 453 33 4 894 1343 452243122 452243571 1.620000e-172 616
23 TraesCS7A01G274700 chr2A 94.314 1196 24 12 306 1488 748227197 748228361 0.000000e+00 1792
24 TraesCS7A01G274700 chr2A 98.723 940 7 2 1 940 728781933 728780999 0.000000e+00 1664
25 TraesCS7A01G274700 chr2A 98.858 438 5 0 2739 3176 206353731 206354168 0.000000e+00 782
26 TraesCS7A01G274700 chr5B 92.863 1191 73 11 1557 2743 486696905 486698087 0.000000e+00 1718
27 TraesCS7A01G274700 chr3A 92.904 916 57 6 1 915 598918719 598919627 0.000000e+00 1325
28 TraesCS7A01G274700 chr3A 99.087 438 4 0 2739 3176 464769183 464769620 0.000000e+00 787
29 TraesCS7A01G274700 chr6B 85.963 919 112 13 1 914 100716221 100717127 0.000000e+00 966
30 TraesCS7A01G274700 chr7B 92.143 560 37 2 1 560 705830389 705830941 0.000000e+00 784
31 TraesCS7A01G274700 chr6A 98.630 438 6 0 2739 3176 45687426 45686989 0.000000e+00 776
32 TraesCS7A01G274700 chr6A 98.630 438 6 0 2739 3176 48129272 48129709 0.000000e+00 776
33 TraesCS7A01G274700 chr6A 98.630 438 6 0 2739 3176 222609600 222610037 0.000000e+00 776


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 TraesCS7A01G274700 chr7A 287612013 287615188 3175 False 2988.5 5866 92.9905 1 3176 2 chr7A.!!$F3 3175
1 TraesCS7A01G274700 chr7A 660199396 660200560 1164 True 1775.0 1775 94.0640 306 1488 1 chr7A.!!$R2 1182
2 TraesCS7A01G274700 chr7A 207882507 207884028 1521 False 1007.5 1339 89.2285 1 1492 2 chr7A.!!$F2 1491
3 TraesCS7A01G274700 chr2B 457193552 457196292 2740 False 4909.0 4909 98.9790 1 2743 1 chr2B.!!$F1 2742
4 TraesCS7A01G274700 chr2B 25338396 25340899 2503 True 2232.5 2442 97.3845 306 2742 2 chr2B.!!$R1 2436
5 TraesCS7A01G274700 chr3B 465041525 465044250 2725 True 4590.0 4590 96.9740 1 2742 1 chr3B.!!$R1 2741
6 TraesCS7A01G274700 chr3B 656601882 656604409 2527 True 1587.0 1703 87.6450 221 2743 2 chr3B.!!$R2 2522
7 TraesCS7A01G274700 chr1B 573062360 573068345 5985 False 2416.0 2416 98.9630 1390 2739 2 chr1B.!!$F1 1349
8 TraesCS7A01G274700 chr4B 649663854 649665226 1372 True 2289.0 2289 96.7950 1376 2745 1 chr4B.!!$R1 1369
9 TraesCS7A01G274700 chr5A 634169241 634172131 2890 True 1800.5 1927 88.8630 1 2739 2 chr5A.!!$R3 2738
10 TraesCS7A01G274700 chr5A 452242195 452243571 1376 False 970.5 1325 91.1635 1 1343 2 chr5A.!!$F1 1342
11 TraesCS7A01G274700 chr2A 748227197 748228361 1164 False 1792.0 1792 94.3140 306 1488 1 chr2A.!!$F2 1182
12 TraesCS7A01G274700 chr2A 728780999 728781933 934 True 1664.0 1664 98.7230 1 940 1 chr2A.!!$R1 939
13 TraesCS7A01G274700 chr5B 486696905 486698087 1182 False 1718.0 1718 92.8630 1557 2743 1 chr5B.!!$F1 1186
14 TraesCS7A01G274700 chr3A 598918719 598919627 908 False 1325.0 1325 92.9040 1 915 1 chr3A.!!$F2 914
15 TraesCS7A01G274700 chr6B 100716221 100717127 906 False 966.0 966 85.9630 1 914 1 chr6B.!!$F1 913
16 TraesCS7A01G274700 chr7B 705830389 705830941 552 False 784.0 784 92.1430 1 560 1 chr7B.!!$F1 559

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
212 213 3.434167 GGGGACAACACATGATGCTCTAT 60.434 47.826 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 3251 2.753452 TGGTGTTGTTTTAACCTTCGCA 59.247 40.909 0.0 0.0 34.9 5.1 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
212 213 3.434167 GGGGACAACACATGATGCTCTAT 60.434 47.826 0.00 0.00 0.00 1.98
1368 1608 7.744087 TTTGTTTATGCTCATGAGTACTTGT 57.256 32.000 23.38 7.19 0.00 3.16
2507 2986 9.261035 TCCTTCCATTAAAAGGTGCAAATTATA 57.739 29.630 4.68 0.00 43.22 0.98
2666 3146 4.473196 ACCCTTCCAACCAAACAGAAAAAT 59.527 37.500 0.00 0.00 0.00 1.82
2745 3225 6.488683 CCTAAACCAAACACATCCTTAGTTGA 59.511 38.462 0.00 0.00 0.00 3.18
2746 3226 6.783708 AAACCAAACACATCCTTAGTTGAA 57.216 33.333 0.00 0.00 0.00 2.69
2747 3227 5.767816 ACCAAACACATCCTTAGTTGAAC 57.232 39.130 0.00 0.00 0.00 3.18
2748 3228 4.583073 ACCAAACACATCCTTAGTTGAACC 59.417 41.667 0.00 0.00 0.00 3.62
2750 3230 4.345859 AACACATCCTTAGTTGAACCGA 57.654 40.909 0.00 0.00 0.00 4.69
2751 3231 3.926616 ACACATCCTTAGTTGAACCGAG 58.073 45.455 0.00 0.00 0.00 4.63
2752 3232 3.323979 ACACATCCTTAGTTGAACCGAGT 59.676 43.478 0.00 0.00 0.00 4.18
2754 3234 3.323979 ACATCCTTAGTTGAACCGAGTGT 59.676 43.478 0.00 0.00 0.00 3.55
2755 3235 3.380479 TCCTTAGTTGAACCGAGTGTG 57.620 47.619 0.00 0.00 0.00 3.82
2756 3236 2.036733 TCCTTAGTTGAACCGAGTGTGG 59.963 50.000 0.00 0.00 0.00 4.17
2757 3237 1.798813 CTTAGTTGAACCGAGTGTGGC 59.201 52.381 0.00 0.00 0.00 5.01
2758 3238 1.045407 TAGTTGAACCGAGTGTGGCT 58.955 50.000 0.00 0.00 0.00 4.75
2759 3239 1.045407 AGTTGAACCGAGTGTGGCTA 58.955 50.000 0.00 0.00 0.00 3.93
2760 3240 1.145803 GTTGAACCGAGTGTGGCTAC 58.854 55.000 0.00 0.00 0.00 3.58
2761 3241 0.319211 TTGAACCGAGTGTGGCTACG 60.319 55.000 0.00 0.00 0.00 3.51
2762 3242 2.048503 AACCGAGTGTGGCTACGC 60.049 61.111 5.50 5.50 37.58 4.42
2772 3252 4.832608 GGCTACGCCCGGTCCTTG 62.833 72.222 0.00 0.00 44.06 3.61
2791 3271 3.423996 TGCGAAGGTTAAAACAACACC 57.576 42.857 0.00 0.00 0.00 4.16
2792 3272 2.753452 TGCGAAGGTTAAAACAACACCA 59.247 40.909 0.00 0.00 32.43 4.17
2793 3273 3.192844 TGCGAAGGTTAAAACAACACCAA 59.807 39.130 0.00 0.00 32.43 3.67
2794 3274 3.548668 GCGAAGGTTAAAACAACACCAAC 59.451 43.478 0.00 0.00 32.43 3.77
2796 3276 5.404096 CGAAGGTTAAAACAACACCAACTT 58.596 37.500 0.00 0.00 32.43 2.66
2798 3278 5.986501 AGGTTAAAACAACACCAACTTGA 57.013 34.783 0.00 0.00 32.43 3.02
2799 3279 5.716094 AGGTTAAAACAACACCAACTTGAC 58.284 37.500 0.00 0.00 32.43 3.18
2800 3280 5.244178 AGGTTAAAACAACACCAACTTGACA 59.756 36.000 0.00 0.00 32.43 3.58
2802 3282 6.424207 GGTTAAAACAACACCAACTTGACAAA 59.576 34.615 0.00 0.00 0.00 2.83
2803 3283 5.915812 AAAACAACACCAACTTGACAAAC 57.084 34.783 0.00 0.00 0.00 2.93
2804 3284 4.864704 AACAACACCAACTTGACAAACT 57.135 36.364 0.00 0.00 0.00 2.66
2805 3285 5.968528 AACAACACCAACTTGACAAACTA 57.031 34.783 0.00 0.00 0.00 2.24
2806 3286 6.524101 AACAACACCAACTTGACAAACTAT 57.476 33.333 0.00 0.00 0.00 2.12
2807 3287 6.131544 ACAACACCAACTTGACAAACTATC 57.868 37.500 0.00 0.00 0.00 2.08
2809 3289 4.448210 ACACCAACTTGACAAACTATCGT 58.552 39.130 0.00 0.00 0.00 3.73
2810 3290 4.879545 ACACCAACTTGACAAACTATCGTT 59.120 37.500 0.00 0.00 34.03 3.85
2813 3293 5.204833 CCAACTTGACAAACTATCGTTGTG 58.795 41.667 12.18 3.87 32.65 3.33
2814 3294 5.204833 CAACTTGACAAACTATCGTTGTGG 58.795 41.667 7.30 0.00 32.65 4.17
2815 3295 4.448210 ACTTGACAAACTATCGTTGTGGT 58.552 39.130 0.00 0.00 32.65 4.16
2816 3296 4.879545 ACTTGACAAACTATCGTTGTGGTT 59.120 37.500 0.00 0.00 32.65 3.67
2817 3297 5.355910 ACTTGACAAACTATCGTTGTGGTTT 59.644 36.000 0.00 0.00 32.65 3.27
2818 3298 5.821516 TGACAAACTATCGTTGTGGTTTT 57.178 34.783 0.00 0.00 32.65 2.43
2819 3299 5.574082 TGACAAACTATCGTTGTGGTTTTG 58.426 37.500 0.00 0.00 32.65 2.44
2820 3300 5.354513 TGACAAACTATCGTTGTGGTTTTGA 59.645 36.000 0.00 0.00 32.65 2.69
2821 3301 6.038825 TGACAAACTATCGTTGTGGTTTTGAT 59.961 34.615 0.00 0.00 32.65 2.57
2826 4625 2.210961 TCGTTGTGGTTTTGATGCGTA 58.789 42.857 0.00 0.00 0.00 4.42
2829 4628 2.264005 TGTGGTTTTGATGCGTAGGT 57.736 45.000 0.00 0.00 0.00 3.08
2840 4639 4.439057 TGATGCGTAGGTAAGATTGGTTC 58.561 43.478 0.00 0.00 0.00 3.62
2843 4642 4.250464 TGCGTAGGTAAGATTGGTTCTTG 58.750 43.478 0.00 0.00 44.54 3.02
2846 4645 4.935808 CGTAGGTAAGATTGGTTCTTGCTT 59.064 41.667 3.97 0.00 44.54 3.91
2847 4646 6.103997 CGTAGGTAAGATTGGTTCTTGCTTA 58.896 40.000 3.97 0.00 44.54 3.09
2848 4647 6.592607 CGTAGGTAAGATTGGTTCTTGCTTAA 59.407 38.462 3.97 0.00 44.54 1.85
2849 4648 7.201530 CGTAGGTAAGATTGGTTCTTGCTTAAG 60.202 40.741 0.00 0.00 44.54 1.85
2850 4649 5.416013 AGGTAAGATTGGTTCTTGCTTAAGC 59.584 40.000 20.84 20.84 44.54 3.09
2852 4651 3.092301 AGATTGGTTCTTGCTTAAGCCC 58.908 45.455 24.30 17.34 41.18 5.19
2854 4653 0.109723 TGGTTCTTGCTTAAGCCCGT 59.890 50.000 24.30 0.00 41.18 5.28
2856 4655 2.007608 GGTTCTTGCTTAAGCCCGTAG 58.992 52.381 24.30 15.33 41.18 3.51
2857 4656 1.397343 GTTCTTGCTTAAGCCCGTAGC 59.603 52.381 24.30 7.07 41.18 3.58
2859 4658 1.009829 CTTGCTTAAGCCCGTAGCAG 58.990 55.000 24.30 5.52 44.80 4.24
2860 4659 1.024579 TTGCTTAAGCCCGTAGCAGC 61.025 55.000 24.30 0.00 44.80 5.25
2866 4665 4.137872 GCCCGTAGCAGCCACGTA 62.138 66.667 12.50 0.00 42.97 3.57
2867 4666 2.574929 CCCGTAGCAGCCACGTAA 59.425 61.111 12.50 0.00 37.71 3.18
2868 4667 1.079681 CCCGTAGCAGCCACGTAAA 60.080 57.895 12.50 0.00 37.71 2.01
2870 4669 0.441145 CCGTAGCAGCCACGTAAAAC 59.559 55.000 12.50 0.00 37.71 2.43
2871 4670 1.425412 CGTAGCAGCCACGTAAAACT 58.575 50.000 5.07 0.00 34.74 2.66
2872 4671 1.796459 CGTAGCAGCCACGTAAAACTT 59.204 47.619 5.07 0.00 34.74 2.66
2874 4673 0.310854 AGCAGCCACGTAAAACTTGC 59.689 50.000 0.00 0.00 0.00 4.01
2876 4675 1.535015 GCAGCCACGTAAAACTTGCAA 60.535 47.619 0.00 0.00 0.00 4.08
2877 4676 2.116366 CAGCCACGTAAAACTTGCAAC 58.884 47.619 0.00 0.00 0.00 4.17
2878 4677 1.746220 AGCCACGTAAAACTTGCAACA 59.254 42.857 0.00 0.00 0.00 3.33
2879 4678 2.164624 AGCCACGTAAAACTTGCAACAA 59.835 40.909 0.00 0.00 0.00 2.83
2880 4679 2.280445 GCCACGTAAAACTTGCAACAAC 59.720 45.455 0.00 0.00 0.00 3.32
2881 4680 3.502920 CCACGTAAAACTTGCAACAACA 58.497 40.909 0.00 0.00 0.00 3.33
2882 4681 3.921021 CCACGTAAAACTTGCAACAACAA 59.079 39.130 0.00 0.00 0.00 2.83
2884 4683 5.443955 CCACGTAAAACTTGCAACAACAAAG 60.444 40.000 0.00 0.00 0.00 2.77
2885 4684 5.117897 CACGTAAAACTTGCAACAACAAAGT 59.882 36.000 0.00 0.00 0.00 2.66
2886 4685 6.305877 CACGTAAAACTTGCAACAACAAAGTA 59.694 34.615 0.00 0.00 0.00 2.24
2888 4687 6.743627 CGTAAAACTTGCAACAACAAAGTAGA 59.256 34.615 0.00 0.00 0.00 2.59
2889 4688 7.044966 CGTAAAACTTGCAACAACAAAGTAGAG 60.045 37.037 0.00 0.00 0.00 2.43
2891 4690 4.523083 ACTTGCAACAACAAAGTAGAGGA 58.477 39.130 0.00 0.00 0.00 3.71
2892 4691 4.335594 ACTTGCAACAACAAAGTAGAGGAC 59.664 41.667 0.00 0.00 0.00 3.85
2893 4692 2.869801 TGCAACAACAAAGTAGAGGACG 59.130 45.455 0.00 0.00 0.00 4.79
2894 4693 2.870411 GCAACAACAAAGTAGAGGACGT 59.130 45.455 0.00 0.00 0.00 4.34
2895 4694 3.059800 GCAACAACAAAGTAGAGGACGTC 60.060 47.826 7.13 7.13 0.00 4.34
2896 4695 4.369182 CAACAACAAAGTAGAGGACGTCT 58.631 43.478 16.46 2.78 39.59 4.18
2897 4696 5.526115 CAACAACAAAGTAGAGGACGTCTA 58.474 41.667 16.46 0.69 36.64 2.59
2898 4697 5.779529 ACAACAAAGTAGAGGACGTCTAA 57.220 39.130 16.46 0.00 39.61 2.10
2899 4698 5.527033 ACAACAAAGTAGAGGACGTCTAAC 58.473 41.667 16.46 8.55 39.61 2.34
2900 4699 5.301298 ACAACAAAGTAGAGGACGTCTAACT 59.699 40.000 16.46 13.92 39.61 2.24
2902 4701 5.770417 ACAAAGTAGAGGACGTCTAACTTG 58.230 41.667 16.46 17.64 39.61 3.16
2904 4703 6.183360 ACAAAGTAGAGGACGTCTAACTTGTT 60.183 38.462 16.46 7.74 39.56 2.83
2905 4704 6.402456 AAGTAGAGGACGTCTAACTTGTTT 57.598 37.500 16.46 5.47 39.61 2.83
2909 4708 4.272748 AGAGGACGTCTAACTTGTTTTTGC 59.727 41.667 16.46 0.00 31.71 3.68
2910 4709 3.942748 AGGACGTCTAACTTGTTTTTGCA 59.057 39.130 16.46 0.00 0.00 4.08
2912 4711 4.279659 GACGTCTAACTTGTTTTTGCAGG 58.720 43.478 8.70 0.00 0.00 4.85
2914 4713 3.381045 GTCTAACTTGTTTTTGCAGGGC 58.619 45.455 0.00 0.00 0.00 5.19
2916 4715 3.640967 TCTAACTTGTTTTTGCAGGGCAT 59.359 39.130 0.00 0.00 38.76 4.40
2919 4718 2.093021 ACTTGTTTTTGCAGGGCATGTT 60.093 40.909 0.00 0.00 38.76 2.71
2920 4719 1.950828 TGTTTTTGCAGGGCATGTTG 58.049 45.000 0.00 0.00 38.76 3.33
2921 4720 1.209019 TGTTTTTGCAGGGCATGTTGT 59.791 42.857 0.00 0.00 38.76 3.32
2922 4721 1.598601 GTTTTTGCAGGGCATGTTGTG 59.401 47.619 0.00 0.00 38.76 3.33
2926 4725 0.540133 TGCAGGGCATGTTGTGATGT 60.540 50.000 0.00 0.00 31.71 3.06
2927 4726 0.108992 GCAGGGCATGTTGTGATGTG 60.109 55.000 0.00 0.00 0.00 3.21
2928 4727 1.536940 CAGGGCATGTTGTGATGTGA 58.463 50.000 0.00 0.00 0.00 3.58
2929 4728 2.097036 CAGGGCATGTTGTGATGTGAT 58.903 47.619 0.00 0.00 0.00 3.06
2931 4730 3.887110 CAGGGCATGTTGTGATGTGATAT 59.113 43.478 0.00 0.00 0.00 1.63
2932 4731 3.887110 AGGGCATGTTGTGATGTGATATG 59.113 43.478 0.00 0.00 0.00 1.78
2933 4732 3.005050 GGGCATGTTGTGATGTGATATGG 59.995 47.826 0.00 0.00 0.00 2.74
2935 4734 4.261322 GGCATGTTGTGATGTGATATGGTC 60.261 45.833 0.00 0.00 0.00 4.02
2936 4735 4.336153 GCATGTTGTGATGTGATATGGTCA 59.664 41.667 0.00 0.00 0.00 4.02
2937 4736 5.163632 GCATGTTGTGATGTGATATGGTCAA 60.164 40.000 0.00 0.00 38.90 3.18
2938 4737 6.492254 CATGTTGTGATGTGATATGGTCAAG 58.508 40.000 0.00 0.00 38.90 3.02
2939 4738 5.803552 TGTTGTGATGTGATATGGTCAAGA 58.196 37.500 0.00 0.00 38.90 3.02
2943 5353 5.818857 TGTGATGTGATATGGTCAAGACATG 59.181 40.000 2.29 0.00 38.90 3.21
2948 5358 5.061853 GTGATATGGTCAAGACATGATGCT 58.938 41.667 0.00 0.00 40.97 3.79
2949 5359 6.183360 TGTGATATGGTCAAGACATGATGCTA 60.183 38.462 0.00 0.00 40.97 3.49
2953 5363 8.701908 ATATGGTCAAGACATGATGCTAAATT 57.298 30.769 0.00 0.00 40.97 1.82
2955 5365 7.230849 TGGTCAAGACATGATGCTAAATTTT 57.769 32.000 0.00 0.00 40.97 1.82
2958 5368 9.807649 GGTCAAGACATGATGCTAAATTTTATT 57.192 29.630 0.00 0.00 40.97 1.40
2986 5396 6.169800 TGAGATGATCATGTTTTGTAACCGA 58.830 36.000 14.30 0.00 30.72 4.69
2987 5397 6.313658 TGAGATGATCATGTTTTGTAACCGAG 59.686 38.462 14.30 0.00 30.72 4.63
2989 5399 6.655003 AGATGATCATGTTTTGTAACCGAGTT 59.345 34.615 14.30 0.00 33.15 3.01
3002 5412 2.006772 CGAGTTATCGGCAACTGGC 58.993 57.895 7.21 0.00 45.39 4.85
3019 5429 3.502164 GCAGGAGCCATATGGTTGT 57.498 52.632 22.79 8.28 37.57 3.32
3020 5430 1.312815 GCAGGAGCCATATGGTTGTC 58.687 55.000 22.79 15.96 37.57 3.18
3021 5431 1.586422 CAGGAGCCATATGGTTGTCG 58.414 55.000 22.79 5.98 37.57 4.35
3022 5432 0.179045 AGGAGCCATATGGTTGTCGC 60.179 55.000 22.79 7.84 37.57 5.19
3029 5684 4.036734 AGCCATATGGTTGTCGCTTTATTG 59.963 41.667 22.79 0.00 37.57 1.90
3032 5687 6.293955 GCCATATGGTTGTCGCTTTATTGTAT 60.294 38.462 22.79 0.00 37.57 2.29
3033 5688 7.077605 CCATATGGTTGTCGCTTTATTGTATG 58.922 38.462 14.09 0.00 0.00 2.39
3035 5690 3.753797 TGGTTGTCGCTTTATTGTATGCA 59.246 39.130 0.00 0.00 0.00 3.96
3048 5703 0.317269 GTATGCAATGCAATCGCGCT 60.317 50.000 13.45 0.00 43.62 5.92
3049 5704 0.317186 TATGCAATGCAATCGCGCTG 60.317 50.000 13.45 1.77 43.62 5.18
3050 5705 2.202518 GCAATGCAATCGCGCTGT 60.203 55.556 5.56 0.00 42.97 4.40
3053 5708 1.861202 GCAATGCAATCGCGCTGTAAT 60.861 47.619 5.56 0.00 42.97 1.89
3054 5709 1.776897 CAATGCAATCGCGCTGTAATG 59.223 47.619 5.56 0.19 42.97 1.90
3055 5710 0.317269 ATGCAATCGCGCTGTAATGC 60.317 50.000 5.56 9.58 42.97 3.56
3056 5711 1.353103 GCAATCGCGCTGTAATGCT 59.647 52.632 5.56 0.00 0.00 3.79
3057 5712 0.248215 GCAATCGCGCTGTAATGCTT 60.248 50.000 5.56 0.00 0.00 3.91
3058 5713 1.795162 GCAATCGCGCTGTAATGCTTT 60.795 47.619 5.56 0.00 0.00 3.51
3059 5714 2.538737 GCAATCGCGCTGTAATGCTTTA 60.539 45.455 5.56 0.00 0.00 1.85
3060 5715 3.029074 CAATCGCGCTGTAATGCTTTAC 58.971 45.455 14.02 14.02 38.56 2.01
3061 5716 2.004583 TCGCGCTGTAATGCTTTACT 57.995 45.000 19.69 0.00 38.81 2.24
3062 5717 2.343101 TCGCGCTGTAATGCTTTACTT 58.657 42.857 19.69 0.00 38.81 2.24
3063 5718 2.739913 TCGCGCTGTAATGCTTTACTTT 59.260 40.909 19.69 0.00 38.81 2.66
3065 5720 4.569162 TCGCGCTGTAATGCTTTACTTTAT 59.431 37.500 19.69 0.00 38.81 1.40
3066 5721 4.898488 CGCGCTGTAATGCTTTACTTTATC 59.102 41.667 19.69 7.67 38.81 1.75
3067 5722 5.501736 CGCGCTGTAATGCTTTACTTTATCA 60.502 40.000 19.69 2.15 38.81 2.15
3068 5723 5.677178 GCGCTGTAATGCTTTACTTTATCAC 59.323 40.000 19.69 0.00 38.81 3.06
3069 5724 6.456988 GCGCTGTAATGCTTTACTTTATCACT 60.457 38.462 19.69 0.00 38.81 3.41
3070 5725 7.254319 GCGCTGTAATGCTTTACTTTATCACTA 60.254 37.037 19.69 0.31 38.81 2.74
3071 5726 8.600625 CGCTGTAATGCTTTACTTTATCACTAA 58.399 33.333 19.69 0.00 38.81 2.24
3072 5727 9.922305 GCTGTAATGCTTTACTTTATCACTAAG 57.078 33.333 19.69 8.62 38.81 2.18
3075 5730 6.604735 ATGCTTTACTTTATCACTAAGCGG 57.395 37.500 0.00 0.00 40.51 5.52
3076 5731 4.873827 TGCTTTACTTTATCACTAAGCGGG 59.126 41.667 0.00 0.00 40.51 6.13
3077 5732 5.114081 GCTTTACTTTATCACTAAGCGGGA 58.886 41.667 0.00 0.00 0.00 5.14
3092 6468 1.721664 CGGGAGCGATAGTCGTGGAA 61.722 60.000 1.11 0.00 42.81 3.53
3094 6470 0.595310 GGAGCGATAGTCGTGGAAGC 60.595 60.000 1.11 0.00 42.81 3.86
3098 6474 2.361119 AGCGATAGTCGTGGAAGCATAA 59.639 45.455 1.11 0.00 42.81 1.90
3100 6476 3.550233 GCGATAGTCGTGGAAGCATAAGA 60.550 47.826 1.11 0.00 42.81 2.10
3102 6478 5.223382 CGATAGTCGTGGAAGCATAAGATT 58.777 41.667 0.00 0.00 34.72 2.40
3103 6479 5.117745 CGATAGTCGTGGAAGCATAAGATTG 59.882 44.000 0.00 0.00 34.72 2.67
3106 6482 1.003545 CGTGGAAGCATAAGATTGGCG 60.004 52.381 0.00 0.00 0.00 5.69
3112 6488 3.758755 AGCATAAGATTGGCGAGATGA 57.241 42.857 0.00 0.00 0.00 2.92
3113 6489 3.397482 AGCATAAGATTGGCGAGATGAC 58.603 45.455 0.00 0.00 0.00 3.06
3121 6497 1.302366 TGGCGAGATGACAATGATGC 58.698 50.000 0.00 0.00 26.81 3.91
3123 6499 2.102925 TGGCGAGATGACAATGATGCTA 59.897 45.455 0.00 0.00 26.81 3.49
3125 6501 2.154580 GCGAGATGACAATGATGCTACG 59.845 50.000 0.00 0.00 0.00 3.51
3126 6502 3.632189 CGAGATGACAATGATGCTACGA 58.368 45.455 0.00 0.00 0.00 3.43
3127 6503 4.233005 CGAGATGACAATGATGCTACGAT 58.767 43.478 0.00 0.00 0.00 3.73
3129 6505 3.744942 AGATGACAATGATGCTACGATGC 59.255 43.478 0.00 0.00 0.00 3.91
3131 6507 2.867975 TGACAATGATGCTACGATGCAG 59.132 45.455 11.87 2.38 46.71 4.41
3132 6508 3.126073 GACAATGATGCTACGATGCAGA 58.874 45.455 11.87 3.28 46.71 4.26
3134 6510 3.744942 ACAATGATGCTACGATGCAGATC 59.255 43.478 11.87 7.01 46.71 2.75
3135 6511 3.672767 ATGATGCTACGATGCAGATCA 57.327 42.857 11.87 11.37 46.71 2.92
3136 6512 3.457610 TGATGCTACGATGCAGATCAA 57.542 42.857 11.87 0.00 46.71 2.57
3138 6514 2.229675 TGCTACGATGCAGATCAAGG 57.770 50.000 0.00 0.00 38.12 3.61
3139 6515 1.482182 TGCTACGATGCAGATCAAGGT 59.518 47.619 0.00 0.00 38.12 3.50
3140 6516 1.863454 GCTACGATGCAGATCAAGGTG 59.137 52.381 0.00 0.00 0.00 4.00
3142 6518 2.015736 ACGATGCAGATCAAGGTGTC 57.984 50.000 0.00 0.00 0.00 3.67
3144 6520 0.654683 GATGCAGATCAAGGTGTCGC 59.345 55.000 0.00 0.00 0.00 5.19
3145 6521 1.086067 ATGCAGATCAAGGTGTCGCG 61.086 55.000 0.00 0.00 0.00 5.87
3146 6522 3.084579 CAGATCAAGGTGTCGCGC 58.915 61.111 0.00 0.00 0.00 6.86
3147 6523 2.125512 AGATCAAGGTGTCGCGCC 60.126 61.111 0.00 0.00 0.00 6.53
3148 6524 3.554692 GATCAAGGTGTCGCGCCG 61.555 66.667 0.00 0.00 39.30 6.46
3166 6542 2.665777 GGTGACGATGGTGATCACG 58.334 57.895 19.33 10.62 43.03 4.35
3167 6543 0.172578 GGTGACGATGGTGATCACGA 59.827 55.000 19.33 16.39 43.03 4.35
3168 6544 1.202417 GGTGACGATGGTGATCACGAT 60.202 52.381 21.67 21.67 43.03 3.73
3169 6545 1.854743 GTGACGATGGTGATCACGATG 59.145 52.381 25.74 19.00 33.94 3.84
3170 6546 1.202405 TGACGATGGTGATCACGATGG 60.202 52.381 25.74 25.01 33.04 3.51
3171 6547 0.824109 ACGATGGTGATCACGATGGT 59.176 50.000 25.52 25.52 34.70 3.55
3172 6548 1.211743 CGATGGTGATCACGATGGTG 58.788 55.000 25.74 12.58 45.78 4.17
3173 6549 0.940126 GATGGTGATCACGATGGTGC 59.060 55.000 25.74 9.39 44.03 5.01
3174 6550 0.543277 ATGGTGATCACGATGGTGCT 59.457 50.000 20.99 0.00 44.03 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 213 4.267452 ACGTTCTAAAGCGTCACGTAAAAA 59.733 37.500 0.00 0.00 42.06 1.94
2769 3249 3.794564 GGTGTTGTTTTAACCTTCGCAAG 59.205 43.478 0.00 0.00 0.00 4.01
2770 3250 3.192844 TGGTGTTGTTTTAACCTTCGCAA 59.807 39.130 0.00 0.00 34.90 4.85
2771 3251 2.753452 TGGTGTTGTTTTAACCTTCGCA 59.247 40.909 0.00 0.00 34.90 5.10
2772 3252 3.423996 TGGTGTTGTTTTAACCTTCGC 57.576 42.857 0.00 0.00 34.90 4.70
2773 3253 4.989044 AGTTGGTGTTGTTTTAACCTTCG 58.011 39.130 0.00 0.00 34.90 3.79
2774 3254 6.309494 GTCAAGTTGGTGTTGTTTTAACCTTC 59.691 38.462 2.34 0.00 34.90 3.46
2775 3255 6.160684 GTCAAGTTGGTGTTGTTTTAACCTT 58.839 36.000 2.34 0.00 34.90 3.50
2776 3256 5.244178 TGTCAAGTTGGTGTTGTTTTAACCT 59.756 36.000 2.34 0.00 34.90 3.50
2777 3257 5.471257 TGTCAAGTTGGTGTTGTTTTAACC 58.529 37.500 2.34 0.00 34.38 2.85
2778 3258 7.170151 AGTTTGTCAAGTTGGTGTTGTTTTAAC 59.830 33.333 2.34 0.00 0.00 2.01
2779 3259 7.210873 AGTTTGTCAAGTTGGTGTTGTTTTAA 58.789 30.769 2.34 0.00 0.00 1.52
2780 3260 6.750148 AGTTTGTCAAGTTGGTGTTGTTTTA 58.250 32.000 2.34 0.00 0.00 1.52
2781 3261 5.606505 AGTTTGTCAAGTTGGTGTTGTTTT 58.393 33.333 2.34 0.00 0.00 2.43
2782 3262 5.208463 AGTTTGTCAAGTTGGTGTTGTTT 57.792 34.783 2.34 0.00 0.00 2.83
2783 3263 4.864704 AGTTTGTCAAGTTGGTGTTGTT 57.135 36.364 2.34 0.00 0.00 2.83
2784 3264 5.220777 CGATAGTTTGTCAAGTTGGTGTTGT 60.221 40.000 2.34 0.00 0.00 3.32
2785 3265 5.204833 CGATAGTTTGTCAAGTTGGTGTTG 58.795 41.667 2.34 0.00 0.00 3.33
2786 3266 5.418310 CGATAGTTTGTCAAGTTGGTGTT 57.582 39.130 2.34 0.00 0.00 3.32
2803 3283 3.120338 ACGCATCAAAACCACAACGATAG 60.120 43.478 0.00 0.00 46.19 2.08
2804 3284 2.809119 ACGCATCAAAACCACAACGATA 59.191 40.909 0.00 0.00 0.00 2.92
2805 3285 1.606668 ACGCATCAAAACCACAACGAT 59.393 42.857 0.00 0.00 0.00 3.73
2806 3286 1.018148 ACGCATCAAAACCACAACGA 58.982 45.000 0.00 0.00 0.00 3.85
2807 3287 2.570169 CTACGCATCAAAACCACAACG 58.430 47.619 0.00 0.00 0.00 4.10
2809 3289 2.577700 ACCTACGCATCAAAACCACAA 58.422 42.857 0.00 0.00 0.00 3.33
2810 3290 2.264005 ACCTACGCATCAAAACCACA 57.736 45.000 0.00 0.00 0.00 4.17
2813 3293 5.448632 CCAATCTTACCTACGCATCAAAACC 60.449 44.000 0.00 0.00 0.00 3.27
2814 3294 5.123344 ACCAATCTTACCTACGCATCAAAAC 59.877 40.000 0.00 0.00 0.00 2.43
2815 3295 5.250200 ACCAATCTTACCTACGCATCAAAA 58.750 37.500 0.00 0.00 0.00 2.44
2816 3296 4.839121 ACCAATCTTACCTACGCATCAAA 58.161 39.130 0.00 0.00 0.00 2.69
2817 3297 4.481368 ACCAATCTTACCTACGCATCAA 57.519 40.909 0.00 0.00 0.00 2.57
2818 3298 4.161565 AGAACCAATCTTACCTACGCATCA 59.838 41.667 0.00 0.00 33.39 3.07
2819 3299 4.694339 AGAACCAATCTTACCTACGCATC 58.306 43.478 0.00 0.00 33.39 3.91
2820 3300 4.755266 AGAACCAATCTTACCTACGCAT 57.245 40.909 0.00 0.00 33.39 4.73
2821 3301 4.250464 CAAGAACCAATCTTACCTACGCA 58.750 43.478 0.00 0.00 46.80 5.24
2826 4625 5.416013 GCTTAAGCAAGAACCAATCTTACCT 59.584 40.000 22.59 0.00 46.80 3.08
2829 4628 4.705023 GGGCTTAAGCAAGAACCAATCTTA 59.295 41.667 27.83 0.00 46.80 2.10
2840 4639 1.009829 CTGCTACGGGCTTAAGCAAG 58.990 55.000 27.83 21.70 45.04 4.01
2843 4642 2.180862 GGCTGCTACGGGCTTAAGC 61.181 63.158 19.53 19.53 42.39 3.09
2846 4645 2.582436 GTGGCTGCTACGGGCTTA 59.418 61.111 0.00 0.00 42.39 3.09
2847 4646 4.760047 CGTGGCTGCTACGGGCTT 62.760 66.667 27.68 0.00 42.39 4.35
2849 4648 3.652539 TTACGTGGCTGCTACGGGC 62.653 63.158 35.30 3.98 45.24 6.13
2850 4649 0.671163 TTTTACGTGGCTGCTACGGG 60.671 55.000 35.30 15.11 45.24 5.28
2852 4651 1.425412 AGTTTTACGTGGCTGCTACG 58.575 50.000 32.13 32.13 46.31 3.51
2854 4653 1.533731 GCAAGTTTTACGTGGCTGCTA 59.466 47.619 0.00 0.00 0.00 3.49
2856 4655 0.030101 TGCAAGTTTTACGTGGCTGC 59.970 50.000 0.00 0.00 0.00 5.25
2857 4656 2.116366 GTTGCAAGTTTTACGTGGCTG 58.884 47.619 0.00 0.00 0.00 4.85
2858 4657 1.746220 TGTTGCAAGTTTTACGTGGCT 59.254 42.857 0.00 0.00 0.00 4.75
2859 4658 2.196295 TGTTGCAAGTTTTACGTGGC 57.804 45.000 0.00 0.00 0.00 5.01
2860 4659 3.502920 TGTTGTTGCAAGTTTTACGTGG 58.497 40.909 0.00 0.00 0.00 4.94
2862 4661 5.224135 ACTTTGTTGTTGCAAGTTTTACGT 58.776 33.333 0.00 0.00 0.00 3.57
2863 4662 5.755330 ACTTTGTTGTTGCAAGTTTTACG 57.245 34.783 0.00 0.00 0.00 3.18
2864 4663 7.220108 CCTCTACTTTGTTGTTGCAAGTTTTAC 59.780 37.037 0.00 0.00 0.00 2.01
2865 4664 7.121463 TCCTCTACTTTGTTGTTGCAAGTTTTA 59.879 33.333 0.00 0.00 0.00 1.52
2866 4665 6.071616 TCCTCTACTTTGTTGTTGCAAGTTTT 60.072 34.615 0.00 0.00 0.00 2.43
2867 4666 5.417580 TCCTCTACTTTGTTGTTGCAAGTTT 59.582 36.000 0.00 0.00 0.00 2.66
2868 4667 4.947388 TCCTCTACTTTGTTGTTGCAAGTT 59.053 37.500 0.00 0.00 0.00 2.66
2870 4669 4.552767 CGTCCTCTACTTTGTTGTTGCAAG 60.553 45.833 0.00 0.00 0.00 4.01
2871 4670 3.311322 CGTCCTCTACTTTGTTGTTGCAA 59.689 43.478 0.00 0.00 0.00 4.08
2872 4671 2.869801 CGTCCTCTACTTTGTTGTTGCA 59.130 45.455 0.00 0.00 0.00 4.08
2874 4673 4.369182 AGACGTCCTCTACTTTGTTGTTG 58.631 43.478 13.01 0.00 0.00 3.33
2876 4675 5.301298 AGTTAGACGTCCTCTACTTTGTTGT 59.699 40.000 13.01 0.00 30.56 3.32
2877 4676 5.770417 AGTTAGACGTCCTCTACTTTGTTG 58.230 41.667 13.01 0.00 30.56 3.33
2878 4677 6.183360 ACAAGTTAGACGTCCTCTACTTTGTT 60.183 38.462 13.01 1.75 36.11 2.83
2879 4678 5.301298 ACAAGTTAGACGTCCTCTACTTTGT 59.699 40.000 13.01 11.00 35.43 2.83
2880 4679 5.770417 ACAAGTTAGACGTCCTCTACTTTG 58.230 41.667 13.01 10.40 34.27 2.77
2881 4680 6.402456 AACAAGTTAGACGTCCTCTACTTT 57.598 37.500 13.01 5.57 30.56 2.66
2882 4681 6.402456 AAACAAGTTAGACGTCCTCTACTT 57.598 37.500 13.01 13.18 30.56 2.24
2884 4683 6.563567 GCAAAAACAAGTTAGACGTCCTCTAC 60.564 42.308 13.01 5.43 30.56 2.59
2885 4684 5.464389 GCAAAAACAAGTTAGACGTCCTCTA 59.536 40.000 13.01 0.00 0.00 2.43
2886 4685 4.272748 GCAAAAACAAGTTAGACGTCCTCT 59.727 41.667 13.01 5.43 0.00 3.69
2888 4687 3.942748 TGCAAAAACAAGTTAGACGTCCT 59.057 39.130 13.01 0.00 0.00 3.85
2889 4688 4.279659 CTGCAAAAACAAGTTAGACGTCC 58.720 43.478 13.01 0.00 0.00 4.79
2891 4690 3.066203 CCCTGCAAAAACAAGTTAGACGT 59.934 43.478 0.00 0.00 0.00 4.34
2892 4691 3.628017 CCCTGCAAAAACAAGTTAGACG 58.372 45.455 0.00 0.00 0.00 4.18
2893 4692 3.181480 TGCCCTGCAAAAACAAGTTAGAC 60.181 43.478 0.00 0.00 34.76 2.59
2894 4693 3.027412 TGCCCTGCAAAAACAAGTTAGA 58.973 40.909 0.00 0.00 34.76 2.10
2895 4694 3.451141 TGCCCTGCAAAAACAAGTTAG 57.549 42.857 0.00 0.00 34.76 2.34
2896 4695 3.133721 ACATGCCCTGCAAAAACAAGTTA 59.866 39.130 0.00 0.00 43.62 2.24
2897 4696 2.093021 ACATGCCCTGCAAAAACAAGTT 60.093 40.909 0.00 0.00 43.62 2.66
2898 4697 1.485895 ACATGCCCTGCAAAAACAAGT 59.514 42.857 0.00 0.00 43.62 3.16
2899 4698 2.243602 ACATGCCCTGCAAAAACAAG 57.756 45.000 0.00 0.00 43.62 3.16
2900 4699 2.286872 CAACATGCCCTGCAAAAACAA 58.713 42.857 0.00 0.00 43.62 2.83
2902 4701 1.598601 CACAACATGCCCTGCAAAAAC 59.401 47.619 0.00 0.00 43.62 2.43
2904 4703 1.117994 TCACAACATGCCCTGCAAAA 58.882 45.000 0.00 0.00 43.62 2.44
2905 4704 1.001068 CATCACAACATGCCCTGCAAA 59.999 47.619 0.00 0.00 43.62 3.68
2909 4708 1.536940 TCACATCACAACATGCCCTG 58.463 50.000 0.00 0.00 0.00 4.45
2910 4709 2.519771 ATCACATCACAACATGCCCT 57.480 45.000 0.00 0.00 0.00 5.19
2912 4711 3.633525 ACCATATCACATCACAACATGCC 59.366 43.478 0.00 0.00 0.00 4.40
2914 4713 6.316890 TCTTGACCATATCACATCACAACATG 59.683 38.462 0.00 0.00 36.92 3.21
2916 4715 5.643348 GTCTTGACCATATCACATCACAACA 59.357 40.000 0.00 0.00 36.92 3.33
2919 4718 5.419239 TGTCTTGACCATATCACATCACA 57.581 39.130 0.00 0.00 36.92 3.58
2920 4719 6.051074 TCATGTCTTGACCATATCACATCAC 58.949 40.000 0.00 0.00 36.92 3.06
2921 4720 6.237887 TCATGTCTTGACCATATCACATCA 57.762 37.500 0.00 0.00 36.92 3.07
2922 4721 6.348295 GCATCATGTCTTGACCATATCACATC 60.348 42.308 0.00 0.00 36.92 3.06
2926 4725 5.300411 AGCATCATGTCTTGACCATATCA 57.700 39.130 0.00 0.00 37.11 2.15
2927 4726 7.734924 TTTAGCATCATGTCTTGACCATATC 57.265 36.000 0.00 0.00 37.11 1.63
2928 4727 8.701908 AATTTAGCATCATGTCTTGACCATAT 57.298 30.769 0.00 0.00 37.11 1.78
2929 4728 8.523915 AAATTTAGCATCATGTCTTGACCATA 57.476 30.769 0.00 0.00 37.11 2.74
2931 4730 6.839124 AAATTTAGCATCATGTCTTGACCA 57.161 33.333 0.00 0.00 37.11 4.02
2932 4731 9.807649 AATAAAATTTAGCATCATGTCTTGACC 57.192 29.630 0.00 0.00 37.11 4.02
2958 5368 8.892723 GGTTACAAAACATGATCATCTCATACA 58.107 33.333 4.86 0.00 42.91 2.29
2962 5372 6.169800 TCGGTTACAAAACATGATCATCTCA 58.830 36.000 4.86 0.00 37.34 3.27
2963 5373 6.313905 ACTCGGTTACAAAACATGATCATCTC 59.686 38.462 4.86 0.00 37.34 2.75
2967 5377 7.201487 CGATAACTCGGTTACAAAACATGATCA 60.201 37.037 0.00 0.00 41.27 2.92
2970 5380 6.397831 CGATAACTCGGTTACAAAACATGA 57.602 37.500 0.00 0.00 41.27 3.07
2984 5394 0.739462 TGCCAGTTGCCGATAACTCG 60.739 55.000 1.91 0.00 44.62 4.18
2986 5396 0.392998 CCTGCCAGTTGCCGATAACT 60.393 55.000 0.00 0.00 41.37 2.24
2987 5397 0.392461 TCCTGCCAGTTGCCGATAAC 60.392 55.000 0.00 0.00 40.16 1.89
2989 5399 1.522092 CTCCTGCCAGTTGCCGATA 59.478 57.895 0.00 0.00 40.16 2.92
3001 5411 1.312815 GACAACCATATGGCTCCTGC 58.687 55.000 22.18 3.09 39.32 4.85
3002 5412 1.586422 CGACAACCATATGGCTCCTG 58.414 55.000 22.18 15.33 39.32 3.86
3003 5413 0.179045 GCGACAACCATATGGCTCCT 60.179 55.000 22.18 0.00 39.32 3.69
3004 5414 0.179045 AGCGACAACCATATGGCTCC 60.179 55.000 22.18 7.70 39.32 4.70
3005 5415 1.668419 AAGCGACAACCATATGGCTC 58.332 50.000 22.18 12.36 39.32 4.70
3006 5416 2.128771 AAAGCGACAACCATATGGCT 57.871 45.000 22.18 6.77 39.32 4.75
3007 5417 4.202010 ACAATAAAGCGACAACCATATGGC 60.202 41.667 22.18 6.47 39.32 4.40
3008 5418 5.499139 ACAATAAAGCGACAACCATATGG 57.501 39.130 20.68 20.68 42.17 2.74
3009 5419 6.578545 GCATACAATAAAGCGACAACCATATG 59.421 38.462 0.00 0.00 0.00 1.78
3010 5420 6.262049 TGCATACAATAAAGCGACAACCATAT 59.738 34.615 0.00 0.00 0.00 1.78
3011 5421 5.586643 TGCATACAATAAAGCGACAACCATA 59.413 36.000 0.00 0.00 0.00 2.74
3012 5422 4.397730 TGCATACAATAAAGCGACAACCAT 59.602 37.500 0.00 0.00 0.00 3.55
3013 5423 3.753797 TGCATACAATAAAGCGACAACCA 59.246 39.130 0.00 0.00 0.00 3.67
3014 5424 4.349663 TGCATACAATAAAGCGACAACC 57.650 40.909 0.00 0.00 0.00 3.77
3016 5426 4.797868 GCATTGCATACAATAAAGCGACAA 59.202 37.500 3.15 0.00 44.83 3.18
3017 5427 4.142513 TGCATTGCATACAATAAAGCGACA 60.143 37.500 7.38 0.00 44.83 4.35
3018 5428 4.350346 TGCATTGCATACAATAAAGCGAC 58.650 39.130 7.38 0.00 44.83 5.19
3019 5429 4.629251 TGCATTGCATACAATAAAGCGA 57.371 36.364 7.38 0.00 44.83 4.93
3020 5430 5.386627 CGATTGCATTGCATACAATAAAGCG 60.387 40.000 12.95 5.57 44.83 4.68
3021 5431 5.610982 GCGATTGCATTGCATACAATAAAGC 60.611 40.000 12.95 6.12 44.83 3.51
3022 5432 5.386627 CGCGATTGCATTGCATACAATAAAG 60.387 40.000 12.95 0.24 44.83 1.85
3029 5684 0.317269 AGCGCGATTGCATTGCATAC 60.317 50.000 12.10 8.63 42.97 2.39
3032 5687 1.642952 TACAGCGCGATTGCATTGCA 61.643 50.000 12.10 7.38 42.97 4.08
3033 5688 0.523125 TTACAGCGCGATTGCATTGC 60.523 50.000 12.10 0.46 42.97 3.56
3035 5690 1.861202 GCATTACAGCGCGATTGCATT 60.861 47.619 12.10 0.00 42.97 3.56
3044 5699 5.677178 GTGATAAAGTAAAGCATTACAGCGC 59.323 40.000 13.81 0.00 43.20 5.92
3045 5700 7.005062 AGTGATAAAGTAAAGCATTACAGCG 57.995 36.000 13.81 0.00 43.20 5.18
3048 5703 8.600625 CGCTTAGTGATAAAGTAAAGCATTACA 58.399 33.333 13.81 0.00 43.20 2.41
3049 5704 8.062448 CCGCTTAGTGATAAAGTAAAGCATTAC 58.938 37.037 3.64 3.64 41.45 1.89
3050 5705 7.225931 CCCGCTTAGTGATAAAGTAAAGCATTA 59.774 37.037 5.79 0.00 0.00 1.90
3053 5708 4.873827 CCCGCTTAGTGATAAAGTAAAGCA 59.126 41.667 5.79 0.00 0.00 3.91
3054 5709 5.114081 TCCCGCTTAGTGATAAAGTAAAGC 58.886 41.667 0.00 0.00 0.00 3.51
3055 5710 5.234543 GCTCCCGCTTAGTGATAAAGTAAAG 59.765 44.000 0.00 0.00 0.00 1.85
3056 5711 5.114081 GCTCCCGCTTAGTGATAAAGTAAA 58.886 41.667 0.00 0.00 0.00 2.01
3057 5712 4.690122 GCTCCCGCTTAGTGATAAAGTAA 58.310 43.478 0.00 0.00 0.00 2.24
3058 5713 3.243301 CGCTCCCGCTTAGTGATAAAGTA 60.243 47.826 0.00 0.00 0.00 2.24
3059 5714 2.481449 CGCTCCCGCTTAGTGATAAAGT 60.481 50.000 0.00 0.00 0.00 2.66
3060 5715 2.128035 CGCTCCCGCTTAGTGATAAAG 58.872 52.381 0.00 0.00 0.00 1.85
3061 5716 1.752498 TCGCTCCCGCTTAGTGATAAA 59.248 47.619 0.00 0.00 0.00 1.40
3062 5717 1.395635 TCGCTCCCGCTTAGTGATAA 58.604 50.000 0.00 0.00 0.00 1.75
3063 5718 1.617322 ATCGCTCCCGCTTAGTGATA 58.383 50.000 0.00 0.00 41.27 2.15
3065 5720 0.952280 CTATCGCTCCCGCTTAGTGA 59.048 55.000 0.00 0.00 37.84 3.41
3066 5721 0.669077 ACTATCGCTCCCGCTTAGTG 59.331 55.000 0.00 0.00 34.25 2.74
3067 5722 0.953003 GACTATCGCTCCCGCTTAGT 59.047 55.000 0.00 0.00 36.50 2.24
3068 5723 0.110147 CGACTATCGCTCCCGCTTAG 60.110 60.000 0.00 0.00 31.14 2.18
3069 5724 0.816825 ACGACTATCGCTCCCGCTTA 60.817 55.000 0.00 0.00 45.12 3.09
3070 5725 2.119655 ACGACTATCGCTCCCGCTT 61.120 57.895 0.00 0.00 45.12 4.68
3071 5726 2.516460 ACGACTATCGCTCCCGCT 60.516 61.111 0.00 0.00 45.12 5.52
3072 5727 2.353607 CACGACTATCGCTCCCGC 60.354 66.667 0.00 0.00 45.12 6.13
3075 5730 0.595310 GCTTCCACGACTATCGCTCC 60.595 60.000 0.00 0.00 45.12 4.70
3076 5731 0.100682 TGCTTCCACGACTATCGCTC 59.899 55.000 0.00 0.00 45.12 5.03
3077 5732 0.747255 ATGCTTCCACGACTATCGCT 59.253 50.000 0.00 0.00 45.12 4.93
3080 5735 5.406780 CCAATCTTATGCTTCCACGACTATC 59.593 44.000 0.00 0.00 0.00 2.08
3081 5736 5.300752 CCAATCTTATGCTTCCACGACTAT 58.699 41.667 0.00 0.00 0.00 2.12
3082 5737 4.693283 CCAATCTTATGCTTCCACGACTA 58.307 43.478 0.00 0.00 0.00 2.59
3085 6461 2.288666 GCCAATCTTATGCTTCCACGA 58.711 47.619 0.00 0.00 0.00 4.35
3088 6464 2.170397 TCTCGCCAATCTTATGCTTCCA 59.830 45.455 0.00 0.00 0.00 3.53
3092 6468 3.181462 TGTCATCTCGCCAATCTTATGCT 60.181 43.478 0.00 0.00 0.00 3.79
3094 6470 5.467735 TCATTGTCATCTCGCCAATCTTATG 59.532 40.000 0.00 0.00 0.00 1.90
3098 6474 3.548745 TCATTGTCATCTCGCCAATCT 57.451 42.857 0.00 0.00 0.00 2.40
3100 6476 2.292569 GCATCATTGTCATCTCGCCAAT 59.707 45.455 0.00 0.00 0.00 3.16
3102 6478 1.134310 AGCATCATTGTCATCTCGCCA 60.134 47.619 0.00 0.00 0.00 5.69
3103 6479 1.590932 AGCATCATTGTCATCTCGCC 58.409 50.000 0.00 0.00 0.00 5.54
3106 6482 4.143158 GCATCGTAGCATCATTGTCATCTC 60.143 45.833 0.00 0.00 0.00 2.75
3112 6488 3.183793 TCTGCATCGTAGCATCATTGT 57.816 42.857 5.11 0.00 44.68 2.71
3113 6489 3.744426 TGATCTGCATCGTAGCATCATTG 59.256 43.478 5.11 0.00 44.68 2.82
3115 6491 3.672767 TGATCTGCATCGTAGCATCAT 57.327 42.857 5.11 1.68 44.68 2.45
3116 6492 3.387397 CTTGATCTGCATCGTAGCATCA 58.613 45.455 5.11 4.91 44.68 3.07
3117 6493 2.735663 CCTTGATCTGCATCGTAGCATC 59.264 50.000 5.11 2.61 44.68 3.91
3120 6496 1.863454 CACCTTGATCTGCATCGTAGC 59.137 52.381 0.00 0.00 0.00 3.58
3121 6497 3.119291 GACACCTTGATCTGCATCGTAG 58.881 50.000 0.00 0.00 0.00 3.51
3123 6499 1.737029 CGACACCTTGATCTGCATCGT 60.737 52.381 0.00 0.00 0.00 3.73
3125 6501 0.654683 GCGACACCTTGATCTGCATC 59.345 55.000 0.00 0.00 0.00 3.91
3126 6502 1.086067 CGCGACACCTTGATCTGCAT 61.086 55.000 0.00 0.00 0.00 3.96
3127 6503 1.737735 CGCGACACCTTGATCTGCA 60.738 57.895 0.00 0.00 0.00 4.41
3129 6505 2.456119 GGCGCGACACCTTGATCTG 61.456 63.158 12.10 0.00 0.00 2.90
3131 6507 3.554692 CGGCGCGACACCTTGATC 61.555 66.667 14.85 0.00 0.00 2.92
3144 6520 3.716539 ATCACCATCGTCACCGGCG 62.717 63.158 0.00 0.00 33.95 6.46
3145 6521 1.883084 GATCACCATCGTCACCGGC 60.883 63.158 0.00 0.00 33.95 6.13
3146 6522 0.806102 GTGATCACCATCGTCACCGG 60.806 60.000 15.31 0.00 37.00 5.28
3147 6523 1.139816 CGTGATCACCATCGTCACCG 61.140 60.000 20.03 0.38 39.17 4.94
3148 6524 0.172578 TCGTGATCACCATCGTCACC 59.827 55.000 20.03 0.00 39.17 4.02
3153 6529 1.211743 CACCATCGTGATCACCATCG 58.788 55.000 20.03 8.35 43.14 3.84
3155 6531 0.543277 AGCACCATCGTGATCACCAT 59.457 50.000 20.03 10.35 43.14 3.55
3156 6532 0.324614 AAGCACCATCGTGATCACCA 59.675 50.000 20.03 8.09 43.14 4.17
3157 6533 3.159298 AAGCACCATCGTGATCACC 57.841 52.632 20.03 4.16 43.14 4.02


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

AutoCloner maintained by Alex Coulton.