Multiple sequence alignment - TraesCS6A01G217300

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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 TraesCS6A01G217300 chr6A 100.000 4356 0 0 1 4356 399882532 399878177 0.000000e+00 8045.0
1 TraesCS6A01G217300 chr6D 95.482 1173 34 11 816 1971 276129279 276130449 0.000000e+00 1855.0
2 TraesCS6A01G217300 chr6D 91.042 1161 48 20 2821 3929 276131260 276132416 0.000000e+00 1517.0
3 TraesCS6A01G217300 chr6D 95.935 738 25 4 2010 2743 276130522 276131258 0.000000e+00 1192.0
4 TraesCS6A01G217300 chr6D 94.301 193 9 2 4164 4356 276133131 276133321 1.180000e-75 294.0
5 TraesCS6A01G217300 chr6D 90.909 99 9 0 3957 4055 276133037 276133135 2.730000e-27 134.0
6 TraesCS6A01G217300 chr6D 95.588 68 3 0 2760 2827 168293777 168293844 4.610000e-20 110.0
7 TraesCS6A01G217300 chr6D 93.151 73 5 0 2760 2832 309072526 309072598 1.660000e-19 108.0
8 TraesCS6A01G217300 chr6D 94.203 69 4 0 2760 2828 363038100 363038168 5.960000e-19 106.0
9 TraesCS6A01G217300 chr6D 94.203 69 3 1 2760 2827 185368103 185368171 2.140000e-18 104.0
10 TraesCS6A01G217300 chr6B 90.335 1045 46 14 2820 3811 438094857 438095899 0.000000e+00 1319.0
11 TraesCS6A01G217300 chr6B 93.073 895 37 11 816 1696 438093005 438093888 0.000000e+00 1286.0
12 TraesCS6A01G217300 chr6B 88.987 1017 60 20 1742 2746 438093883 438094859 0.000000e+00 1210.0
13 TraesCS6A01G217300 chr6B 93.827 243 14 1 4114 4356 438095927 438096168 8.900000e-97 364.0
14 TraesCS6A01G217300 chr6B 100.000 40 0 0 1 40 630535605 630535644 1.680000e-09 75.0
15 TraesCS6A01G217300 chr7B 88.984 817 58 11 1 797 368206799 368207603 0.000000e+00 981.0
16 TraesCS6A01G217300 chr7B 87.148 817 66 12 1 797 696387811 696388608 0.000000e+00 891.0
17 TraesCS6A01G217300 chr7B 86.722 241 14 4 1 223 20843757 20843997 7.230000e-63 252.0
18 TraesCS6A01G217300 chr2B 88.499 826 62 13 1 807 519417763 519418574 0.000000e+00 968.0
19 TraesCS6A01G217300 chr2B 88.491 391 32 4 1 378 93032922 93032532 1.100000e-125 460.0
20 TraesCS6A01G217300 chr7A 88.386 818 67 13 1 797 49406364 49405554 0.000000e+00 959.0
21 TraesCS6A01G217300 chr7A 91.304 161 10 2 38 195 485186983 485187142 2.640000e-52 217.0
22 TraesCS6A01G217300 chr3B 88.600 807 64 12 1 787 250580213 250579415 0.000000e+00 955.0
23 TraesCS6A01G217300 chr3B 89.203 778 58 12 38 805 772911118 772911879 0.000000e+00 948.0
24 TraesCS6A01G217300 chr3B 86.190 811 78 12 1 792 191948438 191947643 0.000000e+00 846.0
25 TraesCS6A01G217300 chr4B 88.736 799 61 7 1 784 578464655 578465439 0.000000e+00 950.0
26 TraesCS6A01G217300 chr4B 88.471 798 64 6 1 784 578313915 578314698 0.000000e+00 939.0
27 TraesCS6A01G217300 chr4B 93.151 73 4 1 2760 2831 491017663 491017735 5.960000e-19 106.0
28 TraesCS6A01G217300 chr2A 88.185 821 58 9 1 801 20012104 20011303 0.000000e+00 942.0
29 TraesCS6A01G217300 chr2A 88.703 239 14 5 1 227 334575523 334575760 3.320000e-71 279.0
30 TraesCS6A01G217300 chr5A 87.696 829 75 12 1 807 692040597 692039774 0.000000e+00 941.0
31 TraesCS6A01G217300 chr1D 87.990 816 72 7 1 797 34662898 34662090 0.000000e+00 941.0
32 TraesCS6A01G217300 chr1D 98.462 65 1 0 2760 2824 196440523 196440587 9.900000e-22 115.0
33 TraesCS6A01G217300 chr1D 94.203 69 4 0 2760 2828 301353527 301353595 5.960000e-19 106.0
34 TraesCS6A01G217300 chr1D 96.825 63 2 0 2760 2822 355171597 355171659 5.960000e-19 106.0
35 TraesCS6A01G217300 chr1D 92.000 75 4 2 2760 2832 196440563 196440489 2.140000e-18 104.0
36 TraesCS6A01G217300 chr1D 95.312 64 3 0 2760 2823 252473168 252473231 7.710000e-18 102.0
37 TraesCS6A01G217300 chr1D 95.312 64 3 0 2760 2823 337216869 337216806 7.710000e-18 102.0
38 TraesCS6A01G217300 chr1D 95.238 63 3 0 2760 2822 295954238 295954300 2.770000e-17 100.0
39 TraesCS6A01G217300 chr1D 95.238 63 3 0 2760 2822 337065211 337065273 2.770000e-17 100.0
40 TraesCS6A01G217300 chr1D 92.647 68 5 0 2760 2827 339110921 339110988 9.970000e-17 99.0
41 TraesCS6A01G217300 chr1D 90.541 74 5 2 2760 2831 431958086 431958013 3.590000e-16 97.1
42 TraesCS6A01G217300 chr2D 87.685 812 58 11 1 792 35335870 35335081 0.000000e+00 907.0
43 TraesCS6A01G217300 chr3D 87.271 817 64 11 1 797 456728412 456729208 0.000000e+00 896.0
44 TraesCS6A01G217300 chr3D 96.923 65 2 0 2760 2824 303788479 303788543 4.610000e-20 110.0
45 TraesCS6A01G217300 chr3D 94.203 69 4 0 2760 2828 570848690 570848758 5.960000e-19 106.0
46 TraesCS6A01G217300 chr1A 86.829 782 63 18 1 761 36817689 36816927 0.000000e+00 837.0
47 TraesCS6A01G217300 chr1A 89.362 47 5 0 3970 4016 230653300 230653346 4.700000e-05 60.2
48 TraesCS6A01G217300 chr7D 84.390 820 88 14 1 798 316501393 316500592 0.000000e+00 769.0
49 TraesCS6A01G217300 chr7D 89.130 92 8 2 2760 2849 5068108 5068199 3.560000e-21 113.0
50 TraesCS6A01G217300 chr7D 91.026 78 6 1 2760 2836 289566415 289566338 2.140000e-18 104.0
51 TraesCS6A01G217300 chr5D 93.056 72 4 1 2760 2830 111788706 111788635 2.140000e-18 104.0
52 TraesCS6A01G217300 chrUn 95.238 63 3 0 2760 2822 65138891 65138953 2.770000e-17 100.0
53 TraesCS6A01G217300 chrUn 92.537 67 5 0 2760 2826 104668870 104668804 3.590000e-16 97.1
54 TraesCS6A01G217300 chrUn 93.651 63 4 0 2760 2822 31861232 31861294 1.290000e-15 95.3
55 TraesCS6A01G217300 chrUn 93.750 64 3 1 2760 2822 84435402 84435465 1.290000e-15 95.3
56 TraesCS6A01G217300 chrUn 90.141 71 6 1 2760 2829 84435443 84435373 1.670000e-14 91.6
57 TraesCS6A01G217300 chrUn 92.188 64 5 0 2760 2823 208649116 208649053 1.670000e-14 91.6
58 TraesCS6A01G217300 chrUn 92.188 64 5 0 2760 2823 226179948 226179885 1.670000e-14 91.6
59 TraesCS6A01G217300 chrUn 92.063 63 5 0 2760 2822 68883290 68883352 6.000000e-14 89.8
60 TraesCS6A01G217300 chrUn 88.000 75 9 0 2760 2834 336469359 336469285 6.000000e-14 89.8
61 TraesCS6A01G217300 chrUn 88.000 75 9 0 2760 2834 397152034 397151960 6.000000e-14 89.8
62 TraesCS6A01G217300 chr1B 84.746 59 9 0 3968 4026 209140354 209140296 4.700000e-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 TraesCS6A01G217300 chr6A 399878177 399882532 4355 True 8045.00 8045 100.0000 1 4356 1 chr6A.!!$R1 4355
1 TraesCS6A01G217300 chr6D 276129279 276133321 4042 False 998.40 1855 93.5338 816 4356 5 chr6D.!!$F5 3540
2 TraesCS6A01G217300 chr6B 438093005 438096168 3163 False 1044.75 1319 91.5555 816 4356 4 chr6B.!!$F2 3540
3 TraesCS6A01G217300 chr7B 368206799 368207603 804 False 981.00 981 88.9840 1 797 1 chr7B.!!$F2 796
4 TraesCS6A01G217300 chr7B 696387811 696388608 797 False 891.00 891 87.1480 1 797 1 chr7B.!!$F3 796
5 TraesCS6A01G217300 chr2B 519417763 519418574 811 False 968.00 968 88.4990 1 807 1 chr2B.!!$F1 806
6 TraesCS6A01G217300 chr7A 49405554 49406364 810 True 959.00 959 88.3860 1 797 1 chr7A.!!$R1 796
7 TraesCS6A01G217300 chr3B 250579415 250580213 798 True 955.00 955 88.6000 1 787 1 chr3B.!!$R2 786
8 TraesCS6A01G217300 chr3B 772911118 772911879 761 False 948.00 948 89.2030 38 805 1 chr3B.!!$F1 767
9 TraesCS6A01G217300 chr3B 191947643 191948438 795 True 846.00 846 86.1900 1 792 1 chr3B.!!$R1 791
10 TraesCS6A01G217300 chr4B 578464655 578465439 784 False 950.00 950 88.7360 1 784 1 chr4B.!!$F3 783
11 TraesCS6A01G217300 chr4B 578313915 578314698 783 False 939.00 939 88.4710 1 784 1 chr4B.!!$F2 783
12 TraesCS6A01G217300 chr2A 20011303 20012104 801 True 942.00 942 88.1850 1 801 1 chr2A.!!$R1 800
13 TraesCS6A01G217300 chr5A 692039774 692040597 823 True 941.00 941 87.6960 1 807 1 chr5A.!!$R1 806
14 TraesCS6A01G217300 chr1D 34662090 34662898 808 True 941.00 941 87.9900 1 797 1 chr1D.!!$R1 796
15 TraesCS6A01G217300 chr2D 35335081 35335870 789 True 907.00 907 87.6850 1 792 1 chr2D.!!$R1 791
16 TraesCS6A01G217300 chr3D 456728412 456729208 796 False 896.00 896 87.2710 1 797 1 chr3D.!!$F2 796
17 TraesCS6A01G217300 chr1A 36816927 36817689 762 True 837.00 837 86.8290 1 761 1 chr1A.!!$R1 760
18 TraesCS6A01G217300 chr7D 316500592 316501393 801 True 769.00 769 84.3900 1 798 1 chr7D.!!$R2 797

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
814 856 0.602638 CAACAAGTAGCACCCTCGCA 60.603 55.0 0.00 0.0 0.00 5.10 F
1349 1397 0.179045 ATTTCGAGCCGAATGGAGGG 60.179 55.0 10.19 0.0 45.28 4.30 F
1364 1412 1.393603 GAGGGGATTAGCCAGTTTGC 58.606 55.0 0.00 0.0 38.95 3.68 F
2756 2877 0.104304 AATGATGTACTCCCGCCGTC 59.896 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 2873 0.237498 GAAAAACGCTCTTGGGACGG 59.763 55.0 0.0 0.0 0.0 4.79 R
2753 2874 0.941542 TGAAAAACGCTCTTGGGACG 59.058 50.0 0.0 0.0 0.0 4.79 R
3008 3160 1.081094 CACTGCAATGATGAGCGACA 58.919 50.0 0.0 0.0 0.0 4.35 R
4102 4900 0.107945 GGACCACAGAGAGGATGCAC 60.108 60.0 0.0 0.0 0.0 4.57 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
200 219 1.078848 GCCCTGACACTCATCGCTT 60.079 57.895 0.00 0.00 0.00 4.68
209 228 0.888619 ACTCATCGCTTCACTTCGGA 59.111 50.000 0.00 0.00 0.00 4.55
227 246 4.338012 TCGGACTATTGTGTCTACCTTGA 58.662 43.478 0.00 0.00 37.16 3.02
256 275 1.830279 TATCTCGTGGTCGTCCAAGT 58.170 50.000 13.45 0.00 46.15 3.16
319 338 2.045708 GCGGTGGCCAATGTCATCA 61.046 57.895 7.24 0.00 0.00 3.07
371 393 0.676151 GAGCTCTCTTGCCCTGTTGG 60.676 60.000 6.43 0.00 37.09 3.77
404 426 1.607628 AGTCTACTGCGACAACGTCTT 59.392 47.619 0.00 0.00 41.98 3.01
484 507 7.124147 AGTTGGATATTCATTTTGTTCGGGAAT 59.876 33.333 0.00 0.00 33.22 3.01
491 514 3.791953 TTTTGTTCGGGAATAGGTGGA 57.208 42.857 0.00 0.00 0.00 4.02
496 519 2.767960 GTTCGGGAATAGGTGGACCTTA 59.232 50.000 3.03 0.00 46.09 2.69
541 564 2.896685 CCTACTTCCCAACAATTTGCCA 59.103 45.455 0.00 0.00 0.00 4.92
626 649 4.717629 CGGTGCCGCTTCGACTGA 62.718 66.667 0.00 0.00 0.00 3.41
649 689 2.938798 GGATGGGTGGGTGGGTGA 60.939 66.667 0.00 0.00 0.00 4.02
650 690 2.543797 GGATGGGTGGGTGGGTGAA 61.544 63.158 0.00 0.00 0.00 3.18
687 727 8.273780 TGTGTTATGTGCATATTGTGTATTGA 57.726 30.769 0.00 0.00 0.00 2.57
723 764 5.479375 AGTTTCTTGTATAGTTGAGGTCCGA 59.521 40.000 0.00 0.00 0.00 4.55
798 840 6.248420 GTCGTGCAATTACAACATCATACAAC 59.752 38.462 0.00 0.00 0.00 3.32
802 844 7.594758 GTGCAATTACAACATCATACAACAAGT 59.405 33.333 0.00 0.00 0.00 3.16
804 846 9.277565 GCAATTACAACATCATACAACAAGTAG 57.722 33.333 0.00 0.00 35.85 2.57
805 847 9.277565 CAATTACAACATCATACAACAAGTAGC 57.722 33.333 0.00 0.00 35.85 3.58
806 848 7.971183 TTACAACATCATACAACAAGTAGCA 57.029 32.000 0.00 0.00 35.85 3.49
807 849 6.241207 ACAACATCATACAACAAGTAGCAC 57.759 37.500 0.00 0.00 35.85 4.40
808 850 5.181245 ACAACATCATACAACAAGTAGCACC 59.819 40.000 0.00 0.00 35.85 5.01
809 851 4.261801 ACATCATACAACAAGTAGCACCC 58.738 43.478 0.00 0.00 35.85 4.61
810 852 4.019321 ACATCATACAACAAGTAGCACCCT 60.019 41.667 0.00 0.00 35.85 4.34
811 853 4.202245 TCATACAACAAGTAGCACCCTC 57.798 45.455 0.00 0.00 35.85 4.30
812 854 2.736144 TACAACAAGTAGCACCCTCG 57.264 50.000 0.00 0.00 0.00 4.63
813 855 0.602905 ACAACAAGTAGCACCCTCGC 60.603 55.000 0.00 0.00 0.00 5.03
814 856 0.602638 CAACAAGTAGCACCCTCGCA 60.603 55.000 0.00 0.00 0.00 5.10
1196 1243 2.041819 CCGCCTCCCCTCCTACTT 60.042 66.667 0.00 0.00 0.00 2.24
1211 1258 2.561569 CTACTTATTTCCCTGGTGGCG 58.438 52.381 0.00 0.00 0.00 5.69
1306 1353 1.069978 TCGACATGGTGTCTGCTGAAA 59.930 47.619 8.30 0.00 44.85 2.69
1349 1397 0.179045 ATTTCGAGCCGAATGGAGGG 60.179 55.000 10.19 0.00 45.28 4.30
1364 1412 1.393603 GAGGGGATTAGCCAGTTTGC 58.606 55.000 0.00 0.00 38.95 3.68
1381 1436 6.348540 CCAGTTTGCTTATTTGTCTGTAGACC 60.349 42.308 9.37 0.00 44.15 3.85
1461 1517 3.159213 AGATGTGTTGCATTCCCTTGA 57.841 42.857 0.00 0.00 38.06 3.02
1470 1526 2.236146 TGCATTCCCTTGATCGTAGTGT 59.764 45.455 0.00 0.00 0.00 3.55
1693 1752 7.873719 TTACACTGGTATGATAAAATGGTGG 57.126 36.000 0.00 0.00 0.00 4.61
1721 1780 7.201444 CGAAGCATAACTTAGAGTGTTACCTTG 60.201 40.741 0.00 0.00 39.29 3.61
1795 1854 6.098695 TGGTACACTTAGGTTGAACAGTTAGT 59.901 38.462 0.00 0.00 0.00 2.24
1850 1909 1.656587 AGGCTCAGGGTGACACATTA 58.343 50.000 8.08 0.00 0.00 1.90
1882 1947 3.555547 GGTTTGCTTGGTGTTGAAATGTC 59.444 43.478 0.00 0.00 0.00 3.06
2172 2286 6.479990 TCAATGGCATCGTCTACTTTATTCTG 59.520 38.462 0.00 0.00 0.00 3.02
2173 2287 5.592104 TGGCATCGTCTACTTTATTCTGA 57.408 39.130 0.00 0.00 0.00 3.27
2204 2318 7.007116 AGGTTCCTTTTCTCTGCTAAAGATTT 58.993 34.615 0.00 0.00 34.11 2.17
2231 2345 5.300752 TCTTCATTTGCGAAGAAAGACTCT 58.699 37.500 8.70 0.00 46.45 3.24
2281 2395 2.092375 GGTAGGGCTGCATAACCTTCTT 60.092 50.000 8.97 0.00 35.84 2.52
2531 2649 5.482163 TTGCCGTGGATTATCATGAGATA 57.518 39.130 0.09 0.00 35.67 1.98
2574 2692 6.013032 AGCATCCAGTATTGCTATTCCTGTAT 60.013 38.462 0.00 0.00 46.92 2.29
2681 2800 6.718522 AAAAGTAGCTAGGACAGGACTATC 57.281 41.667 0.00 0.00 0.00 2.08
2746 2867 8.810427 CCTTGATTTTGCAACATAATGATGTAC 58.190 33.333 0.00 0.00 45.93 2.90
2747 2868 9.577110 CTTGATTTTGCAACATAATGATGTACT 57.423 29.630 0.00 0.00 45.93 2.73
2748 2869 9.571810 TTGATTTTGCAACATAATGATGTACTC 57.428 29.630 0.00 0.00 45.93 2.59
2749 2870 8.190122 TGATTTTGCAACATAATGATGTACTCC 58.810 33.333 0.00 0.00 45.93 3.85
2750 2871 6.449635 TTTGCAACATAATGATGTACTCCC 57.550 37.500 0.00 0.00 45.93 4.30
2751 2872 4.126437 TGCAACATAATGATGTACTCCCG 58.874 43.478 0.00 0.00 45.93 5.14
2752 2873 3.058914 GCAACATAATGATGTACTCCCGC 60.059 47.826 0.00 0.00 45.93 6.13
2753 2874 3.402628 ACATAATGATGTACTCCCGCC 57.597 47.619 0.00 0.00 44.77 6.13
2754 2875 2.288825 ACATAATGATGTACTCCCGCCG 60.289 50.000 0.00 0.00 44.77 6.46
2755 2876 1.405872 TAATGATGTACTCCCGCCGT 58.594 50.000 0.00 0.00 0.00 5.68
2756 2877 0.104304 AATGATGTACTCCCGCCGTC 59.896 55.000 0.00 0.00 0.00 4.79
2757 2878 1.745320 ATGATGTACTCCCGCCGTCC 61.745 60.000 0.00 0.00 0.00 4.79
2758 2879 3.148031 GATGTACTCCCGCCGTCCC 62.148 68.421 0.00 0.00 0.00 4.46
2759 2880 3.968837 ATGTACTCCCGCCGTCCCA 62.969 63.158 0.00 0.00 0.00 4.37
2760 2881 3.384532 GTACTCCCGCCGTCCCAA 61.385 66.667 0.00 0.00 0.00 4.12
2761 2882 3.072468 TACTCCCGCCGTCCCAAG 61.072 66.667 0.00 0.00 0.00 3.61
2762 2883 3.588817 TACTCCCGCCGTCCCAAGA 62.589 63.158 0.00 0.00 0.00 3.02
2763 2884 4.148825 CTCCCGCCGTCCCAAGAG 62.149 72.222 0.00 0.00 0.00 2.85
2768 2889 2.668550 GCCGTCCCAAGAGCGTTT 60.669 61.111 0.00 0.00 0.00 3.60
2769 2890 2.258726 GCCGTCCCAAGAGCGTTTT 61.259 57.895 0.00 0.00 0.00 2.43
2770 2891 1.792118 GCCGTCCCAAGAGCGTTTTT 61.792 55.000 0.00 0.00 0.00 1.94
2771 2892 0.237498 CCGTCCCAAGAGCGTTTTTC 59.763 55.000 0.00 0.00 0.00 2.29
2772 2893 0.941542 CGTCCCAAGAGCGTTTTTCA 59.058 50.000 0.00 0.00 0.00 2.69
2773 2894 1.333791 CGTCCCAAGAGCGTTTTTCAC 60.334 52.381 0.00 0.00 0.00 3.18
2774 2895 1.673920 GTCCCAAGAGCGTTTTTCACA 59.326 47.619 0.00 0.00 0.00 3.58
2775 2896 1.673920 TCCCAAGAGCGTTTTTCACAC 59.326 47.619 0.00 0.00 0.00 3.82
2776 2897 1.676006 CCCAAGAGCGTTTTTCACACT 59.324 47.619 0.00 0.00 0.00 3.55
2777 2898 2.875933 CCCAAGAGCGTTTTTCACACTA 59.124 45.455 0.00 0.00 0.00 2.74
2778 2899 3.058914 CCCAAGAGCGTTTTTCACACTAG 60.059 47.826 0.00 0.00 0.00 2.57
2779 2900 3.545633 CAAGAGCGTTTTTCACACTAGC 58.454 45.455 0.00 0.00 0.00 3.42
2780 2901 1.792949 AGAGCGTTTTTCACACTAGCG 59.207 47.619 0.00 0.00 0.00 4.26
2781 2902 1.525619 GAGCGTTTTTCACACTAGCGT 59.474 47.619 0.00 0.00 0.00 5.07
2782 2903 2.727798 GAGCGTTTTTCACACTAGCGTA 59.272 45.455 0.00 0.00 0.00 4.42
2783 2904 2.729882 AGCGTTTTTCACACTAGCGTAG 59.270 45.455 0.00 0.00 0.00 3.51
2784 2905 2.473984 GCGTTTTTCACACTAGCGTAGT 59.526 45.455 0.00 0.00 40.28 2.73
2799 2920 3.854286 CGTAGTGTGAAAAACGCTCTT 57.146 42.857 0.00 0.00 46.98 2.85
2800 2921 4.959631 CGTAGTGTGAAAAACGCTCTTA 57.040 40.909 0.00 0.00 46.98 2.10
2801 2922 5.511088 CGTAGTGTGAAAAACGCTCTTAT 57.489 39.130 0.00 0.00 46.98 1.73
2802 2923 6.621737 CGTAGTGTGAAAAACGCTCTTATA 57.378 37.500 0.00 0.00 46.98 0.98
2803 2924 7.218145 CGTAGTGTGAAAAACGCTCTTATAT 57.782 36.000 0.00 0.00 46.98 0.86
2804 2925 7.672738 CGTAGTGTGAAAAACGCTCTTATATT 58.327 34.615 0.00 0.00 46.98 1.28
2805 2926 8.800972 CGTAGTGTGAAAAACGCTCTTATATTA 58.199 33.333 0.00 0.00 46.98 0.98
2808 2929 8.612619 AGTGTGAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 46.98 2.74
2809 2930 7.855904 GTGTGAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 36.31 4.00
2810 2931 7.771361 TGTGAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
2811 2932 8.068380 GTGAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2812 2933 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2813 2934 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2814 2935 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2815 2936 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2816 2937 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2817 2938 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2818 2939 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2819 2940 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2820 2941 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2821 2942 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2960 3081 3.942539 TCAGTGTGTTGTTTGATGTCG 57.057 42.857 0.00 0.00 0.00 4.35
3001 3147 3.836949 CCATCACTTATTTGTGTGTGCC 58.163 45.455 0.00 0.00 38.90 5.01
3038 3190 5.533528 TCATCATTGCAGTGCTATTGCTTAT 59.466 36.000 17.60 0.29 42.02 1.73
3191 3343 8.846943 TCAAGTAACATGATACATCAAACACT 57.153 30.769 14.73 0.00 40.69 3.55
3205 3357 4.650734 TCAAACACTGATATGTTGCTCCA 58.349 39.130 0.00 0.00 42.01 3.86
3249 3401 6.635755 ACTGAGAAGTTTACTCCTATTCTGC 58.364 40.000 0.00 0.00 33.95 4.26
3274 3426 6.202226 GTTTGTCTGGTTGAAAGATTCACTC 58.798 40.000 0.00 0.00 39.87 3.51
3470 3627 8.156820 TGGAATTCAGACATCTTTTGAAGTAGA 58.843 33.333 7.93 0.00 34.64 2.59
3574 3731 1.835483 CTCGTTGTGTCTGCTGTGGC 61.835 60.000 0.00 0.00 39.26 5.01
3576 3733 1.835483 CGTTGTGTCTGCTGTGGCTC 61.835 60.000 0.00 0.00 39.59 4.70
3655 3812 2.159240 TGGCTACTACGATGACTGCAAG 60.159 50.000 0.00 0.00 42.29 4.01
3678 3835 3.688272 CGCTAACGGAATCGAAGTCTTA 58.312 45.455 0.00 0.00 40.11 2.10
3694 3851 4.563061 AGTCTTATTTTACTCAACGCCGT 58.437 39.130 0.00 0.00 0.00 5.68
3735 3912 0.320771 GGCATCTCCAACACACGTCT 60.321 55.000 0.00 0.00 34.01 4.18
3775 3956 1.755380 GACCTATGCCACGTAGGACTT 59.245 52.381 17.69 0.00 41.01 3.01
3819 4163 0.039180 CCTTACCGGGCCTTTCCTTT 59.961 55.000 6.32 0.00 34.39 3.11
3826 4170 0.603707 GGGCCTTTCCTTTGCTTTGC 60.604 55.000 0.84 0.00 34.39 3.68
3831 4175 2.037511 CCTTTCCTTTGCTTTGCATCCA 59.962 45.455 0.00 0.00 38.76 3.41
3834 4178 1.340889 TCCTTTGCTTTGCATCCACAC 59.659 47.619 0.00 0.00 38.76 3.82
3848 4192 1.697432 TCCACACCCTCTTTGTTCGAT 59.303 47.619 0.00 0.00 0.00 3.59
3858 4202 4.152402 CCTCTTTGTTCGATGTCGTCATTT 59.848 41.667 2.04 0.00 40.80 2.32
3876 4220 1.909700 TTTACCTCTTTGGCTGCCAG 58.090 50.000 22.17 11.60 40.22 4.85
3895 4239 1.454201 GCCTAGGCTTGTTGGACTTC 58.546 55.000 27.17 0.00 38.26 3.01
3896 4240 1.003696 GCCTAGGCTTGTTGGACTTCT 59.996 52.381 27.17 0.00 38.26 2.85
3897 4241 2.704572 CCTAGGCTTGTTGGACTTCTG 58.295 52.381 0.00 0.00 0.00 3.02
3900 4244 0.595095 GGCTTGTTGGACTTCTGCAG 59.405 55.000 7.63 7.63 0.00 4.41
3909 4253 1.835927 GACTTCTGCAGCCCTCACCT 61.836 60.000 9.47 0.00 0.00 4.00
3921 4265 3.649277 CTCACCTACGCGCTTGCCT 62.649 63.158 5.73 0.00 34.11 4.75
3933 4277 1.308783 GCTTGCCTGCCTTGGACTAC 61.309 60.000 0.00 0.00 0.00 2.73
4004 4802 2.810274 TGAAGACTTTGTGCTCATGCTC 59.190 45.455 0.00 0.00 40.48 4.26
4005 4803 2.855209 AGACTTTGTGCTCATGCTCT 57.145 45.000 0.00 0.00 40.48 4.09
4014 4812 3.943381 TGTGCTCATGCTCTAAAGGATTG 59.057 43.478 0.00 0.00 40.48 2.67
4041 4839 2.038557 AGATTAAGTTGTCGTGCCACCT 59.961 45.455 0.00 0.00 0.00 4.00
4048 4846 0.678366 TGTCGTGCCACCTTGTTGTT 60.678 50.000 0.00 0.00 0.00 2.83
4050 4848 0.107410 TCGTGCCACCTTGTTGTTCT 60.107 50.000 0.00 0.00 0.00 3.01
4051 4849 1.139256 TCGTGCCACCTTGTTGTTCTA 59.861 47.619 0.00 0.00 0.00 2.10
4052 4850 2.151202 CGTGCCACCTTGTTGTTCTAT 58.849 47.619 0.00 0.00 0.00 1.98
4053 4851 2.095768 CGTGCCACCTTGTTGTTCTATG 60.096 50.000 0.00 0.00 0.00 2.23
4054 4852 2.228822 GTGCCACCTTGTTGTTCTATGG 59.771 50.000 0.00 0.00 0.00 2.74
4055 4853 2.158534 TGCCACCTTGTTGTTCTATGGT 60.159 45.455 0.00 0.00 0.00 3.55
4056 4854 2.228822 GCCACCTTGTTGTTCTATGGTG 59.771 50.000 0.00 0.00 43.06 4.17
4057 4855 3.750371 CCACCTTGTTGTTCTATGGTGA 58.250 45.455 11.02 0.00 45.37 4.02
4058 4856 3.502211 CCACCTTGTTGTTCTATGGTGAC 59.498 47.826 11.02 0.00 45.37 3.67
4059 4857 4.133820 CACCTTGTTGTTCTATGGTGACA 58.866 43.478 4.14 0.00 45.37 3.58
4090 4888 8.507524 ACTAAATTAGTCTTCTTTGGTATGCC 57.492 34.615 0.00 0.00 32.47 4.40
4091 4889 8.107095 ACTAAATTAGTCTTCTTTGGTATGCCA 58.893 33.333 0.00 0.00 37.46 4.92
4092 4890 7.961326 AAATTAGTCTTCTTTGGTATGCCAT 57.039 32.000 2.33 0.00 45.56 4.40
4093 4891 7.961326 AATTAGTCTTCTTTGGTATGCCATT 57.039 32.000 2.33 0.00 45.56 3.16
4094 4892 7.961326 ATTAGTCTTCTTTGGTATGCCATTT 57.039 32.000 2.33 0.00 45.56 2.32
4095 4893 7.775053 TTAGTCTTCTTTGGTATGCCATTTT 57.225 32.000 2.33 0.00 45.56 1.82
4096 4894 6.670695 AGTCTTCTTTGGTATGCCATTTTT 57.329 33.333 2.33 0.00 45.56 1.94
4125 4923 2.396608 CATCCTCTCTGTGGTCCATCT 58.603 52.381 0.00 0.00 0.00 2.90
4143 4941 7.414540 GGTCCATCTGATCAACAAATACTTGAC 60.415 40.741 0.00 0.00 36.33 3.18
4171 4969 5.111989 TGCTTCTGAAGAAAGTATGGATCG 58.888 41.667 21.06 0.00 33.07 3.69
4174 4972 5.932619 TCTGAAGAAAGTATGGATCGGAA 57.067 39.130 0.00 0.00 0.00 4.30
4232 5030 3.464720 TGTTTGCCTAAATCCCATGGA 57.535 42.857 15.22 0.00 35.55 3.41
4255 5053 9.170890 TGGAGGACTTGGTATTTTAGATATCAT 57.829 33.333 5.32 0.00 0.00 2.45
4317 5115 0.393077 CTTCAACGGAGTGGACACCT 59.607 55.000 0.00 0.00 42.13 4.00
4336 5134 4.235079 CCTCTTGGGTCAACATTATCCA 57.765 45.455 0.00 0.00 0.00 3.41
4338 5136 4.080356 CCTCTTGGGTCAACATTATCCAGA 60.080 45.833 0.00 0.00 0.00 3.86
4349 5147 9.614792 GTCAACATTATCCAGAAAACCTACTAT 57.385 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 112 1.415659 AGATCCATAGTGCCACAGAGC 59.584 52.381 0.00 0.00 0.00 4.09
103 113 3.464907 CAAGATCCATAGTGCCACAGAG 58.535 50.000 0.00 0.00 0.00 3.35
200 219 4.157289 GGTAGACACAATAGTCCGAAGTGA 59.843 45.833 0.00 0.00 39.34 3.41
209 228 4.844655 AGGGTTCAAGGTAGACACAATAGT 59.155 41.667 0.00 0.00 0.00 2.12
227 246 2.496470 GACCACGAGATAAGTGAGGGTT 59.504 50.000 0.00 0.00 41.83 4.11
256 275 0.251787 TGAGAGACTGTAGGCTGCCA 60.252 55.000 22.65 3.92 0.00 4.92
371 393 0.594284 GTAGACTATCGTGGCACGGC 60.594 60.000 36.30 20.99 42.81 5.68
491 514 6.093082 GTGTAAAACACGAATATGGCTAAGGT 59.907 38.462 0.00 0.00 39.53 3.50
541 564 2.961062 GCAAGCCCTTGGTCATGATATT 59.039 45.455 9.81 0.00 40.74 1.28
570 593 3.009033 TGGACCGAAACTCCTCAAATGAT 59.991 43.478 0.00 0.00 0.00 2.45
634 674 1.387737 CATTCACCCACCCACCCAT 59.612 57.895 0.00 0.00 0.00 4.00
639 679 0.850100 ACTCAACATTCACCCACCCA 59.150 50.000 0.00 0.00 0.00 4.51
641 681 5.296780 CACATATACTCAACATTCACCCACC 59.703 44.000 0.00 0.00 0.00 4.61
643 683 6.061022 ACACATATACTCAACATTCACCCA 57.939 37.500 0.00 0.00 0.00 4.51
647 687 8.611757 GCACATAACACATATACTCAACATTCA 58.388 33.333 0.00 0.00 0.00 2.57
649 689 8.504812 TGCACATAACACATATACTCAACATT 57.495 30.769 0.00 0.00 0.00 2.71
650 690 8.681486 ATGCACATAACACATATACTCAACAT 57.319 30.769 0.00 0.00 0.00 2.71
687 727 1.630878 CAAGAAACTAGGAGGTGGGCT 59.369 52.381 0.00 0.00 0.00 5.19
752 794 2.674852 CACATTGCTCTTCGTGCATAGT 59.325 45.455 0.00 0.00 40.34 2.12
771 813 4.140518 TGATGTTGTAATTGCACGACAC 57.859 40.909 3.56 0.00 43.81 3.67
773 815 5.863898 TGTATGATGTTGTAATTGCACGAC 58.136 37.500 0.00 0.00 33.99 4.34
798 840 1.234821 TTTTGCGAGGGTGCTACTTG 58.765 50.000 0.00 0.00 35.36 3.16
853 900 1.639298 GCCGCTTGAAGATTCGTGCT 61.639 55.000 0.00 0.00 0.00 4.40
1196 1243 1.223487 GAGCGCCACCAGGGAAATA 59.777 57.895 2.29 0.00 40.01 1.40
1211 1258 1.668047 GCACCAAACAAGCATCAGAGC 60.668 52.381 0.00 0.00 0.00 4.09
1306 1353 2.364324 TCAAGCAAACCGAGACTGTACT 59.636 45.455 0.00 0.00 0.00 2.73
1349 1397 5.965922 ACAAATAAGCAAACTGGCTAATCC 58.034 37.500 0.00 0.00 45.07 3.01
1364 1412 4.495422 ACGCAGGTCTACAGACAAATAAG 58.505 43.478 11.31 0.79 46.47 1.73
1381 1436 2.873170 TTCTCGTGCAAATTACGCAG 57.127 45.000 2.84 0.00 40.78 5.18
1461 1517 3.233578 CGCAATGCAAAAACACTACGAT 58.766 40.909 5.91 0.00 0.00 3.73
1534 1593 0.249280 ACGCACAACACATGACTCGA 60.249 50.000 0.00 0.00 0.00 4.04
1685 1744 3.686016 AGTTATGCTTCGACCACCATTT 58.314 40.909 0.00 0.00 0.00 2.32
1693 1752 6.253083 GGTAACACTCTAAGTTATGCTTCGAC 59.747 42.308 0.00 0.00 38.57 4.20
1778 1837 7.128234 ACTGGTAACTAACTGTTCAACCTAA 57.872 36.000 0.00 0.00 37.87 2.69
1795 1854 6.096987 TCTGCAACACCAAATTTAACTGGTAA 59.903 34.615 0.00 0.00 44.30 2.85
1850 1909 3.573967 CACCAAGCAAACCTAGGAAACAT 59.426 43.478 17.98 0.00 0.00 2.71
1882 1947 7.951530 AAAATAGAATGCAACCAAGAAACAG 57.048 32.000 0.00 0.00 0.00 3.16
1948 2013 3.409026 ACCGAGCAGAATTCAAGAAGT 57.591 42.857 8.44 0.00 0.00 3.01
1960 2025 2.871182 TACTGAAGCATACCGAGCAG 57.129 50.000 0.00 0.00 0.00 4.24
2172 2286 4.878971 GCAGAGAAAAGGAACCTAGGAATC 59.121 45.833 17.98 13.03 0.00 2.52
2173 2287 4.538089 AGCAGAGAAAAGGAACCTAGGAAT 59.462 41.667 17.98 3.24 0.00 3.01
2218 2332 7.357951 AGAGCAAAATAAGAGTCTTTCTTCG 57.642 36.000 11.40 0.00 42.54 3.79
2255 2369 2.498167 GTTATGCAGCCCTACCATCAG 58.502 52.381 0.00 0.00 0.00 2.90
2658 2777 6.436890 AGATAGTCCTGTCCTAGCTACTTTT 58.563 40.000 0.00 0.00 29.80 2.27
2746 2867 4.148825 CTCTTGGGACGGCGGGAG 62.149 72.222 13.24 4.98 0.00 4.30
2751 2872 1.792118 AAAAACGCTCTTGGGACGGC 61.792 55.000 0.00 0.00 0.00 5.68
2752 2873 0.237498 GAAAAACGCTCTTGGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
2753 2874 0.941542 TGAAAAACGCTCTTGGGACG 59.058 50.000 0.00 0.00 0.00 4.79
2754 2875 1.673920 TGTGAAAAACGCTCTTGGGAC 59.326 47.619 0.00 0.00 0.00 4.46
2755 2876 1.673920 GTGTGAAAAACGCTCTTGGGA 59.326 47.619 0.00 0.00 36.31 4.37
2756 2877 1.676006 AGTGTGAAAAACGCTCTTGGG 59.324 47.619 0.00 0.00 46.98 4.12
2757 2878 3.607078 GCTAGTGTGAAAAACGCTCTTGG 60.607 47.826 0.00 0.00 46.98 3.61
2758 2879 3.545633 GCTAGTGTGAAAAACGCTCTTG 58.454 45.455 0.00 0.00 46.98 3.02
2759 2880 2.221055 CGCTAGTGTGAAAAACGCTCTT 59.779 45.455 0.00 0.00 46.98 2.85
2760 2881 1.792949 CGCTAGTGTGAAAAACGCTCT 59.207 47.619 0.00 0.00 46.98 4.09
2761 2882 1.525619 ACGCTAGTGTGAAAAACGCTC 59.474 47.619 8.45 0.00 46.98 5.03
2763 2884 2.473984 ACTACGCTAGTGTGAAAAACGC 59.526 45.455 19.20 0.00 37.69 4.84
2779 2900 3.854286 AAGAGCGTTTTTCACACTACG 57.146 42.857 0.00 0.00 37.09 3.51
2782 2903 8.612619 CCATAATATAAGAGCGTTTTTCACACT 58.387 33.333 0.00 0.00 0.00 3.55
2783 2904 7.855904 CCCATAATATAAGAGCGTTTTTCACAC 59.144 37.037 0.00 0.00 0.00 3.82
2784 2905 7.771361 TCCCATAATATAAGAGCGTTTTTCACA 59.229 33.333 0.00 0.00 0.00 3.58
2785 2906 8.068380 GTCCCATAATATAAGAGCGTTTTTCAC 58.932 37.037 0.00 0.00 0.00 3.18
2786 2907 7.042321 CGTCCCATAATATAAGAGCGTTTTTCA 60.042 37.037 0.00 0.00 0.00 2.69
2787 2908 7.288672 CGTCCCATAATATAAGAGCGTTTTTC 58.711 38.462 0.00 0.00 0.00 2.29
2788 2909 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2789 2910 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2790 2911 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2791 2912 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2792 2913 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2793 2914 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2794 2915 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2795 2916 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2796 2917 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2797 2918 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2798 2919 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2799 2920 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2800 2921 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2801 2922 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2802 2923 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2803 2924 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2804 2925 2.969950 CAAATACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
2805 2926 1.768870 CAAATACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
2806 2927 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
2807 2928 1.201424 ACAAATACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
2808 2929 3.345508 AAACAAATACTCCCTCCGTCC 57.654 47.619 0.00 0.00 0.00 4.79
2809 2930 3.119955 GCAAAACAAATACTCCCTCCGTC 60.120 47.826 0.00 0.00 0.00 4.79
2810 2931 2.817844 GCAAAACAAATACTCCCTCCGT 59.182 45.455 0.00 0.00 0.00 4.69
2811 2932 2.817258 TGCAAAACAAATACTCCCTCCG 59.183 45.455 0.00 0.00 0.00 4.63
2812 2933 3.826729 AGTGCAAAACAAATACTCCCTCC 59.173 43.478 0.00 0.00 0.00 4.30
2813 2934 4.321230 CCAGTGCAAAACAAATACTCCCTC 60.321 45.833 0.00 0.00 0.00 4.30
2814 2935 3.573967 CCAGTGCAAAACAAATACTCCCT 59.426 43.478 0.00 0.00 0.00 4.20
2815 2936 3.306019 CCCAGTGCAAAACAAATACTCCC 60.306 47.826 0.00 0.00 0.00 4.30
2816 2937 3.572255 TCCCAGTGCAAAACAAATACTCC 59.428 43.478 0.00 0.00 0.00 3.85
2817 2938 4.546570 GTCCCAGTGCAAAACAAATACTC 58.453 43.478 0.00 0.00 0.00 2.59
2818 2939 3.004315 CGTCCCAGTGCAAAACAAATACT 59.996 43.478 0.00 0.00 0.00 2.12
2819 2940 3.305110 CGTCCCAGTGCAAAACAAATAC 58.695 45.455 0.00 0.00 0.00 1.89
2820 2941 2.287909 GCGTCCCAGTGCAAAACAAATA 60.288 45.455 0.00 0.00 0.00 1.40
2821 2942 1.537990 GCGTCCCAGTGCAAAACAAAT 60.538 47.619 0.00 0.00 0.00 2.32
3008 3160 1.081094 CACTGCAATGATGAGCGACA 58.919 50.000 0.00 0.00 0.00 4.35
3038 3190 9.502091 AAGATGCTGTATGTTAAAGTACAAAGA 57.498 29.630 0.00 0.00 31.05 2.52
3175 3327 8.347771 GCAACATATCAGTGTTTGATGTATCAT 58.652 33.333 0.12 0.00 46.01 2.45
3191 3343 8.985315 AGATAGAAAATTGGAGCAACATATCA 57.015 30.769 0.00 0.00 0.00 2.15
3249 3401 4.970003 GTGAATCTTTCAACCAGACAAACG 59.030 41.667 0.00 0.00 42.15 3.60
3274 3426 2.166459 TCTACCTGTGGAATGAAGCTCG 59.834 50.000 0.00 0.00 0.00 5.03
3416 3569 5.420409 AGTTAATGCACAAGCTCTAGTACC 58.580 41.667 0.00 0.00 42.74 3.34
3470 3627 4.764823 TCAGGAAGAAAACCGTGCATAAAT 59.235 37.500 0.00 0.00 0.00 1.40
3472 3629 3.745799 TCAGGAAGAAAACCGTGCATAA 58.254 40.909 0.00 0.00 0.00 1.90
3473 3630 3.410631 TCAGGAAGAAAACCGTGCATA 57.589 42.857 0.00 0.00 0.00 3.14
3574 3731 2.586258 ATTCAGTTGGATCCGACGAG 57.414 50.000 23.85 20.17 35.57 4.18
3669 3826 5.548250 GGCGTTGAGTAAAATAAGACTTCG 58.452 41.667 0.00 0.00 0.00 3.79
3678 3835 5.349543 CCTAAGTTACGGCGTTGAGTAAAAT 59.650 40.000 21.24 0.49 35.01 1.82
3694 3851 5.310451 CCCTTAACTTGTGTGCCTAAGTTA 58.690 41.667 0.00 0.00 43.25 2.24
3735 3912 1.534697 GGACACCCACAAACCTCCA 59.465 57.895 0.00 0.00 0.00 3.86
3775 3956 0.247460 CAGTTGGCTGAGGATGTCGA 59.753 55.000 0.00 0.00 45.28 4.20
3802 3983 0.896479 GCAAAGGAAAGGCCCGGTAA 60.896 55.000 0.00 0.00 37.37 2.85
3813 4157 2.037901 TGTGGATGCAAAGCAAAGGAA 58.962 42.857 0.00 0.00 43.62 3.36
3814 4158 1.340889 GTGTGGATGCAAAGCAAAGGA 59.659 47.619 0.00 0.00 43.62 3.36
3819 4163 0.895100 GAGGGTGTGGATGCAAAGCA 60.895 55.000 8.95 0.00 44.86 3.91
3826 4170 1.806542 CGAACAAAGAGGGTGTGGATG 59.193 52.381 0.00 0.00 0.00 3.51
3831 4175 2.767505 GACATCGAACAAAGAGGGTGT 58.232 47.619 0.00 0.00 0.00 4.16
3834 4178 1.993370 GACGACATCGAACAAAGAGGG 59.007 52.381 8.54 0.00 43.02 4.30
3848 4192 3.500680 GCCAAAGAGGTAAAATGACGACA 59.499 43.478 0.00 0.00 40.61 4.35
3858 4202 0.609131 GCTGGCAGCCAAAGAGGTAA 60.609 55.000 28.87 0.00 40.61 2.85
3876 4220 1.003696 AGAAGTCCAACAAGCCTAGGC 59.996 52.381 27.19 27.19 42.33 3.93
3879 4223 1.419762 TGCAGAAGTCCAACAAGCCTA 59.580 47.619 0.00 0.00 0.00 3.93
3893 4237 1.888436 CGTAGGTGAGGGCTGCAGAA 61.888 60.000 20.43 0.00 0.00 3.02
3895 4239 2.185350 CGTAGGTGAGGGCTGCAG 59.815 66.667 10.11 10.11 0.00 4.41
3896 4240 4.082523 GCGTAGGTGAGGGCTGCA 62.083 66.667 0.50 0.00 0.00 4.41
3900 4244 4.452733 AAGCGCGTAGGTGAGGGC 62.453 66.667 8.43 0.00 45.09 5.19
3909 4253 4.697756 AAGGCAGGCAAGCGCGTA 62.698 61.111 8.43 0.00 39.92 4.42
3921 4265 1.292223 GACAGCGTAGTCCAAGGCA 59.708 57.895 0.00 0.00 32.74 4.75
3933 4277 1.807226 TCCTATGTGGACGACAGCG 59.193 57.895 0.00 0.00 40.56 5.18
3944 4288 3.069729 GGCTCAAGTTACGGATCCTATGT 59.930 47.826 10.75 2.90 0.00 2.29
3957 4301 4.348168 TCTTGGTTTAGAGAGGCTCAAGTT 59.652 41.667 18.26 0.00 33.85 2.66
3958 4302 3.904339 TCTTGGTTTAGAGAGGCTCAAGT 59.096 43.478 18.26 2.80 33.85 3.16
3959 4303 4.543590 TCTTGGTTTAGAGAGGCTCAAG 57.456 45.455 18.26 9.44 32.06 3.02
3997 4795 5.946942 AGTCTCAATCCTTTAGAGCATGA 57.053 39.130 0.00 0.00 0.00 3.07
3998 4796 7.048629 TCTAGTCTCAATCCTTTAGAGCATG 57.951 40.000 0.00 0.00 0.00 4.06
4014 4812 4.799428 GGCACGACAACTTAATCTAGTCTC 59.201 45.833 0.00 0.00 0.00 3.36
4029 4827 0.678366 AACAACAAGGTGGCACGACA 60.678 50.000 12.17 0.00 0.00 4.35
4041 4839 8.908903 AGTTAATTTGTCACCATAGAACAACAA 58.091 29.630 0.00 0.00 0.00 2.83
4064 4862 8.957466 GGCATACCAAAGAAGACTAATTTAGTT 58.043 33.333 10.32 0.00 35.86 2.24
4065 4863 8.107095 TGGCATACCAAAGAAGACTAATTTAGT 58.893 33.333 8.81 8.81 45.37 2.24
4066 4864 8.506168 TGGCATACCAAAGAAGACTAATTTAG 57.494 34.615 1.79 1.79 45.37 1.85
4095 4893 4.701651 CCACAGAGAGGATGCACATAAAAA 59.298 41.667 0.00 0.00 0.00 1.94
4096 4894 4.263462 ACCACAGAGAGGATGCACATAAAA 60.263 41.667 0.00 0.00 0.00 1.52
4097 4895 3.264193 ACCACAGAGAGGATGCACATAAA 59.736 43.478 0.00 0.00 0.00 1.40
4098 4896 2.840038 ACCACAGAGAGGATGCACATAA 59.160 45.455 0.00 0.00 0.00 1.90
4099 4897 2.432146 GACCACAGAGAGGATGCACATA 59.568 50.000 0.00 0.00 0.00 2.29
4100 4898 1.209019 GACCACAGAGAGGATGCACAT 59.791 52.381 0.00 0.00 0.00 3.21
4101 4899 0.610174 GACCACAGAGAGGATGCACA 59.390 55.000 0.00 0.00 0.00 4.57
4102 4900 0.107945 GGACCACAGAGAGGATGCAC 60.108 60.000 0.00 0.00 0.00 4.57
4103 4901 0.545071 TGGACCACAGAGAGGATGCA 60.545 55.000 0.00 0.00 0.00 3.96
4104 4902 0.835941 ATGGACCACAGAGAGGATGC 59.164 55.000 0.00 0.00 0.00 3.91
4105 4903 2.102757 CAGATGGACCACAGAGAGGATG 59.897 54.545 0.00 0.00 0.00 3.51
4106 4904 2.023598 TCAGATGGACCACAGAGAGGAT 60.024 50.000 0.00 0.00 0.00 3.24
4107 4905 1.359130 TCAGATGGACCACAGAGAGGA 59.641 52.381 0.00 0.00 0.00 3.71
4108 4906 1.857965 TCAGATGGACCACAGAGAGG 58.142 55.000 0.00 0.00 0.00 3.69
4109 4907 3.029570 TGATCAGATGGACCACAGAGAG 58.970 50.000 0.00 0.00 0.00 3.20
4110 4908 3.105959 TGATCAGATGGACCACAGAGA 57.894 47.619 0.00 0.00 0.00 3.10
4111 4909 3.055602 TGTTGATCAGATGGACCACAGAG 60.056 47.826 0.00 0.00 0.00 3.35
4112 4910 2.905736 TGTTGATCAGATGGACCACAGA 59.094 45.455 0.00 0.00 0.00 3.41
4125 4923 6.862608 GCAATGTGTCAAGTATTTGTTGATCA 59.137 34.615 0.00 0.00 36.35 2.92
4143 4941 6.149973 TCCATACTTTCTTCAGAAGCAATGTG 59.850 38.462 5.15 1.21 35.21 3.21
4171 4969 4.021544 TCAGAGTCAGCTTCTTTCTCTTCC 60.022 45.833 0.00 0.00 33.92 3.46
4174 4972 5.743636 AATCAGAGTCAGCTTCTTTCTCT 57.256 39.130 0.00 0.00 36.15 3.10
4186 4984 5.882557 GCTTTATCCCAAGAAATCAGAGTCA 59.117 40.000 0.00 0.00 0.00 3.41
4255 5053 5.554070 TCAGAAGAGCTTGATTGTGAATGA 58.446 37.500 5.11 0.00 0.00 2.57
4317 5115 5.512942 TTCTGGATAATGTTGACCCAAGA 57.487 39.130 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.