Multiple sequence alignment - TraesCS2D01G203500

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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 TraesCS2D01G203500 chr2D 100.000 5087 0 0 1 5087 155515035 155509949 0.000000e+00 9395.0
1 TraesCS2D01G203500 chr2D 100.000 1260 0 0 5355 6614 155509681 155508422 0.000000e+00 2327.0
2 TraesCS2D01G203500 chr2D 99.284 559 4 0 4529 5087 179127591 179128149 0.000000e+00 1011.0
3 TraesCS2D01G203500 chr2D 98.938 565 5 1 4523 5087 603523556 603522993 0.000000e+00 1009.0
4 TraesCS2D01G203500 chr2D 91.667 720 33 11 5921 6614 572791213 572790495 0.000000e+00 972.0
5 TraesCS2D01G203500 chr2D 96.364 440 14 1 5921 6360 30144770 30144333 0.000000e+00 723.0
6 TraesCS2D01G203500 chr2D 95.672 439 18 1 5921 6359 642825485 642825922 0.000000e+00 704.0
7 TraesCS2D01G203500 chr2D 95.011 441 22 0 5919 6359 534952738 534953178 0.000000e+00 693.0
8 TraesCS2D01G203500 chr2D 98.062 258 5 0 6357 6614 30081095 30080838 3.640000e-122 449.0
9 TraesCS2D01G203500 chr2D 97.674 258 6 0 6357 6614 30185910 30185653 1.690000e-120 444.0
10 TraesCS2D01G203500 chr2D 97.674 258 6 0 6357 6614 453729586 453729329 1.690000e-120 444.0
11 TraesCS2D01G203500 chr2D 86.093 151 18 2 583 732 38633990 38634138 6.860000e-35 159.0
12 TraesCS2D01G203500 chr2D 94.828 58 3 0 342 399 383554665 383554722 2.540000e-14 91.6
13 TraesCS2D01G203500 chr2D 100.000 31 0 0 5355 5385 179128175 179128205 2.580000e-04 58.4
14 TraesCS2D01G203500 chr2D 100.000 30 0 0 5355 5384 483627753 483627782 1.000000e-03 56.5
15 TraesCS2D01G203500 chr2A 94.341 1820 84 15 2346 4160 144653829 144655634 0.000000e+00 2772.0
16 TraesCS2D01G203500 chr2A 87.014 978 49 29 832 1777 144652004 144652935 0.000000e+00 1031.0
17 TraesCS2D01G203500 chr2A 93.211 545 19 7 5384 5915 144656309 144656848 0.000000e+00 785.0
18 TraesCS2D01G203500 chr2A 92.675 314 11 1 4158 4459 144655747 144656060 6.090000e-120 442.0
19 TraesCS2D01G203500 chr2A 89.655 319 17 7 1864 2179 144652939 144653244 6.220000e-105 392.0
20 TraesCS2D01G203500 chr2A 76.531 294 50 12 402 693 733415828 733415552 6.910000e-30 143.0
21 TraesCS2D01G203500 chr2A 94.253 87 5 0 1775 1861 628780924 628781010 4.160000e-27 134.0
22 TraesCS2D01G203500 chr2A 94.253 87 5 0 1776 1862 753210726 753210640 4.160000e-27 134.0
23 TraesCS2D01G203500 chr2A 94.186 86 5 0 1777 1862 41474164 41474249 1.500000e-26 132.0
24 TraesCS2D01G203500 chr2B 96.661 1168 28 8 2617 3779 212934677 212933516 0.000000e+00 1930.0
25 TraesCS2D01G203500 chr2B 95.669 785 28 2 48 832 8536082 8536860 0.000000e+00 1256.0
26 TraesCS2D01G203500 chr2B 92.438 886 33 12 832 1707 212936536 212935675 0.000000e+00 1234.0
27 TraesCS2D01G203500 chr2B 94.620 539 24 4 3967 4500 212933518 212932980 0.000000e+00 830.0
28 TraesCS2D01G203500 chr2B 97.018 436 11 2 48 482 777637329 777636895 0.000000e+00 732.0
29 TraesCS2D01G203500 chr2B 89.474 570 27 3 5384 5921 212932754 212932186 0.000000e+00 689.0
30 TraesCS2D01G203500 chr2B 94.420 448 16 5 48 494 198174717 198175156 0.000000e+00 680.0
31 TraesCS2D01G203500 chr2B 87.817 394 33 8 2177 2568 212935367 212934987 1.310000e-121 448.0
32 TraesCS2D01G203500 chr2B 90.813 283 14 5 1872 2153 212935625 212935354 1.050000e-97 368.0
33 TraesCS2D01G203500 chr2B 95.215 209 5 1 477 685 777636331 777636128 6.400000e-85 326.0
34 TraesCS2D01G203500 chr2B 96.364 165 6 0 672 836 198175577 198175741 8.450000e-69 272.0
35 TraesCS2D01G203500 chr2B 94.186 86 5 0 1776 1861 535031457 535031542 1.500000e-26 132.0
36 TraesCS2D01G203500 chr2B 96.078 51 2 0 1 51 8536005 8536055 4.250000e-12 84.2
37 TraesCS2D01G203500 chr2B 94.118 51 3 0 1 51 777637406 777637356 1.980000e-10 78.7
38 TraesCS2D01G203500 chr3A 96.778 838 21 5 1 838 28727835 28728666 0.000000e+00 1393.0
39 TraesCS2D01G203500 chr3A 96.539 838 22 5 1 838 28662026 28662856 0.000000e+00 1380.0
40 TraesCS2D01G203500 chr3A 96.226 477 13 3 358 832 28758647 28759120 0.000000e+00 776.0
41 TraesCS2D01G203500 chr3A 98.962 289 3 0 1 289 28758107 28758395 9.830000e-143 518.0
42 TraesCS2D01G203500 chr3A 93.407 91 6 0 1775 1865 686127537 686127447 1.160000e-27 135.0
43 TraesCS2D01G203500 chr3A 92.000 50 4 0 508 557 28662462 28662511 3.310000e-08 71.3
44 TraesCS2D01G203500 chr3A 92.000 50 4 0 508 557 28728272 28728321 3.310000e-08 71.3
45 TraesCS2D01G203500 chr1A 96.763 834 23 3 1 833 560828033 560828863 0.000000e+00 1387.0
46 TraesCS2D01G203500 chr1A 94.186 86 5 0 1777 1862 409786918 409787003 1.500000e-26 132.0
47 TraesCS2D01G203500 chr1A 94.118 85 5 0 1777 1861 448911837 448911921 5.380000e-26 130.0
48 TraesCS2D01G203500 chr1A 94.118 85 5 0 1780 1864 462746814 462746730 5.380000e-26 130.0
49 TraesCS2D01G203500 chr1A 89.109 101 8 3 1763 1861 518044802 518044901 9.010000e-24 122.0
50 TraesCS2D01G203500 chr1A 91.860 86 7 0 1776 1861 286008393 286008308 3.240000e-23 121.0
51 TraesCS2D01G203500 chr1A 89.091 55 3 3 780 832 465246866 465246813 1.540000e-06 65.8
52 TraesCS2D01G203500 chr1A 100.000 30 0 0 5355 5384 543651256 543651227 1.000000e-03 56.5
53 TraesCS2D01G203500 chr1D 99.643 561 2 0 4527 5087 388964870 388965430 0.000000e+00 1026.0
54 TraesCS2D01G203500 chr1D 94.805 77 4 0 1777 1853 317998636 317998712 3.240000e-23 121.0
55 TraesCS2D01G203500 chr1D 100.000 31 0 0 5355 5385 388965454 388965484 2.580000e-04 58.4
56 TraesCS2D01G203500 chr4D 99.287 561 4 0 4527 5087 15922319 15921759 0.000000e+00 1014.0
57 TraesCS2D01G203500 chr4D 93.023 86 6 0 1777 1862 47533267 47533182 6.960000e-25 126.0
58 TraesCS2D01G203500 chr3D 99.286 560 4 0 4528 5087 223480051 223479492 0.000000e+00 1013.0
59 TraesCS2D01G203500 chr3D 98.930 561 5 1 4527 5087 91808628 91809187 0.000000e+00 1002.0
60 TraesCS2D01G203500 chr3D 98.754 562 7 0 4526 5087 11348137 11347576 0.000000e+00 1000.0
61 TraesCS2D01G203500 chr3D 98.752 561 7 0 4527 5087 553902301 553901741 0.000000e+00 998.0
62 TraesCS2D01G203500 chr3D 96.811 439 14 0 5921 6359 602047884 602048322 0.000000e+00 734.0
63 TraesCS2D01G203500 chr3D 96.145 441 17 0 5919 6359 80220422 80219982 0.000000e+00 721.0
64 TraesCS2D01G203500 chr3D 98.062 258 5 0 6357 6614 80218438 80218181 3.640000e-122 449.0
65 TraesCS2D01G203500 chr7D 99.278 554 4 0 4534 5087 38864512 38865065 0.000000e+00 1002.0
66 TraesCS2D01G203500 chr7D 87.078 681 65 14 139 810 20448840 20448174 0.000000e+00 749.0
67 TraesCS2D01G203500 chr7D 95.270 444 18 1 5919 6359 500222325 500222768 0.000000e+00 701.0
68 TraesCS2D01G203500 chr7D 100.000 31 0 0 5355 5385 511080764 511080734 2.580000e-04 58.4
69 TraesCS2D01G203500 chr6D 86.517 801 78 17 48 836 425078210 425077428 0.000000e+00 854.0
70 TraesCS2D01G203500 chr6D 95.444 439 17 1 5921 6359 108455740 108455305 0.000000e+00 697.0
71 TraesCS2D01G203500 chr6D 84.768 151 20 2 583 732 176897824 176897972 1.490000e-31 148.0
72 TraesCS2D01G203500 chr6D 93.182 88 6 0 1775 1862 446513279 446513192 5.380000e-26 130.0
73 TraesCS2D01G203500 chr6D 92.045 88 7 0 1775 1862 367006878 367006965 2.500000e-24 124.0
74 TraesCS2D01G203500 chr6D 91.765 85 7 0 1777 1861 57486339 57486255 1.170000e-22 119.0
75 TraesCS2D01G203500 chr6D 91.765 85 7 0 1777 1861 68082945 68082861 1.170000e-22 119.0
76 TraesCS2D01G203500 chr6D 90.698 86 8 0 1776 1861 385917026 385916941 1.510000e-21 115.0
77 TraesCS2D01G203500 chr6D 88.889 90 9 1 1777 1866 248004002 248004090 7.010000e-20 110.0
78 TraesCS2D01G203500 chr6D 89.535 86 9 0 1777 1862 441898296 441898381 7.010000e-20 110.0
79 TraesCS2D01G203500 chr5D 95.918 441 16 1 5919 6359 529804433 529803995 0.000000e+00 713.0
80 TraesCS2D01G203500 chr5D 98.084 261 5 0 6354 6614 374628830 374629090 7.820000e-124 455.0
81 TraesCS2D01G203500 chr5D 97.318 261 7 0 6354 6614 332784177 332784437 1.690000e-120 444.0
82 TraesCS2D01G203500 chr5D 94.186 86 5 0 1777 1862 231475606 231475691 1.500000e-26 132.0
83 TraesCS2D01G203500 chr5D 94.048 84 5 0 1775 1858 480349480 480349563 1.940000e-25 128.0
84 TraesCS2D01G203500 chr5D 90.526 95 9 0 1767 1861 260795158 260795064 6.960000e-25 126.0
85 TraesCS2D01G203500 chr5D 92.222 90 6 1 1777 1866 482890057 482890145 6.960000e-25 126.0
86 TraesCS2D01G203500 chr5D 100.000 30 0 0 5355 5384 349375742 349375713 1.000000e-03 56.5
87 TraesCS2D01G203500 chrUn 95.506 445 15 2 5915 6359 20486135 20485696 0.000000e+00 706.0
88 TraesCS2D01G203500 chrUn 97.318 261 7 0 6354 6614 370576170 370576430 1.690000e-120 444.0
89 TraesCS2D01G203500 chrUn 90.805 87 8 0 1776 1862 371558048 371558134 4.190000e-22 117.0
90 TraesCS2D01G203500 chrUn 90.805 87 8 0 1776 1862 371616855 371616941 4.190000e-22 117.0
91 TraesCS2D01G203500 chrUn 88.636 88 10 0 1777 1864 47471788 47471701 2.520000e-19 108.0
92 TraesCS2D01G203500 chrUn 88.889 81 9 0 1777 1857 36436975 36436895 4.220000e-17 100.0
93 TraesCS2D01G203500 chrUn 86.667 90 12 0 1775 1864 50239246 50239157 4.220000e-17 100.0
94 TraesCS2D01G203500 chrUn 87.209 86 11 0 1777 1862 16341743 16341828 1.520000e-16 99.0
95 TraesCS2D01G203500 chrUn 89.474 76 7 1 1779 1853 19207535 19207460 1.960000e-15 95.3
96 TraesCS2D01G203500 chrUn 91.176 68 6 0 1794 1861 41929477 41929544 7.060000e-15 93.5
97 TraesCS2D01G203500 chrUn 88.312 77 9 0 1775 1851 263124938 263125014 7.060000e-15 93.5
98 TraesCS2D01G203500 chr6B 84.148 757 70 29 48 775 197770863 197770128 0.000000e+00 688.0
99 TraesCS2D01G203500 chr6B 85.276 652 66 17 188 832 197769541 197768913 0.000000e+00 645.0
100 TraesCS2D01G203500 chr6B 93.182 88 6 0 1776 1863 531739478 531739565 5.380000e-26 130.0
101 TraesCS2D01G203500 chr6B 83.217 143 19 4 551 693 14632564 14632427 6.960000e-25 126.0
102 TraesCS2D01G203500 chr6B 85.345 116 14 3 1776 1888 55994089 55993974 4.190000e-22 117.0
103 TraesCS2D01G203500 chr4B 93.133 466 29 3 48 513 438095231 438095693 0.000000e+00 680.0
104 TraesCS2D01G203500 chr4B 86.866 335 27 8 508 833 438095619 438095945 6.310000e-95 359.0
105 TraesCS2D01G203500 chr4B 93.182 88 6 0 1775 1862 29271924 29271837 5.380000e-26 130.0
106 TraesCS2D01G203500 chr4B 95.122 82 4 0 1775 1856 454519252 454519333 5.380000e-26 130.0
107 TraesCS2D01G203500 chr4B 93.023 86 6 0 1777 1862 600126334 600126419 6.960000e-25 126.0
108 TraesCS2D01G203500 chr4B 89.691 97 10 0 1769 1865 535283720 535283816 2.500000e-24 124.0
109 TraesCS2D01G203500 chr4B 100.000 30 0 0 5355 5384 393459413 393459384 1.000000e-03 56.5
110 TraesCS2D01G203500 chr5A 94.550 367 17 2 6248 6614 83967726 83967363 1.250000e-156 564.0
111 TraesCS2D01G203500 chr5A 94.783 115 6 0 4973 5087 677775362 677775476 5.270000e-41 180.0
112 TraesCS2D01G203500 chr5A 94.382 89 5 0 1776 1864 479846123 479846211 3.220000e-28 137.0
113 TraesCS2D01G203500 chr5A 94.186 86 5 0 1777 1862 413843423 413843508 1.500000e-26 132.0
114 TraesCS2D01G203500 chr5A 91.304 92 8 0 1777 1868 25892276 25892367 6.960000e-25 126.0
115 TraesCS2D01G203500 chr5A 74.830 294 57 12 402 693 688504930 688505208 4.190000e-22 117.0
116 TraesCS2D01G203500 chr5A 100.000 30 0 0 5355 5384 677775502 677775531 1.000000e-03 56.5
117 TraesCS2D01G203500 chr7B 86.232 138 16 2 583 719 41332974 41333109 5.340000e-31 147.0
118 TraesCS2D01G203500 chr4A 81.714 175 27 4 227 399 686056747 686056918 2.490000e-29 141.0
119 TraesCS2D01G203500 chr4A 94.186 86 5 0 1777 1862 710175365 710175450 1.500000e-26 132.0
120 TraesCS2D01G203500 chr4A 97.561 41 1 0 402 442 603404550 603404590 3.310000e-08 71.3
121 TraesCS2D01G203500 chr4A 100.000 30 0 0 5355 5384 62546780 62546751 1.000000e-03 56.5
122 TraesCS2D01G203500 chr1B 92.857 98 5 2 1777 1873 22881965 22881869 2.490000e-29 141.0
123 TraesCS2D01G203500 chr3B 94.318 88 5 0 1775 1862 818896587 818896674 1.160000e-27 135.0
124 TraesCS2D01G203500 chr6A 88.421 95 11 0 1767 1861 108175331 108175425 1.510000e-21 115.0
125 TraesCS2D01G203500 chr6A 86.022 93 13 0 553 645 57948829 57948737 4.220000e-17 100.0
126 TraesCS2D01G203500 chr6A 100.000 30 0 0 5355 5384 103303424 103303453 1.000000e-03 56.5
127 TraesCS2D01G203500 chr5B 82.353 119 16 3 597 715 647953305 647953192 1.520000e-16 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G203500 chr2D 155508422 155515035 6613 True 5861.00 9395 100.000000 1 6614 2 chr2D.!!$R7 6613
1 TraesCS2D01G203500 chr2D 603522993 603523556 563 True 1009.00 1009 98.938000 4523 5087 1 chr2D.!!$R6 564
2 TraesCS2D01G203500 chr2D 572790495 572791213 718 True 972.00 972 91.667000 5921 6614 1 chr2D.!!$R5 693
3 TraesCS2D01G203500 chr2D 179127591 179128205 614 False 534.70 1011 99.642000 4529 5385 2 chr2D.!!$F6 856
4 TraesCS2D01G203500 chr2A 144652004 144656848 4844 False 1084.40 2772 91.379200 832 5915 5 chr2A.!!$F3 5083
5 TraesCS2D01G203500 chr2B 212932186 212936536 4350 True 916.50 1930 91.970500 832 5921 6 chr2B.!!$R1 5089
6 TraesCS2D01G203500 chr2B 8536005 8536860 855 False 670.10 1256 95.873500 1 832 2 chr2B.!!$F2 831
7 TraesCS2D01G203500 chr2B 198174717 198175741 1024 False 476.00 680 95.392000 48 836 2 chr2B.!!$F3 788
8 TraesCS2D01G203500 chr2B 777636128 777637406 1278 True 378.90 732 95.450333 1 685 3 chr2B.!!$R2 684
9 TraesCS2D01G203500 chr3A 28727835 28728666 831 False 732.15 1393 94.389000 1 838 2 chr3A.!!$F2 837
10 TraesCS2D01G203500 chr3A 28662026 28662856 830 False 725.65 1380 94.269500 1 838 2 chr3A.!!$F1 837
11 TraesCS2D01G203500 chr3A 28758107 28759120 1013 False 647.00 776 97.594000 1 832 2 chr3A.!!$F3 831
12 TraesCS2D01G203500 chr1A 560828033 560828863 830 False 1387.00 1387 96.763000 1 833 1 chr1A.!!$F4 832
13 TraesCS2D01G203500 chr1D 388964870 388965484 614 False 542.20 1026 99.821500 4527 5385 2 chr1D.!!$F2 858
14 TraesCS2D01G203500 chr4D 15921759 15922319 560 True 1014.00 1014 99.287000 4527 5087 1 chr4D.!!$R1 560
15 TraesCS2D01G203500 chr3D 223479492 223480051 559 True 1013.00 1013 99.286000 4528 5087 1 chr3D.!!$R2 559
16 TraesCS2D01G203500 chr3D 91808628 91809187 559 False 1002.00 1002 98.930000 4527 5087 1 chr3D.!!$F1 560
17 TraesCS2D01G203500 chr3D 11347576 11348137 561 True 1000.00 1000 98.754000 4526 5087 1 chr3D.!!$R1 561
18 TraesCS2D01G203500 chr3D 553901741 553902301 560 True 998.00 998 98.752000 4527 5087 1 chr3D.!!$R3 560
19 TraesCS2D01G203500 chr3D 80218181 80220422 2241 True 585.00 721 97.103500 5919 6614 2 chr3D.!!$R4 695
20 TraesCS2D01G203500 chr7D 38864512 38865065 553 False 1002.00 1002 99.278000 4534 5087 1 chr7D.!!$F1 553
21 TraesCS2D01G203500 chr7D 20448174 20448840 666 True 749.00 749 87.078000 139 810 1 chr7D.!!$R1 671
22 TraesCS2D01G203500 chr6D 425077428 425078210 782 True 854.00 854 86.517000 48 836 1 chr6D.!!$R5 788
23 TraesCS2D01G203500 chr6B 197768913 197770863 1950 True 666.50 688 84.712000 48 832 2 chr6B.!!$R3 784
24 TraesCS2D01G203500 chr4B 438095231 438095945 714 False 519.50 680 89.999500 48 833 2 chr4B.!!$F4 785

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
992 3199 0.179081 GGCGTAACCATCACTCCTCC 60.179 60.000 0.00 0.0 38.86 4.30 F
1560 3797 0.179029 GTGGGTTGCCGGCATATACT 60.179 55.000 33.25 0.0 0.00 2.12 F
1631 3868 0.817654 GGCTTAGAATGCACAACCCC 59.182 55.000 0.00 0.0 0.00 4.95 F
1668 3905 1.273606 GCTGACTGGTAGCTGACTTCA 59.726 52.381 5.76 0.0 38.14 3.02 F
1785 4022 2.043801 AGCCTTCTTCTGTACTCCCTCT 59.956 50.000 0.00 0.0 0.00 3.69 F
1786 4023 2.167487 GCCTTCTTCTGTACTCCCTCTG 59.833 54.545 0.00 0.0 0.00 3.35 F
3177 6098 2.473235 GACTGCTGAACAAACTCTCGTC 59.527 50.000 0.00 0.0 0.00 4.20 F
3909 6837 0.178932 AAACCCTCCTTTTGCCTCCC 60.179 55.000 0.00 0.0 0.00 4.30 F
4064 6993 1.421268 TGGTGCACTCATCCTTCAAGT 59.579 47.619 17.98 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 4081 0.415029 AGGTACCCCCTCCGTAAACT 59.585 55.000 8.74 0.00 40.71 2.66 R
2899 5820 2.195741 AGACATCAGCACAAGCATGT 57.804 45.000 0.00 0.00 45.49 3.21 R
3592 6516 1.737793 CTTGCCTACAAACGGTGATCC 59.262 52.381 0.00 0.00 34.74 3.36 R
3638 6562 1.628340 TGGAAGTTCCGATGGTGATGT 59.372 47.619 17.13 0.00 40.17 3.06 R
3642 6566 2.185004 ACTTGGAAGTTCCGATGGTG 57.815 50.000 17.13 6.05 40.17 4.17 R
3643 6567 2.504367 CAACTTGGAAGTTCCGATGGT 58.496 47.619 17.13 7.73 45.65 3.55 R
4925 8334 0.464554 GCCGCTTCTCCATTAGGCTT 60.465 55.000 0.00 0.00 41.21 4.35 R
5523 8932 0.110486 ACACGCCATCCACTTCCTTT 59.890 50.000 0.00 0.00 0.00 3.11 R
5682 9100 0.654683 CAGCCAGCGCTTGACTTATC 59.345 55.000 13.50 0.00 45.55 1.75 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
213 255 4.202192 TGTTCCTAATGCATGCAACACAAA 60.202 37.500 26.68 13.69 0.00 2.83
465 696 1.520564 ACGACGTTGTCAGCAGCAA 60.521 52.632 1.48 0.00 32.09 3.91
645 2654 5.045942 TGTGCTCTATCATCCACCTTGTAAA 60.046 40.000 0.00 0.00 0.00 2.01
655 2667 4.798882 TCCACCTTGTAAAATTGTGACCT 58.201 39.130 0.00 0.00 0.00 3.85
656 2668 5.942961 TCCACCTTGTAAAATTGTGACCTA 58.057 37.500 0.00 0.00 0.00 3.08
657 2669 5.766174 TCCACCTTGTAAAATTGTGACCTAC 59.234 40.000 0.00 0.00 0.00 3.18
658 2670 5.768164 CCACCTTGTAAAATTGTGACCTACT 59.232 40.000 0.00 0.00 0.00 2.57
659 2671 6.293955 CCACCTTGTAAAATTGTGACCTACTG 60.294 42.308 0.00 0.00 0.00 2.74
867 3074 3.589988 CACTCACATACCAGGTTCACTC 58.410 50.000 0.00 0.00 0.00 3.51
873 3080 3.451178 ACATACCAGGTTCACTCGCTAAT 59.549 43.478 0.00 0.00 0.00 1.73
874 3081 2.386661 ACCAGGTTCACTCGCTAATG 57.613 50.000 0.00 0.00 0.00 1.90
919 3126 1.138671 CCGAATTCGCCGCCAAAAT 59.861 52.632 22.36 0.00 38.18 1.82
989 3196 2.171725 GCGGCGTAACCATCACTCC 61.172 63.158 9.37 0.00 39.03 3.85
990 3197 1.515954 CGGCGTAACCATCACTCCT 59.484 57.895 0.00 0.00 39.03 3.69
991 3198 0.527817 CGGCGTAACCATCACTCCTC 60.528 60.000 0.00 0.00 39.03 3.71
992 3199 0.179081 GGCGTAACCATCACTCCTCC 60.179 60.000 0.00 0.00 38.86 4.30
996 3203 2.159085 CGTAACCATCACTCCTCCTTCC 60.159 54.545 0.00 0.00 0.00 3.46
1125 3341 4.069232 CGCACCGCCTCTTCCTCA 62.069 66.667 0.00 0.00 0.00 3.86
1317 3533 0.256752 TCAGCCTAGGCACGTACCTA 59.743 55.000 34.70 13.96 44.88 3.08
1338 3554 4.374689 AACCTTCCTCTCCTTTTCCTTC 57.625 45.455 0.00 0.00 0.00 3.46
1349 3565 3.646637 TCCTTTTCCTTCCTCTCGTTTCT 59.353 43.478 0.00 0.00 0.00 2.52
1360 3577 1.301677 CTCGTTTCTGCTCCTTGGGC 61.302 60.000 0.00 0.00 0.00 5.36
1375 3595 5.517924 TCCTTGGGCAATTTGATTATCTGA 58.482 37.500 0.00 0.00 0.00 3.27
1514 3748 7.010091 CCGGAAATGTTTATTTTCCATGCTTAC 59.990 37.037 13.80 0.00 36.66 2.34
1559 3796 1.170290 GGTGGGTTGCCGGCATATAC 61.170 60.000 33.25 25.41 0.00 1.47
1560 3797 0.179029 GTGGGTTGCCGGCATATACT 60.179 55.000 33.25 0.00 0.00 2.12
1561 3798 1.071071 GTGGGTTGCCGGCATATACTA 59.929 52.381 33.25 11.89 0.00 1.82
1562 3799 1.071071 TGGGTTGCCGGCATATACTAC 59.929 52.381 33.25 23.80 0.00 2.73
1563 3800 1.346722 GGGTTGCCGGCATATACTACT 59.653 52.381 33.25 0.00 0.00 2.57
1564 3801 2.564062 GGGTTGCCGGCATATACTACTA 59.436 50.000 33.25 9.15 0.00 1.82
1565 3802 3.582780 GGTTGCCGGCATATACTACTAC 58.417 50.000 33.25 21.43 0.00 2.73
1566 3803 3.006110 GGTTGCCGGCATATACTACTACA 59.994 47.826 33.25 7.59 0.00 2.74
1567 3804 4.235360 GTTGCCGGCATATACTACTACAG 58.765 47.826 33.25 0.00 0.00 2.74
1568 3805 2.230508 TGCCGGCATATACTACTACAGC 59.769 50.000 29.03 0.00 0.00 4.40
1569 3806 2.230508 GCCGGCATATACTACTACAGCA 59.769 50.000 24.80 0.00 0.00 4.41
1570 3807 3.673594 GCCGGCATATACTACTACAGCAG 60.674 52.174 24.80 0.00 0.00 4.24
1571 3808 3.506455 CCGGCATATACTACTACAGCAGT 59.494 47.826 0.00 0.00 41.62 4.40
1572 3809 4.698780 CCGGCATATACTACTACAGCAGTA 59.301 45.833 0.00 0.00 38.80 2.74
1592 3829 6.313164 GCAGTAGTACCTAGTGGAATTGTTTC 59.687 42.308 7.90 0.00 37.72 2.78
1628 3865 1.474077 CCTGGGCTTAGAATGCACAAC 59.526 52.381 0.00 0.00 43.74 3.32
1631 3868 0.817654 GGCTTAGAATGCACAACCCC 59.182 55.000 0.00 0.00 0.00 4.95
1668 3905 1.273606 GCTGACTGGTAGCTGACTTCA 59.726 52.381 5.76 0.00 38.14 3.02
1669 3906 2.928731 GCTGACTGGTAGCTGACTTCAC 60.929 54.545 5.76 0.00 38.14 3.18
1670 3907 2.297315 CTGACTGGTAGCTGACTTCACA 59.703 50.000 5.76 0.00 0.00 3.58
1777 4014 9.959721 AATATTTCTGTTTAGCCTTCTTCTGTA 57.040 29.630 0.00 0.00 0.00 2.74
1778 4015 7.674471 ATTTCTGTTTAGCCTTCTTCTGTAC 57.326 36.000 0.00 0.00 0.00 2.90
1779 4016 6.420913 TTCTGTTTAGCCTTCTTCTGTACT 57.579 37.500 0.00 0.00 0.00 2.73
1780 4017 6.026947 TCTGTTTAGCCTTCTTCTGTACTC 57.973 41.667 0.00 0.00 0.00 2.59
1781 4018 5.047235 TCTGTTTAGCCTTCTTCTGTACTCC 60.047 44.000 0.00 0.00 0.00 3.85
1782 4019 4.020485 TGTTTAGCCTTCTTCTGTACTCCC 60.020 45.833 0.00 0.00 0.00 4.30
1783 4020 2.632763 AGCCTTCTTCTGTACTCCCT 57.367 50.000 0.00 0.00 0.00 4.20
1784 4021 2.462723 AGCCTTCTTCTGTACTCCCTC 58.537 52.381 0.00 0.00 0.00 4.30
1785 4022 2.043801 AGCCTTCTTCTGTACTCCCTCT 59.956 50.000 0.00 0.00 0.00 3.69
1786 4023 2.167487 GCCTTCTTCTGTACTCCCTCTG 59.833 54.545 0.00 0.00 0.00 3.35
1787 4024 3.436243 CCTTCTTCTGTACTCCCTCTGT 58.564 50.000 0.00 0.00 0.00 3.41
1788 4025 4.601084 CCTTCTTCTGTACTCCCTCTGTA 58.399 47.826 0.00 0.00 0.00 2.74
1789 4026 5.017490 CCTTCTTCTGTACTCCCTCTGTAA 58.983 45.833 0.00 0.00 0.00 2.41
1790 4027 5.126384 CCTTCTTCTGTACTCCCTCTGTAAG 59.874 48.000 0.00 0.00 0.00 2.34
1791 4028 4.017808 TCTTCTGTACTCCCTCTGTAAGC 58.982 47.826 0.00 0.00 0.00 3.09
1792 4029 3.451402 TCTGTACTCCCTCTGTAAGCA 57.549 47.619 0.00 0.00 0.00 3.91
1793 4030 3.774734 TCTGTACTCCCTCTGTAAGCAA 58.225 45.455 0.00 0.00 0.00 3.91
1794 4031 4.157246 TCTGTACTCCCTCTGTAAGCAAA 58.843 43.478 0.00 0.00 0.00 3.68
1795 4032 4.777896 TCTGTACTCCCTCTGTAAGCAAAT 59.222 41.667 0.00 0.00 0.00 2.32
1796 4033 5.955959 TCTGTACTCCCTCTGTAAGCAAATA 59.044 40.000 0.00 0.00 0.00 1.40
1797 4034 6.611642 TCTGTACTCCCTCTGTAAGCAAATAT 59.388 38.462 0.00 0.00 0.00 1.28
1798 4035 7.783119 TCTGTACTCCCTCTGTAAGCAAATATA 59.217 37.037 0.00 0.00 0.00 0.86
1799 4036 8.313944 TGTACTCCCTCTGTAAGCAAATATAA 57.686 34.615 0.00 0.00 0.00 0.98
1800 4037 8.421784 TGTACTCCCTCTGTAAGCAAATATAAG 58.578 37.037 0.00 0.00 0.00 1.73
1801 4038 7.676683 ACTCCCTCTGTAAGCAAATATAAGA 57.323 36.000 0.00 0.00 0.00 2.10
1802 4039 7.731054 ACTCCCTCTGTAAGCAAATATAAGAG 58.269 38.462 0.00 0.00 0.00 2.85
1803 4040 6.525629 TCCCTCTGTAAGCAAATATAAGAGC 58.474 40.000 0.00 0.00 0.00 4.09
1804 4041 5.406780 CCCTCTGTAAGCAAATATAAGAGCG 59.593 44.000 0.00 0.00 0.00 5.03
1805 4042 5.986135 CCTCTGTAAGCAAATATAAGAGCGT 59.014 40.000 0.00 0.00 0.00 5.07
1806 4043 6.480320 CCTCTGTAAGCAAATATAAGAGCGTT 59.520 38.462 0.00 0.00 0.00 4.84
1807 4044 7.011482 CCTCTGTAAGCAAATATAAGAGCGTTT 59.989 37.037 0.00 0.00 0.00 3.60
1808 4045 8.936070 TCTGTAAGCAAATATAAGAGCGTTTA 57.064 30.769 0.00 0.00 0.00 2.01
1809 4046 9.031360 TCTGTAAGCAAATATAAGAGCGTTTAG 57.969 33.333 0.00 0.00 0.00 1.85
1810 4047 8.936070 TGTAAGCAAATATAAGAGCGTTTAGA 57.064 30.769 0.00 0.00 0.00 2.10
1811 4048 9.542462 TGTAAGCAAATATAAGAGCGTTTAGAT 57.458 29.630 0.00 0.00 0.00 1.98
1813 4050 8.662781 AAGCAAATATAAGAGCGTTTAGATCA 57.337 30.769 0.00 0.00 37.82 2.92
1814 4051 8.077836 AGCAAATATAAGAGCGTTTAGATCAC 57.922 34.615 0.00 0.00 37.82 3.06
1815 4052 7.928706 AGCAAATATAAGAGCGTTTAGATCACT 59.071 33.333 0.00 0.00 37.82 3.41
1816 4053 9.193133 GCAAATATAAGAGCGTTTAGATCACTA 57.807 33.333 0.00 0.00 37.82 2.74
1827 4064 9.310716 AGCGTTTAGATCACTAAAATAGTAACC 57.689 33.333 0.00 0.00 45.97 2.85
1828 4065 9.310716 GCGTTTAGATCACTAAAATAGTAACCT 57.689 33.333 0.00 0.00 45.97 3.50
1855 4092 8.543862 AACACTCTTAAATTAGTTTACGGAGG 57.456 34.615 16.72 11.48 35.93 4.30
1856 4093 7.101700 ACACTCTTAAATTAGTTTACGGAGGG 58.898 38.462 14.81 14.81 38.23 4.30
1857 4094 6.537660 CACTCTTAAATTAGTTTACGGAGGGG 59.462 42.308 16.72 9.65 35.93 4.79
1858 4095 5.993055 TCTTAAATTAGTTTACGGAGGGGG 58.007 41.667 0.00 0.00 29.82 5.40
1859 4096 5.488561 TCTTAAATTAGTTTACGGAGGGGGT 59.511 40.000 0.00 0.00 29.82 4.95
1860 4097 6.671779 TCTTAAATTAGTTTACGGAGGGGGTA 59.328 38.462 0.00 0.00 29.82 3.69
1861 4098 4.760530 AATTAGTTTACGGAGGGGGTAC 57.239 45.455 0.00 0.00 0.00 3.34
1862 4099 6.352651 TTAAATTAGTTTACGGAGGGGGTACC 60.353 42.308 2.17 2.17 37.36 3.34
1908 4145 9.807649 ATTATTGTGCCTTTTCTTATTGTCATC 57.192 29.630 0.00 0.00 0.00 2.92
1909 4146 6.647334 TTGTGCCTTTTCTTATTGTCATCA 57.353 33.333 0.00 0.00 0.00 3.07
1911 4148 6.623486 TGTGCCTTTTCTTATTGTCATCATG 58.377 36.000 0.00 0.00 0.00 3.07
1912 4149 6.209192 TGTGCCTTTTCTTATTGTCATCATGT 59.791 34.615 0.00 0.00 0.00 3.21
1913 4150 6.749118 GTGCCTTTTCTTATTGTCATCATGTC 59.251 38.462 0.00 0.00 0.00 3.06
1914 4151 6.433716 TGCCTTTTCTTATTGTCATCATGTCA 59.566 34.615 0.00 0.00 0.00 3.58
1915 4152 7.123098 TGCCTTTTCTTATTGTCATCATGTCAT 59.877 33.333 0.00 0.00 0.00 3.06
1916 4153 7.434307 GCCTTTTCTTATTGTCATCATGTCATG 59.566 37.037 6.47 6.47 0.00 3.07
1918 4155 9.850628 CTTTTCTTATTGTCATCATGTCATGTT 57.149 29.630 12.54 1.55 0.00 2.71
1922 4159 8.603181 TCTTATTGTCATCATGTCATGTTAACG 58.397 33.333 12.54 0.00 0.00 3.18
1923 4160 6.983474 ATTGTCATCATGTCATGTTAACGA 57.017 33.333 12.54 8.99 0.00 3.85
1924 4161 6.983474 TTGTCATCATGTCATGTTAACGAT 57.017 33.333 12.54 0.00 0.00 3.73
1925 4162 6.983474 TGTCATCATGTCATGTTAACGATT 57.017 33.333 12.54 0.00 0.00 3.34
1929 4166 9.210426 GTCATCATGTCATGTTAACGATTTAAC 57.790 33.333 12.54 0.00 45.13 2.01
2099 4336 9.110502 CCTTAGTGGTTCAGGTAATTAAAGATC 57.889 37.037 0.00 0.00 0.00 2.75
2120 4357 6.769822 AGATCACCTGGATTTATTGTGATGTC 59.230 38.462 8.05 0.00 44.33 3.06
2129 4366 7.774625 TGGATTTATTGTGATGTCTGCTTCATA 59.225 33.333 0.00 0.00 32.53 2.15
2135 4372 6.822667 TGTGATGTCTGCTTCATAAAATGT 57.177 33.333 0.00 0.00 32.53 2.71
2140 4377 4.218200 TGTCTGCTTCATAAAATGTGGGTG 59.782 41.667 0.00 0.00 0.00 4.61
2179 4417 8.147704 TGTTCAAGTATGAGTCATTCAACTACA 58.852 33.333 11.68 7.56 39.77 2.74
2180 4418 9.155975 GTTCAAGTATGAGTCATTCAACTACAT 57.844 33.333 11.68 0.00 39.77 2.29
2212 4743 7.471120 GCCTACAGACCGGTATATCTTTACTTT 60.471 40.741 7.34 0.00 0.00 2.66
2214 4745 9.890352 CTACAGACCGGTATATCTTTACTTTAC 57.110 37.037 7.34 0.00 0.00 2.01
2257 4789 5.071653 ACACAATTGATTAAGGCCAAAAGGT 59.928 36.000 13.59 0.00 0.00 3.50
2268 4800 4.677182 AGGCCAAAAGGTGTCAATTCTAT 58.323 39.130 5.01 0.00 0.00 1.98
2293 4825 9.624373 ATGACTCTTCATAATTTAGCTGTCAAT 57.376 29.630 0.00 0.00 40.96 2.57
2324 4857 9.941664 CATATTGTTATTGTTCACTCCATCTTC 57.058 33.333 0.00 0.00 0.00 2.87
2329 4862 8.539544 TGTTATTGTTCACTCCATCTTCATAGA 58.460 33.333 0.00 0.00 34.21 1.98
2339 4872 9.152595 CACTCCATCTTCATAGATTACATCATG 57.847 37.037 0.00 0.00 39.11 3.07
2340 4873 8.878211 ACTCCATCTTCATAGATTACATCATGT 58.122 33.333 0.00 0.00 39.11 3.21
2342 4875 9.498176 TCCATCTTCATAGATTACATCATGTTG 57.502 33.333 0.00 2.12 39.11 3.33
2343 4876 9.498176 CCATCTTCATAGATTACATCATGTTGA 57.502 33.333 10.74 0.00 39.11 3.18
2395 5052 3.340337 GTTGTGAAAGGTCAACTCTGC 57.660 47.619 0.00 0.00 40.20 4.26
2396 5053 2.945668 GTTGTGAAAGGTCAACTCTGCT 59.054 45.455 0.00 0.00 40.20 4.24
2413 5070 6.998802 ACTCTGCTAAATTGTCAAGAGTACT 58.001 36.000 10.70 0.00 34.18 2.73
2473 5130 2.741759 TGTTCATCGTGCTTGCTAGA 57.258 45.000 0.00 0.00 0.00 2.43
2525 5182 5.106396 ACATTGCAGTAAATCAGAACTCTGC 60.106 40.000 7.83 7.83 45.39 4.26
2555 5212 6.978080 TGAAGAGACAATTTGCCAACTAAAAC 59.022 34.615 0.00 0.00 0.00 2.43
2556 5213 6.463995 AGAGACAATTTGCCAACTAAAACA 57.536 33.333 0.00 0.00 0.00 2.83
2559 5216 7.653311 AGAGACAATTTGCCAACTAAAACATTC 59.347 33.333 0.00 0.00 0.00 2.67
2562 5219 8.587952 ACAATTTGCCAACTAAAACATTCTAC 57.412 30.769 0.00 0.00 0.00 2.59
2596 5412 6.483640 AGCATTTATTCTCGATGTAAACCTCC 59.516 38.462 0.00 0.00 0.00 4.30
2600 5416 8.857694 TTTATTCTCGATGTAAACCTCCTTTT 57.142 30.769 0.00 0.00 0.00 2.27
2601 5417 9.947433 TTTATTCTCGATGTAAACCTCCTTTTA 57.053 29.630 0.00 0.00 0.00 1.52
2605 5421 8.857694 TCTCGATGTAAACCTCCTTTTATTTT 57.142 30.769 0.00 0.00 0.00 1.82
2606 5422 9.947433 TCTCGATGTAAACCTCCTTTTATTTTA 57.053 29.630 0.00 0.00 0.00 1.52
2607 5423 9.983804 CTCGATGTAAACCTCCTTTTATTTTAC 57.016 33.333 0.00 0.00 34.58 2.01
2608 5424 9.729281 TCGATGTAAACCTCCTTTTATTTTACT 57.271 29.630 0.00 0.00 34.91 2.24
2609 5425 9.769093 CGATGTAAACCTCCTTTTATTTTACTG 57.231 33.333 0.00 0.00 34.91 2.74
3177 6098 2.473235 GACTGCTGAACAAACTCTCGTC 59.527 50.000 0.00 0.00 0.00 4.20
3543 6467 8.651588 GCTTAGATGTATTGATGCACATACTAC 58.348 37.037 11.77 7.33 35.55 2.73
3552 6476 8.972262 ATTGATGCACATACTACGTAGATTAG 57.028 34.615 28.74 16.31 0.00 1.73
3592 6516 3.734231 GGTGTTACGTATGATCATCGTGG 59.266 47.826 28.11 14.65 38.27 4.94
3638 6562 5.070685 TCTGTCTCTAACTGCACAACTAGA 58.929 41.667 0.00 0.00 0.00 2.43
3642 6566 5.802956 GTCTCTAACTGCACAACTAGACATC 59.197 44.000 0.00 0.00 33.86 3.06
3643 6567 5.476945 TCTCTAACTGCACAACTAGACATCA 59.523 40.000 0.00 0.00 0.00 3.07
3654 6578 3.366396 ACTAGACATCACCATCGGAACT 58.634 45.455 0.00 0.00 0.00 3.01
3657 6581 2.093447 AGACATCACCATCGGAACTTCC 60.093 50.000 0.00 0.00 0.00 3.46
3740 6666 1.741706 AGCTCCATCGCATTCAAGTTG 59.258 47.619 0.00 0.00 0.00 3.16
3741 6667 1.470098 GCTCCATCGCATTCAAGTTGT 59.530 47.619 2.11 0.00 0.00 3.32
3742 6668 2.095059 GCTCCATCGCATTCAAGTTGTT 60.095 45.455 2.11 0.00 0.00 2.83
3746 6672 4.744137 TCCATCGCATTCAAGTTGTTTTTG 59.256 37.500 2.11 0.00 0.00 2.44
3748 6674 5.332506 CCATCGCATTCAAGTTGTTTTTGTC 60.333 40.000 2.11 0.00 0.00 3.18
3814 6740 9.673454 GACAACTATTAAACATCTTTTTCGGTT 57.327 29.630 0.00 0.00 0.00 4.44
3817 6743 8.515473 ACTATTAAACATCTTTTTCGGTTTGC 57.485 30.769 0.00 0.00 35.33 3.68
3844 6772 4.530161 TGCATTTTTATGTTGGGTTAGGCT 59.470 37.500 0.00 0.00 0.00 4.58
3851 6779 3.359695 TGTTGGGTTAGGCTGTTATCC 57.640 47.619 0.00 0.00 0.00 2.59
3870 6798 4.270245 TCCAGTTGGAAATGGAAAATGC 57.730 40.909 6.09 0.00 42.61 3.56
3875 6803 4.347583 AGTTGGAAATGGAAAATGCAAGGA 59.652 37.500 0.00 0.00 0.00 3.36
3909 6837 0.178932 AAACCCTCCTTTTGCCTCCC 60.179 55.000 0.00 0.00 0.00 4.30
3916 6844 3.564352 CCTCCTTTTGCCTCCCATACTTT 60.564 47.826 0.00 0.00 0.00 2.66
3973 6901 7.266922 TGTGGGTACTTATTTTCACTTTGTC 57.733 36.000 0.00 0.00 0.00 3.18
4064 6993 1.421268 TGGTGCACTCATCCTTCAAGT 59.579 47.619 17.98 0.00 0.00 3.16
4153 7082 5.428496 AAATTGCGAGGTACATCATCATG 57.572 39.130 8.44 0.00 35.92 3.07
4265 7309 7.661536 AGTAGTTGGCTCACTGATATTCTAA 57.338 36.000 0.70 0.00 0.00 2.10
4312 7356 2.676839 AGAGCACGCTTCATCATCTTTG 59.323 45.455 0.00 0.00 0.00 2.77
4360 7416 5.786401 ACATGCTAAAGAGAATCGTCAAC 57.214 39.130 0.00 0.00 42.67 3.18
4367 7423 3.883830 AGAGAATCGTCAACATGCTCT 57.116 42.857 0.00 0.00 42.67 4.09
4382 7438 4.202202 ACATGCTCTATACTTGAGGACAGC 60.202 45.833 0.00 0.00 34.86 4.40
4436 7492 5.103290 ACCAAGTACACTGTTTAAATGCG 57.897 39.130 0.00 0.00 0.00 4.73
4461 7517 7.044249 CGTAGGTTGATCTTTACTGTGAATACG 60.044 40.741 0.00 0.00 0.00 3.06
5389 8798 2.135933 GAGTGCGTCAGGCCATAATAC 58.864 52.381 5.01 0.00 42.61 1.89
5428 8837 5.446473 CCGCTTGTAAGAAGTTGTCATGATC 60.446 44.000 0.00 0.00 0.00 2.92
5436 8845 3.533606 AGTTGTCATGATCTCTTCGGG 57.466 47.619 0.00 0.00 0.00 5.14
5485 8894 2.031870 GCCAGTTTTGTCCTTCACCTT 58.968 47.619 0.00 0.00 0.00 3.50
5498 8907 4.681835 CTTCACCTTGAAGCATGAAGAG 57.318 45.455 22.70 6.74 46.03 2.85
5523 8932 6.762702 TTGCTTTGATTGCAGATTGAGATA 57.237 33.333 0.00 0.00 41.71 1.98
5578 8987 0.457166 CATGGCGGCACAAGTGATTG 60.457 55.000 16.34 1.40 0.00 2.67
5795 9245 3.064207 TGTTAACTTCTGTTAGCTGCGG 58.936 45.455 7.22 0.00 39.54 5.69
5841 9291 2.124403 GGCATCCAGAGCAGGGTG 60.124 66.667 0.00 0.00 42.89 4.61
5855 9309 2.039348 GCAGGGTGGTAGGAGTTTGTTA 59.961 50.000 0.00 0.00 0.00 2.41
5871 9325 7.092137 AGTTTGTTACTAATTTATTCGCCCC 57.908 36.000 0.00 0.00 34.56 5.80
5979 9433 3.366883 CCGCAAATTTAGCCAGTTTAGCA 60.367 43.478 0.00 0.00 0.00 3.49
6071 9525 0.592148 GGTCGGATTCGCTATCTCGT 59.408 55.000 0.00 0.00 36.13 4.18
6086 9540 0.672401 CTCGTGCGGTGTATTTGGGT 60.672 55.000 0.00 0.00 0.00 4.51
6230 9684 0.190069 TCACCCCATCCTATAGCCGT 59.810 55.000 0.00 0.00 0.00 5.68
6240 9694 1.524863 CTATAGCCGTGACCCCTCCG 61.525 65.000 0.00 0.00 0.00 4.63
6411 11411 1.307309 CCACCATGGGAGGCATGAA 59.693 57.895 18.09 0.00 32.67 2.57
6532 11532 1.880027 GAAGATCTTGCCAACACCGTT 59.120 47.619 14.00 0.00 0.00 4.44
6585 11585 4.411869 GGAGAGGGAGGAAGATTCATCTTT 59.588 45.833 7.13 0.00 46.47 2.52
6606 11606 1.405661 GGAGGCGGAAGAATCGTCTTT 60.406 52.381 0.00 0.00 44.42 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 255 6.709281 CAGATCTATGCAGATAAGGGATGTT 58.291 40.000 0.00 0.00 41.78 2.71
719 2926 3.320826 GCCAGGGTACAGTTCACAAAAAT 59.679 43.478 0.00 0.00 0.00 1.82
867 3074 1.852077 GCTGCAAAGCGTACATTAGCG 60.852 52.381 0.00 0.00 38.61 4.26
919 3126 4.703897 CCAGGAATCGGATTACTTGCTAA 58.296 43.478 12.83 0.00 28.64 3.09
1111 3318 1.002274 AGGATGAGGAAGAGGCGGT 59.998 57.895 0.00 0.00 0.00 5.68
1119 3335 2.316067 TGAAGAGGAGGAGGATGAGGAA 59.684 50.000 0.00 0.00 0.00 3.36
1125 3341 1.118838 CGCTTGAAGAGGAGGAGGAT 58.881 55.000 0.00 0.00 0.00 3.24
1204 3420 3.631046 GCCTGCTATCCTCCCCGG 61.631 72.222 0.00 0.00 0.00 5.73
1317 3533 3.074687 GGAAGGAAAAGGAGAGGAAGGTT 59.925 47.826 0.00 0.00 0.00 3.50
1338 3554 1.674221 CCAAGGAGCAGAAACGAGAGG 60.674 57.143 0.00 0.00 0.00 3.69
1349 3565 1.941377 ATCAAATTGCCCAAGGAGCA 58.059 45.000 0.00 0.00 38.81 4.26
1360 3577 6.584942 CCGCATTGGATCAGATAATCAAATTG 59.415 38.462 0.00 0.00 42.00 2.32
1375 3595 0.396139 AGGCATCAACCGCATTGGAT 60.396 50.000 0.00 0.00 42.00 3.41
1562 3799 4.778579 TCCACTAGGTACTACTGCTGTAG 58.221 47.826 24.46 24.46 42.69 2.74
1563 3800 4.849813 TCCACTAGGTACTACTGCTGTA 57.150 45.455 3.25 3.25 41.75 2.74
1564 3801 3.733883 TCCACTAGGTACTACTGCTGT 57.266 47.619 0.66 0.66 41.75 4.40
1565 3802 5.105310 ACAATTCCACTAGGTACTACTGCTG 60.105 44.000 0.00 0.00 41.75 4.41
1566 3803 5.024118 ACAATTCCACTAGGTACTACTGCT 58.976 41.667 0.00 0.00 41.75 4.24
1567 3804 5.340439 ACAATTCCACTAGGTACTACTGC 57.660 43.478 0.00 0.00 41.75 4.40
1568 3805 7.829378 GAAACAATTCCACTAGGTACTACTG 57.171 40.000 0.00 0.00 41.75 2.74
1592 3829 3.633986 GCCCAGGTCAAGATTTCAATAGG 59.366 47.826 0.00 0.00 0.00 2.57
1628 3865 0.551396 GATGTAACAAGGGGAGGGGG 59.449 60.000 0.00 0.00 0.00 5.40
1631 3868 0.541863 AGCGATGTAACAAGGGGAGG 59.458 55.000 0.00 0.00 0.00 4.30
1668 3905 2.842496 TCTTCCTTGAGCTCCATGATGT 59.158 45.455 12.15 0.00 0.00 3.06
1669 3906 3.555527 TCTTCCTTGAGCTCCATGATG 57.444 47.619 12.15 5.53 0.00 3.07
1670 3907 4.792513 ATTCTTCCTTGAGCTCCATGAT 57.207 40.909 12.15 0.00 0.00 2.45
1715 3952 3.811083 TCAAGTAGAACCCTCGCAAAAA 58.189 40.909 0.00 0.00 0.00 1.94
1716 3953 3.478857 TCAAGTAGAACCCTCGCAAAA 57.521 42.857 0.00 0.00 0.00 2.44
1718 3955 2.565391 TCATCAAGTAGAACCCTCGCAA 59.435 45.455 0.00 0.00 0.00 4.85
1719 3956 2.094182 GTCATCAAGTAGAACCCTCGCA 60.094 50.000 0.00 0.00 0.00 5.10
1721 3958 3.868757 TGTCATCAAGTAGAACCCTCG 57.131 47.619 0.00 0.00 0.00 4.63
1722 3959 4.878397 CCAATGTCATCAAGTAGAACCCTC 59.122 45.833 0.00 0.00 0.00 4.30
1723 3960 4.848357 CCAATGTCATCAAGTAGAACCCT 58.152 43.478 0.00 0.00 0.00 4.34
1724 3961 3.378427 GCCAATGTCATCAAGTAGAACCC 59.622 47.826 0.00 0.00 0.00 4.11
1726 3963 5.627499 TTGCCAATGTCATCAAGTAGAAC 57.373 39.130 0.00 0.00 0.00 3.01
1773 4010 4.537135 TTTGCTTACAGAGGGAGTACAG 57.463 45.455 0.00 0.00 0.00 2.74
1777 4014 7.676683 TCTTATATTTGCTTACAGAGGGAGT 57.323 36.000 0.00 0.00 0.00 3.85
1778 4015 6.648725 GCTCTTATATTTGCTTACAGAGGGAG 59.351 42.308 0.00 0.00 0.00 4.30
1779 4016 6.525629 GCTCTTATATTTGCTTACAGAGGGA 58.474 40.000 0.00 0.00 0.00 4.20
1780 4017 5.406780 CGCTCTTATATTTGCTTACAGAGGG 59.593 44.000 0.00 0.00 34.68 4.30
1781 4018 5.986135 ACGCTCTTATATTTGCTTACAGAGG 59.014 40.000 0.00 0.00 0.00 3.69
1782 4019 7.470289 AACGCTCTTATATTTGCTTACAGAG 57.530 36.000 0.00 0.00 0.00 3.35
1783 4020 7.843490 AAACGCTCTTATATTTGCTTACAGA 57.157 32.000 0.00 0.00 0.00 3.41
1784 4021 9.031360 TCTAAACGCTCTTATATTTGCTTACAG 57.969 33.333 0.00 0.00 0.00 2.74
1785 4022 8.936070 TCTAAACGCTCTTATATTTGCTTACA 57.064 30.769 0.00 0.00 0.00 2.41
1787 4024 9.758651 TGATCTAAACGCTCTTATATTTGCTTA 57.241 29.630 0.00 0.00 0.00 3.09
1788 4025 8.552034 GTGATCTAAACGCTCTTATATTTGCTT 58.448 33.333 0.00 0.00 0.00 3.91
1789 4026 7.928706 AGTGATCTAAACGCTCTTATATTTGCT 59.071 33.333 0.00 0.00 0.00 3.91
1790 4027 8.077836 AGTGATCTAAACGCTCTTATATTTGC 57.922 34.615 0.00 0.00 0.00 3.68
1801 4038 9.310716 GGTTACTATTTTAGTGATCTAAACGCT 57.689 33.333 0.00 0.00 43.20 5.07
1802 4039 9.310716 AGGTTACTATTTTAGTGATCTAAACGC 57.689 33.333 0.00 0.00 43.20 4.84
1829 4066 8.996271 CCTCCGTAAACTAATTTAAGAGTGTTT 58.004 33.333 0.00 0.00 34.25 2.83
1830 4067 7.605309 CCCTCCGTAAACTAATTTAAGAGTGTT 59.395 37.037 4.99 0.00 34.25 3.32
1831 4068 7.101700 CCCTCCGTAAACTAATTTAAGAGTGT 58.898 38.462 4.99 0.00 34.25 3.55
1832 4069 6.537660 CCCCTCCGTAAACTAATTTAAGAGTG 59.462 42.308 4.99 0.00 34.25 3.51
1833 4070 6.352479 CCCCCTCCGTAAACTAATTTAAGAGT 60.352 42.308 4.99 0.00 34.25 3.24
1834 4071 6.053650 CCCCCTCCGTAAACTAATTTAAGAG 58.946 44.000 0.00 0.00 35.05 2.85
1835 4072 5.488561 ACCCCCTCCGTAAACTAATTTAAGA 59.511 40.000 0.00 0.00 33.14 2.10
1836 4073 5.748402 ACCCCCTCCGTAAACTAATTTAAG 58.252 41.667 0.00 0.00 32.04 1.85
1837 4074 5.777526 ACCCCCTCCGTAAACTAATTTAA 57.222 39.130 0.00 0.00 32.04 1.52
1838 4075 5.130311 GGTACCCCCTCCGTAAACTAATTTA 59.870 44.000 0.00 0.00 0.00 1.40
1839 4076 4.080356 GGTACCCCCTCCGTAAACTAATTT 60.080 45.833 0.00 0.00 0.00 1.82
1840 4077 3.455910 GGTACCCCCTCCGTAAACTAATT 59.544 47.826 0.00 0.00 0.00 1.40
1841 4078 3.041211 GGTACCCCCTCCGTAAACTAAT 58.959 50.000 0.00 0.00 0.00 1.73
1842 4079 2.044353 AGGTACCCCCTCCGTAAACTAA 59.956 50.000 8.74 0.00 40.71 2.24
1843 4080 1.645919 AGGTACCCCCTCCGTAAACTA 59.354 52.381 8.74 0.00 40.71 2.24
1844 4081 0.415029 AGGTACCCCCTCCGTAAACT 59.585 55.000 8.74 0.00 40.71 2.66
1845 4082 2.159179 TAGGTACCCCCTCCGTAAAC 57.841 55.000 8.74 0.00 44.81 2.01
1846 4083 2.314549 TCTTAGGTACCCCCTCCGTAAA 59.685 50.000 8.74 0.00 44.81 2.01
1847 4084 1.929494 TCTTAGGTACCCCCTCCGTAA 59.071 52.381 8.74 0.00 44.81 3.18
1848 4085 1.607225 TCTTAGGTACCCCCTCCGTA 58.393 55.000 8.74 0.00 44.81 4.02
1849 4086 0.939698 ATCTTAGGTACCCCCTCCGT 59.060 55.000 8.74 0.00 44.81 4.69
1850 4087 1.133262 TGATCTTAGGTACCCCCTCCG 60.133 57.143 8.74 0.00 44.81 4.63
1851 4088 2.789323 TGATCTTAGGTACCCCCTCC 57.211 55.000 8.74 0.00 44.81 4.30
1852 4089 6.954352 ATAAATGATCTTAGGTACCCCCTC 57.046 41.667 8.74 0.00 44.81 4.30
1854 4091 8.625467 AGATATAAATGATCTTAGGTACCCCC 57.375 38.462 8.74 0.00 28.94 5.40
1916 4153 7.232300 GCCTTCTACACAGTTAAATCGTTAAC 58.768 38.462 0.00 0.00 46.43 2.01
1918 4155 5.574055 CGCCTTCTACACAGTTAAATCGTTA 59.426 40.000 0.00 0.00 0.00 3.18
1919 4156 4.387862 CGCCTTCTACACAGTTAAATCGTT 59.612 41.667 0.00 0.00 0.00 3.85
1920 4157 3.924686 CGCCTTCTACACAGTTAAATCGT 59.075 43.478 0.00 0.00 0.00 3.73
1921 4158 4.171005 TCGCCTTCTACACAGTTAAATCG 58.829 43.478 0.00 0.00 0.00 3.34
1922 4159 5.408356 TCTCGCCTTCTACACAGTTAAATC 58.592 41.667 0.00 0.00 0.00 2.17
1923 4160 5.401531 TCTCGCCTTCTACACAGTTAAAT 57.598 39.130 0.00 0.00 0.00 1.40
1924 4161 4.859304 TCTCGCCTTCTACACAGTTAAA 57.141 40.909 0.00 0.00 0.00 1.52
1925 4162 4.038282 TGTTCTCGCCTTCTACACAGTTAA 59.962 41.667 0.00 0.00 0.00 2.01
1929 4166 2.229062 TCTGTTCTCGCCTTCTACACAG 59.771 50.000 0.00 0.00 33.00 3.66
2099 4336 5.449588 GCAGACATCACAATAAATCCAGGTG 60.450 44.000 0.00 0.00 0.00 4.00
2120 4357 3.056678 TGCACCCACATTTTATGAAGCAG 60.057 43.478 0.00 0.00 0.00 4.24
2154 4392 8.534333 TGTAGTTGAATGACTCATACTTGAAC 57.466 34.615 0.00 0.00 32.78 3.18
2217 4748 8.945481 TCAATTGTGTTGAACTGAAATGATTT 57.055 26.923 5.13 0.00 0.00 2.17
2229 4760 5.798125 TGGCCTTAATCAATTGTGTTGAA 57.202 34.783 3.32 0.00 31.55 2.69
2231 4762 6.073112 CCTTTTGGCCTTAATCAATTGTGTTG 60.073 38.462 3.32 0.00 0.00 3.33
2232 4763 5.997129 CCTTTTGGCCTTAATCAATTGTGTT 59.003 36.000 3.32 4.87 0.00 3.32
2241 4772 4.864704 TTGACACCTTTTGGCCTTAATC 57.135 40.909 3.32 0.00 45.59 1.75
2268 4800 9.453572 AATTGACAGCTAAATTATGAAGAGTCA 57.546 29.630 0.00 0.00 38.41 3.41
2377 5034 4.415881 TTAGCAGAGTTGACCTTTCACA 57.584 40.909 0.00 0.00 0.00 3.58
2386 5043 6.291377 ACTCTTGACAATTTAGCAGAGTTGA 58.709 36.000 0.00 0.00 32.27 3.18
2473 5130 5.105917 ACATTGGTGAAGAACAAACGAAACT 60.106 36.000 0.00 0.00 0.00 2.66
2525 5182 7.373493 AGTTGGCAAATTGTCTCTTCAAATAG 58.627 34.615 0.00 0.00 0.00 1.73
2569 5385 8.958119 AGGTTTACATCGAGAATAAATGCTAA 57.042 30.769 0.00 0.00 0.00 3.09
2601 5417 9.956720 GCACTAATAAAGCATCATCAGTAAAAT 57.043 29.630 0.00 0.00 0.00 1.82
2605 5421 6.830912 AGGCACTAATAAAGCATCATCAGTA 58.169 36.000 0.00 0.00 36.02 2.74
2606 5422 5.688807 AGGCACTAATAAAGCATCATCAGT 58.311 37.500 0.00 0.00 36.02 3.41
2607 5423 6.630444 AAGGCACTAATAAAGCATCATCAG 57.370 37.500 0.00 0.00 38.49 2.90
2608 5424 8.696043 ATAAAGGCACTAATAAAGCATCATCA 57.304 30.769 0.00 0.00 38.49 3.07
2609 5425 9.007901 AGATAAAGGCACTAATAAAGCATCATC 57.992 33.333 0.00 0.00 38.49 2.92
2610 5426 8.930846 AGATAAAGGCACTAATAAAGCATCAT 57.069 30.769 0.00 0.00 38.49 2.45
2640 5561 9.767684 TGACAATGCGAAGTAAAAACAATATAG 57.232 29.630 0.00 0.00 0.00 1.31
2650 5571 6.621316 TTTACCTTGACAATGCGAAGTAAA 57.379 33.333 0.00 0.00 0.00 2.01
2652 5573 5.761234 ACTTTTACCTTGACAATGCGAAGTA 59.239 36.000 0.00 0.00 0.00 2.24
2653 5574 4.578928 ACTTTTACCTTGACAATGCGAAGT 59.421 37.500 0.00 0.00 0.00 3.01
2654 5575 5.108385 ACTTTTACCTTGACAATGCGAAG 57.892 39.130 0.00 0.00 0.00 3.79
2656 5577 4.453136 GGTACTTTTACCTTGACAATGCGA 59.547 41.667 0.00 0.00 44.24 5.10
2657 5578 4.719040 GGTACTTTTACCTTGACAATGCG 58.281 43.478 0.00 0.00 44.24 4.73
2899 5820 2.195741 AGACATCAGCACAAGCATGT 57.804 45.000 0.00 0.00 45.49 3.21
2910 5831 4.003648 GGGTGGACAGTAAAAGACATCAG 58.996 47.826 0.00 0.00 0.00 2.90
2912 5833 4.015872 TGGGTGGACAGTAAAAGACATC 57.984 45.455 0.00 0.00 0.00 3.06
2915 5836 4.558697 GCAAATGGGTGGACAGTAAAAGAC 60.559 45.833 0.00 0.00 0.00 3.01
3527 6451 8.577296 ACTAATCTACGTAGTATGTGCATCAAT 58.423 33.333 21.53 1.14 44.56 2.57
3552 6476 9.057365 CGTAACACCATTACACAATGAAAATAC 57.943 33.333 0.00 0.00 43.67 1.89
3558 6482 7.097834 TCATACGTAACACCATTACACAATGA 58.902 34.615 0.00 0.00 43.67 2.57
3592 6516 1.737793 CTTGCCTACAAACGGTGATCC 59.262 52.381 0.00 0.00 34.74 3.36
3638 6562 1.628340 TGGAAGTTCCGATGGTGATGT 59.372 47.619 17.13 0.00 40.17 3.06
3642 6566 2.185004 ACTTGGAAGTTCCGATGGTG 57.815 50.000 17.13 6.05 40.17 4.17
3643 6567 2.504367 CAACTTGGAAGTTCCGATGGT 58.496 47.619 17.13 7.73 45.65 3.55
3740 6666 9.387123 CTTGTCTTAAGCATTAGAGACAAAAAC 57.613 33.333 15.83 0.00 45.90 2.43
3741 6667 9.337396 TCTTGTCTTAAGCATTAGAGACAAAAA 57.663 29.630 15.83 7.23 45.90 1.94
3742 6668 8.902540 TCTTGTCTTAAGCATTAGAGACAAAA 57.097 30.769 15.83 3.72 45.90 2.44
3746 6672 7.600752 ACTGTTCTTGTCTTAAGCATTAGAGAC 59.399 37.037 0.00 0.00 38.26 3.36
3748 6674 7.897575 ACTGTTCTTGTCTTAAGCATTAGAG 57.102 36.000 0.00 0.00 0.00 2.43
3817 6743 3.648009 ACCCAACATAAAAATGCACACG 58.352 40.909 0.00 0.00 0.00 4.49
3828 6756 5.044772 TGGATAACAGCCTAACCCAACATAA 60.045 40.000 0.00 0.00 0.00 1.90
3831 6759 2.645297 TGGATAACAGCCTAACCCAACA 59.355 45.455 0.00 0.00 0.00 3.33
3844 6772 6.985653 TTTTCCATTTCCAACTGGATAACA 57.014 33.333 0.00 0.00 44.98 2.41
3851 6779 4.453136 CCTTGCATTTTCCATTTCCAACTG 59.547 41.667 0.00 0.00 0.00 3.16
3897 6825 3.578282 ACAAAAGTATGGGAGGCAAAAGG 59.422 43.478 0.00 0.00 0.00 3.11
3909 6837 8.320295 CACTGCAAAAACTTACACAAAAGTATG 58.680 33.333 0.00 0.00 38.76 2.39
3916 6844 8.988064 TTATTTCACTGCAAAAACTTACACAA 57.012 26.923 0.00 0.00 0.00 3.33
3973 6901 1.813513 AGAATGGTCAAACAGAGGCG 58.186 50.000 0.00 0.00 0.00 5.52
4064 6993 8.562892 CAGAAAGACAAAATTAGAGCTTGAAGA 58.437 33.333 0.00 0.00 0.00 2.87
4312 7356 5.335127 AGCATGCGTTCTTGATTATGTTTC 58.665 37.500 13.01 0.00 0.00 2.78
4360 7416 4.202192 TGCTGTCCTCAAGTATAGAGCATG 60.202 45.833 0.00 0.00 0.00 4.06
4367 7423 5.133941 CCTCTAGTGCTGTCCTCAAGTATA 58.866 45.833 0.00 0.00 0.00 1.47
4382 7438 6.931281 CCATATCAAACATGTACCCTCTAGTG 59.069 42.308 0.00 0.00 0.00 2.74
4424 7480 6.422776 AGATCAACCTACGCATTTAAACAG 57.577 37.500 0.00 0.00 0.00 3.16
4427 7483 8.447833 CAGTAAAGATCAACCTACGCATTTAAA 58.552 33.333 0.00 0.00 0.00 1.52
4436 7492 7.254017 GCGTATTCACAGTAAAGATCAACCTAC 60.254 40.741 0.00 0.00 0.00 3.18
4461 7517 6.020678 GCTGTAAATTCAACGTTTATGATGGC 60.021 38.462 0.00 0.00 0.00 4.40
4925 8334 0.464554 GCCGCTTCTCCATTAGGCTT 60.465 55.000 0.00 0.00 41.21 4.35
5428 8837 0.610687 AGGAAAGAGCACCCGAAGAG 59.389 55.000 0.00 0.00 0.00 2.85
5436 8845 0.884704 TCAACGGCAGGAAAGAGCAC 60.885 55.000 0.00 0.00 0.00 4.40
5498 8907 5.224888 TCTCAATCTGCAATCAAAGCAAAC 58.775 37.500 0.00 0.00 42.17 2.93
5523 8932 0.110486 ACACGCCATCCACTTCCTTT 59.890 50.000 0.00 0.00 0.00 3.11
5578 8987 2.159028 AGCCTTTGTCCTCGAGATAAGC 60.159 50.000 15.71 7.27 0.00 3.09
5682 9100 0.654683 CAGCCAGCGCTTGACTTATC 59.345 55.000 13.50 0.00 45.55 1.75
5707 9125 9.768662 AATCTGAACAAGCACAGAAAATAAAAT 57.231 25.926 0.00 0.00 44.47 1.82
5712 9130 5.069516 ACCAATCTGAACAAGCACAGAAAAT 59.930 36.000 0.00 0.00 44.47 1.82
5795 9245 6.089417 GCAATTTACACACTACATTTTCCTGC 59.911 38.462 0.00 0.00 0.00 4.85
5855 9309 4.595986 AGTTGTGGGGCGAATAAATTAGT 58.404 39.130 0.00 0.00 0.00 2.24
6071 9525 2.036006 GCGACCCAAATACACCGCA 61.036 57.895 0.00 0.00 41.89 5.69
6127 9581 1.134037 GGAGGCGGAGAAGAGAGAGTA 60.134 57.143 0.00 0.00 0.00 2.59
6411 11411 3.629087 CCTCCCATGAGAGAAGCAAAAT 58.371 45.455 5.69 0.00 41.42 1.82
6532 11532 1.737735 CGCATCACGTGAAGCTCCA 60.738 57.895 34.46 8.66 36.69 3.86
6585 11585 0.970937 AGACGATTCTTCCGCCTCCA 60.971 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.