Multiple sequence alignment - TraesCS2D01G494400

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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 TraesCS2D01G494400 chr2D 100.000 2375 0 0 1 2375 591547258 591549632 0.000000e+00 4386.0
1 TraesCS2D01G494400 chr2D 92.997 871 38 11 813 1673 591437680 591438537 0.000000e+00 1249.0
2 TraesCS2D01G494400 chr2D 87.347 980 72 17 717 1672 591388442 591389393 0.000000e+00 1075.0
3 TraesCS2D01G494400 chr2D 85.177 877 74 28 505 1366 591320010 591320845 0.000000e+00 848.0
4 TraesCS2D01G494400 chr2D 89.146 562 40 8 1818 2375 501696717 501696173 0.000000e+00 680.0
5 TraesCS2D01G494400 chr2D 82.124 772 73 35 603 1363 591300574 591301291 3.380000e-168 601.0
6 TraesCS2D01G494400 chr2D 92.147 191 9 3 1821 2011 247104955 247104771 5.030000e-67 265.0
7 TraesCS2D01G494400 chr2D 87.817 197 18 1 1821 2011 387481758 387481562 2.380000e-55 226.0
8 TraesCS2D01G494400 chr2D 94.565 92 5 0 605 696 591437529 591437620 2.460000e-30 143.0
9 TraesCS2D01G494400 chr2D 89.583 96 10 0 1669 1764 17793836 17793741 3.210000e-24 122.0
10 TraesCS2D01G494400 chr2D 89.583 96 10 0 1669 1764 376349409 376349504 3.210000e-24 122.0
11 TraesCS2D01G494400 chr2D 92.683 82 6 0 599 680 591388359 591388440 4.150000e-23 119.0
12 TraesCS2D01G494400 chr2D 88.542 96 11 0 1669 1764 361347197 361347292 1.490000e-22 117.0
13 TraesCS2D01G494400 chr2D 86.598 97 11 2 1669 1764 54128263 54128168 3.230000e-19 106.0
14 TraesCS2D01G494400 chr2D 92.308 52 4 0 1758 1809 531437732 531437681 9.100000e-10 75.0
15 TraesCS2D01G494400 chr2D 100.000 34 0 0 766 799 591437650 591437683 1.970000e-06 63.9
16 TraesCS2D01G494400 chr2D 84.127 63 9 1 1612 1673 591603951 591604013 2.550000e-05 60.2
17 TraesCS2D01G494400 chr2A 84.233 1186 84 52 505 1670 726295502 726296604 0.000000e+00 1059.0
18 TraesCS2D01G494400 chr2A 85.427 844 84 15 841 1673 726223882 726224697 0.000000e+00 841.0
19 TraesCS2D01G494400 chr2A 87.854 741 58 12 921 1660 726273240 726273949 0.000000e+00 841.0
20 TraesCS2D01G494400 chr2A 94.485 272 14 1 196 467 686223597 686223327 3.650000e-113 418.0
21 TraesCS2D01G494400 chr2A 79.577 426 37 18 505 912 726272621 726273014 2.340000e-65 259.0
22 TraesCS2D01G494400 chr2A 95.714 140 6 0 1821 1960 771998838 771998699 2.380000e-55 226.0
23 TraesCS2D01G494400 chr2A 88.820 161 8 4 601 761 726223722 726223872 3.120000e-44 189.0
24 TraesCS2D01G494400 chr2A 96.154 52 2 0 1760 1811 107381619 107381568 4.210000e-13 86.1
25 TraesCS2D01G494400 chr2A 97.297 37 1 0 468 504 686221918 686221882 1.970000e-06 63.9
26 TraesCS2D01G494400 chr2B 89.625 800 57 12 608 1402 717097761 717098539 0.000000e+00 994.0
27 TraesCS2D01G494400 chr2B 83.418 784 80 29 599 1366 717043143 717043892 0.000000e+00 682.0
28 TraesCS2D01G494400 chr2B 91.558 154 12 1 1 154 678015512 678015360 6.650000e-51 211.0
29 TraesCS2D01G494400 chrUn 89.931 576 29 14 1808 2375 69331554 69332108 0.000000e+00 715.0
30 TraesCS2D01G494400 chrUn 83.481 678 60 29 711 1366 317867454 317868101 3.400000e-163 584.0
31 TraesCS2D01G494400 chrUn 91.000 100 8 1 599 697 317867307 317867406 1.480000e-27 134.0
32 TraesCS2D01G494400 chr6B 87.965 565 45 10 1821 2375 578694835 578695386 0.000000e+00 645.0
33 TraesCS2D01G494400 chr6B 87.367 562 43 11 1822 2375 192061865 192062406 9.330000e-174 619.0
34 TraesCS2D01G494400 chr4B 87.478 567 48 7 1816 2372 69464696 69465249 1.200000e-177 632.0
35 TraesCS2D01G494400 chr4B 98.162 272 5 0 196 467 14571896 14572167 2.140000e-130 475.0
36 TraesCS2D01G494400 chr4B 96.691 272 6 1 196 467 80009034 80009302 1.290000e-122 449.0
37 TraesCS2D01G494400 chr4B 100.000 39 0 0 466 504 7743710 7743748 3.270000e-09 73.1
38 TraesCS2D01G494400 chr4B 87.500 64 5 3 1768 1830 166701467 166701406 1.180000e-08 71.3
39 TraesCS2D01G494400 chr3B 86.911 573 41 19 1821 2375 719849343 719848787 1.560000e-171 612.0
40 TraesCS2D01G494400 chr3B 98.162 272 5 0 196 467 718682870 718682599 2.140000e-130 475.0
41 TraesCS2D01G494400 chr3B 95.539 269 10 2 199 467 752379947 752379681 1.690000e-116 429.0
42 TraesCS2D01G494400 chr3B 93.750 272 16 1 196 467 296064134 296064404 7.900000e-110 407.0
43 TraesCS2D01G494400 chr3B 98.701 154 2 0 1 154 718684884 718684731 8.360000e-70 274.0
44 TraesCS2D01G494400 chr3B 98.052 154 3 0 1 154 296062205 296062358 3.890000e-68 268.0
45 TraesCS2D01G494400 chr3B 98.052 154 3 0 1 154 752381882 752381729 3.890000e-68 268.0
46 TraesCS2D01G494400 chr3B 97.403 154 4 0 1 154 20828939 20829092 1.810000e-66 263.0
47 TraesCS2D01G494400 chr3B 96.000 50 2 0 1760 1809 41010284 41010235 5.440000e-12 82.4
48 TraesCS2D01G494400 chr3B 97.619 42 1 0 465 506 296066925 296066966 3.270000e-09 73.1
49 TraesCS2D01G494400 chr3B 100.000 39 0 0 466 504 752377682 752377644 3.270000e-09 73.1
50 TraesCS2D01G494400 chr3B 100.000 37 0 0 468 504 718680983 718680947 4.240000e-08 69.4
51 TraesCS2D01G494400 chr3D 86.726 565 43 17 1821 2375 609838273 609837731 1.210000e-167 599.0
52 TraesCS2D01G494400 chr3D 87.931 232 22 4 1821 2051 56544259 56544033 3.890000e-68 268.0
53 TraesCS2D01G494400 chr3D 87.500 96 12 0 1669 1764 368949044 368948949 6.940000e-21 111.0
54 TraesCS2D01G494400 chr3D 85.859 99 14 0 1666 1764 55189426 55189524 3.230000e-19 106.0
55 TraesCS2D01G494400 chr3D 94.000 50 3 0 1760 1809 254338994 254339043 2.530000e-10 76.8
56 TraesCS2D01G494400 chr4D 85.714 567 49 17 1821 2370 294015183 294014632 9.530000e-159 569.0
57 TraesCS2D01G494400 chr4D 84.536 97 13 2 1668 1764 187503806 187503900 6.990000e-16 95.3
58 TraesCS2D01G494400 chr4D 100.000 37 0 0 468 504 482951895 482951859 4.240000e-08 69.4
59 TraesCS2D01G494400 chr4A 88.222 450 37 11 1940 2375 676260874 676260427 7.520000e-145 523.0
60 TraesCS2D01G494400 chr4A 89.691 291 11 6 196 467 618565936 618566226 1.040000e-93 353.0
61 TraesCS2D01G494400 chr4A 97.122 139 4 0 1822 1960 676261032 676260894 3.950000e-58 235.0
62 TraesCS2D01G494400 chr4A 88.542 96 10 1 1669 1764 641380500 641380594 5.360000e-22 115.0
63 TraesCS2D01G494400 chr5B 97.426 272 7 0 196 467 599323808 599323537 4.620000e-127 464.0
64 TraesCS2D01G494400 chr5B 90.426 282 16 2 196 467 691988097 691988377 6.240000e-96 361.0
65 TraesCS2D01G494400 chr5B 98.701 154 2 0 1 154 599325828 599325675 8.360000e-70 274.0
66 TraesCS2D01G494400 chr5D 89.347 291 12 2 196 467 547985304 547985594 4.860000e-92 348.0
67 TraesCS2D01G494400 chr1A 94.472 199 9 2 1821 2018 581028802 581028999 2.970000e-79 305.0
68 TraesCS2D01G494400 chr1A 86.000 100 14 0 1665 1764 409501858 409501759 8.980000e-20 108.0
69 TraesCS2D01G494400 chr1A 85.484 62 7 2 1703 1764 13581846 13581787 1.970000e-06 63.9
70 TraesCS2D01G494400 chr3A 98.701 154 2 0 1 154 40288264 40288417 8.360000e-70 274.0
71 TraesCS2D01G494400 chr3A 87.662 154 19 0 1 154 309006200 309006047 1.880000e-41 180.0
72 TraesCS2D01G494400 chr3A 81.395 86 9 6 1725 1809 693357088 693357167 1.970000e-06 63.9
73 TraesCS2D01G494400 chr5A 97.403 154 4 0 1 154 585422821 585422974 1.810000e-66 263.0
74 TraesCS2D01G494400 chr7B 90.052 191 14 2 1821 2011 444155714 444155899 2.360000e-60 243.0
75 TraesCS2D01G494400 chr7B 97.143 140 4 0 1821 1960 431354172 431354033 1.100000e-58 237.0
76 TraesCS2D01G494400 chr7B 87.500 192 19 2 1821 2012 664615728 664615914 1.430000e-52 217.0
77 TraesCS2D01G494400 chr7B 90.625 96 9 0 1669 1764 118266714 118266809 6.890000e-26 128.0
78 TraesCS2D01G494400 chr7B 89.362 94 9 1 1669 1762 184337758 184337850 1.490000e-22 117.0
79 TraesCS2D01G494400 chr7B 92.982 57 3 1 1760 1815 508180471 508180415 5.440000e-12 82.4
80 TraesCS2D01G494400 chr6D 89.583 96 10 0 1669 1764 161556507 161556412 3.210000e-24 122.0
81 TraesCS2D01G494400 chr6D 83.838 99 16 0 1666 1764 462478815 462478913 6.990000e-16 95.3
82 TraesCS2D01G494400 chr6D 94.000 50 3 0 1760 1809 130643564 130643515 2.530000e-10 76.8
83 TraesCS2D01G494400 chr6D 80.000 105 18 3 1662 1764 170425142 170425039 9.100000e-10 75.0
84 TraesCS2D01G494400 chr6D 100.000 37 0 0 468 504 116493388 116493424 4.240000e-08 69.4
85 TraesCS2D01G494400 chr6D 83.871 62 9 1 1666 1727 24378447 24378507 9.170000e-05 58.4
86 TraesCS2D01G494400 chr6D 100.000 29 0 0 1681 1709 42248583 42248555 1.000000e-03 54.7
87 TraesCS2D01G494400 chr1D 84.848 99 9 4 1668 1764 30365561 30365655 6.990000e-16 95.3
88 TraesCS2D01G494400 chr1D 97.674 43 1 0 1666 1708 6693479 6693521 9.100000e-10 75.0
89 TraesCS2D01G494400 chr7D 87.500 80 10 0 1685 1764 582148973 582149052 2.510000e-15 93.5
90 TraesCS2D01G494400 chr7D 81.443 97 16 2 1668 1764 1541673 1541767 7.040000e-11 78.7
91 TraesCS2D01G494400 chr7D 94.595 37 2 0 468 504 546768712 546768676 9.170000e-05 58.4
92 TraesCS2D01G494400 chr7A 82.558 86 8 5 1726 1810 617115286 617115365 4.240000e-08 69.4


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 TraesCS2D01G494400 chr2D 591547258 591549632 2374 False 4386.000000 4386 100.000000 1 2375 1 chr2D.!!$F5 2374
1 TraesCS2D01G494400 chr2D 591320010 591320845 835 False 848.000000 848 85.177000 505 1366 1 chr2D.!!$F4 861
2 TraesCS2D01G494400 chr2D 501696173 501696717 544 True 680.000000 680 89.146000 1818 2375 1 chr2D.!!$R5 557
3 TraesCS2D01G494400 chr2D 591300574 591301291 717 False 601.000000 601 82.124000 603 1363 1 chr2D.!!$F3 760
4 TraesCS2D01G494400 chr2D 591388359 591389393 1034 False 597.000000 1075 90.015000 599 1672 2 chr2D.!!$F7 1073
5 TraesCS2D01G494400 chr2D 591437529 591438537 1008 False 485.300000 1249 95.854000 605 1673 3 chr2D.!!$F8 1068
6 TraesCS2D01G494400 chr2A 726295502 726296604 1102 False 1059.000000 1059 84.233000 505 1670 1 chr2A.!!$F1 1165
7 TraesCS2D01G494400 chr2A 726272621 726273949 1328 False 550.000000 841 83.715500 505 1660 2 chr2A.!!$F3 1155
8 TraesCS2D01G494400 chr2A 726223722 726224697 975 False 515.000000 841 87.123500 601 1673 2 chr2A.!!$F2 1072
9 TraesCS2D01G494400 chr2A 686221882 686223597 1715 True 240.950000 418 95.891000 196 504 2 chr2A.!!$R3 308
10 TraesCS2D01G494400 chr2B 717097761 717098539 778 False 994.000000 994 89.625000 608 1402 1 chr2B.!!$F2 794
11 TraesCS2D01G494400 chr2B 717043143 717043892 749 False 682.000000 682 83.418000 599 1366 1 chr2B.!!$F1 767
12 TraesCS2D01G494400 chrUn 69331554 69332108 554 False 715.000000 715 89.931000 1808 2375 1 chrUn.!!$F1 567
13 TraesCS2D01G494400 chrUn 317867307 317868101 794 False 359.000000 584 87.240500 599 1366 2 chrUn.!!$F2 767
14 TraesCS2D01G494400 chr6B 578694835 578695386 551 False 645.000000 645 87.965000 1821 2375 1 chr6B.!!$F2 554
15 TraesCS2D01G494400 chr6B 192061865 192062406 541 False 619.000000 619 87.367000 1822 2375 1 chr6B.!!$F1 553
16 TraesCS2D01G494400 chr4B 69464696 69465249 553 False 632.000000 632 87.478000 1816 2372 1 chr4B.!!$F3 556
17 TraesCS2D01G494400 chr3B 719848787 719849343 556 True 612.000000 612 86.911000 1821 2375 1 chr3B.!!$R2 554
18 TraesCS2D01G494400 chr3B 718680947 718684884 3937 True 272.800000 475 98.954333 1 504 3 chr3B.!!$R3 503
19 TraesCS2D01G494400 chr3B 752377644 752381882 4238 True 256.700000 429 97.863667 1 504 3 chr3B.!!$R4 503
20 TraesCS2D01G494400 chr3B 296062205 296066966 4761 False 249.366667 407 96.473667 1 506 3 chr3B.!!$F2 505
21 TraesCS2D01G494400 chr3D 609837731 609838273 542 True 599.000000 599 86.726000 1821 2375 1 chr3D.!!$R3 554
22 TraesCS2D01G494400 chr4D 294014632 294015183 551 True 569.000000 569 85.714000 1821 2370 1 chr4D.!!$R1 549
23 TraesCS2D01G494400 chr4A 676260427 676261032 605 True 379.000000 523 92.672000 1822 2375 2 chr4A.!!$R1 553
24 TraesCS2D01G494400 chr5B 599323537 599325828 2291 True 369.000000 464 98.063500 1 467 2 chr5B.!!$R1 466

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
524 5722 0.670546 ACCACGTGCTCCATTTCGAG 60.671 55.0 10.91 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 7377 1.064208 CACAGACGAGTACTCCATCCG 59.936 57.143 17.23 8.27 0.0 4.18 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
182 456 9.903682 AACATATATTCAAGCATCAAATACAGC 57.096 29.630 0.00 0.00 0.00 4.40
183 457 9.293404 ACATATATTCAAGCATCAAATACAGCT 57.707 29.630 0.00 0.00 39.37 4.24
184 458 9.556030 CATATATTCAAGCATCAAATACAGCTG 57.444 33.333 13.48 13.48 37.41 4.24
185 459 3.770263 TCAAGCATCAAATACAGCTGC 57.230 42.857 15.27 0.00 37.41 5.25
186 460 3.083293 TCAAGCATCAAATACAGCTGCA 58.917 40.909 15.27 0.00 37.41 4.41
187 461 3.119743 TCAAGCATCAAATACAGCTGCAC 60.120 43.478 15.27 0.00 37.41 4.57
189 463 1.473677 GCATCAAATACAGCTGCACCA 59.526 47.619 15.27 0.00 33.13 4.17
190 464 2.479049 GCATCAAATACAGCTGCACCAG 60.479 50.000 15.27 1.30 33.13 4.00
292 2240 1.078143 CTACAGCAGCAACCCTCCC 60.078 63.158 0.00 0.00 0.00 4.30
524 5722 0.670546 ACCACGTGCTCCATTTCGAG 60.671 55.000 10.91 0.00 0.00 4.04
577 5776 2.755650 GAACTCGACATGCCCGATTAT 58.244 47.619 10.59 1.95 35.35 1.28
627 5849 6.004574 AGAGATACTAATGTCGTGCCAGATA 58.995 40.000 0.00 0.00 30.76 1.98
718 5988 2.419198 GATGCCTGCGGATCTCGT 59.581 61.111 0.00 0.00 41.72 4.18
761 6034 2.594529 CGCAGCGACACAAAAACTAT 57.405 45.000 9.98 0.00 0.00 2.12
813 6101 3.047877 GCCAACCCCAAGACGACG 61.048 66.667 0.00 0.00 0.00 5.12
815 6103 3.047877 CAACCCCAAGACGACGCC 61.048 66.667 0.00 0.00 0.00 5.68
1412 6968 1.227147 GAACGATCGGGCGATGGAA 60.227 57.895 20.98 0.00 34.96 3.53
1496 7060 3.403057 CGCGTACGCACAGCAACT 61.403 61.111 36.44 0.00 42.06 3.16
1503 7067 2.253452 GCACAGCAACTGCCGAAG 59.747 61.111 0.00 0.00 43.38 3.79
1591 7162 4.212716 CTGGTGCTGGGTAGTACAGTATA 58.787 47.826 2.06 0.00 40.81 1.47
1634 7213 4.499183 AGTAACTGATTGAAGAAGGCGAG 58.501 43.478 0.00 0.00 0.00 5.03
1635 7214 2.393271 ACTGATTGAAGAAGGCGAGG 57.607 50.000 0.00 0.00 0.00 4.63
1673 7252 9.924650 TTGTTTTCTCTGTAACTATTCTACTCC 57.075 33.333 0.00 0.00 0.00 3.85
1674 7253 8.529476 TGTTTTCTCTGTAACTATTCTACTCCC 58.471 37.037 0.00 0.00 0.00 4.30
1675 7254 8.751242 GTTTTCTCTGTAACTATTCTACTCCCT 58.249 37.037 0.00 0.00 0.00 4.20
1676 7255 8.522542 TTTCTCTGTAACTATTCTACTCCCTC 57.477 38.462 0.00 0.00 0.00 4.30
1677 7256 6.603224 TCTCTGTAACTATTCTACTCCCTCC 58.397 44.000 0.00 0.00 0.00 4.30
1678 7257 5.374921 TCTGTAACTATTCTACTCCCTCCG 58.625 45.833 0.00 0.00 0.00 4.63
1679 7258 5.104193 TCTGTAACTATTCTACTCCCTCCGT 60.104 44.000 0.00 0.00 0.00 4.69
1680 7259 5.513233 TGTAACTATTCTACTCCCTCCGTT 58.487 41.667 0.00 0.00 0.00 4.44
1681 7260 5.954150 TGTAACTATTCTACTCCCTCCGTTT 59.046 40.000 0.00 0.00 0.00 3.60
1682 7261 5.595257 AACTATTCTACTCCCTCCGTTTC 57.405 43.478 0.00 0.00 0.00 2.78
1683 7262 4.869451 ACTATTCTACTCCCTCCGTTTCT 58.131 43.478 0.00 0.00 0.00 2.52
1684 7263 6.011122 ACTATTCTACTCCCTCCGTTTCTA 57.989 41.667 0.00 0.00 0.00 2.10
1685 7264 6.430007 ACTATTCTACTCCCTCCGTTTCTAA 58.570 40.000 0.00 0.00 0.00 2.10
1686 7265 6.894103 ACTATTCTACTCCCTCCGTTTCTAAA 59.106 38.462 0.00 0.00 0.00 1.85
1687 7266 6.809976 ATTCTACTCCCTCCGTTTCTAAAT 57.190 37.500 0.00 0.00 0.00 1.40
1688 7267 7.909485 ATTCTACTCCCTCCGTTTCTAAATA 57.091 36.000 0.00 0.00 0.00 1.40
1689 7268 7.909485 TTCTACTCCCTCCGTTTCTAAATAT 57.091 36.000 0.00 0.00 0.00 1.28
1690 7269 7.521871 TCTACTCCCTCCGTTTCTAAATATC 57.478 40.000 0.00 0.00 0.00 1.63
1691 7270 7.296098 TCTACTCCCTCCGTTTCTAAATATCT 58.704 38.462 0.00 0.00 0.00 1.98
1692 7271 6.163135 ACTCCCTCCGTTTCTAAATATCTG 57.837 41.667 0.00 0.00 0.00 2.90
1693 7272 5.661759 ACTCCCTCCGTTTCTAAATATCTGT 59.338 40.000 0.00 0.00 0.00 3.41
1694 7273 6.158023 TCCCTCCGTTTCTAAATATCTGTC 57.842 41.667 0.00 0.00 0.00 3.51
1695 7274 5.897824 TCCCTCCGTTTCTAAATATCTGTCT 59.102 40.000 0.00 0.00 0.00 3.41
1696 7275 6.383147 TCCCTCCGTTTCTAAATATCTGTCTT 59.617 38.462 0.00 0.00 0.00 3.01
1697 7276 7.048512 CCCTCCGTTTCTAAATATCTGTCTTT 58.951 38.462 0.00 0.00 0.00 2.52
1698 7277 7.224949 CCCTCCGTTTCTAAATATCTGTCTTTC 59.775 40.741 0.00 0.00 0.00 2.62
1699 7278 7.982354 CCTCCGTTTCTAAATATCTGTCTTTCT 59.018 37.037 0.00 0.00 0.00 2.52
1763 7342 9.440761 AGACATATTTTAGAGGGTAGATTCACT 57.559 33.333 0.00 0.00 0.00 3.41
1765 7344 9.838339 ACATATTTTAGAGGGTAGATTCACTTG 57.162 33.333 0.00 0.00 0.00 3.16
1766 7345 9.277783 CATATTTTAGAGGGTAGATTCACTTGG 57.722 37.037 0.00 0.00 0.00 3.61
1767 7346 6.697641 TTTTAGAGGGTAGATTCACTTGGT 57.302 37.500 0.00 0.00 0.00 3.67
1768 7347 5.677319 TTAGAGGGTAGATTCACTTGGTG 57.323 43.478 0.00 0.00 34.45 4.17
1769 7348 3.791320 AGAGGGTAGATTCACTTGGTGA 58.209 45.455 0.00 0.00 41.09 4.02
1785 7364 8.744652 TCACTTGGTGAAATCTTTAAAAAGACA 58.255 29.630 7.29 0.00 42.31 3.41
1786 7365 9.364989 CACTTGGTGAAATCTTTAAAAAGACAA 57.635 29.630 7.29 5.76 40.68 3.18
1787 7366 9.936759 ACTTGGTGAAATCTTTAAAAAGACAAA 57.063 25.926 7.29 0.00 46.80 2.83
1804 7383 9.855021 AAAAGACAAATATTTAGAAACGGATGG 57.145 29.630 0.00 0.00 0.00 3.51
1805 7384 8.801882 AAGACAAATATTTAGAAACGGATGGA 57.198 30.769 0.00 0.00 0.00 3.41
1806 7385 8.438676 AGACAAATATTTAGAAACGGATGGAG 57.561 34.615 0.00 0.00 0.00 3.86
1807 7386 8.047310 AGACAAATATTTAGAAACGGATGGAGT 58.953 33.333 0.00 0.00 0.00 3.85
1808 7387 9.321562 GACAAATATTTAGAAACGGATGGAGTA 57.678 33.333 0.00 0.00 0.00 2.59
1809 7388 9.106070 ACAAATATTTAGAAACGGATGGAGTAC 57.894 33.333 0.00 0.00 0.00 2.73
1810 7389 9.326413 CAAATATTTAGAAACGGATGGAGTACT 57.674 33.333 0.00 0.00 0.00 2.73
1811 7390 9.543783 AAATATTTAGAAACGGATGGAGTACTC 57.456 33.333 14.87 14.87 0.00 2.59
1812 7391 4.627611 TTAGAAACGGATGGAGTACTCG 57.372 45.455 16.56 8.02 0.00 4.18
1813 7392 2.444421 AGAAACGGATGGAGTACTCGT 58.556 47.619 16.56 8.68 35.48 4.18
1814 7393 2.422832 AGAAACGGATGGAGTACTCGTC 59.577 50.000 16.56 15.69 33.34 4.20
1819 7398 2.093106 GGATGGAGTACTCGTCTGTGT 58.907 52.381 16.56 0.00 0.00 3.72
1850 7429 4.952262 TGTGTACATGTACGTAGGTCTC 57.048 45.455 26.59 12.07 38.85 3.36
1947 7527 7.673082 GGTCGCACCCCTTATACCTATATATAT 59.327 40.741 0.00 0.00 30.04 0.86
1948 7528 9.745018 GTCGCACCCCTTATACCTATATATATA 57.255 37.037 2.49 2.49 0.00 0.86
1984 7614 3.059325 GCCTAGTGCACGATCAATCAATC 60.059 47.826 12.01 0.00 40.77 2.67
2029 7659 4.937201 ACATGGTATCTATCGCAAGTCA 57.063 40.909 0.00 0.00 39.48 3.41
2352 8058 2.555565 CTTCTCGCTGCTCTTCCGCT 62.556 60.000 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.828877 ACAAGTCGATTTGTGTTCCGA 58.171 42.857 23.53 0.00 39.68 4.55
156 157 9.903682 GCTGTATTTGATGCTTGAATATATGTT 57.096 29.630 0.00 0.00 0.00 2.71
157 158 9.293404 AGCTGTATTTGATGCTTGAATATATGT 57.707 29.630 0.00 0.00 30.96 2.29
159 160 8.242053 GCAGCTGTATTTGATGCTTGAATATAT 58.758 33.333 16.64 0.00 42.68 0.86
160 161 7.229106 TGCAGCTGTATTTGATGCTTGAATATA 59.771 33.333 16.64 0.00 45.69 0.86
161 162 6.040054 TGCAGCTGTATTTGATGCTTGAATAT 59.960 34.615 16.64 0.00 45.69 1.28
162 163 5.357596 TGCAGCTGTATTTGATGCTTGAATA 59.642 36.000 16.64 0.00 45.69 1.75
563 5762 2.154462 CTGGGAATAATCGGGCATGTC 58.846 52.381 0.00 0.00 0.00 3.06
577 5776 1.641552 CGCCCCCTAATTCCTGGGAA 61.642 60.000 11.40 4.43 46.15 3.97
706 5972 0.590230 GACGAGAACGAGATCCGCAG 60.590 60.000 0.00 0.00 43.32 5.18
707 5973 1.428219 GACGAGAACGAGATCCGCA 59.572 57.895 0.00 0.00 43.32 5.69
708 5974 1.298488 GGACGAGAACGAGATCCGC 60.298 63.158 0.00 0.00 43.32 5.54
709 5975 1.355916 GGGACGAGAACGAGATCCG 59.644 63.158 0.00 2.55 42.66 4.18
761 6034 1.872234 GCACGACGATGAGCGCTAA 60.872 57.895 11.50 1.72 46.04 3.09
1280 6826 1.228644 TCGGAGTGGGACGAGGAAA 60.229 57.895 0.00 0.00 34.67 3.13
1408 6964 2.223803 ACAAACTGGGTTGTGTTCCA 57.776 45.000 3.02 0.00 40.22 3.53
1416 6972 3.119193 CGCAGCACAAACTGGGTT 58.881 55.556 0.00 0.00 43.54 4.11
1444 7003 1.686587 TGTGTGTCAGTCACCAGTAGG 59.313 52.381 0.00 0.00 45.61 3.18
1446 7005 1.066454 CGTGTGTGTCAGTCACCAGTA 59.934 52.381 0.00 0.00 45.61 2.74
1503 7067 2.514824 GGCCCTTCGGATCAGTGC 60.515 66.667 0.00 0.00 0.00 4.40
1538 7102 4.012895 GATGGCCGGCATTACGCG 62.013 66.667 30.85 3.53 43.84 6.01
1573 7137 5.480422 CCATCATATACTGTACTACCCAGCA 59.520 44.000 0.00 0.00 33.09 4.41
1591 7162 8.639761 GTTACTAACTAGTACCATCACCATCAT 58.360 37.037 0.00 0.00 38.43 2.45
1673 7252 7.982354 AGAAAGACAGATATTTAGAAACGGAGG 59.018 37.037 0.00 0.00 0.00 4.30
1674 7253 8.934507 AGAAAGACAGATATTTAGAAACGGAG 57.065 34.615 0.00 0.00 0.00 4.63
1737 7316 9.440761 AGTGAATCTACCCTCTAAAATATGTCT 57.559 33.333 0.00 0.00 0.00 3.41
1739 7318 9.838339 CAAGTGAATCTACCCTCTAAAATATGT 57.162 33.333 0.00 0.00 0.00 2.29
1740 7319 9.277783 CCAAGTGAATCTACCCTCTAAAATATG 57.722 37.037 0.00 0.00 0.00 1.78
1741 7320 9.004231 ACCAAGTGAATCTACCCTCTAAAATAT 57.996 33.333 0.00 0.00 0.00 1.28
1742 7321 8.265055 CACCAAGTGAATCTACCCTCTAAAATA 58.735 37.037 0.00 0.00 35.23 1.40
1743 7322 7.037586 TCACCAAGTGAATCTACCCTCTAAAAT 60.038 37.037 0.00 0.00 39.78 1.82
1744 7323 6.271391 TCACCAAGTGAATCTACCCTCTAAAA 59.729 38.462 0.00 0.00 39.78 1.52
1745 7324 5.783360 TCACCAAGTGAATCTACCCTCTAAA 59.217 40.000 0.00 0.00 39.78 1.85
1746 7325 5.338632 TCACCAAGTGAATCTACCCTCTAA 58.661 41.667 0.00 0.00 39.78 2.10
1747 7326 4.942944 TCACCAAGTGAATCTACCCTCTA 58.057 43.478 0.00 0.00 39.78 2.43
1748 7327 3.791320 TCACCAAGTGAATCTACCCTCT 58.209 45.455 0.00 0.00 39.78 3.69
1749 7328 4.553330 TTCACCAAGTGAATCTACCCTC 57.447 45.455 6.08 0.00 45.88 4.30
1758 7337 9.581099 GTCTTTTTAAAGATTTCACCAAGTGAA 57.419 29.630 6.08 6.08 45.85 3.18
1759 7338 8.744652 TGTCTTTTTAAAGATTTCACCAAGTGA 58.255 29.630 8.07 0.00 45.83 3.41
1760 7339 8.925161 TGTCTTTTTAAAGATTTCACCAAGTG 57.075 30.769 8.07 0.00 45.83 3.16
1761 7340 9.936759 TTTGTCTTTTTAAAGATTTCACCAAGT 57.063 25.926 8.07 0.00 45.83 3.16
1778 7357 9.855021 CCATCCGTTTCTAAATATTTGTCTTTT 57.145 29.630 11.05 0.00 0.00 2.27
1779 7358 9.238368 TCCATCCGTTTCTAAATATTTGTCTTT 57.762 29.630 11.05 0.00 0.00 2.52
1780 7359 8.801882 TCCATCCGTTTCTAAATATTTGTCTT 57.198 30.769 11.05 0.00 0.00 3.01
1781 7360 8.047310 ACTCCATCCGTTTCTAAATATTTGTCT 58.953 33.333 11.05 0.00 0.00 3.41
1782 7361 8.209917 ACTCCATCCGTTTCTAAATATTTGTC 57.790 34.615 11.05 0.00 0.00 3.18
1783 7362 9.106070 GTACTCCATCCGTTTCTAAATATTTGT 57.894 33.333 11.05 0.00 0.00 2.83
1784 7363 9.326413 AGTACTCCATCCGTTTCTAAATATTTG 57.674 33.333 11.05 1.65 0.00 2.32
1785 7364 9.543783 GAGTACTCCATCCGTTTCTAAATATTT 57.456 33.333 12.13 5.89 0.00 1.40
1786 7365 7.866393 CGAGTACTCCATCCGTTTCTAAATATT 59.134 37.037 17.23 0.00 0.00 1.28
1787 7366 7.014038 ACGAGTACTCCATCCGTTTCTAAATAT 59.986 37.037 17.23 0.00 0.00 1.28
1788 7367 6.319658 ACGAGTACTCCATCCGTTTCTAAATA 59.680 38.462 17.23 0.00 0.00 1.40
1789 7368 5.126707 ACGAGTACTCCATCCGTTTCTAAAT 59.873 40.000 17.23 0.00 0.00 1.40
1790 7369 4.460382 ACGAGTACTCCATCCGTTTCTAAA 59.540 41.667 17.23 0.00 0.00 1.85
1791 7370 4.012374 ACGAGTACTCCATCCGTTTCTAA 58.988 43.478 17.23 0.00 0.00 2.10
1792 7371 3.614092 ACGAGTACTCCATCCGTTTCTA 58.386 45.455 17.23 0.00 0.00 2.10
1793 7372 2.422832 GACGAGTACTCCATCCGTTTCT 59.577 50.000 17.23 0.00 33.32 2.52
1794 7373 2.422832 AGACGAGTACTCCATCCGTTTC 59.577 50.000 17.23 1.57 33.32 2.78
1795 7374 2.163815 CAGACGAGTACTCCATCCGTTT 59.836 50.000 17.23 4.41 33.32 3.60
1796 7375 1.743958 CAGACGAGTACTCCATCCGTT 59.256 52.381 17.23 1.12 33.32 4.44
1797 7376 1.339824 ACAGACGAGTACTCCATCCGT 60.340 52.381 17.23 11.58 36.08 4.69
1798 7377 1.064208 CACAGACGAGTACTCCATCCG 59.936 57.143 17.23 8.27 0.00 4.18
1799 7378 2.093106 ACACAGACGAGTACTCCATCC 58.907 52.381 17.23 4.12 0.00 3.51
1800 7379 3.057456 ACAACACAGACGAGTACTCCATC 60.057 47.826 17.23 14.32 0.00 3.51
1801 7380 2.891580 ACAACACAGACGAGTACTCCAT 59.108 45.455 17.23 5.64 0.00 3.41
1802 7381 2.304092 ACAACACAGACGAGTACTCCA 58.696 47.619 17.23 0.00 0.00 3.86
1803 7382 3.050619 CAACAACACAGACGAGTACTCC 58.949 50.000 17.23 4.19 0.00 3.85
1804 7383 3.961182 TCAACAACACAGACGAGTACTC 58.039 45.455 13.18 13.18 0.00 2.59
1805 7384 4.110482 GTTCAACAACACAGACGAGTACT 58.890 43.478 0.00 0.00 32.14 2.73
1806 7385 3.861113 TGTTCAACAACACAGACGAGTAC 59.139 43.478 0.00 0.00 37.61 2.73
1807 7386 4.112716 TGTTCAACAACACAGACGAGTA 57.887 40.909 0.00 0.00 37.61 2.59
1808 7387 2.967362 TGTTCAACAACACAGACGAGT 58.033 42.857 0.00 0.00 37.61 4.18
1809 7388 3.309682 ACATGTTCAACAACACAGACGAG 59.690 43.478 0.00 0.00 45.47 4.18
1810 7389 3.063316 CACATGTTCAACAACACAGACGA 59.937 43.478 0.00 0.00 45.47 4.20
1811 7390 3.181511 ACACATGTTCAACAACACAGACG 60.182 43.478 0.00 0.00 45.47 4.18
1812 7391 4.355543 ACACATGTTCAACAACACAGAC 57.644 40.909 0.00 0.00 45.47 3.51
1813 7392 4.938226 TGTACACATGTTCAACAACACAGA 59.062 37.500 0.00 0.00 45.47 3.41
1814 7393 5.228579 TGTACACATGTTCAACAACACAG 57.771 39.130 0.00 0.00 45.47 3.66
1850 7429 2.961526 AGGTACTGCATACAAGACCG 57.038 50.000 0.00 0.00 37.18 4.79
1984 7614 4.275196 AGAGAATGATTTGGTGCATCGATG 59.725 41.667 21.27 21.27 0.00 3.84
2352 8058 3.513912 ACATGATCCACGAGGTTGTTCTA 59.486 43.478 0.00 0.00 35.89 2.10


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

AutoCloner maintained by Alex Coulton.