Multiple sequence alignment - TraesCS6A01G045400

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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 TraesCS6A01G045400 chr6A 100.000 4922 0 0 1 4922 23445089 23440168 0.000000e+00 9090.0
1 TraesCS6A01G045400 chr6A 86.911 3713 437 35 641 4345 22815668 22819339 0.000000e+00 4119.0
2 TraesCS6A01G045400 chr6A 84.247 3282 467 29 926 4186 22690823 22694075 0.000000e+00 3151.0
3 TraesCS6A01G045400 chr6A 88.300 453 44 4 914 1365 22826154 22826598 7.250000e-148 534.0
4 TraesCS6A01G045400 chr6A 89.937 318 24 7 1 315 22815239 22815551 2.130000e-108 403.0
5 TraesCS6A01G045400 chr6A 78.689 549 60 28 4400 4922 22989495 22990012 3.700000e-81 313.0
6 TraesCS6A01G045400 chr6A 80.980 347 37 16 4333 4673 22824002 22824325 1.060000e-61 248.0
7 TraesCS6A01G045400 chr6A 97.273 110 2 1 422 531 22815553 22815661 8.410000e-43 185.0
8 TraesCS6A01G045400 chr6A 94.215 121 6 1 486 606 27148136 27148017 3.030000e-42 183.0
9 TraesCS6A01G045400 chr6A 87.778 90 8 2 11 97 83351863 83351952 8.720000e-18 102.0
10 TraesCS6A01G045400 chr6A 91.549 71 5 1 11 80 83346810 83346880 4.060000e-16 97.1
11 TraesCS6A01G045400 chr6D 91.310 3291 265 13 1579 4860 24429616 24432894 0.000000e+00 4473.0
12 TraesCS6A01G045400 chr6D 86.752 3691 415 34 561 4243 24349250 24345626 0.000000e+00 4039.0
13 TraesCS6A01G045400 chr6D 86.742 3696 412 36 558 4243 24390074 24393701 0.000000e+00 4039.0
14 TraesCS6A01G045400 chr6D 93.374 2294 134 10 2574 4860 24339996 24337714 0.000000e+00 3378.0
15 TraesCS6A01G045400 chr6D 88.565 2641 257 23 1582 4211 24335147 24332541 0.000000e+00 3162.0
16 TraesCS6A01G045400 chr6D 88.584 2628 255 30 1858 4477 24364541 24361951 0.000000e+00 3149.0
17 TraesCS6A01G045400 chr6D 84.620 3056 411 38 1147 4186 24225995 24229007 0.000000e+00 2985.0
18 TraesCS6A01G045400 chr6D 88.214 2503 250 23 1883 4378 24403007 24405471 0.000000e+00 2946.0
19 TraesCS6A01G045400 chr6D 86.540 2578 301 27 2014 4581 24353407 24350866 0.000000e+00 2796.0
20 TraesCS6A01G045400 chr6D 90.924 1212 90 12 605 1812 24358501 24357306 0.000000e+00 1611.0
21 TraesCS6A01G045400 chr6D 89.068 558 55 5 984 1535 24402183 24402740 0.000000e+00 688.0
22 TraesCS6A01G045400 chr6D 88.854 323 25 6 1 313 24389704 24390025 2.150000e-103 387.0
23 TraesCS6A01G045400 chr6D 79.963 534 67 17 4401 4922 24296110 24295605 1.680000e-94 357.0
24 TraesCS6A01G045400 chr6D 88.182 220 17 6 84 299 24358971 24358757 2.270000e-63 254.0
25 TraesCS6A01G045400 chr6D 96.350 137 3 2 441 577 24358634 24358500 1.780000e-54 224.0
26 TraesCS6A01G045400 chr6D 94.643 112 2 2 4811 4922 24337713 24337606 2.360000e-38 171.0
27 TraesCS6A01G045400 chr6D 94.643 112 2 2 4811 4922 24432895 24433002 2.360000e-38 171.0
28 TraesCS6A01G045400 chr6D 94.444 90 5 0 4833 4922 24322856 24322767 6.640000e-29 139.0
29 TraesCS6A01G045400 chr6D 94.444 90 5 0 4833 4922 24354520 24354431 6.640000e-29 139.0
30 TraesCS6A01G045400 chr6D 94.444 90 5 0 4833 4922 24405846 24405935 6.640000e-29 139.0
31 TraesCS6A01G045400 chr6D 94.253 87 4 1 441 526 24349585 24349499 1.110000e-26 132.0
32 TraesCS6A01G045400 chr6B 84.533 2625 378 19 1576 4186 39193755 39196365 0.000000e+00 2573.0
33 TraesCS6A01G045400 chr6B 92.365 1336 73 10 421 1752 39754262 39755572 0.000000e+00 1875.0
34 TraesCS6A01G045400 chr6B 89.433 1306 105 15 3294 4588 39455652 39456935 0.000000e+00 1616.0
35 TraesCS6A01G045400 chr6B 84.967 612 84 4 926 1533 39193132 39193739 9.050000e-172 614.0
36 TraesCS6A01G045400 chr6B 83.604 555 76 7 984 1535 39431504 39432046 1.580000e-139 507.0
37 TraesCS6A01G045400 chr6B 86.486 333 30 8 1 319 39753931 39754262 7.840000e-93 351.0
38 TraesCS6A01G045400 chr6B 79.063 363 46 23 4118 4477 39757761 39758096 6.410000e-54 222.0
39 TraesCS6A01G045400 chr6B 92.000 150 9 3 164 313 39343934 39343788 1.800000e-49 207.0
40 TraesCS6A01G045400 chr6B 93.220 118 8 0 313 430 460495299 460495416 1.820000e-39 174.0
41 TraesCS6A01G045400 chr6B 91.818 110 9 0 313 422 44112512 44112403 2.370000e-33 154.0
42 TraesCS6A01G045400 chr6B 82.209 163 26 1 1701 1863 40591911 40591752 2.390000e-28 137.0
43 TraesCS6A01G045400 chr6B 89.815 108 8 2 4815 4922 39429015 39429119 8.590000e-28 135.0
44 TraesCS6A01G045400 chr4A 75.335 2838 600 70 1109 3899 607274026 607271242 0.000000e+00 1271.0
45 TraesCS6A01G045400 chr4A 92.920 113 7 1 310 422 671596414 671596303 3.940000e-36 163.0
46 TraesCS6A01G045400 chr1B 91.729 133 7 3 298 427 683469687 683469556 1.090000e-41 182.0
47 TraesCS6A01G045400 chr1B 91.549 71 5 1 11 80 14048759 14048689 4.060000e-16 97.1
48 TraesCS6A01G045400 chr1B 91.549 71 5 1 11 80 14053558 14053488 4.060000e-16 97.1
49 TraesCS6A01G045400 chr5D 96.330 109 4 0 314 422 257163168 257163276 3.910000e-41 180.0
50 TraesCS6A01G045400 chr5D 92.683 123 8 1 313 435 94343226 94343105 5.060000e-40 176.0
51 TraesCS6A01G045400 chr3B 93.388 121 6 2 315 433 189150385 189150265 1.410000e-40 178.0
52 TraesCS6A01G045400 chr3B 93.277 119 8 0 306 424 205478188 205478070 5.060000e-40 176.0
53 TraesCS6A01G045400 chr1D 94.737 114 5 1 311 423 414643236 414643349 5.060000e-40 176.0
54 TraesCS6A01G045400 chr7B 92.437 119 9 0 304 422 674193658 674193776 2.360000e-38 171.0
55 TraesCS6A01G045400 chr7B 90.984 122 11 0 301 422 78694839 78694960 1.100000e-36 165.0
56 TraesCS6A01G045400 chr7B 82.353 102 15 2 20 118 733748713 733748814 8.780000e-13 86.1
57 TraesCS6A01G045400 chr5B 91.870 123 9 1 306 427 427250027 427250149 2.360000e-38 171.0
58 TraesCS6A01G045400 chr7D 91.129 124 11 0 305 428 90544365 90544242 8.470000e-38 169.0
59 TraesCS6A01G045400 chr2B 89.831 118 11 1 316 432 37903055 37902938 3.070000e-32 150.0
60 TraesCS6A01G045400 chr4B 91.549 71 5 1 11 80 617328104 617328034 4.060000e-16 97.1
61 TraesCS6A01G045400 chr4B 91.549 71 5 1 11 80 617332893 617332823 4.060000e-16 97.1


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 TraesCS6A01G045400 chr6A 23440168 23445089 4921 True 9090.000000 9090 100.000000 1 4922 1 chr6A.!!$R1 4921
1 TraesCS6A01G045400 chr6A 22690823 22694075 3252 False 3151.000000 3151 84.247000 926 4186 1 chr6A.!!$F1 3260
2 TraesCS6A01G045400 chr6A 22815239 22819339 4100 False 1569.000000 4119 91.373667 1 4345 3 chr6A.!!$F5 4344
3 TraesCS6A01G045400 chr6A 22824002 22826598 2596 False 391.000000 534 84.640000 914 4673 2 chr6A.!!$F6 3759
4 TraesCS6A01G045400 chr6A 22989495 22990012 517 False 313.000000 313 78.689000 4400 4922 1 chr6A.!!$F2 522
5 TraesCS6A01G045400 chr6D 24225995 24229007 3012 False 2985.000000 2985 84.620000 1147 4186 1 chr6D.!!$F1 3039
6 TraesCS6A01G045400 chr6D 24429616 24433002 3386 False 2322.000000 4473 92.976500 1579 4922 2 chr6D.!!$F4 3343
7 TraesCS6A01G045400 chr6D 24332541 24339996 7455 True 2237.000000 3378 92.194000 1582 4922 3 chr6D.!!$R3 3340
8 TraesCS6A01G045400 chr6D 24389704 24393701 3997 False 2213.000000 4039 87.798000 1 4243 2 chr6D.!!$F2 4242
9 TraesCS6A01G045400 chr6D 24345626 24364541 18915 True 1543.000000 4039 90.753625 84 4922 8 chr6D.!!$R4 4838
10 TraesCS6A01G045400 chr6D 24402183 24405935 3752 False 1257.666667 2946 90.575333 984 4922 3 chr6D.!!$F3 3938
11 TraesCS6A01G045400 chr6D 24295605 24296110 505 True 357.000000 357 79.963000 4401 4922 1 chr6D.!!$R1 521
12 TraesCS6A01G045400 chr6B 39455652 39456935 1283 False 1616.000000 1616 89.433000 3294 4588 1 chr6B.!!$F1 1294
13 TraesCS6A01G045400 chr6B 39193132 39196365 3233 False 1593.500000 2573 84.750000 926 4186 2 chr6B.!!$F3 3260
14 TraesCS6A01G045400 chr6B 39753931 39758096 4165 False 816.000000 1875 85.971333 1 4477 3 chr6B.!!$F5 4476
15 TraesCS6A01G045400 chr6B 39429015 39432046 3031 False 321.000000 507 86.709500 984 4922 2 chr6B.!!$F4 3938
16 TraesCS6A01G045400 chr4A 607271242 607274026 2784 True 1271.000000 1271 75.335000 1109 3899 1 chr4A.!!$R1 2790

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
219 5712 0.182061 CCACACAGATGGATGGGGAG 59.818 60.0 0.0 0.0 42.53 4.30 F
1693 7277 0.179004 TCCGGTGGTGAACATGCTTT 60.179 50.0 0.0 0.0 0.00 3.51 F
2173 7757 0.255318 CCTGAGCTGGCTGGATCTTT 59.745 55.0 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 7390 0.039472 TGGGTGTGCCATGCTTATGT 59.961 50.000 0.0 0.0 36.17 2.29 R
3540 18465 1.079503 GGTTCAGGCGACTCAATGAC 58.920 55.000 0.0 0.0 40.21 3.06 R
4067 19026 1.451387 GCATACCAACCCCAGTCGG 60.451 63.158 0.0 0.0 0.00 4.79 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
153 5640 1.131315 GATGCAGACTTTCCTTTCGGC 59.869 52.381 0.00 0.00 33.99 5.54
207 5696 4.339247 GGGATTCATCATTTACCCACACAG 59.661 45.833 0.00 0.00 37.50 3.66
216 5709 4.993307 CCCACACAGATGGATGGG 57.007 61.111 8.73 8.73 45.79 4.00
219 5712 0.182061 CCACACAGATGGATGGGGAG 59.818 60.000 0.00 0.00 42.53 4.30
305 5823 5.384145 AGTGGGATTCATCATTCACATCT 57.616 39.130 0.00 0.00 0.00 2.90
325 5843 9.144747 CACATCTCAAATATTATACTCCTTCCG 57.855 37.037 0.00 0.00 0.00 4.30
326 5844 8.871125 ACATCTCAAATATTATACTCCTTCCGT 58.129 33.333 0.00 0.00 0.00 4.69
327 5845 9.712305 CATCTCAAATATTATACTCCTTCCGTT 57.288 33.333 0.00 0.00 0.00 4.44
329 5847 8.080417 TCTCAAATATTATACTCCTTCCGTTCG 58.920 37.037 0.00 0.00 0.00 3.95
331 5849 6.906157 AATATTATACTCCTTCCGTTCGGA 57.094 37.500 10.00 10.00 0.00 4.55
332 5850 6.906157 ATATTATACTCCTTCCGTTCGGAA 57.094 37.500 22.42 22.42 41.48 4.30
333 5851 5.803237 ATTATACTCCTTCCGTTCGGAAT 57.197 39.130 23.69 13.41 42.61 3.01
334 5852 5.603170 TTATACTCCTTCCGTTCGGAATT 57.397 39.130 23.69 12.73 42.61 2.17
336 5854 3.242549 ACTCCTTCCGTTCGGAATTAC 57.757 47.619 23.69 0.00 42.61 1.89
341 5859 3.864003 CCTTCCGTTCGGAATTACTCTTC 59.136 47.826 23.69 0.00 42.61 2.87
342 5860 3.515330 TCCGTTCGGAATTACTCTTCC 57.485 47.619 11.66 0.00 41.16 3.46
345 5863 3.617263 CCGTTCGGAATTACTCTTCCAAG 59.383 47.826 5.19 0.00 44.18 3.61
347 5865 4.927425 CGTTCGGAATTACTCTTCCAAGAA 59.073 41.667 0.00 0.00 44.18 2.52
354 5872 7.912250 CGGAATTACTCTTCCAAGAAATGAATG 59.088 37.037 3.95 0.00 44.18 2.67
359 5877 9.739276 TTACTCTTCCAAGAAATGAATGTATGT 57.261 29.630 0.00 0.00 34.03 2.29
361 5879 9.388506 ACTCTTCCAAGAAATGAATGTATGTAG 57.611 33.333 0.00 0.00 34.03 2.74
362 5880 9.605275 CTCTTCCAAGAAATGAATGTATGTAGA 57.395 33.333 0.00 0.00 34.03 2.59
408 5926 9.236691 CATCCATTTTTATGACAAGTAATTCCG 57.763 33.333 0.00 0.00 0.00 4.30
409 5927 8.568676 TCCATTTTTATGACAAGTAATTCCGA 57.431 30.769 0.00 0.00 0.00 4.55
410 5928 9.015367 TCCATTTTTATGACAAGTAATTCCGAA 57.985 29.630 0.00 0.00 0.00 4.30
411 5929 9.072294 CCATTTTTATGACAAGTAATTCCGAAC 57.928 33.333 0.00 0.00 0.00 3.95
412 5930 8.785101 CATTTTTATGACAAGTAATTCCGAACG 58.215 33.333 0.00 0.00 0.00 3.95
413 5931 6.411630 TTTATGACAAGTAATTCCGAACGG 57.588 37.500 6.94 6.94 0.00 4.44
414 5932 3.663995 TGACAAGTAATTCCGAACGGA 57.336 42.857 12.04 12.04 43.52 4.69
415 5933 3.581755 TGACAAGTAATTCCGAACGGAG 58.418 45.455 15.34 5.60 46.06 4.63
416 5934 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
417 5935 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
418 5936 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
419 5937 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
436 5954 2.563179 GGGAGTAGAAGTCAAGCACTCA 59.437 50.000 0.00 0.00 37.87 3.41
526 6044 1.953686 GCCACCAGAGCTAACACAAAA 59.046 47.619 0.00 0.00 0.00 2.44
568 6086 1.597663 GTTAGCGACCAATGGAATCCG 59.402 52.381 6.16 5.07 0.00 4.18
573 6091 1.017387 GACCAATGGAATCCGTCAGC 58.983 55.000 6.16 0.00 0.00 4.26
646 6167 7.573968 ATTCCTAGAATGTTTACAATCAGGC 57.426 36.000 0.00 0.00 30.78 4.85
751 6272 5.095490 GTCCAGTTGCTTTAATCAAATCCG 58.905 41.667 0.00 0.00 0.00 4.18
856 6402 1.179152 CTGCAAGCCATCATTGGTCA 58.821 50.000 0.00 0.00 45.57 4.02
932 6479 1.067916 CTTGGCAGGCAACACCAAC 59.932 57.895 5.03 0.00 46.47 3.77
1118 6684 3.346631 CTGCCCTGCATCCAAACGC 62.347 63.158 0.00 0.00 38.13 4.84
1122 6688 0.676466 CCCTGCATCCAAACGCTACA 60.676 55.000 0.00 0.00 0.00 2.74
1153 6719 1.134670 GTATTGCTGGCGAGAGGTCTT 60.135 52.381 0.00 0.00 0.00 3.01
1261 6827 1.160137 CTACTGCAGCAACAGAACCC 58.840 55.000 15.27 0.00 40.25 4.11
1409 6993 2.833794 CCAGAACAGGTTCGACAAGAA 58.166 47.619 6.52 0.00 43.97 2.52
1497 7081 0.469917 CTGGAAGGATACCACCGCAT 59.530 55.000 0.00 0.00 35.41 4.73
1693 7277 0.179004 TCCGGTGGTGAACATGCTTT 60.179 50.000 0.00 0.00 0.00 3.51
1697 7281 2.030007 CGGTGGTGAACATGCTTTCAAT 60.030 45.455 0.65 0.00 37.24 2.57
1801 7385 2.169769 ACACTTGACCTCTCCGAAAACA 59.830 45.455 0.00 0.00 0.00 2.83
1806 7390 4.675976 TGACCTCTCCGAAAACAAGTTA 57.324 40.909 0.00 0.00 0.00 2.24
1816 7400 6.607689 TCCGAAAACAAGTTACATAAGCATG 58.392 36.000 0.00 0.00 38.21 4.06
1871 7455 5.009210 GCCTCAAGTATCTAGACATCTCGTT 59.991 44.000 0.00 0.00 0.00 3.85
1877 7461 6.442952 AGTATCTAGACATCTCGTTCAATGC 58.557 40.000 0.00 0.00 0.00 3.56
2002 7586 8.041323 TGAAGAACCTATGTAATTTGGAGAGAC 58.959 37.037 0.00 0.00 0.00 3.36
2052 7636 8.658499 ACGGGAGTATAACAGAATTATTCAAC 57.342 34.615 7.74 0.00 44.60 3.18
2173 7757 0.255318 CCTGAGCTGGCTGGATCTTT 59.745 55.000 0.00 0.00 0.00 2.52
2174 7758 1.666054 CTGAGCTGGCTGGATCTTTC 58.334 55.000 0.00 0.00 0.00 2.62
2278 7863 1.006878 TGGATGGGGTCATGCATGAAA 59.993 47.619 30.24 16.48 44.85 2.69
2364 7949 0.476771 TGAGTCCAACTTGGGTTCCC 59.523 55.000 8.01 0.12 38.32 3.97
2392 7977 8.777865 TTCCAGTCTAACAATGATTCTACTTG 57.222 34.615 0.00 0.00 0.00 3.16
2441 8026 3.055963 CCAACATGGCTTAGATGGCAAAA 60.056 43.478 0.00 0.00 45.43 2.44
2442 8027 4.178540 CAACATGGCTTAGATGGCAAAAG 58.821 43.478 0.00 0.00 45.43 2.27
2448 8033 4.022068 TGGCTTAGATGGCAAAAGAACTTG 60.022 41.667 10.65 0.00 39.58 3.16
2739 8324 4.082571 CCAGGGCTTGAAACACTTATTCTG 60.083 45.833 0.00 0.00 0.00 3.02
2836 8421 7.870509 TCAAGAAATAACCTCAATGGATCAG 57.129 36.000 0.00 0.00 39.71 2.90
2839 8424 8.526147 CAAGAAATAACCTCAATGGATCAGTTT 58.474 33.333 0.00 0.00 39.71 2.66
3007 8592 1.286248 ATTCTCTGGGGCTTTACCGT 58.714 50.000 0.00 0.00 40.62 4.83
3033 8618 3.308046 GGATTGGGGAGAAGCTATCATCC 60.308 52.174 0.00 0.00 0.00 3.51
3144 8729 7.112779 ACCTTGCCTACAATAATATATCAGGC 58.887 38.462 10.33 10.33 45.82 4.85
3167 8752 6.697892 GGCAGCATACCGAGATCTATTATTAC 59.302 42.308 0.00 0.00 0.00 1.89
3192 8777 1.067516 ACAGGCATGACACAAACAAGC 59.932 47.619 4.84 0.00 0.00 4.01
3200 8785 2.486203 TGACACAAACAAGCGACAACTT 59.514 40.909 0.00 0.00 0.00 2.66
3202 8787 3.908213 ACACAAACAAGCGACAACTTTT 58.092 36.364 0.00 0.00 0.00 2.27
3203 8788 4.303282 ACACAAACAAGCGACAACTTTTT 58.697 34.783 0.00 0.00 0.00 1.94
3254 8857 1.902508 TGAGGATGGTGAGAGTCAACC 59.097 52.381 7.85 7.85 31.76 3.77
3275 8878 5.181748 ACCAGTTGACTATGCTGAGAATTC 58.818 41.667 0.00 0.00 32.39 2.17
3306 8909 4.810790 TCACGAAAGGTCAAGAGAGATTC 58.189 43.478 0.00 0.00 0.00 2.52
3405 9008 7.707624 AATCAGCACTCTTATGGAATTGAAA 57.292 32.000 0.00 0.00 0.00 2.69
3469 9072 4.661222 TGAGAATGTTGGTGCCTTAATGA 58.339 39.130 0.00 0.00 0.00 2.57
3540 18465 1.202302 TCAAGCTTATCGGCTCTCACG 60.202 52.381 0.00 0.00 42.24 4.35
3648 18573 6.435277 CAGCATCTATTTATATTGGCAACCCT 59.565 38.462 0.00 0.00 0.00 4.34
3910 18847 4.323104 CCTGGACTTCCTTCAGAGGTAAAG 60.323 50.000 0.00 0.00 43.97 1.85
3917 18857 6.655425 ACTTCCTTCAGAGGTAAAGTTAATGC 59.345 38.462 0.00 0.00 43.97 3.56
3918 18858 6.121776 TCCTTCAGAGGTAAAGTTAATGCA 57.878 37.500 0.00 0.00 43.97 3.96
4065 19024 6.487668 CAGGATATGTATTCAAGGTGCATTCA 59.512 38.462 0.00 0.00 0.00 2.57
4067 19026 7.013655 AGGATATGTATTCAAGGTGCATTCAAC 59.986 37.037 0.00 0.00 0.00 3.18
4076 19035 1.303236 TGCATTCAACCGACTGGGG 60.303 57.895 0.00 0.00 41.60 4.96
4132 19096 2.738321 GCACTTGTGGTTCTTGGTTTGG 60.738 50.000 2.81 0.00 0.00 3.28
4134 19098 3.697045 CACTTGTGGTTCTTGGTTTGGTA 59.303 43.478 0.00 0.00 0.00 3.25
4295 19284 0.825010 CTAGGGGCATGCCATTGACC 60.825 60.000 36.56 27.01 44.81 4.02
4300 19289 2.404789 CATGCCATTGACCGACGC 59.595 61.111 0.00 0.00 0.00 5.19
4363 19354 6.162777 TCTGTTGTTGGTCCTTTTCTTTTTG 58.837 36.000 0.00 0.00 0.00 2.44
4395 19387 8.611757 GTTTATGGTTCTTTTCAATGTGCTTTT 58.388 29.630 0.00 0.00 0.00 2.27
4547 19566 7.543238 CTGCAAGATGTTCAATTCTGCAAGAC 61.543 42.308 0.00 0.00 39.00 3.01
4568 19593 5.251700 AGACCAATAGTTGAGAAGAACCCAT 59.748 40.000 0.00 0.00 0.00 4.00
4592 19617 6.037786 ACAACACTATGGAGAGAAAATCGA 57.962 37.500 0.00 0.00 0.00 3.59
4629 19659 2.102252 CTGAGGTCTCCATGTAAGAGGC 59.898 54.545 0.00 0.00 35.16 4.70
4814 19874 4.126437 TGTGGTAATGACTGTCAGTTGTG 58.874 43.478 16.37 0.00 0.00 3.33
4829 19889 3.254166 CAGTTGTGTGCCTCTGCTTTATT 59.746 43.478 0.00 0.00 38.71 1.40
4830 19890 4.455533 CAGTTGTGTGCCTCTGCTTTATTA 59.544 41.667 0.00 0.00 38.71 0.98
4874 20085 2.355009 GCAACCCAAGCGCTGTTG 60.355 61.111 26.29 26.29 41.69 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 5640 5.004630 TCGGCGTAAATTTATGTAACTCACG 59.995 40.000 16.79 9.08 0.00 4.35
207 5696 0.179006 GAAGCCACTCCCCATCCATC 60.179 60.000 0.00 0.00 0.00 3.51
230 5723 1.226030 GTTCCAACCTTGGGACGTCG 61.226 60.000 9.92 0.00 46.28 5.12
305 5823 7.014518 TCCGAACGGAAGGAGTATAATATTTGA 59.985 37.037 13.65 0.00 42.05 2.69
333 5851 9.739276 ACATACATTCATTTCTTGGAAGAGTAA 57.261 29.630 0.00 0.00 36.22 2.24
336 5854 9.605275 TCTACATACATTCATTTCTTGGAAGAG 57.395 33.333 0.00 0.00 36.22 2.85
382 5900 9.236691 CGGAATTACTTGTCATAAAAATGGATG 57.763 33.333 0.00 0.00 0.00 3.51
383 5901 9.184523 TCGGAATTACTTGTCATAAAAATGGAT 57.815 29.630 0.00 0.00 0.00 3.41
384 5902 8.568676 TCGGAATTACTTGTCATAAAAATGGA 57.431 30.769 0.00 0.00 0.00 3.41
385 5903 9.072294 GTTCGGAATTACTTGTCATAAAAATGG 57.928 33.333 0.00 0.00 0.00 3.16
386 5904 8.785101 CGTTCGGAATTACTTGTCATAAAAATG 58.215 33.333 0.00 0.00 0.00 2.32
387 5905 7.966204 CCGTTCGGAATTACTTGTCATAAAAAT 59.034 33.333 5.19 0.00 0.00 1.82
388 5906 7.172875 TCCGTTCGGAATTACTTGTCATAAAAA 59.827 33.333 11.66 0.00 0.00 1.94
390 5908 6.164876 TCCGTTCGGAATTACTTGTCATAAA 58.835 36.000 11.66 0.00 0.00 1.40
391 5909 5.722263 TCCGTTCGGAATTACTTGTCATAA 58.278 37.500 11.66 0.00 0.00 1.90
393 5911 4.181578 CTCCGTTCGGAATTACTTGTCAT 58.818 43.478 14.79 0.00 33.41 3.06
394 5912 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
395 5913 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
396 5914 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
397 5915 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
398 5916 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
400 5918 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
401 5919 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
404 5922 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
405 5923 0.329261 TTCTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
406 5924 0.739561 CTTCTACTCCCTCCGTTCGG 59.260 60.000 4.74 4.74 0.00 4.30
407 5925 1.401199 GACTTCTACTCCCTCCGTTCG 59.599 57.143 0.00 0.00 0.00 3.95
408 5926 2.444421 TGACTTCTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
409 5927 2.599408 TGACTTCTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
410 5928 2.448453 CTTGACTTCTACTCCCTCCGT 58.552 52.381 0.00 0.00 0.00 4.69
411 5929 1.135333 GCTTGACTTCTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
412 5930 2.093921 GTGCTTGACTTCTACTCCCTCC 60.094 54.545 0.00 0.00 0.00 4.30
413 5931 2.829120 AGTGCTTGACTTCTACTCCCTC 59.171 50.000 0.00 0.00 0.00 4.30
414 5932 2.829120 GAGTGCTTGACTTCTACTCCCT 59.171 50.000 0.00 0.00 33.83 4.20
415 5933 2.563179 TGAGTGCTTGACTTCTACTCCC 59.437 50.000 0.00 0.00 37.54 4.30
416 5934 3.944055 TGAGTGCTTGACTTCTACTCC 57.056 47.619 0.00 0.00 37.54 3.85
417 5935 5.040635 GCTATGAGTGCTTGACTTCTACTC 58.959 45.833 0.00 0.00 38.52 2.59
418 5936 4.709397 AGCTATGAGTGCTTGACTTCTACT 59.291 41.667 0.00 0.00 37.52 2.57
419 5937 4.803088 CAGCTATGAGTGCTTGACTTCTAC 59.197 45.833 0.00 0.00 38.92 2.59
526 6044 2.171840 AGTTAGCTCTGGTGTCGATGT 58.828 47.619 0.00 0.00 0.00 3.06
553 6071 1.290203 CTGACGGATTCCATTGGTCG 58.710 55.000 1.86 5.89 0.00 4.79
568 6086 7.905493 GTGTGCTCTTATATAAAAACAGCTGAC 59.095 37.037 23.35 1.77 0.00 3.51
633 6151 6.403309 GGTTAGTAGCAAGCCTGATTGTAAAC 60.403 42.308 0.00 0.00 32.56 2.01
646 6167 5.447818 GCACTATGCTTTGGTTAGTAGCAAG 60.448 44.000 0.00 0.00 46.78 4.01
751 6272 0.969409 AATCAGGGCTTGCAGGCTTC 60.969 55.000 21.07 12.98 41.09 3.86
856 6402 1.899142 GAGAGTGAAGTTGAGGGAGCT 59.101 52.381 0.00 0.00 0.00 4.09
1118 6684 5.163723 CCAGCAATACAACTGGTGATTGTAG 60.164 44.000 0.00 3.10 46.95 2.74
1153 6719 3.713650 CCTGAAGGCGAGAAGGGA 58.286 61.111 0.00 0.00 0.00 4.20
1409 6993 3.267483 CCGATGAACTCCGGTATTTGTT 58.733 45.455 0.00 0.20 40.78 2.83
1497 7081 5.338632 TGTAAGTTGGAGAGATTACCCAGA 58.661 41.667 0.00 0.00 0.00 3.86
1697 7281 6.288294 TCGGAAAGATGAAGAACTTTCAGAA 58.712 36.000 15.59 4.88 45.89 3.02
1717 7301 4.501571 GCTACTTCTAAGATGGCAATCGGA 60.502 45.833 0.00 0.00 37.92 4.55
1801 7385 3.443681 GGTGTGCCATGCTTATGTAACTT 59.556 43.478 0.00 0.00 34.09 2.66
1806 7390 0.039472 TGGGTGTGCCATGCTTATGT 59.961 50.000 0.00 0.00 36.17 2.29
1871 7455 1.064758 ACGGGCCATAGAAAGCATTGA 60.065 47.619 4.39 0.00 0.00 2.57
1877 7461 2.017049 CTGGAAACGGGCCATAGAAAG 58.983 52.381 4.39 0.00 34.33 2.62
1933 7517 7.386059 CCCACAAGGTTATTTTCTGCTAAATT 58.614 34.615 0.00 0.00 0.00 1.82
1939 7523 2.298729 TGCCCACAAGGTTATTTTCTGC 59.701 45.455 0.00 0.00 38.26 4.26
2014 7598 2.019249 ACTCCCGTCGATATTGTTCGA 58.981 47.619 0.00 0.00 45.27 3.71
2026 7610 8.762426 GTTGAATAATTCTGTTATACTCCCGTC 58.238 37.037 0.00 0.00 0.00 4.79
2050 7634 3.495434 TGAACAACTGGGTAATCGGTT 57.505 42.857 0.00 0.00 36.75 4.44
2052 7636 4.069304 TCTTTGAACAACTGGGTAATCGG 58.931 43.478 0.00 0.00 0.00 4.18
2095 7679 4.281435 TCCAGTCAGATTGTTGTACGGTAA 59.719 41.667 0.00 0.00 0.00 2.85
2173 7757 3.450817 TGACCAGTGAGTTTGTTCTCAGA 59.549 43.478 0.00 0.00 43.76 3.27
2174 7758 3.797039 TGACCAGTGAGTTTGTTCTCAG 58.203 45.455 0.00 0.00 43.76 3.35
2234 7818 6.093633 CAGGTTATTAGAGTTAAGCACCAACC 59.906 42.308 0.00 0.00 31.52 3.77
2278 7863 5.011125 ACATAGCTAGACGTGATAAATGGCT 59.989 40.000 0.00 0.00 36.88 4.75
2364 7949 5.749462 AGAATCATTGTTAGACTGGAAGGG 58.251 41.667 0.00 0.00 39.30 3.95
2441 8026 9.842775 TTGATATATCAAGATTCTGCAAGTTCT 57.157 29.630 21.67 0.00 41.51 3.01
2448 8033 9.661187 CTTGTGTTTGATATATCAAGATTCTGC 57.339 33.333 23.61 13.41 46.34 4.26
2449 8034 9.661187 GCTTGTGTTTGATATATCAAGATTCTG 57.339 33.333 23.61 16.10 46.34 3.02
2739 8324 4.757149 GCCCCAGAGATCATGTTGTTATAC 59.243 45.833 0.00 0.00 0.00 1.47
2836 8421 3.938963 TCATTGACTAGGCAATCGGAAAC 59.061 43.478 21.38 0.00 36.39 2.78
2839 8424 2.766263 ACTCATTGACTAGGCAATCGGA 59.234 45.455 21.38 14.97 36.39 4.55
2943 8528 3.511540 AGATGAGTCGTGGACATTTCTGA 59.488 43.478 0.00 0.00 34.60 3.27
3007 8592 1.600058 AGCTTCTCCCCAATCCATGA 58.400 50.000 0.00 0.00 0.00 3.07
3103 8688 4.336713 GGCAAGGTCCAAATACTGAAGATC 59.663 45.833 0.00 0.00 0.00 2.75
3144 8729 9.295214 CAAGTAATAATAGATCTCGGTATGCTG 57.705 37.037 0.00 0.00 0.00 4.41
3167 8752 1.608055 TTGTGTCATGCCTGTCCAAG 58.392 50.000 0.00 0.00 0.00 3.61
3200 8785 3.921119 ACGCATGCTCAAGATCAAAAA 57.079 38.095 17.13 0.00 0.00 1.94
3202 8787 4.455533 AGTTAACGCATGCTCAAGATCAAA 59.544 37.500 17.13 0.00 0.00 2.69
3203 8788 4.002982 AGTTAACGCATGCTCAAGATCAA 58.997 39.130 17.13 0.00 0.00 2.57
3254 8857 5.064452 GTGGAATTCTCAGCATAGTCAACTG 59.936 44.000 5.23 0.00 0.00 3.16
3275 8878 2.094906 TGACCTTTCGTGAGTATCGTGG 60.095 50.000 0.00 0.00 38.61 4.94
3405 9008 6.777580 AGTTGTTCCATGATAAGTTCAGGTTT 59.222 34.615 0.00 0.00 37.89 3.27
3540 18465 1.079503 GGTTCAGGCGACTCAATGAC 58.920 55.000 0.00 0.00 40.21 3.06
3648 18573 1.774217 AGGAGGACCACAAAGGCCA 60.774 57.895 5.01 0.00 43.14 5.36
3910 18847 6.927936 TCTCATCTCAGCTTCTATGCATTAAC 59.072 38.462 3.54 0.00 34.99 2.01
3917 18857 4.022068 GGTCCTCTCATCTCAGCTTCTATG 60.022 50.000 0.00 0.00 0.00 2.23
3918 18858 4.151883 GGTCCTCTCATCTCAGCTTCTAT 58.848 47.826 0.00 0.00 0.00 1.98
3994 18934 9.447040 CTGAACATTGATTGATACATTCATGAC 57.553 33.333 0.00 0.00 33.34 3.06
4067 19026 1.451387 GCATACCAACCCCAGTCGG 60.451 63.158 0.00 0.00 0.00 4.79
4076 19035 6.146898 ACAATACGAAAAACAGCATACCAAC 58.853 36.000 0.00 0.00 0.00 3.77
4547 19566 6.414732 TGTATGGGTTCTTCTCAACTATTGG 58.585 40.000 0.00 0.00 0.00 3.16
4568 19593 7.165460 TCGATTTTCTCTCCATAGTGTTGTA 57.835 36.000 0.00 0.00 0.00 2.41
4592 19617 3.326297 ACCTCAGCTAGAGCAAAGACTTT 59.674 43.478 4.01 0.00 43.31 2.66
4629 19659 4.920927 ACAAAACAAACAAAACAGAGACCG 59.079 37.500 0.00 0.00 0.00 4.79
4874 20085 4.238514 CCTGCGCTAAGATAAGGATACAC 58.761 47.826 9.73 0.00 41.41 2.90


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

AutoCloner maintained by Alex Coulton.