Multiple sequence alignment - TraesCS4B01G317200

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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 TraesCS4B01G317200 chr4B 100.000 3578 0 0 1 3578 606910149 606906572 0.000000e+00 6608.0
1 TraesCS4B01G317200 chr4B 92.284 1918 117 15 892 2780 606867820 606865905 0.000000e+00 2693.0
2 TraesCS4B01G317200 chr4B 92.952 1816 115 10 974 2780 606828487 606826676 0.000000e+00 2632.0
3 TraesCS4B01G317200 chr4B 95.995 799 29 3 2780 3578 658554709 658555504 0.000000e+00 1295.0
4 TraesCS4B01G317200 chr4B 92.974 797 54 2 2782 3578 267659128 267659922 0.000000e+00 1160.0
5 TraesCS4B01G317200 chr4B 84.728 478 55 13 346 819 606869415 606868952 2.520000e-126 462.0
6 TraesCS4B01G317200 chr4D 94.751 2515 106 9 278 2779 479677171 479674670 0.000000e+00 3890.0
7 TraesCS4B01G317200 chr4D 90.887 2030 124 31 341 2328 479639438 479637428 0.000000e+00 2667.0
8 TraesCS4B01G317200 chr4D 96.263 1579 59 0 972 2550 479637327 479635749 0.000000e+00 2590.0
9 TraesCS4B01G317200 chr4D 89.437 142 12 3 36 176 479677307 479677168 3.670000e-40 176.0
10 TraesCS4B01G317200 chr4D 92.593 108 8 0 175 282 371212212 371212105 4.780000e-34 156.0
11 TraesCS4B01G317200 chr4A 94.248 2434 125 9 282 2711 686140840 686138418 0.000000e+00 3705.0
12 TraesCS4B01G317200 chr4A 91.327 2087 116 32 512 2550 685941526 685939457 0.000000e+00 2791.0
13 TraesCS4B01G317200 chr4A 91.826 1933 117 23 780 2677 686170408 686168482 0.000000e+00 2656.0
14 TraesCS4B01G317200 chr4A 94.743 1655 70 4 913 2550 685998857 685997203 0.000000e+00 2558.0
15 TraesCS4B01G317200 chr4A 80.477 461 48 22 278 725 686171148 686170717 7.460000e-82 315.0
16 TraesCS4B01G317200 chr4A 96.774 93 3 0 74 166 686140926 686140834 4.780000e-34 156.0
17 TraesCS4B01G317200 chr4A 90.123 81 6 2 4 82 686144202 686144122 1.760000e-18 104.0
18 TraesCS4B01G317200 chrUn 93.695 1824 99 8 972 2780 61732957 61731135 0.000000e+00 2717.0
19 TraesCS4B01G317200 chrUn 90.703 2033 123 35 339 2328 61735067 61733058 0.000000e+00 2647.0
20 TraesCS4B01G317200 chr7B 95.995 799 28 4 2780 3578 610641075 610641869 0.000000e+00 1295.0
21 TraesCS4B01G317200 chr7B 94.618 799 43 0 2780 3578 594132363 594133161 0.000000e+00 1238.0
22 TraesCS4B01G317200 chr5A 93.750 800 49 1 2779 3578 602045162 602044364 0.000000e+00 1199.0
23 TraesCS4B01G317200 chr5A 92.866 799 56 1 2780 3578 130313758 130312961 0.000000e+00 1158.0
24 TraesCS4B01G317200 chr2B 92.453 795 58 2 2784 3578 618881247 618880455 0.000000e+00 1134.0
25 TraesCS4B01G317200 chr1B 92.221 797 61 1 2782 3578 614170806 614170011 0.000000e+00 1127.0
26 TraesCS4B01G317200 chr1B 93.407 91 6 0 192 282 530049977 530050067 6.230000e-28 135.0
27 TraesCS4B01G317200 chr3B 92.405 790 59 1 2782 3571 50675180 50674392 0.000000e+00 1125.0
28 TraesCS4B01G317200 chr3B 91.667 108 9 0 175 282 371351472 371351365 2.230000e-32 150.0
29 TraesCS4B01G317200 chr3B 87.755 98 12 0 175 272 59221542 59221639 8.120000e-22 115.0
30 TraesCS4B01G317200 chr5B 88.983 118 3 1 175 282 517216988 517217105 1.730000e-28 137.0
31 TraesCS4B01G317200 chr6B 88.785 107 12 0 175 281 461267535 461267641 8.060000e-27 132.0
32 TraesCS4B01G317200 chr6B 85.714 119 7 1 173 281 260542968 260542850 2.260000e-22 117.0
33 TraesCS4B01G317200 chr7D 87.288 118 5 1 174 281 50726612 50726729 3.750000e-25 126.0
34 TraesCS4B01G317200 chr6D 95.946 74 3 0 211 284 382078450 382078523 1.740000e-23 121.0
35 TraesCS4B01G317200 chr3D 84.091 132 10 2 175 296 292034861 292034731 2.260000e-22 117.0
36 TraesCS4B01G317200 chr7A 84.034 119 9 1 174 282 200511784 200511902 4.890000e-19 106.0
37 TraesCS4B01G317200 chr5D 85.075 67 9 1 175 241 319101276 319101211 2.310000e-07 67.6


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 TraesCS4B01G317200 chr4B 606906572 606910149 3577 True 6608.000000 6608 100.0000 1 3578 1 chr4B.!!$R2 3577
1 TraesCS4B01G317200 chr4B 606826676 606828487 1811 True 2632.000000 2632 92.9520 974 2780 1 chr4B.!!$R1 1806
2 TraesCS4B01G317200 chr4B 606865905 606869415 3510 True 1577.500000 2693 88.5060 346 2780 2 chr4B.!!$R3 2434
3 TraesCS4B01G317200 chr4B 658554709 658555504 795 False 1295.000000 1295 95.9950 2780 3578 1 chr4B.!!$F2 798
4 TraesCS4B01G317200 chr4B 267659128 267659922 794 False 1160.000000 1160 92.9740 2782 3578 1 chr4B.!!$F1 796
5 TraesCS4B01G317200 chr4D 479635749 479639438 3689 True 2628.500000 2667 93.5750 341 2550 2 chr4D.!!$R2 2209
6 TraesCS4B01G317200 chr4D 479674670 479677307 2637 True 2033.000000 3890 92.0940 36 2779 2 chr4D.!!$R3 2743
7 TraesCS4B01G317200 chr4A 685939457 685941526 2069 True 2791.000000 2791 91.3270 512 2550 1 chr4A.!!$R1 2038
8 TraesCS4B01G317200 chr4A 685997203 685998857 1654 True 2558.000000 2558 94.7430 913 2550 1 chr4A.!!$R2 1637
9 TraesCS4B01G317200 chr4A 686168482 686171148 2666 True 1485.500000 2656 86.1515 278 2677 2 chr4A.!!$R4 2399
10 TraesCS4B01G317200 chr4A 686138418 686144202 5784 True 1321.666667 3705 93.7150 4 2711 3 chr4A.!!$R3 2707
11 TraesCS4B01G317200 chrUn 61731135 61735067 3932 True 2682.000000 2717 92.1990 339 2780 2 chrUn.!!$R1 2441
12 TraesCS4B01G317200 chr7B 610641075 610641869 794 False 1295.000000 1295 95.9950 2780 3578 1 chr7B.!!$F2 798
13 TraesCS4B01G317200 chr7B 594132363 594133161 798 False 1238.000000 1238 94.6180 2780 3578 1 chr7B.!!$F1 798
14 TraesCS4B01G317200 chr5A 602044364 602045162 798 True 1199.000000 1199 93.7500 2779 3578 1 chr5A.!!$R2 799
15 TraesCS4B01G317200 chr5A 130312961 130313758 797 True 1158.000000 1158 92.8660 2780 3578 1 chr5A.!!$R1 798
16 TraesCS4B01G317200 chr2B 618880455 618881247 792 True 1134.000000 1134 92.4530 2784 3578 1 chr2B.!!$R1 794
17 TraesCS4B01G317200 chr1B 614170011 614170806 795 True 1127.000000 1127 92.2210 2782 3578 1 chr1B.!!$R1 796
18 TraesCS4B01G317200 chr3B 50674392 50675180 788 True 1125.000000 1125 92.4050 2782 3571 1 chr3B.!!$R1 789

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
190 3397 0.113776 AAGTACACCCTCCGTCCTGA 59.886 55.000 0.00 0.00 0.00 3.86 F
191 3398 0.113776 AGTACACCCTCCGTCCTGAA 59.886 55.000 0.00 0.00 0.00 3.02 F
271 3478 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79 F
276 3483 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30 F
1041 7107 1.071436 GTGTTGAAAGCACTCGACGTC 60.071 52.381 5.18 5.18 33.04 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 7896 0.760945 AGAAGAGGCCCCAGGTATCG 60.761 60.000 0.00 0.0 0.00 2.92 R
1961 8027 4.464262 GGATCCACCCGATCTTGC 57.536 61.111 6.95 0.0 45.90 4.01 R
2250 8316 0.033601 TGAAGGTTGTGCTGTTGGGT 60.034 50.000 0.00 0.0 0.00 4.51 R
2286 8352 4.082523 CGGAGCCTCGCAGGGAAA 62.083 66.667 4.65 0.0 35.37 3.13 R
2988 9072 0.252881 ATCTCCCCAGTCCAAGCAGA 60.253 55.000 0.00 0.0 0.00 4.26 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
87 90 8.816894 TCCTACATTTCTAGAACAATGAGAACT 58.183 33.333 19.47 4.16 34.89 3.01
172 3379 5.828299 ATTTTGTTCTGAAACTGTCCGAA 57.172 34.783 0.00 0.00 36.30 4.30
173 3380 4.875544 TTTGTTCTGAAACTGTCCGAAG 57.124 40.909 0.00 0.00 36.30 3.79
174 3381 3.536956 TGTTCTGAAACTGTCCGAAGT 57.463 42.857 0.00 0.00 36.30 3.01
175 3382 4.659111 TGTTCTGAAACTGTCCGAAGTA 57.341 40.909 0.00 0.00 36.30 2.24
176 3383 4.365723 TGTTCTGAAACTGTCCGAAGTAC 58.634 43.478 0.00 0.00 36.30 2.73
177 3384 4.142116 TGTTCTGAAACTGTCCGAAGTACA 60.142 41.667 0.00 0.00 36.30 2.90
178 3385 3.973657 TCTGAAACTGTCCGAAGTACAC 58.026 45.455 0.00 0.00 0.00 2.90
179 3386 3.057734 CTGAAACTGTCCGAAGTACACC 58.942 50.000 0.00 0.00 0.00 4.16
180 3387 2.224113 TGAAACTGTCCGAAGTACACCC 60.224 50.000 0.00 0.00 0.00 4.61
181 3388 1.713297 AACTGTCCGAAGTACACCCT 58.287 50.000 0.00 0.00 0.00 4.34
182 3389 1.254954 ACTGTCCGAAGTACACCCTC 58.745 55.000 0.00 0.00 0.00 4.30
183 3390 0.531200 CTGTCCGAAGTACACCCTCC 59.469 60.000 0.00 0.00 0.00 4.30
184 3391 1.246056 TGTCCGAAGTACACCCTCCG 61.246 60.000 0.00 0.00 0.00 4.63
185 3392 1.075482 TCCGAAGTACACCCTCCGT 59.925 57.895 0.00 0.00 0.00 4.69
186 3393 0.962356 TCCGAAGTACACCCTCCGTC 60.962 60.000 0.00 0.00 0.00 4.79
187 3394 1.509923 CGAAGTACACCCTCCGTCC 59.490 63.158 0.00 0.00 0.00 4.79
188 3395 0.964358 CGAAGTACACCCTCCGTCCT 60.964 60.000 0.00 0.00 0.00 3.85
189 3396 0.531200 GAAGTACACCCTCCGTCCTG 59.469 60.000 0.00 0.00 0.00 3.86
190 3397 0.113776 AAGTACACCCTCCGTCCTGA 59.886 55.000 0.00 0.00 0.00 3.86
191 3398 0.113776 AGTACACCCTCCGTCCTGAA 59.886 55.000 0.00 0.00 0.00 3.02
192 3399 0.971386 GTACACCCTCCGTCCTGAAA 59.029 55.000 0.00 0.00 0.00 2.69
193 3400 1.553704 GTACACCCTCCGTCCTGAAAT 59.446 52.381 0.00 0.00 0.00 2.17
194 3401 1.946984 ACACCCTCCGTCCTGAAATA 58.053 50.000 0.00 0.00 0.00 1.40
195 3402 1.553704 ACACCCTCCGTCCTGAAATAC 59.446 52.381 0.00 0.00 0.00 1.89
196 3403 1.831736 CACCCTCCGTCCTGAAATACT 59.168 52.381 0.00 0.00 0.00 2.12
197 3404 2.236395 CACCCTCCGTCCTGAAATACTT 59.764 50.000 0.00 0.00 0.00 2.24
198 3405 2.236395 ACCCTCCGTCCTGAAATACTTG 59.764 50.000 0.00 0.00 0.00 3.16
199 3406 2.236395 CCCTCCGTCCTGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
200 3407 3.522553 CCTCCGTCCTGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
201 3408 3.056107 CCTCCGTCCTGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
202 3409 4.177026 CTCCGTCCTGAAATACTTGTCAG 58.823 47.826 0.00 0.00 40.84 3.51
203 3410 3.830178 TCCGTCCTGAAATACTTGTCAGA 59.170 43.478 2.28 0.00 43.32 3.27
204 3411 4.082190 TCCGTCCTGAAATACTTGTCAGAG 60.082 45.833 2.28 0.00 43.32 3.35
205 3412 4.082190 CCGTCCTGAAATACTTGTCAGAGA 60.082 45.833 2.28 0.00 43.32 3.10
206 3413 5.470368 CGTCCTGAAATACTTGTCAGAGAA 58.530 41.667 2.28 0.00 43.32 2.87
207 3414 5.926542 CGTCCTGAAATACTTGTCAGAGAAA 59.073 40.000 2.28 0.00 43.32 2.52
208 3415 6.591834 CGTCCTGAAATACTTGTCAGAGAAAT 59.408 38.462 2.28 0.00 43.32 2.17
209 3416 7.412346 CGTCCTGAAATACTTGTCAGAGAAATG 60.412 40.741 2.28 0.00 43.32 2.32
210 3417 6.881065 TCCTGAAATACTTGTCAGAGAAATGG 59.119 38.462 2.28 0.00 43.32 3.16
211 3418 6.881065 CCTGAAATACTTGTCAGAGAAATGGA 59.119 38.462 2.28 0.00 43.32 3.41
212 3419 7.555554 CCTGAAATACTTGTCAGAGAAATGGAT 59.444 37.037 2.28 0.00 43.32 3.41
213 3420 8.272545 TGAAATACTTGTCAGAGAAATGGATG 57.727 34.615 0.00 0.00 0.00 3.51
214 3421 7.884877 TGAAATACTTGTCAGAGAAATGGATGT 59.115 33.333 0.00 0.00 0.00 3.06
215 3422 9.383519 GAAATACTTGTCAGAGAAATGGATGTA 57.616 33.333 0.00 0.00 0.00 2.29
216 3423 9.911788 AAATACTTGTCAGAGAAATGGATGTAT 57.088 29.630 0.00 0.00 0.00 2.29
217 3424 9.911788 AATACTTGTCAGAGAAATGGATGTATT 57.088 29.630 0.00 0.00 0.00 1.89
218 3425 9.911788 ATACTTGTCAGAGAAATGGATGTATTT 57.088 29.630 0.00 0.00 33.19 1.40
219 3426 8.641498 ACTTGTCAGAGAAATGGATGTATTTT 57.359 30.769 0.00 0.00 30.78 1.82
220 3427 9.739276 ACTTGTCAGAGAAATGGATGTATTTTA 57.261 29.630 0.00 0.00 30.78 1.52
222 3429 9.739276 TTGTCAGAGAAATGGATGTATTTTAGT 57.261 29.630 0.00 0.00 30.78 2.24
223 3430 9.739276 TGTCAGAGAAATGGATGTATTTTAGTT 57.261 29.630 0.00 0.00 30.78 2.24
255 3462 8.450578 ACATCCAATTTTATCTATTTCTGCGA 57.549 30.769 0.00 0.00 0.00 5.10
256 3463 8.345565 ACATCCAATTTTATCTATTTCTGCGAC 58.654 33.333 0.00 0.00 0.00 5.19
257 3464 7.857734 TCCAATTTTATCTATTTCTGCGACA 57.142 32.000 0.00 0.00 0.00 4.35
258 3465 8.275015 TCCAATTTTATCTATTTCTGCGACAA 57.725 30.769 0.00 0.00 0.00 3.18
259 3466 8.397906 TCCAATTTTATCTATTTCTGCGACAAG 58.602 33.333 0.00 0.00 0.00 3.16
260 3467 8.184192 CCAATTTTATCTATTTCTGCGACAAGT 58.816 33.333 0.00 0.00 0.00 3.16
266 3473 6.903883 TCTATTTCTGCGACAAGTAATTCC 57.096 37.500 0.00 0.00 0.00 3.01
267 3474 4.600012 ATTTCTGCGACAAGTAATTCCG 57.400 40.909 0.00 0.00 0.00 4.30
268 3475 2.004583 TCTGCGACAAGTAATTCCGG 57.995 50.000 0.00 0.00 0.00 5.14
269 3476 1.546923 TCTGCGACAAGTAATTCCGGA 59.453 47.619 0.00 0.00 0.00 5.14
270 3477 1.659098 CTGCGACAAGTAATTCCGGAC 59.341 52.381 1.83 0.00 0.00 4.79
271 3478 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
272 3479 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
273 3480 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
274 3481 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
275 3482 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
276 3483 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
367 3584 3.808265 GCAGGACCTAGCATTGCATATCA 60.808 47.826 11.91 0.00 34.99 2.15
374 3591 7.972277 GGACCTAGCATTGCATATCAATTTATG 59.028 37.037 11.91 0.00 42.48 1.90
467 3688 6.437477 CCTGCCATACCATGTAGTTATAGAGA 59.563 42.308 0.00 0.00 0.00 3.10
468 3689 7.363355 CCTGCCATACCATGTAGTTATAGAGAG 60.363 44.444 0.00 0.00 0.00 3.20
469 3690 6.437477 TGCCATACCATGTAGTTATAGAGAGG 59.563 42.308 0.00 0.00 0.00 3.69
470 3691 6.437793 GCCATACCATGTAGTTATAGAGAGGT 59.562 42.308 0.00 0.00 0.00 3.85
802 4317 5.954434 TGACTCCGCGTATATTTTTGTAC 57.046 39.130 4.92 0.00 0.00 2.90
908 5486 2.284754 TGTGCCTTCACCTTGCATTA 57.715 45.000 0.00 0.00 42.46 1.90
940 5529 7.281774 GCCTATATATACGTACTAGAAGCACCA 59.718 40.741 0.00 0.00 0.00 4.17
945 5534 4.267349 ACGTACTAGAAGCACCAAACAT 57.733 40.909 0.00 0.00 0.00 2.71
1041 7107 1.071436 GTGTTGAAAGCACTCGACGTC 60.071 52.381 5.18 5.18 33.04 4.34
1272 7338 1.376553 GCTCTTCTTCGGCTGGCTT 60.377 57.895 0.00 0.00 0.00 4.35
1275 7341 2.672996 TTCTTCGGCTGGCTTGGC 60.673 61.111 0.00 0.00 0.00 4.52
1552 7618 3.597377 TTGGTACTATCGTCACGATCG 57.403 47.619 17.88 13.51 43.45 3.69
1665 7731 1.570813 GCATCATCGTCATGTTCGGA 58.429 50.000 11.51 4.63 0.00 4.55
1668 7734 2.734276 TCATCGTCATGTTCGGAACA 57.266 45.000 24.32 24.32 46.94 3.18
1681 7747 4.796495 GAACAATCCCGGCCGCCT 62.796 66.667 22.85 2.45 0.00 5.52
1692 7758 1.745320 CGGCCGCCTTGACCTACTAT 61.745 60.000 14.67 0.00 0.00 2.12
1758 7824 2.896801 CGGCAACACGAAGCAAGCT 61.897 57.895 0.00 0.00 35.47 3.74
1794 7860 3.307691 CCAAGGTGCTCAACAAGGAGATA 60.308 47.826 0.00 0.00 37.05 1.98
1809 7875 5.352700 AGGAGATATCAGAGGAGGATGTT 57.647 43.478 5.32 0.00 0.00 2.71
1861 7927 1.551452 CCTCTTCTCCCGACAGTTCT 58.449 55.000 0.00 0.00 0.00 3.01
2175 8241 1.933500 GCAATCGCCATACCGTACGAT 60.934 52.381 18.76 0.25 46.43 3.73
2202 8268 1.344953 TGAAGCCAGGACACCACACT 61.345 55.000 0.00 0.00 0.00 3.55
2247 8313 3.945285 TCACTTTCTTCTTCGCCAACTTT 59.055 39.130 0.00 0.00 0.00 2.66
2286 8352 1.522355 CATCGTGCCAGCCGAGATT 60.522 57.895 8.69 0.00 37.81 2.40
2313 8379 2.607750 AGGCTCCGGTCCACATGT 60.608 61.111 15.84 0.00 0.00 3.21
2316 8382 1.221840 GCTCCGGTCCACATGTCAT 59.778 57.895 0.00 0.00 0.00 3.06
2373 8439 4.440127 GGCGCGTTCGGGTTCCTA 62.440 66.667 8.43 0.00 35.95 2.94
2696 8766 8.226819 TCTGAATTTGTTGTGTTGTAATGGTA 57.773 30.769 0.00 0.00 0.00 3.25
2719 8789 1.961793 ATGTAATGCGTTGGCCGTAT 58.038 45.000 0.08 0.00 44.15 3.06
2726 8796 1.693083 GCGTTGGCCGTATCAGTGAC 61.693 60.000 0.00 0.00 39.32 3.67
2733 8803 2.866762 GGCCGTATCAGTGACTCAATTC 59.133 50.000 0.00 0.00 0.00 2.17
2897 8981 0.036952 CAGCCCAGACAACACGAGAT 60.037 55.000 0.00 0.00 0.00 2.75
2988 9072 2.347490 CCACCAGCGCCTAAGTGT 59.653 61.111 2.29 0.00 0.00 3.55
3093 9177 2.615912 GTCAATAATCTCCACTGCTGCC 59.384 50.000 0.00 0.00 0.00 4.85
3220 9304 2.008242 CCCACCCAAAACAATCTCCA 57.992 50.000 0.00 0.00 0.00 3.86
3317 9401 6.118170 CCAAGATCTGATACAACACCAGAAT 58.882 40.000 0.00 0.00 39.94 2.40
3338 9422 7.549134 CAGAATAGATTAGCCAACACACAGTTA 59.451 37.037 0.00 0.00 38.74 2.24
3354 9438 9.120538 ACACACAGTTAAAGAAAATATGTGACT 57.879 29.630 9.20 0.00 39.03 3.41
3411 9495 3.061848 CCGGGCCATTTCGCTTGT 61.062 61.111 4.39 0.00 0.00 3.16
3505 9589 1.493871 AGCCCTCCAGATCCAATTGAG 59.506 52.381 7.12 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 3301 6.785076 TGGTCATCTGTTACATAAAAAGGGA 58.215 36.000 0.00 0.00 0.00 4.20
169 3376 0.964358 AGGACGGAGGGTGTACTTCG 60.964 60.000 0.00 0.00 44.95 3.79
172 3379 0.113776 TTCAGGACGGAGGGTGTACT 59.886 55.000 0.00 0.00 0.00 2.73
173 3380 0.971386 TTTCAGGACGGAGGGTGTAC 59.029 55.000 0.00 0.00 0.00 2.90
174 3381 1.946984 ATTTCAGGACGGAGGGTGTA 58.053 50.000 0.00 0.00 0.00 2.90
175 3382 1.553704 GTATTTCAGGACGGAGGGTGT 59.446 52.381 0.00 0.00 0.00 4.16
176 3383 1.831736 AGTATTTCAGGACGGAGGGTG 59.168 52.381 0.00 0.00 0.00 4.61
177 3384 2.236395 CAAGTATTTCAGGACGGAGGGT 59.764 50.000 0.00 0.00 0.00 4.34
178 3385 2.236395 ACAAGTATTTCAGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
179 3386 3.056107 TGACAAGTATTTCAGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
180 3387 4.082190 TCTGACAAGTATTTCAGGACGGAG 60.082 45.833 0.00 0.00 39.86 4.63
181 3388 3.830178 TCTGACAAGTATTTCAGGACGGA 59.170 43.478 0.00 0.00 39.86 4.69
182 3389 4.082190 TCTCTGACAAGTATTTCAGGACGG 60.082 45.833 0.00 0.00 39.86 4.79
183 3390 5.060662 TCTCTGACAAGTATTTCAGGACG 57.939 43.478 0.00 0.00 39.86 4.79
184 3391 7.148340 CCATTTCTCTGACAAGTATTTCAGGAC 60.148 40.741 0.00 0.00 39.86 3.85
185 3392 6.881065 CCATTTCTCTGACAAGTATTTCAGGA 59.119 38.462 0.00 0.00 39.86 3.86
186 3393 6.881065 TCCATTTCTCTGACAAGTATTTCAGG 59.119 38.462 0.00 0.00 39.86 3.86
187 3394 7.912056 TCCATTTCTCTGACAAGTATTTCAG 57.088 36.000 0.00 0.00 40.65 3.02
188 3395 7.884877 ACATCCATTTCTCTGACAAGTATTTCA 59.115 33.333 0.00 0.00 0.00 2.69
189 3396 8.273780 ACATCCATTTCTCTGACAAGTATTTC 57.726 34.615 0.00 0.00 0.00 2.17
190 3397 9.911788 ATACATCCATTTCTCTGACAAGTATTT 57.088 29.630 0.00 0.00 0.00 1.40
191 3398 9.911788 AATACATCCATTTCTCTGACAAGTATT 57.088 29.630 0.00 0.00 0.00 1.89
192 3399 9.911788 AAATACATCCATTTCTCTGACAAGTAT 57.088 29.630 0.00 0.00 0.00 2.12
193 3400 9.739276 AAAATACATCCATTTCTCTGACAAGTA 57.261 29.630 0.00 0.00 0.00 2.24
194 3401 8.641498 AAAATACATCCATTTCTCTGACAAGT 57.359 30.769 0.00 0.00 0.00 3.16
196 3403 9.739276 ACTAAAATACATCCATTTCTCTGACAA 57.261 29.630 0.00 0.00 0.00 3.18
197 3404 9.739276 AACTAAAATACATCCATTTCTCTGACA 57.261 29.630 0.00 0.00 0.00 3.58
229 3436 9.554395 TCGCAGAAATAGATAAAATTGGATGTA 57.446 29.630 0.00 0.00 0.00 2.29
230 3437 8.345565 GTCGCAGAAATAGATAAAATTGGATGT 58.654 33.333 0.00 0.00 39.69 3.06
231 3438 8.344831 TGTCGCAGAAATAGATAAAATTGGATG 58.655 33.333 0.00 0.00 39.69 3.51
232 3439 8.450578 TGTCGCAGAAATAGATAAAATTGGAT 57.549 30.769 0.00 0.00 39.69 3.41
233 3440 7.857734 TGTCGCAGAAATAGATAAAATTGGA 57.142 32.000 0.00 0.00 39.69 3.53
234 3441 8.184192 ACTTGTCGCAGAAATAGATAAAATTGG 58.816 33.333 0.00 0.00 39.69 3.16
240 3447 9.042008 GGAATTACTTGTCGCAGAAATAGATAA 57.958 33.333 0.00 0.00 39.69 1.75
241 3448 7.381408 CGGAATTACTTGTCGCAGAAATAGATA 59.619 37.037 0.00 0.00 39.69 1.98
242 3449 6.201044 CGGAATTACTTGTCGCAGAAATAGAT 59.799 38.462 0.00 0.00 39.69 1.98
243 3450 5.518847 CGGAATTACTTGTCGCAGAAATAGA 59.481 40.000 0.00 0.00 39.69 1.98
244 3451 5.276868 CCGGAATTACTTGTCGCAGAAATAG 60.277 44.000 0.00 0.00 39.69 1.73
245 3452 4.569162 CCGGAATTACTTGTCGCAGAAATA 59.431 41.667 0.00 0.00 39.69 1.40
246 3453 3.374058 CCGGAATTACTTGTCGCAGAAAT 59.626 43.478 0.00 0.00 39.69 2.17
247 3454 2.739913 CCGGAATTACTTGTCGCAGAAA 59.260 45.455 0.00 0.00 39.69 2.52
248 3455 2.028839 TCCGGAATTACTTGTCGCAGAA 60.029 45.455 0.00 0.00 39.69 3.02
249 3456 1.546923 TCCGGAATTACTTGTCGCAGA 59.453 47.619 0.00 0.00 0.00 4.26
250 3457 1.659098 GTCCGGAATTACTTGTCGCAG 59.341 52.381 5.23 0.00 0.00 5.18
251 3458 1.717194 GTCCGGAATTACTTGTCGCA 58.283 50.000 5.23 0.00 0.00 5.10
252 3459 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
253 3460 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
254 3461 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
255 3462 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
256 3463 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
257 3464 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
258 3465 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
259 3466 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
260 3467 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
261 3468 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
262 3469 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
263 3470 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
264 3471 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
265 3472 0.754217 TTCATACTCCCTCCGTCCGG 60.754 60.000 0.00 0.00 0.00 5.14
266 3473 1.108776 TTTCATACTCCCTCCGTCCG 58.891 55.000 0.00 0.00 0.00 4.79
267 3474 3.840124 AATTTCATACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
268 3475 5.786264 TCTAATTTCATACTCCCTCCGTC 57.214 43.478 0.00 0.00 0.00 4.79
269 3476 6.749036 AATCTAATTTCATACTCCCTCCGT 57.251 37.500 0.00 0.00 0.00 4.69
270 3477 9.209175 CTAAAATCTAATTTCATACTCCCTCCG 57.791 37.037 0.00 0.00 0.00 4.63
271 3478 9.004717 GCTAAAATCTAATTTCATACTCCCTCC 57.995 37.037 0.00 0.00 0.00 4.30
272 3479 9.561069 TGCTAAAATCTAATTTCATACTCCCTC 57.439 33.333 0.00 0.00 0.00 4.30
273 3480 9.920946 TTGCTAAAATCTAATTTCATACTCCCT 57.079 29.630 0.00 0.00 0.00 4.20
274 3481 9.952188 GTTGCTAAAATCTAATTTCATACTCCC 57.048 33.333 0.00 0.00 0.00 4.30
436 3657 3.737559 ACATGGTATGGCAGGAAGAAA 57.262 42.857 0.00 0.00 33.60 2.52
467 3688 4.463050 TGGGGTTAATTTGTTCTCACCT 57.537 40.909 0.00 0.00 0.00 4.00
468 3689 5.016831 AGATGGGGTTAATTTGTTCTCACC 58.983 41.667 0.00 0.00 0.00 4.02
469 3690 5.946377 AGAGATGGGGTTAATTTGTTCTCAC 59.054 40.000 0.00 0.00 32.68 3.51
470 3691 5.945784 CAGAGATGGGGTTAATTTGTTCTCA 59.054 40.000 0.00 0.00 32.68 3.27
802 4317 6.147821 GGATTGTACATTATCAGGATGGTTCG 59.852 42.308 9.25 0.00 36.16 3.95
940 5529 4.023707 GCTCTCTTGTTGTGTGCTATGTTT 60.024 41.667 0.00 0.00 0.00 2.83
945 5534 2.759191 CTGCTCTCTTGTTGTGTGCTA 58.241 47.619 0.00 0.00 32.12 3.49
1041 7107 1.491563 GTACAGTTGCGTCTTGGCG 59.508 57.895 0.00 0.00 35.06 5.69
1552 7618 1.872679 GGAATGCGGACGAGACGAC 60.873 63.158 0.00 0.00 0.00 4.34
1665 7731 4.360405 AAGGCGGCCGGGATTGTT 62.360 61.111 29.38 0.00 0.00 2.83
1668 7734 4.796495 GTCAAGGCGGCCGGGATT 62.796 66.667 29.38 0.00 0.00 3.01
1681 7747 2.169561 TCATGCGCCAATAGTAGGTCAA 59.830 45.455 4.18 0.00 0.00 3.18
1758 7824 3.619733 GCACCTTGGACATGTCTGATGTA 60.620 47.826 24.50 3.09 31.52 2.29
1794 7860 2.293452 ACCCTGAACATCCTCCTCTGAT 60.293 50.000 0.00 0.00 0.00 2.90
1830 7896 0.760945 AGAAGAGGCCCCAGGTATCG 60.761 60.000 0.00 0.00 0.00 2.92
1961 8027 4.464262 GGATCCACCCGATCTTGC 57.536 61.111 6.95 0.00 45.90 4.01
2202 8268 3.484524 GTAGAGCACGACGAAACCA 57.515 52.632 0.00 0.00 0.00 3.67
2247 8313 1.454847 GGTTGTGCTGTTGGGTCCA 60.455 57.895 0.00 0.00 0.00 4.02
2250 8316 0.033601 TGAAGGTTGTGCTGTTGGGT 60.034 50.000 0.00 0.00 0.00 4.51
2286 8352 4.082523 CGGAGCCTCGCAGGGAAA 62.083 66.667 4.65 0.00 35.37 3.13
2313 8379 1.613925 GTAGCGGCAGAGATACCATGA 59.386 52.381 1.45 0.00 0.00 3.07
2373 8439 1.068083 CTGGTCCTGCGACGCATAT 59.932 57.895 24.71 0.00 40.17 1.78
2526 8592 0.941542 CGCCAACGTTCTCCTTTGAA 59.058 50.000 0.00 0.00 33.53 2.69
2529 8595 1.219522 CGTCGCCAACGTTCTCCTTT 61.220 55.000 0.00 0.00 46.42 3.11
2696 8766 1.402194 CGGCCAACGCATTACATTGTT 60.402 47.619 2.24 0.00 36.38 2.83
2744 8828 1.580059 TGGGAGGGAATACAGGTGAC 58.420 55.000 0.00 0.00 0.00 3.67
2897 8981 6.378745 TGGGAGCCATGTACTTAGACTATTA 58.621 40.000 0.00 0.00 0.00 0.98
2988 9072 0.252881 ATCTCCCCAGTCCAAGCAGA 60.253 55.000 0.00 0.00 0.00 4.26
3059 9143 7.791766 TGGAGATTATTGACTAAGGAGGAAGAT 59.208 37.037 0.00 0.00 0.00 2.40
3128 9212 4.138290 TCGAACATGTTTTCCCTGCTAAA 58.862 39.130 13.36 0.00 0.00 1.85
3220 9304 1.955458 TTCTTTGGTTGGGGCCCAGT 61.955 55.000 27.05 0.00 33.81 4.00
3317 9401 7.446769 TCTTTAACTGTGTGTTGGCTAATCTA 58.553 34.615 0.00 0.00 39.55 1.98
3338 9422 9.566432 AGAGAAGACAAGTCACATATTTTCTTT 57.434 29.630 2.72 0.00 0.00 2.52
3354 9438 5.545063 TTGTGTGGTATGAGAGAAGACAA 57.455 39.130 0.00 0.00 0.00 3.18
3411 9495 1.890876 CCGACAGGTGACCAAATTCA 58.109 50.000 3.63 0.00 0.00 2.57
3505 9589 1.228459 GGGTCCACCACCTCCAAAC 60.228 63.158 0.00 0.00 45.95 2.93


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

AutoCloner maintained by Alex Coulton.