Multiple sequence alignment - TraesCS2B01G251600

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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 TraesCS2B01G251600 chr2B 100.000 1967 0 0 773 2739 263832143 263834109 0.000000e+00 3633.0
1 TraesCS2B01G251600 chr2B 96.224 1748 55 3 995 2739 772923892 772922153 0.000000e+00 2852.0
2 TraesCS2B01G251600 chr2B 100.000 495 0 0 1 495 263831371 263831865 0.000000e+00 915.0
3 TraesCS2B01G251600 chr2B 93.697 476 26 2 1031 1506 714782686 714782215 0.000000e+00 710.0
4 TraesCS2B01G251600 chr2B 96.279 430 10 4 1 429 772924919 772924495 0.000000e+00 701.0
5 TraesCS2B01G251600 chr2B 88.235 136 4 3 2616 2739 106852006 106852141 4.720000e-33 152.0
6 TraesCS2B01G251600 chr2B 97.143 35 0 1 462 495 772924256 772924222 1.060000e-04 58.4
7 TraesCS2B01G251600 chr2A 96.246 1971 70 3 773 2739 687889658 687891628 0.000000e+00 3227.0
8 TraesCS2B01G251600 chr2A 95.689 1786 67 7 961 2739 485199712 485201494 0.000000e+00 2863.0
9 TraesCS2B01G251600 chr2A 95.337 1780 74 6 968 2739 485220280 485222058 0.000000e+00 2819.0
10 TraesCS2B01G251600 chr2A 93.151 511 24 4 1003 1506 724520798 724520292 0.000000e+00 739.0
11 TraesCS2B01G251600 chr2A 89.421 397 21 8 1504 1880 724520239 724519844 5.300000e-132 481.0
12 TraesCS2B01G251600 chr2A 96.071 280 10 1 2008 2286 724518957 724518678 3.220000e-124 455.0
13 TraesCS2B01G251600 chr2A 93.421 228 14 1 774 1000 92185313 92185540 1.220000e-88 337.0
14 TraesCS2B01G251600 chr2A 88.316 291 20 5 2332 2621 724518683 724518406 1.220000e-88 337.0
15 TraesCS2B01G251600 chr2A 94.326 141 7 1 1873 2012 724519176 724519036 5.940000e-52 215.0
16 TraesCS2B01G251600 chr2A 95.122 41 2 0 443 483 580600573 580600613 6.330000e-07 65.8
17 TraesCS2B01G251600 chr6B 96.215 1770 63 3 974 2739 95969819 95971588 0.000000e+00 2894.0
18 TraesCS2B01G251600 chr6B 94.366 497 19 4 1 495 464517328 464517817 0.000000e+00 754.0
19 TraesCS2B01G251600 chr6B 95.373 389 14 2 1 385 95968647 95969035 1.390000e-172 616.0
20 TraesCS2B01G251600 chr6B 96.257 374 12 2 1 373 91948351 91948723 1.800000e-171 612.0
21 TraesCS2B01G251600 chr2D 91.888 752 41 8 1876 2622 590151578 590150842 0.000000e+00 1033.0
22 TraesCS2B01G251600 chr2D 92.070 454 25 8 1053 1506 590153130 590152688 1.790000e-176 628.0
23 TraesCS2B01G251600 chr2D 96.042 379 12 2 1504 1880 590152635 590152258 5.010000e-172 614.0
24 TraesCS2B01G251600 chr5B 94.378 498 18 5 1 495 676287485 676286995 0.000000e+00 756.0
25 TraesCS2B01G251600 chr1A 92.000 500 19 15 2 495 566574123 566574607 0.000000e+00 682.0
26 TraesCS2B01G251600 chr1A 92.140 229 15 3 773 1000 66228577 66228803 1.220000e-83 320.0
27 TraesCS2B01G251600 chr1A 82.569 109 13 6 392 495 23085607 23085714 1.040000e-14 91.6
28 TraesCS2B01G251600 chr5A 91.583 499 22 15 2 495 702266133 702266616 0.000000e+00 671.0
29 TraesCS2B01G251600 chr5A 93.421 228 14 1 774 1000 511921495 511921268 1.220000e-88 337.0
30 TraesCS2B01G251600 chr5A 91.667 228 16 2 774 1000 573419272 573419497 2.050000e-81 313.0
31 TraesCS2B01G251600 chr3A 91.583 499 22 14 2 495 701655810 701655327 0.000000e+00 671.0
32 TraesCS2B01G251600 chr3A 94.298 228 12 1 774 1000 207114908 207114681 5.610000e-92 348.0
33 TraesCS2B01G251600 chr3A 95.169 207 10 0 774 980 189292200 189292406 7.310000e-86 327.0
34 TraesCS2B01G251600 chr1B 96.791 374 11 1 1 373 585353396 585353769 8.330000e-175 623.0
35 TraesCS2B01G251600 chr6A 94.298 228 12 1 774 1000 17431364 17431137 5.610000e-92 348.0
36 TraesCS2B01G251600 chr6A 93.860 228 13 1 774 1000 413092674 413092901 2.610000e-90 342.0
37 TraesCS2B01G251600 chr6A 88.125 160 12 2 337 495 1326732 1326885 1.680000e-42 183.0
38 TraesCS2B01G251600 chr4B 94.805 77 3 1 2664 2739 96936251 96936175 4.790000e-23 119.0
39 TraesCS2B01G251600 chr4B 100.000 51 0 0 2616 2666 96936388 96936338 8.070000e-16 95.3
40 TraesCS2B01G251600 chr4A 93.421 76 5 0 2664 2739 515001623 515001548 2.230000e-21 113.0
41 TraesCS2B01G251600 chr4A 100.000 51 0 0 2616 2666 515001764 515001714 8.070000e-16 95.3
42 TraesCS2B01G251600 chr4D 92.105 76 6 0 2664 2739 66316462 66316387 1.040000e-19 108.0
43 TraesCS2B01G251600 chr4D 100.000 51 0 0 2616 2666 66316599 66316549 8.070000e-16 95.3
44 TraesCS2B01G251600 chr1D 96.296 54 1 1 443 495 393125524 393125577 1.350000e-13 87.9


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 TraesCS2B01G251600 chr2B 263831371 263834109 2738 False 2274.000000 3633 100.000000 1 2739 2 chr2B.!!$F2 2738
1 TraesCS2B01G251600 chr2B 772922153 772924919 2766 True 1203.800000 2852 96.548667 1 2739 3 chr2B.!!$R2 2738
2 TraesCS2B01G251600 chr2A 687889658 687891628 1970 False 3227.000000 3227 96.246000 773 2739 1 chr2A.!!$F5 1966
3 TraesCS2B01G251600 chr2A 485199712 485201494 1782 False 2863.000000 2863 95.689000 961 2739 1 chr2A.!!$F2 1778
4 TraesCS2B01G251600 chr2A 485220280 485222058 1778 False 2819.000000 2819 95.337000 968 2739 1 chr2A.!!$F3 1771
5 TraesCS2B01G251600 chr2A 724518406 724520798 2392 True 445.400000 739 92.257000 1003 2621 5 chr2A.!!$R1 1618
6 TraesCS2B01G251600 chr6B 95968647 95971588 2941 False 1755.000000 2894 95.794000 1 2739 2 chr6B.!!$F3 2738
7 TraesCS2B01G251600 chr2D 590150842 590153130 2288 True 758.333333 1033 93.333333 1053 2622 3 chr2D.!!$R1 1569

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
491 857 0.031616 GTCTCCCACCATCTCCCTCT 60.032 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 3669 0.315886 ACAGAACACGTATGTCGGCA 59.684 50.0 0.0 0.0 44.69 5.69 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
80 81 6.349243 TGAGCACTGAAAAATGGAATGAAT 57.651 33.333 0.00 0.00 0.00 2.57
311 318 4.907875 TCTTTCTTTCTTTCTCTCCCTCCA 59.092 41.667 0.00 0.00 0.00 3.86
395 403 1.597461 CCACCCTCGTCCTTTCCTC 59.403 63.158 0.00 0.00 0.00 3.71
460 826 1.305381 CCACCGTCCTTCCCTCTCT 60.305 63.158 0.00 0.00 0.00 3.10
489 855 0.326048 CTGTCTCCCACCATCTCCCT 60.326 60.000 0.00 0.00 0.00 4.20
490 856 0.325671 TGTCTCCCACCATCTCCCTC 60.326 60.000 0.00 0.00 0.00 4.30
491 857 0.031616 GTCTCCCACCATCTCCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
492 858 0.263172 TCTCCCACCATCTCCCTCTC 59.737 60.000 0.00 0.00 0.00 3.20
880 1251 4.179599 CTCTCCCCTCCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
910 1281 1.202940 AGATCCGATCTCCCATCGACA 60.203 52.381 4.96 0.00 43.59 4.35
929 1300 0.641601 ATCCTCCTTCCTCCTGCTCT 59.358 55.000 0.00 0.00 0.00 4.09
980 1351 4.155733 CATCCCACCACCGCGCTA 62.156 66.667 5.56 0.00 0.00 4.26
1231 1614 2.990479 GACGACCCCATTCTGGCT 59.010 61.111 0.00 0.00 35.79 4.75
1362 1745 1.807814 ATATGGCCCTCTTCGAACCT 58.192 50.000 0.00 0.00 0.00 3.50
1390 1773 6.296374 CCCACATTTTTGTCCAAATCCCTTAT 60.296 38.462 0.00 0.00 0.00 1.73
1495 1878 2.165998 GCTCAAGGATTTGAAGCTGGT 58.834 47.619 0.00 0.00 42.48 4.00
1688 2129 2.102252 GGCACTGTTGATCCACCAAAAA 59.898 45.455 0.00 0.00 0.00 1.94
1819 2269 7.491682 AGTCATGTTTTAGTTTGACTTTGCAT 58.508 30.769 0.00 0.00 44.77 3.96
1842 2300 8.777413 GCATTGTGTATTGAATAGCTGAATCTA 58.223 33.333 0.00 0.00 0.00 1.98
2049 3275 8.091449 AGCTAAGGAGAATATAATGTTCGAAGG 58.909 37.037 0.00 0.00 0.00 3.46
2229 3456 5.175090 TGTCTGATATAACGAGAGCACTG 57.825 43.478 0.00 0.00 0.00 3.66
2390 3621 7.395190 TCAACTAATTTATTGCTGTGCAGAT 57.605 32.000 3.02 0.00 40.61 2.90
2435 3669 9.687210 GGGAAAAATAAACTGAGAAAATTACGT 57.313 29.630 0.00 0.00 0.00 3.57
2694 3928 9.445878 ACATCGATTCTTATCATGCATAATCTT 57.554 29.630 13.17 2.01 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
345 353 1.585895 GAAGAGAGGGGCTAGGGTTT 58.414 55.000 0.00 0.00 0.00 3.27
385 393 0.974383 TGAAGGACGGAGGAAAGGAC 59.026 55.000 0.00 0.00 0.00 3.85
395 403 2.107141 GGCGGATCTGAAGGACGG 59.893 66.667 5.48 0.00 0.00 4.79
430 438 4.752879 CGGTGGTAGTGGCGGTGG 62.753 72.222 0.00 0.00 0.00 4.61
431 439 3.927163 GACGGTGGTAGTGGCGGTG 62.927 68.421 0.00 0.00 0.00 4.94
432 440 3.688159 GACGGTGGTAGTGGCGGT 61.688 66.667 0.00 0.00 0.00 5.68
433 441 4.446413 GGACGGTGGTAGTGGCGG 62.446 72.222 0.00 0.00 0.00 6.13
434 442 2.830704 GAAGGACGGTGGTAGTGGCG 62.831 65.000 0.00 0.00 0.00 5.69
435 443 1.079336 GAAGGACGGTGGTAGTGGC 60.079 63.158 0.00 0.00 0.00 5.01
436 444 1.595357 GGAAGGACGGTGGTAGTGG 59.405 63.158 0.00 0.00 0.00 4.00
437 445 0.903454 AGGGAAGGACGGTGGTAGTG 60.903 60.000 0.00 0.00 0.00 2.74
438 446 0.614134 GAGGGAAGGACGGTGGTAGT 60.614 60.000 0.00 0.00 0.00 2.73
439 447 0.324460 AGAGGGAAGGACGGTGGTAG 60.324 60.000 0.00 0.00 0.00 3.18
440 448 0.324091 GAGAGGGAAGGACGGTGGTA 60.324 60.000 0.00 0.00 0.00 3.25
441 449 1.609794 GAGAGGGAAGGACGGTGGT 60.610 63.158 0.00 0.00 0.00 4.16
442 450 1.305381 AGAGAGGGAAGGACGGTGG 60.305 63.158 0.00 0.00 0.00 4.61
443 451 1.893786 CAGAGAGGGAAGGACGGTG 59.106 63.158 0.00 0.00 0.00 4.94
444 452 1.985116 GCAGAGAGGGAAGGACGGT 60.985 63.158 0.00 0.00 0.00 4.83
445 453 2.726351 GGCAGAGAGGGAAGGACGG 61.726 68.421 0.00 0.00 0.00 4.79
446 454 1.671901 GAGGCAGAGAGGGAAGGACG 61.672 65.000 0.00 0.00 0.00 4.79
460 826 3.071206 GGAGACAGAGGCGAGGCA 61.071 66.667 0.00 0.00 0.00 4.75
904 1275 1.219213 AGGAGGAAGGAGGATGTCGAT 59.781 52.381 0.00 0.00 0.00 3.59
910 1281 0.641601 AGAGCAGGAGGAAGGAGGAT 59.358 55.000 0.00 0.00 0.00 3.24
943 1314 0.187361 TTGGTTGGAGGTTGGAAGGG 59.813 55.000 0.00 0.00 0.00 3.95
980 1351 4.974438 TTGGAGGGAGGGCGTGGT 62.974 66.667 0.00 0.00 0.00 4.16
1362 1745 1.403814 TTGGACAAAAATGTGGGCGA 58.596 45.000 0.00 0.00 0.00 5.54
1710 2151 7.933577 TGTGACCCTCAGCTTATTTAGATAATG 59.066 37.037 0.00 0.00 0.00 1.90
1819 2269 9.836864 ACATAGATTCAGCTATTCAATACACAA 57.163 29.630 0.00 0.00 0.00 3.33
1842 2300 6.263168 GCAGGCTTGAATAACCTTATGTACAT 59.737 38.462 13.93 13.93 0.00 2.29
2049 3275 7.100409 AGCTCATACTTCTTTAAGAGGACAAC 58.900 38.462 11.06 0.00 36.50 3.32
2229 3456 1.949525 TGCCAAGAACTCTTTGCAGTC 59.050 47.619 12.75 0.00 45.74 3.51
2390 3621 7.432148 TTTCCCAGCATCTAGTAATGTTCTA 57.568 36.000 0.00 0.00 0.00 2.10
2435 3669 0.315886 ACAGAACACGTATGTCGGCA 59.684 50.000 0.00 0.00 44.69 5.69
2581 3815 5.186198 GGAATACAATACAAGCCTGACAGT 58.814 41.667 0.93 0.00 0.00 3.55
2694 3928 5.989777 CAGAGTATGATTGCATCAGATGTCA 59.010 40.000 12.18 8.27 43.53 3.58


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

AutoCloner maintained by Alex Coulton.