Multiple sequence alignment - TraesCS2A01G433200

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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 TraesCS2A01G433200 chr2A 100.000 3139 0 0 1 3139 686323581 686320443 0.000000e+00 5797.0
1 TraesCS2A01G433200 chr2A 97.598 2873 53 4 1 2867 686524591 686521729 0.000000e+00 4909.0
2 TraesCS2A01G433200 chr2A 98.057 1956 33 2 598 2551 686297401 686295449 0.000000e+00 3397.0
3 TraesCS2A01G433200 chr2A 98.422 1901 21 1 506 2406 686614956 686613065 0.000000e+00 3336.0
4 TraesCS2A01G433200 chr2A 95.410 719 33 0 2420 3138 686608872 686608154 0.000000e+00 1146.0
5 TraesCS2A01G433200 chr2A 93.010 515 34 2 188 700 686623037 686622523 0.000000e+00 750.0
6 TraesCS2A01G433200 chr2A 93.810 420 25 1 188 606 686299389 686298970 5.710000e-177 630.0
7 TraesCS2A01G433200 chr2A 93.391 348 17 4 424 770 686623764 686623422 7.770000e-141 510.0
8 TraesCS2A01G433200 chr2A 93.035 201 8 3 1 195 686623320 686623120 3.960000e-74 289.0
9 TraesCS2A01G433200 chr2A 97.917 96 2 0 100 195 686299567 686299472 1.940000e-37 167.0
10 TraesCS2A01G433200 chr2A 97.059 68 2 0 1 68 686299814 686299747 7.110000e-22 115.0
11 TraesCS2A01G433200 chr2A 78.814 118 20 4 186 300 67984196 67984311 1.210000e-09 75.0
12 TraesCS2A01G433200 chr2B 90.476 1554 90 23 790 2330 648931637 648930129 0.000000e+00 1997.0
13 TraesCS2A01G433200 chr2B 89.872 1323 102 26 834 2142 649370753 649369449 0.000000e+00 1672.0
14 TraesCS2A01G433200 chr2B 87.755 833 62 10 1893 2717 649192246 649191446 0.000000e+00 937.0
15 TraesCS2A01G433200 chr2B 85.106 376 45 9 2766 3136 373745741 373745372 1.060000e-99 374.0
16 TraesCS2A01G433200 chr2B 89.474 76 7 1 751 826 649215155 649215081 9.270000e-16 95.3
17 TraesCS2A01G433200 chr2B 98.077 52 1 0 548 599 649053782 649053731 1.200000e-14 91.6
18 TraesCS2A01G433200 chr2D 89.028 1513 113 33 836 2331 543532118 543530642 0.000000e+00 1825.0
19 TraesCS2A01G433200 chr2D 87.260 1617 122 41 784 2371 543762098 543760537 0.000000e+00 1768.0
20 TraesCS2A01G433200 chr2D 87.548 1558 121 39 834 2371 543813744 543812240 0.000000e+00 1735.0
21 TraesCS2A01G433200 chr2D 85.684 1425 124 42 886 2277 543589155 543587778 0.000000e+00 1428.0
22 TraesCS2A01G433200 chr2D 87.728 383 40 6 2760 3138 391226565 391226186 1.030000e-119 440.0
23 TraesCS2A01G433200 chr2D 85.039 381 41 11 2762 3137 305476689 305476320 1.060000e-99 374.0
24 TraesCS2A01G433200 chr2D 89.815 216 18 3 579 794 543589501 543589290 1.110000e-69 274.0
25 TraesCS2A01G433200 chr2D 89.450 218 17 3 513 730 543816142 543815931 1.430000e-68 270.0
26 TraesCS2A01G433200 chr2D 91.489 188 14 2 601 788 543532429 543532244 1.120000e-64 257.0
27 TraesCS2A01G433200 chr5D 88.032 376 42 3 2762 3135 344934892 344934518 2.870000e-120 442.0
28 TraesCS2A01G433200 chr5D 87.599 379 41 4 2762 3138 107775720 107775346 4.810000e-118 435.0
29 TraesCS2A01G433200 chr5D 85.224 379 49 7 2763 3138 525483164 525483538 1.770000e-102 383.0
30 TraesCS2A01G433200 chr5D 76.289 291 60 8 187 473 536277591 536277876 2.520000e-31 147.0
31 TraesCS2A01G433200 chr5A 85.789 380 49 5 2762 3138 110645960 110645583 6.310000e-107 398.0
32 TraesCS2A01G433200 chr5B 85.372 376 45 10 2767 3138 406613301 406613670 6.350000e-102 381.0
33 TraesCS2A01G433200 chr1B 75.862 580 122 12 1368 1941 14138326 14138893 2.380000e-71 279.0
34 TraesCS2A01G433200 chr1D 75.904 581 113 24 1371 1941 9745210 9745773 3.990000e-69 272.0
35 TraesCS2A01G433200 chr1A 75.345 580 118 21 1371 1941 11555192 11555755 4.020000e-64 255.0
36 TraesCS2A01G433200 chr4D 73.597 303 61 10 186 473 415302672 415302374 7.160000e-17 99.0
37 TraesCS2A01G433200 chr3D 73.490 298 61 15 187 473 572654831 572654541 2.580000e-16 97.1
38 TraesCS2A01G433200 chr3D 83.750 80 12 1 187 265 566893105 566893026 1.210000e-09 75.0
39 TraesCS2A01G433200 chr3B 72.964 307 63 14 182 473 792853717 792853416 4.310000e-14 89.8
40 TraesCS2A01G433200 chr7A 79.508 122 22 3 354 473 510163082 510162962 2.010000e-12 84.2


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 TraesCS2A01G433200 chr2A 686320443 686323581 3138 True 5797.000000 5797 100.000000 1 3139 1 chr2A.!!$R1 3138
1 TraesCS2A01G433200 chr2A 686521729 686524591 2862 True 4909.000000 4909 97.598000 1 2867 1 chr2A.!!$R2 2866
2 TraesCS2A01G433200 chr2A 686613065 686614956 1891 True 3336.000000 3336 98.422000 506 2406 1 chr2A.!!$R4 1900
3 TraesCS2A01G433200 chr2A 686608154 686608872 718 True 1146.000000 1146 95.410000 2420 3138 1 chr2A.!!$R3 718
4 TraesCS2A01G433200 chr2A 686295449 686299814 4365 True 1077.250000 3397 96.710750 1 2551 4 chr2A.!!$R5 2550
5 TraesCS2A01G433200 chr2A 686622523 686623764 1241 True 516.333333 750 93.145333 1 770 3 chr2A.!!$R6 769
6 TraesCS2A01G433200 chr2B 648930129 648931637 1508 True 1997.000000 1997 90.476000 790 2330 1 chr2B.!!$R2 1540
7 TraesCS2A01G433200 chr2B 649369449 649370753 1304 True 1672.000000 1672 89.872000 834 2142 1 chr2B.!!$R6 1308
8 TraesCS2A01G433200 chr2B 649191446 649192246 800 True 937.000000 937 87.755000 1893 2717 1 chr2B.!!$R4 824
9 TraesCS2A01G433200 chr2D 543760537 543762098 1561 True 1768.000000 1768 87.260000 784 2371 1 chr2D.!!$R3 1587
10 TraesCS2A01G433200 chr2D 543530642 543532429 1787 True 1041.000000 1825 90.258500 601 2331 2 chr2D.!!$R4 1730
11 TraesCS2A01G433200 chr2D 543812240 543816142 3902 True 1002.500000 1735 88.499000 513 2371 2 chr2D.!!$R6 1858
12 TraesCS2A01G433200 chr2D 543587778 543589501 1723 True 851.000000 1428 87.749500 579 2277 2 chr2D.!!$R5 1698
13 TraesCS2A01G433200 chr1B 14138326 14138893 567 False 279.000000 279 75.862000 1368 1941 1 chr1B.!!$F1 573
14 TraesCS2A01G433200 chr1D 9745210 9745773 563 False 272.000000 272 75.904000 1371 1941 1 chr1D.!!$F1 570
15 TraesCS2A01G433200 chr1A 11555192 11555755 563 False 255.000000 255 75.345000 1371 1941 1 chr1A.!!$F1 570

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
267 950 3.119955 TCCGTGTTGATCTAGTCTTCGTG 60.12 47.826 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 6980 3.919834 ACTACCCTATACACCGGACAAT 58.08 45.455 9.46 0.0 0.0 2.71 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
267 950 3.119955 TCCGTGTTGATCTAGTCTTCGTG 60.120 47.826 0.00 0.00 0.00 4.35
275 958 4.758165 TGATCTAGTCTTCGTGTGTGTGTA 59.242 41.667 0.00 0.00 0.00 2.90
278 961 6.806388 TCTAGTCTTCGTGTGTGTGTATAA 57.194 37.500 0.00 0.00 0.00 0.98
294 977 9.243637 TGTGTGTATAAAAGTTTGATCTTTTGC 57.756 29.630 12.64 5.76 44.15 3.68
358 1041 4.462280 CGGCCCGTGGGACCTTAC 62.462 72.222 9.72 0.00 41.23 2.34
1908 6319 3.185082 GACGACGTCCACGGTGTGA 62.185 63.158 17.25 1.41 44.95 3.58
2579 7012 4.419875 TGTATAGGGTAGTAGGGTTAGCCA 59.580 45.833 2.44 0.00 40.35 4.75
2620 7053 1.402720 CCGGCATTGTTTGATGGTGAC 60.403 52.381 0.00 0.00 0.00 3.67
2641 7074 5.104693 TGACGGCTTCAGGGATAAGAATAAA 60.105 40.000 0.00 0.00 0.00 1.40
2662 7095 1.038130 AGACCTCAGATCCGGTTCCG 61.038 60.000 8.95 4.08 32.62 4.30
2846 7279 8.672823 TTTCTCTTAGTTAGGAACAAGGTTTC 57.327 34.615 0.00 0.00 0.00 2.78
2874 7307 1.915078 ATAGGAGGCACCACACCAGC 61.915 60.000 3.18 0.00 42.04 4.85
2882 7315 1.078072 ACCACACCAGCAACGTGAA 60.078 52.632 5.01 0.00 35.17 3.18
2933 7366 1.747774 CACCCAACAAAGGCAAGGG 59.252 57.895 0.00 0.00 45.20 3.95
2934 7367 1.459348 ACCCAACAAAGGCAAGGGG 60.459 57.895 0.00 0.00 43.96 4.79
2958 7391 2.644676 GTCACTCCCCTTATTCTTGCC 58.355 52.381 0.00 0.00 0.00 4.52
3007 7440 8.026607 GTGATAGGCAAAGCAATACAAAGTAAA 58.973 33.333 0.00 0.00 0.00 2.01
3041 7474 3.674753 GCAAGCGAACAAAGTAATTGCAT 59.325 39.130 0.00 0.00 43.13 3.96
3110 7543 2.175202 AGTGGCATCTCTCTCGAAAGT 58.825 47.619 0.00 0.00 0.00 2.66
3115 7548 5.239744 GTGGCATCTCTCTCGAAAGTATAGA 59.760 44.000 0.00 0.00 0.00 1.98
3118 7551 7.014711 TGGCATCTCTCTCGAAAGTATAGAAAT 59.985 37.037 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 958 7.750903 GCGTAGAGCAAAAGATCAAACTTTTAT 59.249 33.333 0.00 0.00 44.73 1.40
294 977 3.673338 TCGTCAATGAACAAAGCGTAGAG 59.327 43.478 0.00 0.00 0.00 2.43
358 1041 4.384056 AGACAGTCAGAAAGTCATTGTGG 58.616 43.478 2.66 0.00 33.26 4.17
2547 6980 3.919834 ACTACCCTATACACCGGACAAT 58.080 45.455 9.46 0.00 0.00 2.71
2579 7012 3.305471 GGACGAAGAGCACTCACTTAACT 60.305 47.826 0.00 0.00 0.00 2.24
2620 7053 7.332182 GTCTATTTATTCTTATCCCTGAAGCCG 59.668 40.741 0.00 0.00 0.00 5.52
2641 7074 2.599677 GGAACCGGATCTGAGGTCTAT 58.400 52.381 9.46 0.00 40.37 1.98
2735 7168 0.255033 GACGGGGGAATAGCCAAACT 59.745 55.000 0.00 0.00 38.95 2.66
2846 7279 2.290896 TGGTGCCTCCTATTGGTTCAAG 60.291 50.000 0.00 0.00 37.07 3.02
2855 7288 1.915078 GCTGGTGTGGTGCCTCCTAT 61.915 60.000 0.00 0.00 37.07 2.57
2874 7307 3.488310 GTGTGTAGGTACTGTTCACGTTG 59.512 47.826 0.00 0.00 41.52 4.10
2882 7315 2.292569 CGTGTCTGTGTGTAGGTACTGT 59.707 50.000 0.00 0.00 41.52 3.55
2933 7366 1.138464 GAATAAGGGGAGTGACGACCC 59.862 57.143 9.24 9.24 45.06 4.46
2934 7367 2.108970 AGAATAAGGGGAGTGACGACC 58.891 52.381 0.00 0.00 0.00 4.79
2958 7391 8.506437 TCACTATCAGTTTTAATCTTGCAACTG 58.494 33.333 0.00 8.53 45.04 3.16
3007 7440 7.704899 ACTTTGTTCGCTTGCTTTTATTTACTT 59.295 29.630 0.00 0.00 0.00 2.24
3024 7457 7.801547 AAGAATCATGCAATTACTTTGTTCG 57.198 32.000 0.00 0.00 37.65 3.95
3041 7474 7.568738 TCCCTTCTCCATCAATACTAAGAATCA 59.431 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.