Multiple sequence alignment - TraesCS2A01G509100

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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 TraesCS2A01G509100 chr2A 100.000 9570 0 0 1 9570 735172801 735182370 0.000000e+00 17673
1 TraesCS2A01G509100 chr7B 98.064 9609 127 17 1 9570 743066307 743075895 0.000000e+00 16659
2 TraesCS2A01G509100 chr7B 98.152 2543 30 4 7044 9570 743105850 743103309 0.000000e+00 4420
3 TraesCS2A01G509100 chr7A 98.023 9611 143 13 1 9570 671960566 671950962 0.000000e+00 16652
4 TraesCS2A01G509100 chr7A 97.678 5469 90 6 4139 9570 120921586 120916118 0.000000e+00 9361
5 TraesCS2A01G509100 chr4B 97.533 9605 197 15 1 9570 209149605 209140006 0.000000e+00 16388
6 TraesCS2A01G509100 chr4D 97.813 8642 131 21 1 8607 123578594 123587212 0.000000e+00 14859
7 TraesCS2A01G509100 chr4D 97.528 4450 66 9 4192 8604 123371980 123376422 0.000000e+00 7568
8 TraesCS2A01G509100 chr4A 97.366 8656 166 19 1 8607 67554915 67546273 0.000000e+00 14665
9 TraesCS2A01G509100 chr4A 97.154 8643 197 13 1 8607 332381428 332372799 0.000000e+00 14552
10 TraesCS2A01G509100 chr7D 96.944 8639 199 21 1 8607 307064892 307056287 0.000000e+00 14430
11 TraesCS2A01G509100 chr7D 98.160 6957 84 11 1687 8607 382012479 382005531 0.000000e+00 12098
12 TraesCS2A01G509100 chr7D 97.040 1892 21 6 6751 8607 382004607 382002716 0.000000e+00 3151
13 TraesCS2A01G509100 chr2D 97.911 7994 119 12 1 7962 635037262 635045239 0.000000e+00 13793
14 TraesCS2A01G509100 chr2D 96.189 6928 220 24 1 6911 39607246 39614146 0.000000e+00 11291
15 TraesCS2A01G509100 chr2D 97.354 5254 94 13 3386 8607 17963831 17958591 0.000000e+00 8890
16 TraesCS2A01G509100 chr5A 98.703 7016 84 7 4 7013 16623270 16616256 0.000000e+00 12445
17 TraesCS2A01G509100 chr5A 97.898 5660 83 8 3944 9570 300052914 300058570 0.000000e+00 9760
18 TraesCS2A01G509100 chr5A 98.232 2262 26 2 7323 9570 16615478 16613217 0.000000e+00 3943
19 TraesCS2A01G509100 chr3B 98.224 6532 106 9 487 7013 92179893 92186419 0.000000e+00 11411
20 TraesCS2A01G509100 chr3B 97.354 5404 96 14 4207 9570 201631327 201625931 0.000000e+00 9143
21 TraesCS2A01G509100 chr3B 97.791 2535 39 4 7052 9570 92186768 92189301 0.000000e+00 4355
22 TraesCS2A01G509100 chr3B 98.968 775 7 1 1 775 92178951 92179724 0.000000e+00 1386
23 TraesCS2A01G509100 chr3B 97.872 799 15 2 1 798 575684407 575683610 0.000000e+00 1380
24 TraesCS2A01G509100 chr6B 97.708 5411 82 11 4200 9570 525682386 525687794 0.000000e+00 9267
25 TraesCS2A01G509100 chr3A 92.188 128 10 0 6280 6407 99999470 99999597 2.120000e-41 182
26 TraesCS2A01G509100 chr3A 98.438 64 1 0 6802 6865 615608751 615608688 7.860000e-21 113


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 TraesCS2A01G509100 chr2A 735172801 735182370 9569 False 17673.000000 17673 100.000000 1 9570 1 chr2A.!!$F1 9569
1 TraesCS2A01G509100 chr7B 743066307 743075895 9588 False 16659.000000 16659 98.064000 1 9570 1 chr7B.!!$F1 9569
2 TraesCS2A01G509100 chr7B 743103309 743105850 2541 True 4420.000000 4420 98.152000 7044 9570 1 chr7B.!!$R1 2526
3 TraesCS2A01G509100 chr7A 671950962 671960566 9604 True 16652.000000 16652 98.023000 1 9570 1 chr7A.!!$R2 9569
4 TraesCS2A01G509100 chr7A 120916118 120921586 5468 True 9361.000000 9361 97.678000 4139 9570 1 chr7A.!!$R1 5431
5 TraesCS2A01G509100 chr4B 209140006 209149605 9599 True 16388.000000 16388 97.533000 1 9570 1 chr4B.!!$R1 9569
6 TraesCS2A01G509100 chr4D 123578594 123587212 8618 False 14859.000000 14859 97.813000 1 8607 1 chr4D.!!$F2 8606
7 TraesCS2A01G509100 chr4D 123371980 123376422 4442 False 7568.000000 7568 97.528000 4192 8604 1 chr4D.!!$F1 4412
8 TraesCS2A01G509100 chr4A 67546273 67554915 8642 True 14665.000000 14665 97.366000 1 8607 1 chr4A.!!$R1 8606
9 TraesCS2A01G509100 chr4A 332372799 332381428 8629 True 14552.000000 14552 97.154000 1 8607 1 chr4A.!!$R2 8606
10 TraesCS2A01G509100 chr7D 307056287 307064892 8605 True 14430.000000 14430 96.944000 1 8607 1 chr7D.!!$R1 8606
11 TraesCS2A01G509100 chr7D 382002716 382012479 9763 True 7624.500000 12098 97.600000 1687 8607 2 chr7D.!!$R2 6920
12 TraesCS2A01G509100 chr2D 635037262 635045239 7977 False 13793.000000 13793 97.911000 1 7962 1 chr2D.!!$F2 7961
13 TraesCS2A01G509100 chr2D 39607246 39614146 6900 False 11291.000000 11291 96.189000 1 6911 1 chr2D.!!$F1 6910
14 TraesCS2A01G509100 chr2D 17958591 17963831 5240 True 8890.000000 8890 97.354000 3386 8607 1 chr2D.!!$R1 5221
15 TraesCS2A01G509100 chr5A 300052914 300058570 5656 False 9760.000000 9760 97.898000 3944 9570 1 chr5A.!!$F1 5626
16 TraesCS2A01G509100 chr5A 16613217 16623270 10053 True 8194.000000 12445 98.467500 4 9570 2 chr5A.!!$R1 9566
17 TraesCS2A01G509100 chr3B 201625931 201631327 5396 True 9143.000000 9143 97.354000 4207 9570 1 chr3B.!!$R1 5363
18 TraesCS2A01G509100 chr3B 92178951 92189301 10350 False 5717.333333 11411 98.327667 1 9570 3 chr3B.!!$F1 9569
19 TraesCS2A01G509100 chr3B 575683610 575684407 797 True 1380.000000 1380 97.872000 1 798 1 chr3B.!!$R2 797
20 TraesCS2A01G509100 chr6B 525682386 525687794 5408 False 9267.000000 9267 97.708000 4200 9570 1 chr6B.!!$F1 5370

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
748 1222 6.555463 AGATTCCCGGATAAAGTTCAGTAA 57.445 37.500 0.73 0.0 0.00 2.24 F
1323 1803 2.159057 CCCTATTTGCATTTCAGTGGGC 60.159 50.000 0.00 0.0 0.00 5.36 F
1774 2255 0.838608 TAGGGGGTGTGTTTGTTCGT 59.161 50.000 0.00 0.0 0.00 3.85 F
2863 3350 1.668751 GGCGACACTTTGTTTCACTCA 59.331 47.619 0.00 0.0 0.00 3.41 F
3837 4329 0.249398 GTGACCAGTACAGCGGGAAT 59.751 55.000 0.00 0.0 36.26 3.01 F
4996 5511 0.616679 ACCTGCCTAACCCTTCGCTA 60.617 55.000 0.00 0.0 0.00 4.26 F
5012 5527 0.743097 GCTACGAGGGACCGTACAAT 59.257 55.000 0.00 0.0 43.20 2.71 F
5739 6273 1.283321 GAGCCTTGTCTTCCCTCCAAT 59.717 52.381 0.00 0.0 0.00 3.16 F
6645 7195 0.535797 GAGTTTACCCGGCACTAGCT 59.464 55.000 0.00 0.0 41.70 3.32 F
7872 8910 0.611062 TCTCAACGGATCCTCCACGT 60.611 55.000 10.75 0.0 43.43 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2255 5.152623 ACTTGACGAGGAATTCATTCTCA 57.847 39.130 7.93 2.4 37.00 3.27 R
3123 3614 2.326897 CGCCTCGAATCGACGCTA 59.673 61.111 20.45 0.0 36.19 4.26 R
3205 3696 2.361483 TGTCTGCGTAGGGCCGTA 60.361 61.111 0.00 0.0 42.61 4.02 R
4152 4659 0.411452 TTCTGGTCTCTCTCTGCCCT 59.589 55.000 0.00 0.0 0.00 5.19 R
5570 6104 0.105504 ACCCCCTGCTTGCTTCTTTT 60.106 50.000 0.00 0.0 0.00 2.27 R
6284 6834 3.269643 TCTCAGAGATCTGGTAACCTCCA 59.730 47.826 0.00 0.0 43.91 3.86 R
6645 7195 6.601332 AGATTAGAAATTCCCCGATAAAGCA 58.399 36.000 0.00 0.0 0.00 3.91 R
7115 7987 0.175073 GTTATTGGCTCGTCCGACCT 59.825 55.000 8.86 0.0 37.80 3.85 R
8149 12003 2.975732 TCGCTAGACGGAGAGTAAGA 57.024 50.000 0.00 0.0 43.89 2.10 R
8728 12582 3.593442 TTGAGGACCACAATTTCCTGT 57.407 42.857 1.00 0.0 42.68 4.00 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
748 1222 6.555463 AGATTCCCGGATAAAGTTCAGTAA 57.445 37.500 0.73 0.00 0.00 2.24
1087 1566 6.950619 AGGAAGCATTACTCCTCTTTTCATTT 59.049 34.615 0.00 0.00 28.40 2.32
1323 1803 2.159057 CCCTATTTGCATTTCAGTGGGC 60.159 50.000 0.00 0.00 0.00 5.36
1396 1877 4.438148 TCGTGAATTTCTAATGATCGCCA 58.562 39.130 0.00 0.00 0.00 5.69
1774 2255 0.838608 TAGGGGGTGTGTTTGTTCGT 59.161 50.000 0.00 0.00 0.00 3.85
2525 3011 5.412904 GGGTTCGAGACAAAGAAAGATCAAT 59.587 40.000 0.00 0.00 0.00 2.57
2537 3023 7.526142 AAGAAAGATCAATGCAGCATATCAT 57.474 32.000 17.06 5.71 0.00 2.45
2863 3350 1.668751 GGCGACACTTTGTTTCACTCA 59.331 47.619 0.00 0.00 0.00 3.41
2997 3484 8.927675 TTTGGTGACTATTGGTATGTTTAGTT 57.072 30.769 0.00 0.00 0.00 2.24
3123 3614 4.503741 AAACTTAGCATGTCGCAACAAT 57.496 36.364 0.00 0.00 46.13 2.71
3155 3646 2.713154 GCGTCAGCAAAACACCGT 59.287 55.556 0.00 0.00 44.35 4.83
3290 3781 4.105486 GCTTTCCCGTGAATAAGAATTGC 58.895 43.478 0.00 0.00 0.00 3.56
3430 3921 4.657504 TGGCCTGATCTGTTCTGATAGATT 59.342 41.667 3.32 0.00 34.32 2.40
3821 4313 2.889045 ACTTCCTACAGCTAACACGTGA 59.111 45.455 25.01 0.00 0.00 4.35
3827 4319 1.958579 ACAGCTAACACGTGACCAGTA 59.041 47.619 25.01 5.16 0.00 2.74
3837 4329 0.249398 GTGACCAGTACAGCGGGAAT 59.751 55.000 0.00 0.00 36.26 3.01
4152 4659 1.075305 GGTAAGTTTTGGGGCGGGA 59.925 57.895 0.00 0.00 0.00 5.14
4656 5171 3.406512 AGGGCCACTCACTATAGAAGT 57.593 47.619 6.18 6.73 39.81 3.01
4713 5228 1.686800 GCCAAACCCCCATGCTCAT 60.687 57.895 0.00 0.00 0.00 2.90
4996 5511 0.616679 ACCTGCCTAACCCTTCGCTA 60.617 55.000 0.00 0.00 0.00 4.26
5009 5524 1.369091 TTCGCTACGAGGGACCGTAC 61.369 60.000 0.00 0.00 43.20 3.67
5012 5527 0.743097 GCTACGAGGGACCGTACAAT 59.257 55.000 0.00 0.00 43.20 2.71
5070 5585 3.490348 GGGCCTATGTATTTGCATGACT 58.510 45.455 0.84 0.00 0.00 3.41
5570 6104 2.307309 CGAGCTCCGCGTCAAACAA 61.307 57.895 8.47 0.00 0.00 2.83
5739 6273 1.283321 GAGCCTTGTCTTCCCTCCAAT 59.717 52.381 0.00 0.00 0.00 3.16
5937 6474 6.966021 AGCTCTCTTTTTACAATAAAACGCA 58.034 32.000 0.00 0.00 0.00 5.24
6099 6648 1.541233 CGAAGGGCAGAACTTCAGTGT 60.541 52.381 6.07 0.00 43.43 3.55
6284 6834 3.862845 GGAAGCGTGTTGTCAAAAATGTT 59.137 39.130 0.00 0.00 0.00 2.71
6314 6864 4.877773 ACCAGATCTCTGAGACTACCATT 58.122 43.478 10.00 0.00 46.59 3.16
6361 6911 7.283354 CCAGAAAAAGAAGTGGAGTTAGAAAGT 59.717 37.037 0.00 0.00 31.04 2.66
6390 6940 8.777578 ATGATAGGTGGTAACTATCTTGTACA 57.222 34.615 13.33 0.00 44.46 2.90
6645 7195 0.535797 GAGTTTACCCGGCACTAGCT 59.464 55.000 0.00 0.00 41.70 3.32
7115 7987 1.371337 GCGACTCATGAATGCTGCCA 61.371 55.000 0.00 0.00 0.00 4.92
7872 8910 0.611062 TCTCAACGGATCCTCCACGT 60.611 55.000 10.75 0.00 43.43 4.49
7914 8952 1.348538 CGTGCGTCTTTATCGTGGCA 61.349 55.000 0.00 0.00 0.00 4.92
7921 8959 3.185594 CGTCTTTATCGTGGCAGAAACAA 59.814 43.478 0.00 0.00 0.00 2.83
8149 12003 2.694109 GGTCCGGTGCTAATAGAAGTCT 59.306 50.000 0.00 0.00 0.00 3.24
8303 12157 2.891580 GTCATATGGGAACTCTCGGCTA 59.108 50.000 2.13 0.00 0.00 3.93
8332 12186 9.635404 AACAATCCTTATGGTTTTTATATCCGA 57.365 29.630 0.00 0.00 34.23 4.55
8728 12582 4.526650 TCTGAAATCACTACAGGCACAGTA 59.473 41.667 0.00 0.00 33.19 2.74
8815 12669 4.811969 TCTGGTTATGCGTTTTCCTCTA 57.188 40.909 0.00 0.00 0.00 2.43
8921 12775 1.299468 CGCTACGCCAGGAGATGAC 60.299 63.158 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1087 1566 7.977293 TCGTATCGGTCTTATTGAAGAATTTGA 59.023 33.333 0.00 0.00 43.38 2.69
1323 1803 4.697352 CCAAAACTTCTCATACCAGACCAG 59.303 45.833 0.00 0.00 0.00 4.00
1396 1877 0.178998 GGATCCAGCATGCAGGACAT 60.179 55.000 31.59 18.62 40.66 3.06
1774 2255 5.152623 ACTTGACGAGGAATTCATTCTCA 57.847 39.130 7.93 2.40 37.00 3.27
2863 3350 7.891183 ATCGCGCTTAGAGTATAAATGAAAT 57.109 32.000 5.56 0.00 0.00 2.17
2909 3396 6.287589 AGATCGATCTGTCTTAAAGTGGTT 57.712 37.500 26.78 0.00 35.42 3.67
3075 3566 4.348168 CCCCTATTGCTAGTAGGTTGATGT 59.652 45.833 0.00 0.00 37.58 3.06
3123 3614 2.326897 CGCCTCGAATCGACGCTA 59.673 61.111 20.45 0.00 36.19 4.26
3155 3646 4.336153 GGGTTTTGTTTTAGGAACAGACGA 59.664 41.667 0.00 0.00 0.00 4.20
3205 3696 2.361483 TGTCTGCGTAGGGCCGTA 60.361 61.111 0.00 0.00 42.61 4.02
3821 4313 1.078426 GCATTCCCGCTGTACTGGT 60.078 57.895 1.65 0.00 0.00 4.00
3827 4319 3.127533 GCTTCGCATTCCCGCTGT 61.128 61.111 0.00 0.00 0.00 4.40
3854 4346 2.035961 GGATTCGGTATAGCAGCTCACA 59.964 50.000 0.00 0.00 0.00 3.58
4152 4659 0.411452 TTCTGGTCTCTCTCTGCCCT 59.589 55.000 0.00 0.00 0.00 5.19
4656 5171 6.818281 TGGCTAGGGCTTTTCTAGTTATAA 57.182 37.500 0.00 0.00 37.22 0.98
4713 5228 8.797350 ACTCAATCAATATCAAGAACATGTCA 57.203 30.769 0.00 0.00 0.00 3.58
4996 5511 0.612732 TCCATTGTACGGTCCCTCGT 60.613 55.000 0.00 0.00 45.88 4.18
5009 5524 3.057596 TGTTTAGAAGGCGCTTTCCATTG 60.058 43.478 26.48 0.00 0.00 2.82
5012 5527 2.264005 TGTTTAGAAGGCGCTTTCCA 57.736 45.000 26.48 12.60 0.00 3.53
5535 6069 3.984732 GCAGCCTCCCCACCCTTT 61.985 66.667 0.00 0.00 0.00 3.11
5565 6099 3.534554 CCCTGCTTGCTTCTTTTTGTTT 58.465 40.909 0.00 0.00 0.00 2.83
5570 6104 0.105504 ACCCCCTGCTTGCTTCTTTT 60.106 50.000 0.00 0.00 0.00 2.27
5739 6273 4.505039 GGAACAAGAAAAGGGAGCTAGTCA 60.505 45.833 0.00 0.00 0.00 3.41
6099 6648 3.311596 CGAGGTGACATACTACGATCACA 59.688 47.826 5.66 0.00 42.66 3.58
6284 6834 3.269643 TCTCAGAGATCTGGTAACCTCCA 59.730 47.826 0.00 0.00 43.91 3.86
6361 6911 9.209048 ACAAGATAGTTACCACCTATCATACAA 57.791 33.333 9.40 0.00 42.06 2.41
6645 7195 6.601332 AGATTAGAAATTCCCCGATAAAGCA 58.399 36.000 0.00 0.00 0.00 3.91
7115 7987 0.175073 GTTATTGGCTCGTCCGACCT 59.825 55.000 8.86 0.00 37.80 3.85
7388 8408 8.974408 CCAGATCTATAGAGATATTACGAGTCG 58.026 40.741 11.85 11.85 42.80 4.18
7914 8952 5.127194 GGTCTTTCCCTCTTGTTTTGTTTCT 59.873 40.000 0.00 0.00 0.00 2.52
8149 12003 2.975732 TCGCTAGACGGAGAGTAAGA 57.024 50.000 0.00 0.00 43.89 2.10
8728 12582 3.593442 TTGAGGACCACAATTTCCTGT 57.407 42.857 1.00 0.00 42.68 4.00


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

AutoCloner maintained by Alex Coulton.