Multiple sequence alignment - TraesCS5A01G553100

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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 TraesCS5A01G553100 chr5A 100.000 2961 0 0 1 2961 705781330 705784290 0.000000e+00 5469.0
1 TraesCS5A01G553100 chr5A 100.000 478 0 0 3075 3552 705784404 705784881 0.000000e+00 883.0
2 TraesCS5A01G553100 chr5A 78.223 799 145 24 1597 2376 529080406 529079618 5.330000e-133 484.0
3 TraesCS5A01G553100 chr4B 97.251 2983 18 24 1 2961 665819362 665822302 0.000000e+00 4996.0
4 TraesCS5A01G553100 chr4B 99.163 478 4 0 3075 3552 665822372 665822849 0.000000e+00 861.0
5 TraesCS5A01G553100 chr4B 95.161 62 3 0 1 62 42938214 42938153 8.120000e-17 99.0
6 TraesCS5A01G553100 chr4B 84.314 102 11 4 368 466 283253506 283253605 1.050000e-15 95.3
7 TraesCS5A01G553100 chrUn 95.367 1921 54 11 878 2766 108385372 108383455 0.000000e+00 3022.0
8 TraesCS5A01G553100 chrUn 84.820 527 71 8 248 773 108385929 108385411 4.060000e-144 521.0
9 TraesCS5A01G553100 chrUn 83.936 249 30 6 532 772 312499448 312499694 2.760000e-56 230.0
10 TraesCS5A01G553100 chrUn 84.946 93 13 1 368 459 240280148 240280056 3.780000e-15 93.5
11 TraesCS5A01G553100 chr2B 77.510 1574 288 46 1010 2539 19075088 19073537 0.000000e+00 885.0
12 TraesCS5A01G553100 chr2B 81.712 946 154 15 1594 2528 18949707 18948770 0.000000e+00 771.0
13 TraesCS5A01G553100 chr2B 80.583 927 155 19 1597 2506 18954882 18953964 0.000000e+00 691.0
14 TraesCS5A01G553100 chr2B 79.519 957 159 23 1594 2524 18922762 18923707 0.000000e+00 647.0
15 TraesCS5A01G553100 chr2B 81.010 495 83 6 1013 1497 18955479 18954986 2.000000e-102 383.0
16 TraesCS5A01G553100 chr2B 84.322 236 31 6 532 764 614246081 614246313 3.570000e-55 226.0
17 TraesCS5A01G553100 chr2B 82.661 248 36 4 532 773 489027684 489027930 2.780000e-51 213.0
18 TraesCS5A01G553100 chr2B 94.643 56 3 0 1 56 717691286 717691341 1.760000e-13 87.9
19 TraesCS5A01G553100 chr2B 91.935 62 5 0 1 62 779174911 779174972 1.760000e-13 87.9
20 TraesCS5A01G553100 chr2A 80.797 953 154 19 1594 2524 13004112 13003167 0.000000e+00 719.0
21 TraesCS5A01G553100 chr2A 80.683 937 151 20 1594 2506 12990990 12991920 0.000000e+00 701.0
22 TraesCS5A01G553100 chr2A 81.584 505 78 9 1006 1497 13004702 13004200 1.540000e-108 403.0
23 TraesCS5A01G553100 chr2A 80.404 495 86 6 1013 1497 12990414 12990907 2.010000e-97 366.0
24 TraesCS5A01G553100 chr2D 80.978 941 142 26 1594 2506 12551266 12552197 0.000000e+00 712.0
25 TraesCS5A01G553100 chr2D 81.410 468 70 6 1013 1464 12550679 12551145 2.010000e-97 366.0
26 TraesCS5A01G553100 chr2D 79.070 215 35 10 3179 3387 134480053 134479843 4.780000e-29 139.0
27 TraesCS5A01G553100 chr2D 93.333 60 4 0 1 60 20689633 20689574 4.880000e-14 89.8
28 TraesCS5A01G553100 chr5D 89.037 374 39 1 3181 3552 297051506 297051879 2.500000e-126 462.0
29 TraesCS5A01G553100 chr6A 75.371 674 137 24 1769 2426 592817754 592817094 7.450000e-77 298.0
30 TraesCS5A01G553100 chr6A 82.734 278 41 6 1012 1284 553913268 553912993 1.270000e-59 241.0
31 TraesCS5A01G553100 chr6A 86.250 80 8 3 2845 2923 60102148 60102071 2.270000e-12 84.2
32 TraesCS5A01G553100 chr6D 82.609 276 45 2 1012 1284 408157055 408156780 1.270000e-59 241.0
33 TraesCS5A01G553100 chr6B 81.754 285 49 2 1012 1293 612745121 612744837 5.930000e-58 235.0
34 TraesCS5A01G553100 chr4D 84.211 247 32 5 533 773 120352147 120352392 2.130000e-57 233.0
35 TraesCS5A01G553100 chr4D 83.071 254 37 3 525 772 419245629 419245882 3.570000e-55 226.0
36 TraesCS5A01G553100 chr7D 83.468 248 35 3 531 772 600893513 600893760 3.570000e-55 226.0
37 TraesCS5A01G553100 chr7D 82.869 251 36 5 528 772 33204028 33204277 5.970000e-53 219.0
38 TraesCS5A01G553100 chr7D 88.372 86 10 0 368 453 388715751 388715666 1.740000e-18 104.0
39 TraesCS5A01G553100 chr3D 75.325 385 70 24 3182 3552 264591855 264592228 1.020000e-35 161.0
40 TraesCS5A01G553100 chr4A 74.865 370 71 19 3185 3541 152611378 152611018 7.940000e-32 148.0
41 TraesCS5A01G553100 chr7B 88.372 86 10 0 368 453 383854775 383854690 1.740000e-18 104.0
42 TraesCS5A01G553100 chr1B 95.000 60 3 0 1 60 17975805 17975746 1.050000e-15 95.3
43 TraesCS5A01G553100 chr1B 84.000 100 15 1 368 466 281034861 281034762 1.050000e-15 95.3
44 TraesCS5A01G553100 chr1B 84.000 100 15 1 368 466 321029119 321029218 1.050000e-15 95.3
45 TraesCS5A01G553100 chr1B 93.548 62 4 0 1 62 314731568 314731507 3.780000e-15 93.5
46 TraesCS5A01G553100 chr3B 83.333 102 12 4 368 466 420655775 420655676 4.880000e-14 89.8
47 TraesCS5A01G553100 chr1D 90.385 52 5 0 1 52 438211149 438211200 6.360000e-08 69.4


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 TraesCS5A01G553100 chr5A 705781330 705784881 3551 False 3176.0 5469 100.0000 1 3552 2 chr5A.!!$F1 3551
1 TraesCS5A01G553100 chr5A 529079618 529080406 788 True 484.0 484 78.2230 1597 2376 1 chr5A.!!$R1 779
2 TraesCS5A01G553100 chr4B 665819362 665822849 3487 False 2928.5 4996 98.2070 1 3552 2 chr4B.!!$F2 3551
3 TraesCS5A01G553100 chrUn 108383455 108385929 2474 True 1771.5 3022 90.0935 248 2766 2 chrUn.!!$R2 2518
4 TraesCS5A01G553100 chr2B 19073537 19075088 1551 True 885.0 885 77.5100 1010 2539 1 chr2B.!!$R2 1529
5 TraesCS5A01G553100 chr2B 18948770 18949707 937 True 771.0 771 81.7120 1594 2528 1 chr2B.!!$R1 934
6 TraesCS5A01G553100 chr2B 18922762 18923707 945 False 647.0 647 79.5190 1594 2524 1 chr2B.!!$F1 930
7 TraesCS5A01G553100 chr2B 18953964 18955479 1515 True 537.0 691 80.7965 1013 2506 2 chr2B.!!$R3 1493
8 TraesCS5A01G553100 chr2A 13003167 13004702 1535 True 561.0 719 81.1905 1006 2524 2 chr2A.!!$R1 1518
9 TraesCS5A01G553100 chr2A 12990414 12991920 1506 False 533.5 701 80.5435 1013 2506 2 chr2A.!!$F1 1493
10 TraesCS5A01G553100 chr2D 12550679 12552197 1518 False 539.0 712 81.1940 1013 2506 2 chr2D.!!$F1 1493
11 TraesCS5A01G553100 chr6A 592817094 592817754 660 True 298.0 298 75.3710 1769 2426 1 chr6A.!!$R3 657

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
400 401 2.156917 ACCACACGTACATTCTCTCGA 58.843 47.619 0.0 0.00 0.00 4.04 F
450 451 3.213249 AACTCGCGTGAGGTTAACTAG 57.787 47.619 28.3 2.78 39.90 2.57 F
535 536 6.663953 TGGACTGCCCAATCTATATACTACTC 59.336 42.308 0.0 0.00 43.29 2.59 F
1569 1621 5.955488 ACTGCTAATATATGCTAGTCGTGG 58.045 41.667 0.0 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1618 2.280592 GACCACCACGACCACCAC 60.281 66.667 0.0 0.00 0.00 4.16 R
1569 1621 2.660552 CACGACCACCACGACCAC 60.661 66.667 0.0 0.00 34.70 4.16 R
1571 1623 3.608662 TCCACGACCACCACGACC 61.609 66.667 0.0 0.00 34.70 4.79 R
3454 3608 0.528466 TGGCGCATTTGCAAAAACGA 60.528 45.000 30.0 14.73 42.21 3.85 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
400 401 2.156917 ACCACACGTACATTCTCTCGA 58.843 47.619 0.00 0.00 0.00 4.04
450 451 3.213249 AACTCGCGTGAGGTTAACTAG 57.787 47.619 28.30 2.78 39.90 2.57
535 536 6.663953 TGGACTGCCCAATCTATATACTACTC 59.336 42.308 0.00 0.00 43.29 2.59
870 872 7.068839 GGGACTAGAGTCTGTCTATCAATTTGA 59.931 40.741 16.95 0.75 44.20 2.69
1563 1615 7.313646 ACGTGGTAACTGCTAATATATGCTAG 58.686 38.462 0.00 0.00 37.61 3.42
1565 1617 7.485277 CGTGGTAACTGCTAATATATGCTAGTC 59.515 40.741 0.00 0.00 37.61 2.59
1566 1618 7.485277 GTGGTAACTGCTAATATATGCTAGTCG 59.515 40.741 0.00 0.00 37.61 4.18
1567 1619 7.176165 TGGTAACTGCTAATATATGCTAGTCGT 59.824 37.037 0.00 0.00 37.61 4.34
1568 1620 7.485277 GGTAACTGCTAATATATGCTAGTCGTG 59.515 40.741 0.00 0.00 0.00 4.35
1569 1621 5.955488 ACTGCTAATATATGCTAGTCGTGG 58.045 41.667 0.00 0.00 0.00 4.94
1570 1622 5.477291 ACTGCTAATATATGCTAGTCGTGGT 59.523 40.000 0.00 0.00 0.00 4.16
1571 1623 5.709966 TGCTAATATATGCTAGTCGTGGTG 58.290 41.667 0.00 0.00 0.00 4.17
2941 3095 7.436376 GGGTTAATACACTAGTTAGGCGTAAAG 59.564 40.741 0.00 0.00 0.00 1.85
3183 3337 1.888436 AAGCCTCGGCACATCTCGAA 61.888 55.000 11.02 0.00 44.88 3.71
3334 3488 7.702386 ACACTTTATTTTTGCAAAATCAACCC 58.298 30.769 24.39 0.00 0.00 4.11
3346 3500 5.682212 GCAAAATCAACCCAGTTCAACTCTT 60.682 40.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 372 6.789262 AGAATGTACGTGTGGTATGTAGTAC 58.211 40.000 0.00 0.00 36.11 2.73
535 536 3.560068 GCACTACATTATGAAACGGAGGG 59.440 47.826 0.00 0.00 0.00 4.30
1314 1334 4.354162 GGCGGCCCAACCCTGTTA 62.354 66.667 8.12 0.00 33.26 2.41
1563 1615 2.660552 CACCACGACCACCACGAC 60.661 66.667 0.00 0.00 34.70 4.34
1565 1617 4.230002 ACCACCACGACCACCACG 62.230 66.667 0.00 0.00 0.00 4.94
1566 1618 2.280592 GACCACCACGACCACCAC 60.281 66.667 0.00 0.00 0.00 4.16
1567 1619 3.918977 CGACCACCACGACCACCA 61.919 66.667 0.00 0.00 0.00 4.17
1568 1620 3.920196 ACGACCACCACGACCACC 61.920 66.667 0.00 0.00 34.70 4.61
1569 1621 2.660552 CACGACCACCACGACCAC 60.661 66.667 0.00 0.00 34.70 4.16
1570 1622 3.918977 CCACGACCACCACGACCA 61.919 66.667 0.00 0.00 34.70 4.02
1571 1623 3.608662 TCCACGACCACCACGACC 61.609 66.667 0.00 0.00 34.70 4.79
3183 3337 4.571580 TCGTTTGTTTCACAGGATACGTTT 59.428 37.500 0.00 0.00 46.39 3.60
3334 3488 1.220529 TCGCAGCAAGAGTTGAACTG 58.779 50.000 0.90 0.00 0.00 3.16
3346 3500 2.009051 CACTGTATGGAAATCGCAGCA 58.991 47.619 0.00 0.00 0.00 4.41
3454 3608 0.528466 TGGCGCATTTGCAAAAACGA 60.528 45.000 30.00 14.73 42.21 3.85


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

AutoCloner maintained by Alex Coulton.