Multiple sequence alignment - TraesCS5A01G299000

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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 TraesCS5A01G299000 chr5A 100.000 1520 0 0 775 2294 507565737 507564218 0.000000e+00 2808
1 TraesCS5A01G299000 chr5A 100.000 605 0 0 1 605 507566511 507565907 0.000000e+00 1118
2 TraesCS5A01G299000 chr5A 95.238 609 22 5 1 605 603018407 603019012 0.000000e+00 957
3 TraesCS5A01G299000 chr1A 95.511 1537 52 5 775 2294 380400781 380402317 0.000000e+00 2440
4 TraesCS5A01G299000 chr1A 94.068 1534 73 8 777 2293 531840080 531838548 0.000000e+00 2313
5 TraesCS5A01G299000 chr1A 95.888 608 21 4 1 605 11027112 11026506 0.000000e+00 981
6 TraesCS5A01G299000 chr1A 94.894 470 22 2 1 468 504201248 504201717 0.000000e+00 734
7 TraesCS5A01G299000 chr7A 95.687 1507 48 4 805 2294 707844389 707845895 0.000000e+00 2407
8 TraesCS5A01G299000 chr7A 94.922 1536 61 4 775 2294 650260775 650259241 0.000000e+00 2388
9 TraesCS5A01G299000 chr7A 95.003 1521 59 4 791 2294 650324575 650323055 0.000000e+00 2372
10 TraesCS5A01G299000 chr7A 95.862 580 21 3 1 579 707843430 707844007 0.000000e+00 935
11 TraesCS5A01G299000 chr7A 95.361 582 26 1 1 581 650261676 650261095 0.000000e+00 924
12 TraesCS5A01G299000 chr7A 93.307 508 32 2 1 506 650325352 650324845 0.000000e+00 749
13 TraesCS5A01G299000 chr2A 95.410 1525 47 6 792 2294 600113448 600111925 0.000000e+00 2407
14 TraesCS5A01G299000 chr2A 95.547 1482 50 3 829 2294 23796207 23797688 0.000000e+00 2357
15 TraesCS5A01G299000 chr2A 95.417 1440 49 4 871 2294 571019198 571020636 0.000000e+00 2278
16 TraesCS5A01G299000 chr2A 95.936 566 20 3 1 565 571018345 571018908 0.000000e+00 915
17 TraesCS5A01G299000 chr2A 93.245 607 38 3 1 605 23795340 23795945 0.000000e+00 891
18 TraesCS5A01G299000 chr1B 94.118 1496 70 5 816 2294 658504122 658502628 0.000000e+00 2259
19 TraesCS5A01G299000 chr1B 92.851 1203 69 4 787 1973 235897779 235898980 0.000000e+00 1729
20 TraesCS5A01G299000 chr1B 93.503 354 21 2 250 602 235897031 235897383 2.020000e-145 525
21 TraesCS5A01G299000 chr3B 95.399 1304 52 3 999 2294 59100235 59101538 0.000000e+00 2069
22 TraesCS5A01G299000 chr2B 93.201 1162 62 4 828 1973 811339 810179 0.000000e+00 1692
23 TraesCS5A01G299000 chrUn 95.094 530 23 3 1 528 248381400 248380872 0.000000e+00 832
24 TraesCS5A01G299000 chr7B 93.557 357 22 1 250 605 544972344 544972700 4.340000e-147 531
25 TraesCS5A01G299000 chr6B 92.717 357 25 1 250 605 363202951 363203307 4.370000e-142 514


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 TraesCS5A01G299000 chr5A 507564218 507566511 2293 True 1963.0 2808 100.0000 1 2294 2 chr5A.!!$R1 2293
1 TraesCS5A01G299000 chr5A 603018407 603019012 605 False 957.0 957 95.2380 1 605 1 chr5A.!!$F1 604
2 TraesCS5A01G299000 chr1A 380400781 380402317 1536 False 2440.0 2440 95.5110 775 2294 1 chr1A.!!$F1 1519
3 TraesCS5A01G299000 chr1A 531838548 531840080 1532 True 2313.0 2313 94.0680 777 2293 1 chr1A.!!$R2 1516
4 TraesCS5A01G299000 chr1A 11026506 11027112 606 True 981.0 981 95.8880 1 605 1 chr1A.!!$R1 604
5 TraesCS5A01G299000 chr7A 707843430 707845895 2465 False 1671.0 2407 95.7745 1 2294 2 chr7A.!!$F1 2293
6 TraesCS5A01G299000 chr7A 650259241 650261676 2435 True 1656.0 2388 95.1415 1 2294 2 chr7A.!!$R1 2293
7 TraesCS5A01G299000 chr7A 650323055 650325352 2297 True 1560.5 2372 94.1550 1 2294 2 chr7A.!!$R2 2293
8 TraesCS5A01G299000 chr2A 600111925 600113448 1523 True 2407.0 2407 95.4100 792 2294 1 chr2A.!!$R1 1502
9 TraesCS5A01G299000 chr2A 23795340 23797688 2348 False 1624.0 2357 94.3960 1 2294 2 chr2A.!!$F1 2293
10 TraesCS5A01G299000 chr2A 571018345 571020636 2291 False 1596.5 2278 95.6765 1 2294 2 chr2A.!!$F2 2293
11 TraesCS5A01G299000 chr1B 658502628 658504122 1494 True 2259.0 2259 94.1180 816 2294 1 chr1B.!!$R1 1478
12 TraesCS5A01G299000 chr1B 235897031 235898980 1949 False 1127.0 1729 93.1770 250 1973 2 chr1B.!!$F1 1723
13 TraesCS5A01G299000 chr3B 59100235 59101538 1303 False 2069.0 2069 95.3990 999 2294 1 chr3B.!!$F1 1295
14 TraesCS5A01G299000 chr2B 810179 811339 1160 True 1692.0 1692 93.2010 828 1973 1 chr2B.!!$R1 1145
15 TraesCS5A01G299000 chrUn 248380872 248381400 528 True 832.0 832 95.0940 1 528 1 chrUn.!!$R1 527

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
361 367 0.892755 TCCAACGTCTCCTAACGCAT 59.107 50.0 0.0 0.0 46.4 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 2017 0.106066 CAGCCTATGCCCCCAATTCA 60.106 55.0 0.0 0.0 38.69 2.57 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
108 109 2.640184 TCGATCTCCACACGTGATAGT 58.360 47.619 25.01 0.00 0.00 2.12
111 112 3.181500 CGATCTCCACACGTGATAGTTCA 60.181 47.826 25.01 0.00 0.00 3.18
307 311 1.995626 CCTTCCCACGGATCACCCT 60.996 63.158 0.00 0.00 0.00 4.34
361 367 0.892755 TCCAACGTCTCCTAACGCAT 59.107 50.000 0.00 0.00 46.40 4.73
473 479 2.681273 GATCTCCCTCCCCGACCCAT 62.681 65.000 0.00 0.00 0.00 4.00
590 596 2.941583 GTTGCCCCCTCCTTCCCT 60.942 66.667 0.00 0.00 0.00 4.20
794 1011 1.749334 GCGAGGAGATCCATTCCCGT 61.749 60.000 0.92 0.00 38.89 5.28
949 1379 2.378522 CCCCTCCCTTCCCCTCAT 59.621 66.667 0.00 0.00 0.00 2.90
1130 1570 2.025719 CGCCTGCTCGTCTAGATCA 58.974 57.895 0.00 0.00 0.00 2.92
1188 1628 1.444119 GGCGTGCAGAGTTCACCAAA 61.444 55.000 0.00 0.00 0.00 3.28
1281 1721 2.754552 CCCCATCAACAACATCATCGTT 59.245 45.455 0.00 0.00 0.00 3.85
1366 1806 0.765510 AGACTTGGGTCCTGTTGTCC 59.234 55.000 0.00 0.00 43.05 4.02
1495 1942 9.231297 CAATTTCTACCTTGTTAGGAGAATTCA 57.769 33.333 8.44 0.00 45.05 2.57
1528 1975 2.504175 GGTAATCAGCTGTGGGGAACTA 59.496 50.000 14.67 0.00 0.00 2.24
1621 2068 4.284234 CCACACAATTTGGGAAAAGAGGAT 59.716 41.667 5.47 0.00 0.00 3.24
1681 2128 1.635663 CGCCCAAGTTGGTGTCGATC 61.636 60.000 20.54 0.44 35.17 3.69
1740 2187 6.930731 GGTTACATACCAATGTTTGTCCATT 58.069 36.000 0.00 0.00 44.07 3.16
1772 2219 9.612066 TGCTATGTGTCAATGTATTCTTCATTA 57.388 29.630 0.00 0.00 34.34 1.90
1939 2388 8.046708 TCTATACTTTAATGCACCTGTGTTCAT 58.953 33.333 0.00 0.00 0.00 2.57
1956 2405 1.958579 TCATGCATGGCCAGCTTTATC 59.041 47.619 25.97 4.31 0.00 1.75
2199 2654 2.519302 GTGTGGTGCCAACTGCCT 60.519 61.111 0.00 0.00 40.16 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.181500 TGAACTATCACGTGTGGAGATCG 60.181 47.826 16.51 0.00 0.00 3.69
307 311 0.397114 TGGCTCAGATCGGCTTAGGA 60.397 55.000 7.93 0.00 0.00 2.94
361 367 2.012824 TAGGGTTTGGTTGGCCAGCA 62.013 55.000 22.07 12.13 46.91 4.41
396 402 1.311371 AGAGGGAGAGGGAGGGGAT 60.311 63.158 0.00 0.00 0.00 3.85
433 439 4.779733 GTCGGGGAGAGGGAGGCA 62.780 72.222 0.00 0.00 0.00 4.75
473 479 0.335361 GGACAGTGGAGAGGGAGGTA 59.665 60.000 0.00 0.00 0.00 3.08
574 580 0.697854 GATAGGGAAGGAGGGGGCAA 60.698 60.000 0.00 0.00 0.00 4.52
826 1043 0.984230 TGGGAGGATGTGGTCTGAAC 59.016 55.000 0.00 0.00 0.00 3.18
1130 1570 4.403734 TGGCGAAAGAGGAAAAATAACCT 58.596 39.130 0.00 0.00 39.41 3.50
1135 1575 4.397417 CAGATCTGGCGAAAGAGGAAAAAT 59.603 41.667 15.38 0.00 0.00 1.82
1136 1576 3.753272 CAGATCTGGCGAAAGAGGAAAAA 59.247 43.478 15.38 0.00 0.00 1.94
1366 1806 2.743752 CCAACAGATCACAGCGCGG 61.744 63.158 8.83 5.83 0.00 6.46
1416 1856 9.270640 TCTACTAAAATCTAGCTTACTAGGTCG 57.729 37.037 0.00 0.00 45.20 4.79
1495 1942 4.036518 AGCTGATTACCCTTGACTCATCT 58.963 43.478 0.00 0.00 0.00 2.90
1528 1975 3.019564 GCAATGACTTAAGCATGACCCT 58.980 45.455 1.29 0.00 0.00 4.34
1570 2017 0.106066 CAGCCTATGCCCCCAATTCA 60.106 55.000 0.00 0.00 38.69 2.57
1621 2068 3.435105 ACAGCGAAACATTGCAAAAGA 57.565 38.095 1.71 0.00 0.00 2.52
1740 2187 3.398406 ACATTGACACATAGCACGAACA 58.602 40.909 0.00 0.00 0.00 3.18
1772 2219 3.611530 GCGTGAACACAGGTGCATTAAAT 60.612 43.478 5.80 0.00 34.29 1.40
1939 2388 2.854963 CTAGATAAAGCTGGCCATGCA 58.145 47.619 23.46 8.50 0.00 3.96
1956 2405 1.081442 TCACACGCGACACTGCTAG 60.081 57.895 15.93 0.00 0.00 3.42
2045 2495 3.795688 TTGGAAGAGCTCAGGAAACAT 57.204 42.857 17.77 0.00 0.00 2.71
2199 2654 6.579666 ATTGACATCAGCTAGCAAAGAAAA 57.420 33.333 18.83 3.39 0.00 2.29


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

AutoCloner maintained by Alex Coulton.