Multiple sequence alignment - TraesCS2A01G150900

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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 TraesCS2A01G150900 chr2A 100.000 2754 0 0 1 2754 98721626 98724379 0.000000e+00 5086.0
1 TraesCS2A01G150900 chr2A 91.712 1291 60 20 556 1822 98578239 98579506 0.000000e+00 1748.0
2 TraesCS2A01G150900 chr2A 90.216 1155 68 21 695 1822 98603030 98604166 0.000000e+00 1465.0
3 TraesCS2A01G150900 chr2A 86.512 1164 89 40 582 1706 98455858 98456992 0.000000e+00 1218.0
4 TraesCS2A01G150900 chr2A 83.405 693 98 13 1064 1745 19913922 19914608 6.470000e-176 627.0
5 TraesCS2A01G150900 chr2A 83.154 558 61 15 1 555 98467638 98468165 1.920000e-131 479.0
6 TraesCS2A01G150900 chr2A 91.618 346 22 6 1760 2101 98457096 98457438 3.210000e-129 472.0
7 TraesCS2A01G150900 chr2A 85.615 431 36 11 2110 2514 733096416 733096846 1.960000e-116 429.0
8 TraesCS2A01G150900 chr2A 91.255 263 19 3 1848 2107 98604164 98604425 3.370000e-94 355.0
9 TraesCS2A01G150900 chr2A 92.638 163 11 1 536 698 98584238 98584399 1.650000e-57 233.0
10 TraesCS2A01G150900 chr2A 85.165 182 13 6 1848 2028 98579504 98579672 1.010000e-39 174.0
11 TraesCS2A01G150900 chr2B 93.380 1420 49 14 536 1941 151486351 151484963 0.000000e+00 2060.0
12 TraesCS2A01G150900 chr2B 88.792 1151 92 25 978 2107 151489985 151488851 0.000000e+00 1376.0
13 TraesCS2A01G150900 chr2B 90.955 398 29 4 1 397 151487360 151486969 1.880000e-146 529.0
14 TraesCS2A01G150900 chr2B 79.699 133 11 11 898 1020 30637261 30637135 6.320000e-12 82.4
15 TraesCS2A01G150900 chr2D 91.334 1304 66 23 536 1822 99572130 99573403 0.000000e+00 1738.0
16 TraesCS2A01G150900 chr2D 87.868 1393 113 36 752 2107 99654294 99655667 0.000000e+00 1585.0
17 TraesCS2A01G150900 chr2D 91.536 1146 54 16 698 1822 99560932 99562055 0.000000e+00 1539.0
18 TraesCS2A01G150900 chr2D 90.592 659 48 9 2110 2754 490592272 490592930 0.000000e+00 861.0
19 TraesCS2A01G150900 chr2D 89.866 671 41 5 2110 2754 151987522 151986853 0.000000e+00 837.0
20 TraesCS2A01G150900 chr2D 93.750 560 20 8 1 554 99563772 99564322 0.000000e+00 826.0
21 TraesCS2A01G150900 chr2D 87.466 734 59 16 1382 2101 99360557 99361271 0.000000e+00 815.0
22 TraesCS2A01G150900 chr2D 89.053 676 42 6 2110 2754 424682159 424682833 0.000000e+00 809.0
23 TraesCS2A01G150900 chr2D 88.905 676 43 10 2110 2754 620209504 620208830 0.000000e+00 804.0
24 TraesCS2A01G150900 chr2D 98.467 261 2 2 1848 2107 99573401 99573660 2.500000e-125 459.0
25 TraesCS2A01G150900 chr2D 91.635 263 17 5 1848 2107 99562053 99562313 2.610000e-95 359.0
26 TraesCS2A01G150900 chr2D 78.709 573 77 25 1 551 99657359 99657908 9.450000e-90 340.0
27 TraesCS2A01G150900 chr6D 91.896 654 42 9 2110 2754 16719678 16720329 0.000000e+00 904.0
28 TraesCS2A01G150900 chr7A 90.520 654 51 7 2110 2754 712080133 712079482 0.000000e+00 854.0
29 TraesCS2A01G150900 chr7A 90.072 554 50 5 2202 2752 177100528 177101079 0.000000e+00 713.0
30 TraesCS2A01G150900 chr5B 90.367 654 52 6 2110 2754 695839491 695838840 0.000000e+00 848.0
31 TraesCS2A01G150900 chr3D 90.779 629 49 5 2134 2754 61934067 61934694 0.000000e+00 832.0
32 TraesCS2A01G150900 chr1B 89.039 666 53 8 2109 2754 397992564 397993229 0.000000e+00 808.0
33 TraesCS2A01G150900 chr5D 89.060 649 45 11 2110 2754 4327467 4328093 0.000000e+00 782.0
34 TraesCS2A01G150900 chr1D 91.867 541 42 2 2216 2754 48907292 48906752 0.000000e+00 754.0
35 TraesCS2A01G150900 chr6A 82.000 350 58 4 1323 1669 565424559 565424906 2.680000e-75 292.0
36 TraesCS2A01G150900 chrUn 90.625 64 5 1 955 1018 24365688 24365626 1.760000e-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 TraesCS2A01G150900 chr2A 98721626 98724379 2753 False 5086.000000 5086 100.000000 1 2754 1 chr2A.!!$F4 2753
1 TraesCS2A01G150900 chr2A 98578239 98579672 1433 False 961.000000 1748 88.438500 556 2028 2 chr2A.!!$F7 1472
2 TraesCS2A01G150900 chr2A 98603030 98604425 1395 False 910.000000 1465 90.735500 695 2107 2 chr2A.!!$F8 1412
3 TraesCS2A01G150900 chr2A 98455858 98457438 1580 False 845.000000 1218 89.065000 582 2101 2 chr2A.!!$F6 1519
4 TraesCS2A01G150900 chr2A 19913922 19914608 686 False 627.000000 627 83.405000 1064 1745 1 chr2A.!!$F1 681
5 TraesCS2A01G150900 chr2A 98467638 98468165 527 False 479.000000 479 83.154000 1 555 1 chr2A.!!$F2 554
6 TraesCS2A01G150900 chr2B 151484963 151489985 5022 True 1321.666667 2060 91.042333 1 2107 3 chr2B.!!$R2 2106
7 TraesCS2A01G150900 chr2D 99572130 99573660 1530 False 1098.500000 1738 94.900500 536 2107 2 chr2D.!!$F5 1571
8 TraesCS2A01G150900 chr2D 99654294 99657908 3614 False 962.500000 1585 83.288500 1 2107 2 chr2D.!!$F6 2106
9 TraesCS2A01G150900 chr2D 99560932 99564322 3390 False 908.000000 1539 92.307000 1 2107 3 chr2D.!!$F4 2106
10 TraesCS2A01G150900 chr2D 490592272 490592930 658 False 861.000000 861 90.592000 2110 2754 1 chr2D.!!$F3 644
11 TraesCS2A01G150900 chr2D 151986853 151987522 669 True 837.000000 837 89.866000 2110 2754 1 chr2D.!!$R1 644
12 TraesCS2A01G150900 chr2D 99360557 99361271 714 False 815.000000 815 87.466000 1382 2101 1 chr2D.!!$F1 719
13 TraesCS2A01G150900 chr2D 424682159 424682833 674 False 809.000000 809 89.053000 2110 2754 1 chr2D.!!$F2 644
14 TraesCS2A01G150900 chr2D 620208830 620209504 674 True 804.000000 804 88.905000 2110 2754 1 chr2D.!!$R2 644
15 TraesCS2A01G150900 chr6D 16719678 16720329 651 False 904.000000 904 91.896000 2110 2754 1 chr6D.!!$F1 644
16 TraesCS2A01G150900 chr7A 712079482 712080133 651 True 854.000000 854 90.520000 2110 2754 1 chr7A.!!$R1 644
17 TraesCS2A01G150900 chr7A 177100528 177101079 551 False 713.000000 713 90.072000 2202 2752 1 chr7A.!!$F1 550
18 TraesCS2A01G150900 chr5B 695838840 695839491 651 True 848.000000 848 90.367000 2110 2754 1 chr5B.!!$R1 644
19 TraesCS2A01G150900 chr3D 61934067 61934694 627 False 832.000000 832 90.779000 2134 2754 1 chr3D.!!$F1 620
20 TraesCS2A01G150900 chr1B 397992564 397993229 665 False 808.000000 808 89.039000 2109 2754 1 chr1B.!!$F1 645
21 TraesCS2A01G150900 chr5D 4327467 4328093 626 False 782.000000 782 89.060000 2110 2754 1 chr5D.!!$F1 644
22 TraesCS2A01G150900 chr1D 48906752 48907292 540 True 754.000000 754 91.867000 2216 2754 1 chr1D.!!$R1 538

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
760 763 0.112995 TGACTGCCAGCAAGGGAAAT 59.887 50.000 0.0 0.0 37.23 2.17 F
1421 1493 1.413077 GCGCAGGGGTTCTACTTCTAT 59.587 52.381 0.3 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1677 0.851469 TAGTAGAGGCCCTCGATGGT 59.149 55.000 4.80 0.0 35.36 3.55 R
2705 6655 1.007238 AGGTAGCAGAGAGTGGCCTTA 59.993 52.381 3.32 0.0 0.00 2.69 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
329 330 9.920946 ACATCCCAGTAATTTCAGTACATATTT 57.079 29.630 0.00 0.00 0.00 1.40
377 378 9.613428 ATCGATCATACTTTTCAGGTATTTCAA 57.387 29.630 0.00 0.00 0.00 2.69
525 526 5.128827 TCATTAGCTCCGGAGACAACTATTT 59.871 40.000 35.69 13.28 0.00 1.40
527 528 2.159226 AGCTCCGGAGACAACTATTTCG 60.159 50.000 35.69 4.75 0.00 3.46
532 533 5.585390 TCCGGAGACAACTATTTCGATAAC 58.415 41.667 0.00 0.00 0.00 1.89
535 536 7.067372 TCCGGAGACAACTATTTCGATAACTTA 59.933 37.037 0.00 0.00 0.00 2.24
740 742 2.048312 CTCATCGCGAGGCTGACGTA 62.048 60.000 17.25 0.00 38.18 3.57
760 763 0.112995 TGACTGCCAGCAAGGGAAAT 59.887 50.000 0.00 0.00 37.23 2.17
897 907 1.437625 GCTTGGAGTGCAAGAGAGAC 58.562 55.000 26.63 5.93 0.00 3.36
1061 1125 3.220124 CGATTCTTCGGAGCAGTTGCG 62.220 57.143 0.00 0.00 43.05 4.85
1084 1148 1.547372 GTGAACAATGCAAGGCCTCAT 59.453 47.619 5.23 2.69 0.00 2.90
1114 1178 2.479412 AAGCTGTCTCTGACCGTCGC 62.479 60.000 0.00 0.00 0.00 5.19
1115 1179 2.179517 CTGTCTCTGACCGTCGCC 59.820 66.667 0.00 0.00 0.00 5.54
1169 1236 4.742201 CACGGCCTGACGAGGGTG 62.742 72.222 0.00 0.00 40.19 4.61
1421 1493 1.413077 GCGCAGGGGTTCTACTTCTAT 59.587 52.381 0.30 0.00 0.00 1.98
1544 1616 4.070552 GCCACGCGGGACTTCTCT 62.071 66.667 11.66 0.00 40.01 3.10
1577 1649 1.741401 CGGCGACTTCTTCATGGCA 60.741 57.895 0.00 0.00 0.00 4.92
1605 1677 0.884259 CACAACCATCCGCACTGACA 60.884 55.000 0.00 0.00 0.00 3.58
1687 1760 2.420372 TCTGACTCTGACGATACAGCAC 59.580 50.000 0.00 0.00 37.75 4.40
1749 1844 8.402798 TGATGTTGTTTATGCTTCTCCTTAAA 57.597 30.769 0.00 0.00 0.00 1.52
1750 1845 8.514594 TGATGTTGTTTATGCTTCTCCTTAAAG 58.485 33.333 0.00 0.00 0.00 1.85
1751 1846 8.635765 ATGTTGTTTATGCTTCTCCTTAAAGA 57.364 30.769 0.00 0.00 0.00 2.52
1752 1847 8.458573 TGTTGTTTATGCTTCTCCTTAAAGAA 57.541 30.769 0.00 0.00 34.22 2.52
1753 1848 8.908903 TGTTGTTTATGCTTCTCCTTAAAGAAA 58.091 29.630 0.00 0.00 34.95 2.52
1754 1849 9.744468 GTTGTTTATGCTTCTCCTTAAAGAAAA 57.256 29.630 0.00 0.00 34.95 2.29
1796 1931 2.810439 TGGGTTTTATGCTTGTGTGC 57.190 45.000 0.00 0.00 0.00 4.57
1833 1968 3.814842 CCCATAAGTATGCGAAATGCTCA 59.185 43.478 0.00 0.00 46.63 4.26
2040 2181 4.083537 TGAAATGAACAGTATTCACACGGC 60.084 41.667 0.00 0.00 0.00 5.68
2107 2250 1.818674 CACATTTAGGGCAAGGTGGAC 59.181 52.381 0.00 0.00 0.00 4.02
2114 2998 4.643387 GCAAGGTGGACGCCCTGT 62.643 66.667 0.00 0.00 30.99 4.00
2344 5151 4.974438 TGGGAGTCCGCTTGGGGT 62.974 66.667 2.26 0.00 36.01 4.95
2514 6384 0.107993 CGATCTGGATGCAGTGGTGT 60.108 55.000 14.43 0.00 0.00 4.16
2603 6473 1.339151 GCACGAGAGTTGGATCCCTTT 60.339 52.381 9.90 0.00 46.40 3.11
2612 6482 5.003096 AGTTGGATCCCTTTGAACTGATT 57.997 39.130 9.90 0.00 0.00 2.57
2705 6655 1.298859 GCATCGCCGTGGAGAAGTTT 61.299 55.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
294 295 8.642935 TGAAATTACTGGGATGTATGTTTCAA 57.357 30.769 0.00 0.00 36.13 2.69
344 345 9.784531 ACCTGAAAAGTATGATCGATGAAATAT 57.215 29.630 0.54 0.00 0.00 1.28
346 347 9.784531 ATACCTGAAAAGTATGATCGATGAAAT 57.215 29.630 0.54 0.00 0.00 2.17
349 350 9.261180 GAAATACCTGAAAAGTATGATCGATGA 57.739 33.333 0.54 0.00 30.86 2.92
368 369 9.573133 CCACTCTTGTGAAATAATTGAAATACC 57.427 33.333 0.00 0.00 46.55 2.73
504 505 4.439700 CGAAATAGTTGTCTCCGGAGCTAA 60.440 45.833 27.39 19.71 0.00 3.09
510 511 5.589192 AGTTATCGAAATAGTTGTCTCCGG 58.411 41.667 0.00 0.00 0.00 5.14
558 560 1.264557 CGCATGGTTGGTACGTCAAAA 59.735 47.619 0.00 0.00 0.00 2.44
740 742 0.112995 TTTCCCTTGCTGGCAGTCAT 59.887 50.000 17.16 0.00 0.00 3.06
760 763 1.522092 CTATTGGGCAGCCGACTCA 59.478 57.895 5.00 0.00 0.00 3.41
780 783 6.443792 ACCCTAAAAACGATTAAGCACTTTG 58.556 36.000 0.00 0.00 0.00 2.77
784 787 5.118050 GCAAACCCTAAAAACGATTAAGCAC 59.882 40.000 0.00 0.00 0.00 4.40
866 876 2.034558 CACTCCAAGCGACCAATTGTTT 59.965 45.455 4.43 0.00 0.00 2.83
869 879 0.109597 GCACTCCAAGCGACCAATTG 60.110 55.000 0.00 0.00 0.00 2.32
1061 1125 1.069049 AGGCCTTGCATTGTTCACAAC 59.931 47.619 0.00 0.00 38.86 3.32
1062 1126 1.340889 GAGGCCTTGCATTGTTCACAA 59.659 47.619 6.77 0.00 40.51 3.33
1066 1130 1.134907 CCATGAGGCCTTGCATTGTTC 60.135 52.381 6.77 0.00 0.00 3.18
1084 1148 0.694771 AGACAGCTTGGAAGATGCCA 59.305 50.000 4.57 0.00 45.85 4.92
1114 1178 0.234884 GAGCAGAAAAACCACGACGG 59.765 55.000 0.00 0.00 42.50 4.79
1115 1179 0.111266 CGAGCAGAAAAACCACGACG 60.111 55.000 0.00 0.00 0.00 5.12
1124 1188 2.689785 CGCCATGCCGAGCAGAAAA 61.690 57.895 0.00 0.00 43.65 2.29
1421 1493 1.135139 GTCAGCGACTCCTGCTTATCA 59.865 52.381 0.00 0.00 41.72 2.15
1577 1649 4.980805 ATGGTTGTGACGCCGCGT 62.981 61.111 20.31 20.31 45.10 6.01
1605 1677 0.851469 TAGTAGAGGCCCTCGATGGT 59.149 55.000 4.80 0.00 35.36 3.55
1687 1760 2.979676 ACACACACAGGGCATGCG 60.980 61.111 12.44 0.00 0.00 4.73
1749 1844 4.021544 ACACACACACACACCAAATTTTCT 60.022 37.500 0.00 0.00 0.00 2.52
1750 1845 4.091220 CACACACACACACACCAAATTTTC 59.909 41.667 0.00 0.00 0.00 2.29
1751 1846 3.993081 CACACACACACACACCAAATTTT 59.007 39.130 0.00 0.00 0.00 1.82
1752 1847 3.006323 ACACACACACACACACCAAATTT 59.994 39.130 0.00 0.00 0.00 1.82
1753 1848 2.560542 ACACACACACACACACCAAATT 59.439 40.909 0.00 0.00 0.00 1.82
1754 1849 2.094803 CACACACACACACACACCAAAT 60.095 45.455 0.00 0.00 0.00 2.32
1796 1931 1.159285 ATGGGCATATGCGACAATCG 58.841 50.000 22.30 0.00 43.89 3.34
1809 1944 2.293122 GCATTTCGCATACTTATGGGCA 59.707 45.455 8.14 0.00 43.75 5.36
1922 2059 5.924254 TGACACCGACAAACTTAATCTGTAG 59.076 40.000 0.00 0.00 0.00 2.74
2040 2181 2.430244 ACCGTCGCGTAACTGCAG 60.430 61.111 13.48 13.48 34.15 4.41
2283 4419 2.760385 GAGCCCTACTGTCGCCCT 60.760 66.667 0.00 0.00 0.00 5.19
2432 5426 2.755876 AGACAGAGCCGCCGATCA 60.756 61.111 0.00 0.00 0.00 2.92
2603 6473 5.659463 CAAGTTTTCACCCAAATCAGTTCA 58.341 37.500 0.00 0.00 0.00 3.18
2612 6482 1.407258 CGAAGGCAAGTTTTCACCCAA 59.593 47.619 0.00 0.00 0.00 4.12
2664 6602 3.545703 CTTCAAGAAGGGAACACACAGT 58.454 45.455 1.86 0.00 34.87 3.55
2705 6655 1.007238 AGGTAGCAGAGAGTGGCCTTA 59.993 52.381 3.32 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.