Multiple sequence alignment - TraesCS1D01G027500

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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 TraesCS1D01G027500 chr1D 100.000 2456 0 0 1 2456 11043877 11041422 0.000000e+00 4536.0
1 TraesCS1D01G027500 chr1D 98.955 1531 14 2 928 2456 11091665 11090135 0.000000e+00 2737.0
2 TraesCS1D01G027500 chr1D 94.106 1476 44 11 928 2364 11126232 11124761 0.000000e+00 2204.0
3 TraesCS1D01G027500 chr1D 98.300 941 14 1 1 939 454651657 454650717 0.000000e+00 1648.0
4 TraesCS1D01G027500 chr1D 76.214 618 86 32 934 1534 11202240 11201667 1.120000e-68 270.0
5 TraesCS1D01G027500 chr1A 92.264 1422 54 11 986 2364 22631680 22633088 0.000000e+00 1965.0
6 TraesCS1D01G027500 chr1A 84.938 644 52 19 927 1554 12680087 12680701 5.810000e-171 610.0
7 TraesCS1D01G027500 chr1A 93.333 300 18 2 2057 2355 12688659 12688957 2.240000e-120 442.0
8 TraesCS1D01G027500 chr1A 92.806 139 1 4 1925 2056 12686574 12686710 2.490000e-45 193.0
9 TraesCS1D01G027500 chr1A 96.552 58 2 0 928 985 22631516 22631573 2.010000e-16 97.1
10 TraesCS1D01G027500 chr1A 84.932 73 4 5 1657 1727 108106603 108106536 1.580000e-07 67.6
11 TraesCS1D01G027500 chr1B 90.508 1475 61 29 934 2364 16480834 16479395 0.000000e+00 1875.0
12 TraesCS1D01G027500 chr1B 87.260 832 50 24 1580 2364 16647074 16646252 0.000000e+00 898.0
13 TraesCS1D01G027500 chr1B 95.430 372 14 2 1214 1582 16652557 16652186 7.560000e-165 590.0
14 TraesCS1D01G027500 chr1B 91.822 269 13 4 928 1187 16652819 16652551 1.390000e-97 366.0
15 TraesCS1D01G027500 chr1B 91.566 83 7 0 2374 2456 460633088 460633006 5.550000e-22 115.0
16 TraesCS1D01G027500 chr7D 99.032 930 8 1 1 929 605573982 605574911 0.000000e+00 1666.0
17 TraesCS1D01G027500 chr7D 98.719 937 10 1 1 935 89272805 89273741 0.000000e+00 1663.0
18 TraesCS1D01G027500 chr7D 98.818 931 9 1 1 929 224463404 224462474 0.000000e+00 1657.0
19 TraesCS1D01G027500 chr3D 99.031 929 8 1 1 928 297460453 297461381 0.000000e+00 1664.0
20 TraesCS1D01G027500 chr3D 98.926 931 8 1 1 929 491628683 491627753 0.000000e+00 1663.0
21 TraesCS1D01G027500 chr3D 98.610 935 11 1 1 933 46547678 46546744 0.000000e+00 1653.0
22 TraesCS1D01G027500 chr6D 98.926 931 8 1 1 929 290841968 290842898 0.000000e+00 1663.0
23 TraesCS1D01G027500 chr5D 98.406 941 13 1 1 939 43965021 43964081 0.000000e+00 1653.0
24 TraesCS1D01G027500 chr7B 84.938 644 52 19 927 1554 192779608 192780222 5.810000e-171 610.0
25 TraesCS1D01G027500 chr7B 92.806 139 1 4 1925 2056 192786095 192786231 2.490000e-45 193.0
26 TraesCS1D01G027500 chr7B 81.522 92 17 0 2365 2456 104219625 104219534 2.620000e-10 76.8
27 TraesCS1D01G027500 chr2B 84.938 644 52 19 927 1554 47190676 47190062 5.810000e-171 610.0
28 TraesCS1D01G027500 chr2B 92.806 139 1 4 1925 2056 47184189 47184053 2.490000e-45 193.0
29 TraesCS1D01G027500 chr2B 85.556 90 13 0 2367 2456 68905660 68905571 7.230000e-16 95.3
30 TraesCS1D01G027500 chr2B 83.721 86 12 2 2366 2450 150394380 150394464 2.020000e-11 80.5
31 TraesCS1D01G027500 chrUn 88.652 282 22 7 928 1205 351922124 351921849 3.910000e-88 335.0
32 TraesCS1D01G027500 chr7A 89.691 97 9 1 2360 2456 706517642 706517737 3.320000e-24 122.0
33 TraesCS1D01G027500 chr4D 89.062 64 7 0 2384 2447 470862017 470862080 2.020000e-11 80.5
34 TraesCS1D01G027500 chr6B 88.136 59 7 0 2364 2422 574426571 574426629 1.220000e-08 71.3
35 TraesCS1D01G027500 chr4B 82.278 79 13 1 2364 2441 123495312 123495234 1.580000e-07 67.6


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 TraesCS1D01G027500 chr1D 11041422 11043877 2455 True 4536.00 4536 100.0000 1 2456 1 chr1D.!!$R1 2455
1 TraesCS1D01G027500 chr1D 11090135 11091665 1530 True 2737.00 2737 98.9550 928 2456 1 chr1D.!!$R2 1528
2 TraesCS1D01G027500 chr1D 11124761 11126232 1471 True 2204.00 2204 94.1060 928 2364 1 chr1D.!!$R3 1436
3 TraesCS1D01G027500 chr1D 454650717 454651657 940 True 1648.00 1648 98.3000 1 939 1 chr1D.!!$R5 938
4 TraesCS1D01G027500 chr1D 11201667 11202240 573 True 270.00 270 76.2140 934 1534 1 chr1D.!!$R4 600
5 TraesCS1D01G027500 chr1A 22631516 22633088 1572 False 1031.05 1965 94.4080 928 2364 2 chr1A.!!$F3 1436
6 TraesCS1D01G027500 chr1A 12680087 12680701 614 False 610.00 610 84.9380 927 1554 1 chr1A.!!$F1 627
7 TraesCS1D01G027500 chr1A 12686574 12688957 2383 False 317.50 442 93.0695 1925 2355 2 chr1A.!!$F2 430
8 TraesCS1D01G027500 chr1B 16479395 16480834 1439 True 1875.00 1875 90.5080 934 2364 1 chr1B.!!$R1 1430
9 TraesCS1D01G027500 chr1B 16646252 16647074 822 True 898.00 898 87.2600 1580 2364 1 chr1B.!!$R2 784
10 TraesCS1D01G027500 chr1B 16652186 16652819 633 True 478.00 590 93.6260 928 1582 2 chr1B.!!$R4 654
11 TraesCS1D01G027500 chr7D 605573982 605574911 929 False 1666.00 1666 99.0320 1 929 1 chr7D.!!$F2 928
12 TraesCS1D01G027500 chr7D 89272805 89273741 936 False 1663.00 1663 98.7190 1 935 1 chr7D.!!$F1 934
13 TraesCS1D01G027500 chr7D 224462474 224463404 930 True 1657.00 1657 98.8180 1 929 1 chr7D.!!$R1 928
14 TraesCS1D01G027500 chr3D 297460453 297461381 928 False 1664.00 1664 99.0310 1 928 1 chr3D.!!$F1 927
15 TraesCS1D01G027500 chr3D 491627753 491628683 930 True 1663.00 1663 98.9260 1 929 1 chr3D.!!$R2 928
16 TraesCS1D01G027500 chr3D 46546744 46547678 934 True 1653.00 1653 98.6100 1 933 1 chr3D.!!$R1 932
17 TraesCS1D01G027500 chr6D 290841968 290842898 930 False 1663.00 1663 98.9260 1 929 1 chr6D.!!$F1 928
18 TraesCS1D01G027500 chr5D 43964081 43965021 940 True 1653.00 1653 98.4060 1 939 1 chr5D.!!$R1 938
19 TraesCS1D01G027500 chr7B 192779608 192780222 614 False 610.00 610 84.9380 927 1554 1 chr7B.!!$F1 627
20 TraesCS1D01G027500 chr2B 47190062 47190676 614 True 610.00 610 84.9380 927 1554 1 chr2B.!!$R2 627

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
221 222 2.691252 ATCCCCGGGTTCCTCACC 60.691 66.667 21.85 0.0 46.46 4.02 F
1059 1179 2.627515 TGCTAGCCTGTCAATCATCC 57.372 50.000 13.29 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1455 0.750911 CTCCTTGGCCTCCTTGATGC 60.751 60.000 3.32 0.0 0.0 3.91 R
2176 4342 1.265365 GAAGCAGAGAGGTGTTGTTGC 59.735 52.381 0.00 0.0 0.0 4.17 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
182 183 6.096705 TCCTGAAATCTCTTTTGCTGTTCAAA 59.903 34.615 0.00 0.0 42.50 2.69
221 222 2.691252 ATCCCCGGGTTCCTCACC 60.691 66.667 21.85 0.0 46.46 4.02
310 311 4.602340 TTCTTCTCCAAACTCGCTTACT 57.398 40.909 0.00 0.0 0.00 2.24
564 565 6.590234 TGTCTACTGTGACAACATATCAGT 57.410 37.500 9.56 0.0 43.08 3.41
1059 1179 2.627515 TGCTAGCCTGTCAATCATCC 57.372 50.000 13.29 0.0 0.00 3.51
1304 1455 3.721706 GGAGGTGGTGGGGCTGAG 61.722 72.222 0.00 0.0 0.00 3.35
2416 4589 4.019141 ACAAAGATACCAATTACACCCGGA 60.019 41.667 0.73 0.0 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 183 6.598457 GGATCATGCATATAGAGACATGCTTT 59.402 38.462 0.00 0.00 46.19 3.51
221 222 7.112009 CCGAAGAATGCGTTTAACATGATTATG 59.888 37.037 0.00 0.00 32.87 1.90
564 565 4.030216 TGGATTGCTGGTCATGTAGACTA 58.970 43.478 0.00 0.00 46.72 2.59
635 636 2.031870 ACCAAGAGCAACCTTTTCACC 58.968 47.619 0.00 0.00 0.00 4.02
1039 1159 2.239402 TGGATGATTGACAGGCTAGCAA 59.761 45.455 18.24 1.46 0.00 3.91
1040 1160 1.839354 TGGATGATTGACAGGCTAGCA 59.161 47.619 18.24 0.00 0.00 3.49
1059 1179 1.983605 GACGTACGGCCGATGATATTG 59.016 52.381 35.90 14.13 0.00 1.90
1304 1455 0.750911 CTCCTTGGCCTCCTTGATGC 60.751 60.000 3.32 0.00 0.00 3.91
2176 4342 1.265365 GAAGCAGAGAGGTGTTGTTGC 59.735 52.381 0.00 0.00 0.00 4.17
2395 4568 4.226620 AGTCCGGGTGTAATTGGTATCTTT 59.773 41.667 0.00 0.00 0.00 2.52
2416 4589 7.607991 CCTTTGAACATCTTGTTGGTATAGAGT 59.392 37.037 0.00 0.00 41.28 3.24


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

AutoCloner maintained by Alex Coulton.