Multiple sequence alignment - TraesCS3A01G217100

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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 TraesCS3A01G217100 chr3A 100.000 2399 0 0 1 2399 395990804 395993202 0.000000e+00 4431.0
1 TraesCS3A01G217100 chr3A 95.499 822 31 5 1582 2399 571279746 571278927 0.000000e+00 1308.0
2 TraesCS3A01G217100 chr3A 95.388 824 28 5 1582 2399 37782614 37783433 0.000000e+00 1303.0
3 TraesCS3A01G217100 chr3A 95.383 823 31 5 1582 2399 600472810 600471990 0.000000e+00 1303.0
4 TraesCS3A01G217100 chr3A 95.371 821 34 3 1582 2399 654301732 654300913 0.000000e+00 1303.0
5 TraesCS3A01G217100 chr7A 92.992 1584 90 13 6 1586 711981018 711982583 0.000000e+00 2290.0
6 TraesCS3A01G217100 chr7A 95.706 815 31 3 1588 2399 30371095 30371908 0.000000e+00 1308.0
7 TraesCS3A01G217100 chr7A 83.622 751 91 13 839 1583 727873989 727874713 0.000000e+00 676.0
8 TraesCS3A01G217100 chr7A 84.834 422 57 7 412 828 727873629 727874048 3.690000e-113 418.0
9 TraesCS3A01G217100 chr2B 92.672 1583 103 8 6 1585 1894280 1892708 0.000000e+00 2268.0
10 TraesCS3A01G217100 chr2B 92.261 827 57 5 32 854 699825277 699826100 0.000000e+00 1166.0
11 TraesCS3A01G217100 chr2B 95.735 633 27 0 950 1582 699826403 699827035 0.000000e+00 1020.0
12 TraesCS3A01G217100 chr2B 93.503 354 23 0 1229 1582 504550925 504551278 5.870000e-146 527.0
13 TraesCS3A01G217100 chr6B 91.335 1581 83 15 6 1582 245266884 245265354 0.000000e+00 2111.0
14 TraesCS3A01G217100 chr5A 85.822 1594 188 29 6 1584 35199842 35198272 0.000000e+00 1657.0
15 TraesCS3A01G217100 chr5A 95.488 820 31 4 1582 2399 349004579 349003764 0.000000e+00 1304.0
16 TraesCS3A01G217100 chr2A 96.098 820 27 3 1582 2399 581509409 581508593 0.000000e+00 1332.0
17 TraesCS3A01G217100 chr2A 93.409 789 46 4 6 791 766354872 766355657 0.000000e+00 1164.0
18 TraesCS3A01G217100 chr2A 92.848 755 40 6 834 1582 766355653 766356399 0.000000e+00 1083.0
19 TraesCS3A01G217100 chr4A 95.864 822 30 3 1582 2399 490377870 490378691 0.000000e+00 1327.0
20 TraesCS3A01G217100 chr4A 95.284 827 30 4 1582 2399 45286419 45285593 0.000000e+00 1303.0
21 TraesCS3A01G217100 chr3B 85.538 650 83 6 938 1583 49851692 49851050 0.000000e+00 669.0
22 TraesCS3A01G217100 chr7B 84.810 79 11 1 1519 1596 750532559 750532481 7.110000e-11 78.7


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 TraesCS3A01G217100 chr3A 395990804 395993202 2398 False 4431.0 4431 100.0000 1 2399 1 chr3A.!!$F2 2398
1 TraesCS3A01G217100 chr3A 571278927 571279746 819 True 1308.0 1308 95.4990 1582 2399 1 chr3A.!!$R1 817
2 TraesCS3A01G217100 chr3A 37782614 37783433 819 False 1303.0 1303 95.3880 1582 2399 1 chr3A.!!$F1 817
3 TraesCS3A01G217100 chr3A 600471990 600472810 820 True 1303.0 1303 95.3830 1582 2399 1 chr3A.!!$R2 817
4 TraesCS3A01G217100 chr3A 654300913 654301732 819 True 1303.0 1303 95.3710 1582 2399 1 chr3A.!!$R3 817
5 TraesCS3A01G217100 chr7A 711981018 711982583 1565 False 2290.0 2290 92.9920 6 1586 1 chr7A.!!$F2 1580
6 TraesCS3A01G217100 chr7A 30371095 30371908 813 False 1308.0 1308 95.7060 1588 2399 1 chr7A.!!$F1 811
7 TraesCS3A01G217100 chr7A 727873629 727874713 1084 False 547.0 676 84.2280 412 1583 2 chr7A.!!$F3 1171
8 TraesCS3A01G217100 chr2B 1892708 1894280 1572 True 2268.0 2268 92.6720 6 1585 1 chr2B.!!$R1 1579
9 TraesCS3A01G217100 chr2B 699825277 699827035 1758 False 1093.0 1166 93.9980 32 1582 2 chr2B.!!$F2 1550
10 TraesCS3A01G217100 chr6B 245265354 245266884 1530 True 2111.0 2111 91.3350 6 1582 1 chr6B.!!$R1 1576
11 TraesCS3A01G217100 chr5A 35198272 35199842 1570 True 1657.0 1657 85.8220 6 1584 1 chr5A.!!$R1 1578
12 TraesCS3A01G217100 chr5A 349003764 349004579 815 True 1304.0 1304 95.4880 1582 2399 1 chr5A.!!$R2 817
13 TraesCS3A01G217100 chr2A 581508593 581509409 816 True 1332.0 1332 96.0980 1582 2399 1 chr2A.!!$R1 817
14 TraesCS3A01G217100 chr2A 766354872 766356399 1527 False 1123.5 1164 93.1285 6 1582 2 chr2A.!!$F1 1576
15 TraesCS3A01G217100 chr4A 490377870 490378691 821 False 1327.0 1327 95.8640 1582 2399 1 chr4A.!!$F1 817
16 TraesCS3A01G217100 chr4A 45285593 45286419 826 True 1303.0 1303 95.2840 1582 2399 1 chr4A.!!$R1 817
17 TraesCS3A01G217100 chr3B 49851050 49851692 642 True 669.0 669 85.5380 938 1583 1 chr3B.!!$R1 645

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
585 624 2.287547 GGTTTCATGCAAGCGACTTCAA 60.288 45.455 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1882 1.448985 GGTTCACCATACGTGCATGT 58.551 50.0 17.19 17.19 42.69 3.21 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
72 73 3.705604 TCTTTCGAAAAGGCAAAAGCAG 58.294 40.909 12.41 0.00 0.00 4.24
75 76 2.297701 TCGAAAAGGCAAAAGCAGAGT 58.702 42.857 0.00 0.00 0.00 3.24
360 394 5.414454 GGCAACTTCCACAATACTCATACAA 59.586 40.000 0.00 0.00 0.00 2.41
407 441 2.426738 CAACTTCCACAGTGCTCCAAAA 59.573 45.455 0.00 0.00 35.12 2.44
440 474 4.036734 TCAAGAATGTTCAACTTCCACAGC 59.963 41.667 0.00 0.00 0.00 4.40
525 562 6.831664 AGAATGTTCTCATACCCATTACCT 57.168 37.500 0.00 0.00 33.49 3.08
585 624 2.287547 GGTTTCATGCAAGCGACTTCAA 60.288 45.455 0.00 0.00 0.00 2.69
657 696 8.623769 ACACTCCTATAAATGGGCCATAATATT 58.376 33.333 21.54 12.91 0.00 1.28
913 957 9.629878 TTAAAAACTCTTATGGTTGTAGTCCAA 57.370 29.630 0.00 0.00 38.52 3.53
1067 1318 4.255301 AGTTATTTCGCCGGTTTCATGTA 58.745 39.130 1.90 0.00 0.00 2.29
1112 1367 6.741992 CATACTTTTCTACAGGATGCAACA 57.258 37.500 0.00 0.00 42.53 3.33
1149 1404 4.188247 TGTTCTACCCTCTTCATCAACG 57.812 45.455 0.00 0.00 0.00 4.10
1215 1474 2.299867 AGACATGAAAAATGCCACCACC 59.700 45.455 0.00 0.00 0.00 4.61
1263 1522 0.033504 AGGACGCACGTGAAGACAAT 59.966 50.000 22.23 2.79 0.00 2.71
1386 1645 3.292936 AACCGCGTGGACGACTCT 61.293 61.111 24.59 0.00 43.02 3.24
1517 1780 9.891828 GTTAATTGAAATATCCATGTCGCATTA 57.108 29.630 0.00 0.00 0.00 1.90
1586 1849 4.094442 GCGTGGGGAATTGTCTAGTTTAAG 59.906 45.833 0.00 0.00 0.00 1.85
1619 1882 6.318144 TGTGTTAAAGTTTGTGATTCCCGTAA 59.682 34.615 0.00 0.00 0.00 3.18
1720 1983 1.492720 GGGACGAGCGATGATCTTTC 58.507 55.000 0.00 0.00 0.00 2.62
1738 2001 2.320681 TCCCTACCAATCTATCCCCG 57.679 55.000 0.00 0.00 0.00 5.73
1828 2091 6.925610 TTATGACTAATGTTGAGTCCATGC 57.074 37.500 0.61 0.00 42.29 4.06
1904 2171 1.884579 CGCCGGTATCATACACCTACT 59.115 52.381 1.90 0.00 33.62 2.57
2013 2283 4.628333 ACCGTTCCGTTTATTATGACACAG 59.372 41.667 0.00 0.00 0.00 3.66
2047 2317 4.530553 TCATATTGCATATCCCGGTACACT 59.469 41.667 0.00 0.00 0.00 3.55
2075 2345 7.144661 CGGAGGCATTCATATAGAGTCATATC 58.855 42.308 0.00 0.00 0.00 1.63
2174 2447 4.162320 TGTCCCAGTGAGTAAAGGATGATC 59.838 45.833 0.00 0.00 0.00 2.92
2196 2469 3.118408 CGAGACTATGATTCCCCCACAAA 60.118 47.826 0.00 0.00 0.00 2.83
2336 2624 8.159229 AGGGACAATGTTACTATCCTTTTACT 57.841 34.615 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 7.584122 TGGGAAGTAATACATACTCTCACTC 57.416 40.000 0.00 0.00 44.22 3.51
75 76 8.867097 GGTAATGGGAAGTAATACATACTCTCA 58.133 37.037 0.00 0.00 44.22 3.27
281 291 9.860898 AGAAATGCAACAATTATTAGAAGTTCC 57.139 29.630 0.00 0.00 0.00 3.62
351 361 2.038952 TGTGGAAGCTGCTTGTATGAGT 59.961 45.455 21.25 0.00 0.00 3.41
360 394 4.837085 AGCATTGTGGAAGCTGCT 57.163 50.000 0.00 0.00 40.02 4.24
440 474 2.253452 GCTGGCAGTGTCAAAGCG 59.747 61.111 17.16 0.00 0.00 4.68
477 514 5.580691 CGGTCACAATAGAAGTTGAGCAATA 59.419 40.000 0.00 0.00 33.37 1.90
478 515 4.393062 CGGTCACAATAGAAGTTGAGCAAT 59.607 41.667 0.00 0.00 33.37 3.56
520 557 9.754382 GACATCTCGGTTACAATATAAAGGTAA 57.246 33.333 0.00 0.00 0.00 2.85
759 800 7.433680 ACCGAGCAATGAATTTTTAGAAACTT 58.566 30.769 0.00 0.00 0.00 2.66
836 879 7.928307 ACACTATTAACTGAGCAATGAATGT 57.072 32.000 0.00 0.00 0.00 2.71
931 975 6.261435 TGTAGATATAGGTTGTATGGGAGGG 58.739 44.000 0.00 0.00 0.00 4.30
934 978 6.785466 TGCTTGTAGATATAGGTTGTATGGGA 59.215 38.462 0.00 0.00 0.00 4.37
963 1213 7.396540 AGTGAAGTTTTCAGTGTGAGAAAAT 57.603 32.000 4.65 0.00 44.10 1.82
1067 1318 4.141981 TGCGGGCAAATTGTGAAATATCAT 60.142 37.500 0.00 0.00 38.01 2.45
1149 1404 4.300803 TGTGAGTTTTTCTTGATGCATGC 58.699 39.130 11.82 11.82 0.00 4.06
1215 1474 2.424601 AGTGATCCATGTTGCGGATTTG 59.575 45.455 0.00 0.00 43.49 2.32
1263 1522 4.530553 TGTTCCTGGAGTAGCTTTGTGATA 59.469 41.667 0.00 0.00 0.00 2.15
1566 1829 6.457159 TTCCTTAAACTAGACAATTCCCCA 57.543 37.500 0.00 0.00 0.00 4.96
1586 1849 9.744468 AATCACAAACTTTAACACAAGTATTCC 57.256 29.630 0.00 0.00 35.87 3.01
1619 1882 1.448985 GGTTCACCATACGTGCATGT 58.551 50.000 17.19 17.19 42.69 3.21
1714 1977 4.852697 GGGGATAGATTGGTAGGGAAAGAT 59.147 45.833 0.00 0.00 0.00 2.40
1720 1983 2.025636 ACGGGGATAGATTGGTAGGG 57.974 55.000 0.00 0.00 0.00 3.53
1738 2001 1.719780 GTATTACGCGCATGCTCCTAC 59.280 52.381 17.13 5.23 39.65 3.18
1828 2091 3.735237 AGGGTGAGAGTGCGTATAATG 57.265 47.619 0.00 0.00 0.00 1.90
1904 2171 6.354130 GTGGCTGTTTTGAGGAAGGTATATA 58.646 40.000 0.00 0.00 0.00 0.86
2013 2283 7.415989 GGGATATGCAATATGACAATGATGGAC 60.416 40.741 0.00 0.00 40.26 4.02
2174 2447 2.039418 TGTGGGGGAATCATAGTCTCG 58.961 52.381 0.00 0.00 0.00 4.04
2336 2624 4.447290 TGCTACTTTGAAGCACAAGTGTA 58.553 39.130 1.79 0.00 44.78 2.90


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

AutoCloner maintained by Alex Coulton.