Multiple sequence alignment - TraesCS3A01G155700

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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 TraesCS3A01G155700 chr3A 100.000 3731 0 0 1 3731 149208877 149212607 0 6890
1 TraesCS3A01G155700 chr3A 98.400 2188 34 1 1544 3730 642858659 642860846 0 3845
2 TraesCS3A01G155700 chr3A 97.669 2188 51 0 1544 3731 665687022 665684835 0 3759
3 TraesCS3A01G155700 chr3A 97.306 2190 42 2 1542 3731 92259123 92256951 0 3701
4 TraesCS3A01G155700 chr3A 97.547 1549 37 1 1 1548 92260798 92259250 0 2649
5 TraesCS3A01G155700 chr3A 96.036 883 32 3 1 881 642856782 642857663 0 1434
6 TraesCS3A01G155700 chr3A 94.983 877 41 3 7 881 665688893 665688018 0 1373
7 TraesCS3A01G155700 chr3A 94.749 876 45 1 7 881 219227323 219226448 0 1362
8 TraesCS3A01G155700 chr3A 98.110 688 13 0 861 1548 642857615 642858302 0 1199
9 TraesCS3A01G155700 chr3A 97.807 684 15 0 865 1548 665688062 665687379 0 1181
10 TraesCS3A01G155700 chr6A 98.218 2189 37 2 1544 3731 450322180 450324367 0 3825
11 TraesCS3A01G155700 chr6A 96.899 1548 48 0 1 1548 450320505 450322052 0 2593
12 TraesCS3A01G155700 chr1A 97.989 2188 42 2 1544 3731 177381741 177383926 0 3795
13 TraesCS3A01G155700 chr1A 97.943 2188 45 0 1544 3731 270718843 270716656 0 3792
14 TraesCS3A01G155700 chr1A 96.708 1549 50 1 1 1548 270720748 270719200 0 2577
15 TraesCS3A01G155700 chr1A 94.829 1547 50 16 4 1548 177379866 177381384 0 2386
16 TraesCS3A01G155700 chr5A 97.441 2188 56 0 1544 3731 685307878 685310065 0 3731
17 TraesCS3A01G155700 chr5A 96.984 2188 55 1 1544 3731 518788346 518786170 0 3664
18 TraesCS3A01G155700 chr5A 96.755 2188 42 2 1544 3731 155928797 155930955 0 3620
19 TraesCS3A01G155700 chr5A 96.708 1549 50 1 1 1548 685305973 685307521 0 2577
20 TraesCS3A01G155700 chr5A 95.696 883 36 2 1 881 155926920 155927802 0 1419
21 TraesCS3A01G155700 chr5A 98.246 684 12 0 865 1548 155927758 155928441 0 1197
22 TraesCS3A01G155700 chr7A 98.134 1661 30 1 2072 3731 271152929 271151269 0 2894
23 TraesCS3A01G155700 chr5B 96.637 684 23 0 865 1548 521054932 521054249 0 1136


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 TraesCS3A01G155700 chr3A 149208877 149212607 3730 False 6890.000000 6890 100.000000 1 3731 1 chr3A.!!$F1 3730
1 TraesCS3A01G155700 chr3A 92256951 92260798 3847 True 3175.000000 3701 97.426500 1 3731 2 chr3A.!!$R2 3730
2 TraesCS3A01G155700 chr3A 642856782 642860846 4064 False 2159.333333 3845 97.515333 1 3730 3 chr3A.!!$F2 3729
3 TraesCS3A01G155700 chr3A 665684835 665688893 4058 True 2104.333333 3759 96.819667 7 3731 3 chr3A.!!$R3 3724
4 TraesCS3A01G155700 chr3A 219226448 219227323 875 True 1362.000000 1362 94.749000 7 881 1 chr3A.!!$R1 874
5 TraesCS3A01G155700 chr6A 450320505 450324367 3862 False 3209.000000 3825 97.558500 1 3731 2 chr6A.!!$F1 3730
6 TraesCS3A01G155700 chr1A 270716656 270720748 4092 True 3184.500000 3792 97.325500 1 3731 2 chr1A.!!$R1 3730
7 TraesCS3A01G155700 chr1A 177379866 177383926 4060 False 3090.500000 3795 96.409000 4 3731 2 chr1A.!!$F1 3727
8 TraesCS3A01G155700 chr5A 518786170 518788346 2176 True 3664.000000 3664 96.984000 1544 3731 1 chr5A.!!$R1 2187
9 TraesCS3A01G155700 chr5A 685305973 685310065 4092 False 3154.000000 3731 97.074500 1 3731 2 chr5A.!!$F2 3730
10 TraesCS3A01G155700 chr5A 155926920 155930955 4035 False 2078.666667 3620 96.899000 1 3731 3 chr5A.!!$F1 3730
11 TraesCS3A01G155700 chr7A 271151269 271152929 1660 True 2894.000000 2894 98.134000 2072 3731 1 chr7A.!!$R1 1659
12 TraesCS3A01G155700 chr5B 521054249 521054932 683 True 1136.000000 1136 96.637000 865 1548 1 chr5B.!!$R1 683

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
863 867 1.603802 CGTGCTCATTGTGTTTGACCT 59.396 47.619 0.0 0.0 0.0 3.85 F
1593 1985 1.534476 TTGGTGGCTACGGGACTCA 60.534 57.895 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2709 4.024893 CCAGTATTGAATGTACCACATCGC 60.025 45.833 0.0 0.0 37.97 4.58 R
3206 3614 2.224161 ACTTTGCCCGAGAGATAGCATC 60.224 50.000 0.0 0.0 34.72 3.91 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
162 163 2.872038 GCCGGATCTGAACAAGAACACT 60.872 50.000 5.05 0.0 38.79 3.55
476 477 3.208173 AGGTACCCTCTTCCTCTCCTTA 58.792 50.000 8.74 0.0 0.00 2.69
477 478 3.052717 AGGTACCCTCTTCCTCTCCTTAC 60.053 52.174 8.74 0.0 0.00 2.34
480 481 3.208173 ACCCTCTTCCTCTCCTTACCTA 58.792 50.000 0.00 0.0 0.00 3.08
637 639 5.864474 ACTCTTGCTGTTCTACATACTTTCG 59.136 40.000 0.00 0.0 0.00 3.46
661 663 2.330216 ACCACTATCATACTCCAGGCC 58.670 52.381 0.00 0.0 0.00 5.19
844 848 2.244117 ATACCCACACAGCCAGCTCG 62.244 60.000 0.00 0.0 0.00 5.03
863 867 1.603802 CGTGCTCATTGTGTTTGACCT 59.396 47.619 0.00 0.0 0.00 3.85
1483 1514 5.777449 TGAATCATCCCTCTTCTGTAGGTA 58.223 41.667 0.00 0.0 31.70 3.08
1584 1976 4.752879 GGCGCGAGTTGGTGGCTA 62.753 66.667 12.10 0.0 39.61 3.93
1593 1985 1.534476 TTGGTGGCTACGGGACTCA 60.534 57.895 0.00 0.0 0.00 3.41
3206 3614 5.446741 GCATAAATGGCATCAAAACTGCTTG 60.447 40.000 0.00 0.0 39.60 4.01
3232 3640 4.262249 GCTATCTCTCGGGCAAAGTAGATT 60.262 45.833 0.00 0.0 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.046988 CGCTGGTGATGGAGCACA 60.047 61.111 0.00 0.00 40.52 4.57
162 163 1.003118 GCCAGGTACATGAACCACTCA 59.997 52.381 9.54 0.00 42.40 3.41
361 362 3.482783 GTGGAAGAGCAGCGTCGC 61.483 66.667 9.80 9.80 0.00 5.19
368 369 3.610791 CTCGTCGCGTGGAAGAGCA 62.611 63.158 5.77 0.00 42.83 4.26
476 477 2.897823 ATTGGAGGTGAGGGATAGGT 57.102 50.000 0.00 0.00 0.00 3.08
477 478 3.863086 AGTATTGGAGGTGAGGGATAGG 58.137 50.000 0.00 0.00 0.00 2.57
661 663 4.100529 CGTGGAATTGCAATTCTAAGCAG 58.899 43.478 37.77 24.71 43.33 4.24
844 848 2.030805 GGAGGTCAAACACAATGAGCAC 60.031 50.000 8.24 2.22 45.36 4.40
848 852 2.158623 AGCTGGAGGTCAAACACAATGA 60.159 45.455 0.00 0.00 0.00 2.57
850 854 2.508526 GAGCTGGAGGTCAAACACAAT 58.491 47.619 0.00 0.00 41.81 2.71
851 855 1.810031 CGAGCTGGAGGTCAAACACAA 60.810 52.381 0.00 0.00 42.28 3.33
1328 1359 8.612619 GTGATTCAGAGTTTCAAAGTGAAGTTA 58.387 33.333 0.00 0.00 37.70 2.24
1483 1514 7.182060 TCCCTTAGTTCCAAAGCTTCATAAAT 58.818 34.615 0.00 0.00 0.00 1.40
1584 1976 4.657824 CGTGCCGTTGAGTCCCGT 62.658 66.667 0.00 0.00 0.00 5.28
1593 1985 1.795768 CATATATGAGCCGTGCCGTT 58.204 50.000 6.92 0.00 0.00 4.44
2304 2709 4.024893 CCAGTATTGAATGTACCACATCGC 60.025 45.833 0.00 0.00 37.97 4.58
3167 3574 7.068470 TGCCATTTATGCATTATTTCTGAGACA 59.932 33.333 3.54 0.00 32.85 3.41
3206 3614 2.224161 ACTTTGCCCGAGAGATAGCATC 60.224 50.000 0.00 0.00 34.72 3.91
3232 3640 9.470399 TGATGTACAGATAGTAACCAAACTAGA 57.530 33.333 0.33 0.00 35.50 2.43
3510 3936 9.161629 CATAACATTAGACAGACCAACACATAA 57.838 33.333 0.00 0.00 0.00 1.90
3665 4091 2.222227 AATTCTGGACAGGGCCTTTC 57.778 50.000 11.36 11.36 0.00 2.62


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

AutoCloner maintained by Alex Coulton.