Multiple sequence alignment - TraesCS4A01G432700

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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 TraesCS4A01G432700 chr4A 100.000 2984 0 0 1 2984 703440590 703443573 0.000000e+00 5511.0
1 TraesCS4A01G432700 chr4A 97.247 908 19 3 1 902 26415720 26414813 0.000000e+00 1533.0
2 TraesCS4A01G432700 chrUn 99.698 2985 8 1 1 2984 50427748 50430732 0.000000e+00 5461.0
3 TraesCS4A01G432700 chrUn 97.484 914 16 5 1 907 316447987 316447074 0.000000e+00 1554.0
4 TraesCS4A01G432700 chrUn 92.857 910 55 7 1 902 85703364 85702457 0.000000e+00 1312.0
5 TraesCS4A01G432700 chrUn 93.351 737 47 2 2249 2984 45191756 45192491 0.000000e+00 1088.0
6 TraesCS4A01G432700 chrUn 97.436 78 2 0 904 981 189406877 189406954 1.870000e-27 134.0
7 TraesCS4A01G432700 chrUn 97.436 78 2 0 904 981 251409718 251409641 1.870000e-27 134.0
8 TraesCS4A01G432700 chrUn 97.436 78 2 0 904 981 360799108 360799185 1.870000e-27 134.0
9 TraesCS4A01G432700 chr7A 97.094 1101 29 1 983 2080 27462128 27463228 0.000000e+00 1853.0
10 TraesCS4A01G432700 chr7A 96.552 203 7 0 2044 2246 27463323 27463525 1.330000e-88 337.0
11 TraesCS4A01G432700 chr7A 78.814 118 25 0 1753 1870 581137430 581137547 2.470000e-11 80.5
12 TraesCS4A01G432700 chr2B 98.232 905 14 1 1 903 46006158 46005254 0.000000e+00 1581.0
13 TraesCS4A01G432700 chr2B 93.377 906 51 7 1 902 752879006 752878106 0.000000e+00 1332.0
14 TraesCS4A01G432700 chr5A 98.228 903 15 1 1 902 687367607 687366705 0.000000e+00 1578.0
15 TraesCS4A01G432700 chr2A 98.009 904 16 1 1 902 32556588 32555685 0.000000e+00 1568.0
16 TraesCS4A01G432700 chr2A 93.333 735 48 1 2249 2982 765633095 765633829 0.000000e+00 1085.0
17 TraesCS4A01G432700 chr5B 93.619 909 49 7 1 906 576074533 576073631 0.000000e+00 1349.0
18 TraesCS4A01G432700 chr3A 94.437 737 40 1 2249 2984 623390672 623391408 0.000000e+00 1133.0
19 TraesCS4A01G432700 chr5D 93.496 738 46 2 2249 2984 395707193 395707930 0.000000e+00 1096.0
20 TraesCS4A01G432700 chr5D 93.505 739 45 2 2249 2984 540016633 540015895 0.000000e+00 1096.0
21 TraesCS4A01G432700 chr4D 93.225 738 47 2 2248 2984 467192896 467193631 0.000000e+00 1083.0
22 TraesCS4A01G432700 chr1D 93.216 737 49 1 2249 2984 775403 776139 0.000000e+00 1083.0
23 TraesCS4A01G432700 chr1D 93.216 737 49 1 2249 2984 778758 779494 0.000000e+00 1083.0
24 TraesCS4A01G432700 chr1D 97.436 78 2 0 904 981 141317342 141317265 1.870000e-27 134.0
25 TraesCS4A01G432700 chr7B 75.344 945 182 37 1007 1928 639379596 639378680 9.960000e-110 407.0
26 TraesCS4A01G432700 chr7B 88.333 60 5 2 1769 1827 640864828 640864770 1.480000e-08 71.3
27 TraesCS4A01G432700 chr7B 75.333 150 31 5 1484 1630 623757387 623757533 1.920000e-07 67.6
28 TraesCS4A01G432700 chr7D 97.436 78 2 0 904 981 203514386 203514463 1.870000e-27 134.0
29 TraesCS4A01G432700 chr7D 84.000 75 12 0 1753 1827 510339916 510339990 4.130000e-09 73.1
30 TraesCS4A01G432700 chr7D 86.667 60 6 2 1769 1827 577510891 577510833 6.900000e-07 65.8
31 TraesCS4A01G432700 chr7D 86.667 60 6 2 1769 1827 577537552 577537494 6.900000e-07 65.8
32 TraesCS4A01G432700 chr6D 97.436 78 2 0 904 981 124531915 124531992 1.870000e-27 134.0
33 TraesCS4A01G432700 chr6D 97.436 78 2 0 904 981 283221528 283221605 1.870000e-27 134.0
34 TraesCS4A01G432700 chr6D 97.436 78 2 0 904 981 458912574 458912651 1.870000e-27 134.0


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 TraesCS4A01G432700 chr4A 703440590 703443573 2983 False 5511 5511 100.000 1 2984 1 chr4A.!!$F1 2983
1 TraesCS4A01G432700 chr4A 26414813 26415720 907 True 1533 1533 97.247 1 902 1 chr4A.!!$R1 901
2 TraesCS4A01G432700 chrUn 50427748 50430732 2984 False 5461 5461 99.698 1 2984 1 chrUn.!!$F2 2983
3 TraesCS4A01G432700 chrUn 316447074 316447987 913 True 1554 1554 97.484 1 907 1 chrUn.!!$R3 906
4 TraesCS4A01G432700 chrUn 85702457 85703364 907 True 1312 1312 92.857 1 902 1 chrUn.!!$R1 901
5 TraesCS4A01G432700 chrUn 45191756 45192491 735 False 1088 1088 93.351 2249 2984 1 chrUn.!!$F1 735
6 TraesCS4A01G432700 chr7A 27462128 27463525 1397 False 1095 1853 96.823 983 2246 2 chr7A.!!$F2 1263
7 TraesCS4A01G432700 chr2B 46005254 46006158 904 True 1581 1581 98.232 1 903 1 chr2B.!!$R1 902
8 TraesCS4A01G432700 chr2B 752878106 752879006 900 True 1332 1332 93.377 1 902 1 chr2B.!!$R2 901
9 TraesCS4A01G432700 chr5A 687366705 687367607 902 True 1578 1578 98.228 1 902 1 chr5A.!!$R1 901
10 TraesCS4A01G432700 chr2A 32555685 32556588 903 True 1568 1568 98.009 1 902 1 chr2A.!!$R1 901
11 TraesCS4A01G432700 chr2A 765633095 765633829 734 False 1085 1085 93.333 2249 2982 1 chr2A.!!$F1 733
12 TraesCS4A01G432700 chr5B 576073631 576074533 902 True 1349 1349 93.619 1 906 1 chr5B.!!$R1 905
13 TraesCS4A01G432700 chr3A 623390672 623391408 736 False 1133 1133 94.437 2249 2984 1 chr3A.!!$F1 735
14 TraesCS4A01G432700 chr5D 395707193 395707930 737 False 1096 1096 93.496 2249 2984 1 chr5D.!!$F1 735
15 TraesCS4A01G432700 chr5D 540015895 540016633 738 True 1096 1096 93.505 2249 2984 1 chr5D.!!$R1 735
16 TraesCS4A01G432700 chr4D 467192896 467193631 735 False 1083 1083 93.225 2248 2984 1 chr4D.!!$F1 736
17 TraesCS4A01G432700 chr1D 775403 779494 4091 False 1083 1083 93.216 2249 2984 2 chr1D.!!$F1 735
18 TraesCS4A01G432700 chr7B 639378680 639379596 916 True 407 407 75.344 1007 1928 1 chr7B.!!$R1 921

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
976 991 1.003118 CAGGACCAGGAACCAATTCGA 59.997 52.381 0.0 0.0 35.48 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 6266 0.107017 ACTATTTCCCGCAGCAGCAT 60.107 50.0 0.82 0.0 42.27 3.79 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
498 513 3.882326 CGGCCAGGGCAGATGGAT 61.882 66.667 14.59 0.0 44.11 3.41
976 991 1.003118 CAGGACCAGGAACCAATTCGA 59.997 52.381 0.00 0.0 35.48 3.71
2738 6266 4.035612 ACTGACTTGTACTCAGCCTCTA 57.964 45.455 9.82 0.0 39.08 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2738 6266 0.107017 ACTATTTCCCGCAGCAGCAT 60.107 50.0 0.82 0.0 42.27 3.79


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

AutoCloner maintained by Alex Coulton.