Multiple sequence alignment - TraesCS5A01G550500

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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 TraesCS5A01G550500 chr5A 100.000 3137 0 0 1 3137 704100998 704097862 0.000000e+00 5794.0
1 TraesCS5A01G550500 chr5A 98.942 2835 11 2 1 2817 704261792 704258959 0.000000e+00 5051.0
2 TraesCS5A01G550500 chr5A 97.607 2215 41 9 183 2394 704017007 704014802 0.000000e+00 3786.0
3 TraesCS5A01G550500 chr5A 97.048 2236 54 9 183 2415 703970492 703968266 0.000000e+00 3753.0
4 TraesCS5A01G550500 chr5A 99.557 2031 7 2 786 2816 704208887 704206859 0.000000e+00 3699.0
5 TraesCS5A01G550500 chr5A 97.695 2039 40 6 377 2415 703964451 703962420 0.000000e+00 3498.0
6 TraesCS5A01G550500 chr5A 97.401 2039 46 6 377 2415 703958584 703956553 0.000000e+00 3465.0
7 TraesCS5A01G550500 chr5A 95.056 2043 66 9 377 2415 703952739 703950728 0.000000e+00 3181.0
8 TraesCS5A01G550500 chr5A 95.541 1413 50 8 433 1840 703936704 703935300 0.000000e+00 2248.0
9 TraesCS5A01G550500 chr5A 99.428 1224 7 0 1 1224 704221490 704220267 0.000000e+00 2222.0
10 TraesCS5A01G550500 chr5A 99.723 721 2 0 1 721 704130905 704130185 0.000000e+00 1321.0
11 TraesCS5A01G550500 chr5A 94.772 746 18 4 2412 3137 703968045 703967301 0.000000e+00 1142.0
12 TraesCS5A01G550500 chr5A 94.504 746 20 4 2412 3137 703956332 703955588 0.000000e+00 1131.0
13 TraesCS5A01G550500 chr5A 94.951 713 9 3 2445 3137 704014802 704014097 0.000000e+00 1092.0
14 TraesCS5A01G550500 chr5A 97.574 577 13 1 1837 2413 703922203 703921628 0.000000e+00 987.0
15 TraesCS5A01G550500 chr5A 99.425 348 2 0 1 348 704218317 704217970 1.590000e-177 632.0
16 TraesCS5A01G550500 chr5A 93.473 429 10 1 2412 2822 703962198 703961770 3.440000e-174 621.0
17 TraesCS5A01G550500 chr5A 93.062 418 11 3 2412 2811 703921404 703920987 2.080000e-166 595.0
18 TraesCS5A01G550500 chr5A 98.198 333 6 0 2412 2744 703950507 703950175 1.620000e-162 582.0
19 TraesCS5A01G550500 chr5A 100.000 277 0 0 2861 3137 704128483 704128207 2.160000e-141 512.0
20 TraesCS5A01G550500 chr5A 100.000 277 0 0 2861 3137 704206770 704206494 2.160000e-141 512.0
21 TraesCS5A01G550500 chr5A 100.000 277 0 0 2861 3137 704258406 704258130 2.160000e-141 512.0
22 TraesCS5A01G550500 chr5A 96.727 275 7 1 2863 3137 703949798 703949526 1.030000e-124 457.0
23 TraesCS5A01G550500 chr5A 94.881 293 11 1 2845 3137 703920778 703920490 3.690000e-124 455.0
24 TraesCS5A01G550500 chr5A 97.436 234 5 1 2904 3137 703961664 703961432 6.300000e-107 398.0
25 TraesCS5A01G550500 chr5A 88.060 134 15 1 2412 2545 703703995 703703863 1.160000e-34 158.0
26 TraesCS5A01G550500 chr5A 96.154 78 2 1 300 377 704197399 704197323 3.280000e-25 126.0
27 TraesCS5A01G550500 chr5A 96.154 78 2 1 300 377 704328153 704328077 3.280000e-25 126.0
28 TraesCS5A01G550500 chr5A 94.872 78 3 1 300 377 704088589 704088513 1.530000e-23 121.0
29 TraesCS5A01G550500 chr5A 84.746 59 8 1 124 182 562488522 562488579 1.220000e-04 58.4
30 TraesCS5A01G550500 chrUn 91.277 2052 119 23 377 2415 109056050 109058054 0.000000e+00 2743.0
31 TraesCS5A01G550500 chr4B 89.525 821 81 4 1569 2388 664052264 664053080 0.000000e+00 1035.0
32 TraesCS5A01G550500 chr7A 95.082 122 6 0 183 304 10848025 10848146 3.190000e-45 193.0
33 TraesCS5A01G550500 chr7D 94.262 122 7 0 183 304 408031743 408031622 1.490000e-43 187.0
34 TraesCS5A01G550500 chr3A 94.215 121 7 0 184 304 200681375 200681495 5.340000e-43 185.0
35 TraesCS5A01G550500 chr3A 95.455 44 2 0 139 182 26258905 26258862 1.560000e-08 71.3
36 TraesCS5A01G550500 chr3A 93.333 45 3 0 139 183 140954825 140954781 2.020000e-07 67.6
37 TraesCS5A01G550500 chr3B 87.719 57 6 1 126 182 810706036 810706091 7.260000e-07 65.8
38 TraesCS5A01G550500 chr4A 85.714 56 7 1 127 182 398504944 398504890 1.220000e-04 58.4


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 TraesCS5A01G550500 chr5A 704097862 704100998 3136 True 5794.0 5794 100.000000 1 3137 1 chr5A.!!$R4 3136
1 TraesCS5A01G550500 chr5A 704258130 704261792 3662 True 2781.5 5051 99.471000 1 3137 2 chr5A.!!$R13 3136
2 TraesCS5A01G550500 chr5A 704014097 704017007 2910 True 2439.0 3786 96.279000 183 3137 2 chr5A.!!$R9 2954
3 TraesCS5A01G550500 chr5A 703935300 703936704 1404 True 2248.0 2248 95.541000 433 1840 1 chr5A.!!$R2 1407
4 TraesCS5A01G550500 chr5A 704206494 704208887 2393 True 2105.5 3699 99.778500 786 3137 2 chr5A.!!$R11 2351
5 TraesCS5A01G550500 chr5A 703949526 703970492 20966 True 1822.8 3753 96.231000 183 3137 10 chr5A.!!$R8 2954
6 TraesCS5A01G550500 chr5A 704217970 704221490 3520 True 1427.0 2222 99.426500 1 1224 2 chr5A.!!$R12 1223
7 TraesCS5A01G550500 chr5A 704128207 704130905 2698 True 916.5 1321 99.861500 1 3137 2 chr5A.!!$R10 3136
8 TraesCS5A01G550500 chr5A 703920490 703922203 1713 True 679.0 987 95.172333 1837 3137 3 chr5A.!!$R7 1300
9 TraesCS5A01G550500 chrUn 109056050 109058054 2004 False 2743.0 2743 91.277000 377 2415 1 chrUn.!!$F1 2038
10 TraesCS5A01G550500 chr4B 664052264 664053080 816 False 1035.0 1035 89.525000 1569 2388 1 chr4B.!!$F1 819

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
192 193 1.659794 CGGCCCTGTTCAAAAGTGG 59.34 57.895 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2832 16330 2.46788 CCTCTATAGGGGTGTGTGTGT 58.532 52.381 10.89 0.0 39.48 3.72 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
192 193 1.659794 CGGCCCTGTTCAAAAGTGG 59.340 57.895 0.0 0.00 0.00 4.00
1812 8857 0.036388 GCGAGGAGAACATTGACCCA 60.036 55.000 0.0 0.00 0.00 4.51
2600 10214 3.054065 GTCCAACCTTCTCCTCCATCAAT 60.054 47.826 0.0 0.00 0.00 2.57
2794 16292 0.462581 GAACATGCTCCAGCGGATCA 60.463 55.000 0.0 4.12 45.83 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
784 6642 8.76600 TTAATTAGAGTAGACATGTTTTGCGA 57.234 30.769 0.00 0.0 0.00 5.10
2832 16330 2.46788 CCTCTATAGGGGTGTGTGTGT 58.532 52.381 10.89 0.0 39.48 3.72


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

AutoCloner maintained by Alex Coulton.