Multiple sequence alignment - TraesCS7A01G492100

Loading Multiple Alignment...

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 TraesCS7A01G492100 chr7A 100.000 3437 0 0 1 3437 680681703 680678267 0.000000e+00 6348.0
1 TraesCS7A01G492100 chr7B 94.359 2588 109 20 548 3126 663751620 663749061 0.000000e+00 3936.0
2 TraesCS7A01G492100 chr7B 95.679 1967 79 4 546 2509 663842857 663844820 0.000000e+00 3157.0
3 TraesCS7A01G492100 chr7B 89.051 411 31 10 2722 3126 663846258 663846660 6.620000e-137 497.0
4 TraesCS7A01G492100 chr7B 92.636 258 16 1 3 260 663842621 663842875 5.420000e-98 368.0
5 TraesCS7A01G492100 chr7B 84.848 66 8 2 3373 3437 643329671 643329735 7.960000e-07 65.8
6 TraesCS7A01G492100 chr7D 94.192 2600 100 22 563 3126 589391688 589389104 0.000000e+00 3917.0
7 TraesCS7A01G492100 chr7D 90.260 308 26 4 239 545 263324536 263324840 1.920000e-107 399.0
8 TraesCS7A01G492100 chr2B 83.141 1910 247 48 700 2554 138993596 138991707 0.000000e+00 1674.0
9 TraesCS7A01G492100 chr2B 80.653 1959 288 55 622 2515 12421937 12423869 0.000000e+00 1434.0
10 TraesCS7A01G492100 chr2B 80.935 1883 280 45 625 2446 11518691 11516827 0.000000e+00 1415.0
11 TraesCS7A01G492100 chr2B 82.829 1619 201 36 917 2480 12996047 12994451 0.000000e+00 1378.0
12 TraesCS7A01G492100 chr2B 82.403 1631 213 29 902 2480 11445348 11446956 0.000000e+00 1354.0
13 TraesCS7A01G492100 chr2B 77.612 134 21 5 2527 2657 13066996 13066869 4.760000e-09 73.1
14 TraesCS7A01G492100 chr2B 92.157 51 4 0 127 177 13342907 13342857 4.760000e-09 73.1
15 TraesCS7A01G492100 chr2D 82.661 1909 251 40 700 2554 85929887 85928005 0.000000e+00 1618.0
16 TraesCS7A01G492100 chr2D 81.622 1948 274 43 546 2433 19586562 19588485 0.000000e+00 1537.0
17 TraesCS7A01G492100 chr2D 83.119 1635 195 37 902 2480 9665345 9663736 0.000000e+00 1415.0
18 TraesCS7A01G492100 chr2D 80.640 1875 275 50 638 2446 9604386 9606238 0.000000e+00 1371.0
19 TraesCS7A01G492100 chr2D 81.990 1427 225 14 1000 2395 8659797 8661222 0.000000e+00 1182.0
20 TraesCS7A01G492100 chr2D 92.177 294 21 2 253 545 180879717 180879425 6.860000e-112 414.0
21 TraesCS7A01G492100 chr2A 81.583 1428 229 17 1000 2395 7727400 7728825 0.000000e+00 1149.0
22 TraesCS7A01G492100 chr2A 91.837 294 22 2 253 545 177014164 177014456 3.190000e-110 409.0
23 TraesCS7A01G492100 chr2A 92.157 51 4 0 127 177 9947604 9947654 4.760000e-09 73.1
24 TraesCS7A01G492100 chr2A 76.596 141 23 6 2527 2663 9092976 9092842 6.150000e-08 69.4
25 TraesCS7A01G492100 chr4B 92.177 294 21 2 253 545 322760395 322760103 6.860000e-112 414.0
26 TraesCS7A01G492100 chr5D 91.837 294 22 2 253 545 292148187 292147895 3.190000e-110 409.0
27 TraesCS7A01G492100 chr5D 84.211 76 12 0 3360 3435 357503054 357503129 1.320000e-09 75.0
28 TraesCS7A01G492100 chr5D 100.000 31 0 0 132 162 404501616 404501586 1.330000e-04 58.4
29 TraesCS7A01G492100 chr5A 91.837 294 22 2 253 545 366235117 366234825 3.190000e-110 409.0
30 TraesCS7A01G492100 chr4D 91.837 294 22 2 253 545 428568246 428568538 3.190000e-110 409.0
31 TraesCS7A01G492100 chr3A 91.837 294 22 2 253 545 308688838 308688546 3.190000e-110 409.0
32 TraesCS7A01G492100 chr4A 91.554 296 23 2 253 547 588567678 588567384 1.150000e-109 407.0
33 TraesCS7A01G492100 chr3D 85.000 80 12 0 3358 3437 230778260 230778339 7.910000e-12 82.4


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 TraesCS7A01G492100 chr7A 680678267 680681703 3436 True 6348.000000 6348 100.000000 1 3437 1 chr7A.!!$R1 3436
1 TraesCS7A01G492100 chr7B 663749061 663751620 2559 True 3936.000000 3936 94.359000 548 3126 1 chr7B.!!$R1 2578
2 TraesCS7A01G492100 chr7B 663842621 663846660 4039 False 1340.666667 3157 92.455333 3 3126 3 chr7B.!!$F2 3123
3 TraesCS7A01G492100 chr7D 589389104 589391688 2584 True 3917.000000 3917 94.192000 563 3126 1 chr7D.!!$R1 2563
4 TraesCS7A01G492100 chr2B 138991707 138993596 1889 True 1674.000000 1674 83.141000 700 2554 1 chr2B.!!$R5 1854
5 TraesCS7A01G492100 chr2B 12421937 12423869 1932 False 1434.000000 1434 80.653000 622 2515 1 chr2B.!!$F2 1893
6 TraesCS7A01G492100 chr2B 11516827 11518691 1864 True 1415.000000 1415 80.935000 625 2446 1 chr2B.!!$R1 1821
7 TraesCS7A01G492100 chr2B 12994451 12996047 1596 True 1378.000000 1378 82.829000 917 2480 1 chr2B.!!$R2 1563
8 TraesCS7A01G492100 chr2B 11445348 11446956 1608 False 1354.000000 1354 82.403000 902 2480 1 chr2B.!!$F1 1578
9 TraesCS7A01G492100 chr2D 85928005 85929887 1882 True 1618.000000 1618 82.661000 700 2554 1 chr2D.!!$R2 1854
10 TraesCS7A01G492100 chr2D 19586562 19588485 1923 False 1537.000000 1537 81.622000 546 2433 1 chr2D.!!$F3 1887
11 TraesCS7A01G492100 chr2D 9663736 9665345 1609 True 1415.000000 1415 83.119000 902 2480 1 chr2D.!!$R1 1578
12 TraesCS7A01G492100 chr2D 9604386 9606238 1852 False 1371.000000 1371 80.640000 638 2446 1 chr2D.!!$F2 1808
13 TraesCS7A01G492100 chr2D 8659797 8661222 1425 False 1182.000000 1182 81.990000 1000 2395 1 chr2D.!!$F1 1395
14 TraesCS7A01G492100 chr2A 7727400 7728825 1425 False 1149.000000 1149 81.583000 1000 2395 1 chr2A.!!$F1 1395


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
65 66 0.040351 CACCTCCTCCTCTCACCTGA 59.960 60.0 0.00 0.0 0.00 3.86 F
108 109 0.178955 TTGACCCACGGTGTCCTCTA 60.179 55.0 7.45 0.0 35.25 2.43 F
439 440 0.179004 ATGGACAAGGGTGCGTGAAA 60.179 50.0 0.00 0.0 38.35 2.69 F
440 441 0.817634 TGGACAAGGGTGCGTGAAAG 60.818 55.0 0.00 0.0 38.35 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2086 1.270625 TGCAACTCCCTGGTAAACTCG 60.271 52.381 0.0 0.0 0.0 4.18 R
2185 2279 2.030274 GCAAAGCAAGGTCCGTTATGTT 60.030 45.455 0.0 0.0 0.0 2.71 R
2408 2523 2.100603 GTCCTCGTCGCTTCCTCG 59.899 66.667 0.0 0.0 0.0 4.63 R
2494 2611 4.516323 CCACATGAACACATCCATCTGTA 58.484 43.478 0.0 0.0 0.0 2.74 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)



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

AutoCloner maintained by Alex Coulton.