Multiple sequence alignment - TraesCS5A01G039300

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 TraesCS5A01G039300 chr5A 100.000 5309 0 0 1 5309 36111747 36106439 0.000000e+00 9804.0
1 TraesCS5A01G039300 chr5A 97.014 4019 45 17 1 4007 36083656 36079701 0.000000e+00 6687.0
2 TraesCS5A01G039300 chr5A 98.455 2912 25 8 367 3269 36145159 36142259 0.000000e+00 5110.0
3 TraesCS5A01G039300 chr5A 98.019 2776 35 2 2553 5309 36171762 36168988 0.000000e+00 4804.0
4 TraesCS5A01G039300 chr5A 97.295 2773 33 13 367 3130 36056480 36053741 0.000000e+00 4667.0
5 TraesCS5A01G039300 chr5A 96.698 1938 20 13 1232 3167 36200995 36199100 0.000000e+00 3184.0
6 TraesCS5A01G039300 chr5A 98.046 1740 14 3 368 2105 36173818 36172097 0.000000e+00 3007.0
7 TraesCS5A01G039300 chr5A 97.668 1458 14 2 3871 5309 36053160 36051704 0.000000e+00 2486.0
8 TraesCS5A01G039300 chr5A 97.984 1290 6 2 4039 5309 36136261 36134973 0.000000e+00 2220.0
9 TraesCS5A01G039300 chr5A 97.061 1259 17 6 4070 5309 36079729 36078472 0.000000e+00 2102.0
10 TraesCS5A01G039300 chr5A 98.832 856 8 2 367 1221 36202083 36201229 0.000000e+00 1524.0
11 TraesCS5A01G039300 chr5A 96.837 822 7 1 4140 4942 36198829 36198008 0.000000e+00 1356.0
12 TraesCS5A01G039300 chr5A 99.197 747 3 1 3300 4043 36142262 36141516 0.000000e+00 1343.0
13 TraesCS5A01G039300 chr5A 88.117 547 52 4 3715 4252 36247517 36248059 5.800000e-179 638.0
14 TraesCS5A01G039300 chr5A 97.051 373 9 1 1 371 36145594 36145222 1.260000e-175 627.0
15 TraesCS5A01G039300 chr5A 97.051 373 8 2 1 371 36202519 36202148 4.510000e-175 625.0
16 TraesCS5A01G039300 chr5A 96.783 373 10 1 1 371 36056917 36056545 5.840000e-174 621.0
17 TraesCS5A01G039300 chr5A 98.830 342 4 0 2164 2505 36172100 36171759 1.260000e-170 610.0
18 TraesCS5A01G039300 chr5A 96.247 373 12 1 1 371 36174253 36173881 1.260000e-170 610.0
19 TraesCS5A01G039300 chr5A 78.416 1010 157 33 1571 2560 36128603 36127635 7.610000e-168 601.0
20 TraesCS5A01G039300 chr5A 78.993 814 124 25 1763 2560 36099689 36098907 3.670000e-141 512.0
21 TraesCS5A01G039300 chr5A 97.071 239 5 2 1336 1572 87418711 87418949 8.280000e-108 401.0
22 TraesCS5A01G039300 chr5A 99.052 211 2 0 3888 4098 36199034 36198824 3.880000e-101 379.0
23 TraesCS5A01G039300 chr5A 80.806 422 58 15 2970 3372 36246620 36247037 5.160000e-80 309.0
24 TraesCS5A01G039300 chr5A 98.649 74 1 0 3769 3842 36199105 36199032 1.200000e-26 132.0
25 TraesCS5A01G039300 chr5D 94.707 2116 66 13 1589 3658 45253238 45251123 0.000000e+00 3245.0
26 TraesCS5A01G039300 chr5D 89.925 665 56 5 3654 4311 45251088 45250428 0.000000e+00 846.0
27 TraesCS5A01G039300 chr5D 80.395 811 110 26 1571 2335 45256685 45257492 5.960000e-159 571.0
28 TraesCS5A01G039300 chr5D 79.178 754 105 22 2640 3372 45257823 45258545 4.810000e-130 475.0
29 TraesCS5A01G039300 chr5D 79.196 572 107 11 4739 5307 552794312 552793750 2.320000e-103 387.0
30 TraesCS5A01G039300 chr5D 83.681 288 39 5 3372 3658 45258573 45258853 1.130000e-66 265.0
31 TraesCS5A01G039300 chr5D 94.048 84 4 1 3654 3736 45258888 45258971 5.580000e-25 126.0
32 TraesCS5A01G039300 chrUn 96.906 1713 6 6 2593 4305 380818623 380816958 0.000000e+00 2826.0
33 TraesCS5A01G039300 chrUn 100.000 1006 0 0 3300 4305 451704538 451705543 0.000000e+00 1858.0
34 TraesCS5A01G039300 chrUn 82.343 572 96 4 4739 5307 332529144 332528575 4.780000e-135 492.0
35 TraesCS5A01G039300 chrUn 92.405 79 6 0 1 79 262706642 262706564 4.350000e-21 113.0
36 TraesCS5A01G039300 chr1A 89.381 452 45 3 4739 5189 13849385 13849834 2.780000e-157 566.0
37 TraesCS5A01G039300 chr7A 82.425 569 95 4 4739 5304 734476659 734477225 4.780000e-135 492.0
38 TraesCS5A01G039300 chr7A 94.714 227 10 2 1336 1560 48826189 48825963 8.460000e-93 351.0
39 TraesCS5A01G039300 chr7A 92.771 83 6 0 1 83 709603341 709603423 2.600000e-23 121.0
40 TraesCS5A01G039300 chr2B 80.249 562 95 15 4739 5293 513251993 513251441 4.950000e-110 409.0
41 TraesCS5A01G039300 chr2B 89.583 240 11 5 1336 1573 771509160 771508933 5.200000e-75 292.0
42 TraesCS5A01G039300 chr2A 94.400 250 10 4 1328 1574 25475363 25475611 1.080000e-101 381.0
43 TraesCS5A01G039300 chr2A 85.333 75 10 1 367 441 79458557 79458630 5.700000e-10 76.8
44 TraesCS5A01G039300 chr1D 92.913 254 15 3 1326 1577 416111571 416111319 3.020000e-97 366.0
45 TraesCS5A01G039300 chr1D 84.270 89 13 1 369 457 378302602 378302689 9.470000e-13 86.1
46 TraesCS5A01G039300 chr7B 87.029 239 26 5 1330 1565 746821341 746821105 1.130000e-66 265.0
47 TraesCS5A01G039300 chr7D 85.477 241 32 3 1326 1565 129851131 129851369 1.140000e-61 248.0
48 TraesCS5A01G039300 chr3B 95.000 80 4 0 1 80 191001 190922 5.580000e-25 126.0
49 TraesCS5A01G039300 chr3A 92.500 80 6 0 1 80 733871970 733871891 1.210000e-21 115.0
50 TraesCS5A01G039300 chr4A 84.884 86 12 1 372 457 626026557 626026641 9.470000e-13 86.1
51 TraesCS5A01G039300 chr6B 83.516 91 14 1 367 457 704417413 704417324 3.410000e-12 84.2
52 TraesCS5A01G039300 chr6D 91.071 56 2 3 637 690 324811244 324811298 7.380000e-09 73.1


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 TraesCS5A01G039300 chr5A 36106439 36111747 5308 True 9804.000000 9804 100.000000 1 5309 1 chr5A.!!$R2 5308
1 TraesCS5A01G039300 chr5A 36078472 36083656 5184 True 4394.500000 6687 97.037500 1 5309 2 chr5A.!!$R6 5308
2 TraesCS5A01G039300 chr5A 36051704 36056917 5213 True 2591.333333 4667 97.248667 1 5309 3 chr5A.!!$R5 5308
3 TraesCS5A01G039300 chr5A 36141516 36145594 4078 True 2360.000000 5110 98.234333 1 4043 3 chr5A.!!$R7 4042
4 TraesCS5A01G039300 chr5A 36168988 36174253 5265 True 2257.750000 4804 97.785500 1 5309 4 chr5A.!!$R8 5308
5 TraesCS5A01G039300 chr5A 36134973 36136261 1288 True 2220.000000 2220 97.984000 4039 5309 1 chr5A.!!$R4 1270
6 TraesCS5A01G039300 chr5A 36198008 36202519 4511 True 1200.000000 3184 97.853167 1 4942 6 chr5A.!!$R9 4941
7 TraesCS5A01G039300 chr5A 36127635 36128603 968 True 601.000000 601 78.416000 1571 2560 1 chr5A.!!$R3 989
8 TraesCS5A01G039300 chr5A 36098907 36099689 782 True 512.000000 512 78.993000 1763 2560 1 chr5A.!!$R1 797
9 TraesCS5A01G039300 chr5A 36246620 36248059 1439 False 473.500000 638 84.461500 2970 4252 2 chr5A.!!$F2 1282
10 TraesCS5A01G039300 chr5D 45250428 45253238 2810 True 2045.500000 3245 92.316000 1589 4311 2 chr5D.!!$R2 2722
11 TraesCS5A01G039300 chr5D 552793750 552794312 562 True 387.000000 387 79.196000 4739 5307 1 chr5D.!!$R1 568
12 TraesCS5A01G039300 chr5D 45256685 45258971 2286 False 359.250000 571 84.325500 1571 3736 4 chr5D.!!$F1 2165
13 TraesCS5A01G039300 chrUn 380816958 380818623 1665 True 2826.000000 2826 96.906000 2593 4305 1 chrUn.!!$R3 1712
14 TraesCS5A01G039300 chrUn 451704538 451705543 1005 False 1858.000000 1858 100.000000 3300 4305 1 chrUn.!!$F1 1005
15 TraesCS5A01G039300 chrUn 332528575 332529144 569 True 492.000000 492 82.343000 4739 5307 1 chrUn.!!$R2 568
16 TraesCS5A01G039300 chr7A 734476659 734477225 566 False 492.000000 492 82.425000 4739 5304 1 chr7A.!!$F2 565
17 TraesCS5A01G039300 chr2B 513251441 513251993 552 True 409.000000 409 80.249000 4739 5293 1 chr2B.!!$R1 554

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
477 549 1.153329 GTCGTGGGTGTGTTGGACA 60.153 57.895 0.0 0.0 0.00 4.02 F
498 570 1.745232 ACGAACACAAGGTGCTCAAA 58.255 45.000 0.0 0.0 36.98 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2417 1.425825 CTCGTGCTCGTCATCTCGT 59.574 57.895 8.17 0.0 38.33 4.18 R
4637 5501 9.800433 ATCAATGAAATGATACGCAAACATTAA 57.200 25.926 0.00 0.0 38.25 1.40 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
477 549 1.153329 GTCGTGGGTGTGTTGGACA 60.153 57.895 0.0 0.0 0.00 4.02
498 570 1.745232 ACGAACACAAGGTGCTCAAA 58.255 45.000 0.0 0.0 36.98 2.69
2757 3281 1.459450 GCCTGAAATAAGGTTGGCGA 58.541 50.000 0.0 0.0 39.75 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
477 549 1.745232 TGAGCACCTTGTGTTCGTTT 58.255 45.000 6.59 0.0 44.63 3.60
498 570 2.495669 CTCATACGGCAACCCCATTTTT 59.504 45.455 0.00 0.0 0.00 1.94
1476 1791 3.641437 TTTCGGCTGAAATTTGACCAG 57.359 42.857 16.83 0.0 39.13 4.00
2037 2417 1.425825 CTCGTGCTCGTCATCTCGT 59.574 57.895 8.17 0.0 38.33 4.18
4637 5501 9.800433 ATCAATGAAATGATACGCAAACATTAA 57.200 25.926 0.00 0.0 38.25 1.40


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

AutoCloner maintained by Alex Coulton.