Multiple sequence alignment - TraesCS7D01G302000

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 TraesCS7D01G302000 chr7D 100.000 4494 0 0 1 4494 382254410 382258903 0.000000e+00 8299.0
1 TraesCS7D01G302000 chr7D 84.211 228 31 5 1655 1881 438368655 438368878 2.720000e-52 217.0
2 TraesCS7D01G302000 chr7D 88.281 128 13 2 1632 1758 215096309 215096183 7.790000e-33 152.0
3 TraesCS7D01G302000 chr7A 92.002 2013 103 26 2402 4401 430241427 430243394 0.000000e+00 2772.0
4 TraesCS7D01G302000 chr7A 90.412 1043 57 23 1320 2351 430240420 430241430 0.000000e+00 1332.0
5 TraesCS7D01G302000 chr7A 91.868 455 9 4 818 1268 430239976 430240406 1.070000e-170 610.0
6 TraesCS7D01G302000 chr7A 79.245 583 81 18 6 576 430239305 430239859 1.970000e-98 370.0
7 TraesCS7D01G302000 chr7A 83.772 228 32 5 1655 1881 489163240 489163463 1.270000e-50 211.0
8 TraesCS7D01G302000 chr7A 95.413 109 5 0 4386 4494 430271883 430271991 1.660000e-39 174.0
9 TraesCS7D01G302000 chr7A 92.308 65 3 2 2342 2405 360611190 360611253 1.720000e-14 91.6
10 TraesCS7D01G302000 chr7B 93.442 1540 62 12 2402 3925 376432281 376433797 0.000000e+00 2248.0
11 TraesCS7D01G302000 chr7B 90.650 877 41 22 1493 2351 376431427 376432280 0.000000e+00 1127.0
12 TraesCS7D01G302000 chr7B 88.058 762 32 16 684 1431 376430678 376431394 0.000000e+00 848.0
13 TraesCS7D01G302000 chr7B 88.862 413 27 10 4087 4494 376436044 376436442 1.450000e-134 490.0
14 TraesCS7D01G302000 chr7B 80.032 621 84 26 6 617 376430072 376430661 1.490000e-114 424.0
15 TraesCS7D01G302000 chr7B 84.211 228 31 5 1655 1881 455272016 455271793 2.720000e-52 217.0
16 TraesCS7D01G302000 chr7B 95.652 46 2 0 3913 3958 376435279 376435324 1.730000e-09 75.0
17 TraesCS7D01G302000 chr2D 87.747 253 28 3 1629 1881 568801800 568802049 4.400000e-75 292.0
18 TraesCS7D01G302000 chr2D 79.894 189 26 3 1004 1180 568801320 568801508 1.310000e-25 128.0
19 TraesCS7D01G302000 chr2D 82.222 90 14 2 1794 1882 398086987 398086899 4.820000e-10 76.8
20 TraesCS7D01G302000 chr2A 87.352 253 29 2 1629 1881 708059137 708059386 2.050000e-73 287.0
21 TraesCS7D01G302000 chr2A 95.918 49 1 1 627 674 377135607 377135559 1.340000e-10 78.7
22 TraesCS7D01G302000 chr2B 87.805 246 27 2 1629 1874 681409271 681409513 7.360000e-73 285.0
23 TraesCS7D01G302000 chr2B 82.320 181 27 4 1004 1180 681408801 681408980 7.790000e-33 152.0
24 TraesCS7D01G302000 chr2B 91.429 70 2 4 2344 2410 38218223 38218291 4.790000e-15 93.5
25 TraesCS7D01G302000 chr6A 96.552 58 1 1 2349 2405 454654059 454654002 1.330000e-15 95.3
26 TraesCS7D01G302000 chr6A 87.692 65 5 3 613 674 17700407 17700343 6.240000e-09 73.1
27 TraesCS7D01G302000 chr5B 96.552 58 1 1 2349 2405 69548107 69548050 1.330000e-15 95.3
28 TraesCS7D01G302000 chr5D 93.651 63 3 1 2344 2405 273117881 273117943 4.790000e-15 93.5
29 TraesCS7D01G302000 chr3A 95.000 60 2 1 2347 2405 466806948 466807007 4.790000e-15 93.5
30 TraesCS7D01G302000 chr3A 95.918 49 1 1 627 674 620767136 620767184 1.340000e-10 78.7
31 TraesCS7D01G302000 chr3A 92.593 54 3 1 622 674 594510490 594510543 4.820000e-10 76.8
32 TraesCS7D01G302000 chr3B 92.308 65 4 1 2348 2411 525999187 525999123 1.720000e-14 91.6
33 TraesCS7D01G302000 chr1A 88.158 76 7 2 2350 2424 137852083 137852009 6.190000e-14 89.8
34 TraesCS7D01G302000 chr3D 90.769 65 6 0 2341 2405 74197494 74197558 2.230000e-13 87.9
35 TraesCS7D01G302000 chr4D 76.506 166 32 7 1018 1181 46293024 46292864 2.880000e-12 84.2
36 TraesCS7D01G302000 chr4D 90.909 55 3 2 627 679 360102137 360102191 6.240000e-09 73.1
37 TraesCS7D01G302000 chr4B 76.647 167 30 9 1015 1178 67771414 67771574 2.880000e-12 84.2
38 TraesCS7D01G302000 chr4B 95.918 49 1 1 627 674 387795129 387795177 1.340000e-10 78.7
39 TraesCS7D01G302000 chr4B 92.727 55 2 2 627 679 629952328 629952382 1.340000e-10 78.7
40 TraesCS7D01G302000 chr4A 76.506 166 32 7 1015 1178 552698531 552698691 2.880000e-12 84.2
41 TraesCS7D01G302000 chr5A 90.000 60 4 2 622 679 461871459 461871400 4.820000e-10 76.8
42 TraesCS7D01G302000 chr6B 90.909 55 3 2 627 679 601049784 601049838 6.240000e-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 TraesCS7D01G302000 chr7D 382254410 382258903 4493 False 8299.000000 8299 100.000000 1 4494 1 chr7D.!!$F1 4493
1 TraesCS7D01G302000 chr7A 430239305 430243394 4089 False 1271.000000 2772 88.381750 6 4401 4 chr7A.!!$F4 4395
2 TraesCS7D01G302000 chr7B 376430072 376436442 6370 False 868.666667 2248 89.449333 6 4494 6 chr7B.!!$F1 4488
3 TraesCS7D01G302000 chr2D 568801320 568802049 729 False 210.000000 292 83.820500 1004 1881 2 chr2D.!!$F1 877
4 TraesCS7D01G302000 chr2B 681408801 681409513 712 False 218.500000 285 85.062500 1004 1874 2 chr2B.!!$F2 870


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
506 509 0.040692 CATGCTCGATGGCGATTTGG 60.041 55.0 0.00 0.0 46.80 3.28 F
958 979 0.178935 CCCTCCATCTCTCCCTCTCC 60.179 65.0 0.00 0.0 0.00 3.71 F
1209 1245 0.248289 TTCCTACTTGCTACGTGCCC 59.752 55.0 0.00 0.0 42.00 5.36 F
1490 1543 0.313987 CCCGGGTTTGAACTTTGAGC 59.686 55.0 14.18 0.0 0.00 4.26 F
2707 2879 0.319900 CAGGTCAACTCCACAGTCCG 60.320 60.0 0.00 0.0 29.93 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1510 0.538746 AAAGTTCAAACCCGGGCGAT 60.539 50.0 24.08 3.77 0.00 4.58 R
2227 2395 0.584876 CACTTTGGGGAACGAACGTC 59.415 55.0 0.00 0.00 28.11 4.34 R
2723 2895 0.872388 CTGGCGTAAACACTGGAACC 59.128 55.0 0.00 0.00 0.00 3.62 R
3242 3426 0.036765 TCAAAGGCGATGTAGGCGTT 60.037 50.0 0.00 0.00 39.89 4.84 R
3969 5654 0.606401 TGCCGCTTTTTCTCTCCTGG 60.606 55.0 0.00 0.00 0.00 4.45 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.