Multiple sequence alignment - TraesCS7A01G498200

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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 TraesCS7A01G498200 chr7A 100.000 9646 0 0 1 9646 688694088 688684443 0.000000e+00 17813.0
1 TraesCS7A01G498200 chr7A 80.942 892 102 28 7971 8847 688457232 688456394 2.270000e-180 643.0
2 TraesCS7A01G498200 chr7A 81.096 529 60 19 7971 8488 688663185 688662686 4.230000e-103 387.0
3 TraesCS7A01G498200 chr7A 80.583 515 65 22 7484 7974 688457817 688457314 1.980000e-96 364.0
4 TraesCS7A01G498200 chr7A 83.288 371 48 10 8119 8486 688627292 688626933 7.220000e-86 329.0
5 TraesCS7A01G498200 chr7A 85.809 303 26 10 9316 9611 688625965 688625673 1.220000e-78 305.0
6 TraesCS7A01G498200 chr7A 83.270 263 25 9 6597 6857 688459549 688459304 3.510000e-54 224.0
7 TraesCS7A01G498200 chr7A 85.520 221 20 8 9316 9532 688638930 688638718 4.530000e-53 220.0
8 TraesCS7A01G498200 chr7A 88.095 168 12 6 8563 8725 688662656 688662492 9.890000e-45 193.0
9 TraesCS7A01G498200 chr7A 74.629 607 68 40 8889 9453 688662071 688661509 1.280000e-43 189.0
10 TraesCS7A01G498200 chr7A 85.430 151 18 3 7972 8122 688641090 688640944 4.670000e-33 154.0
11 TraesCS7A01G498200 chr7A 84.810 79 10 2 8802 8879 688662483 688662406 2.890000e-10 78.7
12 TraesCS7A01G498200 chr7D 96.462 5285 157 15 3517 8792 595728496 595723233 0.000000e+00 8696.0
13 TraesCS7A01G498200 chr7D 95.064 2512 91 20 1 2504 595731731 595729245 0.000000e+00 3921.0
14 TraesCS7A01G498200 chr7D 97.486 716 16 1 2805 3518 595729246 595728531 0.000000e+00 1221.0
15 TraesCS7A01G498200 chr7D 85.369 786 50 22 8900 9646 595722748 595721989 0.000000e+00 754.0
16 TraesCS7A01G498200 chr7D 80.624 898 100 27 7973 8847 595578345 595577499 2.290000e-175 627.0
17 TraesCS7A01G498200 chr7D 82.749 371 51 6 8119 8486 595613555 595613195 1.560000e-82 318.0
18 TraesCS7A01G498200 chr7D 86.184 304 21 12 9316 9610 595612252 595611961 9.410000e-80 309.0
19 TraesCS7A01G498200 chr7D 81.935 310 39 6 6597 6903 595581364 595581069 7.480000e-61 246.0
20 TraesCS7A01G498200 chr7D 82.818 291 21 10 8563 8848 595665559 595665293 5.820000e-57 233.0
21 TraesCS7A01G498200 chr7D 74.633 682 82 52 8900 9543 595664911 595664283 5.870000e-52 217.0
22 TraesCS7A01G498200 chr7D 81.655 278 32 3 7718 7976 595666651 595666374 7.590000e-51 213.0
23 TraesCS7A01G498200 chr7D 76.728 434 59 19 7084 7488 595606037 595605617 4.570000e-48 204.0
24 TraesCS7A01G498200 chr7D 92.647 136 6 2 8754 8889 595723234 595723103 9.890000e-45 193.0
25 TraesCS7A01G498200 chr7D 83.333 192 10 10 8889 9076 595612601 595612428 3.610000e-34 158.0
26 TraesCS7A01G498200 chr7D 94.898 98 4 1 7393 7490 595531873 595531777 1.680000e-32 152.0
27 TraesCS7A01G498200 chr7D 91.045 67 6 0 6953 7019 595580493 595580427 3.710000e-14 91.6
28 TraesCS7A01G498200 chr7B 96.308 4659 121 19 3517 8163 673309504 673304885 0.000000e+00 7603.0
29 TraesCS7A01G498200 chr7B 93.034 2541 117 24 1 2504 673312654 673310137 0.000000e+00 3657.0
30 TraesCS7A01G498200 chr7B 91.168 702 41 9 8193 8889 673304885 673304200 0.000000e+00 933.0
31 TraesCS7A01G498200 chr7B 97.148 526 15 0 2992 3517 673310065 673309540 0.000000e+00 889.0
32 TraesCS7A01G498200 chr7B 86.090 798 49 15 8903 9646 673303885 673303096 0.000000e+00 802.0
33 TraesCS7A01G498200 chr7B 82.367 845 115 20 7971 8798 672915088 672914261 0.000000e+00 704.0
34 TraesCS7A01G498200 chr7B 80.778 900 94 32 7973 8854 672841824 672840986 1.770000e-176 630.0
35 TraesCS7A01G498200 chr7B 79.038 520 65 22 7484 7974 672842411 672841907 5.620000e-82 316.0
36 TraesCS7A01G498200 chr7B 81.671 371 54 6 8119 8486 673124011 673123652 7.320000e-76 296.0
37 TraesCS7A01G498200 chr7B 85.016 307 25 13 9311 9611 673122695 673122404 9.480000e-75 292.0
38 TraesCS7A01G498200 chr7B 83.453 278 27 12 6749 7019 672843771 672843506 3.480000e-59 241.0
39 TraesCS7A01G498200 chr7B 75.129 583 71 44 8900 9453 673135925 673135388 1.270000e-48 206.0
40 TraesCS7A01G498200 chr7B 84.653 202 16 4 8900 9090 672913663 672913466 4.600000e-43 187.0
41 TraesCS7A01G498200 chr7B 94.872 78 4 0 2805 2882 673310138 673310061 1.320000e-23 122.0
42 TraesCS7A01G498200 chr7B 87.952 83 9 1 8797 8879 673136346 673136265 7.970000e-16 97.1
43 TraesCS7A01G498200 chr4A 96.078 306 11 1 2502 2806 209332212 209331907 1.870000e-136 497.0
44 TraesCS7A01G498200 chr4A 95.098 306 14 1 2502 2806 486117719 486118024 1.880000e-131 481.0
45 TraesCS7A01G498200 chr4A 94.481 308 16 1 2500 2806 628560850 628561157 3.150000e-129 473.0
46 TraesCS7A01G498200 chr3A 94.771 306 15 1 2502 2806 545355077 545354772 8.770000e-130 475.0
47 TraesCS7A01G498200 chr6A 93.910 312 17 2 2498 2808 12373223 12372913 4.080000e-128 470.0
48 TraesCS7A01G498200 chr4D 94.444 306 16 1 2502 2806 444466644 444466339 4.080000e-128 470.0
49 TraesCS7A01G498200 chr4D 100.000 30 0 0 3912 3941 123635851 123635880 1.000000e-03 56.5
50 TraesCS7A01G498200 chr2A 94.156 308 17 1 2503 2809 540047976 540047669 1.470000e-127 468.0
51 TraesCS7A01G498200 chr2A 93.871 310 17 2 2502 2809 565266902 565266593 5.280000e-127 466.0
52 TraesCS7A01G498200 chr2A 82.135 459 57 19 1820 2275 714211858 714211422 4.260000e-98 370.0
53 TraesCS7A01G498200 chr5B 92.260 323 22 3 2498 2819 383920928 383920608 1.140000e-123 455.0
54 TraesCS7A01G498200 chr2B 90.226 266 25 1 2002 2267 692167160 692166896 7.170000e-91 346.0
55 TraesCS7A01G498200 chr2D 90.421 261 24 1 2002 2262 576195691 576195432 9.280000e-90 342.0
56 TraesCS7A01G498200 chrUn 100.000 30 0 0 3912 3941 86461787 86461816 1.000000e-03 56.5
57 TraesCS7A01G498200 chrUn 100.000 30 0 0 3912 3941 222673487 222673458 1.000000e-03 56.5
58 TraesCS7A01G498200 chrUn 100.000 30 0 0 3912 3941 229496815 229496786 1.000000e-03 56.5
59 TraesCS7A01G498200 chrUn 100.000 30 0 0 3912 3941 237101258 237101229 1.000000e-03 56.5
60 TraesCS7A01G498200 chr6D 100.000 30 0 0 3912 3941 168781986 168782015 1.000000e-03 56.5
61 TraesCS7A01G498200 chr1D 100.000 30 0 0 3912 3941 141328896 141328867 1.000000e-03 56.5


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 TraesCS7A01G498200 chr7A 688684443 688694088 9645 True 17813.000000 17813 100.000000 1 9646 1 chr7A.!!$R1 9645
1 TraesCS7A01G498200 chr7A 688456394 688459549 3155 True 410.333333 643 81.598333 6597 8847 3 chr7A.!!$R2 2250
2 TraesCS7A01G498200 chr7A 688625673 688627292 1619 True 317.000000 329 84.548500 8119 9611 2 chr7A.!!$R3 1492
3 TraesCS7A01G498200 chr7A 688661509 688663185 1676 True 211.925000 387 82.157500 7971 9453 4 chr7A.!!$R5 1482
4 TraesCS7A01G498200 chr7D 595721989 595731731 9742 True 2957.000000 8696 93.405600 1 9646 5 chr7D.!!$R6 9645
5 TraesCS7A01G498200 chr7D 595577499 595581364 3865 True 321.533333 627 84.534667 6597 8847 3 chr7D.!!$R3 2250
6 TraesCS7A01G498200 chr7D 595611961 595613555 1594 True 261.666667 318 84.088667 8119 9610 3 chr7D.!!$R4 1491
7 TraesCS7A01G498200 chr7D 595664283 595666651 2368 True 221.000000 233 79.702000 7718 9543 3 chr7D.!!$R5 1825
8 TraesCS7A01G498200 chr7B 673303096 673312654 9558 True 2334.333333 7603 93.103333 1 9646 6 chr7B.!!$R5 9645
9 TraesCS7A01G498200 chr7B 672913466 672915088 1622 True 445.500000 704 83.510000 7971 9090 2 chr7B.!!$R2 1119
10 TraesCS7A01G498200 chr7B 672840986 672843771 2785 True 395.666667 630 81.089667 6749 8854 3 chr7B.!!$R1 2105
11 TraesCS7A01G498200 chr7B 673122404 673124011 1607 True 294.000000 296 83.343500 8119 9611 2 chr7B.!!$R3 1492


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
518 532 0.102844 TCTGCTTTTGTTGCCACAGC 59.897 50.000 0.00 0.0 40.48 4.40 F
554 568 0.171231 GTTGCCCTGAAAGCGGAATC 59.829 55.000 0.00 0.0 0.00 2.52 F
1934 1971 0.392461 TACCTTCACCATGCCTTCGC 60.392 55.000 0.00 0.0 0.00 4.70 F
2579 2617 0.981183 AGGCCACCAACAGTAATCGA 59.019 50.000 5.01 0.0 0.00 3.59 F
2580 2618 1.066143 AGGCCACCAACAGTAATCGAG 60.066 52.381 5.01 0.0 0.00 4.04 F
2583 2621 1.338674 CCACCAACAGTAATCGAGGCA 60.339 52.381 0.00 0.0 0.00 4.75 F
2782 2820 1.349688 TGTAATCCGAGTTTGTGGCCT 59.650 47.619 3.32 0.0 0.00 5.19 F
3217 3257 1.610038 CACTGAATGCTTCCACTTGCA 59.390 47.619 0.00 0.0 43.67 4.08 F
4682 4760 2.143602 CTCCTTTTCCCCCATATCCCA 58.856 52.381 0.00 0.0 0.00 4.37 F
5592 5673 1.153005 GCTGGCATTCAGGAGGGAG 60.153 63.158 0.00 0.0 43.54 4.30 F
6155 6240 1.250328 TGAGTTGGCTCATTGCTTGG 58.750 50.000 0.00 0.0 45.94 3.61 F
8224 10231 0.178953 ATGGGCCTGACTGCAAAAGT 60.179 50.000 4.53 0.0 43.85 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1971 1.229428 TGAAGCAGAAAAGTCGGCAG 58.771 50.000 0.00 0.00 46.27 4.85 R
2079 2116 1.473434 GCCATAACCTCCCTCTTGACG 60.473 57.143 0.00 0.00 0.00 4.35 R
2762 2800 1.349688 AGGCCACAAACTCGGATTACA 59.650 47.619 5.01 0.00 0.00 2.41 R
4435 4513 0.747283 CTTGCAGGATGGGCTCTCAC 60.747 60.000 0.00 0.00 35.86 3.51 R
4682 4760 9.359653 CAGAGATTATATGTTTCCCCTTGAAAT 57.640 33.333 0.00 0.00 44.44 2.17 R
4711 4789 7.257722 TCATGAGAAAAGGAGACAAAACAAAC 58.742 34.615 0.00 0.00 0.00 2.93 R
4840 4918 2.751436 GCAGATCGCAAGGCCCAA 60.751 61.111 0.00 0.00 41.79 4.12 R
5412 5493 5.185828 GGGCACACTTTCCAGAATTATCTTT 59.814 40.000 0.00 0.00 32.03 2.52 R
5759 5840 0.321564 CACGGATTGCTTCCAGTCCA 60.322 55.000 6.14 0.00 45.43 4.02 R
7692 9278 1.067213 GCTCTCTGTCTGTCTCCCAAC 60.067 57.143 0.00 0.00 0.00 3.77 R
8305 10312 1.279271 ACTCAGAATTTACTGCCGGCT 59.721 47.619 29.70 11.31 37.75 5.52 R
9115 12149 0.466124 GCTCTACTAGGGGCCAACAG 59.534 60.000 4.39 0.68 0.00 3.16 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)



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AutoCloner maintained by Alex Coulton.