Multiple sequence alignment - TraesCS2A01G378000

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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 TraesCS2A01G378000 chr2A 100.000 4121 0 0 1 4121 620706265 620710385 0.000000e+00 7611.0
1 TraesCS2A01G378000 chr2A 99.388 3595 19 1 530 4121 736454395 736450801 0.000000e+00 6514.0
2 TraesCS2A01G378000 chr2A 95.759 1344 48 7 733 2074 21215527 21216863 0.000000e+00 2158.0
3 TraesCS2A01G378000 chr2A 96.080 995 31 3 2158 3152 21218121 21219107 0.000000e+00 1615.0
4 TraesCS2A01G378000 chr2A 99.622 529 2 0 1 529 736458753 736458225 0.000000e+00 966.0
5 TraesCS2A01G378000 chr2A 95.098 204 6 1 3922 4121 744844904 744844701 6.650000e-83 318.0
6 TraesCS2A01G378000 chr2A 92.647 204 11 1 3922 4121 21219681 21219884 1.450000e-74 291.0
7 TraesCS2A01G378000 chr2A 100.000 30 0 0 3852 3881 744844937 744844908 5.750000e-04 56.5
8 TraesCS2A01G378000 chr2A 100.000 29 0 0 3852 3880 21219648 21219676 2.000000e-03 54.7
9 TraesCS2A01G378000 chr6B 99.054 3595 16 2 530 4121 707179627 707176048 0.000000e+00 6434.0
10 TraesCS2A01G378000 chr6B 96.841 1678 50 3 2158 3833 11701799 11700123 0.000000e+00 2802.0
11 TraesCS2A01G378000 chr6B 97.616 755 17 1 1409 2163 11702734 11701981 0.000000e+00 1293.0
12 TraesCS2A01G378000 chr6B 99.244 529 4 0 1 529 707183987 707183459 0.000000e+00 955.0
13 TraesCS2A01G378000 chr6B 96.408 529 19 0 1 529 11704550 11704022 0.000000e+00 872.0
14 TraesCS2A01G378000 chr6B 100.000 43 0 0 2071 2113 11701972 11701930 3.410000e-11 80.5
15 TraesCS2A01G378000 chr7B 96.280 1344 44 5 733 2074 585480075 585478736 0.000000e+00 2200.0
16 TraesCS2A01G378000 chr7B 96.181 995 31 4 2158 3152 585477479 585476492 0.000000e+00 1620.0
17 TraesCS2A01G378000 chr7B 94.253 261 13 2 530 789 585480215 585479956 8.300000e-107 398.0
18 TraesCS2A01G378000 chr7B 82.979 423 41 8 3373 3766 743627803 743628223 1.820000e-93 353.0
19 TraesCS2A01G378000 chr7B 92.647 204 11 1 3922 4121 585475918 585475715 1.450000e-74 291.0
20 TraesCS2A01G378000 chr7B 82.890 263 26 12 3504 3761 744062766 744063014 6.940000e-53 219.0
21 TraesCS2A01G378000 chr7B 94.792 96 5 0 4026 4121 537734160 537734065 2.570000e-32 150.0
22 TraesCS2A01G378000 chr7B 89.474 114 6 4 3652 3759 745255295 745255408 5.550000e-29 139.0
23 TraesCS2A01G378000 chr7B 95.000 80 3 1 3373 3451 743625607 743625686 1.560000e-24 124.0
24 TraesCS2A01G378000 chr7B 89.247 93 10 0 3373 3465 645580088 645579996 2.600000e-22 117.0
25 TraesCS2A01G378000 chr7B 100.000 29 0 0 3852 3880 585475951 585475923 2.000000e-03 54.7
26 TraesCS2A01G378000 chr2B 95.578 1357 54 5 647 2001 576685616 576684264 0.000000e+00 2169.0
27 TraesCS2A01G378000 chr2B 98.213 1231 17 3 2895 4121 721700662 721701891 0.000000e+00 2146.0
28 TraesCS2A01G378000 chr2B 98.110 529 10 0 1 529 721697727 721698255 0.000000e+00 922.0
29 TraesCS2A01G378000 chr2B 80.569 422 42 16 3373 3761 782163418 782163004 5.210000e-74 289.0
30 TraesCS2A01G378000 chr2B 97.436 39 1 0 2071 2109 109404492 109404530 2.660000e-07 67.6
31 TraesCS2A01G378000 chrUn 95.578 1357 53 6 647 2001 38658884 38660235 0.000000e+00 2167.0
32 TraesCS2A01G378000 chrUn 97.898 999 16 4 1077 2074 316936553 316937547 0.000000e+00 1724.0
33 TraesCS2A01G378000 chrUn 96.382 995 33 2 2158 3152 316938806 316939797 0.000000e+00 1635.0
34 TraesCS2A01G378000 chrUn 96.181 995 35 2 2158 3152 379280354 379279363 0.000000e+00 1624.0
35 TraesCS2A01G378000 chrUn 93.103 261 14 3 530 789 431333118 431333375 3.010000e-101 379.0
36 TraesCS2A01G378000 chr1B 95.280 1356 59 4 647 2001 32422892 32424243 0.000000e+00 2145.0
37 TraesCS2A01G378000 chr4A 98.050 1231 19 3 2895 4121 622189808 622191037 0.000000e+00 2135.0
38 TraesCS2A01G378000 chr4A 98.488 529 8 0 1 529 622186873 622187401 0.000000e+00 933.0
39 TraesCS2A01G378000 chr4A 100.000 31 0 0 3892 3922 622190736 622190766 1.600000e-04 58.4
40 TraesCS2A01G378000 chr5B 93.363 1356 67 15 647 2001 591688175 591686842 0.000000e+00 1984.0
41 TraesCS2A01G378000 chr5A 96.023 880 31 2 2238 3117 78916001 78915126 0.000000e+00 1428.0
42 TraesCS2A01G378000 chr5A 96.023 880 31 2 2238 3117 395306238 395307113 0.000000e+00 1428.0
43 TraesCS2A01G378000 chr5A 93.191 514 30 4 1562 2074 458335058 458335567 0.000000e+00 750.0
44 TraesCS2A01G378000 chr5A 95.833 96 4 0 4026 4121 78914221 78914126 5.520000e-34 156.0
45 TraesCS2A01G378000 chr3B 99.235 784 3 1 3341 4121 785318798 785319581 0.000000e+00 1411.0
46 TraesCS2A01G378000 chr3B 99.622 529 2 0 1 529 785317966 785318494 0.000000e+00 966.0
47 TraesCS2A01G378000 chr3B 93.191 514 30 4 1562 2074 9284826 9285335 0.000000e+00 750.0
48 TraesCS2A01G378000 chr3B 89.820 167 13 1 530 696 42497235 42497397 1.160000e-50 211.0
49 TraesCS2A01G378000 chr3B 95.385 65 1 2 109 173 216365006 216365068 7.290000e-18 102.0
50 TraesCS2A01G378000 chr7A 92.996 514 31 4 1562 2074 66645701 66645192 0.000000e+00 745.0
51 TraesCS2A01G378000 chr7A 88.889 54 6 0 3954 4007 1701649 1701596 2.660000e-07 67.6
52 TraesCS2A01G378000 chr7A 79.310 87 9 5 3150 3236 736336649 736336572 7.000000e-03 52.8
53 TraesCS2A01G378000 chr3A 98.551 414 6 0 116 529 671167975 671167562 0.000000e+00 732.0
54 TraesCS2A01G378000 chr3A 98.824 340 4 0 190 529 153336043 153336382 1.270000e-169 606.0
55 TraesCS2A01G378000 chr1A 98.551 414 6 0 116 529 551839019 551839432 0.000000e+00 732.0


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 TraesCS2A01G378000 chr2A 620706265 620710385 4120 False 7611.000000 7611 100.00000 1 4121 1 chr2A.!!$F1 4120
1 TraesCS2A01G378000 chr2A 736450801 736458753 7952 True 3740.000000 6514 99.50500 1 4121 2 chr2A.!!$R1 4120
2 TraesCS2A01G378000 chr2A 21215527 21219884 4357 False 1029.675000 2158 96.12150 733 4121 4 chr2A.!!$F2 3388
3 TraesCS2A01G378000 chr6B 707176048 707183987 7939 True 3694.500000 6434 99.14900 1 4121 2 chr6B.!!$R2 4120
4 TraesCS2A01G378000 chr6B 11700123 11704550 4427 True 1261.875000 2802 97.71625 1 3833 4 chr6B.!!$R1 3832
5 TraesCS2A01G378000 chr7B 585475715 585480215 4500 True 912.740000 2200 95.87220 530 4121 5 chr7B.!!$R3 3591
6 TraesCS2A01G378000 chr7B 743625607 743628223 2616 False 238.500000 353 88.98950 3373 3766 2 chr7B.!!$F3 393
7 TraesCS2A01G378000 chr2B 576684264 576685616 1352 True 2169.000000 2169 95.57800 647 2001 1 chr2B.!!$R1 1354
8 TraesCS2A01G378000 chr2B 721697727 721701891 4164 False 1534.000000 2146 98.16150 1 4121 2 chr2B.!!$F2 4120
9 TraesCS2A01G378000 chrUn 38658884 38660235 1351 False 2167.000000 2167 95.57800 647 2001 1 chrUn.!!$F1 1354
10 TraesCS2A01G378000 chrUn 316936553 316939797 3244 False 1679.500000 1724 97.14000 1077 3152 2 chrUn.!!$F3 2075
11 TraesCS2A01G378000 chrUn 379279363 379280354 991 True 1624.000000 1624 96.18100 2158 3152 1 chrUn.!!$R1 994
12 TraesCS2A01G378000 chr1B 32422892 32424243 1351 False 2145.000000 2145 95.28000 647 2001 1 chr1B.!!$F1 1354
13 TraesCS2A01G378000 chr4A 622186873 622191037 4164 False 1042.133333 2135 98.84600 1 4121 3 chr4A.!!$F1 4120
14 TraesCS2A01G378000 chr5B 591686842 591688175 1333 True 1984.000000 1984 93.36300 647 2001 1 chr5B.!!$R1 1354
15 TraesCS2A01G378000 chr5A 395306238 395307113 875 False 1428.000000 1428 96.02300 2238 3117 1 chr5A.!!$F1 879
16 TraesCS2A01G378000 chr5A 78914126 78916001 1875 True 792.000000 1428 95.92800 2238 4121 2 chr5A.!!$R1 1883
17 TraesCS2A01G378000 chr5A 458335058 458335567 509 False 750.000000 750 93.19100 1562 2074 1 chr5A.!!$F2 512
18 TraesCS2A01G378000 chr3B 785317966 785319581 1615 False 1188.500000 1411 99.42850 1 4121 2 chr3B.!!$F4 4120
19 TraesCS2A01G378000 chr3B 9284826 9285335 509 False 750.000000 750 93.19100 1562 2074 1 chr3B.!!$F1 512
20 TraesCS2A01G378000 chr7A 66645192 66645701 509 True 745.000000 745 92.99600 1562 2074 1 chr7A.!!$R2 512

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
554 4387 3.004629 TGACATGATGTTGCACCAGAAAC 59.995 43.478 0.0 0.0 33.58 2.78 F
632 4465 4.550076 ATTCTGAAGAGGAACCAGAGTG 57.450 45.455 0.0 0.0 38.08 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 6083 8.749499 CAAGATTCAAAGTCAAAAGACATGAAC 58.251 33.333 14.65 10.73 36.62 3.18 R
3927 12613 5.536161 AGGAAGAAAAACTGCACACATACAT 59.464 36.000 0.00 0.00 0.00 2.29 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
332 333 9.905713 AATGTTTAGAAAGGATATGCAGTTCTA 57.094 29.630 13.13 13.13 31.28 2.10
532 4365 4.090786 GCAAGTTGCGTGTTTAGTTTTGTT 59.909 37.500 12.95 0.00 31.71 2.83
554 4387 3.004629 TGACATGATGTTGCACCAGAAAC 59.995 43.478 0.00 0.00 33.58 2.78
632 4465 4.550076 ATTCTGAAGAGGAACCAGAGTG 57.450 45.455 0.00 0.00 38.08 3.51
3927 12613 9.520204 GTTAGCTACGTACAAATGTATTTCCTA 57.480 33.333 0.00 0.00 32.54 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
514 515 4.795268 TGTCAACAAAACTAAACACGCAA 58.205 34.783 0.00 0.00 0.00 4.85
532 4365 2.565046 TCTGGTGCAACATCATGTCA 57.435 45.000 4.06 0.00 39.98 3.58
554 4387 5.335191 GCCAACTCTTTTGGATCAGTAACAG 60.335 44.000 7.23 0.00 42.06 3.16
632 4465 8.932791 CCCGATACAACACATAATTATTCTACC 58.067 37.037 0.00 0.00 0.00 3.18
1863 6083 8.749499 CAAGATTCAAAGTCAAAAGACATGAAC 58.251 33.333 14.65 10.73 36.62 3.18
3927 12613 5.536161 AGGAAGAAAAACTGCACACATACAT 59.464 36.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.