Multiple sequence alignment - TraesCS2D01G005500

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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 TraesCS2D01G005500 chr2D 100.000 6354 0 0 1 6354 2889470 2895823 0.000000e+00 11734.0
1 TraesCS2D01G005500 chr2D 89.320 309 33 0 3599 3907 598718528 598718836 7.730000e-104 388.0
2 TraesCS2D01G005500 chr2B 92.932 3834 202 35 98 3907 8239233 8235445 0.000000e+00 5515.0
3 TraesCS2D01G005500 chr2B 92.510 3832 210 33 98 3907 8083756 8079980 0.000000e+00 5415.0
4 TraesCS2D01G005500 chr2B 92.410 3834 218 37 98 3907 7913990 7910206 0.000000e+00 5400.0
5 TraesCS2D01G005500 chr2B 92.598 2837 152 29 98 2923 7804643 7801854 0.000000e+00 4023.0
6 TraesCS2D01G005500 chr2B 93.732 2473 123 20 3905 6354 8235395 8232932 0.000000e+00 3679.0
7 TraesCS2D01G005500 chr2B 93.530 2473 128 20 3905 6354 8079930 8077467 0.000000e+00 3651.0
8 TraesCS2D01G005500 chr2B 92.473 1953 106 17 3905 5825 7800736 7798793 0.000000e+00 2754.0
9 TraesCS2D01G005500 chr2B 93.754 1633 76 10 4740 6354 7909357 7907733 0.000000e+00 2427.0
10 TraesCS2D01G005500 chr2B 95.251 1074 46 4 2836 3907 7801856 7800786 0.000000e+00 1696.0
11 TraesCS2D01G005500 chr2B 93.835 811 42 7 3905 4710 7910156 7909349 0.000000e+00 1214.0
12 TraesCS2D01G005500 chr2B 92.793 222 12 2 5901 6118 7798798 7798577 1.030000e-82 318.0
13 TraesCS2D01G005500 chr2B 87.571 177 17 4 326 502 41181016 41180845 3.880000e-47 200.0
14 TraesCS2D01G005500 chr5D 83.240 716 103 11 5644 6354 28949819 28950522 5.370000e-180 641.0
15 TraesCS2D01G005500 chr5D 85.574 305 35 8 5644 5943 48727341 48727641 1.720000e-80 311.0
16 TraesCS2D01G005500 chr6A 84.253 616 83 9 5740 6354 546622846 546623448 7.100000e-164 588.0
17 TraesCS2D01G005500 chr6A 87.151 179 20 1 319 497 143068141 143067966 3.880000e-47 200.0
18 TraesCS2D01G005500 chr5A 80.992 726 112 14 5644 6354 19682430 19683144 2.590000e-153 553.0
19 TraesCS2D01G005500 chr6B 81.168 685 99 15 5671 6354 32003792 32004447 2.030000e-144 523.0
20 TraesCS2D01G005500 chr2A 89.032 310 34 0 3598 3907 633949188 633948879 9.990000e-103 385.0
21 TraesCS2D01G005500 chr2A 84.639 332 45 3 6023 6354 3792037 3791712 6.140000e-85 326.0
22 TraesCS2D01G005500 chr2A 89.286 168 14 3 326 493 628342207 628342370 2.320000e-49 207.0
23 TraesCS2D01G005500 chr2A 88.439 173 15 4 321 493 26381743 26381576 3.000000e-48 204.0
24 TraesCS2D01G005500 chr3A 88.997 309 34 0 3599 3907 701221320 701221012 3.590000e-102 383.0
25 TraesCS2D01G005500 chr3A 79.949 389 73 3 1997 2381 52727928 52728315 1.350000e-71 281.0
26 TraesCS2D01G005500 chr3A 79.949 389 73 3 1997 2381 52774228 52774615 1.350000e-71 281.0
27 TraesCS2D01G005500 chr3A 79.692 389 74 3 1997 2381 52682073 52682460 6.270000e-70 276.0
28 TraesCS2D01G005500 chr3A 79.434 389 75 3 1997 2381 52589739 52590126 2.920000e-68 270.0
29 TraesCS2D01G005500 chr3A 79.434 389 75 3 1997 2381 52822120 52822507 2.920000e-68 270.0
30 TraesCS2D01G005500 chr3A 78.671 286 59 2 5033 5317 52685707 52685991 8.410000e-44 189.0
31 TraesCS2D01G005500 chr3A 78.596 285 61 0 5033 5317 52826010 52826294 8.410000e-44 189.0
32 TraesCS2D01G005500 chr3A 78.246 285 62 0 5033 5317 52593553 52593837 3.910000e-42 183.0
33 TraesCS2D01G005500 chr3A 78.246 285 62 0 5033 5317 52640087 52640371 3.910000e-42 183.0
34 TraesCS2D01G005500 chr3A 78.246 285 62 0 5033 5317 52778142 52778426 3.910000e-42 183.0
35 TraesCS2D01G005500 chr3A 84.375 160 25 0 2 161 59925885 59926044 2.370000e-34 158.0
36 TraesCS2D01G005500 chr3A 75.874 286 55 8 1252 1530 52589259 52589537 4.000000e-27 134.0
37 TraesCS2D01G005500 chr3A 75.874 286 55 8 1252 1530 52635602 52635880 4.000000e-27 134.0
38 TraesCS2D01G005500 chr3A 75.874 286 55 8 1252 1530 52681593 52681871 4.000000e-27 134.0
39 TraesCS2D01G005500 chr3A 75.874 286 55 7 1252 1530 52821640 52821918 4.000000e-27 134.0
40 TraesCS2D01G005500 chr3A 75.524 286 56 8 1252 1530 52727448 52727726 1.860000e-25 128.0
41 TraesCS2D01G005500 chr3B 88.050 318 34 3 3599 3915 663132081 663132395 2.160000e-99 374.0
42 TraesCS2D01G005500 chr1A 88.050 318 32 4 3592 3907 313906873 313906560 7.780000e-99 372.0
43 TraesCS2D01G005500 chr1A 81.319 91 16 1 5930 6020 578215836 578215925 8.840000e-09 73.1
44 TraesCS2D01G005500 chr7B 84.366 339 52 1 6017 6354 187595914 187596252 1.320000e-86 331.0
45 TraesCS2D01G005500 chr5B 83.784 296 42 5 5644 5937 51218483 51218774 6.270000e-70 276.0
46 TraesCS2D01G005500 chr4A 89.017 173 14 3 322 493 625818893 625819061 6.460000e-50 209.0
47 TraesCS2D01G005500 chr7A 100.000 32 0 0 5574 5605 135710253 135710222 6.880000e-05 60.2


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 TraesCS2D01G005500 chr2D 2889470 2895823 6353 False 11734.000000 11734 100.00000 1 6354 1 chr2D.!!$F1 6353
1 TraesCS2D01G005500 chr2B 8232932 8239233 6301 True 4597.000000 5515 93.33200 98 6354 2 chr2B.!!$R5 6256
2 TraesCS2D01G005500 chr2B 8077467 8083756 6289 True 4533.000000 5415 93.02000 98 6354 2 chr2B.!!$R4 6256
3 TraesCS2D01G005500 chr2B 7907733 7913990 6257 True 3013.666667 5400 93.33300 98 6354 3 chr2B.!!$R3 6256
4 TraesCS2D01G005500 chr2B 7798577 7804643 6066 True 2197.750000 4023 93.27875 98 6118 4 chr2B.!!$R2 6020
5 TraesCS2D01G005500 chr5D 28949819 28950522 703 False 641.000000 641 83.24000 5644 6354 1 chr5D.!!$F1 710
6 TraesCS2D01G005500 chr6A 546622846 546623448 602 False 588.000000 588 84.25300 5740 6354 1 chr6A.!!$F1 614
7 TraesCS2D01G005500 chr5A 19682430 19683144 714 False 553.000000 553 80.99200 5644 6354 1 chr5A.!!$F1 710
8 TraesCS2D01G005500 chr6B 32003792 32004447 655 False 523.000000 523 81.16800 5671 6354 1 chr6B.!!$F1 683
9 TraesCS2D01G005500 chr3A 52774228 52778426 4198 False 232.000000 281 79.09750 1997 5317 2 chr3A.!!$F7 3320
10 TraesCS2D01G005500 chr3A 52727448 52728315 867 False 204.500000 281 77.73650 1252 2381 2 chr3A.!!$F6 1129


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
778 779 0.036010 ACTTGGGAGGCAGACGATTG 60.036 55.000 0.00 0.00 0.00 2.67 F
899 900 0.106918 TTTTTCACAGACCCACGCCT 60.107 50.000 0.00 0.00 0.00 5.52 F
900 901 0.106918 TTTTCACAGACCCACGCCTT 60.107 50.000 0.00 0.00 0.00 4.35 F
1029 1034 0.249676 CCTCTCATGCTGCTGACACT 59.750 55.000 0.00 0.00 0.00 3.55 F
2249 2316 0.320697 GCGTGTAAGAGGGTGGAAGT 59.679 55.000 0.00 0.00 0.00 3.01 F
2986 3864 1.509463 ACGTATGACATCCGTGCGT 59.491 52.632 5.15 0.00 45.84 5.24 F
3714 5996 0.177604 TTGTGGCCCTTTTGCAACAG 59.822 50.000 5.59 5.59 45.50 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 3415 0.106519 ATGTGTGCTAATCCCAGCCC 60.107 55.000 0.0 0.0 41.04 5.19 R
2661 3454 4.828704 GCATTTGCATGATACAACATTGC 58.171 39.130 0.0 0.0 41.59 3.56 R
2686 3479 8.964476 AGACATATGGAGAAAATTATGTTCGT 57.036 30.769 7.8 0.0 0.00 3.85 R
2976 3854 0.319040 CCTCTATGGACGCACGGATG 60.319 60.000 0.0 0.0 38.35 3.51 R
3636 5913 0.740868 AATGACGGATGGCAGACACG 60.741 55.000 0.0 0.0 0.00 4.49 R
4341 6680 0.666913 CCATGCAGCCATCAGTAAGC 59.333 55.000 0.0 0.0 0.00 3.09 R
5572 7981 0.029834 GCAATGCATGGGCGTTCTAG 59.970 55.000 0.0 0.0 46.01 2.43 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.