Multiple sequence alignment - TraesCS2B01G122200

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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 TraesCS2B01G122200 chr2B 100.000 8692 0 0 1 8692 89541999 89550690 0.000000e+00 16052.0
1 TraesCS2B01G122200 chr2B 99.432 176 1 0 3340 3515 385772978 385773153 3.920000e-83 320.0
2 TraesCS2B01G122200 chr2B 88.800 125 12 2 519 642 705874260 705874383 1.510000e-32 152.0
3 TraesCS2B01G122200 chr2D 91.240 2637 147 43 744 3342 56533554 56536144 0.000000e+00 3513.0
4 TraesCS2B01G122200 chr2D 94.561 2151 90 9 3516 5657 56536136 56538268 0.000000e+00 3299.0
5 TraesCS2B01G122200 chr2D 94.578 1291 49 13 5656 6935 56538312 56539592 0.000000e+00 1977.0
6 TraesCS2B01G122200 chr2D 89.880 919 75 13 6977 7884 56539591 56540502 0.000000e+00 1166.0
7 TraesCS2B01G122200 chr2D 92.857 420 27 3 8275 8692 56541154 56541572 2.680000e-169 606.0
8 TraesCS2B01G122200 chr2D 85.677 384 31 9 7914 8277 56540617 56540996 4.920000e-102 383.0
9 TraesCS2B01G122200 chr2D 80.556 108 13 6 400 500 611247221 611247327 9.360000e-10 76.8
10 TraesCS2B01G122200 chr2A 95.911 2152 72 7 3516 5660 57989426 57991568 0.000000e+00 3472.0
11 TraesCS2B01G122200 chr2A 89.975 2005 106 40 744 2701 57987268 57989224 0.000000e+00 2501.0
12 TraesCS2B01G122200 chr2A 94.465 1337 58 14 5656 6981 57991609 57992940 0.000000e+00 2045.0
13 TraesCS2B01G122200 chr2A 91.005 1423 96 19 6976 8373 57995483 57996898 0.000000e+00 1890.0
14 TraesCS2B01G122200 chr2A 90.592 287 22 4 8402 8684 57997312 57997597 8.240000e-100 375.0
15 TraesCS2B01G122200 chr2A 93.370 181 12 0 3162 3342 57989254 57989434 1.440000e-67 268.0
16 TraesCS2B01G122200 chr2A 78.788 198 27 7 335 521 57987028 57987221 1.530000e-22 119.0
17 TraesCS2B01G122200 chr4A 98.378 185 2 1 3331 3515 662620986 662621169 3.030000e-84 324.0
18 TraesCS2B01G122200 chr1B 99.438 178 1 0 3340 3517 25246056 25246233 3.030000e-84 324.0
19 TraesCS2B01G122200 chr1B 96.078 102 4 0 528 629 423961640 423961539 5.400000e-37 167.0
20 TraesCS2B01G122200 chr5B 100.000 174 0 0 3343 3516 363665473 363665300 1.090000e-83 322.0
21 TraesCS2B01G122200 chr7B 98.352 182 1 2 3340 3519 662001631 662001450 1.410000e-82 318.0
22 TraesCS2B01G122200 chr7B 94.898 196 8 2 3327 3521 668908586 668908780 1.100000e-78 305.0
23 TraesCS2B01G122200 chr7B 99.010 101 1 0 531 631 659404281 659404181 1.930000e-41 182.0
24 TraesCS2B01G122200 chr4B 99.425 174 1 0 3343 3516 328009284 328009111 5.060000e-82 316.0
25 TraesCS2B01G122200 chr4B 83.333 90 12 3 1651 1737 55922877 55922788 7.230000e-11 80.5
26 TraesCS2B01G122200 chr6B 95.833 192 6 2 3334 3524 695088424 695088614 8.470000e-80 309.0
27 TraesCS2B01G122200 chr6B 92.793 111 8 0 519 629 633054004 633054114 2.510000e-35 161.0
28 TraesCS2B01G122200 chr1D 90.455 220 19 2 3319 3537 372878607 372878825 1.100000e-73 289.0
29 TraesCS2B01G122200 chr3A 84.659 176 19 5 526 701 77404924 77405091 1.500000e-37 169.0
30 TraesCS2B01G122200 chr5D 94.495 109 5 1 529 637 266749456 266749349 5.400000e-37 167.0
31 TraesCS2B01G122200 chr7A 96.907 97 3 0 533 629 203965835 203965931 6.980000e-36 163.0
32 TraesCS2B01G122200 chr1A 82.234 197 18 13 504 688 590991833 590992024 4.200000e-33 154.0
33 TraesCS2B01G122200 chr1A 83.784 111 12 5 377 484 497224479 497224372 5.550000e-17 100.0
34 TraesCS2B01G122200 chr3B 89.256 121 11 2 526 646 219440344 219440226 5.440000e-32 150.0
35 TraesCS2B01G122200 chr4D 81.818 110 19 1 1618 1726 38449113 38449222 3.340000e-14 91.6
36 TraesCS2B01G122200 chr5A 81.818 88 11 5 400 484 533564525 533564440 1.570000e-07 69.4


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 TraesCS2B01G122200 chr2B 89541999 89550690 8691 False 16052.000000 16052 100.000000 1 8692 1 chr2B.!!$F1 8691
1 TraesCS2B01G122200 chr2D 56533554 56541572 8018 False 1824.000000 3513 91.465500 744 8692 6 chr2D.!!$F2 7948
2 TraesCS2B01G122200 chr2A 57987028 57997597 10569 False 1524.285714 3472 90.586571 335 8684 7 chr2A.!!$F1 8349


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
81 82 0.339859 TCCTCCCATGTACCTCTGCT 59.660 55.0 0.00 0.00 0.00 4.24 F
82 83 1.207791 CCTCCCATGTACCTCTGCTT 58.792 55.0 0.00 0.00 0.00 3.91 F
1336 1369 0.033920 TGGACAGTAGTGCAGTGCAG 59.966 55.0 20.42 9.05 41.46 4.41 F
1337 1370 0.034059 GGACAGTAGTGCAGTGCAGT 59.966 55.0 27.60 27.60 44.89 4.40 F
1394 1427 0.099436 GATTTCGGCCACTGATGTGC 59.901 55.0 2.24 0.00 42.54 4.57 F
3165 3244 0.182537 AACCAACACCAGTAGCAGCA 59.817 50.0 0.00 0.00 0.00 4.41 F
3427 3506 0.394938 ATACAACCCACGTCAGCACA 59.605 50.0 0.00 0.00 0.00 4.57 F
3831 3910 0.511653 GGTCACTTTTCCTCGCGTTC 59.488 55.0 5.77 0.00 0.00 3.95 F
4021 4100 0.671472 GGGGCAATGCAGAAGTTTGC 60.671 55.0 12.50 12.50 43.83 3.68 F
5137 5222 0.872388 CAGGCTCGGGTTTTGTGTAC 59.128 55.0 0.00 0.00 0.00 2.90 F
7061 9768 0.106918 ACTGGGTCCTAGCTCTCTCG 60.107 60.0 1.33 0.00 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1350 0.033920 CTGCACTGCACTACTGTCCA 59.966 55.000 0.00 0.00 33.79 4.02 R
1484 1517 0.035056 ACAGTAGCCATGGGTTCAGC 60.035 55.000 23.79 10.25 0.00 4.26 R
3152 3231 0.097674 GCGAAATGCTGCTACTGGTG 59.902 55.000 0.00 0.00 41.73 4.17 R
3165 3244 1.153823 CACCGGACTCTCGCGAAAT 60.154 57.895 9.46 0.00 0.00 2.17 R
3168 3247 3.429141 GACACCGGACTCTCGCGA 61.429 66.667 9.46 9.26 0.00 5.87 R
3976 4055 0.462759 GGACTGCCATGTCTGTAGCC 60.463 60.000 0.00 0.00 37.16 3.93 R
5333 5428 1.270358 TGTGTAACCATGTAGCACGCA 60.270 47.619 0.00 0.00 34.36 5.24 R
5614 5709 0.909623 TAGCTTTCACCAGGTAGGGC 59.090 55.000 0.00 0.00 43.89 5.19 R
5840 5980 1.554617 TGCAGATTCTGACATTCCCGA 59.445 47.619 17.87 0.00 32.44 5.14 R
7130 9837 0.610785 GGTTTCGGGGATTTCAGCCA 60.611 55.000 0.00 0.00 0.00 4.75 R
8041 10850 0.950836 CACGGTGTTTCCTTGCATCA 59.049 50.000 0.00 0.00 0.00 3.07 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.