Multiple sequence alignment - TraesCS1A01G116800

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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 TraesCS1A01G116800 chr1A 100.000 2597 0 0 1 2597 124015422 124012826 0.000000e+00 4796
1 TraesCS1A01G116800 chr1A 96.203 395 14 1 2142 2536 569788785 569789178 0.000000e+00 645
2 TraesCS1A01G116800 chr1A 96.429 364 12 1 1748 2110 569788424 569788787 1.330000e-167 599
3 TraesCS1A01G116800 chr3B 98.457 1750 20 3 1 1748 10254795 10256539 0.000000e+00 3075
4 TraesCS1A01G116800 chr5A 95.976 845 32 1 1751 2595 310966926 310967768 0.000000e+00 1371
5 TraesCS1A01G116800 chr5A 96.292 836 27 4 1752 2586 109335407 109334575 0.000000e+00 1369
6 TraesCS1A01G116800 chr2A 96.368 826 27 1 1752 2577 651616231 651617053 0.000000e+00 1356
7 TraesCS1A01G116800 chr3A 94.947 851 32 9 1752 2597 587599614 587600458 0.000000e+00 1323
8 TraesCS1A01G116800 chr4A 96.456 790 26 2 1748 2536 623784484 623785272 0.000000e+00 1303
9 TraesCS1A01G116800 chr5D 92.512 828 32 11 1754 2577 327625596 327624795 0.000000e+00 1158
10 TraesCS1A01G116800 chr5D 88.597 877 41 26 1751 2577 520432199 520433066 0.000000e+00 1011
11 TraesCS1A01G116800 chr5D 88.588 517 30 15 1752 2241 378788796 378789310 3.700000e-168 601
12 TraesCS1A01G116800 chr6B 84.401 718 81 12 795 1507 656035534 656036225 0.000000e+00 676
13 TraesCS1A01G116800 chr6B 82.493 714 92 15 799 1509 656163936 656164619 1.720000e-166 595
14 TraesCS1A01G116800 chr6B 88.856 341 35 3 181 519 656162333 656162672 1.440000e-112 416
15 TraesCS1A01G116800 chr6B 86.897 290 32 2 507 791 656162720 656163008 1.160000e-83 320
16 TraesCS1A01G116800 chr6B 92.405 158 10 2 1 158 656160390 656160545 9.350000e-55 224
17 TraesCS1A01G116800 chr5B 86.907 527 38 12 1752 2247 453006163 453006689 1.740000e-156 562
18 TraesCS1A01G116800 chr6D 92.373 354 19 4 2224 2577 117374595 117374940 4.990000e-137 497
19 TraesCS1A01G116800 chr6D 86.334 461 50 4 1051 1509 433877265 433877714 8.350000e-135 490
20 TraesCS1A01G116800 chr6D 90.000 350 31 3 174 521 433878258 433878605 1.420000e-122 449
21 TraesCS1A01G116800 chr6D 83.948 461 61 5 1050 1509 433894026 433894474 1.850000e-116 429
22 TraesCS1A01G116800 chr6D 86.897 290 32 2 507 791 433878624 433878912 1.160000e-83 320
23 TraesCS1A01G116800 chr6D 88.048 251 23 4 799 1046 433770229 433770475 9.090000e-75 291
24 TraesCS1A01G116800 chr6D 84.962 266 25 6 795 1056 433879870 433880124 3.320000e-64 255
25 TraesCS1A01G116800 chr6D 93.038 158 8 3 1 158 433877986 433878140 7.230000e-56 228


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 TraesCS1A01G116800 chr1A 124012826 124015422 2596 True 4796.00 4796 100.00000 1 2597 1 chr1A.!!$R1 2596
1 TraesCS1A01G116800 chr1A 569788424 569789178 754 False 622.00 645 96.31600 1748 2536 2 chr1A.!!$F1 788
2 TraesCS1A01G116800 chr3B 10254795 10256539 1744 False 3075.00 3075 98.45700 1 1748 1 chr3B.!!$F1 1747
3 TraesCS1A01G116800 chr5A 310966926 310967768 842 False 1371.00 1371 95.97600 1751 2595 1 chr5A.!!$F1 844
4 TraesCS1A01G116800 chr5A 109334575 109335407 832 True 1369.00 1369 96.29200 1752 2586 1 chr5A.!!$R1 834
5 TraesCS1A01G116800 chr2A 651616231 651617053 822 False 1356.00 1356 96.36800 1752 2577 1 chr2A.!!$F1 825
6 TraesCS1A01G116800 chr3A 587599614 587600458 844 False 1323.00 1323 94.94700 1752 2597 1 chr3A.!!$F1 845
7 TraesCS1A01G116800 chr4A 623784484 623785272 788 False 1303.00 1303 96.45600 1748 2536 1 chr4A.!!$F1 788
8 TraesCS1A01G116800 chr5D 327624795 327625596 801 True 1158.00 1158 92.51200 1754 2577 1 chr5D.!!$R1 823
9 TraesCS1A01G116800 chr5D 520432199 520433066 867 False 1011.00 1011 88.59700 1751 2577 1 chr5D.!!$F2 826
10 TraesCS1A01G116800 chr5D 378788796 378789310 514 False 601.00 601 88.58800 1752 2241 1 chr5D.!!$F1 489
11 TraesCS1A01G116800 chr6B 656035534 656036225 691 False 676.00 676 84.40100 795 1507 1 chr6B.!!$F1 712
12 TraesCS1A01G116800 chr6B 656160390 656164619 4229 False 388.75 595 87.66275 1 1509 4 chr6B.!!$F2 1508
13 TraesCS1A01G116800 chr5B 453006163 453006689 526 False 562.00 562 86.90700 1752 2247 1 chr5B.!!$F1 495
14 TraesCS1A01G116800 chr6D 433877265 433880124 2859 False 348.40 490 88.24620 1 1509 5 chr6D.!!$F4 1508

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
267 2762 1.271856 TCTCCGCAATGTAGGAACCA 58.728 50.0 1.82 0.0 35.9 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 5342 1.418097 ATGTGGGCCTGTGAGACACA 61.418 55.0 10.56 10.56 44.91 3.72 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
42 764 5.241506 GTCATGTCCAGTGAATTTTTCTCCA 59.758 40.000 0.00 0.00 0.00 3.86
267 2762 1.271856 TCTCCGCAATGTAGGAACCA 58.728 50.000 1.82 0.00 35.90 3.67
907 4426 7.886970 ACAATATATTGGTCATCTCCTTCATGG 59.113 37.037 25.45 0.00 41.96 3.66
1209 4729 1.295423 GCCTCCACAGACGGCTTTA 59.705 57.895 0.00 0.00 40.62 1.85
1456 4984 4.123745 AGGAATAGATTGGGGGTTTACCA 58.876 43.478 0.69 0.00 42.91 3.25
1664 5192 3.624777 GGATTGGGAAAGAGATGCAGAA 58.375 45.455 0.00 0.00 0.00 3.02
1814 5342 1.376424 CTCCTTCACAGCACGCCAT 60.376 57.895 0.00 0.00 0.00 4.40
1934 5496 2.859404 TCTGTTCCATCTCCTCCCTCTA 59.141 50.000 0.00 0.00 0.00 2.43
2018 5580 1.274712 CTGCTCACCTTCTCTCCCTT 58.725 55.000 0.00 0.00 0.00 3.95
2068 5630 1.416373 CATGTGAGAGATCCATCGCG 58.584 55.000 0.00 0.00 0.00 5.87
2355 5967 2.866028 GCTGCAGTGAAGCTTCGG 59.134 61.111 21.11 13.96 37.69 4.30
2389 6001 2.042831 GCTGCGGTGGAGCTTTGAT 61.043 57.895 2.86 0.00 38.13 2.57
2465 6077 2.690778 GCAATGAAGCTTCGCCGGT 61.691 57.895 21.11 1.95 0.00 5.28
2541 6153 2.257302 TTGCAATGAAGCGCCACGA 61.257 52.632 2.29 0.00 37.31 4.35
2544 6156 2.048597 AATGAAGCGCCACGACGA 60.049 55.556 2.29 0.00 34.06 4.20
2578 6190 1.956170 CGAGGTTGCAGTGAAGCGT 60.956 57.895 0.00 0.00 37.31 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 764 4.887071 TCTCTGTGTTTAAAATGTGCAGGT 59.113 37.500 0.00 0.00 0.00 4.00
176 898 9.787532 CTTGATGTGAGAAAAGTGAGTTTTTAA 57.212 29.630 0.00 0.00 38.54 1.52
177 899 7.915397 GCTTGATGTGAGAAAAGTGAGTTTTTA 59.085 33.333 0.00 0.00 38.54 1.52
907 4426 2.036256 AGCCCATGGTCAAGTGCC 59.964 61.111 11.73 0.00 0.00 5.01
1233 4753 3.329889 ATTGGAGGAGCCGTGCCA 61.330 61.111 0.00 0.00 40.66 4.92
1456 4984 2.117156 GCCACGCAGCAATCCATCT 61.117 57.895 0.00 0.00 0.00 2.90
1664 5192 1.995626 CACCTTCTCCCGGACCCAT 60.996 63.158 0.73 0.00 0.00 4.00
1748 5276 5.504337 CGGTTGATTGTAAACGTTTTCCAGA 60.504 40.000 20.19 0.00 36.09 3.86
1749 5277 4.673311 CGGTTGATTGTAAACGTTTTCCAG 59.327 41.667 20.19 0.00 36.09 3.86
1814 5342 1.418097 ATGTGGGCCTGTGAGACACA 61.418 55.000 10.56 10.56 44.91 3.72
1934 5496 1.813102 GGGATTGAGGGGTGAGAGAT 58.187 55.000 0.00 0.00 0.00 2.75
1987 5549 1.476833 GGTGAGCAGGAAGGTTGTTGA 60.477 52.381 0.00 0.00 0.00 3.18
2018 5580 2.357034 GTGTTGGAGCTTCGCCGA 60.357 61.111 0.00 0.00 0.00 5.54
2068 5630 4.802051 TTGGAGCAGCGATGCCCC 62.802 66.667 24.00 22.14 32.91 5.80
2363 5975 4.320456 CCACCGCAGCACCAGACT 62.320 66.667 0.00 0.00 0.00 3.24
2465 6077 3.702048 GTAGCACCCCGACAGCCA 61.702 66.667 0.00 0.00 0.00 4.75
2469 6081 2.665089 CCATGGTAGCACCCCGACA 61.665 63.158 2.57 0.00 37.50 4.35
2541 6153 1.079127 CCGGAGCTCCAACAATCGT 60.079 57.895 31.67 0.00 35.14 3.73
2544 6156 2.436646 CGCCGGAGCTCCAACAAT 60.437 61.111 31.67 0.00 36.60 2.71


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

AutoCloner maintained by Alex Coulton.