Multiple sequence alignment - TraesCS5B01G018100

Loading Multiple Alignment...

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 TraesCS5B01G018100 chr5B 100.000 2885 0 0 1 2885 17597262 17600146 0.000000e+00 5328
1 TraesCS5B01G018100 chr5B 94.619 1914 99 4 1 1913 671135441 671137351 0.000000e+00 2961
2 TraesCS5B01G018100 chr5B 96.263 990 18 9 1913 2885 386862515 386861528 0.000000e+00 1605
3 TraesCS5B01G018100 chr5B 92.308 520 40 0 1394 1913 690067883 690067364 0.000000e+00 739
4 TraesCS5B01G018100 chr7B 95.124 1456 68 3 1 1455 744718384 744716931 0.000000e+00 2292
5 TraesCS5B01G018100 chr7B 95.991 848 17 7 2052 2882 108526127 108526974 0.000000e+00 1362
6 TraesCS5B01G018100 chr6A 87.956 1918 226 4 1 1915 23759145 23757230 0.000000e+00 2257
7 TraesCS5B01G018100 chr6A 81.270 1906 338 13 15 1915 616905988 616904097 0.000000e+00 1524
8 TraesCS5B01G018100 chr5A 85.655 1917 268 6 1 1914 433204691 433202779 0.000000e+00 2010
9 TraesCS5B01G018100 chr1A 84.800 1921 272 11 1 1915 558600014 558601920 0.000000e+00 1912
10 TraesCS5B01G018100 chr1B 96.465 990 18 7 1913 2885 80959124 80960113 0.000000e+00 1618
11 TraesCS5B01G018100 chr1B 95.005 1001 22 8 1913 2885 46930303 46931303 0.000000e+00 1546
12 TraesCS5B01G018100 chr1B 77.380 1397 305 10 431 1821 62019247 62020638 0.000000e+00 819
13 TraesCS5B01G018100 chr1B 92.832 572 19 8 2336 2885 321235042 321234471 0.000000e+00 809
14 TraesCS5B01G018100 chr2A 83.450 1716 262 14 202 1913 207776316 207774619 0.000000e+00 1576
15 TraesCS5B01G018100 chr2A 97.225 865 17 3 1913 2771 2613369 2614232 0.000000e+00 1458
16 TraesCS5B01G018100 chr2A 85.273 713 101 4 1205 1915 7310455 7309745 0.000000e+00 732
17 TraesCS5B01G018100 chr2A 87.857 140 1 2 2762 2885 2616072 2616211 1.790000e-32 150
18 TraesCS5B01G018100 chr2D 94.795 999 19 12 1913 2885 578032500 578031509 0.000000e+00 1526
19 TraesCS5B01G018100 chr2D 92.748 979 28 13 1913 2885 377261087 377262028 0.000000e+00 1375
20 TraesCS5B01G018100 chr7D 93.054 979 24 14 1913 2885 553413654 553412714 0.000000e+00 1391
21 TraesCS5B01G018100 chr3D 91.122 980 24 11 1913 2885 67055561 67056484 0.000000e+00 1269
22 TraesCS5B01G018100 chr3B 95.630 778 24 1 1913 2690 59224770 59225537 0.000000e+00 1240
23 TraesCS5B01G018100 chr3B 90.452 199 2 3 2704 2885 59227956 59228154 2.220000e-61 246
24 TraesCS5B01G018100 chr2B 81.057 1362 250 8 557 1914 614232624 614233981 0.000000e+00 1079
25 TraesCS5B01G018100 chr2B 77.976 1571 331 15 6 1568 733990455 733988892 0.000000e+00 970
26 TraesCS5B01G018100 chr7A 77.537 1705 371 11 7 1705 563324523 563326221 0.000000e+00 1016


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 TraesCS5B01G018100 chr5B 17597262 17600146 2884 False 5328 5328 100.000 1 2885 1 chr5B.!!$F1 2884
1 TraesCS5B01G018100 chr5B 671135441 671137351 1910 False 2961 2961 94.619 1 1913 1 chr5B.!!$F2 1912
2 TraesCS5B01G018100 chr5B 386861528 386862515 987 True 1605 1605 96.263 1913 2885 1 chr5B.!!$R1 972
3 TraesCS5B01G018100 chr5B 690067364 690067883 519 True 739 739 92.308 1394 1913 1 chr5B.!!$R2 519
4 TraesCS5B01G018100 chr7B 744716931 744718384 1453 True 2292 2292 95.124 1 1455 1 chr7B.!!$R1 1454
5 TraesCS5B01G018100 chr7B 108526127 108526974 847 False 1362 1362 95.991 2052 2882 1 chr7B.!!$F1 830
6 TraesCS5B01G018100 chr6A 23757230 23759145 1915 True 2257 2257 87.956 1 1915 1 chr6A.!!$R1 1914
7 TraesCS5B01G018100 chr6A 616904097 616905988 1891 True 1524 1524 81.270 15 1915 1 chr6A.!!$R2 1900
8 TraesCS5B01G018100 chr5A 433202779 433204691 1912 True 2010 2010 85.655 1 1914 1 chr5A.!!$R1 1913
9 TraesCS5B01G018100 chr1A 558600014 558601920 1906 False 1912 1912 84.800 1 1915 1 chr1A.!!$F1 1914
10 TraesCS5B01G018100 chr1B 80959124 80960113 989 False 1618 1618 96.465 1913 2885 1 chr1B.!!$F3 972
11 TraesCS5B01G018100 chr1B 46930303 46931303 1000 False 1546 1546 95.005 1913 2885 1 chr1B.!!$F1 972
12 TraesCS5B01G018100 chr1B 62019247 62020638 1391 False 819 819 77.380 431 1821 1 chr1B.!!$F2 1390
13 TraesCS5B01G018100 chr1B 321234471 321235042 571 True 809 809 92.832 2336 2885 1 chr1B.!!$R1 549
14 TraesCS5B01G018100 chr2A 207774619 207776316 1697 True 1576 1576 83.450 202 1913 1 chr2A.!!$R2 1711
15 TraesCS5B01G018100 chr2A 2613369 2616211 2842 False 804 1458 92.541 1913 2885 2 chr2A.!!$F1 972
16 TraesCS5B01G018100 chr2A 7309745 7310455 710 True 732 732 85.273 1205 1915 1 chr2A.!!$R1 710
17 TraesCS5B01G018100 chr2D 578031509 578032500 991 True 1526 1526 94.795 1913 2885 1 chr2D.!!$R1 972
18 TraesCS5B01G018100 chr2D 377261087 377262028 941 False 1375 1375 92.748 1913 2885 1 chr2D.!!$F1 972
19 TraesCS5B01G018100 chr7D 553412714 553413654 940 True 1391 1391 93.054 1913 2885 1 chr7D.!!$R1 972
20 TraesCS5B01G018100 chr3D 67055561 67056484 923 False 1269 1269 91.122 1913 2885 1 chr3D.!!$F1 972
21 TraesCS5B01G018100 chr3B 59224770 59228154 3384 False 743 1240 93.041 1913 2885 2 chr3B.!!$F1 972
22 TraesCS5B01G018100 chr2B 614232624 614233981 1357 False 1079 1079 81.057 557 1914 1 chr2B.!!$F1 1357
23 TraesCS5B01G018100 chr2B 733988892 733990455 1563 True 970 970 77.976 6 1568 1 chr2B.!!$R1 1562
24 TraesCS5B01G018100 chr7A 563324523 563326221 1698 False 1016 1016 77.537 7 1705 1 chr7A.!!$F1 1698

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
247 249 0.037590 TGTCACAATACTGGTGGGGC 59.962 55.0 0.0 0.0 36.90 5.80 F
1094 1108 0.337773 AGAGTGCAGGAGATCTGGGA 59.662 55.0 0.0 0.0 43.54 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1223 0.741915 CGAGCTCCTTCCTAGACACC 59.258 60.0 8.47 0.0 0.0 4.16 R
2231 2256 1.479709 CGTGAGGGAGGATGTCTTCT 58.520 55.0 0.00 0.0 0.0 2.85 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
142 143 4.967084 TGGAGGTAAAGAAGTGTTGCTA 57.033 40.909 0.00 0.0 0.00 3.49
226 228 1.538950 TGCAATGCAATAACGACAGCA 59.461 42.857 5.01 0.0 41.73 4.41
247 249 0.037590 TGTCACAATACTGGTGGGGC 59.962 55.000 0.00 0.0 36.90 5.80
304 307 2.359850 TGGAAGATGTGCGTGCCC 60.360 61.111 0.00 0.0 0.00 5.36
319 322 2.421399 GCCCAAGAGCAATGGAGGC 61.421 63.158 4.19 0.0 40.56 4.70
334 337 1.202746 GGAGGCATGGGATTCAGAGAC 60.203 57.143 0.00 0.0 0.00 3.36
483 487 2.637872 CAAGAAGGGGAGTTCCTACACA 59.362 50.000 0.00 0.0 35.80 3.72
504 508 0.817229 GGCAGAGCTTATGGAGTGGC 60.817 60.000 0.00 0.0 0.00 5.01
513 517 2.107950 TATGGAGTGGCCTTCAAACG 57.892 50.000 3.32 0.0 37.63 3.60
761 775 1.149174 CAACGGGGATGATGGAGGG 59.851 63.158 0.00 0.0 0.00 4.30
1094 1108 0.337773 AGAGTGCAGGAGATCTGGGA 59.662 55.000 0.00 0.0 43.54 4.37
1194 1208 2.951457 TGATGCCAAATGATGCAGTG 57.049 45.000 0.00 0.0 41.46 3.66
1363 1377 1.867233 TGAGAGCAAAGAAGCAACGAC 59.133 47.619 0.00 0.0 36.85 4.34
1431 1445 3.419943 TGTCAGCTTAAATGTGGATGCA 58.580 40.909 0.00 0.0 0.00 3.96
1541 1555 1.154016 CGTTCGTCGAGGATGCAGT 60.154 57.895 8.88 0.0 42.86 4.40
1588 1602 1.762222 CGGGCTAATCCTCGCAAACG 61.762 60.000 0.00 0.0 42.01 3.60
1676 1690 2.626467 GGAATTCCCTGGGGCCAGT 61.626 63.158 14.03 0.0 42.15 4.00
1872 1886 4.026052 CAAATGATGTAGCCCTTTTCCCT 58.974 43.478 0.00 0.0 0.00 4.20
1887 1901 7.425606 CCCTTTTCCCTCATGAAATATAAACG 58.574 38.462 0.00 0.0 34.41 3.60
1956 1970 3.324846 TGCCCTCATCTATTCGCTACAAT 59.675 43.478 0.00 0.0 0.00 2.71
2242 2267 1.276421 CAACGACCCAGAAGACATCCT 59.724 52.381 0.00 0.0 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 228 2.883888 GCCCCACCAGTATTGTGACATT 60.884 50.000 0.00 0.00 35.74 2.71
247 249 1.753649 TGCTTCTTCTCCTCCTCATCG 59.246 52.381 0.00 0.00 0.00 3.84
304 307 0.744874 CCATGCCTCCATTGCTCTTG 59.255 55.000 0.00 0.00 0.00 3.02
319 322 1.293924 GCACGTCTCTGAATCCCATG 58.706 55.000 0.00 0.00 0.00 3.66
334 337 2.116366 GCCAAGTTAAAACAGTGCACG 58.884 47.619 12.01 9.15 0.00 5.34
387 391 2.555757 GGCACATAATGATTCTGGCTCC 59.444 50.000 0.00 0.00 0.00 4.70
483 487 1.142465 CCACTCCATAAGCTCTGCCAT 59.858 52.381 0.00 0.00 0.00 4.40
761 775 8.730970 TTTATTATAGTGCCACGAAACAAAAC 57.269 30.769 0.00 0.00 0.00 2.43
977 991 1.339929 GACGATTTGCCAAAACACCCT 59.660 47.619 0.00 0.00 0.00 4.34
1194 1208 3.537874 ACCTCCGGTAGCATCGGC 61.538 66.667 0.00 0.00 46.43 5.54
1209 1223 0.741915 CGAGCTCCTTCCTAGACACC 59.258 60.000 8.47 0.00 0.00 4.16
1363 1377 1.884926 GCTTCTGGATTCGCCCTCG 60.885 63.158 0.00 0.00 34.97 4.63
1431 1445 1.679944 CCACTGTCCGCATCAAAGGAT 60.680 52.381 0.00 0.00 38.97 3.24
1541 1555 3.515286 CTCTCGCCTCCGCCGTTA 61.515 66.667 0.00 0.00 0.00 3.18
1588 1602 6.240894 TCTCCACCTTATTGCATCCAATATC 58.759 40.000 0.00 0.00 42.00 1.63
1676 1690 1.271856 TTCCTCGTAGATGGTTGCCA 58.728 50.000 0.00 0.00 38.19 4.92
1887 1901 5.659440 TTTTAGGAAAAGCCATCATGACC 57.341 39.130 0.00 0.00 40.02 4.02
2231 2256 1.479709 CGTGAGGGAGGATGTCTTCT 58.520 55.000 0.00 0.00 0.00 2.85
2623 2658 7.716799 TTTGGGAGAACAAATGCAATATAGT 57.283 32.000 0.00 0.00 35.57 2.12


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

AutoCloner maintained by Alex Coulton.