Multiple sequence alignment - TraesCS6A01G020900

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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 TraesCS6A01G020900 chr6A 100.000 2636 0 0 1 2636 9946088 9948723 0.000000e+00 4868.0
1 TraesCS6A01G020900 chr6A 96.216 2643 92 5 1 2636 9855379 9858020 0.000000e+00 4320.0
2 TraesCS6A01G020900 chr6A 93.487 522 30 2 1 518 235160352 235159831 0.000000e+00 773.0
3 TraesCS6A01G020900 chr6A 78.042 1052 186 28 602 1636 11281194 11280171 2.880000e-174 621.0
4 TraesCS6A01G020900 chr6B 91.337 2124 170 7 519 2636 16995853 16997968 0.000000e+00 2891.0
5 TraesCS6A01G020900 chr6B 88.952 1412 129 14 518 1928 16628212 16629597 0.000000e+00 1718.0
6 TraesCS6A01G020900 chr6B 88.952 1412 129 14 518 1928 16683390 16684775 0.000000e+00 1718.0
7 TraesCS6A01G020900 chr6B 81.054 1082 187 10 555 1630 16547445 16546376 0.000000e+00 846.0
8 TraesCS6A01G020900 chr6B 86.557 729 62 15 1920 2636 16640921 16641625 0.000000e+00 771.0
9 TraesCS6A01G020900 chr6B 86.420 729 63 14 1920 2636 16697338 16698042 0.000000e+00 765.0
10 TraesCS6A01G020900 chr6B 84.071 113 16 2 2245 2356 17217120 17217231 9.980000e-20 108.0
11 TraesCS6A01G020900 chr6B 81.416 113 19 2 2245 2356 17220797 17220908 1.000000e-14 91.6
12 TraesCS6A01G020900 chr6D 89.118 2132 166 28 517 2636 9114075 9116152 0.000000e+00 2591.0
13 TraesCS6A01G020900 chr6D 82.239 1081 175 11 555 1627 9027229 9028300 0.000000e+00 917.0
14 TraesCS6A01G020900 chr6D 78.627 1034 189 21 593 1615 9215843 9216855 0.000000e+00 656.0
15 TraesCS6A01G020900 chr4D 93.308 523 30 4 1 518 448936701 448936179 0.000000e+00 767.0
16 TraesCS6A01G020900 chr4A 92.925 523 33 3 1 519 590692364 590692886 0.000000e+00 758.0
17 TraesCS6A01G020900 chr5D 93.077 520 31 3 3 518 158160314 158160832 0.000000e+00 756.0
18 TraesCS6A01G020900 chr5D 92.571 525 33 5 1 519 109699719 109700243 0.000000e+00 749.0
19 TraesCS6A01G020900 chr3A 92.912 522 31 4 3 519 543748860 543749380 0.000000e+00 754.0
20 TraesCS6A01G020900 chr5A 92.748 524 33 4 1 520 95554288 95554810 0.000000e+00 752.0
21 TraesCS6A01G020900 chr2D 92.748 524 33 4 1 519 614653857 614653334 0.000000e+00 752.0


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 TraesCS6A01G020900 chr6A 9946088 9948723 2635 False 4868 4868 100.000 1 2636 1 chr6A.!!$F2 2635
1 TraesCS6A01G020900 chr6A 9855379 9858020 2641 False 4320 4320 96.216 1 2636 1 chr6A.!!$F1 2635
2 TraesCS6A01G020900 chr6A 235159831 235160352 521 True 773 773 93.487 1 518 1 chr6A.!!$R2 517
3 TraesCS6A01G020900 chr6A 11280171 11281194 1023 True 621 621 78.042 602 1636 1 chr6A.!!$R1 1034
4 TraesCS6A01G020900 chr6B 16995853 16997968 2115 False 2891 2891 91.337 519 2636 1 chr6B.!!$F5 2117
5 TraesCS6A01G020900 chr6B 16628212 16629597 1385 False 1718 1718 88.952 518 1928 1 chr6B.!!$F1 1410
6 TraesCS6A01G020900 chr6B 16683390 16684775 1385 False 1718 1718 88.952 518 1928 1 chr6B.!!$F3 1410
7 TraesCS6A01G020900 chr6B 16546376 16547445 1069 True 846 846 81.054 555 1630 1 chr6B.!!$R1 1075
8 TraesCS6A01G020900 chr6B 16640921 16641625 704 False 771 771 86.557 1920 2636 1 chr6B.!!$F2 716
9 TraesCS6A01G020900 chr6B 16697338 16698042 704 False 765 765 86.420 1920 2636 1 chr6B.!!$F4 716
10 TraesCS6A01G020900 chr6D 9114075 9116152 2077 False 2591 2591 89.118 517 2636 1 chr6D.!!$F2 2119
11 TraesCS6A01G020900 chr6D 9027229 9028300 1071 False 917 917 82.239 555 1627 1 chr6D.!!$F1 1072
12 TraesCS6A01G020900 chr6D 9215843 9216855 1012 False 656 656 78.627 593 1615 1 chr6D.!!$F3 1022
13 TraesCS6A01G020900 chr4D 448936179 448936701 522 True 767 767 93.308 1 518 1 chr4D.!!$R1 517
14 TraesCS6A01G020900 chr4A 590692364 590692886 522 False 758 758 92.925 1 519 1 chr4A.!!$F1 518
15 TraesCS6A01G020900 chr5D 158160314 158160832 518 False 756 756 93.077 3 518 1 chr5D.!!$F2 515
16 TraesCS6A01G020900 chr5D 109699719 109700243 524 False 749 749 92.571 1 519 1 chr5D.!!$F1 518
17 TraesCS6A01G020900 chr3A 543748860 543749380 520 False 754 754 92.912 3 519 1 chr3A.!!$F1 516
18 TraesCS6A01G020900 chr5A 95554288 95554810 522 False 752 752 92.748 1 520 1 chr5A.!!$F1 519
19 TraesCS6A01G020900 chr2D 614653334 614653857 523 True 752 752 92.748 1 519 1 chr2D.!!$R1 518

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
716 728 1.747709 AGATGCATGTGCCTCTTCAC 58.252 50.0 2.46 0.0 42.09 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1690 1.003464 ACACATGTAGCTGGTCATGCA 59.997 47.619 20.36 0.0 43.34 3.96 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
316 325 9.438228 CATCTATATCAGATCTCACTTTGCAAT 57.562 33.333 0.00 0.00 42.40 3.56
495 506 6.425210 CCTTTCCTCTTCAAGGGAAAAATT 57.575 37.500 16.45 0.00 42.49 1.82
505 516 4.054671 CAAGGGAAAAATTAACGCAAGCA 58.945 39.130 0.00 0.00 45.62 3.91
598 610 3.136641 AGGAATCAGTGGTAGATGGGT 57.863 47.619 0.00 0.00 0.00 4.51
716 728 1.747709 AGATGCATGTGCCTCTTCAC 58.252 50.000 2.46 0.00 42.09 3.18
733 745 6.989169 CCTCTTCACAGAAACCTTCCATATAG 59.011 42.308 0.00 0.00 0.00 1.31
799 812 7.730364 AATATGCGGTCTTAGGAAGTAAATG 57.270 36.000 0.00 0.00 0.00 2.32
932 945 3.660865 GCCACTATAAATCCACCCTACG 58.339 50.000 0.00 0.00 0.00 3.51
1213 1231 1.679680 TGGCTATCCTAAGTCGGTTCG 59.320 52.381 0.00 0.00 0.00 3.95
1276 1294 0.831307 GGAGACCATTCTTAGCCGGT 59.169 55.000 1.90 0.00 29.47 5.28
1627 1648 6.321435 CCAGATCTACAATGGACACAGTACTA 59.679 42.308 0.00 0.00 36.09 1.82
1669 1690 3.108376 GGAGAGGAATTCCACAGGTAGT 58.892 50.000 26.22 2.56 38.89 2.73
1891 1914 5.826601 TGTTTCATGAGTTAGTTGCAACA 57.173 34.783 30.11 14.17 0.00 3.33
1969 1995 3.007290 TGACTCTTAGCACTGCATCAAGT 59.993 43.478 3.30 1.57 0.00 3.16
2076 2102 4.456911 ACCTGAGCACATGTATTGTTTGAG 59.543 41.667 0.00 0.00 36.00 3.02
2332 2365 1.893544 CATCCTGTGATGGGAGATGC 58.106 55.000 0.00 0.00 43.90 3.91
2333 2366 1.142262 CATCCTGTGATGGGAGATGCA 59.858 52.381 0.00 0.00 43.90 3.96
2375 2408 6.015519 CCCACTACTTTGAAAATGAATGGTGA 60.016 38.462 0.00 0.00 0.00 4.02
2431 2464 3.321682 CCCAAATGTGTTCATTCCACTGT 59.678 43.478 0.00 0.00 42.60 3.55
2601 2643 2.315155 AGGACCCTAGGAGAACTAGCAA 59.685 50.000 11.48 0.00 46.44 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.822990 TCCGTGTCAAGTAGGCCTAAG 59.177 52.381 15.83 7.94 0.00 2.18
15 16 0.594602 TCACGTCCGTGTCAAGTAGG 59.405 55.000 18.23 0.00 45.55 3.18
316 325 3.773418 TGTCAATCCCTTCACGGTTAA 57.227 42.857 0.00 0.00 0.00 2.01
495 506 2.683968 CTACCTCTTGTGCTTGCGTTA 58.316 47.619 0.00 0.00 0.00 3.18
505 516 3.261897 ACTTGCATACTGCTACCTCTTGT 59.738 43.478 0.34 0.00 45.31 3.16
733 745 1.656095 CTCGTCAATCGCTGGAGAAAC 59.344 52.381 0.00 0.00 39.67 2.78
778 790 5.099042 ACATTTACTTCCTAAGACCGCAT 57.901 39.130 0.00 0.00 0.00 4.73
828 841 3.509575 CCAAACTTAATTGTGCCCAGCTA 59.490 43.478 0.00 0.00 0.00 3.32
887 900 2.836262 CTTGCTAGGATGAGGAAGCTG 58.164 52.381 0.00 0.00 37.95 4.24
932 945 2.147150 GGTGAGTCAGAAGCAAGGAAC 58.853 52.381 0.00 0.00 0.00 3.62
1213 1231 1.818785 GCACCTCTGGCATGCTCTC 60.819 63.158 18.92 0.95 36.40 3.20
1276 1294 1.262417 TGTCGGAGTTGTATGAGGCA 58.738 50.000 0.00 0.00 0.00 4.75
1329 1347 0.324738 AGAGAATCCTGGCCTCACGA 60.325 55.000 3.32 0.00 33.66 4.35
1494 1512 2.972505 CCGCCGGTGACATATGGC 60.973 66.667 18.79 4.20 44.09 4.40
1627 1648 9.308000 CTCTCCCTTCTTACATATTCATAGACT 57.692 37.037 0.00 0.00 0.00 3.24
1669 1690 1.003464 ACACATGTAGCTGGTCATGCA 59.997 47.619 20.36 0.00 43.34 3.96
1907 1930 9.352784 CTTGACAAAACAAGTTGACATAAAGAA 57.647 29.630 10.54 0.00 41.32 2.52
1995 2021 2.294979 CATCTTGCTATGCAGAAGCCA 58.705 47.619 18.31 8.91 40.61 4.75
2055 2081 4.696877 TCCTCAAACAATACATGTGCTCAG 59.303 41.667 9.11 0.00 42.99 3.35
2076 2102 6.930667 TGTTTTAGTACACAAGAGGTTTCC 57.069 37.500 0.00 0.00 0.00 3.13
2332 2365 5.371526 AGTGGGAACTGCATTCATATACTG 58.628 41.667 9.92 0.00 39.30 2.74
2333 2366 5.636903 AGTGGGAACTGCATTCATATACT 57.363 39.130 9.92 6.21 39.30 2.12
2350 2383 6.015519 TCACCATTCATTTTCAAAGTAGTGGG 60.016 38.462 0.00 0.00 0.00 4.61
2375 2408 5.163519 GGCCTAATTATGTGTGCACAAATCT 60.164 40.000 25.77 13.88 45.41 2.40
2431 2464 4.264668 TGACCACCTCCCTAGAAAGTATCA 60.265 45.833 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.