Multiple sequence alignment - TraesCS7B01G313200

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 TraesCS7B01G313200 chr7B 100.000 2372 0 0 1 2372 559141907 559139536 0.000000e+00 4381
1 TraesCS7B01G313200 chr6D 96.748 2337 47 10 52 2372 168248078 168245755 0.000000e+00 3868
2 TraesCS7B01G313200 chr2D 95.847 2360 49 14 49 2372 272797352 272799698 0.000000e+00 3770
3 TraesCS7B01G313200 chr3B 95.793 2353 56 15 52 2372 201523549 201521208 0.000000e+00 3757
4 TraesCS7B01G313200 chr6A 95.344 2384 65 12 20 2372 271186351 271183983 0.000000e+00 3746
5 TraesCS7B01G313200 chr3A 95.271 2347 74 15 49 2372 672913465 672915797 0.000000e+00 3685
6 TraesCS7B01G313200 chr4D 94.157 2362 79 16 52 2372 19925338 19922995 0.000000e+00 3542
7 TraesCS7B01G313200 chr2B 95.131 2177 78 14 52 2215 369624585 369622424 0.000000e+00 3408
8 TraesCS7B01G313200 chr5D 95.420 2096 57 14 49 2134 329123561 329125627 0.000000e+00 3302
9 TraesCS7B01G313200 chr1A 94.773 2066 69 23 326 2372 168442037 168444082 0.000000e+00 3181
10 TraesCS7B01G313200 chr1A 96.842 1520 32 5 52 1565 584779983 584778474 0.000000e+00 2527
11 TraesCS7B01G313200 chr4A 95.505 1268 31 8 1126 2372 722779092 722780354 0.000000e+00 2002
12 TraesCS7B01G313200 chr7D 97.273 110 3 0 2263 2372 231603005 231602896 1.120000e-43 187


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 TraesCS7B01G313200 chr7B 559139536 559141907 2371 True 4381 4381 100.000 1 2372 1 chr7B.!!$R1 2371
1 TraesCS7B01G313200 chr6D 168245755 168248078 2323 True 3868 3868 96.748 52 2372 1 chr6D.!!$R1 2320
2 TraesCS7B01G313200 chr2D 272797352 272799698 2346 False 3770 3770 95.847 49 2372 1 chr2D.!!$F1 2323
3 TraesCS7B01G313200 chr3B 201521208 201523549 2341 True 3757 3757 95.793 52 2372 1 chr3B.!!$R1 2320
4 TraesCS7B01G313200 chr6A 271183983 271186351 2368 True 3746 3746 95.344 20 2372 1 chr6A.!!$R1 2352
5 TraesCS7B01G313200 chr3A 672913465 672915797 2332 False 3685 3685 95.271 49 2372 1 chr3A.!!$F1 2323
6 TraesCS7B01G313200 chr4D 19922995 19925338 2343 True 3542 3542 94.157 52 2372 1 chr4D.!!$R1 2320
7 TraesCS7B01G313200 chr2B 369622424 369624585 2161 True 3408 3408 95.131 52 2215 1 chr2B.!!$R1 2163
8 TraesCS7B01G313200 chr5D 329123561 329125627 2066 False 3302 3302 95.420 49 2134 1 chr5D.!!$F1 2085
9 TraesCS7B01G313200 chr1A 168442037 168444082 2045 False 3181 3181 94.773 326 2372 1 chr1A.!!$F1 2046
10 TraesCS7B01G313200 chr1A 584778474 584779983 1509 True 2527 2527 96.842 52 1565 1 chr1A.!!$R1 1513
11 TraesCS7B01G313200 chr4A 722779092 722780354 1262 False 2002 2002 95.505 1126 2372 1 chr4A.!!$F1 1246

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
39 40 0.115944 TTCATTGGGTGGGATGGCAA 59.884 50.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1723 2.750166 TGTCGCAAAGTTGAAACCAAGA 59.25 40.909 0.0 0.0 0.0 3.02 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
38 39 0.324552 CTTCATTGGGTGGGATGGCA 60.325 55.000 0.00 0.00 0.00 4.92
39 40 0.115944 TTCATTGGGTGGGATGGCAA 59.884 50.000 0.00 0.00 0.00 4.52
40 41 0.339162 TCATTGGGTGGGATGGCAAT 59.661 50.000 0.00 0.00 0.00 3.56
41 42 0.754472 CATTGGGTGGGATGGCAATC 59.246 55.000 0.00 0.00 0.00 2.67
42 43 0.339162 ATTGGGTGGGATGGCAATCA 59.661 50.000 2.85 0.00 34.17 2.57
463 478 7.039011 TGCAGTAGAGATGGAACTAAGAAAGAA 60.039 37.037 0.00 0.00 0.00 2.52
470 485 8.712228 AGATGGAACTAAGAAAGAAAACCATT 57.288 30.769 0.00 0.00 36.04 3.16
532 547 9.539194 ACATAGAGGAAGAATGAAAGGAAAATT 57.461 29.630 0.00 0.00 0.00 1.82
534 549 7.150783 AGAGGAAGAATGAAAGGAAAATTCG 57.849 36.000 0.00 0.00 35.83 3.34
535 550 6.942576 AGAGGAAGAATGAAAGGAAAATTCGA 59.057 34.615 0.00 0.00 35.83 3.71
536 551 7.448469 AGAGGAAGAATGAAAGGAAAATTCGAA 59.552 33.333 0.00 0.00 35.83 3.71
537 552 7.951591 AGGAAGAATGAAAGGAAAATTCGAAA 58.048 30.769 0.00 0.00 35.83 3.46
538 553 8.421002 AGGAAGAATGAAAGGAAAATTCGAAAA 58.579 29.630 0.00 0.00 35.83 2.29
539 554 9.208022 GGAAGAATGAAAGGAAAATTCGAAAAT 57.792 29.630 0.00 0.00 35.83 1.82
567 582 5.649557 CCGAGGCAATCATATTTGTTTTGA 58.350 37.500 0.00 0.00 0.00 2.69
665 680 0.179111 ATATGCACGTCGTGGTGGAG 60.179 55.000 25.70 0.45 41.65 3.86
707 722 2.963432 CCGACAAACCGGTTACACTAT 58.037 47.619 22.60 0.00 44.23 2.12
736 751 2.530958 AAACACGTATGGGCTCGGGG 62.531 60.000 0.00 0.00 34.58 5.73
795 810 8.488651 AAACCTGGTCGTATACTTTATGAAAG 57.511 34.615 0.00 0.00 44.10 2.62
867 883 3.869246 AGTAAAATGCCCATACGAAGTCG 59.131 43.478 0.00 0.00 43.93 4.18
1188 1221 5.041287 TCCGAAGTAATTCGAGCTGTAATG 58.959 41.667 25.41 6.50 46.52 1.90
1329 1362 3.955471 TGCCGAGGAATTGAGAGAATTT 58.045 40.909 0.00 0.00 0.00 1.82
1521 1565 3.452627 AGTCTTATGGGCAAGGACACTAG 59.547 47.826 0.00 0.00 0.00 2.57
1532 1576 4.331168 GCAAGGACACTAGTGCTGATTTAG 59.669 45.833 22.90 6.75 46.56 1.85
1933 1980 1.119574 AATCGCCCCGCCTATAGTGT 61.120 55.000 0.00 0.00 0.00 3.55
2090 2153 2.358195 GCCCTACCCAATGGAATGTTCT 60.358 50.000 0.00 0.00 34.81 3.01
2126 2189 1.878211 TGACACCATCATCCTAGGCA 58.122 50.000 2.96 0.00 29.99 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.964772 CCAATGAAGAATAATTCCTCTGAACTT 58.035 33.333 0.00 0.00 32.13 2.66
2 3 7.559170 CCCAATGAAGAATAATTCCTCTGAACT 59.441 37.037 0.00 0.00 32.13 3.01
3 4 7.340487 ACCCAATGAAGAATAATTCCTCTGAAC 59.660 37.037 0.00 0.00 32.13 3.18
4 5 7.340232 CACCCAATGAAGAATAATTCCTCTGAA 59.660 37.037 0.00 0.00 34.33 3.02
5 6 6.830324 CACCCAATGAAGAATAATTCCTCTGA 59.170 38.462 0.00 0.00 0.00 3.27
6 7 6.040166 CCACCCAATGAAGAATAATTCCTCTG 59.960 42.308 0.00 0.00 0.00 3.35
7 8 6.131961 CCACCCAATGAAGAATAATTCCTCT 58.868 40.000 0.00 0.00 0.00 3.69
8 9 5.302823 CCCACCCAATGAAGAATAATTCCTC 59.697 44.000 0.00 0.00 0.00 3.71
9 10 5.043432 TCCCACCCAATGAAGAATAATTCCT 60.043 40.000 0.00 0.00 0.00 3.36
10 11 5.208121 TCCCACCCAATGAAGAATAATTCC 58.792 41.667 0.00 0.00 0.00 3.01
11 12 6.239402 CCATCCCACCCAATGAAGAATAATTC 60.239 42.308 0.00 0.00 0.00 2.17
12 13 5.603813 CCATCCCACCCAATGAAGAATAATT 59.396 40.000 0.00 0.00 0.00 1.40
13 14 5.149976 CCATCCCACCCAATGAAGAATAAT 58.850 41.667 0.00 0.00 0.00 1.28
14 15 4.545678 CCATCCCACCCAATGAAGAATAA 58.454 43.478 0.00 0.00 0.00 1.40
15 16 3.691020 GCCATCCCACCCAATGAAGAATA 60.691 47.826 0.00 0.00 0.00 1.75
16 17 2.956385 GCCATCCCACCCAATGAAGAAT 60.956 50.000 0.00 0.00 0.00 2.40
17 18 1.619432 GCCATCCCACCCAATGAAGAA 60.619 52.381 0.00 0.00 0.00 2.52
18 19 0.033208 GCCATCCCACCCAATGAAGA 60.033 55.000 0.00 0.00 0.00 2.87
463 478 7.013834 TCTTTTGGGGTTATAGTCAATGGTTT 58.986 34.615 0.00 0.00 0.00 3.27
470 485 5.311121 TCTGGTTCTTTTGGGGTTATAGTCA 59.689 40.000 0.00 0.00 0.00 3.41
532 547 1.449601 GCCTCGGCAGGATTTTCGA 60.450 57.895 2.41 0.00 43.65 3.71
533 548 3.102097 GCCTCGGCAGGATTTTCG 58.898 61.111 2.41 0.00 43.65 3.46
665 680 7.276438 GTCGGGAAATATACGTACCCATATTTC 59.724 40.741 22.27 22.27 45.25 2.17
707 722 0.680618 ATACGTGTTTCCGTGGGTCA 59.319 50.000 0.00 0.00 41.92 4.02
748 763 7.067251 GGTTTAACAACGGATACCCAATATTCA 59.933 37.037 0.00 0.00 33.13 2.57
1188 1221 7.642071 TTTGAACTCTTTACATGTACGTACC 57.358 36.000 22.43 5.80 0.00 3.34
1532 1576 6.278363 TGTCCGCATTTCTTATAGAGGTTAC 58.722 40.000 0.00 0.00 0.00 2.50
1678 1723 2.750166 TGTCGCAAAGTTGAAACCAAGA 59.250 40.909 0.00 0.00 0.00 3.02
1734 1779 6.146898 TGATACGCTTTAAAAAGGTTCTTGC 58.853 36.000 4.71 0.00 36.53 4.01
1933 1980 4.164221 AGGAAGGGCGAGATAGAATTTGAA 59.836 41.667 0.00 0.00 0.00 2.69
2090 2153 0.815095 TCATTCTCTAGCCGAACGCA 59.185 50.000 0.00 0.00 41.38 5.24
2126 2189 8.925338 ACTAGACCGTATCTTTCCTGAAATATT 58.075 33.333 0.00 0.00 39.04 1.28
2261 2324 3.065510 TCTTCGCTATCCTTCGAGTCTTG 59.934 47.826 0.00 0.00 36.02 3.02


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

AutoCloner maintained by Alex Coulton.