Multiple sequence alignment - TraesCS1D01G086800

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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 TraesCS1D01G086800 chr1D 100.000 2614 0 0 1 2614 71286596 71289209 0.000000e+00 4828
1 TraesCS1D01G086800 chr1D 97.889 2037 39 4 580 2614 182580738 182582772 0.000000e+00 3520
2 TraesCS1D01G086800 chr2D 98.623 2033 26 2 583 2614 639485012 639482981 0.000000e+00 3598
3 TraesCS1D01G086800 chr2D 96.903 2034 51 4 583 2614 345251459 345253482 0.000000e+00 3397
4 TraesCS1D01G086800 chr5D 97.738 2034 44 2 582 2614 42206481 42208513 0.000000e+00 3500
5 TraesCS1D01G086800 chr7D 95.870 2034 78 6 583 2614 127375811 127377840 0.000000e+00 3286
6 TraesCS1D01G086800 chr7D 97.211 1793 35 5 583 2374 58131751 58129973 0.000000e+00 3020
7 TraesCS1D01G086800 chr7D 96.471 85 2 1 2530 2614 58129996 58129913 3.510000e-29 139
8 TraesCS1D01G086800 chr1A 89.120 1921 154 29 584 2497 546519079 546520951 0.000000e+00 2338
9 TraesCS1D01G086800 chr1A 93.132 597 20 6 1 582 71694336 71694926 0.000000e+00 856
10 TraesCS1D01G086800 chr2A 88.316 1378 118 28 1128 2497 32113979 32115321 0.000000e+00 1613
11 TraesCS1D01G086800 chr2A 91.494 435 33 2 582 1013 32113533 32113966 1.730000e-166 595
12 TraesCS1D01G086800 chr1B 93.651 504 16 4 1 490 112752994 112753495 0.000000e+00 739
13 TraesCS1D01G086800 chr1B 95.455 66 2 1 518 582 112753565 112753630 1.280000e-18 104


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 TraesCS1D01G086800 chr1D 71286596 71289209 2613 False 4828.0 4828 100.000 1 2614 1 chr1D.!!$F1 2613
1 TraesCS1D01G086800 chr1D 182580738 182582772 2034 False 3520.0 3520 97.889 580 2614 1 chr1D.!!$F2 2034
2 TraesCS1D01G086800 chr2D 639482981 639485012 2031 True 3598.0 3598 98.623 583 2614 1 chr2D.!!$R1 2031
3 TraesCS1D01G086800 chr2D 345251459 345253482 2023 False 3397.0 3397 96.903 583 2614 1 chr2D.!!$F1 2031
4 TraesCS1D01G086800 chr5D 42206481 42208513 2032 False 3500.0 3500 97.738 582 2614 1 chr5D.!!$F1 2032
5 TraesCS1D01G086800 chr7D 127375811 127377840 2029 False 3286.0 3286 95.870 583 2614 1 chr7D.!!$F1 2031
6 TraesCS1D01G086800 chr7D 58129913 58131751 1838 True 1579.5 3020 96.841 583 2614 2 chr7D.!!$R1 2031
7 TraesCS1D01G086800 chr1A 546519079 546520951 1872 False 2338.0 2338 89.120 584 2497 1 chr1A.!!$F2 1913
8 TraesCS1D01G086800 chr1A 71694336 71694926 590 False 856.0 856 93.132 1 582 1 chr1A.!!$F1 581
9 TraesCS1D01G086800 chr2A 32113533 32115321 1788 False 1104.0 1613 89.905 582 2497 2 chr2A.!!$F1 1915
10 TraesCS1D01G086800 chr1B 112752994 112753630 636 False 421.5 739 94.553 1 582 2 chr1B.!!$F1 581

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
429 444 0.249953 TACCTTCGCGTTCTTGGCAA 60.25 50.0 5.77 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2086 0.751277 TGCCGTGCATGAATAAGGGG 60.751 55.0 7.72 0.0 31.71 4.79 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
34 35 4.042435 TCCCTTCCAGTGTTTTTACCCTAG 59.958 45.833 0.00 0.00 0.00 3.02
224 225 1.284491 TGGGATTACATGCAAGCCTCA 59.716 47.619 12.58 6.49 34.32 3.86
268 269 1.421410 CCGCGTTGACAGCAGTATCC 61.421 60.000 4.92 0.00 34.19 2.59
275 276 4.202060 CGTTGACAGCAGTATCCTGTAGAT 60.202 45.833 0.00 0.00 43.17 1.98
341 356 3.827008 TCAGATTACCAGTCTGATGCC 57.173 47.619 0.00 0.00 45.19 4.40
367 382 2.818130 GGCAAATTGGCAACTGAGAA 57.182 45.000 14.91 0.00 43.14 2.87
368 383 3.323751 GGCAAATTGGCAACTGAGAAT 57.676 42.857 14.91 0.00 43.14 2.40
373 388 6.204495 GGCAAATTGGCAACTGAGAATTTTTA 59.796 34.615 14.91 0.00 43.14 1.52
374 389 7.094677 GGCAAATTGGCAACTGAGAATTTTTAT 60.095 33.333 14.91 0.00 43.14 1.40
375 390 8.291740 GCAAATTGGCAACTGAGAATTTTTATT 58.708 29.630 13.74 0.00 37.61 1.40
393 408 8.880878 TTTTTATTTCCACCTTTAGTTTGCTC 57.119 30.769 0.00 0.00 0.00 4.26
429 444 0.249953 TACCTTCGCGTTCTTGGCAA 60.250 50.000 5.77 0.00 0.00 4.52
433 448 2.393764 CTTCGCGTTCTTGGCAATTTT 58.606 42.857 5.77 0.00 0.00 1.82
443 458 6.640499 CGTTCTTGGCAATTTTTGAAGTATGA 59.360 34.615 0.00 0.00 0.00 2.15
453 468 2.010145 TGAAGTATGACGAGCAAGGC 57.990 50.000 0.00 0.00 0.00 4.35
454 469 0.924090 GAAGTATGACGAGCAAGGCG 59.076 55.000 0.00 0.00 0.00 5.52
455 470 0.530744 AAGTATGACGAGCAAGGCGA 59.469 50.000 0.00 0.00 0.00 5.54
456 471 0.530744 AGTATGACGAGCAAGGCGAA 59.469 50.000 0.00 0.00 0.00 4.70
457 472 1.137086 AGTATGACGAGCAAGGCGAAT 59.863 47.619 0.00 0.00 0.00 3.34
458 473 1.523095 GTATGACGAGCAAGGCGAATC 59.477 52.381 0.00 0.00 0.00 2.52
585 600 3.774702 GCGTGGTTTCTCGGCGAC 61.775 66.667 4.99 0.00 0.00 5.19
650 665 3.074369 TTCGATCCGCTGGAGGCA 61.074 61.111 3.76 0.00 41.91 4.75
678 693 1.403116 CCCGCTGTATTGTACGTGACA 60.403 52.381 0.00 0.00 35.78 3.58
1051 1069 1.375396 CCAATCGTGCCTTGTCCGA 60.375 57.895 0.00 0.00 34.79 4.55
1078 1096 0.677288 CAGGAACGTGGTGACCTACA 59.323 55.000 2.11 0.00 0.00 2.74
1134 1152 1.909700 ACAAGTGCCGGAATCACAAT 58.090 45.000 5.05 0.00 36.93 2.71
1879 1908 3.107601 TGTCAGAATGGGAGTTAGGAGG 58.892 50.000 0.00 0.00 36.16 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.847111 AAAAACACTGGAAGGGAAAGTAC 57.153 39.130 0.00 0.0 43.23 2.73
34 35 5.565439 GAGTATCAATGGCAATGTTATGGCC 60.565 44.000 1.93 0.0 41.13 5.36
130 131 3.369381 CGTGAAGCGGGAGATGATT 57.631 52.632 0.00 0.0 36.85 2.57
224 225 3.382083 AAACGCCTAGGGAAAATCCAT 57.618 42.857 11.72 0.0 38.64 3.41
275 276 7.098477 CCATGGATTTGCTTTATTTTGTCTCA 58.902 34.615 5.56 0.0 0.00 3.27
341 356 3.187637 CAGTTGCCAATTTGCCATCAAAG 59.812 43.478 0.00 0.0 44.47 2.77
367 382 9.489084 GAGCAAACTAAAGGTGGAAATAAAAAT 57.511 29.630 0.00 0.0 0.00 1.82
368 383 7.650104 CGAGCAAACTAAAGGTGGAAATAAAAA 59.350 33.333 0.00 0.0 0.00 1.94
373 388 4.394729 TCGAGCAAACTAAAGGTGGAAAT 58.605 39.130 0.00 0.0 0.00 2.17
374 389 3.811083 TCGAGCAAACTAAAGGTGGAAA 58.189 40.909 0.00 0.0 0.00 3.13
375 390 3.478857 TCGAGCAAACTAAAGGTGGAA 57.521 42.857 0.00 0.0 0.00 3.53
376 391 3.695830 ATCGAGCAAACTAAAGGTGGA 57.304 42.857 0.00 0.0 0.00 4.02
393 408 2.231478 AGGTATTCCGCCACAGATATCG 59.769 50.000 0.00 0.0 39.05 2.92
429 444 5.619981 GCCTTGCTCGTCATACTTCAAAAAT 60.620 40.000 0.00 0.0 0.00 1.82
433 448 2.346803 GCCTTGCTCGTCATACTTCAA 58.653 47.619 0.00 0.0 0.00 2.69
475 490 5.094387 CCTATACTCCCACCCATACAGATT 58.906 45.833 0.00 0.0 0.00 2.40
678 693 2.612972 CGCACATTAACTGTCCTCACCT 60.613 50.000 0.00 0.0 35.29 4.00
738 753 3.389925 AAACACCGTGAAATCCTCGTA 57.610 42.857 5.28 0.0 0.00 3.43
926 944 0.774491 TGGGGCCAGTCTAGGGTTTT 60.774 55.000 4.39 0.0 0.00 2.43
1051 1069 2.625823 CCACGTTCCTGCCGCAATT 61.626 57.895 0.00 0.0 0.00 2.32
1134 1152 5.534654 CCCAATCCAAGAAACTTGACTTACA 59.465 40.000 12.25 0.0 0.00 2.41
1295 1313 1.337635 ACAGCAGCTTCTCCTTCTTCG 60.338 52.381 0.00 0.0 0.00 3.79
1728 1746 2.736144 TGGTTACATCGTCACTCACC 57.264 50.000 0.00 0.0 0.00 4.02
1879 1908 6.924111 TGACATTCATTCTAAAAAGCCTTCC 58.076 36.000 0.00 0.0 0.00 3.46
1985 2015 7.469043 GCCTGAATATCTGCATACAAACAATGA 60.469 37.037 0.00 0.0 0.00 2.57
2055 2086 0.751277 TGCCGTGCATGAATAAGGGG 60.751 55.000 7.72 0.0 31.71 4.79


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

AutoCloner maintained by Alex Coulton.