Multiple sequence alignment - TraesCS7D01G406800

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 TraesCS7D01G406800 chr7D 100.000 3970 0 0 1 3970 524311338 524315307 0.000000e+00 7332.0
1 TraesCS7D01G406800 chr7D 97.163 3384 83 8 1 3383 524303693 524307064 0.000000e+00 5705.0
2 TraesCS7D01G406800 chr7D 96.103 3387 120 9 1 3384 524248960 524252337 0.000000e+00 5513.0
3 TraesCS7D01G406800 chr7D 94.692 3391 164 11 1 3384 562196519 562199900 0.000000e+00 5251.0
4 TraesCS7D01G406800 chr7D 95.932 590 19 4 2788 3376 524259492 524260077 0.000000e+00 952.0
5 TraesCS7D01G406800 chr7D 91.216 444 38 1 3526 3969 523544636 523545078 1.580000e-168 603.0
6 TraesCS7D01G406800 chr7D 97.297 37 1 0 3393 3429 562201560 562201596 3.310000e-06 63.9
7 TraesCS7D01G406800 chr6A 96.843 3991 98 14 3 3970 74148180 74152165 0.000000e+00 6647.0
8 TraesCS7D01G406800 chr6A 91.061 3401 246 29 1 3387 52290338 52286982 0.000000e+00 4543.0
9 TraesCS7D01G406800 chr7A 94.654 3386 173 4 1 3384 604249827 604253206 0.000000e+00 5243.0
10 TraesCS7D01G406800 chr7A 94.467 3380 180 5 7 3384 604260612 604263986 0.000000e+00 5199.0
11 TraesCS7D01G406800 chr7A 94.034 3386 191 5 1 3384 604255230 604258606 0.000000e+00 5123.0
12 TraesCS7D01G406800 chr7A 96.309 569 10 5 3402 3970 604379160 604379717 0.000000e+00 924.0
13 TraesCS7D01G406800 chr6D 91.048 3396 238 27 1 3387 41624583 41621245 0.000000e+00 4527.0
14 TraesCS7D01G406800 chr7B 94.413 537 21 4 3442 3970 560513760 560514295 0.000000e+00 817.0
15 TraesCS7D01G406800 chr7B 87.147 319 41 0 3651 3969 559630150 559630468 2.920000e-96 363.0


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 TraesCS7D01G406800 chr7D 524311338 524315307 3969 False 7332.000000 7332 100.0000 1 3970 1 chr7D.!!$F5 3969
1 TraesCS7D01G406800 chr7D 524303693 524307064 3371 False 5705.000000 5705 97.1630 1 3383 1 chr7D.!!$F4 3382
2 TraesCS7D01G406800 chr7D 524248960 524252337 3377 False 5513.000000 5513 96.1030 1 3384 1 chr7D.!!$F2 3383
3 TraesCS7D01G406800 chr7D 562196519 562201596 5077 False 2657.450000 5251 95.9945 1 3429 2 chr7D.!!$F6 3428
4 TraesCS7D01G406800 chr7D 524259492 524260077 585 False 952.000000 952 95.9320 2788 3376 1 chr7D.!!$F3 588
5 TraesCS7D01G406800 chr6A 74148180 74152165 3985 False 6647.000000 6647 96.8430 3 3970 1 chr6A.!!$F1 3967
6 TraesCS7D01G406800 chr6A 52286982 52290338 3356 True 4543.000000 4543 91.0610 1 3387 1 chr6A.!!$R1 3386
7 TraesCS7D01G406800 chr7A 604249827 604263986 14159 False 5188.333333 5243 94.3850 1 3384 3 chr7A.!!$F2 3383
8 TraesCS7D01G406800 chr7A 604379160 604379717 557 False 924.000000 924 96.3090 3402 3970 1 chr7A.!!$F1 568
9 TraesCS7D01G406800 chr6D 41621245 41624583 3338 True 4527.000000 4527 91.0480 1 3387 1 chr6D.!!$R1 3386
10 TraesCS7D01G406800 chr7B 560513760 560514295 535 False 817.000000 817 94.4130 3442 3970 1 chr7B.!!$F2 528

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
941 988 1.075374 AGTTGGCTTCCCTATGCAACA 59.925 47.619 0.00 0.0 0.0 3.33 F
1779 1832 0.395311 TTGGCCTAGATCTCGACGGT 60.395 55.000 3.32 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2519 1.078759 GATGTCCGACTCTTGCACCG 61.079 60.0 0.00 0.00 0.00 4.94 R
3530 11740 0.942252 AGAAAGACGGCCGTGTTTTC 59.058 50.0 42.16 38.24 40.83 2.29 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
109 112 9.921637 TTAGCCTTACAATGGAAAACAATTTAG 57.078 29.630 0.00 0.00 0.00 1.85
302 336 1.876156 CTCTTCAAACCGAAAGCTGCT 59.124 47.619 0.00 0.00 31.71 4.24
796 842 6.755607 CGATCCACACATGAGGAATATATCTG 59.244 42.308 0.00 0.00 38.28 2.90
935 982 2.310052 AGAGCAAAGTTGGCTTCCCTAT 59.690 45.455 6.13 0.00 42.78 2.57
941 988 1.075374 AGTTGGCTTCCCTATGCAACA 59.925 47.619 0.00 0.00 0.00 3.33
1007 1054 2.027745 CAGTAGTCTCCACAATGCTGGT 60.028 50.000 2.70 0.00 32.50 4.00
1083 1133 2.307392 TGCCATTACCAAGAGCAAGGTA 59.693 45.455 0.00 0.00 39.31 3.08
1194 1244 2.719354 GTCAACAAGCCGGCGTTT 59.281 55.556 23.20 8.33 0.00 3.60
1197 1247 2.589442 AACAAGCCGGCGTTTCGA 60.589 55.556 23.20 0.00 0.00 3.71
1779 1832 0.395311 TTGGCCTAGATCTCGACGGT 60.395 55.000 3.32 0.00 0.00 4.83
1801 1854 6.755141 CGGTCACGAGAAAATTATTAAGGAGA 59.245 38.462 0.00 0.00 44.60 3.71
1863 1916 1.207329 GAGCGTTGGAGGTAGTGGAAT 59.793 52.381 0.00 0.00 0.00 3.01
2063 2118 5.192927 CCAATTGCCTCATAGTCCTACAAA 58.807 41.667 0.00 0.00 0.00 2.83
2349 2404 3.417069 TGCAGGGCATAATATTAGCGT 57.583 42.857 1.02 0.00 31.71 5.07
2778 2833 4.585526 GACGGGGATGCATCGCGA 62.586 66.667 30.44 13.09 42.00 5.87
2965 3020 3.643320 CACCTCTACCCTCTCATGCATTA 59.357 47.826 0.00 0.00 0.00 1.90
3154 3218 2.132517 TTTCACGTACGAGCGAGCCA 62.133 55.000 24.41 0.00 35.59 4.75
3400 11590 6.035217 CAGCATAGAAGATGAGGTGATATCG 58.965 44.000 0.00 0.00 0.00 2.92
3530 11740 8.636213 AGCCCACTTCATCATCATAAAATAAAG 58.364 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 74 4.124238 TGTAAGGCTAATTCGGGATTTCG 58.876 43.478 0.00 0.00 0.00 3.46
302 336 2.306805 GCCAGGATGATGGACCATATGA 59.693 50.000 7.05 0.00 43.57 2.15
597 639 7.972832 ATCCAAACGTAGTCAAAACAGAATA 57.027 32.000 0.00 0.00 45.00 1.75
796 842 7.823149 ACGTATCTAACACTAAAACATGTCC 57.177 36.000 0.00 0.00 0.00 4.02
935 982 3.761897 AGCTACCCTTGTTATTGTTGCA 58.238 40.909 0.00 0.00 32.99 4.08
1007 1054 2.992543 GACACAACAAAGCAACAGCAAA 59.007 40.909 0.00 0.00 0.00 3.68
1114 1164 4.735132 CGGCGGAAGTGGAAGCGA 62.735 66.667 0.00 0.00 0.00 4.93
1197 1247 3.222053 CATCACGCGATGGATCCAT 57.778 52.632 27.66 27.66 44.59 3.41
1779 1832 7.617225 TGGTCTCCTTAATAATTTTCTCGTGA 58.383 34.615 0.00 0.00 0.00 4.35
1863 1916 4.815108 TCCTGCCTCTCGCCGCTA 62.815 66.667 0.00 0.00 36.24 4.26
1951 2005 2.158623 TGGACTGTGCTTTGACCTCATT 60.159 45.455 0.00 0.00 0.00 2.57
2013 2067 6.261826 CACTAAATTCAATCTAGGCCCTTGAG 59.738 42.308 0.00 0.00 31.11 3.02
2063 2118 7.818997 TTCTCATGGATGACGTATTAGTACT 57.181 36.000 0.00 0.00 32.50 2.73
2349 2404 3.738899 GCGTTTGACGGGTTATCTATGGA 60.739 47.826 2.48 0.00 42.82 3.41
2464 2519 1.078759 GATGTCCGACTCTTGCACCG 61.079 60.000 0.00 0.00 0.00 4.94
2572 2627 1.963855 CCCGCAACAATGGTGTCGA 60.964 57.895 14.62 0.00 36.80 4.20
2654 2709 1.596934 GAGCGGTTCATCCCAGACA 59.403 57.895 0.00 0.00 0.00 3.41
2778 2833 4.287067 ACTCATGGTTGTTCCTAGTGATGT 59.713 41.667 0.00 0.00 37.07 3.06
2965 3020 4.430007 TCGTAGCTCGTTATTTGCTCAAT 58.570 39.130 0.00 0.00 40.80 2.57
3154 3218 1.210155 GCGGCGCATGAAAGAAACT 59.790 52.632 29.21 0.00 0.00 2.66
3400 11590 7.703197 TCTGTTTTCAACCGGACTTTTTATTTC 59.297 33.333 9.46 0.00 0.00 2.17
3445 11647 2.684001 TTGTGACACTCGACCAAACT 57.316 45.000 7.20 0.00 0.00 2.66
3530 11740 0.942252 AGAAAGACGGCCGTGTTTTC 59.058 50.000 42.16 38.24 40.83 2.29


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

AutoCloner maintained by Alex Coulton.