Multiple sequence alignment - TraesCS7A01G528400

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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 TraesCS7A01G528400 chr7A 100.000 2240 0 0 1 2240 708793951 708791712 0.000000e+00 4137.0
1 TraesCS7A01G528400 chr7A 91.284 1526 108 18 715 2236 124272 122768 0.000000e+00 2058.0
2 TraesCS7A01G528400 chr2D 97.545 2240 51 4 1 2240 35052235 35054470 0.000000e+00 3829.0
3 TraesCS7A01G528400 chr6D 97.280 2243 54 6 1 2240 364896901 364894663 0.000000e+00 3797.0
4 TraesCS7A01G528400 chr7B 95.813 2245 64 13 1 2240 568662391 568664610 0.000000e+00 3598.0
5 TraesCS7A01G528400 chr3B 95.637 2246 67 13 1 2240 460377031 460379251 0.000000e+00 3576.0
6 TraesCS7A01G528400 chr2B 91.611 1347 102 6 897 2240 282991098 282992436 0.000000e+00 1851.0
7 TraesCS7A01G528400 chr2B 93.230 709 38 6 3 710 282966854 282967553 0.000000e+00 1035.0
8 TraesCS7A01G528400 chr4B 96.574 759 19 3 1 754 626782510 626781754 0.000000e+00 1251.0
9 TraesCS7A01G528400 chr4B 93.679 443 9 3 403 845 626781728 626781305 0.000000e+00 645.0
10 TraesCS7A01G528400 chr4B 100.000 32 0 0 771 802 626781754 626781723 2.400000e-05 60.2
11 TraesCS7A01G528400 chr6B 96.552 319 9 2 1 319 651215525 651215841 5.480000e-146 527.0
12 TraesCS7A01G528400 chr6B 95.896 268 9 2 475 742 651215839 651216104 1.230000e-117 433.0
13 TraesCS7A01G528400 chr6B 94.886 176 9 0 2065 2240 651216100 651216275 2.190000e-70 276.0


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 TraesCS7A01G528400 chr7A 708791712 708793951 2239 True 4137.000000 4137 100.000 1 2240 1 chr7A.!!$R2 2239
1 TraesCS7A01G528400 chr7A 122768 124272 1504 True 2058.000000 2058 91.284 715 2236 1 chr7A.!!$R1 1521
2 TraesCS7A01G528400 chr2D 35052235 35054470 2235 False 3829.000000 3829 97.545 1 2240 1 chr2D.!!$F1 2239
3 TraesCS7A01G528400 chr6D 364894663 364896901 2238 True 3797.000000 3797 97.280 1 2240 1 chr6D.!!$R1 2239
4 TraesCS7A01G528400 chr7B 568662391 568664610 2219 False 3598.000000 3598 95.813 1 2240 1 chr7B.!!$F1 2239
5 TraesCS7A01G528400 chr3B 460377031 460379251 2220 False 3576.000000 3576 95.637 1 2240 1 chr3B.!!$F1 2239
6 TraesCS7A01G528400 chr2B 282991098 282992436 1338 False 1851.000000 1851 91.611 897 2240 1 chr2B.!!$F2 1343
7 TraesCS7A01G528400 chr2B 282966854 282967553 699 False 1035.000000 1035 93.230 3 710 1 chr2B.!!$F1 707
8 TraesCS7A01G528400 chr4B 626781305 626782510 1205 True 652.066667 1251 96.751 1 845 3 chr4B.!!$R1 844
9 TraesCS7A01G528400 chr6B 651215525 651216275 750 False 412.000000 527 95.778 1 2240 3 chr6B.!!$F1 2239

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
745 1127 2.599645 CTTGCCCGCCATAGACTGCT 62.6 60.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2140 2.610833 CTCAGATGCAAGCTATTCGCAA 59.389 45.455 0.0 0.0 42.61 4.85 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
31 33 2.887151 AATACTCTGCTTTGCCACCT 57.113 45.000 0.00 0.0 0.00 4.00
462 469 2.832838 TCCTAAAGGAGCTCATGGTCA 58.167 47.619 17.19 0.0 42.05 4.02
546 553 8.845227 TCAAGTAATTCATTGCAGTTTCAGTTA 58.155 29.630 0.00 0.0 0.00 2.24
740 1122 4.545706 CGCCTTGCCCGCCATAGA 62.546 66.667 0.00 0.0 0.00 1.98
745 1127 2.599645 CTTGCCCGCCATAGACTGCT 62.600 60.000 0.00 0.0 0.00 4.24
883 1265 9.035607 CAGGGCGATAGATATAAATTGATGTAC 57.964 37.037 0.00 0.0 39.76 2.90
981 1364 8.713708 TGGAGATGGTTAACAATTAAGGAAAA 57.286 30.769 8.10 0.0 0.00 2.29
1083 1466 1.645710 GAAGGGGTGTGGAGAAGAGA 58.354 55.000 0.00 0.0 0.00 3.10
1085 1468 0.191064 AGGGGTGTGGAGAAGAGACA 59.809 55.000 0.00 0.0 0.00 3.41
1242 1625 6.418226 GCAGTTCGATTCTTACTGTATAGGTG 59.582 42.308 14.02 0.0 40.99 4.00
1380 1763 4.388577 AGAGCTTGGAAGGTTGGTAATT 57.611 40.909 0.00 0.0 36.78 1.40
1392 1775 4.765339 AGGTTGGTAATTTGCTTCCTACAC 59.235 41.667 0.00 0.0 0.00 2.90
1411 1794 8.778059 TCCTACACAATAACAGGAAGGATAATT 58.222 33.333 0.00 0.0 34.25 1.40
1457 1840 2.103153 ACCTGGTTCTTGGAGACTCA 57.897 50.000 4.53 0.0 0.00 3.41
1470 1853 6.719829 TCTTGGAGACTCAGAACAGTAATGTA 59.280 38.462 4.53 0.0 0.00 2.29
1472 1855 5.773176 TGGAGACTCAGAACAGTAATGTACA 59.227 40.000 4.53 0.0 0.00 2.90
1569 1958 2.887152 ACTCAAGATGCACCTGGTTTTC 59.113 45.455 0.00 0.0 0.00 2.29
1779 2168 2.424557 AGCTTGCATCTGAGTCAAGTG 58.575 47.619 17.32 0.0 39.36 3.16
1951 2343 1.115326 GTCCTGTTTGGCCCTGCTTT 61.115 55.000 0.00 0.0 35.26 3.51
1958 2350 3.213506 GTTTGGCCCTGCTTTTTGAATT 58.786 40.909 0.00 0.0 0.00 2.17
1977 2369 8.879342 TTGAATTATTGTGTGGGTTACAAAAG 57.121 30.769 0.00 0.0 39.78 2.27
2212 2604 2.338228 GCAACAATGTATTTCACGCACG 59.662 45.455 0.00 0.0 0.00 5.34
2221 2613 3.634568 ATTTCACGCACGAATCCAAAA 57.365 38.095 0.00 0.0 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 308 7.112122 TCCACATGTCAAGCTATATCAGTTTT 58.888 34.615 0.00 0.0 0.00 2.43
462 469 6.365520 AGGTTCAGTTTCACTAAAATGGACT 58.634 36.000 8.96 0.0 44.78 3.85
546 553 2.704572 GTGAGCTGCACCTAAACTGAT 58.295 47.619 1.02 0.0 41.78 2.90
647 1029 9.204570 CTCATTGGTATAAATTAGTTACCCTCG 57.795 37.037 8.24 0.0 35.53 4.63
677 1059 5.722263 CATTATGGTCATGAGAGAGCTAGG 58.278 45.833 0.00 0.0 36.97 3.02
738 1120 2.851102 AGGGGTGTGCAGCAGTCT 60.851 61.111 0.00 0.0 0.00 3.24
740 1122 3.170672 TCAGGGGTGTGCAGCAGT 61.171 61.111 0.00 0.0 0.00 4.40
981 1364 4.832823 CACATGGGGTCCTCTTTAGTTTTT 59.167 41.667 0.00 0.0 0.00 1.94
1083 1466 3.064987 CTCGCCTCCCGTTCGATGT 62.065 63.158 0.00 0.0 38.35 3.06
1085 1468 2.005960 CTTCTCGCCTCCCGTTCGAT 62.006 60.000 0.00 0.0 38.35 3.59
1176 1559 6.655003 TCTGTTGTTTCATGACTCCCTTAATC 59.345 38.462 0.00 0.0 0.00 1.75
1178 1561 5.935945 TCTGTTGTTTCATGACTCCCTTAA 58.064 37.500 0.00 0.0 0.00 1.85
1276 1659 6.055588 CACTTAGTCCTTCCAGTTTCTTGAA 58.944 40.000 0.00 0.0 0.00 2.69
1380 1763 5.235850 TCCTGTTATTGTGTAGGAAGCAA 57.764 39.130 0.00 0.0 36.44 3.91
1411 1794 3.957497 CTCTCTTGCCTTAGCCTCTTCTA 59.043 47.826 0.00 0.0 38.69 2.10
1470 1853 7.765695 ACAACATCTGGTCTATTTGAATTGT 57.234 32.000 0.00 0.0 0.00 2.71
1472 1855 8.408043 TCAACAACATCTGGTCTATTTGAATT 57.592 30.769 0.00 0.0 0.00 2.17
1569 1958 4.825422 TCTAGCAAATGAGTCCAAGTCTG 58.175 43.478 0.00 0.0 0.00 3.51
1751 2140 2.610833 CTCAGATGCAAGCTATTCGCAA 59.389 45.455 0.00 0.0 42.61 4.85
1779 2168 5.640218 ATTGTGCATATTTTTATGTGCGC 57.360 34.783 0.00 0.0 45.36 6.09
1951 2343 9.319143 CTTTTGTAACCCACACAATAATTCAAA 57.681 29.630 0.00 0.0 36.69 2.69
1958 2350 7.589958 ACAATCTTTTGTAACCCACACAATA 57.410 32.000 0.00 0.0 44.22 1.90
2066 2458 9.618890 ACAGTACTAGCAATTGATGATATTGTT 57.381 29.630 10.34 0.0 35.82 2.83
2212 2604 5.359860 CCTACTGGTAATGGGTTTTGGATTC 59.640 44.000 0.00 0.0 0.00 2.52


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

AutoCloner maintained by Alex Coulton.