Multiple sequence alignment - TraesCS6A01G202700

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 TraesCS6A01G202700 chr6A 100.000 2243 0 0 1 2243 338516639 338518881 0 4143
1 TraesCS6A01G202700 chr6A 96.623 1747 46 3 1 1746 155857310 155859044 0 2887
2 TraesCS6A01G202700 chr6A 95.535 1747 64 3 1 1746 375860748 375859015 0 2782
3 TraesCS6A01G202700 chr4B 96.394 1747 49 3 1 1746 209242568 209244301 0 2865
4 TraesCS6A01G202700 chr3B 96.222 1747 52 3 1 1746 483333223 483334956 0 2848
5 TraesCS6A01G202700 chr3B 95.423 1748 66 3 1 1746 575839731 575837996 0 2772
6 TraesCS6A01G202700 chr2A 96.165 1747 54 2 1 1746 750453580 750451846 0 2843
7 TraesCS6A01G202700 chr2A 96.789 1308 29 2 1 1307 755480560 755481855 0 2170
8 TraesCS6A01G202700 chr4A 95.306 1747 69 2 1 1746 350172251 350173985 0 2760
9 TraesCS6A01G202700 chr4A 97.217 503 14 0 1741 2243 105656191 105656693 0 852
10 TraesCS6A01G202700 chr4A 97.206 501 13 1 1741 2241 552129798 552130297 0 846
11 TraesCS6A01G202700 chr3A 95.544 1526 52 5 223 1746 230228527 230227016 0 2427
12 TraesCS6A01G202700 chr7B 96.796 1311 29 2 1 1310 742948727 742947429 0 2176
13 TraesCS6A01G202700 chr7B 96.636 1308 31 2 1 1307 716784618 716785913 0 2159
14 TraesCS6A01G202700 chr7A 96.789 1308 29 2 1 1307 60084947 60086242 0 2170
15 TraesCS6A01G202700 chr7A 96.720 1311 30 2 1 1310 60168756 60167458 0 2170
16 TraesCS6A01G202700 chr5A 96.636 1308 31 2 1 1307 420185713 420187008 0 2159
17 TraesCS6A01G202700 chr5A 97.416 503 13 0 1741 2243 238853302 238853804 0 857
18 TraesCS6A01G202700 chr3D 96.212 1320 44 6 1 1319 308558642 308557328 0 2156
19 TraesCS6A01G202700 chr1D 96.308 1246 33 2 1 1245 185743751 185742518 0 2034
20 TraesCS6A01G202700 chrUn 96.793 873 15 2 1 872 378556550 378557410 0 1445
21 TraesCS6A01G202700 chr6B 92.816 696 47 3 1052 1746 401858413 401859106 0 1005
22 TraesCS6A01G202700 chr7D 97.416 503 13 0 1741 2243 626642086 626642588 0 857
23 TraesCS6A01G202700 chr1A 97.405 501 13 0 1743 2243 292104664 292105164 0 854
24 TraesCS6A01G202700 chr2B 97.217 503 14 0 1741 2243 449207097 449207599 0 852
25 TraesCS6A01G202700 chr1B 97.217 503 14 0 1741 2243 339009316 339008814 0 852
26 TraesCS6A01G202700 chr1B 97.018 503 15 0 1741 2243 338933905 338933403 0 846
27 TraesCS6A01G202700 chr1B 97.024 504 14 1 1741 2243 683694551 683694048 0 846


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 TraesCS6A01G202700 chr6A 338516639 338518881 2242 False 4143 4143 100.000 1 2243 1 chr6A.!!$F2 2242
1 TraesCS6A01G202700 chr6A 155857310 155859044 1734 False 2887 2887 96.623 1 1746 1 chr6A.!!$F1 1745
2 TraesCS6A01G202700 chr6A 375859015 375860748 1733 True 2782 2782 95.535 1 1746 1 chr6A.!!$R1 1745
3 TraesCS6A01G202700 chr4B 209242568 209244301 1733 False 2865 2865 96.394 1 1746 1 chr4B.!!$F1 1745
4 TraesCS6A01G202700 chr3B 483333223 483334956 1733 False 2848 2848 96.222 1 1746 1 chr3B.!!$F1 1745
5 TraesCS6A01G202700 chr3B 575837996 575839731 1735 True 2772 2772 95.423 1 1746 1 chr3B.!!$R1 1745
6 TraesCS6A01G202700 chr2A 750451846 750453580 1734 True 2843 2843 96.165 1 1746 1 chr2A.!!$R1 1745
7 TraesCS6A01G202700 chr2A 755480560 755481855 1295 False 2170 2170 96.789 1 1307 1 chr2A.!!$F1 1306
8 TraesCS6A01G202700 chr4A 350172251 350173985 1734 False 2760 2760 95.306 1 1746 1 chr4A.!!$F2 1745
9 TraesCS6A01G202700 chr4A 105656191 105656693 502 False 852 852 97.217 1741 2243 1 chr4A.!!$F1 502
10 TraesCS6A01G202700 chr3A 230227016 230228527 1511 True 2427 2427 95.544 223 1746 1 chr3A.!!$R1 1523
11 TraesCS6A01G202700 chr7B 742947429 742948727 1298 True 2176 2176 96.796 1 1310 1 chr7B.!!$R1 1309
12 TraesCS6A01G202700 chr7B 716784618 716785913 1295 False 2159 2159 96.636 1 1307 1 chr7B.!!$F1 1306
13 TraesCS6A01G202700 chr7A 60084947 60086242 1295 False 2170 2170 96.789 1 1307 1 chr7A.!!$F1 1306
14 TraesCS6A01G202700 chr7A 60167458 60168756 1298 True 2170 2170 96.720 1 1310 1 chr7A.!!$R1 1309
15 TraesCS6A01G202700 chr5A 420185713 420187008 1295 False 2159 2159 96.636 1 1307 1 chr5A.!!$F2 1306
16 TraesCS6A01G202700 chr5A 238853302 238853804 502 False 857 857 97.416 1741 2243 1 chr5A.!!$F1 502
17 TraesCS6A01G202700 chr3D 308557328 308558642 1314 True 2156 2156 96.212 1 1319 1 chr3D.!!$R1 1318
18 TraesCS6A01G202700 chr1D 185742518 185743751 1233 True 2034 2034 96.308 1 1245 1 chr1D.!!$R1 1244
19 TraesCS6A01G202700 chrUn 378556550 378557410 860 False 1445 1445 96.793 1 872 1 chrUn.!!$F1 871
20 TraesCS6A01G202700 chr6B 401858413 401859106 693 False 1005 1005 92.816 1052 1746 1 chr6B.!!$F1 694
21 TraesCS6A01G202700 chr7D 626642086 626642588 502 False 857 857 97.416 1741 2243 1 chr7D.!!$F1 502
22 TraesCS6A01G202700 chr1A 292104664 292105164 500 False 854 854 97.405 1743 2243 1 chr1A.!!$F1 500
23 TraesCS6A01G202700 chr2B 449207097 449207599 502 False 852 852 97.217 1741 2243 1 chr2B.!!$F1 502
24 TraesCS6A01G202700 chr1B 339008814 339009316 502 True 852 852 97.217 1741 2243 1 chr1B.!!$R2 502
25 TraesCS6A01G202700 chr1B 338933403 338933905 502 True 846 846 97.018 1741 2243 1 chr1B.!!$R1 502
26 TraesCS6A01G202700 chr1B 683694048 683694551 503 True 846 846 97.024 1741 2243 1 chr1B.!!$R3 502

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
912 928 0.95228 TGAAAATTACGGCGGTGCAA 59.048 45.0 13.24 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2024 1.557099 ACCTCTTCACATCGCACCTA 58.443 50.0 0.0 0.0 0.0 3.08 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
42 43 4.448200 CCCCACCAATGTGATCTCCATTAT 60.448 45.833 9.80 1.77 45.76 1.28
217 219 3.081409 GAAGTGGCCGCCTCCCTA 61.081 66.667 14.07 0.00 0.00 3.53
228 230 1.776662 GCCTCCCTAAATTTGGGTCC 58.223 55.000 18.27 7.97 44.84 4.46
765 781 4.798472 GACCCCCTACCTATACCTATACCT 59.202 50.000 0.00 0.00 0.00 3.08
766 782 5.956426 ACCCCCTACCTATACCTATACCTA 58.044 45.833 0.00 0.00 0.00 3.08
767 783 6.547530 ACCCCCTACCTATACCTATACCTAT 58.452 44.000 0.00 0.00 0.00 2.57
768 784 7.695234 ACCCCCTACCTATACCTATACCTATA 58.305 42.308 0.00 0.00 0.00 1.31
769 785 7.578174 ACCCCCTACCTATACCTATACCTATAC 59.422 44.444 0.00 0.00 0.00 1.47
770 786 7.019053 CCCCCTACCTATACCTATACCTATACC 59.981 48.148 0.00 0.00 0.00 2.73
811 827 8.451245 ACCTATACCTGATGATTTTCAATCCAT 58.549 33.333 0.00 0.00 0.00 3.41
902 918 8.760569 CCGCATAACCCAATATTTGAAAATTAC 58.239 33.333 0.00 0.00 0.00 1.89
905 921 8.760569 CATAACCCAATATTTGAAAATTACGGC 58.239 33.333 0.00 0.00 0.00 5.68
912 928 0.952280 TGAAAATTACGGCGGTGCAA 59.048 45.000 13.24 0.00 0.00 4.08
926 942 1.604604 GTGCAAGCCCAAGTACTTCA 58.395 50.000 4.77 0.00 0.00 3.02
947 963 8.591072 ACTTCAAATCATCAACAAGAAATCCAT 58.409 29.630 0.00 0.00 0.00 3.41
1026 1042 6.542370 TGTTAGAAGGTGCTAAATCAATAGGC 59.458 38.462 0.00 0.00 32.58 3.93
1141 1157 6.397272 TCATTGGCTAAACAATCATTTGGTC 58.603 36.000 0.00 0.00 38.94 4.02
1166 1182 2.235402 CCATTTTGGGCTTTGCTCTCAT 59.765 45.455 0.00 0.00 32.67 2.90
1393 1412 5.629079 AGGATTCTGCTTTTCGGTTAAAG 57.371 39.130 0.00 0.00 38.00 1.85
1479 1498 4.346127 AGCTATATCATGACTGCTGGAACA 59.654 41.667 0.00 0.00 0.00 3.18
1519 1538 5.486735 TTTCGTACCACCTTCCAATCTTA 57.513 39.130 0.00 0.00 0.00 2.10
1677 1697 3.735591 AGCTGCCGTTTTCACTACTTTA 58.264 40.909 0.00 0.00 0.00 1.85
1702 1722 5.701290 GTCCCTAGCGATATTGTTGCTTAAT 59.299 40.000 0.01 0.00 45.60 1.40
1779 1799 6.183360 CCGGGAAATAGAAAATTTGGAATCGA 60.183 38.462 0.00 0.00 0.00 3.59
1901 1922 8.932434 ATTTACTGTCAGATAGAGAGATGCTA 57.068 34.615 6.91 0.00 39.94 3.49
2003 2024 2.092753 ACAGAGCACATGATTCGGGATT 60.093 45.455 0.00 0.00 0.00 3.01
2077 2098 4.988540 GTGGAAAGGCAAAACCATTAGTTC 59.011 41.667 0.00 0.00 43.14 3.01
2092 2113 1.605753 AGTTCAAGTTCCCGGCTTTC 58.394 50.000 0.00 0.00 0.00 2.62
2138 2159 7.219484 ACCATTTGAGTCAATTTGGAGTAAG 57.781 36.000 28.85 11.63 33.80 2.34
2155 2176 7.837863 TGGAGTAAGTAGTAAGACTTTGGATG 58.162 38.462 0.00 0.00 40.22 3.51
2205 2226 2.380064 TGGCATCTTTTTCCCACTGT 57.620 45.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.022428 TGGTGGGGATATAGGCCGATAT 60.022 50.000 17.34 17.34 0.00 1.63
42 43 6.775142 TGTTTCCAAACAGATTTGTCCATCTA 59.225 34.615 0.55 0.00 43.45 1.98
217 219 2.668144 TCAAGGTCGGACCCAAATTT 57.332 45.000 23.21 8.12 39.75 1.82
228 230 1.416813 GAGTCGCAGCATCAAGGTCG 61.417 60.000 0.00 0.00 0.00 4.79
768 784 8.857997 AGGTATAGGTAATCATCAGGTATAGGT 58.142 37.037 0.00 0.00 0.00 3.08
769 785 9.137459 CAGGTATAGGTAATCATCAGGTATAGG 57.863 40.741 0.00 0.00 0.00 2.57
770 786 9.922477 TCAGGTATAGGTAATCATCAGGTATAG 57.078 37.037 0.00 0.00 0.00 1.31
905 921 0.889186 AAGTACTTGGGCTTGCACCG 60.889 55.000 7.48 0.00 0.00 4.94
912 928 4.922206 TGATGATTTGAAGTACTTGGGCT 58.078 39.130 14.14 0.00 0.00 5.19
926 942 9.431887 CTTTCATGGATTTCTTGTTGATGATTT 57.568 29.630 0.00 0.00 0.00 2.17
947 963 4.156922 TGTTTTTCCTTCGCTGTTCTTTCA 59.843 37.500 0.00 0.00 0.00 2.69
1026 1042 1.815421 AATTGTAGCAGCTCCGGCG 60.815 57.895 0.00 0.00 44.37 6.46
1393 1412 1.897398 ATCGCCGACTTGTGTTTCGC 61.897 55.000 0.00 0.00 33.78 4.70
1479 1498 5.243207 ACGAAAATACTCATCGGGTCTTTT 58.757 37.500 0.00 0.00 40.71 2.27
1519 1538 8.691661 AGTGGAAAAGTACACAATTGACTAAT 57.308 30.769 13.59 0.00 39.99 1.73
1677 1697 2.700897 AGCAACAATATCGCTAGGGACT 59.299 45.455 12.26 4.52 46.37 3.85
1702 1722 4.715534 TGAACCCACTTTCCATGTTAGA 57.284 40.909 0.00 0.00 0.00 2.10
1855 1876 9.722056 GTAAATATTGCTTTCAATCGATCAGTT 57.278 29.630 0.00 0.00 41.68 3.16
1856 1877 9.113838 AGTAAATATTGCTTTCAATCGATCAGT 57.886 29.630 0.00 0.00 41.68 3.41
2003 2024 1.557099 ACCTCTTCACATCGCACCTA 58.443 50.000 0.00 0.00 0.00 3.08
2077 2098 1.574702 GGACGAAAGCCGGGAACTTG 61.575 60.000 2.18 0.00 43.93 3.16
2092 2113 2.034685 TGACTGAACTTCACAGAGGACG 59.965 50.000 0.00 0.00 38.55 4.79
2138 2159 3.939592 GGTGCCATCCAAAGTCTTACTAC 59.060 47.826 0.00 0.00 0.00 2.73
2150 2171 3.913509 ACATTATGAATGGTGCCATCCA 58.086 40.909 3.96 0.00 43.21 3.41


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

AutoCloner maintained by Alex Coulton.