Multiple sequence alignment - TraesCS1A01G407400

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 TraesCS1A01G407400 chr1A 100.000 2375 0 0 1 2375 570008440 570010814 0.000000e+00 4386
1 TraesCS1A01G407400 chr1A 86.322 329 42 1 271 599 569947513 569947838 2.900000e-94 355
2 TraesCS1A01G407400 chr7A 96.852 1779 48 6 600 2375 652135183 652133410 0.000000e+00 2968
3 TraesCS1A01G407400 chr7A 95.894 1778 60 7 600 2375 546507308 546505542 0.000000e+00 2867
4 TraesCS1A01G407400 chr4A 96.402 1779 61 3 600 2375 620625879 620624101 0.000000e+00 2928
5 TraesCS1A01G407400 chr4A 98.664 599 8 0 1 599 623970034 623970632 0.000000e+00 1062
6 TraesCS1A01G407400 chr4A 87.135 342 39 3 230 569 716980586 716980924 1.330000e-102 383
7 TraesCS1A01G407400 chr4A 86.322 329 42 1 271 599 623950021 623950346 2.900000e-94 355
8 TraesCS1A01G407400 chrUn 96.251 1787 56 7 599 2375 30431624 30429839 0.000000e+00 2918
9 TraesCS1A01G407400 chr6D 96.134 1785 57 8 600 2375 390006827 390008608 0.000000e+00 2904
10 TraesCS1A01G407400 chr5D 96.031 1789 54 11 598 2375 399910098 399911880 0.000000e+00 2894
11 TraesCS1A01G407400 chr5D 95.521 1786 65 8 599 2375 47119053 47117274 0.000000e+00 2841
12 TraesCS1A01G407400 chr5D 85.906 596 58 9 9 599 545402045 545401471 1.560000e-171 612
13 TraesCS1A01G407400 chr3A 95.674 1780 69 8 600 2375 733097458 733099233 0.000000e+00 2854
14 TraesCS1A01G407400 chr3A 87.135 342 39 3 230 569 427779460 427779122 1.330000e-102 383
15 TraesCS1A01G407400 chr2A 95.616 1779 62 10 600 2375 678534726 678536491 0.000000e+00 2839
16 TraesCS1A01G407400 chr5B 88.441 372 38 3 230 599 135804429 135804797 6.020000e-121 444
17 TraesCS1A01G407400 chr7B 88.378 370 38 3 229 596 234388791 234389157 7.790000e-120 440
18 TraesCS1A01G407400 chr3B 87.719 342 37 3 230 569 125576655 125576993 6.150000e-106 394


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 TraesCS1A01G407400 chr1A 570008440 570010814 2374 False 4386 4386 100.000 1 2375 1 chr1A.!!$F2 2374
1 TraesCS1A01G407400 chr7A 652133410 652135183 1773 True 2968 2968 96.852 600 2375 1 chr7A.!!$R2 1775
2 TraesCS1A01G407400 chr7A 546505542 546507308 1766 True 2867 2867 95.894 600 2375 1 chr7A.!!$R1 1775
3 TraesCS1A01G407400 chr4A 620624101 620625879 1778 True 2928 2928 96.402 600 2375 1 chr4A.!!$R1 1775
4 TraesCS1A01G407400 chr4A 623970034 623970632 598 False 1062 1062 98.664 1 599 1 chr4A.!!$F2 598
5 TraesCS1A01G407400 chrUn 30429839 30431624 1785 True 2918 2918 96.251 599 2375 1 chrUn.!!$R1 1776
6 TraesCS1A01G407400 chr6D 390006827 390008608 1781 False 2904 2904 96.134 600 2375 1 chr6D.!!$F1 1775
7 TraesCS1A01G407400 chr5D 399910098 399911880 1782 False 2894 2894 96.031 598 2375 1 chr5D.!!$F1 1777
8 TraesCS1A01G407400 chr5D 47117274 47119053 1779 True 2841 2841 95.521 599 2375 1 chr5D.!!$R1 1776
9 TraesCS1A01G407400 chr5D 545401471 545402045 574 True 612 612 85.906 9 599 1 chr5D.!!$R2 590
10 TraesCS1A01G407400 chr3A 733097458 733099233 1775 False 2854 2854 95.674 600 2375 1 chr3A.!!$F1 1775
11 TraesCS1A01G407400 chr2A 678534726 678536491 1765 False 2839 2839 95.616 600 2375 1 chr2A.!!$F1 1775

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
322 327 2.042831 GGCAGCAAGCTTCCGACAT 61.043 57.895 0.00 0.0 44.79 3.06 F
1112 1130 1.406069 CCTGAAGCGGCTAGTCACAAT 60.406 52.381 1.35 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1354 0.038166 GCACCCTCCAGTTGAATCCA 59.962 55.0 0.00 0.00 0.00 3.41 R
1959 1989 2.435372 AAAGGTGACTGCAGGAAACA 57.565 45.0 19.93 9.66 42.68 2.83 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
126 128 4.681744 AGAAGATCAGAAATCTCACTCGC 58.318 43.478 0.00 0.0 0.00 5.03
322 327 2.042831 GGCAGCAAGCTTCCGACAT 61.043 57.895 0.00 0.0 44.79 3.06
462 467 3.719268 TTTTGCTGATAAGAGAGCCCA 57.281 42.857 0.00 0.0 34.04 5.36
521 526 4.080582 TCTGCCCCGATATCTTTTTCTTCA 60.081 41.667 0.34 0.0 0.00 3.02
650 656 3.620374 GTGTGAATTGTCTCTCATGCGAT 59.380 43.478 0.00 0.0 0.00 4.58
957 975 3.202906 CCGTTGTTGTTCTTCTTCTCCA 58.797 45.455 0.00 0.0 0.00 3.86
1112 1130 1.406069 CCTGAAGCGGCTAGTCACAAT 60.406 52.381 1.35 0.0 0.00 2.71
1278 1296 6.603940 TTTGGGATTTAGGGTTCATCTTTG 57.396 37.500 0.00 0.0 0.00 2.77
1336 1354 5.947663 AGTGGCTAGATGAGTACATAGAGT 58.052 41.667 0.00 0.0 36.82 3.24
1370 1388 3.473647 TGCATCAGGGGAGCTCGG 61.474 66.667 7.83 0.0 0.00 4.63
1373 1391 1.686325 GCATCAGGGGAGCTCGGTTA 61.686 60.000 7.83 0.0 0.00 2.85
1400 1418 2.044946 GGCGGAGAAGTTGGGCAT 60.045 61.111 0.00 0.0 0.00 4.40
1442 1460 4.369591 TGGGGCCCCTGGATCTGT 62.370 66.667 40.66 0.0 36.94 3.41
1537 1555 5.240891 AGAAACTCATCGAATTGCAGAAGA 58.759 37.500 0.00 0.0 0.00 2.87
1542 1560 3.055167 TCATCGAATTGCAGAAGAAGGGA 60.055 43.478 0.00 0.0 0.00 4.20
2332 2363 8.908903 CCCCTTACAACATATAGTGCATAAAAA 58.091 33.333 0.00 0.0 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 2.099921 GGAGAATAAGCAGCGAGTGAGA 59.900 50.000 0.00 0.00 0.00 3.27
126 128 2.019984 GGTTGGCAGGAGAATAAGCAG 58.980 52.381 0.00 0.00 0.00 4.24
322 327 6.950842 AGAAACCTGATGATGATAAGTGTGA 58.049 36.000 0.00 0.00 0.00 3.58
462 467 3.767711 TGCGTCCTATCCTAGATGACAT 58.232 45.455 0.00 0.00 0.00 3.06
650 656 4.021807 TGAGAGCTATTACAACCAACGACA 60.022 41.667 0.00 0.00 0.00 4.35
770 780 0.331616 AAGTTAGTGGGTCCCATGCC 59.668 55.000 15.49 0.59 35.28 4.40
1112 1130 1.234821 GTTGCCATTCTTGTCGGTCA 58.765 50.000 0.00 0.00 0.00 4.02
1336 1354 0.038166 GCACCCTCCAGTTGAATCCA 59.962 55.000 0.00 0.00 0.00 3.41
1370 1388 3.569902 CCGCCTCCAACGGTTAAC 58.430 61.111 0.00 0.00 45.70 2.01
1400 1418 4.690719 ACGCGCCCGATCCAAACA 62.691 61.111 5.73 0.00 38.29 2.83
1442 1460 1.215173 CAGTAGCCCCAATGGAATGGA 59.785 52.381 0.00 0.00 43.54 3.41
1537 1555 2.190538 CAGCCCCATCAAATTTCCCTT 58.809 47.619 0.00 0.00 0.00 3.95
1542 1560 1.487558 GCCATCAGCCCCATCAAATTT 59.512 47.619 0.00 0.00 34.35 1.82
1683 1702 1.631072 CCGAATTCGTACAGCGCAG 59.369 57.895 25.10 3.33 41.07 5.18
1751 1770 4.163078 CCCTCTACCACTGAAACTGATGAT 59.837 45.833 0.00 0.00 0.00 2.45
1959 1989 2.435372 AAAGGTGACTGCAGGAAACA 57.565 45.000 19.93 9.66 42.68 2.83


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

AutoCloner maintained by Alex Coulton.