Multiple sequence alignment - TraesCS7D01G313100

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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 TraesCS7D01G313100 chr7D 100.000 2447 0 0 1 2447 396980537 396982983 0.000000e+00 4519.0
1 TraesCS7D01G313100 chr7D 96.118 747 29 0 20 766 49831220 49830474 0.000000e+00 1219.0
2 TraesCS7D01G313100 chr7D 84.225 748 116 1 19 766 28856957 28856212 0.000000e+00 726.0
3 TraesCS7D01G313100 chr7A 96.027 1636 47 7 825 2447 450962057 450963687 0.000000e+00 2645.0
4 TraesCS7D01G313100 chr7B 95.755 1649 51 7 811 2447 400633792 400635433 0.000000e+00 2639.0
5 TraesCS7D01G313100 chr7B 84.371 755 117 1 13 766 493009711 493008957 0.000000e+00 739.0
6 TraesCS7D01G313100 chr5A 91.963 759 61 0 17 775 676909986 676910744 0.000000e+00 1064.0
7 TraesCS7D01G313100 chr5A 88.639 757 83 3 12 766 306181793 306181038 0.000000e+00 918.0
8 TraesCS7D01G313100 chr5A 87.067 750 97 0 17 766 707538423 707537674 0.000000e+00 848.0
9 TraesCS7D01G313100 chr6B 87.049 749 95 2 19 766 56968888 56968141 0.000000e+00 845.0
10 TraesCS7D01G313100 chr2B 86.631 748 100 0 19 766 225363830 225363083 0.000000e+00 828.0
11 TraesCS7D01G313100 chr4D 81.732 739 130 5 29 766 343547645 343546911 1.610000e-171 612.0
12 TraesCS7D01G313100 chr3D 95.122 41 2 0 1293 1333 481928550 481928590 5.650000e-07 65.8


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 TraesCS7D01G313100 chr7D 396980537 396982983 2446 False 4519 4519 100.000 1 2447 1 chr7D.!!$F1 2446
1 TraesCS7D01G313100 chr7D 49830474 49831220 746 True 1219 1219 96.118 20 766 1 chr7D.!!$R2 746
2 TraesCS7D01G313100 chr7D 28856212 28856957 745 True 726 726 84.225 19 766 1 chr7D.!!$R1 747
3 TraesCS7D01G313100 chr7A 450962057 450963687 1630 False 2645 2645 96.027 825 2447 1 chr7A.!!$F1 1622
4 TraesCS7D01G313100 chr7B 400633792 400635433 1641 False 2639 2639 95.755 811 2447 1 chr7B.!!$F1 1636
5 TraesCS7D01G313100 chr7B 493008957 493009711 754 True 739 739 84.371 13 766 1 chr7B.!!$R1 753
6 TraesCS7D01G313100 chr5A 676909986 676910744 758 False 1064 1064 91.963 17 775 1 chr5A.!!$F1 758
7 TraesCS7D01G313100 chr5A 306181038 306181793 755 True 918 918 88.639 12 766 1 chr5A.!!$R1 754
8 TraesCS7D01G313100 chr5A 707537674 707538423 749 True 848 848 87.067 17 766 1 chr5A.!!$R2 749
9 TraesCS7D01G313100 chr6B 56968141 56968888 747 True 845 845 87.049 19 766 1 chr6B.!!$R1 747
10 TraesCS7D01G313100 chr2B 225363083 225363830 747 True 828 828 86.631 19 766 1 chr2B.!!$R1 747
11 TraesCS7D01G313100 chr4D 343546911 343547645 734 True 612 612 81.732 29 766 1 chr4D.!!$R1 737

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
713 714 1.141053 GGCTAACCCTCACAATCCGAT 59.859 52.381 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 1547 0.249031 AAGCACAAAACAGAAGCGCC 60.249 50.0 2.29 0.0 0.0 6.53 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
175 176 2.575532 CACAGGCCACTTCTCTTTTCA 58.424 47.619 5.01 0.00 0.00 2.69
184 185 3.080319 ACTTCTCTTTTCATGAGCAGGC 58.920 45.455 0.00 0.00 30.94 4.85
234 235 4.446371 CAAAACCCCACAGTAATTTGCAA 58.554 39.130 0.00 0.00 0.00 4.08
382 383 3.541632 GACCAAGCGGGAAATTATCTGA 58.458 45.455 4.35 0.00 41.15 3.27
506 507 3.852286 ACATAATTGTGGCGTCGAACTA 58.148 40.909 7.15 0.00 33.85 2.24
583 584 7.686938 CGGTGATAACAGAAATTAAACTTCGTC 59.313 37.037 0.00 0.00 0.00 4.20
667 668 4.478206 TTAGCTAAGCATGCACTCTCTT 57.522 40.909 21.98 6.65 0.00 2.85
713 714 1.141053 GGCTAACCCTCACAATCCGAT 59.859 52.381 0.00 0.00 0.00 4.18
1467 1473 1.123928 GGATTGATCCGTCTCCCAGT 58.876 55.000 0.00 0.00 37.19 4.00
1541 1547 4.097012 CGTATCATCTGATCTGATCTGCG 58.903 47.826 17.82 12.81 35.12 5.18
1604 1610 3.053619 ACTGCCCTAGGGTTTGGATAAAG 60.054 47.826 28.96 13.86 37.65 1.85
1715 1721 6.647334 TTAATCAGAAACCAGTGAAATGCA 57.353 33.333 0.00 0.00 0.00 3.96
1772 1778 9.829507 ATGATTTGTTTTTCTTGTAATTGGTGA 57.170 25.926 0.00 0.00 0.00 4.02
1912 1918 4.892934 GGTTAATATCATGGGGCTGTTGAA 59.107 41.667 0.00 0.00 0.00 2.69
1934 1940 6.721208 TGAAAGGCCTCTCTTGAATTTATTGT 59.279 34.615 5.23 0.00 0.00 2.71
1988 2007 7.572523 ACCGATACATGTTGAAATTGATCAT 57.427 32.000 2.30 0.00 0.00 2.45
1991 2010 7.136772 CGATACATGTTGAAATTGATCATGCT 58.863 34.615 2.30 0.00 39.27 3.79
2204 2223 6.579666 TCTGGATCAAATTTAGGCATATGC 57.420 37.500 19.79 19.79 41.14 3.14
2365 2391 4.997395 TCACTTCAATAGGCTGAGTTGTTC 59.003 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.370231 ATTTGGTTCCGTGCGGCC 61.370 61.111 5.64 0.00 34.68 6.13
11 12 2.126502 CATTTGGTTCCGTGCGGC 60.127 61.111 5.64 0.00 34.68 6.53
12 13 2.126502 GCATTTGGTTCCGTGCGG 60.127 61.111 3.94 3.94 0.00 5.69
14 15 0.318275 TTTCGCATTTGGTTCCGTGC 60.318 50.000 0.00 0.00 0.00 5.34
15 16 1.268794 TGTTTCGCATTTGGTTCCGTG 60.269 47.619 0.00 0.00 0.00 4.94
99 100 1.122019 GGGCCGTCCAGATAGACCAT 61.122 60.000 0.00 0.00 32.91 3.55
184 185 5.984926 GGATGAGCTCTAGTTCTTTGATGAG 59.015 44.000 16.19 0.00 0.00 2.90
382 383 1.681264 CAAAACCAAAGCCGAACTCCT 59.319 47.619 0.00 0.00 0.00 3.69
457 458 2.839486 TGAAGATCTTCAGCCAACGT 57.161 45.000 30.05 0.00 43.90 3.99
506 507 2.653726 TGTCATCAACAACCTGCTTGT 58.346 42.857 0.00 0.00 45.68 3.16
553 554 8.385898 AGTTTAATTTCTGTTATCACCGAACA 57.614 30.769 0.00 0.00 35.55 3.18
583 584 9.874205 AATGAAATTACATGTAAAATCCACAGG 57.126 29.630 21.57 0.00 32.46 4.00
639 640 4.818546 AGTGCATGCTTAGCTAAACTATGG 59.181 41.667 20.33 5.48 0.00 2.74
830 831 1.715585 GTGGTGCCGTGATCGATTG 59.284 57.895 0.00 0.00 39.71 2.67
1030 1036 2.586079 CTCCCGCATCGACGCAAT 60.586 61.111 3.68 0.00 0.00 3.56
1467 1473 5.392767 AAATACGAAGAAGTCTGAGCAGA 57.607 39.130 0.00 0.00 34.56 4.26
1498 1504 5.681880 ACGAAATAAAATCACGCGAAGAAA 58.318 33.333 15.93 0.00 0.00 2.52
1541 1547 0.249031 AAGCACAAAACAGAAGCGCC 60.249 50.000 2.29 0.00 0.00 6.53
1604 1610 8.585471 ATCCATTAATCCATAATCACACCATC 57.415 34.615 0.00 0.00 31.69 3.51
1715 1721 8.965819 TGTATTAACATGAATGCATAAACTGGT 58.034 29.630 0.00 0.00 32.27 4.00
1772 1778 8.997323 GTGCTAGCATCAGAAATTATAAGATGT 58.003 33.333 22.51 4.16 38.59 3.06
1861 1867 3.395941 ACTGAAACAAGAATGACCCTCCT 59.604 43.478 0.00 0.00 0.00 3.69
1912 1918 6.151817 GTGACAATAAATTCAAGAGAGGCCTT 59.848 38.462 6.77 0.00 0.00 4.35
2204 2223 4.524316 AGATTATAGCTCTGCTGCTCTG 57.476 45.455 0.00 0.00 42.97 3.35
2340 2366 4.202357 ACAACTCAGCCTATTGAAGTGACA 60.202 41.667 0.00 0.00 0.00 3.58
2395 2421 8.569641 GTTTCTGAGTAGACTGAACTCTTCTAA 58.430 37.037 6.88 0.00 43.13 2.10
2396 2422 7.940137 AGTTTCTGAGTAGACTGAACTCTTCTA 59.060 37.037 6.88 0.00 43.13 2.10
2397 2423 6.775629 AGTTTCTGAGTAGACTGAACTCTTCT 59.224 38.462 6.88 0.00 43.13 2.85
2398 2424 6.977213 AGTTTCTGAGTAGACTGAACTCTTC 58.023 40.000 6.88 0.00 43.13 2.87
2399 2425 6.969993 AGTTTCTGAGTAGACTGAACTCTT 57.030 37.500 6.88 0.00 43.13 2.85


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

AutoCloner maintained by Alex Coulton.