Multiple sequence alignment - TraesCS2A01G240400

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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 TraesCS2A01G240400 chr2A 100.000 2694 0 0 1 2694 335805874 335803181 0 4975
1 TraesCS2A01G240400 chr2A 97.774 2695 59 1 1 2694 335822606 335819912 0 4643
2 TraesCS2A01G240400 chr2A 97.716 1751 39 1 945 2694 726905314 726903564 0 3011
3 TraesCS2A01G240400 chr2A 99.031 929 9 0 1 929 726901700 726900772 0 1666
4 TraesCS2A01G240400 chr2A 98.708 929 12 0 1 929 651438664 651439592 0 1650
5 TraesCS2A01G240400 chr3A 97.716 1751 39 1 945 2694 66003992 66002242 0 3011
6 TraesCS2A01G240400 chr3A 98.924 929 10 0 1 929 66000725 65999797 0 1661
7 TraesCS2A01G240400 chr5D 97.544 1751 41 2 945 2694 503263635 503261886 0 2994
8 TraesCS2A01G240400 chr5D 97.430 1751 43 2 945 2694 503246413 503248162 0 2983
9 TraesCS2A01G240400 chr5D 98.708 929 12 0 1 929 503260022 503259094 0 1650
10 TraesCS2A01G240400 chr2D 97.430 1751 44 1 945 2694 272811105 272809355 0 2983
11 TraesCS2A01G240400 chr2D 97.259 1751 47 1 945 2694 591985750 591987500 0 2966
12 TraesCS2A01G240400 chr3D 97.202 1751 47 2 945 2694 589262385 589260636 0 2961
13 TraesCS2A01G240400 chr1A 97.202 1751 48 1 945 2694 532074832 532076582 0 2961
14 TraesCS2A01G240400 chr7B 98.924 929 10 0 1 929 622433215 622432287 0 1661
15 TraesCS2A01G240400 chr3B 98.924 929 10 0 1 929 201548055 201548983 0 1661
16 TraesCS2A01G240400 chr3B 98.924 929 10 0 1 929 201570032 201569104 0 1661
17 TraesCS2A01G240400 chr3B 98.924 929 10 0 1 929 813249123 813250051 0 1661


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 TraesCS2A01G240400 chr2A 335803181 335805874 2693 True 4975.0 4975 100.0000 1 2694 1 chr2A.!!$R1 2693
1 TraesCS2A01G240400 chr2A 335819912 335822606 2694 True 4643.0 4643 97.7740 1 2694 1 chr2A.!!$R2 2693
2 TraesCS2A01G240400 chr2A 726900772 726905314 4542 True 2338.5 3011 98.3735 1 2694 2 chr2A.!!$R3 2693
3 TraesCS2A01G240400 chr2A 651438664 651439592 928 False 1650.0 1650 98.7080 1 929 1 chr2A.!!$F1 928
4 TraesCS2A01G240400 chr3A 65999797 66003992 4195 True 2336.0 3011 98.3200 1 2694 2 chr3A.!!$R1 2693
5 TraesCS2A01G240400 chr5D 503246413 503248162 1749 False 2983.0 2983 97.4300 945 2694 1 chr5D.!!$F1 1749
6 TraesCS2A01G240400 chr5D 503259094 503263635 4541 True 2322.0 2994 98.1260 1 2694 2 chr5D.!!$R1 2693
7 TraesCS2A01G240400 chr2D 272809355 272811105 1750 True 2983.0 2983 97.4300 945 2694 1 chr2D.!!$R1 1749
8 TraesCS2A01G240400 chr2D 591985750 591987500 1750 False 2966.0 2966 97.2590 945 2694 1 chr2D.!!$F1 1749
9 TraesCS2A01G240400 chr3D 589260636 589262385 1749 True 2961.0 2961 97.2020 945 2694 1 chr3D.!!$R1 1749
10 TraesCS2A01G240400 chr1A 532074832 532076582 1750 False 2961.0 2961 97.2020 945 2694 1 chr1A.!!$F1 1749
11 TraesCS2A01G240400 chr7B 622432287 622433215 928 True 1661.0 1661 98.9240 1 929 1 chr7B.!!$R1 928
12 TraesCS2A01G240400 chr3B 201548055 201548983 928 False 1661.0 1661 98.9240 1 929 1 chr3B.!!$F1 928
13 TraesCS2A01G240400 chr3B 201569104 201570032 928 True 1661.0 1661 98.9240 1 929 1 chr3B.!!$R1 928
14 TraesCS2A01G240400 chr3B 813249123 813250051 928 False 1661.0 1661 98.9240 1 929 1 chr3B.!!$F2 928

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
186 187 0.602905 CCCACTTCACACCTCGGAAC 60.603 60.0 0.0 0.0 0.0 3.62 F
539 540 1.006832 CAAGGATAGCGAACGGGTTG 58.993 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1223 0.896226 GCTACACCCTTCCTCGTCTT 59.104 55.0 0.00 0.0 0.00 3.01 R
2529 2531 0.324943 CCTCCATGGACGAACCTTGT 59.675 55.0 11.44 0.0 40.75 3.16 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
57 58 5.008415 AGCTCGATGCCAGAATGATAAAAAG 59.992 40.000 3.66 0.00 44.23 2.27
186 187 0.602905 CCCACTTCACACCTCGGAAC 60.603 60.000 0.00 0.00 0.00 3.62
436 437 3.592059 AGCGGACGTAAAGCTATTGAAA 58.408 40.909 9.71 0.00 39.74 2.69
539 540 1.006832 CAAGGATAGCGAACGGGTTG 58.993 55.000 0.00 0.00 0.00 3.77
553 554 1.875488 GGGTTGCCTACTCCTAAGGA 58.125 55.000 0.00 0.00 36.08 3.36
574 575 5.105187 AGGATCAAAGCAAGCCCTTTAATTC 60.105 40.000 0.00 0.00 33.50 2.17
663 664 3.930634 ACCTACGACCAGTCAGTTAAC 57.069 47.619 0.00 0.00 0.00 2.01
666 667 2.150397 ACGACCAGTCAGTTAACAGC 57.850 50.000 8.61 0.00 0.00 4.40
685 686 2.649034 GACCGCTCGACCACTGAA 59.351 61.111 0.00 0.00 0.00 3.02
687 688 2.432628 CCGCTCGACCACTGAACC 60.433 66.667 0.00 0.00 0.00 3.62
791 792 8.488651 TCTTTCGTAACTCCCATAATTTCTTC 57.511 34.615 0.00 0.00 0.00 2.87
808 809 2.202570 CGTAGTGGCTCCGTTCCG 60.203 66.667 0.00 0.00 0.00 4.30
1019 1020 1.251527 ATGTCAGCGGTTCGAGTCCT 61.252 55.000 7.05 0.00 0.00 3.85
1085 1086 2.547634 GCACCAAATTTTGCCAATTCGT 59.452 40.909 3.50 0.00 32.21 3.85
1201 1202 3.636764 GGTTCAAAAGAGGAAAGGCTTGA 59.363 43.478 0.00 0.00 0.00 3.02
1222 1223 1.209621 GTGGATACCTAGGCACCCAA 58.790 55.000 9.30 0.00 0.00 4.12
1236 1237 0.767060 ACCCAAAGACGAGGAAGGGT 60.767 55.000 6.79 6.79 44.40 4.34
1254 1255 2.264813 GGTGTAGCAAGCGACGAAATA 58.735 47.619 0.00 0.00 0.00 1.40
1505 1506 2.664851 CGAAGCGGTTGAGTGCCA 60.665 61.111 3.70 0.00 0.00 4.92
1562 1563 1.472878 CACTAGCTTACGCTCTGACCA 59.527 52.381 0.00 0.00 45.15 4.02
1791 1792 3.917760 GCCGGCGACTCATAGGCT 61.918 66.667 12.58 0.00 44.06 4.58
1830 1831 2.924101 AACCCACCGGAGCCGTAA 60.924 61.111 9.46 0.00 37.81 3.18
1905 1906 5.026121 GGTGATCTATCCATGACCAGGATA 58.974 45.833 0.00 0.00 43.90 2.59
1938 1939 1.926108 ACTAAGCAGAGGTCCGAACT 58.074 50.000 0.00 0.00 0.00 3.01
2250 2252 2.094182 TGACCGCTCAGTGATAAAGGAC 60.094 50.000 0.00 0.00 0.00 3.85
2543 2545 0.324943 CCTCCACAAGGTTCGTCCAT 59.675 55.000 2.77 0.00 40.67 3.41
2630 2633 3.778629 CCTGTACTACCCCTTGTTGGTAT 59.221 47.826 0.00 0.00 37.70 2.73
2643 2646 1.335132 TTGGTATGGAGGGACGGAGC 61.335 60.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.427245 CGCAGGACCTCCCCTACAG 61.427 68.421 0.00 0.00 34.07 2.74
57 58 9.181805 GAAAAAGTCAAATAAGAGGTGTTAAGC 57.818 33.333 0.00 0.00 0.00 3.09
186 187 5.746245 CCTTTCTCTCTATAAGAACAGTGCG 59.254 44.000 0.00 0.00 32.64 5.34
275 276 1.267574 CCTCTGAGCTACAGGCCCAA 61.268 60.000 0.00 0.00 45.76 4.12
436 437 6.316390 CGACAAAAGGAAAGAGCATACCTAAT 59.684 38.462 0.00 0.00 32.06 1.73
539 540 3.134804 TGCTTTGATCCTTAGGAGTAGGC 59.865 47.826 7.19 7.10 34.05 3.93
553 554 5.743636 TGAATTAAAGGGCTTGCTTTGAT 57.256 34.783 0.00 0.00 0.00 2.57
666 667 4.778415 CAGTGGTCGAGCGGTCGG 62.778 72.222 33.60 17.17 46.80 4.79
676 677 1.048601 TCCTCAGTGGTTCAGTGGTC 58.951 55.000 3.31 0.00 35.69 4.02
685 686 1.427072 CCCCCTTGTTCCTCAGTGGT 61.427 60.000 0.00 0.00 37.07 4.16
808 809 2.620585 GCTTCCCTATGAAATGAGGCAC 59.379 50.000 0.00 0.00 31.06 5.01
972 973 1.447314 GGTAAACCACCGCCTCTCG 60.447 63.158 0.00 0.00 37.63 4.04
1019 1020 1.480954 GTTCACGGGCTGGAGATAAGA 59.519 52.381 0.00 0.00 0.00 2.10
1085 1086 7.981225 TGAATGTGAAATCATAGATCGAACTGA 59.019 33.333 5.31 0.00 0.00 3.41
1222 1223 0.896226 GCTACACCCTTCCTCGTCTT 59.104 55.000 0.00 0.00 0.00 3.01
1236 1237 3.226346 AGTATTTCGTCGCTTGCTACA 57.774 42.857 0.00 0.00 0.00 2.74
1254 1255 3.254903 GCTTATTTTCAACACCCCGAAGT 59.745 43.478 0.00 0.00 0.00 3.01
1562 1563 1.990060 ACGTGCCCCATGCTACTCT 60.990 57.895 0.00 0.00 42.00 3.24
1791 1792 1.816183 CGTTCCCTTAACCAAGCCACA 60.816 52.381 0.00 0.00 34.33 4.17
1830 1831 3.737355 GCCCTATTAAGACTCGCTTTCGT 60.737 47.826 0.00 0.00 38.05 3.85
1938 1939 3.681417 CGCTGATTCTTCAACATCAGTCA 59.319 43.478 10.14 0.00 45.69 3.41
2047 2048 4.202161 ACAGTGCTTTATCCCTAGATGTCG 60.202 45.833 0.00 0.00 33.67 4.35
2093 2094 3.941483 CAGAGTTTGCCTCGATTTGGTAT 59.059 43.478 0.00 0.00 45.44 2.73
2250 2252 2.203280 TGTCTTTGCACCCCCACG 60.203 61.111 0.00 0.00 0.00 4.94
2272 2274 1.611673 GCTGCTTCTAGGCAAACCTCA 60.612 52.381 0.00 0.00 46.34 3.86
2529 2531 0.324943 CCTCCATGGACGAACCTTGT 59.675 55.000 11.44 0.00 40.75 3.16
2543 2545 2.607750 GCCCTGACTCACCCTCCA 60.608 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.