Multiple sequence alignment - TraesCS2A01G435400

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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 TraesCS2A01G435400 chr2A 100.000 4535 0 0 1 4535 687312093 687316627 0.000000e+00 8375.0
1 TraesCS2A01G435400 chr2D 98.243 3757 32 6 1 3748 545729921 545726190 0.000000e+00 6541.0
2 TraesCS2A01G435400 chr2D 88.974 3011 277 37 771 3748 584234607 584237595 0.000000e+00 3670.0
3 TraesCS2A01G435400 chr2D 83.597 2085 244 42 1720 3753 580971426 580973463 0.000000e+00 1866.0
4 TraesCS2A01G435400 chr2D 93.936 808 9 7 3747 4535 545726108 545725322 0.000000e+00 1184.0
5 TraesCS2A01G435400 chr2D 87.621 929 105 6 791 1710 580970459 580971386 0.000000e+00 1070.0
6 TraesCS2A01G435400 chr2D 75.860 1802 291 58 1197 2938 582503815 582502098 0.000000e+00 785.0
7 TraesCS2A01G435400 chr2D 77.550 1412 232 50 2159 3514 435926301 435927683 0.000000e+00 773.0
8 TraesCS2A01G435400 chr2D 85.026 768 59 17 1 754 584233911 584234636 0.000000e+00 730.0
9 TraesCS2A01G435400 chr2D 75.289 1125 201 37 870 1952 435925008 435926097 2.470000e-127 466.0
10 TraesCS2A01G435400 chr2D 87.200 125 9 7 621 745 580970365 580970482 7.910000e-28 135.0
11 TraesCS2A01G435400 chr2D 80.864 162 22 7 4378 4535 558178681 558178525 7.970000e-23 119.0
12 TraesCS2A01G435400 chr2D 90.789 76 7 0 2093 2168 580971841 580971916 8.030000e-18 102.0
13 TraesCS2A01G435400 chr2B 89.103 3010 284 30 771 3748 703349852 703352849 0.000000e+00 3701.0
14 TraesCS2A01G435400 chr2B 85.680 1683 187 21 2094 3753 700206949 700208600 0.000000e+00 1724.0
15 TraesCS2A01G435400 chr2B 77.129 2619 417 93 979 3509 701503285 701500761 0.000000e+00 1351.0
16 TraesCS2A01G435400 chr2B 87.083 929 110 6 791 1710 700205575 700206502 0.000000e+00 1042.0
17 TraesCS2A01G435400 chr2B 77.605 1411 232 53 2159 3514 515049332 515047951 0.000000e+00 778.0
18 TraesCS2A01G435400 chr2B 85.696 769 60 22 1 754 703349148 703349881 0.000000e+00 765.0
19 TraesCS2A01G435400 chr2B 75.567 1146 203 38 870 1973 515050646 515049536 1.130000e-135 494.0
20 TraesCS2A01G435400 chr2B 81.137 387 40 15 1 357 700204974 700205357 3.450000e-71 279.0
21 TraesCS2A01G435400 chr2B 86.486 111 11 2 4416 4523 5831692 5831801 7.970000e-23 119.0
22 TraesCS2A01G435400 chr4A 73.560 677 136 26 2537 3178 603749273 603748605 7.640000e-53 219.0
23 TraesCS2A01G435400 chr1A 83.168 101 17 0 4378 4478 5772468 5772568 4.830000e-15 93.5


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 TraesCS2A01G435400 chr2A 687312093 687316627 4534 False 8375.00 8375 100.000000 1 4535 1 chr2A.!!$F1 4534
1 TraesCS2A01G435400 chr2D 545725322 545729921 4599 True 3862.50 6541 96.089500 1 4535 2 chr2D.!!$R3 4534
2 TraesCS2A01G435400 chr2D 584233911 584237595 3684 False 2200.00 3670 87.000000 1 3748 2 chr2D.!!$F3 3747
3 TraesCS2A01G435400 chr2D 580970365 580973463 3098 False 793.25 1866 87.301750 621 3753 4 chr2D.!!$F2 3132
4 TraesCS2A01G435400 chr2D 582502098 582503815 1717 True 785.00 785 75.860000 1197 2938 1 chr2D.!!$R2 1741
5 TraesCS2A01G435400 chr2D 435925008 435927683 2675 False 619.50 773 76.419500 870 3514 2 chr2D.!!$F1 2644
6 TraesCS2A01G435400 chr2B 703349148 703352849 3701 False 2233.00 3701 87.399500 1 3748 2 chr2B.!!$F3 3747
7 TraesCS2A01G435400 chr2B 701500761 701503285 2524 True 1351.00 1351 77.129000 979 3509 1 chr2B.!!$R1 2530
8 TraesCS2A01G435400 chr2B 700204974 700208600 3626 False 1015.00 1724 84.633333 1 3753 3 chr2B.!!$F2 3752
9 TraesCS2A01G435400 chr2B 515047951 515050646 2695 True 636.00 778 76.586000 870 3514 2 chr2B.!!$R2 2644
10 TraesCS2A01G435400 chr4A 603748605 603749273 668 True 219.00 219 73.560000 2537 3178 1 chr4A.!!$R1 641

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
447 502 3.281727 TTATAGCCCTTTGTGCTGGAG 57.718 47.619 0.00 0.00 39.91 3.86 F
1020 1113 9.234827 GGTGATATGGATGAATCAATTGATGTA 57.765 33.333 21.39 13.49 34.06 2.29 F
1816 1960 0.917259 CGACGTAGAAGTGCTGATGC 59.083 55.000 0.00 0.00 40.20 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1342 3.758554 ACGCTGAGCCATTTTAGACAAAT 59.241 39.130 0.00 0.0 0.00 2.32 R
2770 3096 0.971386 TCCCGGGTGTCACTAACTTC 59.029 55.000 22.86 0.0 0.00 3.01 R
3756 4237 1.003003 AGCACAGCTTCCTTTCCTCTC 59.997 52.381 0.00 0.0 33.89 3.20 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
447 502 3.281727 TTATAGCCCTTTGTGCTGGAG 57.718 47.619 0.00 0.00 39.91 3.86
1020 1113 9.234827 GGTGATATGGATGAATCAATTGATGTA 57.765 33.333 21.39 13.49 34.06 2.29
1249 1342 4.019411 TCAAGGATGCACACAAGGATCTAA 60.019 41.667 0.00 0.00 36.68 2.10
1801 1945 1.712401 TACCAAATTCGAACCCGACG 58.288 50.000 0.00 0.00 45.50 5.12
1816 1960 0.917259 CGACGTAGAAGTGCTGATGC 59.083 55.000 0.00 0.00 40.20 3.91
1954 2158 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1955 2159 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1956 2160 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1957 2161 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1958 2162 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1959 2163 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1960 2164 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1961 2165 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1962 2166 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1963 2167 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1964 2168 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1965 2169 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1966 2170 9.898152 AAGAAGAAGAAGAAGAAGAAGAAGAAA 57.102 29.630 0.00 0.00 0.00 2.52
1967 2171 9.898152 AGAAGAAGAAGAAGAAGAAGAAGAAAA 57.102 29.630 0.00 0.00 0.00 2.29
2632 2940 5.065731 GGTTATGGAGAAGATGCAAAGTCAG 59.934 44.000 0.00 0.00 30.55 3.51
2770 3096 4.778534 AAAGCATTGAGTGAGATTGTGG 57.221 40.909 0.00 0.00 0.00 4.17
3856 4337 2.624674 GAAGTGTGTGGGCTGTGGGT 62.625 60.000 0.00 0.00 0.00 4.51
4040 4521 6.384015 TCAGTTTATGGACACTGAGGATACAT 59.616 38.462 0.00 0.00 43.63 2.29
4041 4522 6.481313 CAGTTTATGGACACTGAGGATACATG 59.519 42.308 0.00 0.00 42.74 3.21
4058 4539 6.038603 GGATACATGTGCAACTGTATGATGTT 59.961 38.462 21.08 3.59 39.51 2.71
4162 4643 2.031163 GTGCGGGCTCACTTCTGT 59.969 61.111 3.77 0.00 34.29 3.41
4301 4782 1.277842 TGGGTAGCATTTTCTCTCGCA 59.722 47.619 0.00 0.00 0.00 5.10
4305 4805 0.801251 AGCATTTTCTCTCGCAGTGC 59.199 50.000 4.58 4.58 0.00 4.40
4420 4920 3.684788 CCTCAACTATACAACAGCCACAC 59.315 47.826 0.00 0.00 0.00 3.82
4431 4931 0.669619 CAGCCACACATGCAGTTTCA 59.330 50.000 0.00 0.00 0.00 2.69
4449 4949 7.649306 GCAGTTTCATAACTTTGATTCACTTGT 59.351 33.333 0.00 0.00 41.85 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
447 502 2.995939 GGAGCAAATTTACAGCAAAGCC 59.004 45.455 2.29 0.00 0.00 4.35
1020 1113 3.353557 AGCATGTGTGAGAGCATCATTT 58.646 40.909 0.00 0.00 40.92 2.32
1249 1342 3.758554 ACGCTGAGCCATTTTAGACAAAT 59.241 39.130 0.00 0.00 0.00 2.32
1801 1945 5.041287 TGTAATACGCATCAGCACTTCTAC 58.959 41.667 0.00 0.00 42.27 2.59
1816 1960 6.020440 CCATTCAAAGCTTGCATTGTAATACG 60.020 38.462 0.00 0.00 0.00 3.06
1980 2184 8.423906 AGAGAAGACCAGTAAAGTAAGATTCA 57.576 34.615 0.00 0.00 0.00 2.57
2000 2207 5.488919 AGAAGTGGGACCAATGAATAGAGAA 59.511 40.000 0.00 0.00 0.00 2.87
2480 2788 7.175119 CCTCATTTCTCATGATTCTATGTGCAT 59.825 37.037 0.00 0.00 0.00 3.96
2632 2940 5.452078 TCACATGAATTTGACTTTGACCC 57.548 39.130 0.00 0.00 0.00 4.46
2770 3096 0.971386 TCCCGGGTGTCACTAACTTC 59.029 55.000 22.86 0.00 0.00 3.01
3755 4236 1.948144 GCACAGCTTCCTTTCCTCTCC 60.948 57.143 0.00 0.00 0.00 3.71
3756 4237 1.003003 AGCACAGCTTCCTTTCCTCTC 59.997 52.381 0.00 0.00 33.89 3.20
3856 4337 9.349713 AGGATAAATGAAGTTTACAACAGACAA 57.650 29.630 0.00 0.00 35.23 3.18
3897 4378 8.289440 CAGTGAACGTACTGTGTTAATCTTAA 57.711 34.615 9.84 0.00 42.38 1.85
3898 4379 7.862741 CAGTGAACGTACTGTGTTAATCTTA 57.137 36.000 9.84 0.00 42.38 2.10
3899 4380 6.764877 CAGTGAACGTACTGTGTTAATCTT 57.235 37.500 9.84 0.00 42.38 2.40
3910 4391 4.008330 TCTAAGCTAGCAGTGAACGTACT 58.992 43.478 18.83 0.00 0.00 2.73
3911 4392 4.352600 TCTAAGCTAGCAGTGAACGTAC 57.647 45.455 18.83 0.00 0.00 3.67
3912 4393 4.638865 TGATCTAAGCTAGCAGTGAACGTA 59.361 41.667 18.83 0.00 0.00 3.57
3913 4394 3.444034 TGATCTAAGCTAGCAGTGAACGT 59.556 43.478 18.83 0.00 0.00 3.99
3914 4395 4.033990 TGATCTAAGCTAGCAGTGAACG 57.966 45.455 18.83 0.00 0.00 3.95
3915 4396 5.691305 CAGATGATCTAAGCTAGCAGTGAAC 59.309 44.000 18.83 10.28 0.00 3.18
3974 4455 1.804151 GTAAGTCGCATGCAAGAACCA 59.196 47.619 19.57 0.00 0.00 3.67
4162 4643 4.253685 CCAAGAGAAATCTACTTTCGGCA 58.746 43.478 0.00 0.00 46.53 5.69
4301 4782 2.368548 TGACTACATTCACTGGTGCACT 59.631 45.455 17.98 0.00 0.00 4.40
4305 4805 3.329386 CAGGTGACTACATTCACTGGTG 58.671 50.000 3.44 0.00 44.63 4.17
4420 4920 7.811236 AGTGAATCAAAGTTATGAAACTGCATG 59.189 33.333 0.00 0.00 45.37 4.06
4449 4949 3.264947 CTTGACCATCGCAGATCTCAAA 58.735 45.455 0.00 0.00 45.12 2.69


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

AutoCloner maintained by Alex Coulton.