Multiple sequence alignment - TraesCS4A01G285500

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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 TraesCS4A01G285500 chr4A 100.000 2970 0 0 1 2970 591673857 591676826 0 5485
1 TraesCS4A01G285500 chr4A 97.308 2972 77 3 1 2970 591346352 591349322 0 5042
2 TraesCS4A01G285500 chr4A 97.274 2971 78 3 1 2970 591292587 591295555 0 5035
3 TraesCS4A01G285500 chr4A 97.274 2971 76 4 1 2970 591415871 591418837 0 5033
4 TraesCS4A01G285500 chr4A 96.938 2972 88 3 1 2970 592363091 592360121 0 4981
5 TraesCS4A01G285500 chr4A 96.809 2977 87 3 1 2970 592336769 592333794 0 4964
6 TraesCS4A01G285500 chr4A 97.538 2031 49 1 1 2031 592928423 592926394 0 3472
7 TraesCS4A01G285500 chr4A 97.371 1940 50 1 1 1940 592310812 592308874 0 3299
8 TraesCS4A01G285500 chr4A 97.010 1940 57 1 1 1940 591285563 591283625 0 3260
9 TraesCS4A01G285500 chr4A 97.609 1380 33 0 1 1380 592639039 592637660 0 2366
10 TraesCS4A01G285500 chr4A 97.076 1402 39 2 1570 2970 592926382 592924982 0 2361
11 TraesCS4A01G285500 chr4A 97.249 945 25 1 2027 2970 592636718 592635774 0 1600
12 TraesCS4A01G285500 chr4A 96.723 946 30 1 2026 2970 592308466 592307521 0 1574
13 TraesCS4A01G285500 chr4A 97.005 935 27 1 2037 2970 591283300 591282366 0 1570
14 TraesCS4A01G285500 chr4D 91.349 1572 113 11 436 1989 10828589 10830155 0 2128


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 TraesCS4A01G285500 chr4A 591673857 591676826 2969 False 5485.0 5485 100.0000 1 2970 1 chr4A.!!$F4 2969
1 TraesCS4A01G285500 chr4A 591346352 591349322 2970 False 5042.0 5042 97.3080 1 2970 1 chr4A.!!$F2 2969
2 TraesCS4A01G285500 chr4A 591292587 591295555 2968 False 5035.0 5035 97.2740 1 2970 1 chr4A.!!$F1 2969
3 TraesCS4A01G285500 chr4A 591415871 591418837 2966 False 5033.0 5033 97.2740 1 2970 1 chr4A.!!$F3 2969
4 TraesCS4A01G285500 chr4A 592360121 592363091 2970 True 4981.0 4981 96.9380 1 2970 1 chr4A.!!$R2 2969
5 TraesCS4A01G285500 chr4A 592333794 592336769 2975 True 4964.0 4964 96.8090 1 2970 1 chr4A.!!$R1 2969
6 TraesCS4A01G285500 chr4A 592924982 592928423 3441 True 2916.5 3472 97.3070 1 2970 2 chr4A.!!$R6 2969
7 TraesCS4A01G285500 chr4A 592307521 592310812 3291 True 2436.5 3299 97.0470 1 2970 2 chr4A.!!$R4 2969
8 TraesCS4A01G285500 chr4A 591282366 591285563 3197 True 2415.0 3260 97.0075 1 2970 2 chr4A.!!$R3 2969
9 TraesCS4A01G285500 chr4A 592635774 592639039 3265 True 1983.0 2366 97.4290 1 2970 2 chr4A.!!$R5 2969
10 TraesCS4A01G285500 chr4D 10828589 10830155 1566 False 2128.0 2128 91.3490 436 1989 1 chr4D.!!$F1 1553

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
71 73 1.005294 GTTCGTCGGCGCTAGTTTCA 61.005 55.0 3.52 0.0 38.14 2.69 F
938 953 1.568504 TTGGGTGCGGTAATCTCTCT 58.431 50.0 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1314 0.747255 GACCAGCTGCCGAAGATCTA 59.253 55.0 8.66 0.0 0.00 1.98 R
2528 3026 0.592637 CTTGCCGTGTCATCTTGCAA 59.407 50.0 0.00 0.0 39.42 4.08 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
71 73 1.005294 GTTCGTCGGCGCTAGTTTCA 61.005 55.000 3.52 0.00 38.14 2.69
132 134 2.329614 CCGATTTTTGGGCGTCGGT 61.330 57.895 4.60 0.00 46.29 4.69
434 436 7.445121 AGCAATGATCGAGATTCATACCTAAA 58.555 34.615 0.59 0.00 0.00 1.85
527 529 5.649395 CCTTAAGAAAGGCTCATCATTCACA 59.351 40.000 3.36 0.00 45.78 3.58
702 709 7.916077 ACATCCTAACTAAGTAACTATGCCT 57.084 36.000 0.00 0.00 0.00 4.75
924 939 2.359249 GGAGGGGATTGCTAATTTGGGT 60.359 50.000 0.00 0.00 0.00 4.51
938 953 1.568504 TTGGGTGCGGTAATCTCTCT 58.431 50.000 0.00 0.00 0.00 3.10
1000 1015 5.643421 ATTAAGCTCCTTCATCCTCACAT 57.357 39.130 0.00 0.00 0.00 3.21
1085 1100 2.664851 GCGGTGCAGCAGTGTACA 60.665 61.111 17.33 0.00 40.85 2.90
1498 1513 0.329596 GGCATCCTGAAGGTCCACTT 59.670 55.000 0.00 0.00 43.65 3.16
1568 1583 2.509336 CAGATCGACGCCGCCTTT 60.509 61.111 0.00 0.00 35.37 3.11
1740 1755 1.349259 CTACGCCACGTTTCTTCCCG 61.349 60.000 0.00 0.00 41.54 5.14
1881 1905 5.003804 TCTGAGCTCATCACGCATATACTA 58.996 41.667 18.63 0.00 33.22 1.82
2023 2519 3.171705 GAGCATCTCTAGCCGTTCG 57.828 57.895 0.00 0.00 0.00 3.95
2024 2520 0.318275 GAGCATCTCTAGCCGTTCGG 60.318 60.000 6.90 6.90 0.00 4.30
2150 2648 0.966179 GATTTTGGCCCACTTTCGGT 59.034 50.000 0.00 0.00 0.00 4.69
2366 2864 0.951558 GCTCCACCAAATCGTGTTGT 59.048 50.000 0.00 0.00 31.47 3.32
2367 2865 1.334960 GCTCCACCAAATCGTGTTGTG 60.335 52.381 0.00 0.00 31.47 3.33
2506 3004 1.876156 GTCAAACACTGGCTCTTCCTG 59.124 52.381 0.00 0.00 39.46 3.86
2528 3026 3.311871 GCTCGCTCTCAATGATCATGTTT 59.688 43.478 9.46 0.00 0.00 2.83
2800 3298 2.827921 GCCCATTGACCTTGAAGTTCAT 59.172 45.455 6.36 0.00 0.00 2.57
2840 3338 4.699257 TCAACAAGCTTGGCAAAAACATTT 59.301 33.333 29.18 8.45 0.00 2.32
2841 3339 4.880886 ACAAGCTTGGCAAAAACATTTC 57.119 36.364 29.18 0.00 0.00 2.17
2855 3353 2.849942 ACATTTCAGCACTGCAGTACA 58.150 42.857 21.20 0.00 0.00 2.90
2922 3420 1.672356 CAGAGGTCCTGTTTGGCCG 60.672 63.158 0.00 0.00 38.10 6.13
2942 3440 2.361789 GCCGCCTCAAATACCAAACTA 58.638 47.619 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 436 1.608590 CTTGCGTGGAACAAATCAGGT 59.391 47.619 0.00 0.00 44.16 4.00
527 529 2.613474 GCAAACATGATGTTGTGGCCAT 60.613 45.455 9.72 0.00 40.14 4.40
702 709 2.558800 GCCCACCCCTTAAAAATCAGGA 60.559 50.000 0.00 0.00 30.81 3.86
924 939 1.686325 GGCCCAGAGAGATTACCGCA 61.686 60.000 0.00 0.00 0.00 5.69
938 953 4.680237 CGCACGTTGAGAGGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
1000 1015 0.532573 GAGGAGAGATTGTGGTGCGA 59.467 55.000 0.00 0.00 0.00 5.10
1299 1314 0.747255 GACCAGCTGCCGAAGATCTA 59.253 55.000 8.66 0.00 0.00 1.98
1400 1415 1.076727 GGTAGCACCCTGGGCTTTT 59.923 57.895 14.08 0.00 42.62 2.27
1498 1513 1.192146 CCCCTTGACTTCCTCACCGA 61.192 60.000 0.00 0.00 0.00 4.69
1568 1583 2.032528 GTGGTGGCTGCAGTGCTA 59.967 61.111 17.60 0.00 0.00 3.49
1881 1905 9.736023 CACGTACACATATGCATATCTACATAT 57.264 33.333 16.46 0.00 39.49 1.78
1971 1995 4.889856 TCGATCGCCGGTGCATGG 62.890 66.667 11.05 6.62 39.14 3.66
2150 2648 1.342819 CCAAAATTGGGCCGACTTTCA 59.657 47.619 3.57 0.00 44.70 2.69
2366 2864 1.887854 CCACATGTGCATCAAGAACCA 59.112 47.619 20.81 0.00 0.00 3.67
2367 2865 1.203052 CCCACATGTGCATCAAGAACC 59.797 52.381 20.81 0.00 0.00 3.62
2506 3004 2.481854 ACATGATCATTGAGAGCGAGC 58.518 47.619 5.16 0.00 34.70 5.03
2528 3026 0.592637 CTTGCCGTGTCATCTTGCAA 59.407 50.000 0.00 0.00 39.42 4.08
2800 3298 0.614697 TGAAGGTCATGCTCCTCCGA 60.615 55.000 9.18 0.00 33.76 4.55
2840 3338 2.837532 TCAATGTACTGCAGTGCTGA 57.162 45.000 30.93 24.51 42.34 4.26
2841 3339 2.745821 ACATCAATGTACTGCAGTGCTG 59.254 45.455 30.93 22.86 42.68 4.41
2855 3353 4.703575 CCAGGAACTCACAATGACATCAAT 59.296 41.667 0.00 0.00 34.60 2.57
2922 3420 1.173913 AGTTTGGTATTTGAGGCGGC 58.826 50.000 0.00 0.00 0.00 6.53
2932 3430 5.010282 CCAAAGGAGCTTGTAGTTTGGTAT 58.990 41.667 13.79 0.00 41.45 2.73
2942 3440 1.777272 AGAGGTTCCAAAGGAGCTTGT 59.223 47.619 0.00 0.00 33.37 3.16


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

AutoCloner maintained by Alex Coulton.