Multiple sequence alignment - TraesCS5A01G243200

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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 TraesCS5A01G243200 chr5A 100.000 4480 0 0 1 4480 457899911 457904390 0.000000e+00 8274
1 TraesCS5A01G243200 chr5D 96.995 4492 92 15 1 4479 356200916 356205377 0.000000e+00 7507
2 TraesCS5A01G243200 chr5B 97.563 3118 46 12 1 3103 421181782 421184884 0.000000e+00 5310
3 TraesCS5A01G243200 chr5B 91.001 1389 79 17 3104 4480 421184995 421186349 0.000000e+00 1831
4 TraesCS5A01G243200 chr6D 77.951 898 99 48 3596 4480 38239378 38238567 1.890000e-128 470
5 TraesCS5A01G243200 chr6B 77.753 899 99 51 3596 4480 89142823 89142012 4.080000e-125 459
6 TraesCS5A01G243200 chr4A 85.714 70 10 0 2585 2654 660080547 660080616 1.730000e-09 75


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 TraesCS5A01G243200 chr5A 457899911 457904390 4479 False 8274.0 8274 100.000 1 4480 1 chr5A.!!$F1 4479
1 TraesCS5A01G243200 chr5D 356200916 356205377 4461 False 7507.0 7507 96.995 1 4479 1 chr5D.!!$F1 4478
2 TraesCS5A01G243200 chr5B 421181782 421186349 4567 False 3570.5 5310 94.282 1 4480 2 chr5B.!!$F1 4479
3 TraesCS5A01G243200 chr6D 38238567 38239378 811 True 470.0 470 77.951 3596 4480 1 chr6D.!!$R1 884
4 TraesCS5A01G243200 chr6B 89142012 89142823 811 True 459.0 459 77.753 3596 4480 1 chr6B.!!$R1 884

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
311 312 2.888594 ACAACGTGGATGAGAATACGG 58.111 47.619 0.0 0.0 40.56 4.02 F
1489 1500 1.875514 GATGTTGAGCAGTTGCAGTCA 59.124 47.619 6.9 0.0 45.16 3.41 F
1822 1833 2.358737 GGGGACTTGTGACTGCGG 60.359 66.667 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2159 1.438651 GTTGTAGCCGCTTGATGTCA 58.561 50.000 0.00 0.0 0.00 3.58 R
2657 2674 1.619654 ATGCAAAACTACAGGCAGCA 58.380 45.000 0.00 0.0 39.95 4.41 R
3800 3944 3.324035 GCGGCGGCTATCTCTTTG 58.676 61.111 9.78 0.0 35.83 2.77 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
255 256 5.444983 CATAAGTTCGTCGGATCTAGACAG 58.555 45.833 17.46 11.94 38.46 3.51
311 312 2.888594 ACAACGTGGATGAGAATACGG 58.111 47.619 0.00 0.00 40.56 4.02
486 487 5.512942 TCCCATTTAGGTCAATCAACTCA 57.487 39.130 0.00 0.00 34.66 3.41
834 838 6.656314 ATCATCGCACGTTTAAGTTATTCA 57.344 33.333 0.00 0.00 0.00 2.57
941 945 6.311690 GCTCTACATTAACTTGAGGACTCAAC 59.688 42.308 10.52 0.00 43.90 3.18
997 1001 3.037549 CCTACCCTTGAAGAGAGCAGAT 58.962 50.000 0.00 0.00 0.00 2.90
1017 1021 6.203723 GCAGATATATGGAGACTGGAAAACAC 59.796 42.308 0.00 0.00 0.00 3.32
1023 1027 4.389374 TGGAGACTGGAAAACACATCTTC 58.611 43.478 0.00 0.00 0.00 2.87
1077 1081 3.381590 TCACAATTCTCTCGATCGATGGT 59.618 43.478 19.78 3.87 0.00 3.55
1489 1500 1.875514 GATGTTGAGCAGTTGCAGTCA 59.124 47.619 6.90 0.00 45.16 3.41
1706 1717 7.951530 AATTTTCAATTGACGCTCTTGATTT 57.048 28.000 7.89 0.00 0.00 2.17
1822 1833 2.358737 GGGGACTTGTGACTGCGG 60.359 66.667 0.00 0.00 0.00 5.69
2023 2037 3.573967 GGGTGCATTTGGTAGGATAATGG 59.426 47.826 0.00 0.00 31.54 3.16
2486 2500 9.817809 TTCTATTATCATGTGACAGGTTAAGAC 57.182 33.333 6.85 0.00 0.00 3.01
2494 2511 4.340097 TGTGACAGGTTAAGACGAAGAAGA 59.660 41.667 0.00 0.00 0.00 2.87
2495 2512 5.163488 TGTGACAGGTTAAGACGAAGAAGAA 60.163 40.000 0.00 0.00 0.00 2.52
2496 2513 5.402867 GTGACAGGTTAAGACGAAGAAGAAG 59.597 44.000 0.00 0.00 0.00 2.85
2497 2514 5.301045 TGACAGGTTAAGACGAAGAAGAAGA 59.699 40.000 0.00 0.00 0.00 2.87
2498 2515 6.158023 ACAGGTTAAGACGAAGAAGAAGAA 57.842 37.500 0.00 0.00 0.00 2.52
2499 2516 6.579865 ACAGGTTAAGACGAAGAAGAAGAAA 58.420 36.000 0.00 0.00 0.00 2.52
2657 2674 4.041691 AGCTGCCAATAATCCGGTACTATT 59.958 41.667 0.00 0.42 0.00 1.73
3307 3436 1.375013 CCAAATGGTGCCTGCTTGC 60.375 57.895 0.00 0.00 0.00 4.01
3477 3616 2.475466 CGCCAAGCAAGATCGCCAT 61.475 57.895 0.00 0.00 0.00 4.40
3509 3648 3.607775 CGGTCTCTTTTGTGTCAATGCTG 60.608 47.826 0.00 0.00 0.00 4.41
3550 3690 2.615447 CTGCATGGCATACACCAGTTAG 59.385 50.000 0.00 0.00 44.71 2.34
3563 3703 8.677300 CATACACCAGTTAGCAATTAGTTGATT 58.323 33.333 1.56 0.00 37.53 2.57
3624 3764 3.763057 TGTAGTGAGGCTTACTGACTGA 58.237 45.455 21.00 0.00 43.80 3.41
3800 3944 3.192922 CGGCGGGACATTCGGAAC 61.193 66.667 0.00 0.00 0.00 3.62
3939 4089 2.297701 TGCCTTTTGAAGAAGAACGCT 58.702 42.857 0.00 0.00 0.00 5.07
3940 4090 2.687935 TGCCTTTTGAAGAAGAACGCTT 59.312 40.909 0.00 0.00 36.96 4.68
3941 4091 3.130340 TGCCTTTTGAAGAAGAACGCTTT 59.870 39.130 0.00 0.00 33.61 3.51
3942 4092 4.336993 TGCCTTTTGAAGAAGAACGCTTTA 59.663 37.500 0.00 0.00 33.61 1.85
3943 4093 4.675565 GCCTTTTGAAGAAGAACGCTTTAC 59.324 41.667 0.00 0.00 33.61 2.01
3944 4094 5.212934 CCTTTTGAAGAAGAACGCTTTACC 58.787 41.667 0.00 0.00 33.61 2.85
3945 4095 4.823790 TTTGAAGAAGAACGCTTTACCC 57.176 40.909 0.00 0.00 33.61 3.69
3946 4096 3.478857 TGAAGAAGAACGCTTTACCCA 57.521 42.857 0.00 0.00 33.61 4.51
3947 4097 3.811083 TGAAGAAGAACGCTTTACCCAA 58.189 40.909 0.00 0.00 33.61 4.12
3948 4098 3.562557 TGAAGAAGAACGCTTTACCCAAC 59.437 43.478 0.00 0.00 33.61 3.77
3949 4099 2.140717 AGAAGAACGCTTTACCCAACG 58.859 47.619 0.00 0.00 33.61 4.10
3950 4100 0.589708 AAGAACGCTTTACCCAACGC 59.410 50.000 0.00 0.00 0.00 4.84
3967 4117 5.337491 CCCAACGCTTTACCCTTTAGTACTA 60.337 44.000 0.00 0.00 0.00 1.82
4078 4231 2.663063 GCGCTTCACTAACTCAAAGCAC 60.663 50.000 0.00 0.00 43.31 4.40
4097 4250 5.717119 AGCACTTCATTTTTATTGGAGCAG 58.283 37.500 0.00 0.00 0.00 4.24
4291 4446 0.040058 ACATTGCAGCATCCAAGGGA 59.960 50.000 0.00 0.00 35.55 4.20
4293 4448 1.033746 ATTGCAGCATCCAAGGGACG 61.034 55.000 0.00 0.00 32.98 4.79
4432 4592 4.697514 AGATTGGTGATCTGTAACCATCG 58.302 43.478 3.65 0.00 45.66 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 222 4.201532 CGACGAACTTATGCAAGTCTTCAG 60.202 45.833 0.00 0.00 44.41 3.02
231 232 4.220572 GTCTAGATCCGACGAACTTATGC 58.779 47.826 0.00 0.00 0.00 3.14
311 312 2.226437 ACGGTTGTTGCATCACTGATTC 59.774 45.455 0.00 0.00 0.00 2.52
813 817 8.882199 CATTATGAATAACTTAAACGTGCGATG 58.118 33.333 0.00 0.00 0.00 3.84
859 863 3.081804 GGCAATGCAGGTAGTGTAAGTT 58.918 45.455 7.79 0.00 0.00 2.66
862 866 2.432444 GTGGCAATGCAGGTAGTGTAA 58.568 47.619 7.79 0.00 0.00 2.41
997 1001 7.437713 AGATGTGTTTTCCAGTCTCCATATA 57.562 36.000 0.00 0.00 0.00 0.86
1017 1021 1.808945 GGTGGTTGTCTGCAGAAGATG 59.191 52.381 20.19 0.00 37.23 2.90
1023 1027 1.392589 AAGTTGGTGGTTGTCTGCAG 58.607 50.000 7.63 7.63 0.00 4.41
1077 1081 2.174685 TGATTCCTCGAATCCCTCCA 57.825 50.000 10.95 0.00 45.37 3.86
1195 1199 2.306847 CCAGGTAAGTGTTGCCTTGTT 58.693 47.619 0.00 0.00 43.78 2.83
1489 1500 6.845758 TCCAAGAATTTGAATCTTCTGCAT 57.154 33.333 0.00 0.00 34.99 3.96
1706 1717 5.241403 ACATAACAGTTTCAGTGGGATGA 57.759 39.130 0.00 0.00 0.00 2.92
2023 2037 3.126831 CTGACAATGAGCGAAGTATCCC 58.873 50.000 0.00 0.00 0.00 3.85
2145 2159 1.438651 GTTGTAGCCGCTTGATGTCA 58.561 50.000 0.00 0.00 0.00 3.58
2307 2321 2.477375 GCATGTGTTTCTTGTGCCATTG 59.523 45.455 0.00 0.00 0.00 2.82
2486 2500 7.969387 TTCATTGTGTTTTTCTTCTTCTTCG 57.031 32.000 0.00 0.00 0.00 3.79
2494 2511 7.614124 ACAAAGCATTCATTGTGTTTTTCTT 57.386 28.000 0.00 0.00 38.29 2.52
2495 2512 7.614124 AACAAAGCATTCATTGTGTTTTTCT 57.386 28.000 0.00 0.00 39.57 2.52
2496 2513 9.584839 GATAACAAAGCATTCATTGTGTTTTTC 57.415 29.630 0.00 0.00 39.57 2.29
2497 2514 9.107177 TGATAACAAAGCATTCATTGTGTTTTT 57.893 25.926 0.00 0.00 39.57 1.94
2498 2515 8.659925 TGATAACAAAGCATTCATTGTGTTTT 57.340 26.923 0.00 0.00 39.57 2.43
2499 2516 8.143193 TCTGATAACAAAGCATTCATTGTGTTT 58.857 29.630 0.00 0.00 39.57 2.83
2541 2558 2.684881 CAAATAAGTTGGAGCAGCGGAT 59.315 45.455 0.00 0.00 33.18 4.18
2657 2674 1.619654 ATGCAAAACTACAGGCAGCA 58.380 45.000 0.00 0.00 39.95 4.41
3307 3436 4.403752 TCATTGGTCTCCTCTATGTCACTG 59.596 45.833 0.00 0.00 0.00 3.66
3381 3518 4.524714 AGCTCATAAGTAGATGCATACCGT 59.475 41.667 0.00 0.00 0.00 4.83
3477 3616 4.994852 CACAAAAGAGACCGGACTTCATTA 59.005 41.667 9.46 0.00 0.00 1.90
3550 3690 8.603181 ACTTCAACAAACAAATCAACTAATTGC 58.397 29.630 0.00 0.00 35.63 3.56
3624 3764 5.817816 GGCGCCTAACATTATCAAGCTATAT 59.182 40.000 22.15 0.00 0.00 0.86
3800 3944 3.324035 GCGGCGGCTATCTCTTTG 58.676 61.111 9.78 0.00 35.83 2.77
3939 4089 2.955342 AGGGTAAAGCGTTGGGTAAA 57.045 45.000 0.00 0.00 0.00 2.01
3940 4090 2.955342 AAGGGTAAAGCGTTGGGTAA 57.045 45.000 0.00 0.00 0.00 2.85
3941 4091 2.955342 AAAGGGTAAAGCGTTGGGTA 57.045 45.000 0.00 0.00 0.00 3.69
3942 4092 2.107031 ACTAAAGGGTAAAGCGTTGGGT 59.893 45.455 0.00 0.00 0.00 4.51
3943 4093 2.786777 ACTAAAGGGTAAAGCGTTGGG 58.213 47.619 0.00 0.00 0.00 4.12
3944 4094 4.572909 AGTACTAAAGGGTAAAGCGTTGG 58.427 43.478 0.00 0.00 0.00 3.77
3945 4095 6.393171 AGTAGTACTAAAGGGTAAAGCGTTG 58.607 40.000 3.61 0.00 0.00 4.10
3946 4096 6.596309 AGTAGTACTAAAGGGTAAAGCGTT 57.404 37.500 3.61 0.00 0.00 4.84
3947 4097 6.209391 TCAAGTAGTACTAAAGGGTAAAGCGT 59.791 38.462 3.61 0.00 0.00 5.07
3948 4098 6.624423 TCAAGTAGTACTAAAGGGTAAAGCG 58.376 40.000 3.61 0.00 0.00 4.68
3949 4099 7.834803 TCTCAAGTAGTACTAAAGGGTAAAGC 58.165 38.462 3.61 0.00 0.00 3.51
3967 4117 2.906389 TCCCAACAGCAGTATCTCAAGT 59.094 45.455 0.00 0.00 0.00 3.16
4078 4231 4.795278 GCGTCTGCTCCAATAAAAATGAAG 59.205 41.667 0.00 0.00 38.39 3.02
4097 4250 1.856265 CTGTTGCCCTGGAAAGCGTC 61.856 60.000 0.00 0.00 0.00 5.19
4245 4400 5.648092 ACAAATCCAACTTGGCAGAGTATAC 59.352 40.000 2.52 0.00 37.47 1.47
4293 4448 2.599645 ATCCTGCAGCCCACGATGTC 62.600 60.000 8.66 0.00 0.00 3.06
4347 4505 4.347000 TGAAAGGCTACCCACCATAGTATC 59.653 45.833 0.00 0.00 0.00 2.24
4348 4506 4.303794 TGAAAGGCTACCCACCATAGTAT 58.696 43.478 0.00 0.00 0.00 2.12
4349 4507 3.726790 TGAAAGGCTACCCACCATAGTA 58.273 45.455 0.00 0.00 0.00 1.82
4350 4508 2.557869 TGAAAGGCTACCCACCATAGT 58.442 47.619 0.00 0.00 0.00 2.12
4351 4509 3.644966 TTGAAAGGCTACCCACCATAG 57.355 47.619 0.00 0.00 0.00 2.23
4352 4510 3.876156 GCTTTGAAAGGCTACCCACCATA 60.876 47.826 7.09 0.00 0.00 2.74
4353 4511 2.807676 CTTTGAAAGGCTACCCACCAT 58.192 47.619 0.00 0.00 0.00 3.55
4354 4512 1.821666 GCTTTGAAAGGCTACCCACCA 60.822 52.381 7.09 0.00 0.00 4.17
4432 4592 2.289569 TGGTGCTCAAAATTTGATGGGC 60.290 45.455 9.02 9.79 39.30 5.36


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

AutoCloner maintained by Alex Coulton.