Multiple sequence alignment - TraesCS2A01G590500

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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 TraesCS2A01G590500 chr2A 100.000 2531 0 0 1 2531 778647326 778649856 0.000000e+00 4674
1 TraesCS2A01G590500 chr6A 96.318 2553 65 7 1 2531 182421822 182419277 0.000000e+00 4167
2 TraesCS2A01G590500 chr6A 93.198 2558 109 11 1 2531 137494905 137492386 0.000000e+00 3699
3 TraesCS2A01G590500 chr3B 95.456 2553 89 6 1 2528 473234221 473236771 0.000000e+00 4047
4 TraesCS2A01G590500 chr7B 94.588 2550 112 5 1 2528 51882339 51884884 0.000000e+00 3921
5 TraesCS2A01G590500 chr7B 84.770 1589 181 32 996 2528 73167298 73168881 0.000000e+00 1537
6 TraesCS2A01G590500 chr7A 94.481 2555 95 12 1 2528 126147079 126149614 0.000000e+00 3895
7 TraesCS2A01G590500 chr6B 94.353 2550 101 9 1 2528 48078039 48080567 0.000000e+00 3871
8 TraesCS2A01G590500 chr4B 93.850 2553 128 8 1 2528 321540569 321543117 0.000000e+00 3818
9 TraesCS2A01G590500 chr4B 93.561 2221 112 9 1 2193 587096930 587099147 0.000000e+00 3280
10 TraesCS2A01G590500 chr4B 96.656 299 9 1 2230 2528 587099150 587099447 1.750000e-136 496
11 TraesCS2A01G590500 chr3A 95.443 2282 80 4 1 2260 153361219 153363498 0.000000e+00 3616
12 TraesCS2A01G590500 chr7D 84.287 1591 187 33 996 2528 83758294 83759879 0.000000e+00 1495
13 TraesCS2A01G590500 chr5B 83.333 570 70 8 1779 2325 489804798 489804231 1.050000e-138 503


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 TraesCS2A01G590500 chr2A 778647326 778649856 2530 False 4674 4674 100.0000 1 2531 1 chr2A.!!$F1 2530
1 TraesCS2A01G590500 chr6A 182419277 182421822 2545 True 4167 4167 96.3180 1 2531 1 chr6A.!!$R2 2530
2 TraesCS2A01G590500 chr6A 137492386 137494905 2519 True 3699 3699 93.1980 1 2531 1 chr6A.!!$R1 2530
3 TraesCS2A01G590500 chr3B 473234221 473236771 2550 False 4047 4047 95.4560 1 2528 1 chr3B.!!$F1 2527
4 TraesCS2A01G590500 chr7B 51882339 51884884 2545 False 3921 3921 94.5880 1 2528 1 chr7B.!!$F1 2527
5 TraesCS2A01G590500 chr7B 73167298 73168881 1583 False 1537 1537 84.7700 996 2528 1 chr7B.!!$F2 1532
6 TraesCS2A01G590500 chr7A 126147079 126149614 2535 False 3895 3895 94.4810 1 2528 1 chr7A.!!$F1 2527
7 TraesCS2A01G590500 chr6B 48078039 48080567 2528 False 3871 3871 94.3530 1 2528 1 chr6B.!!$F1 2527
8 TraesCS2A01G590500 chr4B 321540569 321543117 2548 False 3818 3818 93.8500 1 2528 1 chr4B.!!$F1 2527
9 TraesCS2A01G590500 chr4B 587096930 587099447 2517 False 1888 3280 95.1085 1 2528 2 chr4B.!!$F2 2527
10 TraesCS2A01G590500 chr3A 153361219 153363498 2279 False 3616 3616 95.4430 1 2260 1 chr3A.!!$F1 2259
11 TraesCS2A01G590500 chr7D 83758294 83759879 1585 False 1495 1495 84.2870 996 2528 1 chr7D.!!$F1 1532
12 TraesCS2A01G590500 chr5B 489804231 489804798 567 True 503 503 83.3330 1779 2325 1 chr5B.!!$R1 546

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
322 324 0.460284 ATTAAGCCCGAGCGTCACTG 60.46 55.0 0.0 0.0 46.67 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1691 0.036164 TCACCCAACCTTGATCGGTG 59.964 55.0 7.21 7.21 44.4 4.94 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
23 24 0.882042 CAGCGCCTCACTGTTCAGTT 60.882 55.000 2.29 0.00 0.00 3.16
72 73 2.258591 GTCGAGAAGCAGCACCGA 59.741 61.111 0.00 0.00 0.00 4.69
78 79 1.375908 GAAGCAGCACCGACCATGA 60.376 57.895 0.00 0.00 0.00 3.07
322 324 0.460284 ATTAAGCCCGAGCGTCACTG 60.460 55.000 0.00 0.00 46.67 3.66
346 348 6.600427 TGATGATGACTGTCATGCTACAATTT 59.400 34.615 26.71 5.01 37.20 1.82
686 698 3.290308 TGTTTTGTTTTCGTGTGCAGT 57.710 38.095 0.00 0.00 0.00 4.40
689 701 5.403246 TGTTTTGTTTTCGTGTGCAGTATT 58.597 33.333 0.00 0.00 0.00 1.89
745 757 7.852263 TCCACTTTAACATTCTTTTTCCCAAA 58.148 30.769 0.00 0.00 0.00 3.28
830 842 7.497909 CCCCTAATGTTGATATGTTCTTAACGT 59.502 37.037 0.00 0.00 0.00 3.99
1300 1316 2.243994 GGCCTAAGGGGTACAAGGAATT 59.756 50.000 0.00 0.00 37.43 2.17
1338 1354 6.713903 AGATAGTGGCATCATTCCTTTATGTG 59.286 38.462 0.00 0.00 0.00 3.21
1472 1488 6.206634 CCATTGCTACTTAAGAAACCAGAACA 59.793 38.462 10.09 0.00 0.00 3.18
1480 1496 7.924541 ACTTAAGAAACCAGAACATATACCCA 58.075 34.615 10.09 0.00 0.00 4.51
1490 1506 4.413520 AGAACATATACCCAAGGACTGCAT 59.586 41.667 0.00 0.00 0.00 3.96
1585 1607 5.572896 GGTAAAGATGCTAATGTTTGCACAC 59.427 40.000 4.11 0.00 41.35 3.82
1669 1691 4.406003 TCCCAGCTACTATGAAAGGAAGAC 59.594 45.833 0.00 0.00 0.00 3.01
1727 1751 2.476772 GTGTGTGTGCACCTGACAA 58.523 52.632 15.69 1.05 44.65 3.18
1848 1872 8.790718 CCCTGAAGATCAATATTATCTTGTTGG 58.209 37.037 17.54 15.48 42.38 3.77
2126 2179 4.113354 GACCCACTTGATAATGACGAGAC 58.887 47.826 0.00 0.00 0.00 3.36
2127 2180 3.513912 ACCCACTTGATAATGACGAGACA 59.486 43.478 0.00 0.00 0.00 3.41
2128 2181 4.020573 ACCCACTTGATAATGACGAGACAA 60.021 41.667 0.00 0.00 0.00 3.18
2206 2259 8.520351 TCATTACTTCTATCTCAACTTCGAACA 58.480 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.681538 GACGACTAGATGGCTCTGGA 58.318 55.000 0.00 0.00 34.29 3.86
72 73 4.530946 CCTAACCTAATCCGGTATCATGGT 59.469 45.833 0.00 0.88 35.89 3.55
78 79 3.271153 AGCCCTAACCTAATCCGGTAT 57.729 47.619 0.00 0.00 35.89 2.73
299 301 0.386113 GACGCTCGGGCTTAATCTCT 59.614 55.000 5.36 0.00 36.09 3.10
322 324 6.615264 AATTGTAGCATGACAGTCATCATC 57.385 37.500 13.53 6.04 37.20 2.92
346 348 4.350368 TGTGCAGTTAAGTCATCCTTGA 57.650 40.909 0.00 0.00 34.46 3.02
431 434 4.701956 AACAGGACACAAAGACAAGTTG 57.298 40.909 0.00 0.00 0.00 3.16
433 436 9.959721 ATATATAAACAGGACACAAAGACAAGT 57.040 29.630 0.00 0.00 0.00 3.16
519 526 4.384846 CACGGTCACATATTATTAGCGTCC 59.615 45.833 0.00 0.00 41.73 4.79
689 701 9.982291 GATAAGCGAAAATACAATACACTTCAA 57.018 29.630 0.00 0.00 0.00 2.69
745 757 1.202722 AGGACAACCGATGAACCGTTT 60.203 47.619 0.00 0.00 41.83 3.60
1188 1204 0.457443 CTGCATCGCTCTCACCAGTA 59.543 55.000 0.00 0.00 0.00 2.74
1300 1316 3.326006 GCCACTATCTCCTCCAATGATGA 59.674 47.826 0.00 0.00 0.00 2.92
1472 1488 5.190528 CCATCTATGCAGTCCTTGGGTATAT 59.809 44.000 0.00 0.00 0.00 0.86
1480 1496 5.132648 TCCATTTACCATCTATGCAGTCCTT 59.867 40.000 0.00 0.00 0.00 3.36
1585 1607 9.950680 AAGACAATTCTACAACATAAACAACAG 57.049 29.630 0.00 0.00 0.00 3.16
1669 1691 0.036164 TCACCCAACCTTGATCGGTG 59.964 55.000 7.21 7.21 44.40 4.94
1727 1751 6.767902 CCAGGTAGTATGTAAATGAACTGCAT 59.232 38.462 0.00 0.00 39.43 3.96
1848 1872 1.265635 TCGCATTTGTGTAACCAGCAC 59.734 47.619 0.00 0.00 34.36 4.40
2126 2179 8.034215 TGCCTTCCAATGTTTCTTGTATTATTG 58.966 33.333 0.00 0.00 0.00 1.90
2127 2180 8.133024 TGCCTTCCAATGTTTCTTGTATTATT 57.867 30.769 0.00 0.00 0.00 1.40
2128 2181 7.716799 TGCCTTCCAATGTTTCTTGTATTAT 57.283 32.000 0.00 0.00 0.00 1.28
2206 2259 3.895041 ACATTCCGGAAATTTGTCCACTT 59.105 39.130 23.08 0.00 37.56 3.16


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

AutoCloner maintained by Alex Coulton.