Multiple sequence alignment - TraesCS5D01G300200

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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 TraesCS5D01G300200 chr5D 100.000 2627 0 0 1 2627 397473182 397470556 0.000000e+00 4852.0
1 TraesCS5D01G300200 chr5D 95.475 2630 111 5 1 2627 397466571 397469195 0.000000e+00 4191.0
2 TraesCS5D01G300200 chr5D 95.612 2507 104 5 1 2501 375001990 375004496 0.000000e+00 4015.0
3 TraesCS5D01G300200 chr5D 94.751 2515 115 8 1 2501 184453023 184455534 0.000000e+00 3897.0
4 TraesCS5D01G300200 chr6B 93.301 2508 161 6 1 2501 666360970 666358463 0.000000e+00 3694.0
5 TraesCS5D01G300200 chr3A 94.666 2381 116 8 125 2501 720600566 720598193 0.000000e+00 3683.0
6 TraesCS5D01G300200 chr3A 94.534 2360 121 5 146 2501 117786785 117784430 0.000000e+00 3637.0
7 TraesCS5D01G300200 chr4A 93.742 2381 139 7 125 2501 444377901 444380275 0.000000e+00 3563.0
8 TraesCS5D01G300200 chr4A 90.426 94 7 2 2534 2626 444380275 444380367 3.550000e-24 122.0
9 TraesCS5D01G300200 chr7A 95.415 2094 89 4 1 2091 692229364 692231453 0.000000e+00 3328.0
10 TraesCS5D01G300200 chr2A 94.763 1795 93 1 1 1794 33472831 33471037 0.000000e+00 2793.0
11 TraesCS5D01G300200 chr3B 92.371 970 56 5 1549 2501 442046540 442047508 0.000000e+00 1365.0
12 TraesCS5D01G300200 chr3B 92.537 67 3 2 2561 2627 627584682 627584618 7.740000e-16 95.3
13 TraesCS5D01G300200 chr1D 90.769 65 6 0 2562 2626 85860715 85860779 1.300000e-13 87.9
14 TraesCS5D01G300200 chr3D 79.200 125 19 5 2510 2627 484079364 484079488 2.170000e-11 80.5


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 TraesCS5D01G300200 chr5D 397470556 397473182 2626 True 4852.0 4852 100.000 1 2627 1 chr5D.!!$R1 2626
1 TraesCS5D01G300200 chr5D 397466571 397469195 2624 False 4191.0 4191 95.475 1 2627 1 chr5D.!!$F3 2626
2 TraesCS5D01G300200 chr5D 375001990 375004496 2506 False 4015.0 4015 95.612 1 2501 1 chr5D.!!$F2 2500
3 TraesCS5D01G300200 chr5D 184453023 184455534 2511 False 3897.0 3897 94.751 1 2501 1 chr5D.!!$F1 2500
4 TraesCS5D01G300200 chr6B 666358463 666360970 2507 True 3694.0 3694 93.301 1 2501 1 chr6B.!!$R1 2500
5 TraesCS5D01G300200 chr3A 720598193 720600566 2373 True 3683.0 3683 94.666 125 2501 1 chr3A.!!$R2 2376
6 TraesCS5D01G300200 chr3A 117784430 117786785 2355 True 3637.0 3637 94.534 146 2501 1 chr3A.!!$R1 2355
7 TraesCS5D01G300200 chr4A 444377901 444380367 2466 False 1842.5 3563 92.084 125 2626 2 chr4A.!!$F1 2501
8 TraesCS5D01G300200 chr7A 692229364 692231453 2089 False 3328.0 3328 95.415 1 2091 1 chr7A.!!$F1 2090
9 TraesCS5D01G300200 chr2A 33471037 33472831 1794 True 2793.0 2793 94.763 1 1794 1 chr2A.!!$R1 1793
10 TraesCS5D01G300200 chr3B 442046540 442047508 968 False 1365.0 1365 92.371 1549 2501 1 chr3B.!!$F1 952

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
978 984 0.397564 TCTGCCACTGCTCATTGTCA 59.602 50.0 0.0 0.0 38.71 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2297 1.097232 ACACATGCATCCGACATTGG 58.903 50.0 0.0 0.0 0.0 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
218 219 4.016706 AAGCCCGCCTTGTACGCT 62.017 61.111 0.00 0.00 30.99 5.07
311 313 6.994421 TTATCATAGATCCTGGCTGTAACA 57.006 37.500 0.00 0.00 0.00 2.41
382 384 3.395604 ACCAGACTAGAGGTAGAGGCTA 58.604 50.000 0.00 0.00 36.07 3.93
392 394 4.581409 AGAGGTAGAGGCTAACGATTTCTC 59.419 45.833 0.00 0.00 0.00 2.87
505 508 1.079503 GATGTTGTTCTCGGTGGAGC 58.920 55.000 0.00 0.00 40.26 4.70
761 767 5.382303 CCAGCTGTTGTTCTTGTAAATACG 58.618 41.667 13.81 0.00 0.00 3.06
778 784 2.585869 CGGACGTGCATACCATCGC 61.586 63.158 8.11 0.00 0.00 4.58
978 984 0.397564 TCTGCCACTGCTCATTGTCA 59.602 50.000 0.00 0.00 38.71 3.58
1071 1078 4.619973 ACGTGAGGTAACGAACATTACAA 58.380 39.130 3.45 0.00 46.49 2.41
1103 1110 4.976224 ACTTTTAGCTTTTCCACACGTT 57.024 36.364 0.00 0.00 0.00 3.99
1200 1207 3.758554 GTGATTATGGCAGTGACAAACCT 59.241 43.478 0.77 0.00 0.00 3.50
1284 1291 1.990160 AACTGCCCGGGAGACAAACA 61.990 55.000 29.31 9.95 0.00 2.83
1374 1381 2.418910 CCCCATGAGCTCGACGTCT 61.419 63.158 14.70 0.00 0.00 4.18
1422 1429 4.382541 TCGCTCCCTGCTCCCTCA 62.383 66.667 0.00 0.00 40.11 3.86
1428 1435 0.252881 TCCCTGCTCCCTCATGTTCT 60.253 55.000 0.00 0.00 0.00 3.01
1508 1515 1.709578 CTACCCTCATCCTGCTGCTA 58.290 55.000 0.00 0.00 0.00 3.49
1547 1554 2.092538 ACTGCCCAGAGAATGAATGAGG 60.093 50.000 1.69 0.00 0.00 3.86
1738 1758 3.495806 CCCTAGCTCCCTATTTTCTGCTG 60.496 52.174 0.00 0.00 32.72 4.41
1774 1794 5.031066 TGTTGGTTTAGAACACTAGCAGT 57.969 39.130 0.00 0.00 0.00 4.40
1883 1903 3.677976 GCTTGTGGTAGCCATTACGTAGT 60.678 47.826 0.00 0.00 39.72 2.73
1931 1951 9.851686 AATCATCAGTTCATAGTATTTGGCTTA 57.148 29.630 0.00 0.00 0.00 3.09
1945 1965 4.359434 TTGGCTTATGTGTGTTGGTCTA 57.641 40.909 0.00 0.00 0.00 2.59
1949 1969 4.941263 GGCTTATGTGTGTTGGTCTATGAA 59.059 41.667 0.00 0.00 0.00 2.57
2101 2123 3.434319 CGCCGGTCAAGCAAGCAT 61.434 61.111 1.90 0.00 0.00 3.79
2275 2297 6.972901 GGAGTTTTCCGGATTTGAATATGAAC 59.027 38.462 4.15 0.00 32.79 3.18
2509 2543 6.520913 GCTCCCTAATATGGAAGAACCTTAGG 60.521 46.154 0.00 0.00 40.67 2.69
2529 2563 5.357742 AGGAAACAAAAAGGCTGAATTGT 57.642 34.783 6.92 6.92 37.59 2.71
2557 2591 1.407712 GGCCCGTGCAGAAATTACCTA 60.408 52.381 0.00 0.00 40.13 3.08
2614 2648 3.962063 TGGCCGATATAGACACCAAACTA 59.038 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 5.571784 AAATACACAGGATAACTCGTCGA 57.428 39.130 0.00 0.00 0.00 4.20
311 313 3.806625 AAGTCACAAGCACAAAAGCAT 57.193 38.095 0.00 0.00 36.85 3.79
382 384 4.748102 TGACTAAAACAGCGAGAAATCGTT 59.252 37.500 0.00 0.00 35.26 3.85
392 394 3.002246 TCAAGCACTTGACTAAAACAGCG 59.998 43.478 8.99 0.00 43.90 5.18
505 508 1.429927 CTGCTCATCCTCAAGCGCAG 61.430 60.000 11.47 0.72 41.51 5.18
546 550 9.268282 TGATAAGAACAAAGAACCTACCTATCT 57.732 33.333 0.00 0.00 0.00 1.98
547 551 9.535878 CTGATAAGAACAAAGAACCTACCTATC 57.464 37.037 0.00 0.00 0.00 2.08
656 661 6.386654 CACAACAAGTTTTTACCAGACTGTT 58.613 36.000 0.93 0.00 0.00 3.16
761 767 2.244651 GGCGATGGTATGCACGTCC 61.245 63.158 0.00 0.00 0.00 4.79
778 784 2.638480 TCTCTGTTTGGTGAAGGTGG 57.362 50.000 0.00 0.00 0.00 4.61
816 822 5.010617 GGGGCACTTCTATTTTTCTTGTCAA 59.989 40.000 0.00 0.00 0.00 3.18
978 984 1.512926 GGTGAACGCTCTGTCAACAT 58.487 50.000 0.00 0.00 0.00 2.71
1071 1078 6.428465 GGAAAAGCTAAAAGTTCTCTACTGCT 59.572 38.462 0.00 0.00 37.12 4.24
1200 1207 3.436704 GCAGATCGAAGTCATGGTTTTCA 59.563 43.478 0.00 0.00 0.00 2.69
1284 1291 2.430244 CGCGACAACGGTAGTGCT 60.430 61.111 0.00 0.00 40.15 4.40
1374 1381 1.202769 GGGTGGTGGTTGTAGGGCTA 61.203 60.000 0.00 0.00 0.00 3.93
1422 1429 5.809001 TGAGCTGGACAGATAAAAGAACAT 58.191 37.500 3.00 0.00 0.00 2.71
1428 1435 5.441718 AGGATTGAGCTGGACAGATAAAA 57.558 39.130 3.00 0.00 0.00 1.52
1508 1515 4.095483 GGCAGTTTGATTCGATTGACAGAT 59.905 41.667 0.00 0.00 0.00 2.90
1607 1614 1.470632 GCTAGACGTGAGCAAGAGCAT 60.471 52.381 12.96 0.00 45.49 3.79
1738 1758 2.843701 ACCAACAGAGCATGCTATAGC 58.156 47.619 22.74 18.18 42.50 2.97
1774 1794 7.009179 AGTACGTATACATGGTAGGCTACTA 57.991 40.000 23.01 18.48 33.30 1.82
1883 1903 4.801330 AGTAGACACGGACATGATTCAA 57.199 40.909 0.00 0.00 0.00 2.69
2113 2135 7.505923 ACATCTGCTACTATCCTAACATGTACA 59.494 37.037 0.00 0.00 0.00 2.90
2260 2282 6.039270 TCCGACATTGGTTCATATTCAAATCC 59.961 38.462 0.00 0.00 0.00 3.01
2275 2297 1.097232 ACACATGCATCCGACATTGG 58.903 50.000 0.00 0.00 0.00 3.16
2509 2543 5.220835 CCCAACAATTCAGCCTTTTTGTTTC 60.221 40.000 0.00 0.00 39.55 2.78
2557 2591 8.664669 ATTCAACCCATTTAGTATGTTTTCCT 57.335 30.769 0.00 0.00 0.00 3.36
2597 2631 5.278858 CCCGGTCTAGTTTGGTGTCTATATC 60.279 48.000 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.