Multiple sequence alignment - TraesCS4A01G460300

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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 TraesCS4A01G460300 chr4A 100.000 2624 0 0 1 2624 725754023 725756646 0.000000 4846.0
1 TraesCS4A01G460300 chr4A 97.302 2409 65 0 1 2409 725801144 725803552 0.000000 4089.0
2 TraesCS4A01G460300 chr4A 83.738 1070 145 17 730 1788 726100930 726099879 0.000000 985.0
3 TraesCS4A01G460300 chr4A 96.875 32 1 0 529 560 726087878 726087847 0.001000 54.7
4 TraesCS4A01G460300 chr7D 90.047 2532 188 33 123 2624 12381527 12379030 0.000000 3221.0
5 TraesCS4A01G460300 chr7A 89.632 2527 193 38 123 2624 11992183 11989701 0.000000 3151.0
6 TraesCS4A01G460300 chr7A 82.954 1273 173 26 529 1788 11249374 11250615 0.000000 1109.0
7 TraesCS4A01G460300 chr7A 94.737 38 1 1 2459 2496 21776772 21776736 0.000101 58.4
8 TraesCS4A01G460300 chr5A 90.909 44 4 0 2477 2520 564640945 564640902 0.000028 60.2
9 TraesCS4A01G460300 chr5A 94.872 39 0 2 2454 2492 602793963 602793927 0.000028 60.2
10 TraesCS4A01G460300 chr5A 94.872 39 0 2 2454 2492 602817941 602817905 0.000028 60.2


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 TraesCS4A01G460300 chr4A 725754023 725756646 2623 False 4846 4846 100.000 1 2624 1 chr4A.!!$F1 2623
1 TraesCS4A01G460300 chr4A 725801144 725803552 2408 False 4089 4089 97.302 1 2409 1 chr4A.!!$F2 2408
2 TraesCS4A01G460300 chr4A 726099879 726100930 1051 True 985 985 83.738 730 1788 1 chr4A.!!$R2 1058
3 TraesCS4A01G460300 chr7D 12379030 12381527 2497 True 3221 3221 90.047 123 2624 1 chr7D.!!$R1 2501
4 TraesCS4A01G460300 chr7A 11989701 11992183 2482 True 3151 3151 89.632 123 2624 1 chr7A.!!$R1 2501
5 TraesCS4A01G460300 chr7A 11249374 11250615 1241 False 1109 1109 82.954 529 1788 1 chr7A.!!$F1 1259

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
906 933 0.041576 CCATGCACATCGCTTCATCG 60.042 55.0 0.0 0.0 43.06 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 2571 0.313987 GGGGAAGTGCGAGGTTTTTG 59.686 55.0 0.0 0.0 0.0 2.44 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
33 34 5.729974 ACTTTACGTGACTTCAAGGTTTC 57.270 39.130 0.00 0.00 0.00 2.78
34 35 4.573607 ACTTTACGTGACTTCAAGGTTTCC 59.426 41.667 0.00 0.00 0.00 3.13
102 103 9.733556 ATTCACACAAGGTTACTCATATTTGTA 57.266 29.630 0.00 0.00 0.00 2.41
246 248 3.052036 AGCAACAAATCACACGCATTTC 58.948 40.909 0.00 0.00 0.00 2.17
327 329 5.306678 TGGTTGCACCTTGAGGAATTATTTT 59.693 36.000 3.59 0.00 39.58 1.82
352 354 9.706691 TTTAAGTTTGGTTCTAGAGATGTACAG 57.293 33.333 0.33 0.00 0.00 2.74
518 526 5.648092 AGTATTAATGTGCACCAAAGGAGAC 59.352 40.000 15.69 3.27 0.00 3.36
906 933 0.041576 CCATGCACATCGCTTCATCG 60.042 55.000 0.00 0.00 43.06 3.84
1059 1086 4.573900 CCATCGCTATTATGCTCCTTTCT 58.426 43.478 0.00 0.00 0.00 2.52
1072 1099 2.698797 CTCCTTTCTAATACCCTCGCCA 59.301 50.000 0.00 0.00 0.00 5.69
1082 1109 1.304052 CCCTCGCCACCAAATCCAA 60.304 57.895 0.00 0.00 0.00 3.53
1228 1257 3.247056 TTGGACAATCGGAGCGCCA 62.247 57.895 7.44 0.00 0.00 5.69
1329 1358 1.024271 AACAAATGCTGCACGACACT 58.976 45.000 3.57 0.00 0.00 3.55
1357 1386 2.819595 CGGCTACAATGCGTGCCT 60.820 61.111 9.35 0.00 38.75 4.75
1375 1404 1.068055 CCTTCAGTTTCTGCATGGTGC 60.068 52.381 0.00 0.00 45.29 5.01
2046 2085 2.697654 GTTGCTCTGAAGATCAGCTGT 58.302 47.619 14.67 0.42 43.95 4.40
2183 2222 0.317519 CTGCACCCGTTTTTCGTTCC 60.318 55.000 0.00 0.00 37.94 3.62
2202 2241 1.000938 CCTGAGTGCTTGGTTTTCAGC 60.001 52.381 0.00 0.00 35.18 4.26
2208 2247 2.037901 TGCTTGGTTTTCAGCCATTCA 58.962 42.857 0.00 0.00 35.71 2.57
2335 2374 5.389935 CGAACAACTTCTCAGTTATCTTGCC 60.390 44.000 0.00 0.00 41.69 4.52
2437 2476 4.266976 CGTATCTTGATTGTACACCGGAAC 59.733 45.833 9.46 3.62 0.00 3.62
2439 2478 4.345859 TCTTGATTGTACACCGGAACTT 57.654 40.909 9.46 0.00 0.00 2.66
2446 2485 4.196626 TGTACACCGGAACTTTCTATGG 57.803 45.455 9.46 0.00 0.00 2.74
2531 2570 1.475441 CGTCGCGCTTTTTGCCAAAA 61.475 50.000 5.56 0.00 38.78 2.44
2532 2571 0.043396 GTCGCGCTTTTTGCCAAAAC 60.043 50.000 5.56 0.00 38.78 2.43
2557 2596 0.527565 CCTCGCACTTCCCCAAAATG 59.472 55.000 0.00 0.00 0.00 2.32
2560 2599 2.493278 CTCGCACTTCCCCAAAATGAAT 59.507 45.455 0.00 0.00 0.00 2.57
2564 2603 1.824852 ACTTCCCCAAAATGAATCCGC 59.175 47.619 0.00 0.00 0.00 5.54
2567 2606 1.319614 CCCCAAAATGAATCCGCGGT 61.320 55.000 27.15 6.47 0.00 5.68
2583 2622 1.425412 CGGTCCCGTTTAAGTGTGAG 58.575 55.000 0.00 0.00 34.35 3.51
2617 2656 3.673543 TGTGTTTTGTAGAAACCCCCT 57.326 42.857 0.00 0.00 0.00 4.79
2618 2657 3.292460 TGTGTTTTGTAGAAACCCCCTG 58.708 45.455 0.00 0.00 0.00 4.45
2619 2658 3.053544 TGTGTTTTGTAGAAACCCCCTGA 60.054 43.478 0.00 0.00 0.00 3.86
2620 2659 3.568430 GTGTTTTGTAGAAACCCCCTGAG 59.432 47.826 0.00 0.00 0.00 3.35
2622 2661 2.127651 TTGTAGAAACCCCCTGAGGT 57.872 50.000 0.00 0.00 44.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.573607 GGAAACCTTGAAGTCACGTAAAGT 59.426 41.667 0.00 0.00 0.00 2.66
102 103 9.100197 ACTTATAAAACCCAAAAGTTGATCCAT 57.900 29.630 0.00 0.00 0.00 3.41
127 128 7.404671 ACTACAATTGTCATTTGGGGATTAC 57.595 36.000 15.85 0.00 0.00 1.89
215 217 6.310197 GTGTGATTTGTTGCTCTTAGCTAAG 58.690 40.000 24.90 24.90 42.97 2.18
327 329 7.817962 GCTGTACATCTCTAGAACCAAACTTAA 59.182 37.037 0.00 0.00 0.00 1.85
352 354 4.660352 TTTTGTTGTGCAACTTTCAAGC 57.340 36.364 14.97 0.00 41.67 4.01
906 933 5.083122 TGATGAGTAGGGAAGAGATGGATC 58.917 45.833 0.00 0.00 0.00 3.36
1059 1086 2.158726 GGATTTGGTGGCGAGGGTATTA 60.159 50.000 0.00 0.00 0.00 0.98
1072 1099 1.620524 CCCAGAGGCATTGGATTTGGT 60.621 52.381 8.67 0.00 37.96 3.67
1105 1132 3.888930 TCCAAAATGAAGTTGGTCACCTC 59.111 43.478 0.00 0.00 44.96 3.85
1329 1358 2.772077 TTGTAGCCGTGCCATTCTTA 57.228 45.000 0.00 0.00 0.00 2.10
1375 1404 1.078709 CTCACCATGCGGTTGTAGTG 58.921 55.000 0.00 0.00 46.31 2.74
1455 1484 1.081892 CAGAAGACAGCAACCCATCG 58.918 55.000 0.00 0.00 0.00 3.84
1712 1745 9.515020 GAAAGTGAAAGTAAAATTGATGACACA 57.485 29.630 0.00 0.00 0.00 3.72
1774 1808 8.002433 CGATAGCTATTTTCTAGACAGCTTTC 57.998 38.462 17.64 17.14 42.37 2.62
2046 2085 1.418264 TCCATCGGACCAACAGTTGAA 59.582 47.619 15.36 0.00 0.00 2.69
2183 2222 1.000938 GGCTGAAAACCAAGCACTCAG 60.001 52.381 0.00 0.00 37.23 3.35
2263 2302 9.495572 AAAGTGACCAAAAAGTTTACAATTTCA 57.504 25.926 0.00 0.00 0.00 2.69
2278 2317 3.556775 CGAAGTTCGGTAAAGTGACCAAA 59.443 43.478 17.61 0.00 39.72 3.28
2335 2374 4.701956 AACCTATTTGAGCAATGTTCGG 57.298 40.909 0.00 0.00 0.00 4.30
2401 2440 7.824289 ACAATCAAGATACGGAGAAATTCTTCA 59.176 33.333 1.81 0.00 33.64 3.02
2491 2530 1.468914 GACGGGCAGAAACAATCCTTC 59.531 52.381 0.00 0.00 0.00 3.46
2492 2531 1.534729 GACGGGCAGAAACAATCCTT 58.465 50.000 0.00 0.00 0.00 3.36
2531 2570 1.029681 GGGAAGTGCGAGGTTTTTGT 58.970 50.000 0.00 0.00 0.00 2.83
2532 2571 0.313987 GGGGAAGTGCGAGGTTTTTG 59.686 55.000 0.00 0.00 0.00 2.44
2557 2596 0.740516 TTAAACGGGACCGCGGATTC 60.741 55.000 35.90 20.53 44.19 2.52
2560 2599 2.262292 CTTAAACGGGACCGCGGA 59.738 61.111 35.90 2.60 44.19 5.54
2564 2603 1.269936 ACTCACACTTAAACGGGACCG 60.270 52.381 9.56 9.56 46.03 4.79
2567 2606 5.534207 TTTCTACTCACACTTAAACGGGA 57.466 39.130 0.00 0.00 0.00 5.14
2599 2638 3.435890 CCTCAGGGGGTTTCTACAAAACA 60.436 47.826 3.38 0.00 29.76 2.83


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

AutoCloner maintained by Alex Coulton.