Multiple sequence alignment - TraesCS4A01G244900

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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 TraesCS4A01G244900 chr4A 100.000 2378 0 0 1 2378 554961157 554958780 0 4392
1 TraesCS4A01G244900 chr4A 99.088 658 5 1 1721 2378 133082199 133082855 0 1181
2 TraesCS4A01G244900 chrUn 97.208 1719 47 1 3 1720 237312464 237310746 0 2907
3 TraesCS4A01G244900 chrUn 97.208 1719 47 1 3 1720 245706823 245705105 0 2907
4 TraesCS4A01G244900 chrUn 97.208 1719 47 1 3 1720 274340527 274342245 0 2907
5 TraesCS4A01G244900 chrUn 97.208 1719 47 1 3 1720 291536195 291534477 0 2907
6 TraesCS4A01G244900 chrUn 97.150 1719 48 1 3 1720 229309472 229311190 0 2902
7 TraesCS4A01G244900 chrUn 96.975 1719 51 1 3 1720 67500253 67501971 0 2885
8 TraesCS4A01G244900 chr5D 97.150 1719 48 1 3 1720 18999679 18997961 0 2902
9 TraesCS4A01G244900 chr6B 97.033 1719 50 1 3 1720 111686034 111687752 0 2891
10 TraesCS4A01G244900 chr6B 99.085 656 6 0 1721 2376 614759269 614758614 0 1179
11 TraesCS4A01G244900 chr1B 97.033 1719 50 1 3 1720 544624391 544622673 0 2891
12 TraesCS4A01G244900 chr6A 99.088 658 6 0 1721 2378 533534106 533533449 0 1182
13 TraesCS4A01G244900 chr6A 99.088 658 6 0 1721 2378 533540702 533540045 0 1182
14 TraesCS4A01G244900 chr5B 98.938 659 7 0 1720 2378 459355533 459354875 0 1179
15 TraesCS4A01G244900 chr7B 98.936 658 7 0 1721 2378 177372467 177371810 0 1177
16 TraesCS4A01G244900 chr3B 98.792 662 7 1 1718 2378 704547766 704547105 0 1177
17 TraesCS4A01G244900 chr3A 98.936 658 7 0 1721 2378 656055275 656055932 0 1177
18 TraesCS4A01G244900 chr1A 98.640 662 9 0 1717 2378 81584587 81583926 0 1173


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 TraesCS4A01G244900 chr4A 554958780 554961157 2377 True 4392 4392 100.000 1 2378 1 chr4A.!!$R1 2377
1 TraesCS4A01G244900 chr4A 133082199 133082855 656 False 1181 1181 99.088 1721 2378 1 chr4A.!!$F1 657
2 TraesCS4A01G244900 chrUn 237310746 237312464 1718 True 2907 2907 97.208 3 1720 1 chrUn.!!$R1 1717
3 TraesCS4A01G244900 chrUn 245705105 245706823 1718 True 2907 2907 97.208 3 1720 1 chrUn.!!$R2 1717
4 TraesCS4A01G244900 chrUn 274340527 274342245 1718 False 2907 2907 97.208 3 1720 1 chrUn.!!$F3 1717
5 TraesCS4A01G244900 chrUn 291534477 291536195 1718 True 2907 2907 97.208 3 1720 1 chrUn.!!$R3 1717
6 TraesCS4A01G244900 chrUn 229309472 229311190 1718 False 2902 2902 97.150 3 1720 1 chrUn.!!$F2 1717
7 TraesCS4A01G244900 chrUn 67500253 67501971 1718 False 2885 2885 96.975 3 1720 1 chrUn.!!$F1 1717
8 TraesCS4A01G244900 chr5D 18997961 18999679 1718 True 2902 2902 97.150 3 1720 1 chr5D.!!$R1 1717
9 TraesCS4A01G244900 chr6B 111686034 111687752 1718 False 2891 2891 97.033 3 1720 1 chr6B.!!$F1 1717
10 TraesCS4A01G244900 chr6B 614758614 614759269 655 True 1179 1179 99.085 1721 2376 1 chr6B.!!$R1 655
11 TraesCS4A01G244900 chr1B 544622673 544624391 1718 True 2891 2891 97.033 3 1720 1 chr1B.!!$R1 1717
12 TraesCS4A01G244900 chr6A 533533449 533534106 657 True 1182 1182 99.088 1721 2378 1 chr6A.!!$R1 657
13 TraesCS4A01G244900 chr6A 533540045 533540702 657 True 1182 1182 99.088 1721 2378 1 chr6A.!!$R2 657
14 TraesCS4A01G244900 chr5B 459354875 459355533 658 True 1179 1179 98.938 1720 2378 1 chr5B.!!$R1 658
15 TraesCS4A01G244900 chr7B 177371810 177372467 657 True 1177 1177 98.936 1721 2378 1 chr7B.!!$R1 657
16 TraesCS4A01G244900 chr3B 704547105 704547766 661 True 1177 1177 98.792 1718 2378 1 chr3B.!!$R1 660
17 TraesCS4A01G244900 chr3A 656055275 656055932 657 False 1177 1177 98.936 1721 2378 1 chr3A.!!$F1 657
18 TraesCS4A01G244900 chr1A 81583926 81584587 661 True 1173 1173 98.640 1717 2378 1 chr1A.!!$R1 661

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
119 120 0.759346 AGGATCGGCTTACCCATGTC 59.241 55.0 0.0 0.0 0.0 3.06 F
399 401 1.052617 TTCGACTTCCATGACCACCA 58.947 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1353 1.133606 AGTCGGGTTGTTTGGGAATGT 60.134 47.619 0.0 0.0 0.00 2.71 R
1963 1966 4.454678 TCGCGAAGATAGGAGTTAACCTA 58.545 43.478 6.2 0.0 45.05 3.08 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
119 120 0.759346 AGGATCGGCTTACCCATGTC 59.241 55.000 0.00 0.00 0.00 3.06
126 127 1.271926 GGCTTACCCATGTCCAAGTGT 60.272 52.381 0.00 0.00 0.00 3.55
370 372 2.794910 CAGGTGAGTTGTTACACACTCG 59.205 50.000 16.56 5.34 43.00 4.18
399 401 1.052617 TTCGACTTCCATGACCACCA 58.947 50.000 0.00 0.00 0.00 4.17
416 418 3.370846 CCACCATCCTGCTGTCTTAATCA 60.371 47.826 0.00 0.00 0.00 2.57
446 448 4.635699 CCTTTGTGGGTTCTAGGTTAGT 57.364 45.455 0.00 0.00 0.00 2.24
530 532 3.971702 GGCCCACTTGGAGCACCT 61.972 66.667 0.71 0.00 37.39 4.00
602 604 5.941555 AAGTTTGAGAATAGGTCGAGGAT 57.058 39.130 0.00 0.00 0.00 3.24
614 616 2.511600 GAGGATGTTGCGTCCCCG 60.512 66.667 3.94 0.00 40.21 5.73
649 651 6.721318 TCATTGGCTTTACCTGATAGAACTT 58.279 36.000 0.00 0.00 40.22 2.66
658 660 7.504926 TTACCTGATAGAACTTGTAATGGGT 57.495 36.000 0.00 0.00 0.00 4.51
663 665 6.785076 TGATAGAACTTGTAATGGGTTCCAA 58.215 36.000 0.00 0.00 39.82 3.53
765 767 1.917955 CGATTTGCACGTCAGTATCGT 59.082 47.619 16.71 0.00 42.33 3.73
1225 1227 3.089874 CCATCCGCTTCCCTCCCA 61.090 66.667 0.00 0.00 0.00 4.37
1281 1283 3.328050 AGTCCTTTTCATCTTTCCCTCGT 59.672 43.478 0.00 0.00 0.00 4.18
1497 1499 2.427453 GCCTCTCCAGACTACAATTCGA 59.573 50.000 0.00 0.00 0.00 3.71
1528 1530 1.907739 CCCGATTCTCAAGCTGGGA 59.092 57.895 0.00 0.00 39.03 4.37
1669 1671 2.250939 CGCTTCGTTTGCTGGGTCA 61.251 57.895 0.00 0.00 0.00 4.02
1672 1674 1.000274 GCTTCGTTTGCTGGGTCATTT 60.000 47.619 0.00 0.00 0.00 2.32
1682 1684 1.753073 CTGGGTCATTTTGAGGCCATC 59.247 52.381 5.01 0.00 0.00 3.51
1736 1739 1.741528 AAGTGTCACGACCGGTTTTT 58.258 45.000 9.42 0.00 0.00 1.94
1805 1808 3.543680 TTACTGTTAGCTGATGAGGCC 57.456 47.619 0.00 0.00 0.00 5.19
1963 1966 2.743718 CCACGGGAACAGCTGACT 59.256 61.111 23.35 6.77 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.577328 GATGTGGTGGTTGACGGCTG 61.577 60.000 0.00 0.00 0.00 4.85
1 2 1.302511 GATGTGGTGGTTGACGGCT 60.303 57.895 0.00 0.00 0.00 5.52
63 64 4.326153 GCAGATAGCGCGATCACA 57.674 55.556 28.54 0.00 0.00 3.58
252 254 2.490148 CGATGAGTAGGAGGGCGCA 61.490 63.158 10.83 0.00 0.00 6.09
311 313 1.474077 GAAAATGGATGGCGCTGAAGT 59.526 47.619 7.64 0.00 0.00 3.01
370 372 2.613691 TGGAAGTCGAAATCCGCTAAC 58.386 47.619 11.85 0.00 38.63 2.34
399 401 4.574674 TGGTTGATTAAGACAGCAGGAT 57.425 40.909 0.00 0.00 0.00 3.24
649 651 4.785914 TCAGGATAGTTGGAACCCATTACA 59.214 41.667 0.00 0.00 31.53 2.41
658 660 4.175962 AGTTTCCCTCAGGATAGTTGGAA 58.824 43.478 0.00 0.00 43.54 3.53
663 665 2.766828 CCGAAGTTTCCCTCAGGATAGT 59.233 50.000 0.00 0.00 43.54 2.12
765 767 0.832135 ACTCTGGTGGAGGCTCGAAA 60.832 55.000 8.69 0.00 45.83 3.46
841 843 1.070786 GGGTTCGAGTTGGAGCACA 59.929 57.895 0.00 0.00 0.00 4.57
1156 1158 4.704833 GCTCTTGCTGGTCCGCCA 62.705 66.667 3.72 0.00 43.73 5.69
1225 1227 4.340381 AGTCAAAGAGTGCTTGAAATTGCT 59.660 37.500 0.00 0.00 33.79 3.91
1281 1283 1.820519 ACCGATAGCGAACAAGTACCA 59.179 47.619 0.00 0.00 40.82 3.25
1349 1351 2.885894 GTCGGGTTGTTTGGGAATGTAA 59.114 45.455 0.00 0.00 0.00 2.41
1351 1353 1.133606 AGTCGGGTTGTTTGGGAATGT 60.134 47.619 0.00 0.00 0.00 2.71
1528 1530 4.514577 CGAGCGAACCGGGAGCAT 62.515 66.667 17.92 5.56 0.00 3.79
1736 1739 7.121611 GGTCTTTTCTGGAAATTTATTACCCGA 59.878 37.037 0.00 0.00 0.00 5.14
1805 1808 6.588719 TTGGAATTTCTGTATCAAGTTGGG 57.411 37.500 2.34 0.00 0.00 4.12
1963 1966 4.454678 TCGCGAAGATAGGAGTTAACCTA 58.545 43.478 6.20 0.00 45.05 3.08


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

AutoCloner maintained by Alex Coulton.