Multiple sequence alignment - TraesCS4A01G387200

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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 TraesCS4A01G387200 chr4A 100.000 3623 0 0 1 3623 664504228 664500606 0 6691
1 TraesCS4A01G387200 chr4A 93.353 2362 102 19 3 2312 711324999 711322641 0 3441
2 TraesCS4A01G387200 chr3B 95.940 3645 113 14 3 3623 698407012 698403379 0 5879
3 TraesCS4A01G387200 chr3B 94.820 3668 133 12 3 3623 543542267 543545924 0 5668
4 TraesCS4A01G387200 chr4B 95.369 3649 116 12 3 3623 657437974 657441597 0 5753
5 TraesCS4A01G387200 chr4B 94.361 3671 137 23 3 3623 5275378 5271728 0 5568
6 TraesCS4A01G387200 chr4B 94.142 3670 156 24 3 3623 403105533 403109192 0 5531
7 TraesCS4A01G387200 chr4B 93.855 3629 158 23 3 3569 66843664 66840039 0 5406
8 TraesCS4A01G387200 chr4B 93.422 3679 178 24 3 3623 73282640 73286312 0 5395
9 TraesCS4A01G387200 chr1B 94.849 3669 131 15 3 3623 549442640 549438982 0 5675
10 TraesCS4A01G387200 chr1B 94.607 2874 100 12 3 2828 667349157 667346291 0 4397
11 TraesCS4A01G387200 chr2B 92.840 3687 191 23 3 3621 559131111 559134792 0 5278
12 TraesCS4A01G387200 chr2B 92.809 3685 196 26 3 3623 393872690 393869011 0 5273
13 TraesCS4A01G387200 chr7B 93.972 2505 97 10 3 2460 637698646 637701143 0 3740


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 TraesCS4A01G387200 chr4A 664500606 664504228 3622 True 6691 6691 100.000 1 3623 1 chr4A.!!$R1 3622
1 TraesCS4A01G387200 chr4A 711322641 711324999 2358 True 3441 3441 93.353 3 2312 1 chr4A.!!$R2 2309
2 TraesCS4A01G387200 chr3B 698403379 698407012 3633 True 5879 5879 95.940 3 3623 1 chr3B.!!$R1 3620
3 TraesCS4A01G387200 chr3B 543542267 543545924 3657 False 5668 5668 94.820 3 3623 1 chr3B.!!$F1 3620
4 TraesCS4A01G387200 chr4B 657437974 657441597 3623 False 5753 5753 95.369 3 3623 1 chr4B.!!$F3 3620
5 TraesCS4A01G387200 chr4B 5271728 5275378 3650 True 5568 5568 94.361 3 3623 1 chr4B.!!$R1 3620
6 TraesCS4A01G387200 chr4B 403105533 403109192 3659 False 5531 5531 94.142 3 3623 1 chr4B.!!$F2 3620
7 TraesCS4A01G387200 chr4B 66840039 66843664 3625 True 5406 5406 93.855 3 3569 1 chr4B.!!$R2 3566
8 TraesCS4A01G387200 chr4B 73282640 73286312 3672 False 5395 5395 93.422 3 3623 1 chr4B.!!$F1 3620
9 TraesCS4A01G387200 chr1B 549438982 549442640 3658 True 5675 5675 94.849 3 3623 1 chr1B.!!$R1 3620
10 TraesCS4A01G387200 chr1B 667346291 667349157 2866 True 4397 4397 94.607 3 2828 1 chr1B.!!$R2 2825
11 TraesCS4A01G387200 chr2B 559131111 559134792 3681 False 5278 5278 92.840 3 3621 1 chr2B.!!$F1 3618
12 TraesCS4A01G387200 chr2B 393869011 393872690 3679 True 5273 5273 92.809 3 3623 1 chr2B.!!$R1 3620
13 TraesCS4A01G387200 chr7B 637698646 637701143 2497 False 3740 3740 93.972 3 2460 1 chr7B.!!$F1 2457

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
794 804 2.298729 GGGCTAACATGGCAACTTCAAA 59.701 45.455 0.00 0.0 37.61 2.69 F
1894 1951 0.030101 GTGCGGTGCAAGCAAAACTA 59.970 50.000 18.08 0.0 46.97 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 2643 2.229792 TGAAAGAGTTGCCATGTGGAC 58.770 47.619 2.55 0.00 37.39 4.02 R
3300 3414 0.676151 GAACCTCCTCTTGGCAGCTG 60.676 60.000 10.11 10.11 0.00 4.24 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
47 48 2.472816 CCATGCGGCAACCAAATTATC 58.527 47.619 6.82 0.00 0.00 1.75
168 170 7.603784 GTGGCAACTAATTTTCCTGAATGATTT 59.396 33.333 0.00 0.00 37.61 2.17
330 333 6.000840 TGGCAAATAGAATGTGAACACACTA 58.999 36.000 9.83 8.41 45.05 2.74
674 683 2.406130 CACATTTTTGCCGCTGAACAT 58.594 42.857 0.00 0.00 0.00 2.71
794 804 2.298729 GGGCTAACATGGCAACTTCAAA 59.701 45.455 0.00 0.00 37.61 2.69
864 882 2.692557 TGCAACCAATGTGCTTACTTGT 59.307 40.909 0.00 0.00 0.00 3.16
885 904 5.257108 TGTCACGTTTATGTTTTCGACAAC 58.743 37.500 7.50 7.50 42.62 3.32
895 914 2.940410 GTTTTCGACAACCACAAGAGGA 59.060 45.455 2.96 0.00 0.00 3.71
1007 1031 2.367894 CCTATCTCAGCAGAATGGCTCA 59.632 50.000 0.00 0.00 43.68 4.26
1281 1329 1.079057 GAGCCTCCCAAGAACGACC 60.079 63.158 0.00 0.00 0.00 4.79
1296 1344 1.197721 ACGACCGACTACGTTAACTGG 59.802 52.381 3.71 0.00 39.75 4.00
1762 1811 9.628500 AATGGTCCATCCTTACTACTTTATTTC 57.372 33.333 4.39 0.00 37.07 2.17
1885 1942 1.406898 TGAAAATCTTGTGCGGTGCAA 59.593 42.857 0.00 0.00 41.47 4.08
1894 1951 0.030101 GTGCGGTGCAAGCAAAACTA 59.970 50.000 18.08 0.00 46.97 2.24
1898 1955 2.605366 GCGGTGCAAGCAAAACTAAAAA 59.395 40.909 10.18 0.00 34.19 1.94
1946 2003 0.108186 CATAGCCGACTTCCTGCACA 60.108 55.000 0.00 0.00 0.00 4.57
2329 2434 1.647346 CCGCCTACGCATAAGTTTGA 58.353 50.000 0.00 0.00 38.22 2.69
2382 2487 4.254709 TGCTTGCCGCAGACAGGT 62.255 61.111 0.00 0.00 45.47 4.00
2445 2550 0.957395 CTTTCTCCACACGGCATGCT 60.957 55.000 18.92 0.00 0.00 3.79
2521 2626 1.667236 TATCCATGGCTTTCTGCGTG 58.333 50.000 6.96 0.00 44.05 5.34
2538 2643 2.604914 GCGTGTTGTATCCATGTCTCAG 59.395 50.000 0.00 0.00 0.00 3.35
2589 2694 8.535335 TGCTGAAACTTACATTCTCTCTCTTAT 58.465 33.333 0.00 0.00 0.00 1.73
2910 3024 2.273179 TTGAGGGGTGGACGTCTCG 61.273 63.158 16.46 0.00 0.00 4.04
2919 3033 0.892358 TGGACGTCTCGTAGTGGCTT 60.892 55.000 16.46 0.00 41.37 4.35
3056 3170 4.021104 CACAAGATGAACTAGGTGGAGACA 60.021 45.833 0.00 0.00 33.38 3.41
3128 3242 4.341366 ACCGATGATGATGAACATGCTA 57.659 40.909 0.00 0.00 39.56 3.49
3181 3295 1.212375 CACCATATGTCCCTCCACCA 58.788 55.000 1.24 0.00 0.00 4.17
3203 3317 5.389935 CCAGAGAAAGTCAAAGAACATACGC 60.390 44.000 0.00 0.00 0.00 4.42
3435 3555 3.181477 TGTCTGACAATTGCCACCTTTTG 60.181 43.478 8.27 0.00 0.00 2.44
3465 3585 2.449031 CTTACACGTGCAGGGAGGCA 62.449 60.000 17.22 0.00 42.53 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.439721 AGCTTGATTGTGGCAACTATCATA 58.560 37.500 17.45 8.98 44.43 2.15
1 2 4.275810 AGCTTGATTGTGGCAACTATCAT 58.724 39.130 17.45 2.32 44.43 2.45
47 48 3.062639 GTGGCAACTATCACAGTCATTCG 59.937 47.826 0.00 0.00 36.04 3.34
168 170 3.207265 ACAGTGTGGCAACTATCACAA 57.793 42.857 7.76 0.00 44.19 3.33
741 751 8.788806 AGTACGATAGATAGTCTCAAAATCCTG 58.211 37.037 0.00 0.00 41.38 3.86
794 804 8.190888 TCGTAAATGCACTTGAAAACAAAATT 57.809 26.923 0.00 0.00 0.00 1.82
864 882 4.331992 TGGTTGTCGAAAACATAAACGTGA 59.668 37.500 19.84 0.00 37.82 4.35
885 904 1.069765 ACACGCACTCCTCTTGTGG 59.930 57.895 0.00 0.00 36.08 4.17
895 914 1.136305 ACTAGTGAACACACACGCACT 59.864 47.619 7.68 0.00 44.35 4.40
1054 1078 2.238646 TCCGTCCAGTTGCCTGATTATT 59.761 45.455 0.00 0.00 41.50 1.40
1281 1329 2.624316 TCTGCCAGTTAACGTAGTCG 57.376 50.000 0.00 0.00 45.00 4.18
1291 1339 3.678056 TCGTCAGTAAATCTGCCAGTT 57.322 42.857 0.00 0.00 43.32 3.16
1296 1344 5.447818 CCCTTTTGATCGTCAGTAAATCTGC 60.448 44.000 0.00 0.00 43.32 4.26
1636 1684 8.846943 TGAGTAGCTTCATCTTAAAAACATCA 57.153 30.769 0.00 0.00 0.00 3.07
1762 1811 7.841956 ACATCGGATCTAAATAGATTGTAGGG 58.158 38.462 4.52 0.00 42.79 3.53
1777 1829 4.122776 GCTTTACACATGACATCGGATCT 58.877 43.478 0.00 0.00 0.00 2.75
1898 1955 4.889409 ACACCAGTTCATGTTCTTCACATT 59.111 37.500 0.00 0.00 44.40 2.71
1946 2003 5.163581 GGTACATCTTGCTTGAGAATGCATT 60.164 40.000 12.83 12.83 39.07 3.56
2321 2426 3.628032 TCCACGCACAAACATCAAACTTA 59.372 39.130 0.00 0.00 0.00 2.24
2329 2434 3.052455 TGATAGTCCACGCACAAACAT 57.948 42.857 0.00 0.00 0.00 2.71
2445 2550 5.988561 GGTTGCCTCATGTCAAATTTGTAAA 59.011 36.000 17.47 5.52 0.00 2.01
2538 2643 2.229792 TGAAAGAGTTGCCATGTGGAC 58.770 47.619 2.55 0.00 37.39 4.02
2919 3033 2.530497 GCAACCACGTCGCTGTCAA 61.530 57.895 0.00 0.00 0.00 3.18
3056 3170 2.159043 CGTCATCCTTGCTGATACCAGT 60.159 50.000 0.00 0.00 42.35 4.00
3128 3242 1.602377 GTTAGCACCTGCACGAACTTT 59.398 47.619 0.00 0.00 45.16 2.66
3181 3295 4.691216 GGCGTATGTTCTTTGACTTTCTCT 59.309 41.667 0.00 0.00 0.00 3.10
3300 3414 0.676151 GAACCTCCTCTTGGCAGCTG 60.676 60.000 10.11 10.11 0.00 4.24
3435 3555 2.032290 GCACGTGTAAGTTGGAGGAAAC 60.032 50.000 18.38 0.00 0.00 2.78
3465 3585 2.031163 GCTCGTCCACCAGCTGTT 59.969 61.111 13.81 0.00 32.48 3.16


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

AutoCloner maintained by Alex Coulton.