Multiple sequence alignment - TraesCS5A01G102100

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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 TraesCS5A01G102100 chr5A 100.000 2994 0 0 1 2994 153575858 153572865 0 5529
1 TraesCS5A01G102100 chr5A 94.752 2115 82 16 886 2994 565286118 565284027 0 3264
2 TraesCS5A01G102100 chr5A 94.213 2108 93 16 893 2994 693843667 693845751 0 3190
3 TraesCS5A01G102100 chr2A 97.302 3002 46 19 1 2994 30580111 30583085 0 5062
4 TraesCS5A01G102100 chr2A 96.465 2999 74 18 1 2994 614119 611148 0 4922
5 TraesCS5A01G102100 chr2A 94.077 2161 76 17 791 2919 15750046 15747906 0 3234
6 TraesCS5A01G102100 chr4A 96.999 2999 42 15 1 2994 600514279 600511324 0 4996
7 TraesCS5A01G102100 chr7A 97.333 2100 31 11 433 2527 10993226 10995305 0 3544
8 TraesCS5A01G102100 chr7A 95.873 2108 61 12 891 2994 15520956 15518871 0 3387
9 TraesCS5A01G102100 chr7A 95.067 892 36 7 1 888 15521902 15521015 0 1397
10 TraesCS5A01G102100 chr6A 95.920 2108 56 16 891 2994 555103859 555101778 0 3389
11 TraesCS5A01G102100 chr6A 95.394 2106 70 13 893 2994 597466971 597464889 0 3326
12 TraesCS5A01G102100 chr6A 95.396 2107 68 15 893 2994 602796925 602794843 0 3326
13 TraesCS5A01G102100 chr6A 95.516 892 32 6 1 888 555104805 555103918 0 1419
14 TraesCS5A01G102100 chr3A 99.079 1737 13 2 1259 2994 38170700 38172434 0 3116
15 TraesCS5A01G102100 chr3A 94.183 894 42 9 1 888 17914021 17913132 0 1354
16 TraesCS5A01G102100 chr3A 99.222 643 4 1 433 1074 38170061 38170703 0 1158
17 TraesCS5A01G102100 chr2B 94.038 889 45 8 3 888 512426312 512425429 0 1341
18 TraesCS5A01G102100 chr2B 94.124 885 47 5 3 886 670327043 670327923 0 1341
19 TraesCS5A01G102100 chr2B 87.020 886 57 14 3 886 717673954 717673125 0 946
20 TraesCS5A01G102100 chr2B 87.020 886 57 18 3 886 738147997 738148826 0 946
21 TraesCS5A01G102100 chr7B 94.018 886 47 6 3 886 599829274 599830155 0 1338
22 TraesCS5A01G102100 chr6B 93.671 869 48 7 22 888 353552274 353551411 0 1293


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 TraesCS5A01G102100 chr5A 153572865 153575858 2993 True 5529 5529 100.0000 1 2994 1 chr5A.!!$R1 2993
1 TraesCS5A01G102100 chr5A 565284027 565286118 2091 True 3264 3264 94.7520 886 2994 1 chr5A.!!$R2 2108
2 TraesCS5A01G102100 chr5A 693843667 693845751 2084 False 3190 3190 94.2130 893 2994 1 chr5A.!!$F1 2101
3 TraesCS5A01G102100 chr2A 30580111 30583085 2974 False 5062 5062 97.3020 1 2994 1 chr2A.!!$F1 2993
4 TraesCS5A01G102100 chr2A 611148 614119 2971 True 4922 4922 96.4650 1 2994 1 chr2A.!!$R1 2993
5 TraesCS5A01G102100 chr2A 15747906 15750046 2140 True 3234 3234 94.0770 791 2919 1 chr2A.!!$R2 2128
6 TraesCS5A01G102100 chr4A 600511324 600514279 2955 True 4996 4996 96.9990 1 2994 1 chr4A.!!$R1 2993
7 TraesCS5A01G102100 chr7A 10993226 10995305 2079 False 3544 3544 97.3330 433 2527 1 chr7A.!!$F1 2094
8 TraesCS5A01G102100 chr7A 15518871 15521902 3031 True 2392 3387 95.4700 1 2994 2 chr7A.!!$R1 2993
9 TraesCS5A01G102100 chr6A 597464889 597466971 2082 True 3326 3326 95.3940 893 2994 1 chr6A.!!$R1 2101
10 TraesCS5A01G102100 chr6A 602794843 602796925 2082 True 3326 3326 95.3960 893 2994 1 chr6A.!!$R2 2101
11 TraesCS5A01G102100 chr6A 555101778 555104805 3027 True 2404 3389 95.7180 1 2994 2 chr6A.!!$R3 2993
12 TraesCS5A01G102100 chr3A 38170061 38172434 2373 False 2137 3116 99.1505 433 2994 2 chr3A.!!$F1 2561
13 TraesCS5A01G102100 chr3A 17913132 17914021 889 True 1354 1354 94.1830 1 888 1 chr3A.!!$R1 887
14 TraesCS5A01G102100 chr2B 512425429 512426312 883 True 1341 1341 94.0380 3 888 1 chr2B.!!$R1 885
15 TraesCS5A01G102100 chr2B 670327043 670327923 880 False 1341 1341 94.1240 3 886 1 chr2B.!!$F1 883
16 TraesCS5A01G102100 chr2B 717673125 717673954 829 True 946 946 87.0200 3 886 1 chr2B.!!$R2 883
17 TraesCS5A01G102100 chr2B 738147997 738148826 829 False 946 946 87.0200 3 886 1 chr2B.!!$F2 883
18 TraesCS5A01G102100 chr7B 599829274 599830155 881 False 1338 1338 94.0180 3 886 1 chr7B.!!$F1 883
19 TraesCS5A01G102100 chr6B 353551411 353552274 863 True 1293 1293 93.6710 22 888 1 chr6B.!!$R1 866

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
547 560 0.107456 AGCACTTCTATGGCGGGATG 59.893 55.0 0.0 0.0 0.00 3.51 F
549 562 0.107456 CACTTCTATGGCGGGATGCT 59.893 55.0 0.0 0.0 45.43 3.79 F
550 563 0.839946 ACTTCTATGGCGGGATGCTT 59.160 50.0 0.0 0.0 45.43 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 1870 0.255890 CGGGATCCCTTGGTGTGATT 59.744 55.000 28.42 0.0 0.00 2.57 R
1935 2039 4.159321 TGACATGGTTCAAGCAAAAACAGA 59.841 37.500 0.00 0.0 0.00 3.41 R
2380 2516 4.405116 TTTCTGTTTTCAGCAAGGCAAT 57.595 36.364 0.00 0.0 46.59 3.56 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
132 136 4.579454 AGAGACAGTTGCGTAGTACAAA 57.421 40.909 0.38 0.00 0.00 2.83
532 545 4.212214 CCTGAAGACACTTCAAAGTAGCAC 59.788 45.833 13.78 0.00 37.08 4.40
533 546 5.023533 TGAAGACACTTCAAAGTAGCACT 57.976 39.130 11.06 0.00 37.08 4.40
534 547 5.428253 TGAAGACACTTCAAAGTAGCACTT 58.572 37.500 11.06 0.00 40.80 3.16
535 548 5.523916 TGAAGACACTTCAAAGTAGCACTTC 59.476 40.000 11.06 15.40 37.47 3.01
536 549 5.283457 AGACACTTCAAAGTAGCACTTCT 57.717 39.130 0.00 0.00 37.47 2.85
537 550 6.406692 AGACACTTCAAAGTAGCACTTCTA 57.593 37.500 0.00 0.00 37.47 2.10
538 551 6.998802 AGACACTTCAAAGTAGCACTTCTAT 58.001 36.000 0.00 0.00 37.47 1.98
539 552 6.870965 AGACACTTCAAAGTAGCACTTCTATG 59.129 38.462 0.00 0.00 37.47 2.23
540 553 5.934625 ACACTTCAAAGTAGCACTTCTATGG 59.065 40.000 0.00 0.00 37.47 2.74
541 554 4.938226 ACTTCAAAGTAGCACTTCTATGGC 59.062 41.667 0.00 0.00 37.47 4.40
542 555 3.521560 TCAAAGTAGCACTTCTATGGCG 58.478 45.455 2.65 0.00 37.47 5.69
543 556 2.604046 AAGTAGCACTTCTATGGCGG 57.396 50.000 0.00 0.00 31.77 6.13
544 557 0.753262 AGTAGCACTTCTATGGCGGG 59.247 55.000 0.00 0.00 0.00 6.13
545 558 0.750850 GTAGCACTTCTATGGCGGGA 59.249 55.000 0.00 0.00 0.00 5.14
546 559 1.344763 GTAGCACTTCTATGGCGGGAT 59.655 52.381 0.00 0.00 0.00 3.85
547 560 0.107456 AGCACTTCTATGGCGGGATG 59.893 55.000 0.00 0.00 0.00 3.51
548 561 1.510480 GCACTTCTATGGCGGGATGC 61.510 60.000 0.00 0.00 45.38 3.91
549 562 0.107456 CACTTCTATGGCGGGATGCT 59.893 55.000 0.00 0.00 45.43 3.79
550 563 0.839946 ACTTCTATGGCGGGATGCTT 59.160 50.000 0.00 0.00 45.43 3.91
551 564 1.233019 CTTCTATGGCGGGATGCTTG 58.767 55.000 0.00 0.00 45.43 4.01
1066 1163 5.240623 CCATTGTACTGTACACAACATGGTT 59.759 40.000 26.65 1.88 38.02 3.67
1159 1256 1.228228 GCAATGGAGGCAGATGGGA 59.772 57.895 0.00 0.00 0.00 4.37
1769 1870 6.934056 AGCCATGTTTGACTAAATATTTGCA 58.066 32.000 11.05 3.89 31.04 4.08
1935 2039 6.204882 GTGTTTCTTAGCCTATCAACAAGTGT 59.795 38.462 0.00 0.00 0.00 3.55
2380 2516 3.272574 TGCCCAAACTTTGCATTTGAA 57.727 38.095 11.88 0.00 39.01 2.69
2411 2547 9.950680 CTTGCTGAAAACAGAAAAGAAACTATA 57.049 29.630 0.00 0.00 0.00 1.31
2527 2664 6.670464 TGGGACAGAACTCATTGTACCTTATA 59.330 38.462 7.35 0.00 46.55 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 112 5.694231 TTGTACTACGCAACTGTCTCTTA 57.306 39.130 0.00 0.00 0.00 2.10
183 188 3.417069 TGCAACTGTATACTGGCAACT 57.583 42.857 13.58 0.00 37.61 3.16
253 259 8.360390 CAGCTGAGATAGTTGTTGGTATATGTA 58.640 37.037 8.42 0.00 33.41 2.29
254 260 7.212976 CAGCTGAGATAGTTGTTGGTATATGT 58.787 38.462 8.42 0.00 33.41 2.29
532 545 1.233019 CAAGCATCCCGCCATAGAAG 58.767 55.000 0.00 0.00 44.04 2.85
533 546 0.819259 GCAAGCATCCCGCCATAGAA 60.819 55.000 0.00 0.00 44.04 2.10
534 547 1.227943 GCAAGCATCCCGCCATAGA 60.228 57.895 0.00 0.00 44.04 1.98
535 548 0.820891 AAGCAAGCATCCCGCCATAG 60.821 55.000 0.00 0.00 44.04 2.23
536 549 0.819259 GAAGCAAGCATCCCGCCATA 60.819 55.000 0.00 0.00 44.04 2.74
537 550 2.043652 AAGCAAGCATCCCGCCAT 60.044 55.556 0.00 0.00 44.04 4.40
538 551 2.751436 GAAGCAAGCATCCCGCCA 60.751 61.111 0.00 0.00 44.04 5.69
539 552 3.521796 GGAAGCAAGCATCCCGCC 61.522 66.667 5.04 0.00 44.04 6.13
540 553 3.521796 GGGAAGCAAGCATCCCGC 61.522 66.667 18.41 0.00 42.99 6.13
543 556 0.975887 TTTTGGGGAAGCAAGCATCC 59.024 50.000 7.75 7.75 33.45 3.51
544 557 2.837532 TTTTTGGGGAAGCAAGCATC 57.162 45.000 0.00 0.00 0.00 3.91
545 558 2.638855 TGATTTTTGGGGAAGCAAGCAT 59.361 40.909 0.00 0.00 0.00 3.79
546 559 2.045524 TGATTTTTGGGGAAGCAAGCA 58.954 42.857 0.00 0.00 0.00 3.91
547 560 2.837532 TGATTTTTGGGGAAGCAAGC 57.162 45.000 0.00 0.00 0.00 4.01
548 561 5.065235 ACATTTGATTTTTGGGGAAGCAAG 58.935 37.500 0.00 0.00 34.38 4.01
549 562 5.046288 ACATTTGATTTTTGGGGAAGCAA 57.954 34.783 0.00 0.00 31.32 3.91
550 563 4.703379 ACATTTGATTTTTGGGGAAGCA 57.297 36.364 0.00 0.00 0.00 3.91
551 564 4.320421 GCAACATTTGATTTTTGGGGAAGC 60.320 41.667 0.00 0.00 0.00 3.86
1066 1163 3.306225 GCCACAAATTCTGCATTTCCAGA 60.306 43.478 0.00 0.00 39.94 3.86
1159 1256 0.324943 CGACCCCCATGACTTGACTT 59.675 55.000 0.00 0.00 0.00 3.01
1769 1870 0.255890 CGGGATCCCTTGGTGTGATT 59.744 55.000 28.42 0.00 0.00 2.57
1867 1969 6.094186 GCAGGTTCTTAAAGTTAGAAGATGGG 59.906 42.308 1.98 0.00 32.60 4.00
1868 1970 6.655003 TGCAGGTTCTTAAAGTTAGAAGATGG 59.345 38.462 1.98 0.00 32.60 3.51
1935 2039 4.159321 TGACATGGTTCAAGCAAAAACAGA 59.841 37.500 0.00 0.00 0.00 3.41
2380 2516 4.405116 TTTCTGTTTTCAGCAAGGCAAT 57.595 36.364 0.00 0.00 46.59 3.56
2411 2547 5.590530 TCTACACAAAAACAGTGCCAAAT 57.409 34.783 0.00 0.00 40.59 2.32
2527 2664 5.825679 TGAGGTTTGTAATGTGTTTAGTGCT 59.174 36.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.