Multiple sequence alignment - TraesCS1A01G216600

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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 TraesCS1A01G216600 chr1A 100.000 2327 0 0 1 2327 384104948 384107274 0.000000e+00 4298
1 TraesCS1A01G216600 chr1A 93.794 1563 80 7 769 2327 102379064 102377515 0.000000e+00 2333
2 TraesCS1A01G216600 chr1A 94.171 772 44 1 1 771 102807207 102807978 0.000000e+00 1175
3 TraesCS1A01G216600 chr4A 93.555 1567 82 9 766 2327 140718647 140717095 0.000000e+00 2316
4 TraesCS1A01G216600 chr4A 90.295 711 52 7 895 1599 29295734 29296433 0.000000e+00 915
5 TraesCS1A01G216600 chr3A 93.754 1553 81 7 775 2327 736941142 736939606 0.000000e+00 2316
6 TraesCS1A01G216600 chr3A 92.408 1541 83 11 777 2317 539847930 539849436 0.000000e+00 2167
7 TraesCS1A01G216600 chr3A 93.912 772 43 4 1 771 137672839 137672071 0.000000e+00 1162
8 TraesCS1A01G216600 chr5A 93.505 1555 85 6 775 2327 396387405 396388945 0.000000e+00 2298
9 TraesCS1A01G216600 chr5A 94.825 773 37 3 1 771 365764897 365764126 0.000000e+00 1203
10 TraesCS1A01G216600 chr7A 92.634 1344 67 12 994 2327 33752554 33751233 0.000000e+00 1905
11 TraesCS1A01G216600 chr7A 93.790 773 46 2 1 771 244887205 244887977 0.000000e+00 1160
12 TraesCS1A01G216600 chr7A 93.579 623 31 4 775 1397 33753189 33752576 0.000000e+00 920
13 TraesCS1A01G216600 chr7A 98.104 211 3 1 766 975 299501369 299501579 1.310000e-97 366
14 TraesCS1A01G216600 chr5D 94.696 773 39 2 1 771 196611110 196611882 0.000000e+00 1199
15 TraesCS1A01G216600 chr5D 92.450 596 43 2 1593 2188 31089590 31090183 0.000000e+00 850
16 TraesCS1A01G216600 chr1D 94.675 770 37 4 1 768 176820047 176820814 0.000000e+00 1192
17 TraesCS1A01G216600 chr2D 94.315 774 40 4 1 771 135060054 135059282 0.000000e+00 1182
18 TraesCS1A01G216600 chr2A 93.920 773 45 2 1 771 512767042 512766270 0.000000e+00 1166
19 TraesCS1A01G216600 chr3D 93.790 773 46 2 1 771 350314020 350313248 0.000000e+00 1160
20 TraesCS1A01G216600 chr7D 93.333 735 40 3 1593 2327 623598038 623597313 0.000000e+00 1077
21 TraesCS1A01G216600 chr4B 89.744 702 57 7 903 1599 545148728 545149419 0.000000e+00 883
22 TraesCS1A01G216600 chr7B 90.981 632 56 1 1593 2224 178766768 178767398 0.000000e+00 850
23 TraesCS1A01G216600 chr4D 91.667 612 41 5 988 1599 440038159 440038760 0.000000e+00 839
24 TraesCS1A01G216600 chr6D 88.851 583 32 14 778 1352 291620022 291620579 0.000000e+00 686


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 TraesCS1A01G216600 chr1A 384104948 384107274 2326 False 4298.0 4298 100.0000 1 2327 1 chr1A.!!$F2 2326
1 TraesCS1A01G216600 chr1A 102377515 102379064 1549 True 2333.0 2333 93.7940 769 2327 1 chr1A.!!$R1 1558
2 TraesCS1A01G216600 chr1A 102807207 102807978 771 False 1175.0 1175 94.1710 1 771 1 chr1A.!!$F1 770
3 TraesCS1A01G216600 chr4A 140717095 140718647 1552 True 2316.0 2316 93.5550 766 2327 1 chr4A.!!$R1 1561
4 TraesCS1A01G216600 chr4A 29295734 29296433 699 False 915.0 915 90.2950 895 1599 1 chr4A.!!$F1 704
5 TraesCS1A01G216600 chr3A 736939606 736941142 1536 True 2316.0 2316 93.7540 775 2327 1 chr3A.!!$R2 1552
6 TraesCS1A01G216600 chr3A 539847930 539849436 1506 False 2167.0 2167 92.4080 777 2317 1 chr3A.!!$F1 1540
7 TraesCS1A01G216600 chr3A 137672071 137672839 768 True 1162.0 1162 93.9120 1 771 1 chr3A.!!$R1 770
8 TraesCS1A01G216600 chr5A 396387405 396388945 1540 False 2298.0 2298 93.5050 775 2327 1 chr5A.!!$F1 1552
9 TraesCS1A01G216600 chr5A 365764126 365764897 771 True 1203.0 1203 94.8250 1 771 1 chr5A.!!$R1 770
10 TraesCS1A01G216600 chr7A 33751233 33753189 1956 True 1412.5 1905 93.1065 775 2327 2 chr7A.!!$R1 1552
11 TraesCS1A01G216600 chr7A 244887205 244887977 772 False 1160.0 1160 93.7900 1 771 1 chr7A.!!$F1 770
12 TraesCS1A01G216600 chr5D 196611110 196611882 772 False 1199.0 1199 94.6960 1 771 1 chr5D.!!$F2 770
13 TraesCS1A01G216600 chr5D 31089590 31090183 593 False 850.0 850 92.4500 1593 2188 1 chr5D.!!$F1 595
14 TraesCS1A01G216600 chr1D 176820047 176820814 767 False 1192.0 1192 94.6750 1 768 1 chr1D.!!$F1 767
15 TraesCS1A01G216600 chr2D 135059282 135060054 772 True 1182.0 1182 94.3150 1 771 1 chr2D.!!$R1 770
16 TraesCS1A01G216600 chr2A 512766270 512767042 772 True 1166.0 1166 93.9200 1 771 1 chr2A.!!$R1 770
17 TraesCS1A01G216600 chr3D 350313248 350314020 772 True 1160.0 1160 93.7900 1 771 1 chr3D.!!$R1 770
18 TraesCS1A01G216600 chr7D 623597313 623598038 725 True 1077.0 1077 93.3330 1593 2327 1 chr7D.!!$R1 734
19 TraesCS1A01G216600 chr4B 545148728 545149419 691 False 883.0 883 89.7440 903 1599 1 chr4B.!!$F1 696
20 TraesCS1A01G216600 chr7B 178766768 178767398 630 False 850.0 850 90.9810 1593 2224 1 chr7B.!!$F1 631
21 TraesCS1A01G216600 chr4D 440038159 440038760 601 False 839.0 839 91.6670 988 1599 1 chr4D.!!$F1 611
22 TraesCS1A01G216600 chr6D 291620022 291620579 557 False 686.0 686 88.8510 778 1352 1 chr6D.!!$F1 574

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
125 126 0.555769 GGGGTTATGCATGAGGGGAA 59.444 55.0 10.16 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1897 0.040058 AGTTGATCCCATTGCAGCCA 59.96 50.0 0.0 0.0 0.0 4.75 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
125 126 0.555769 GGGGTTATGCATGAGGGGAA 59.444 55.000 10.16 0.00 0.00 3.97
132 133 5.351458 GTTATGCATGAGGGGAACATTTTC 58.649 41.667 10.16 0.00 0.00 2.29
170 171 7.505248 TGAAGCATGGCCAAACTATATGATTTA 59.495 33.333 10.96 0.00 28.75 1.40
179 180 9.167311 GCCAAACTATATGATTTAGTAGGGATG 57.833 37.037 13.30 3.32 31.02 3.51
690 700 1.301716 GGACGTCAAGGAAGCAGCA 60.302 57.895 18.91 0.00 0.00 4.41
751 763 3.842923 CCTCGCAGCTCCACCGAT 61.843 66.667 0.00 0.00 0.00 4.18
799 811 3.627395 ATAAAGCACGGATTGACTCCA 57.373 42.857 0.00 0.00 45.24 3.86
986 1007 2.363680 CCTCGACCTCATTGCTATCAGT 59.636 50.000 0.00 0.00 0.00 3.41
1046 1067 0.456221 GACATCGTGATCGTGGGAGT 59.544 55.000 0.00 0.00 38.33 3.85
1149 1181 4.678743 GCCTGGGGGTTCGCCTTT 62.679 66.667 5.91 0.00 37.37 3.11
1158 1190 2.193536 GTTCGCCTTTGCCACCTGT 61.194 57.895 0.00 0.00 0.00 4.00
1203 1235 2.280524 CTTGGCGTCGGTGACCAA 60.281 61.111 1.11 0.00 41.08 3.67
1335 1367 2.959484 GCTGCTGTAGGTCCTGGCA 61.959 63.158 0.00 8.56 0.00 4.92
1431 1867 3.157217 GATGCTCCACCTCGCCGAT 62.157 63.158 0.00 0.00 0.00 4.18
1456 1892 1.827399 GACTCTCCGGGCAAAGGTGA 61.827 60.000 0.00 0.00 0.00 4.02
1461 1897 1.606313 CCGGGCAAAGGTGATGGTT 60.606 57.895 0.00 0.00 0.00 3.67
1468 1911 0.469705 AAAGGTGATGGTTGGCTGCA 60.470 50.000 0.50 0.00 0.00 4.41
1470 1913 0.251922 AGGTGATGGTTGGCTGCAAT 60.252 50.000 0.50 0.00 0.00 3.56
1527 1970 2.117156 GCTCACCAAGCCATCGCAT 61.117 57.895 0.00 0.00 45.92 4.73
1534 1978 3.344137 AAGCCATCGCATTCCGGGT 62.344 57.895 0.00 0.00 37.52 5.28
1925 2372 4.626081 GGGCACACCAGCGACAGT 62.626 66.667 0.00 0.00 39.85 3.55
1932 2379 0.952497 CACCAGCGACAGTCAGCAAT 60.952 55.000 16.37 2.65 35.48 3.56
2104 2551 7.229506 GCAGCTCCCAAACAGTAATATTTCTAT 59.770 37.037 0.00 0.00 0.00 1.98
2140 2587 9.268268 ACACGTATTCTATTTGTTTCTCTTCAA 57.732 29.630 0.00 0.00 0.00 2.69
2268 2715 8.839310 ATATGGATTACATAGTTCTGCAAGTC 57.161 34.615 0.00 0.00 44.79 3.01
2295 2744 6.375455 ACATATATATGCCAACAAAGCTAGCC 59.625 38.462 20.46 0.00 37.19 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 3.495193 CCATGCTTCATTTTCGTCACAG 58.505 45.455 0.00 0.00 0.00 3.66
170 171 3.623453 GCCAAAGAAAGCTCATCCCTACT 60.623 47.826 0.00 0.00 0.00 2.57
179 180 8.028938 TCAAAATAACATAGCCAAAGAAAGCTC 58.971 33.333 0.00 0.00 40.56 4.09
394 399 3.677156 AGCATCCCCAAGCTTAATTCT 57.323 42.857 0.00 0.00 38.01 2.40
511 517 7.015389 TCGGTTAATAGGTTTGTCCCAAAAATT 59.985 33.333 0.00 0.00 36.75 1.82
523 529 4.014406 CTGGGCTTTCGGTTAATAGGTTT 58.986 43.478 0.00 0.00 0.00 3.27
656 666 0.898789 GTCCACTCCAAGTCTCCCGA 60.899 60.000 0.00 0.00 0.00 5.14
658 668 1.186267 ACGTCCACTCCAAGTCTCCC 61.186 60.000 0.00 0.00 0.00 4.30
690 700 2.291043 CCTACCTCGTGGCCACCTT 61.291 63.158 29.95 13.73 36.63 3.50
751 763 5.642165 AGGGATATAGGCGAAAGAAGTAGA 58.358 41.667 0.00 0.00 0.00 2.59
799 811 2.706890 GTATTGTGACGGTGAACCCAT 58.293 47.619 0.00 0.00 0.00 4.00
1136 1168 4.986708 TGGCAAAGGCGAACCCCC 62.987 66.667 0.00 0.00 42.47 5.40
1149 1181 4.947147 GCGTTGGGACAGGTGGCA 62.947 66.667 0.00 0.00 42.39 4.92
1456 1892 0.325860 ATCCCATTGCAGCCAACCAT 60.326 50.000 0.00 0.00 32.95 3.55
1461 1897 0.040058 AGTTGATCCCATTGCAGCCA 59.960 50.000 0.00 0.00 0.00 4.75
1653 2097 2.047370 TCGCATGCACCATCGTGT 60.047 55.556 19.57 0.00 42.39 4.49
1759 2203 2.282110 CCACCATGCACCAACGGA 60.282 61.111 0.00 0.00 0.00 4.69
1908 2355 4.626081 ACTGTCGCTGGTGTGCCC 62.626 66.667 0.00 0.00 0.00 5.36
1925 2372 3.493440 CGCTCGCTGCATTGCTGA 61.493 61.111 18.44 8.77 43.06 4.26
1949 2396 2.387445 TTTTCGCATCACGGCTCGG 61.387 57.895 0.00 0.00 43.89 4.63
2027 2474 3.750373 AACAGGTTGCACTCGCCGT 62.750 57.895 0.00 0.00 37.32 5.68
2066 2513 0.246635 GGAGCTGCCTCGAGTGTTAA 59.753 55.000 12.31 0.00 39.06 2.01
2268 2715 6.579666 AGCTTTGTTGGCATATATATGTGG 57.420 37.500 21.10 0.06 36.11 4.17


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

AutoCloner maintained by Alex Coulton.