Multiple sequence alignment - TraesCS5A01G124500

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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 TraesCS5A01G124500 chr5A 100.000 2237 0 0 1 2237 272286001 272288237 0 4132
1 TraesCS5A01G124500 chr7D 96.604 1384 42 4 1 1381 474678226 474679607 0 2290
2 TraesCS5A01G124500 chr7D 91.841 858 65 3 1381 2237 470921977 470921124 0 1192
3 TraesCS5A01G124500 chr1B 96.457 1383 46 2 1 1381 95493322 95494703 0 2279
4 TraesCS5A01G124500 chr1B 96.179 1387 46 4 1 1381 530762844 530761459 0 2261
5 TraesCS5A01G124500 chr2B 96.023 1383 52 2 1 1381 424683736 424682355 0 2246
6 TraesCS5A01G124500 chr2A 95.960 1386 50 3 1 1381 628571087 628572471 0 2244
7 TraesCS5A01G124500 chr2A 95.818 1387 50 6 1 1381 374484955 374486339 0 2233
8 TraesCS5A01G124500 chr2A 95.671 1386 54 3 1 1381 628646932 628645548 0 2222
9 TraesCS5A01G124500 chr2A 95.674 1387 47 6 1 1381 161528151 161529530 0 2217
10 TraesCS5A01G124500 chr2A 91.841 858 61 5 1381 2237 120430834 120431683 0 1188
11 TraesCS5A01G124500 chr1A 95.746 1387 52 4 1 1381 409610515 409611900 0 2228
12 TraesCS5A01G124500 chr2D 92.326 860 57 6 1381 2237 450365177 450366030 0 1214
13 TraesCS5A01G124500 chr3D 91.977 860 61 7 1381 2237 468538092 468538946 0 1199
14 TraesCS5A01G124500 chr3D 92.217 848 59 5 1381 2226 436366370 436367212 0 1194
15 TraesCS5A01G124500 chr3A 91.851 859 62 5 1381 2237 101519731 101518879 0 1192
16 TraesCS5A01G124500 chr5D 91.841 858 63 4 1381 2237 347260669 347261520 0 1190
17 TraesCS5A01G124500 chr1D 91.754 861 60 8 1381 2237 316833280 316834133 0 1186
18 TraesCS5A01G124500 chr1D 91.608 858 66 3 1381 2237 477773418 477774270 0 1181


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 TraesCS5A01G124500 chr5A 272286001 272288237 2236 False 4132 4132 100.000 1 2237 1 chr5A.!!$F1 2236
1 TraesCS5A01G124500 chr7D 474678226 474679607 1381 False 2290 2290 96.604 1 1381 1 chr7D.!!$F1 1380
2 TraesCS5A01G124500 chr7D 470921124 470921977 853 True 1192 1192 91.841 1381 2237 1 chr7D.!!$R1 856
3 TraesCS5A01G124500 chr1B 95493322 95494703 1381 False 2279 2279 96.457 1 1381 1 chr1B.!!$F1 1380
4 TraesCS5A01G124500 chr1B 530761459 530762844 1385 True 2261 2261 96.179 1 1381 1 chr1B.!!$R1 1380
5 TraesCS5A01G124500 chr2B 424682355 424683736 1381 True 2246 2246 96.023 1 1381 1 chr2B.!!$R1 1380
6 TraesCS5A01G124500 chr2A 628571087 628572471 1384 False 2244 2244 95.960 1 1381 1 chr2A.!!$F4 1380
7 TraesCS5A01G124500 chr2A 374484955 374486339 1384 False 2233 2233 95.818 1 1381 1 chr2A.!!$F3 1380
8 TraesCS5A01G124500 chr2A 628645548 628646932 1384 True 2222 2222 95.671 1 1381 1 chr2A.!!$R1 1380
9 TraesCS5A01G124500 chr2A 161528151 161529530 1379 False 2217 2217 95.674 1 1381 1 chr2A.!!$F2 1380
10 TraesCS5A01G124500 chr2A 120430834 120431683 849 False 1188 1188 91.841 1381 2237 1 chr2A.!!$F1 856
11 TraesCS5A01G124500 chr1A 409610515 409611900 1385 False 2228 2228 95.746 1 1381 1 chr1A.!!$F1 1380
12 TraesCS5A01G124500 chr2D 450365177 450366030 853 False 1214 1214 92.326 1381 2237 1 chr2D.!!$F1 856
13 TraesCS5A01G124500 chr3D 468538092 468538946 854 False 1199 1199 91.977 1381 2237 1 chr3D.!!$F2 856
14 TraesCS5A01G124500 chr3D 436366370 436367212 842 False 1194 1194 92.217 1381 2226 1 chr3D.!!$F1 845
15 TraesCS5A01G124500 chr3A 101518879 101519731 852 True 1192 1192 91.851 1381 2237 1 chr3A.!!$R1 856
16 TraesCS5A01G124500 chr5D 347260669 347261520 851 False 1190 1190 91.841 1381 2237 1 chr5D.!!$F1 856
17 TraesCS5A01G124500 chr1D 316833280 316834133 853 False 1186 1186 91.754 1381 2237 1 chr1D.!!$F1 856
18 TraesCS5A01G124500 chr1D 477773418 477774270 852 False 1181 1181 91.608 1381 2237 1 chr1D.!!$F2 856

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
794 797 0.81321 GAATCTTGGAGGAGCTGGCG 60.813 60.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2159 0.813821 GGGTACGTAGACACACTCCC 59.186 60.0 0.0 0.0 0.0 4.3 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
53 54 6.069789 GGGTCTCCCAAAGGTAATAAACTAGT 60.070 42.308 0.00 0.00 44.65 2.57
159 162 4.637534 GGAAATGCAGAAGATAGAGCACAA 59.362 41.667 0.00 0.00 40.14 3.33
327 330 8.171164 ACGAGAAGAAGAAAATCCAAGAAAAT 57.829 30.769 0.00 0.00 0.00 1.82
330 333 9.623350 GAGAAGAAGAAAATCCAAGAAAATGAG 57.377 33.333 0.00 0.00 0.00 2.90
403 406 1.004200 GTTTCATGGGACGACCGGT 60.004 57.895 6.92 6.92 44.64 5.28
419 422 3.097614 ACCGGTAGTGCAAGATTCTAGT 58.902 45.455 4.49 0.00 0.00 2.57
425 428 5.069781 GGTAGTGCAAGATTCTAGTGGATCT 59.930 44.000 0.00 0.00 0.00 2.75
426 429 5.021033 AGTGCAAGATTCTAGTGGATCTG 57.979 43.478 0.00 4.17 0.00 2.90
456 459 9.294030 CTTTGGAAAAACATCATCATAGTAAGC 57.706 33.333 0.00 0.00 0.00 3.09
610 613 5.450965 GGGAGAATTGCATGATGGTTAGTTG 60.451 44.000 0.00 0.00 0.00 3.16
631 634 8.412608 AGTTGTCAACTTCATTCATATACTCG 57.587 34.615 12.62 0.00 39.04 4.18
742 745 7.122948 GGGACATATAACTTCACCTCTATCGAT 59.877 40.741 2.16 2.16 0.00 3.59
794 797 0.813210 GAATCTTGGAGGAGCTGGCG 60.813 60.000 0.00 0.00 0.00 5.69
818 821 6.305272 AGAATCAAGGAGAAACATCAGCTA 57.695 37.500 0.00 0.00 0.00 3.32
996 1002 2.774799 GGCGAATGGTGATGTGGCC 61.775 63.158 0.00 0.00 0.00 5.36
1040 1046 1.276622 ATAAGGACGAAGCAGGTGGT 58.723 50.000 0.00 0.00 0.00 4.16
1070 1076 0.034477 AATAAGCCAAGGGTCGTGGG 60.034 55.000 2.42 0.00 36.58 4.61
1093 1100 5.062308 GGTGAGTACTCTATCAAAAACTGCG 59.938 44.000 23.01 0.00 0.00 5.18
1185 1192 3.799420 CCGAGAACCGAGAGATTTTCATC 59.201 47.826 0.00 0.00 41.76 2.92
1354 1364 7.599630 TTTTCTGCTGAAAATGGATATTTGC 57.400 32.000 22.94 0.00 44.39 3.68
1409 1419 2.352127 GCATCGTCATGATCTCCATCGA 60.352 50.000 0.00 1.26 36.42 3.59
1471 1481 2.024176 TCTCGCCAACTATTGCTTCC 57.976 50.000 0.00 0.00 0.00 3.46
1488 1498 2.572191 TCCACAACTATCGCTAACGG 57.428 50.000 0.00 0.00 40.63 4.44
1539 1549 6.815641 TGGCGTTTGCATTTCATACAATAAAT 59.184 30.769 0.00 0.00 45.35 1.40
1680 1691 6.011476 ACAAGTTAGACGTCCTCTACTTTC 57.989 41.667 13.01 0.00 30.56 2.62
1707 1718 2.412847 GCAAGTTTTACGTGGCTGCTAG 60.413 50.000 0.00 0.00 0.00 3.42
1718 1729 1.051556 GGCTGCTAGGGGCTTCTAGT 61.052 60.000 13.78 0.00 42.39 2.57
1742 1754 2.573941 ACCGTTCTTACCTACGCATC 57.426 50.000 0.00 0.00 36.49 3.91
1901 1913 1.745489 GGAACCGGTCTCATGTGCC 60.745 63.158 8.04 0.00 0.00 5.01
1968 1980 4.998672 ACCGAATCAAAATAAGACGTTGGA 59.001 37.500 0.00 0.00 0.00 3.53
2083 2098 4.591998 AAACGTTGCATGGAAAACAAAC 57.408 36.364 0.00 0.00 0.00 2.93
2086 2101 3.997021 ACGTTGCATGGAAAACAAACAAA 59.003 34.783 0.00 0.00 32.09 2.83
2087 2102 4.452455 ACGTTGCATGGAAAACAAACAAAA 59.548 33.333 0.00 0.00 32.09 2.44
2200 2216 2.228138 AGCGTTTGACAAGACGGTTA 57.772 45.000 16.39 0.00 46.34 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.422479 CCGACCAGAGAAATAGTCACGA 59.578 50.000 0.00 0.00 0.00 4.35
159 162 2.519771 TCTCAAGGCTTGCATTCCAT 57.480 45.000 22.31 0.00 0.00 3.41
256 259 6.984474 TGGTGGAATTTCTTCACTATCGTATC 59.016 38.462 5.98 0.00 32.70 2.24
403 406 5.452496 GCAGATCCACTAGAATCTTGCACTA 60.452 44.000 0.00 0.00 0.00 2.74
419 422 2.673775 TTTCCAAAGTGGCAGATCCA 57.326 45.000 0.00 0.00 44.18 3.41
425 428 4.100653 TGATGATGTTTTTCCAAAGTGGCA 59.899 37.500 0.00 0.00 37.47 4.92
426 429 4.630111 TGATGATGTTTTTCCAAAGTGGC 58.370 39.130 0.00 0.00 37.47 5.01
456 459 9.927668 AAACTTTTAGGGAATAACAATGACATG 57.072 29.630 0.00 0.00 0.00 3.21
610 613 7.488150 TGACACGAGTATATGAATGAAGTTGAC 59.512 37.037 0.00 0.00 0.00 3.18
742 745 5.479724 TGATTGGGTTGAGCAATGTAATGAA 59.520 36.000 0.00 0.00 0.00 2.57
747 750 3.760738 TGTGATTGGGTTGAGCAATGTA 58.239 40.909 0.00 0.00 0.00 2.29
794 797 5.184711 AGCTGATGTTTCTCCTTGATTCTC 58.815 41.667 0.00 0.00 0.00 2.87
818 821 4.107072 TCTCCTCCAAGATTCTCACCATT 58.893 43.478 0.00 0.00 0.00 3.16
996 1002 3.310774 CCAAGTACTTCTCCATCATTGCG 59.689 47.826 4.77 0.00 0.00 4.85
1040 1046 3.137176 CCTTGGCTTATTCCTCTCATCCA 59.863 47.826 0.00 0.00 0.00 3.41
1070 1076 5.634020 ACGCAGTTTTTGATAGAGTACTCAC 59.366 40.000 24.44 14.93 37.78 3.51
1093 1100 4.919754 GTCCATTGTTTTCAGCAGATCAAC 59.080 41.667 0.00 0.00 0.00 3.18
1185 1192 0.037512 CAGTCTCTGGTCTGGCACTG 60.038 60.000 0.00 0.00 0.00 3.66
1225 1232 7.272144 AGGAGTACCTGAGTTATTCCATTTT 57.728 36.000 1.68 0.00 45.92 1.82
1376 1386 4.701651 TCATGACGATGCTTTGGAGAAAAT 59.298 37.500 0.00 0.00 0.00 1.82
1409 1419 3.231736 AAGGTGTCGAGCCGGTGT 61.232 61.111 1.90 0.00 0.00 4.16
1471 1481 4.675565 CACTATCCGTTAGCGATAGTTGTG 59.324 45.833 15.78 7.78 38.30 3.33
1539 1549 4.398358 CGACAGGAGTCTTATGGTTGTCTA 59.602 45.833 0.00 0.00 42.73 2.59
1680 1691 2.533942 GCCACGTAAAACTTGCAACAAG 59.466 45.455 5.80 5.80 0.00 3.16
1901 1913 2.711542 GGACCAACCTTACATGTCCAG 58.288 52.381 0.00 0.00 43.92 3.86
1968 1980 4.278669 CGGTGATAGTCATACTGCTTACCT 59.721 45.833 0.00 0.00 0.00 3.08
2086 2101 4.385825 TCCTTGTGAGTGCGTAGAATTTT 58.614 39.130 0.00 0.00 0.00 1.82
2087 2102 4.002906 TCCTTGTGAGTGCGTAGAATTT 57.997 40.909 0.00 0.00 0.00 1.82
2102 2118 4.019501 GCATCTCCATGGATAGATCCTTGT 60.020 45.833 16.63 0.00 45.61 3.16
2143 2159 0.813821 GGGTACGTAGACACACTCCC 59.186 60.000 0.00 0.00 0.00 4.30
2144 2160 1.742268 GAGGGTACGTAGACACACTCC 59.258 57.143 7.13 0.00 39.39 3.85
2193 2209 7.384387 AGAAGAAGTTTGACTACATTAACCGTC 59.616 37.037 0.00 0.00 0.00 4.79
2200 2216 7.100409 GGAGCTAGAAGAAGTTTGACTACATT 58.900 38.462 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.