Multiple sequence alignment - TraesCS2D01G591900

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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 TraesCS2D01G591900 chr2D 100.000 2288 0 0 1 2288 647091183 647088896 0.000000e+00 4226
1 TraesCS2D01G591900 chr2D 95.577 2306 82 5 1 2288 646800103 646797800 0.000000e+00 3675
2 TraesCS2D01G591900 chr2D 95.447 2306 82 6 1 2288 646883877 646881577 0.000000e+00 3655
3 TraesCS2D01G591900 chr2D 95.405 2307 86 5 1 2288 646961478 646959173 0.000000e+00 3655
4 TraesCS2D01G591900 chr2D 95.506 2292 89 5 1 2288 646863595 646861314 0.000000e+00 3650
5 TraesCS2D01G591900 chr2D 95.222 2051 77 6 256 2288 646928767 646926720 0.000000e+00 3225
6 TraesCS2D01G591900 chr2D 87.799 795 49 15 938 1692 646000096 646000882 0.000000e+00 887
7 TraesCS2D01G591900 chr2D 88.073 436 32 5 1274 1692 587371899 587371467 1.220000e-137 499
8 TraesCS2D01G591900 chr2D 88.940 217 8 1 1492 1692 629244134 629244350 1.050000e-63 254
9 TraesCS2D01G591900 chr6D 93.597 1718 90 5 1 1700 446604638 446602923 0.000000e+00 2545
10 TraesCS2D01G591900 chr1A 93.388 1694 106 5 1 1692 463969302 463970991 0.000000e+00 2503
11 TraesCS2D01G591900 chr1D 92.699 1712 104 7 1 1696 369900550 369902256 0.000000e+00 2449
12 TraesCS2D01G591900 chr3A 91.817 1723 100 9 1 1695 600090327 600088618 0.000000e+00 2362
13 TraesCS2D01G591900 chr2A 91.565 1719 121 11 1 1701 171849915 171851627 0.000000e+00 2350
14 TraesCS2D01G591900 chr2B 91.199 1727 96 21 1 1698 23892244 23890545 0.000000e+00 2296
15 TraesCS2D01G591900 chr2B 91.163 1720 110 17 1 1692 643125131 643126836 0.000000e+00 2296
16 TraesCS2D01G591900 chr7A 91.042 1708 134 5 1 1692 167800040 167798336 0.000000e+00 2289
17 TraesCS2D01G591900 chr3B 89.914 1735 104 18 1 1696 581033388 581035090 0.000000e+00 2169
18 TraesCS2D01G591900 chr3B 82.492 297 43 7 1999 2287 690362612 690362317 3.770000e-63 252
19 TraesCS2D01G591900 chr3B 86.547 223 29 1 1764 1985 741884750 741884528 6.310000e-61 244
20 TraesCS2D01G591900 chr3B 86.283 226 30 1 1761 1985 780262670 780262445 6.310000e-61 244
21 TraesCS2D01G591900 chr5A 90.219 1370 86 19 360 1692 292010809 292012167 0.000000e+00 1744
22 TraesCS2D01G591900 chr5B 90.909 242 6 5 1466 1691 520072939 520073180 6.140000e-81 311
23 TraesCS2D01G591900 chr5B 84.122 296 35 9 2001 2286 454693457 454693164 2.240000e-70 276
24 TraesCS2D01G591900 chr6A 83.871 310 41 8 1981 2283 559205796 559206103 1.030000e-73 287
25 TraesCS2D01G591900 chr4A 82.410 307 43 7 1986 2284 627745397 627745700 8.110000e-65 257
26 TraesCS2D01G591900 chr1B 86.607 224 28 2 1763 1985 576599847 576600069 1.760000e-61 246
27 TraesCS2D01G591900 chr7D 85.217 230 33 1 1757 1985 71075801 71075572 3.800000e-58 235


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 TraesCS2D01G591900 chr2D 647088896 647091183 2287 True 4226 4226 100.000 1 2288 1 chr2D.!!$R7 2287
1 TraesCS2D01G591900 chr2D 646797800 646800103 2303 True 3675 3675 95.577 1 2288 1 chr2D.!!$R2 2287
2 TraesCS2D01G591900 chr2D 646881577 646883877 2300 True 3655 3655 95.447 1 2288 1 chr2D.!!$R4 2287
3 TraesCS2D01G591900 chr2D 646959173 646961478 2305 True 3655 3655 95.405 1 2288 1 chr2D.!!$R6 2287
4 TraesCS2D01G591900 chr2D 646861314 646863595 2281 True 3650 3650 95.506 1 2288 1 chr2D.!!$R3 2287
5 TraesCS2D01G591900 chr2D 646926720 646928767 2047 True 3225 3225 95.222 256 2288 1 chr2D.!!$R5 2032
6 TraesCS2D01G591900 chr2D 646000096 646000882 786 False 887 887 87.799 938 1692 1 chr2D.!!$F2 754
7 TraesCS2D01G591900 chr6D 446602923 446604638 1715 True 2545 2545 93.597 1 1700 1 chr6D.!!$R1 1699
8 TraesCS2D01G591900 chr1A 463969302 463970991 1689 False 2503 2503 93.388 1 1692 1 chr1A.!!$F1 1691
9 TraesCS2D01G591900 chr1D 369900550 369902256 1706 False 2449 2449 92.699 1 1696 1 chr1D.!!$F1 1695
10 TraesCS2D01G591900 chr3A 600088618 600090327 1709 True 2362 2362 91.817 1 1695 1 chr3A.!!$R1 1694
11 TraesCS2D01G591900 chr2A 171849915 171851627 1712 False 2350 2350 91.565 1 1701 1 chr2A.!!$F1 1700
12 TraesCS2D01G591900 chr2B 23890545 23892244 1699 True 2296 2296 91.199 1 1698 1 chr2B.!!$R1 1697
13 TraesCS2D01G591900 chr2B 643125131 643126836 1705 False 2296 2296 91.163 1 1692 1 chr2B.!!$F1 1691
14 TraesCS2D01G591900 chr7A 167798336 167800040 1704 True 2289 2289 91.042 1 1692 1 chr7A.!!$R1 1691
15 TraesCS2D01G591900 chr3B 581033388 581035090 1702 False 2169 2169 89.914 1 1696 1 chr3B.!!$F1 1695
16 TraesCS2D01G591900 chr5A 292010809 292012167 1358 False 1744 1744 90.219 360 1692 1 chr5A.!!$F1 1332

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
964 1010 1.131638 TGGTCCAACTCACTTCTGCT 58.868 50.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2219 0.822121 AAAAACCGTGCTCCAGGTCC 60.822 55.0 0.0 0.0 40.37 4.46 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
147 152 2.203167 CCTCGCTGGCATCTGCAT 60.203 61.111 4.33 0.00 44.36 3.96
383 388 4.081972 TCAGCGTCTTCAGCTCTTCTTTAT 60.082 41.667 0.00 0.00 44.06 1.40
442 447 4.002797 GGCATGGAGGCGAAGTTT 57.997 55.556 0.00 0.00 33.57 2.66
456 461 1.876156 GAAGTTTGAGCACACCTCCAG 59.124 52.381 0.00 0.00 39.98 3.86
495 500 3.936203 GTCACCAGCCGTCCACCA 61.936 66.667 0.00 0.00 0.00 4.17
540 546 2.478803 CCCAAGGGAAGGGGTTGGT 61.479 63.158 0.00 0.00 42.90 3.67
549 555 1.943730 AAGGGGTTGGTGTTGGAGCA 61.944 55.000 0.00 0.00 0.00 4.26
753 762 4.084287 ACTCCATGAATTGTGTGCAGATT 58.916 39.130 0.00 0.00 0.00 2.40
964 1010 1.131638 TGGTCCAACTCACTTCTGCT 58.868 50.000 0.00 0.00 0.00 4.24
1098 1168 0.247736 AGGTGACGGTGAAGCTGATC 59.752 55.000 0.00 0.00 0.00 2.92
1692 1817 2.826738 ACGGCAACCAAACACGCT 60.827 55.556 0.00 0.00 0.00 5.07
1704 1829 1.523758 AACACGCTCCAAATGAGTCC 58.476 50.000 0.00 0.00 43.48 3.85
1712 1837 4.038042 CGCTCCAAATGAGTCCAGTAGATA 59.962 45.833 0.00 0.00 43.48 1.98
1719 1844 3.031736 TGAGTCCAGTAGATAGGGTTGC 58.968 50.000 0.00 0.00 0.00 4.17
1729 1854 0.538118 ATAGGGTTGCGCGTTTCCTA 59.462 50.000 16.88 16.88 34.96 2.94
1861 1986 1.199097 GTGCCATTTGTCGTAACCTGG 59.801 52.381 0.00 0.00 0.00 4.45
1874 1999 5.528690 GTCGTAACCTGGTAGTTTTCCTTTT 59.471 40.000 0.00 0.00 0.00 2.27
2171 2298 2.179018 CAACCATGCCTTTCGCGG 59.821 61.111 6.13 0.00 42.08 6.46
2184 2311 3.057806 CCTTTCGCGGAAGTAAAACCATT 60.058 43.478 24.98 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 3.862402 CCGAGGAGGACGACGACG 61.862 72.222 5.58 5.58 45.00 5.12
102 107 4.003788 CAGGCCGTCGTTCCTGGT 62.004 66.667 18.07 0.00 44.64 4.00
147 152 1.187087 GGAGGAGGAAGAAGAAGCGA 58.813 55.000 0.00 0.00 0.00 4.93
229 234 0.325296 ACTGGGCTCCTAATGACCGA 60.325 55.000 0.00 0.00 0.00 4.69
383 388 1.246056 GCAGTGCTCATGAAGGCCAA 61.246 55.000 8.18 0.00 0.00 4.52
456 461 1.509703 GACCAAGTTCGAGAACACCC 58.490 55.000 17.00 0.00 43.47 4.61
495 500 0.620121 CTGGAGGGCCTTCTTCCTCT 60.620 60.000 14.33 0.00 46.51 3.69
753 762 1.767088 CCCATCTCATTGCTCTCCTCA 59.233 52.381 0.00 0.00 0.00 3.86
948 993 2.563179 GACCTAGCAGAAGTGAGTTGGA 59.437 50.000 0.00 0.00 0.00 3.53
1151 1221 2.037772 ACCATGTAGCCGATCTTGATCC 59.962 50.000 5.18 0.00 0.00 3.36
1633 1758 1.603739 GCACTTCTCCACCCAACCC 60.604 63.158 0.00 0.00 0.00 4.11
1692 1817 4.901849 CCCTATCTACTGGACTCATTTGGA 59.098 45.833 0.00 0.00 0.00 3.53
1704 1829 0.102481 ACGCGCAACCCTATCTACTG 59.898 55.000 5.73 0.00 0.00 2.74
1712 1837 0.535553 TTTAGGAAACGCGCAACCCT 60.536 50.000 5.73 10.66 0.00 4.34
1917 2043 0.999406 CGTTCGAGATTTGGACGCAT 59.001 50.000 0.00 0.00 0.00 4.73
2092 2219 0.822121 AAAAACCGTGCTCCAGGTCC 60.822 55.000 0.00 0.00 40.37 4.46
2171 2298 4.000988 TGCGAGAGGAATGGTTTTACTTC 58.999 43.478 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.