Multiple sequence alignment - TraesCS7D01G424000

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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 TraesCS7D01G424000 chr7D 100.000 2276 0 0 1 2276 544560454 544558179 0.000000e+00 4204.0
1 TraesCS7D01G424000 chr7D 97.243 1306 31 1 1 1306 599239745 599238445 0.000000e+00 2207.0
2 TraesCS7D01G424000 chr4D 98.008 1305 26 0 1 1305 298273073 298274377 0.000000e+00 2266.0
3 TraesCS7D01G424000 chr3D 97.623 1304 31 0 1 1304 31890960 31889657 0.000000e+00 2237.0
4 TraesCS7D01G424000 chr7B 92.868 1304 93 0 1 1304 706500288 706501591 0.000000e+00 1893.0
5 TraesCS7D01G424000 chr7B 92.346 797 44 11 1480 2276 587966679 587965900 0.000000e+00 1118.0
6 TraesCS7D01G424000 chr1A 92.414 1305 99 0 1 1305 65652204 65650900 0.000000e+00 1862.0
7 TraesCS7D01G424000 chr4B 94.103 1221 70 1 1 1221 605895610 605894392 0.000000e+00 1855.0
8 TraesCS7D01G424000 chr4B 84.112 107 11 6 1305 1408 620266973 620266870 5.170000e-17 99.0
9 TraesCS7D01G424000 chr6B 92.178 1304 102 0 1 1304 173438468 173437165 0.000000e+00 1844.0
10 TraesCS7D01G424000 chr6B 84.815 810 73 32 1477 2276 663691080 663691849 0.000000e+00 769.0
11 TraesCS7D01G424000 chr7A 92.037 1306 103 1 1 1306 79128437 79127133 0.000000e+00 1834.0
12 TraesCS7D01G424000 chr7A 93.340 931 42 8 1358 2276 625754286 625753364 0.000000e+00 1358.0
13 TraesCS7D01G424000 chr2B 94.008 1185 70 1 1 1185 683266695 683267878 0.000000e+00 1794.0
14 TraesCS7D01G424000 chr2B 95.161 62 1 1 1252 1313 683268173 683268232 1.860000e-16 97.1
15 TraesCS7D01G424000 chr6A 86.318 804 78 22 1484 2276 586815915 586816697 0.000000e+00 846.0
16 TraesCS7D01G424000 chr6D 86.856 738 61 18 1551 2276 438299122 438299835 0.000000e+00 793.0
17 TraesCS7D01G424000 chr6D 93.651 63 3 1 1304 1366 316625903 316625964 2.410000e-15 93.5
18 TraesCS7D01G424000 chr5D 98.246 57 0 1 1305 1361 452219447 452219392 5.170000e-17 99.0
19 TraesCS7D01G424000 chr5D 93.651 63 3 1 1304 1366 431538637 431538698 2.410000e-15 93.5
20 TraesCS7D01G424000 chr5B 98.214 56 1 0 1303 1358 51965444 51965499 5.170000e-17 99.0
21 TraesCS7D01G424000 chr2A 93.651 63 4 0 1305 1367 200620194 200620132 6.690000e-16 95.3
22 TraesCS7D01G424000 chr1B 92.537 67 2 3 1305 1369 466926209 466926144 2.410000e-15 93.5
23 TraesCS7D01G424000 chr5A 91.045 67 6 0 1307 1373 247191205 247191139 8.660000e-15 91.6
24 TraesCS7D01G424000 chr3A 91.176 68 5 1 1305 1372 737369226 737369160 8.660000e-15 91.6


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 TraesCS7D01G424000 chr7D 544558179 544560454 2275 True 4204.00 4204 100.0000 1 2276 1 chr7D.!!$R1 2275
1 TraesCS7D01G424000 chr7D 599238445 599239745 1300 True 2207.00 2207 97.2430 1 1306 1 chr7D.!!$R2 1305
2 TraesCS7D01G424000 chr4D 298273073 298274377 1304 False 2266.00 2266 98.0080 1 1305 1 chr4D.!!$F1 1304
3 TraesCS7D01G424000 chr3D 31889657 31890960 1303 True 2237.00 2237 97.6230 1 1304 1 chr3D.!!$R1 1303
4 TraesCS7D01G424000 chr7B 706500288 706501591 1303 False 1893.00 1893 92.8680 1 1304 1 chr7B.!!$F1 1303
5 TraesCS7D01G424000 chr7B 587965900 587966679 779 True 1118.00 1118 92.3460 1480 2276 1 chr7B.!!$R1 796
6 TraesCS7D01G424000 chr1A 65650900 65652204 1304 True 1862.00 1862 92.4140 1 1305 1 chr1A.!!$R1 1304
7 TraesCS7D01G424000 chr4B 605894392 605895610 1218 True 1855.00 1855 94.1030 1 1221 1 chr4B.!!$R1 1220
8 TraesCS7D01G424000 chr6B 173437165 173438468 1303 True 1844.00 1844 92.1780 1 1304 1 chr6B.!!$R1 1303
9 TraesCS7D01G424000 chr6B 663691080 663691849 769 False 769.00 769 84.8150 1477 2276 1 chr6B.!!$F1 799
10 TraesCS7D01G424000 chr7A 79127133 79128437 1304 True 1834.00 1834 92.0370 1 1306 1 chr7A.!!$R1 1305
11 TraesCS7D01G424000 chr7A 625753364 625754286 922 True 1358.00 1358 93.3400 1358 2276 1 chr7A.!!$R2 918
12 TraesCS7D01G424000 chr2B 683266695 683268232 1537 False 945.55 1794 94.5845 1 1313 2 chr2B.!!$F1 1312
13 TraesCS7D01G424000 chr6A 586815915 586816697 782 False 846.00 846 86.3180 1484 2276 1 chr6A.!!$F1 792
14 TraesCS7D01G424000 chr6D 438299122 438299835 713 False 793.00 793 86.8560 1551 2276 1 chr6D.!!$F2 725

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
564 565 0.907704 TGCCAAGACTACATCCCCGT 60.908 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1808 0.249398 AGACTTTGCGCCGGTTCTAT 59.751 50.0 4.18 0.0 0.0 1.98 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
112 113 3.379445 GGACGGAGCAGGTTCGGA 61.379 66.667 5.06 0.00 0.00 4.55
152 153 1.798735 CCGCAGCCATTCTGAACAG 59.201 57.895 0.00 0.00 45.72 3.16
249 250 1.181001 CGTATCGTGCTCTCGTGAAC 58.819 55.000 0.00 0.00 0.00 3.18
415 416 1.209128 CGAGTGCACTCTCAAACGTT 58.791 50.000 36.78 6.45 40.75 3.99
423 424 2.805671 CACTCTCAAACGTTGCCACATA 59.194 45.455 0.00 0.00 0.00 2.29
564 565 0.907704 TGCCAAGACTACATCCCCGT 60.908 55.000 0.00 0.00 0.00 5.28
821 822 8.779303 TGAATACATGAAAATCAACACTAACGT 58.221 29.630 0.00 0.00 0.00 3.99
925 926 3.556038 ATCCCGGGGGTGACAGACA 62.556 63.158 23.50 0.00 36.47 3.41
1350 1579 8.682936 ATGCTCTTATATTTGTTTACAGAGGG 57.317 34.615 0.00 0.00 0.00 4.30
1351 1580 7.857456 TGCTCTTATATTTGTTTACAGAGGGA 58.143 34.615 0.00 0.00 0.00 4.20
1352 1581 7.987458 TGCTCTTATATTTGTTTACAGAGGGAG 59.013 37.037 0.00 0.00 0.00 4.30
1353 1582 7.988028 GCTCTTATATTTGTTTACAGAGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
1422 1652 8.986039 AAATGAATGAACAAATGCGTTAAAAC 57.014 26.923 0.00 0.00 0.00 2.43
1504 1734 9.893305 GTAGCATTTATTATGGGTGTATTTCAC 57.107 33.333 0.00 0.00 45.47 3.18
1552 1792 4.852134 TGCAAAGCATCACACAAATAGT 57.148 36.364 0.00 0.00 31.71 2.12
1553 1793 5.956068 TGCAAAGCATCACACAAATAGTA 57.044 34.783 0.00 0.00 31.71 1.82
1559 1799 8.338259 CAAAGCATCACACAAATAGTACTATCC 58.662 37.037 15.72 0.00 0.00 2.59
1567 1807 6.839657 ACACAAATAGTACTATCCACCTAGCT 59.160 38.462 15.72 0.00 0.00 3.32
1568 1808 8.003044 ACACAAATAGTACTATCCACCTAGCTA 58.997 37.037 15.72 0.00 0.00 3.32
1717 1963 2.985406 GAAGTGGTCGAACTCGTAGT 57.015 50.000 0.33 0.00 40.80 2.73
1718 1964 2.849110 GAAGTGGTCGAACTCGTAGTC 58.151 52.381 0.33 0.00 40.80 2.59
1836 2091 3.382832 CCGGAGTCCAGGAACGCT 61.383 66.667 10.49 0.00 0.00 5.07
1914 2172 4.475135 GCCTTCTCTCCACCGCCC 62.475 72.222 0.00 0.00 0.00 6.13
1916 2174 3.382832 CTTCTCTCCACCGCCCGT 61.383 66.667 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 1.592669 CCGGCGCGATGAAGATCTT 60.593 57.895 12.10 7.95 0.00 2.40
415 416 3.378112 GTGCTAATCTGCTTTATGTGGCA 59.622 43.478 0.00 0.00 36.94 4.92
564 565 7.667635 TCACATAAAATGTCTTTGGACCATGTA 59.332 33.333 0.00 0.00 42.70 2.29
925 926 2.441164 AGCCTCCGCGATGAGAGT 60.441 61.111 8.23 0.00 41.18 3.24
1011 1012 3.127425 AGGTTTACTGCCTCAAGACAC 57.873 47.619 0.00 0.00 0.00 3.67
1324 1553 9.125026 CCCTCTGTAAACAAATATAAGAGCATT 57.875 33.333 0.00 0.00 0.00 3.56
1325 1554 8.494433 TCCCTCTGTAAACAAATATAAGAGCAT 58.506 33.333 0.00 0.00 0.00 3.79
1326 1555 7.857456 TCCCTCTGTAAACAAATATAAGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
1327 1556 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
1392 1622 7.424227 ACGCATTTGTTCATTCATTTCAATT 57.576 28.000 0.00 0.00 0.00 2.32
1422 1652 5.023920 GTGAATCAAATGTATGCAGACACG 58.976 41.667 17.79 8.62 30.52 4.49
1504 1734 3.063452 GTGTTTGCATGATACCCGTACTG 59.937 47.826 0.00 0.00 0.00 2.74
1550 1790 7.404481 GGTTCTATAGCTAGGTGGATAGTACT 58.596 42.308 15.37 0.00 0.00 2.73
1551 1791 6.315891 CGGTTCTATAGCTAGGTGGATAGTAC 59.684 46.154 4.27 8.47 0.00 2.73
1552 1792 6.413052 CGGTTCTATAGCTAGGTGGATAGTA 58.587 44.000 4.27 0.00 0.00 1.82
1553 1793 5.254901 CGGTTCTATAGCTAGGTGGATAGT 58.745 45.833 4.27 0.00 0.00 2.12
1559 1799 1.068472 CGCCGGTTCTATAGCTAGGTG 60.068 57.143 1.90 0.00 0.00 4.00
1567 1807 1.479323 AGACTTTGCGCCGGTTCTATA 59.521 47.619 4.18 0.00 0.00 1.31
1568 1808 0.249398 AGACTTTGCGCCGGTTCTAT 59.751 50.000 4.18 0.00 0.00 1.98
1620 1866 1.206578 CGTTCTGCGCAAATTCGGT 59.793 52.632 13.05 0.00 0.00 4.69
1632 1878 1.551452 AGAAGAGGAGGTCCGTTCTG 58.449 55.000 13.19 0.00 40.44 3.02
1716 1962 2.601562 GGCCATGGACGATTACGAC 58.398 57.895 18.40 0.00 42.66 4.34
1941 2202 2.915137 ACGGCGGCAACCCAAAAT 60.915 55.556 13.24 0.00 0.00 1.82
2202 2463 3.175240 CGTGAGAACGCCGAGCTG 61.175 66.667 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.