Multiple sequence alignment - TraesCS5B01G342500

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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 TraesCS5B01G342500 chr5B 100.000 2438 0 0 1 2438 526669563 526667126 0.000000e+00 4503.0
1 TraesCS5B01G342500 chr5B 86.784 227 19 4 486 711 526675128 526674912 2.420000e-60 243.0
2 TraesCS5B01G342500 chr5B 76.327 245 44 12 1125 1359 528570340 528570100 4.260000e-23 119.0
3 TraesCS5B01G342500 chr5D 96.313 1519 47 5 5 1521 433198366 433196855 0.000000e+00 2486.0
4 TraesCS5B01G342500 chr5D 96.939 882 20 5 1530 2405 433192327 433191447 0.000000e+00 1472.0
5 TraesCS5B01G342500 chr5D 85.306 735 85 17 798 1525 433332628 433331910 0.000000e+00 737.0
6 TraesCS5B01G342500 chr5D 76.860 242 48 5 1125 1359 435259060 435258820 1.970000e-26 130.0
7 TraesCS5B01G342500 chr5D 75.207 242 52 6 1125 1359 435255800 435255560 9.220000e-20 108.0
8 TraesCS5B01G342500 chr5D 97.778 45 0 1 1608 1652 433192324 433192367 2.600000e-10 76.8
9 TraesCS5B01G342500 chr5D 91.837 49 3 1 746 793 433218909 433218861 1.560000e-07 67.6
10 TraesCS5B01G342500 chr4B 78.310 355 67 10 313 659 623725886 623726238 1.130000e-53 220.0
11 TraesCS5B01G342500 chr5A 78.226 248 41 11 1122 1359 549196328 549196084 1.950000e-31 147.0


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 TraesCS5B01G342500 chr5B 526667126 526669563 2437 True 4503 4503 100.000 1 2438 1 chr5B.!!$R1 2437
1 TraesCS5B01G342500 chr5D 433196855 433198366 1511 True 2486 2486 96.313 5 1521 1 chr5D.!!$R2 1516
2 TraesCS5B01G342500 chr5D 433191447 433192327 880 True 1472 1472 96.939 1530 2405 1 chr5D.!!$R1 875
3 TraesCS5B01G342500 chr5D 433331910 433332628 718 True 737 737 85.306 798 1525 1 chr5D.!!$R4 727

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
661 664 1.708341 AAAACCAAGCAGCATGAGGT 58.292 45.0 0.0 0.0 39.69 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2201 0.97504 CCTAGAGAGTGCACCCAGCT 60.975 60.0 14.63 8.7 45.94 4.24 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
45 47 9.748708 CTGGATTTTGACTGAATTAGAAAACAA 57.251 29.630 0.00 0.00 0.00 2.83
127 129 6.180472 GGAGGAAGAAACCATTGATGTAGAA 58.820 40.000 0.00 0.00 0.00 2.10
189 191 4.640771 ATGGCAGAAAGTAAGGAAGTGA 57.359 40.909 0.00 0.00 0.00 3.41
200 202 6.969828 AGTAAGGAAGTGATTAAGAAAGCG 57.030 37.500 0.00 0.00 0.00 4.68
219 221 7.489757 AGAAAGCGAGATAAACACAGATAGAAC 59.510 37.037 0.00 0.00 0.00 3.01
259 261 4.683832 CAGGGAATCTGGTACTAGAAACG 58.316 47.826 13.39 0.00 39.76 3.60
263 265 4.804665 GGAATCTGGTACTAGAAACGAAGC 59.195 45.833 13.39 0.00 0.00 3.86
269 271 4.398988 TGGTACTAGAAACGAAGCGGATTA 59.601 41.667 0.00 0.00 0.00 1.75
271 273 5.401674 GGTACTAGAAACGAAGCGGATTATG 59.598 44.000 0.00 0.00 0.00 1.90
277 279 2.743938 ACGAAGCGGATTATGCACTAG 58.256 47.619 0.00 0.00 33.85 2.57
278 280 2.361119 ACGAAGCGGATTATGCACTAGA 59.639 45.455 0.00 0.00 33.85 2.43
279 281 2.726760 CGAAGCGGATTATGCACTAGAC 59.273 50.000 0.00 0.00 33.85 2.59
280 282 3.717707 GAAGCGGATTATGCACTAGACA 58.282 45.455 0.00 0.00 33.85 3.41
281 283 3.099267 AGCGGATTATGCACTAGACAC 57.901 47.619 0.00 0.00 33.85 3.67
282 284 2.695666 AGCGGATTATGCACTAGACACT 59.304 45.455 0.00 0.00 33.85 3.55
283 285 3.889538 AGCGGATTATGCACTAGACACTA 59.110 43.478 0.00 0.00 33.85 2.74
290 292 8.195436 GGATTATGCACTAGACACTAGTTACAA 58.805 37.037 8.46 2.91 0.00 2.41
347 349 6.772716 TGGACAAGCCCTCAGATTTATAAATC 59.227 38.462 24.71 24.71 39.59 2.17
374 376 8.283291 CAGTAAAACACTAAGATCAGTTGGTTC 58.717 37.037 0.00 0.00 34.98 3.62
423 425 7.981789 TCACTTTCCTATATCTCACATCAACAC 59.018 37.037 0.00 0.00 0.00 3.32
446 448 5.817816 ACGTTGAATTAGCCTAGAGAAATGG 59.182 40.000 0.00 0.00 0.00 3.16
467 469 3.509967 GGCCAAGGCTTTGTACTACAAAT 59.490 43.478 13.58 0.00 45.79 2.32
474 476 9.522804 CAAGGCTTTGTACTACAAATAAACAAA 57.477 29.630 13.58 0.00 45.79 2.83
585 588 5.526111 ACGTATACAAACAAACAAGCTCACT 59.474 36.000 3.32 0.00 0.00 3.41
630 633 3.499338 AGATTCAGAACCAATGCAACCA 58.501 40.909 0.00 0.00 0.00 3.67
661 664 1.708341 AAAACCAAGCAGCATGAGGT 58.292 45.000 0.00 0.00 39.69 3.85
677 680 2.705658 TGAGGTAGACTGCCATAATGGG 59.294 50.000 12.54 0.00 38.19 4.00
718 721 5.310857 AGACTGGACCAAGAAAAGGATAACT 59.689 40.000 0.00 0.00 0.00 2.24
728 731 6.547930 AGAAAAGGATAACTAGAGTGGACC 57.452 41.667 0.00 0.00 0.00 4.46
931 935 2.289072 ACTAGCACACAAGCGTCTTCAT 60.289 45.455 0.00 0.00 40.15 2.57
936 940 2.413112 CACACAAGCGTCTTCATACCAG 59.587 50.000 0.00 0.00 0.00 4.00
1525 1533 9.603298 GTGATGCAATGTGTAAATAGATGTATG 57.397 33.333 0.00 0.00 0.00 2.39
1526 1534 9.341078 TGATGCAATGTGTAAATAGATGTATGT 57.659 29.630 0.00 0.00 0.00 2.29
1658 1666 4.406003 AGGGATATTGTACTGACCTGACAC 59.594 45.833 0.00 0.00 0.00 3.67
1686 1694 0.942962 CATTCCAGCGCTCAAGATCC 59.057 55.000 7.13 0.00 0.00 3.36
1697 1705 0.535335 TCAAGATCCCGGTGTGTAGC 59.465 55.000 0.00 0.00 0.00 3.58
1767 1775 0.398318 ACTTCCTCCAGTGAAGGCAC 59.602 55.000 0.00 0.00 42.79 5.01
1840 1848 6.042897 ACCTAGCAAACTACTACCTGTTTTCT 59.957 38.462 0.00 0.00 34.60 2.52
1870 1879 5.353123 TGCCAAGACGTCTTATATTTGGAAC 59.647 40.000 29.28 14.54 37.79 3.62
1906 1915 6.179906 AGACATGGTACTGAAATATGGGAG 57.820 41.667 0.00 0.00 0.00 4.30
1997 2006 3.009363 TCCACATGGAAATTGAGAGCAGA 59.991 43.478 0.00 0.00 42.18 4.26
2043 2056 7.913674 ATCCTTGAAGATCTAACTGAACAAC 57.086 36.000 0.00 0.00 0.00 3.32
2044 2057 6.826668 TCCTTGAAGATCTAACTGAACAACA 58.173 36.000 0.00 0.00 0.00 3.33
2048 2062 9.429359 CTTGAAGATCTAACTGAACAACACTAT 57.571 33.333 0.00 0.00 0.00 2.12
2187 2201 4.416516 TCTCAGTCTCAACCCAATAGTGA 58.583 43.478 0.00 0.00 0.00 3.41
2358 2372 6.695713 CGAGTGATATCATTCGTACAAAAGGA 59.304 38.462 31.34 0.00 46.48 3.36
2361 2375 7.442364 AGTGATATCATTCGTACAAAAGGATGG 59.558 37.037 9.02 0.00 30.53 3.51
2379 2393 1.071699 TGGGTCCTAAGTGTCAACTGC 59.928 52.381 0.00 0.00 36.51 4.40
2382 2396 2.290323 GGTCCTAAGTGTCAACTGCCAT 60.290 50.000 0.00 0.00 36.51 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.226394 TCCAGCTGCCATAGTACCTTTTTA 59.774 41.667 8.66 0.00 0.00 1.52
2 3 2.576191 TCCAGCTGCCATAGTACCTTTT 59.424 45.455 8.66 0.00 0.00 2.27
17 18 7.765695 TTTCTAATTCAGTCAAAATCCAGCT 57.234 32.000 0.00 0.00 0.00 4.24
18 19 7.867403 TGTTTTCTAATTCAGTCAAAATCCAGC 59.133 33.333 0.00 0.00 0.00 4.85
127 129 2.356535 GCTTCCTCCAGATTCCATGTGT 60.357 50.000 0.00 0.00 0.00 3.72
163 165 5.425539 ACTTCCTTACTTTCTGCCATAGCTA 59.574 40.000 0.00 0.00 40.80 3.32
169 171 4.640771 ATCACTTCCTTACTTTCTGCCA 57.359 40.909 0.00 0.00 0.00 4.92
189 191 8.723942 ATCTGTGTTTATCTCGCTTTCTTAAT 57.276 30.769 0.00 0.00 0.00 1.40
200 202 5.460419 CGCAGGTTCTATCTGTGTTTATCTC 59.540 44.000 0.00 0.00 37.80 2.75
236 238 4.443621 GTTTCTAGTACCAGATTCCCTGC 58.556 47.826 0.00 0.00 41.57 4.85
259 261 3.491267 GTGTCTAGTGCATAATCCGCTTC 59.509 47.826 0.00 0.00 0.00 3.86
263 265 5.440234 ACTAGTGTCTAGTGCATAATCCG 57.560 43.478 8.39 0.00 0.00 4.18
269 271 7.611770 TCATTTGTAACTAGTGTCTAGTGCAT 58.388 34.615 9.71 0.00 0.00 3.96
271 273 7.062371 CACTCATTTGTAACTAGTGTCTAGTGC 59.938 40.741 9.71 7.27 34.28 4.40
279 281 5.547465 TGGGACACTCATTTGTAACTAGTG 58.453 41.667 0.00 0.00 42.53 2.74
280 282 5.818678 TGGGACACTCATTTGTAACTAGT 57.181 39.130 0.00 0.00 0.00 2.57
281 283 7.504924 TTTTGGGACACTCATTTGTAACTAG 57.495 36.000 0.00 0.00 39.29 2.57
282 284 7.883391 TTTTTGGGACACTCATTTGTAACTA 57.117 32.000 0.00 0.00 39.29 2.24
283 285 6.783708 TTTTTGGGACACTCATTTGTAACT 57.216 33.333 0.00 0.00 39.29 2.24
321 323 2.206576 AAATCTGAGGGCTTGTCCAC 57.793 50.000 0.00 0.00 36.21 4.02
347 349 6.710744 ACCAACTGATCTTAGTGTTTTACTGG 59.289 38.462 0.00 0.00 40.65 4.00
365 367 7.826260 AAAACACTGTTTATTGAACCAACTG 57.174 32.000 7.59 0.00 37.45 3.16
423 425 5.277538 GCCATTTCTCTAGGCTAATTCAACG 60.278 44.000 0.00 0.00 44.92 4.10
467 469 6.692486 ACCGGTGCATAATTCAATTTGTTTA 58.308 32.000 6.12 0.00 0.00 2.01
474 476 3.360867 TCCAACCGGTGCATAATTCAAT 58.639 40.909 8.52 0.00 0.00 2.57
630 633 5.562113 GCTGCTTGGTTTTACATTCGTAACT 60.562 40.000 0.00 0.00 37.33 2.24
661 664 6.787458 TCTTATTCTCCCATTATGGCAGTCTA 59.213 38.462 5.57 0.00 35.79 2.59
677 680 7.422399 GTCCAGTCTATGTCAGTCTTATTCTC 58.578 42.308 0.00 0.00 0.00 2.87
718 721 2.703536 TCTGCACTTTTGGTCCACTCTA 59.296 45.455 0.00 0.00 0.00 2.43
728 731 6.377327 TTTTCTTCCTAGTCTGCACTTTTG 57.623 37.500 0.00 0.00 33.62 2.44
792 795 3.611766 AAGTCTTGGTGTTATCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
931 935 4.521256 GGTACTTGATGTTTTTGGCTGGTA 59.479 41.667 0.00 0.00 0.00 3.25
936 940 4.506288 GTGTTGGTACTTGATGTTTTTGGC 59.494 41.667 0.00 0.00 0.00 4.52
1087 1094 3.186047 GTTGGCGTCGTGGATCGG 61.186 66.667 0.00 0.00 40.32 4.18
1525 1533 7.558604 TCACTTGTTTACTGGGGTATATGTAC 58.441 38.462 0.00 0.00 0.00 2.90
1526 1534 7.736881 TCACTTGTTTACTGGGGTATATGTA 57.263 36.000 0.00 0.00 0.00 2.29
1527 1535 6.630203 TCACTTGTTTACTGGGGTATATGT 57.370 37.500 0.00 0.00 0.00 2.29
1528 1536 7.335627 TCTTCACTTGTTTACTGGGGTATATG 58.664 38.462 0.00 0.00 0.00 1.78
1594 1602 7.415095 CCAAATAACAATATTCTGCTGTCGGAA 60.415 37.037 0.00 0.00 41.44 4.30
1595 1603 6.038161 CCAAATAACAATATTCTGCTGTCGGA 59.962 38.462 0.00 0.00 31.28 4.55
1686 1694 3.305110 GACAAATTTTGCTACACACCGG 58.695 45.455 9.04 0.00 0.00 5.28
1697 1705 4.300189 TGGAACCTGTCGACAAATTTTG 57.700 40.909 20.49 6.48 0.00 2.44
1767 1775 7.148738 CCATATTATTACTGTCAGTAGCTTGCG 60.149 40.741 12.39 1.72 31.47 4.85
1840 1848 8.447833 CAAATATAAGACGTCTTGGCAGTTTTA 58.552 33.333 35.24 16.26 37.40 1.52
1870 1879 3.366396 ACCATGTCTAGTACACCCTCTG 58.634 50.000 0.00 0.00 42.09 3.35
1906 1915 3.798878 GCTTGAACAAAGAGTGGAAAAGC 59.201 43.478 0.00 0.00 38.24 3.51
2043 2056 7.653713 GGAGTGATTTCAGTACCATGTATAGTG 59.346 40.741 0.00 0.00 0.00 2.74
2044 2057 7.344612 TGGAGTGATTTCAGTACCATGTATAGT 59.655 37.037 0.00 0.00 28.80 2.12
2048 2062 6.170506 GTTGGAGTGATTTCAGTACCATGTA 58.829 40.000 0.00 0.00 31.46 2.29
2187 2201 0.975040 CCTAGAGAGTGCACCCAGCT 60.975 60.000 14.63 8.70 45.94 4.24
2358 2372 2.290323 GCAGTTGACACTTAGGACCCAT 60.290 50.000 0.00 0.00 0.00 4.00
2361 2375 1.071699 TGGCAGTTGACACTTAGGACC 59.928 52.381 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.