Multiple sequence alignment - TraesCS4A01G035600

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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 TraesCS4A01G035600 chr4A 100.000 2369 0 0 1 2369 28185282 28187650 0.000000e+00 4375
1 TraesCS4A01G035600 chr4B 88.889 2385 217 24 1 2369 542581820 542584172 0.000000e+00 2892
2 TraesCS4A01G035600 chr4B 86.078 510 66 4 3 510 215927776 215928282 5.760000e-151 544
3 TraesCS4A01G035600 chr4D 94.883 1407 71 1 451 1857 438681080 438682485 0.000000e+00 2198
4 TraesCS4A01G035600 chr4D 93.504 508 31 2 1863 2369 438704495 438705001 0.000000e+00 754
5 TraesCS4A01G035600 chr4D 92.747 455 27 4 1 455 438671750 438672198 0.000000e+00 652
6 TraesCS4A01G035600 chr4D 89.173 508 54 1 3 510 236401823 236402329 1.190000e-177 632
7 TraesCS4A01G035600 chr7D 83.549 1234 183 14 1143 2369 612164027 612162807 0.000000e+00 1136
8 TraesCS4A01G035600 chr7D 88.583 508 55 2 3 510 271439929 271439425 4.330000e-172 614
9 TraesCS4A01G035600 chr7D 85.185 540 73 6 602 1140 612376479 612377012 4.450000e-152 547
10 TraesCS4A01G035600 chr2D 86.301 949 124 5 616 1561 616755765 616754820 0.000000e+00 1027
11 TraesCS4A01G035600 chr2B 85.714 966 130 7 600 1561 752298860 752299821 0.000000e+00 1013
12 TraesCS4A01G035600 chr2B 86.879 503 60 6 9 509 303437903 303437405 2.060000e-155 558
13 TraesCS4A01G035600 chr7A 88.189 508 59 1 3 510 357457203 357457709 2.600000e-169 604
14 TraesCS4A01G035600 chr6B 88.016 509 59 2 3 510 299587451 299587958 3.370000e-168 601
15 TraesCS4A01G035600 chr6D 87.129 505 61 4 7 510 353959718 353960219 9.500000e-159 569


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 TraesCS4A01G035600 chr4A 28185282 28187650 2368 False 4375 4375 100.000 1 2369 1 chr4A.!!$F1 2368
1 TraesCS4A01G035600 chr4B 542581820 542584172 2352 False 2892 2892 88.889 1 2369 1 chr4B.!!$F2 2368
2 TraesCS4A01G035600 chr4B 215927776 215928282 506 False 544 544 86.078 3 510 1 chr4B.!!$F1 507
3 TraesCS4A01G035600 chr4D 438681080 438682485 1405 False 2198 2198 94.883 451 1857 1 chr4D.!!$F3 1406
4 TraesCS4A01G035600 chr4D 438704495 438705001 506 False 754 754 93.504 1863 2369 1 chr4D.!!$F4 506
5 TraesCS4A01G035600 chr4D 236401823 236402329 506 False 632 632 89.173 3 510 1 chr4D.!!$F1 507
6 TraesCS4A01G035600 chr7D 612162807 612164027 1220 True 1136 1136 83.549 1143 2369 1 chr7D.!!$R2 1226
7 TraesCS4A01G035600 chr7D 271439425 271439929 504 True 614 614 88.583 3 510 1 chr7D.!!$R1 507
8 TraesCS4A01G035600 chr7D 612376479 612377012 533 False 547 547 85.185 602 1140 1 chr7D.!!$F1 538
9 TraesCS4A01G035600 chr2D 616754820 616755765 945 True 1027 1027 86.301 616 1561 1 chr2D.!!$R1 945
10 TraesCS4A01G035600 chr2B 752298860 752299821 961 False 1013 1013 85.714 600 1561 1 chr2B.!!$F1 961
11 TraesCS4A01G035600 chr7A 357457203 357457709 506 False 604 604 88.189 3 510 1 chr7A.!!$F1 507
12 TraesCS4A01G035600 chr6B 299587451 299587958 507 False 601 601 88.016 3 510 1 chr6B.!!$F1 507
13 TraesCS4A01G035600 chr6D 353959718 353960219 501 False 569 569 87.129 7 510 1 chr6D.!!$F1 503

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
404 421 0.884514 GCAAAGGGAAGCAGAGGTTC 59.115 55.0 0.58 0.58 39.04 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 2264 1.412343 GTTGGTGGCTCAAAATGGTGT 59.588 47.619 0.0 0.0 0.0 4.16 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
166 169 7.639113 AAGTTTCAGTCAAACACATAGGAAA 57.361 32.000 0.00 0.00 46.20 3.13
216 219 7.499232 CCCAACTTGTTTATCTCGAGGATAATT 59.501 37.037 13.56 4.20 43.75 1.40
298 313 2.168936 CCACCACATTATGCTTGCCAAT 59.831 45.455 0.00 0.00 0.00 3.16
404 421 0.884514 GCAAAGGGAAGCAGAGGTTC 59.115 55.000 0.58 0.58 39.04 3.62
405 422 1.160137 CAAAGGGAAGCAGAGGTTCG 58.840 55.000 3.26 0.00 40.44 3.95
416 433 1.226128 GAGGTTCGCATGCGCTTTC 60.226 57.895 34.45 22.84 39.59 2.62
488 505 5.206905 ACCCCTTATGATAGCAACCTTTT 57.793 39.130 0.00 0.00 0.00 2.27
594 611 6.048732 TGGACACATATCGGTATAATGCAT 57.951 37.500 0.00 0.00 0.00 3.96
910 928 2.383338 ACCATCCCCTCTTTCAAACCAT 59.617 45.455 0.00 0.00 0.00 3.55
923 941 5.917541 TTCAAACCATAACTCGTGTCTTC 57.082 39.130 0.00 0.00 0.00 2.87
946 964 4.305769 CCCAAGAGCAATATCTCGAGAAG 58.694 47.826 20.91 10.85 38.12 2.85
1140 1158 4.363991 ACAGAGAGCAAAAGAGACCAAT 57.636 40.909 0.00 0.00 0.00 3.16
1171 1189 0.742635 GAAGGCCAAGGAAGAGAGCG 60.743 60.000 5.01 0.00 0.00 5.03
1172 1190 1.484444 AAGGCCAAGGAAGAGAGCGT 61.484 55.000 5.01 0.00 0.00 5.07
1183 1201 2.622064 AGAGAGCGTTGGAACTGTTT 57.378 45.000 0.00 0.00 0.00 2.83
1185 1203 2.103263 AGAGAGCGTTGGAACTGTTTCT 59.897 45.455 0.00 0.00 31.71 2.52
1203 1221 8.254508 ACTGTTTCTAGGTATCTCTTCATGAAC 58.745 37.037 3.38 0.00 0.00 3.18
1204 1222 8.134202 TGTTTCTAGGTATCTCTTCATGAACA 57.866 34.615 3.38 0.00 0.00 3.18
1249 1267 3.258622 GTGCAAGGAGTACTACCAAGAGT 59.741 47.826 0.00 0.00 0.00 3.24
1326 1344 3.727258 ATGCCAACCCCGCAGCTA 61.727 61.111 0.00 0.00 40.15 3.32
1330 1348 2.114670 CCAACCCCGCAGCTACATG 61.115 63.158 0.00 0.00 0.00 3.21
1435 1453 8.777413 TCATTTGAGATATAGTGCTTATGTTGC 58.223 33.333 0.00 0.00 0.00 4.17
1472 1492 0.866906 CGCCGCTTATGTTGCAATGG 60.867 55.000 0.59 0.00 0.00 3.16
1606 1626 7.652105 ACAGAACGGCATATGTATGTTTAGTAG 59.348 37.037 4.29 1.01 36.11 2.57
1767 1790 6.097356 GTCAACTATATTTGACGTCACCTCA 58.903 40.000 19.90 0.00 44.41 3.86
1848 1871 1.479323 GTACGTGACCCCTCATTAGCA 59.521 52.381 0.00 0.00 0.00 3.49
1861 1884 5.454471 CCCTCATTAGCAGCATCTCTAAGTT 60.454 44.000 0.00 0.00 0.00 2.66
1872 1895 5.300792 AGCATCTCTAAGTTCCTACTAGCAC 59.699 44.000 0.00 0.00 33.17 4.40
1882 1905 2.681848 TCCTACTAGCACTGTTCTACGC 59.318 50.000 0.00 0.00 0.00 4.42
1928 1951 3.560068 AGTTTACAACTAGCAGTGTGTGC 59.440 43.478 4.92 0.00 43.05 4.57
2016 2039 5.242795 ACTAGTAGCATTTGTCCCAAGTT 57.757 39.130 0.00 0.00 0.00 2.66
2029 2052 4.536090 TGTCCCAAGTTGATCACTCCTAAT 59.464 41.667 3.87 0.00 32.94 1.73
2075 2116 1.172180 TGCTTTGCACACTAGTGGCC 61.172 55.000 26.12 16.30 45.98 5.36
2242 2284 1.412343 ACACCATTTTGAGCCACCAAC 59.588 47.619 0.00 0.00 0.00 3.77
2254 2296 3.499338 AGCCACCAACATCAAATTCAGA 58.501 40.909 0.00 0.00 0.00 3.27
2342 2384 5.453567 ACCTAGCAATTCTGGAAACAAAC 57.546 39.130 0.00 0.00 42.06 2.93
2352 2394 4.312443 TCTGGAAACAAACTACTTAGCGG 58.688 43.478 0.00 0.00 42.06 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.039574 TGGATTGTGATTGTTTCAATGACTGAT 60.040 33.333 11.71 7.16 35.70 2.90
47 48 9.667107 TGCTAAACAAAGCTCTTATATACACTT 57.333 29.630 0.00 0.00 43.19 3.16
131 132 9.066892 TGTTTGACTGAAACTTTTGCTCTATAT 57.933 29.630 0.00 0.00 43.90 0.86
166 169 5.423931 GTGGTGAACATTATAAACCCCCATT 59.576 40.000 1.68 0.00 0.00 3.16
234 237 2.028476 TCCAGTTGGATGTAGGTGAACG 60.028 50.000 0.00 0.00 39.78 3.95
405 422 3.510719 TCCAAAAATAGAAAGCGCATGC 58.489 40.909 11.47 7.91 43.24 4.06
416 433 5.320549 AGAGCTTGCACATCCAAAAATAG 57.679 39.130 0.00 0.00 0.00 1.73
488 505 1.803334 AAAGCGACGGACTGCATAAA 58.197 45.000 0.00 0.00 0.00 1.40
594 611 8.565896 AAAAGCATGTAGACATTTGTATCTCA 57.434 30.769 0.00 0.00 33.61 3.27
761 778 5.013704 ACATAGGTTGTTGGATAAGGACACA 59.986 40.000 0.00 0.00 33.74 3.72
800 817 4.792521 TGCTACACAACAACAAAGGTTT 57.207 36.364 0.00 0.00 34.21 3.27
855 873 1.152830 TGGAAGTGGGGTCCAAAGC 59.847 57.895 0.00 0.00 42.29 3.51
910 928 2.561419 CTCTTGGGGAAGACACGAGTTA 59.439 50.000 0.00 0.00 31.73 2.24
923 941 2.630098 TCTCGAGATATTGCTCTTGGGG 59.370 50.000 12.08 0.00 29.30 4.96
946 964 8.453238 TTGTGACTAGATGACTAGAAGTATCC 57.547 38.462 10.60 0.00 46.34 2.59
1140 1158 0.179032 TGGCCTTCTCAAAGCGTTCA 60.179 50.000 3.32 0.00 0.00 3.18
1171 1189 6.937392 AGAGATACCTAGAAACAGTTCCAAC 58.063 40.000 0.00 0.00 33.92 3.77
1172 1190 7.234782 TGAAGAGATACCTAGAAACAGTTCCAA 59.765 37.037 0.00 0.00 33.92 3.53
1183 1201 9.513906 CTCTATGTTCATGAAGAGATACCTAGA 57.486 37.037 14.50 11.82 38.16 2.43
1185 1203 8.448816 TCCTCTATGTTCATGAAGAGATACCTA 58.551 37.037 19.42 3.23 38.16 3.08
1203 1221 6.496565 ACTCCTCATGGTTAAGATCCTCTATG 59.503 42.308 0.00 0.00 34.23 2.23
1204 1222 6.496565 CACTCCTCATGGTTAAGATCCTCTAT 59.503 42.308 0.00 0.00 34.23 1.98
1249 1267 2.488204 TCTTGGTTGATCCGCATCAA 57.512 45.000 0.00 0.00 45.20 2.57
1326 1344 4.067896 GTGATTCCACTGAAGACACATGT 58.932 43.478 0.00 0.00 39.41 3.21
1330 1348 4.552767 CGTTTGTGATTCCACTGAAGACAC 60.553 45.833 0.00 0.00 43.55 3.67
1411 1429 8.681486 TGCAACATAAGCACTATATCTCAAAT 57.319 30.769 0.00 0.00 37.02 2.32
1435 1453 3.242413 CGGCGTCCATTATTTCTTCACTG 60.242 47.826 0.00 0.00 0.00 3.66
1519 1539 8.519799 TTCTTTGTTCCATTACAACTCTTTCT 57.480 30.769 0.00 0.00 37.72 2.52
1645 1665 7.500141 AGAAGTTTGTTTGCTCATTAAATGGT 58.500 30.769 0.00 0.00 0.00 3.55
1714 1737 3.641437 TTTTGAAGATCCCTTTGTGCG 57.359 42.857 0.00 0.00 31.62 5.34
1759 1782 4.273148 ACAACAATCTAGGTGAGGTGAC 57.727 45.455 1.07 0.00 0.00 3.67
1796 1819 7.911130 AGAACTCTCTCAAGATATCCATGAA 57.089 36.000 9.40 2.46 0.00 2.57
1848 1871 5.300792 GTGCTAGTAGGAACTTAGAGATGCT 59.699 44.000 0.00 0.00 41.75 3.79
1861 1884 2.681848 GCGTAGAACAGTGCTAGTAGGA 59.318 50.000 0.00 0.00 0.00 2.94
1882 1905 1.952266 GCGAAAGTAGGTGGCGTTCG 61.952 60.000 8.50 8.50 45.53 3.95
1928 1951 6.040166 AGGTTATTCATTAGCAGCATTTGGAG 59.960 38.462 0.00 0.00 0.00 3.86
2016 2039 6.183360 TGTTGATTCGCTATTAGGAGTGATCA 60.183 38.462 0.00 0.00 35.92 2.92
2102 2144 7.033185 GGGTACAACATGCTACCAAATAAAAG 58.967 38.462 13.95 0.00 35.03 2.27
2222 2264 1.412343 GTTGGTGGCTCAAAATGGTGT 59.588 47.619 0.00 0.00 0.00 4.16
2316 2358 5.488341 TGTTTCCAGAATTGCTAGGTACTC 58.512 41.667 0.00 0.00 41.75 2.59
2342 2384 3.106672 CGTGCTTTCTACCGCTAAGTAG 58.893 50.000 0.00 0.00 40.98 2.57


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

AutoCloner maintained by Alex Coulton.