Multiple sequence alignment - TraesCS2A01G446800

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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 TraesCS2A01G446800 chr2A 100.000 2687 0 0 1 2687 695815711 695818397 0.000000e+00 4963
1 TraesCS2A01G446800 chr2A 96.553 2089 47 7 365 2436 695973476 695975556 0.000000e+00 3435
2 TraesCS2A01G446800 chr2A 97.814 366 7 1 1 366 695972978 695973342 4.880000e-177 630
3 TraesCS2A01G446800 chr2D 94.575 2341 108 6 365 2687 556220283 556222622 0.000000e+00 3602
4 TraesCS2A01G446800 chr2D 91.222 2324 178 14 365 2668 564467012 564469329 0.000000e+00 3138
5 TraesCS2A01G446800 chr2D 96.721 366 7 2 1 366 556219789 556220149 2.960000e-169 604
6 TraesCS2A01G446800 chr2D 95.640 367 13 3 1 365 564466506 564466871 1.070000e-163 586
7 TraesCS2A01G446800 chr2B 92.350 2340 151 13 365 2687 663337076 663334748 0.000000e+00 3304
8 TraesCS2A01G446800 chr2B 88.094 1663 145 15 1021 2668 601729757 601731381 0.000000e+00 1925
9 TraesCS2A01G446800 chr2B 87.667 673 69 6 365 1027 601720454 601721122 0.000000e+00 771
10 TraesCS2A01G446800 chr2B 95.640 367 15 1 1 366 663337576 663337210 2.980000e-164 588
11 TraesCS2A01G446800 chr2B 95.355 366 14 2 1 366 601719955 601720317 1.790000e-161 579
12 TraesCS2A01G446800 chr6A 90.571 1803 149 13 880 2668 561448826 561450621 0.000000e+00 2368
13 TraesCS2A01G446800 chr6A 90.349 1803 152 14 880 2668 561605068 561603274 0.000000e+00 2346
14 TraesCS2A01G446800 chr6A 91.386 1335 101 9 1345 2668 561591348 561590017 0.000000e+00 1816
15 TraesCS2A01G446800 chr6A 90.000 530 46 2 365 887 561605775 561605246 0.000000e+00 678
16 TraesCS2A01G446800 chr6A 89.642 531 46 4 365 887 561448119 561448648 0.000000e+00 667
17 TraesCS2A01G446800 chr6A 95.652 368 13 2 1 366 561447614 561447980 2.980000e-164 588
18 TraesCS2A01G446800 chr6A 93.750 368 17 3 1 366 561606277 561605914 5.060000e-152 547
19 TraesCS2A01G446800 chr3D 90.315 1239 88 10 483 1714 482838465 482837252 0.000000e+00 1594
20 TraesCS2A01G446800 chr3D 90.655 931 71 7 1749 2668 482837248 482836323 0.000000e+00 1223
21 TraesCS2A01G446800 chr4A 87.593 1080 97 14 644 1714 30774746 30775797 0.000000e+00 1218
22 TraesCS2A01G446800 chr4A 89.925 933 83 4 1747 2668 30775799 30776731 0.000000e+00 1192
23 TraesCS2A01G446800 chr7D 99.057 106 1 0 178 283 311870728 311870623 9.820000e-45 191
24 TraesCS2A01G446800 chr7A 99.057 106 1 0 178 283 375890820 375890925 9.820000e-45 191


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 TraesCS2A01G446800 chr2A 695815711 695818397 2686 False 4963.000000 4963 100.000000 1 2687 1 chr2A.!!$F1 2686
1 TraesCS2A01G446800 chr2A 695972978 695975556 2578 False 2032.500000 3435 97.183500 1 2436 2 chr2A.!!$F2 2435
2 TraesCS2A01G446800 chr2D 556219789 556222622 2833 False 2103.000000 3602 95.648000 1 2687 2 chr2D.!!$F1 2686
3 TraesCS2A01G446800 chr2D 564466506 564469329 2823 False 1862.000000 3138 93.431000 1 2668 2 chr2D.!!$F2 2667
4 TraesCS2A01G446800 chr2B 663334748 663337576 2828 True 1946.000000 3304 93.995000 1 2687 2 chr2B.!!$R1 2686
5 TraesCS2A01G446800 chr2B 601729757 601731381 1624 False 1925.000000 1925 88.094000 1021 2668 1 chr2B.!!$F1 1647
6 TraesCS2A01G446800 chr2B 601719955 601721122 1167 False 675.000000 771 91.511000 1 1027 2 chr2B.!!$F2 1026
7 TraesCS2A01G446800 chr6A 561590017 561591348 1331 True 1816.000000 1816 91.386000 1345 2668 1 chr6A.!!$R1 1323
8 TraesCS2A01G446800 chr6A 561447614 561450621 3007 False 1207.666667 2368 91.955000 1 2668 3 chr6A.!!$F1 2667
9 TraesCS2A01G446800 chr6A 561603274 561606277 3003 True 1190.333333 2346 91.366333 1 2668 3 chr6A.!!$R2 2667
10 TraesCS2A01G446800 chr3D 482836323 482838465 2142 True 1408.500000 1594 90.485000 483 2668 2 chr3D.!!$R1 2185
11 TraesCS2A01G446800 chr4A 30774746 30776731 1985 False 1205.000000 1218 88.759000 644 2668 2 chr4A.!!$F1 2024

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
767 926 0.617413 CTCTCAGATGCTTGGGTGGT 59.383 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 3195 2.746277 GGCGCGGAAGACCAACAT 60.746 61.111 8.83 0.0 35.59 2.71 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
377 533 4.290942 CTTGGTAGGAGTCAAGGTAGGAT 58.709 47.826 0.00 0.0 37.35 3.24
383 539 4.689062 AGGAGTCAAGGTAGGATGAAGAA 58.311 43.478 0.00 0.0 0.00 2.52
392 548 7.448469 TCAAGGTAGGATGAAGAAAAGAAAAGG 59.552 37.037 0.00 0.0 0.00 3.11
486 642 1.180029 GGCTCCATTGCAACAGTGAT 58.820 50.000 0.00 0.0 34.04 3.06
574 730 2.972505 CGTGCCGTTGCCTGAGTT 60.973 61.111 0.00 0.0 36.33 3.01
582 738 2.607771 CCGTTGCCTGAGTTGGATTTTG 60.608 50.000 0.00 0.0 0.00 2.44
767 926 0.617413 CTCTCAGATGCTTGGGTGGT 59.383 55.000 0.00 0.0 0.00 4.16
1016 1554 2.083774 GGTGATGAAGTTGGCGATTGA 58.916 47.619 0.00 0.0 0.00 2.57
1597 2145 3.557824 CGGTTTCCCACTACGCAC 58.442 61.111 0.00 0.0 0.00 5.34
1732 2281 0.813821 AACGACGCCTAGGTTCCTAC 59.186 55.000 11.31 0.0 0.00 3.18
1884 2433 5.510179 CCATGAAGGTGAAAGATGCAAAACT 60.510 40.000 0.00 0.0 0.00 2.66
1910 2459 1.007964 CGCGGCACCACAAAATCAA 60.008 52.632 0.00 0.0 0.00 2.57
2464 3026 0.953727 GTAAAACCCCCGTGTGAACC 59.046 55.000 0.00 0.0 0.00 3.62
2483 3045 2.225470 ACCCCCTTTACTTCCGACTACT 60.225 50.000 0.00 0.0 0.00 2.57
2527 3089 1.812571 GACGGTTTTCTGCACCATCAT 59.187 47.619 0.00 0.0 33.36 2.45
2563 3125 8.793592 GGTAGTGAGTTGGAATCTGTTTAAATT 58.206 33.333 0.00 0.0 0.00 1.82
2577 3139 6.035112 TCTGTTTAAATTGTTTGGTTTGCGAC 59.965 34.615 0.00 0.0 0.00 5.19
2587 3153 2.961526 GGTTTGCGACCTATCTCTCA 57.038 50.000 2.01 0.0 45.55 3.27
2593 3159 2.832129 TGCGACCTATCTCTCAAGGTTT 59.168 45.455 0.00 0.0 46.22 3.27
2621 3195 5.252863 CCATTATATGTACCCTTGATCCCCA 59.747 44.000 0.00 0.0 0.00 4.96
2633 3207 1.284785 TGATCCCCATGTTGGTCTTCC 59.715 52.381 0.00 0.0 35.17 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
377 533 7.581213 TTCATAGTGCCTTTTCTTTTCTTCA 57.419 32.000 0.00 0.00 0.00 3.02
383 539 8.743714 CCTTAAGATTCATAGTGCCTTTTCTTT 58.256 33.333 3.36 0.00 0.00 2.52
392 548 4.035675 GTGTGGCCTTAAGATTCATAGTGC 59.964 45.833 3.32 0.00 0.00 4.40
486 642 4.975631 TCTAGGGTCAAACAAAATTCCGA 58.024 39.130 0.00 0.00 0.00 4.55
574 730 0.413037 ACATGGGGCCTCAAAATCCA 59.587 50.000 10.86 2.41 0.00 3.41
582 738 3.857157 TGTATCTTTACATGGGGCCTC 57.143 47.619 0.84 0.00 33.37 4.70
767 926 1.473677 CTGCCGCCTTTCATCAATGAA 59.526 47.619 1.30 1.30 44.42 2.57
1016 1554 0.179004 TGACACCCAACGCCATTCTT 60.179 50.000 0.00 0.00 0.00 2.52
1276 1814 0.600255 AGTGGAAGGACAACGCTTCG 60.600 55.000 0.00 0.00 0.00 3.79
1317 1855 2.665185 GTCGTGGCTGGAGCGTTT 60.665 61.111 0.00 0.00 43.26 3.60
1538 2086 4.362476 CCTGCCAAAGCCGTTGCC 62.362 66.667 0.00 0.00 38.69 4.52
1597 2145 4.592192 ATCTCCGCGCCCACATCG 62.592 66.667 0.00 0.00 0.00 3.84
1732 2281 6.728200 TCTTCAAATCATTTAATGCTAGCCG 58.272 36.000 13.29 0.00 0.00 5.52
1884 2433 3.457263 TGGTGCCGCGATCTAGCA 61.457 61.111 8.23 4.98 36.85 3.49
1910 2459 3.216187 TCTCTATGGCTTCGTAGCTCT 57.784 47.619 13.99 4.30 46.90 4.09
2464 3026 2.830321 ACAGTAGTCGGAAGTAAAGGGG 59.170 50.000 0.00 0.00 0.00 4.79
2527 3089 3.576982 CCAACTCACTACCAGAGTACCAA 59.423 47.826 0.00 0.00 45.11 3.67
2577 3139 3.519510 TGGACCAAACCTTGAGAGATAGG 59.480 47.826 0.00 0.00 37.56 2.57
2621 3195 2.746277 GGCGCGGAAGACCAACAT 60.746 61.111 8.83 0.00 35.59 2.71


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

AutoCloner maintained by Alex Coulton.