Multiple sequence alignment - TraesCS5A01G132200

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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 TraesCS5A01G132200 chr5A 100.000 2740 0 0 1 2740 298532450 298535189 0.000000e+00 5060.0
1 TraesCS5A01G132200 chr5A 91.191 2418 173 17 1 2387 118346117 118348525 0.000000e+00 3249.0
2 TraesCS5A01G132200 chr5A 92.910 1904 125 5 1 1897 102841535 102839635 0.000000e+00 2760.0
3 TraesCS5A01G132200 chr5A 92.497 1666 123 2 1 1666 117509783 117508120 0.000000e+00 2383.0
4 TraesCS5A01G132200 chr5A 87.815 755 54 17 1664 2387 117507956 117507209 0.000000e+00 850.0
5 TraesCS5A01G132200 chr5A 90.188 479 35 6 1914 2387 102839492 102839021 5.010000e-172 614.0
6 TraesCS5A01G132200 chr5A 85.279 197 21 6 2551 2740 117507192 117506997 2.150000e-46 196.0
7 TraesCS5A01G132200 chr5A 84.264 197 23 6 2551 2740 118348542 118348737 4.660000e-43 185.0
8 TraesCS5A01G132200 chr5A 83.756 197 24 6 2551 2740 102839004 102838809 2.170000e-41 180.0
9 TraesCS5A01G132200 chr5B 96.462 2770 61 9 1 2740 248757380 248760142 0.000000e+00 4538.0
10 TraesCS5A01G132200 chr5B 91.108 2283 157 25 1 2246 123686189 123688462 0.000000e+00 3049.0
11 TraesCS5A01G132200 chr5B 91.465 2109 145 12 1 2082 122852054 122849954 0.000000e+00 2865.0
12 TraesCS5A01G132200 chr5B 90.415 313 23 4 2081 2387 122849849 122849538 3.290000e-109 405.0
13 TraesCS5A01G132200 chr5B 83.756 197 24 6 2551 2740 122849521 122849326 2.170000e-41 180.0
14 TraesCS5A01G132200 chr5D 93.361 1898 124 2 1 1897 99916400 99918296 0.000000e+00 2806.0
15 TraesCS5A01G132200 chr5D 93.098 1898 129 2 1 1897 109808259 109810155 0.000000e+00 2778.0
16 TraesCS5A01G132200 chr5D 91.060 481 32 5 1910 2387 109810290 109810762 8.270000e-180 640.0
17 TraesCS5A01G132200 chr5D 90.249 482 35 6 1910 2387 99918431 99918904 1.080000e-173 619.0
18 TraesCS5A01G132200 chr5D 84.848 198 20 9 2551 2740 109810779 109810974 1.000000e-44 191.0
19 TraesCS5A01G132200 chr5D 84.264 197 23 6 2551 2740 99918921 99919116 4.660000e-43 185.0
20 TraesCS5A01G132200 chr6B 92.782 1898 135 2 1 1897 184003743 184005639 0.000000e+00 2745.0
21 TraesCS5A01G132200 chr6B 89.212 482 37 8 1910 2387 184005782 184006252 3.040000e-164 588.0
22 TraesCS5A01G132200 chr6B 84.264 197 23 6 2551 2740 184006269 184006464 4.660000e-43 185.0
23 TraesCS5A01G132200 chr6B 90.000 60 6 0 2469 2528 47533133 47533074 8.130000e-11 78.7


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 TraesCS5A01G132200 chr5A 298532450 298535189 2739 False 5060.000000 5060 100.000000 1 2740 1 chr5A.!!$F1 2739
1 TraesCS5A01G132200 chr5A 118346117 118348737 2620 False 1717.000000 3249 87.727500 1 2740 2 chr5A.!!$F2 2739
2 TraesCS5A01G132200 chr5A 102838809 102841535 2726 True 1184.666667 2760 88.951333 1 2740 3 chr5A.!!$R1 2739
3 TraesCS5A01G132200 chr5A 117506997 117509783 2786 True 1143.000000 2383 88.530333 1 2740 3 chr5A.!!$R2 2739
4 TraesCS5A01G132200 chr5B 248757380 248760142 2762 False 4538.000000 4538 96.462000 1 2740 1 chr5B.!!$F2 2739
5 TraesCS5A01G132200 chr5B 123686189 123688462 2273 False 3049.000000 3049 91.108000 1 2246 1 chr5B.!!$F1 2245
6 TraesCS5A01G132200 chr5B 122849326 122852054 2728 True 1150.000000 2865 88.545333 1 2740 3 chr5B.!!$R1 2739
7 TraesCS5A01G132200 chr5D 99916400 99919116 2716 False 1203.333333 2806 89.291333 1 2740 3 chr5D.!!$F1 2739
8 TraesCS5A01G132200 chr5D 109808259 109810974 2715 False 1203.000000 2778 89.668667 1 2740 3 chr5D.!!$F2 2739
9 TraesCS5A01G132200 chr6B 184003743 184006464 2721 False 1172.666667 2745 88.752667 1 2740 3 chr6B.!!$F1 2739

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
307 308 2.352715 GCGGAAAGAATCAACCAAAGGG 60.353 50.0 0.00 0.0 41.29 3.95 F
1035 1041 1.433121 GAGATGAGCTCTGGGGGAAT 58.567 55.0 16.19 0.0 40.61 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1280 4.558226 AGTGTATCTTGAGGCAACATCA 57.442 40.909 0.0 0.0 41.41 3.07 R
2404 2843 1.224870 GCTCTTGGTAGCCCCTTCC 59.775 63.158 0.0 0.0 36.45 3.46 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
307 308 2.352715 GCGGAAAGAATCAACCAAAGGG 60.353 50.000 0.00 0.00 41.29 3.95
802 808 4.411540 ACTGGTCCTCTATGAAGAATGCAT 59.588 41.667 0.00 0.00 38.50 3.96
934 940 5.495640 AGAATCAAGAGTCATGGAGTTTCC 58.504 41.667 0.14 0.00 36.96 3.13
1035 1041 1.433121 GAGATGAGCTCTGGGGGAAT 58.567 55.000 16.19 0.00 40.61 3.01
1101 1107 4.102210 CAGGGTGATCACTTGGTAGATGAT 59.898 45.833 24.50 0.00 35.77 2.45
1274 1280 3.579586 GAGATCATCAGGGAGAAGCTGAT 59.420 47.826 0.00 0.00 38.23 2.90
1558 1564 7.840342 AACATCTGCAGTGATTAGTTCTTAG 57.160 36.000 14.67 0.00 0.00 2.18
1617 1629 3.581755 TCGTGTGCTAACTGATAACCAC 58.418 45.455 0.00 0.00 0.00 4.16
1642 1654 7.231317 ACCTTTGCAGATAGAATTGAAGAAACA 59.769 33.333 0.00 0.00 0.00 2.83
1743 1921 1.477553 TCCTGCTGCCCAATGAATTC 58.522 50.000 0.00 0.00 0.00 2.17
2109 2541 5.710513 TTGCATGCTCTCAGTTTTACAAT 57.289 34.783 20.33 0.00 0.00 2.71
2203 2641 0.968405 GAAATGGCAAGCACCTCCAA 59.032 50.000 0.00 0.00 33.04 3.53
2404 2843 4.402056 TTCCCGAAAATGCTAGACCTAG 57.598 45.455 0.00 0.00 36.29 3.02
2426 2865 0.547712 AGGGGCTACCAAGAGCTTCA 60.548 55.000 0.00 0.00 43.89 3.02
2480 2919 9.396022 TCACTTCCCTGATTTATCAAAAGATAC 57.604 33.333 12.43 0.00 36.18 2.24
2505 2944 6.423905 CCACTTAATCCATTACATAGGTCACG 59.576 42.308 0.00 0.00 0.00 4.35
2506 2945 7.207383 CACTTAATCCATTACATAGGTCACGA 58.793 38.462 0.00 0.00 0.00 4.35
2507 2946 7.709182 CACTTAATCCATTACATAGGTCACGAA 59.291 37.037 0.00 0.00 0.00 3.85
2509 2948 8.657074 TTAATCCATTACATAGGTCACGAAAG 57.343 34.615 0.00 0.00 0.00 2.62
2511 2950 6.479972 TCCATTACATAGGTCACGAAAGAT 57.520 37.500 0.00 0.00 0.00 2.40
2512 2951 6.513180 TCCATTACATAGGTCACGAAAGATC 58.487 40.000 0.00 0.00 0.00 2.75
2599 3065 7.430502 CGGAGATAAATTTCTGTGAAATCTTGC 59.569 37.037 6.08 0.00 0.00 4.01
2609 3075 4.346730 TGTGAAATCTTGCATGGATCCTT 58.653 39.130 14.23 3.29 0.00 3.36
2634 3100 5.450592 TGTTGAAAATCACTGCATTGCTA 57.549 34.783 10.49 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 308 1.508088 CGGCTTCCAATGGCAGAAC 59.492 57.895 2.39 0.00 0.00 3.01
672 673 1.132721 AGAGCAGCCATGGGAGGTATA 60.133 52.381 15.13 0.00 0.00 1.47
934 940 0.381801 CGGGAATTGAGGCAAATCCG 59.618 55.000 7.86 6.52 42.52 4.18
1035 1041 5.449553 TCTGGATCTATAACTGACTGCAGA 58.550 41.667 23.35 0.00 45.17 4.26
1082 1088 8.082852 ACGTTATATCATCTACCAAGTGATCAC 58.917 37.037 18.47 18.47 34.62 3.06
1101 1107 1.406341 GGCTGGTGGCTGAACGTTATA 60.406 52.381 0.00 0.00 41.46 0.98
1274 1280 4.558226 AGTGTATCTTGAGGCAACATCA 57.442 40.909 0.00 0.00 41.41 3.07
1558 1564 8.472683 AGCGAAGAAATGAGCATATATAACTC 57.527 34.615 8.51 8.51 0.00 3.01
1617 1629 7.596494 TGTTTCTTCAATTCTATCTGCAAAGG 58.404 34.615 0.00 0.00 0.00 3.11
1743 1921 5.374080 GTCAATGTGACATGAGTTAACACG 58.626 41.667 8.61 0.00 46.22 4.49
1946 2259 7.335422 GGATGCAAATCCTACATACCAGATAAG 59.665 40.741 0.00 0.00 37.73 1.73
1977 2295 8.885346 CCTATAGGAAAAGAGGACATCCTAATT 58.115 37.037 14.11 0.00 45.14 1.40
1978 2296 7.037945 GCCTATAGGAAAAGAGGACATCCTAAT 60.038 40.741 23.61 0.00 45.14 1.73
2203 2641 8.196771 TGCAAACATTAAGACTTTGTTGAGAAT 58.803 29.630 6.12 0.00 34.04 2.40
2404 2843 1.224870 GCTCTTGGTAGCCCCTTCC 59.775 63.158 0.00 0.00 36.45 3.46
2416 2855 3.190118 GGTGGAAAGTCATGAAGCTCTTG 59.810 47.826 0.00 0.00 0.00 3.02
2426 2865 2.354328 TGGTTAGGGGTGGAAAGTCAT 58.646 47.619 0.00 0.00 0.00 3.06
2480 2919 6.423905 CGTGACCTATGTAATGGATTAAGTGG 59.576 42.308 0.00 0.00 0.00 4.00
2505 2944 7.717568 TGCTACACCTACATAAGAGATCTTTC 58.282 38.462 0.00 0.00 37.40 2.62
2506 2945 7.661536 TGCTACACCTACATAAGAGATCTTT 57.338 36.000 0.00 0.00 37.40 2.52
2507 2946 7.847711 ATGCTACACCTACATAAGAGATCTT 57.152 36.000 0.00 0.07 39.85 2.40
2509 2948 8.798402 AGTAATGCTACACCTACATAAGAGATC 58.202 37.037 0.00 0.00 0.00 2.75
2511 2950 7.778382 TGAGTAATGCTACACCTACATAAGAGA 59.222 37.037 0.00 0.00 0.00 3.10
2512 2951 7.941919 TGAGTAATGCTACACCTACATAAGAG 58.058 38.462 0.00 0.00 0.00 2.85
2599 3065 7.658575 AGTGATTTTCAACAAAAAGGATCCATG 59.341 33.333 15.82 9.71 40.09 3.66
2609 3075 5.585445 AGCAATGCAGTGATTTTCAACAAAA 59.415 32.000 20.00 0.00 35.92 2.44
2661 3127 4.496840 CGGTTAAGTGGTGGTTGTTTTCTC 60.497 45.833 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.