Multiple sequence alignment - TraesCS5B01G214900

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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 TraesCS5B01G214900 chr5B 100.000 2613 0 0 1 2613 387891559 387888947 0.000000e+00 4826
1 TraesCS5B01G214900 chr5B 85.403 781 102 9 660 1434 259727914 259728688 0.000000e+00 800
2 TraesCS5B01G214900 chrUn 96.118 1932 52 10 1 1916 33219348 33217424 0.000000e+00 3131
3 TraesCS5B01G214900 chrUn 84.389 679 65 14 1 641 221036422 221037097 1.710000e-176 628
4 TraesCS5B01G214900 chr6A 95.919 1936 54 7 1 1916 447840068 447841998 0.000000e+00 3114
5 TraesCS5B01G214900 chr6A 95.506 1936 61 9 1 1916 601158374 601156445 0.000000e+00 3070
6 TraesCS5B01G214900 chr6A 89.137 313 31 3 1484 1794 20167320 20167631 1.130000e-103 387
7 TraesCS5B01G214900 chr6A 82.847 274 33 11 1900 2163 46571407 46571676 1.560000e-57 233
8 TraesCS5B01G214900 chr6A 82.784 273 35 10 1900 2163 383584055 383584324 1.560000e-57 233
9 TraesCS5B01G214900 chr5A 94.832 1935 74 9 1 1916 433729619 433727692 0.000000e+00 2996
10 TraesCS5B01G214900 chr3B 92.072 1829 105 13 19 1832 328598079 328599882 0.000000e+00 2538
11 TraesCS5B01G214900 chr3B 88.012 684 70 4 1901 2576 145900893 145901572 0.000000e+00 798
12 TraesCS5B01G214900 chr2D 95.994 724 19 3 1900 2613 463865240 463864517 0.000000e+00 1168
13 TraesCS5B01G214900 chr3A 88.782 731 55 11 1900 2613 549417829 549418549 0.000000e+00 870
14 TraesCS5B01G214900 chr3A 89.865 148 14 1 1 148 469500299 469500445 3.430000e-44 189
15 TraesCS5B01G214900 chr3D 87.671 730 57 11 1900 2613 94843172 94843884 0.000000e+00 819
16 TraesCS5B01G214900 chr2B 84.094 679 67 14 1 641 788440902 788441577 3.690000e-173 617
17 TraesCS5B01G214900 chr1A 84.268 642 86 9 19 649 373587845 373587208 1.720000e-171 612
18 TraesCS5B01G214900 chr1A 88.498 313 31 5 1484 1794 388526819 388526510 8.830000e-100 374
19 TraesCS5B01G214900 chr5D 86.397 544 51 15 2 537 239195348 239195876 8.110000e-160 573
20 TraesCS5B01G214900 chr5D 87.209 86 11 0 541 626 535919786 535919871 5.950000e-17 99
21 TraesCS5B01G214900 chr4B 88.315 368 40 3 660 1024 429721544 429721177 3.090000e-119 438
22 TraesCS5B01G214900 chr7D 89.809 314 31 1 1484 1796 613791753 613792066 4.050000e-108 401
23 TraesCS5B01G214900 chr7D 90.043 231 22 1 1564 1794 116821915 116821686 5.470000e-77 298


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 TraesCS5B01G214900 chr5B 387888947 387891559 2612 True 4826 4826 100.000 1 2613 1 chr5B.!!$R1 2612
1 TraesCS5B01G214900 chr5B 259727914 259728688 774 False 800 800 85.403 660 1434 1 chr5B.!!$F1 774
2 TraesCS5B01G214900 chrUn 33217424 33219348 1924 True 3131 3131 96.118 1 1916 1 chrUn.!!$R1 1915
3 TraesCS5B01G214900 chrUn 221036422 221037097 675 False 628 628 84.389 1 641 1 chrUn.!!$F1 640
4 TraesCS5B01G214900 chr6A 447840068 447841998 1930 False 3114 3114 95.919 1 1916 1 chr6A.!!$F4 1915
5 TraesCS5B01G214900 chr6A 601156445 601158374 1929 True 3070 3070 95.506 1 1916 1 chr6A.!!$R1 1915
6 TraesCS5B01G214900 chr5A 433727692 433729619 1927 True 2996 2996 94.832 1 1916 1 chr5A.!!$R1 1915
7 TraesCS5B01G214900 chr3B 328598079 328599882 1803 False 2538 2538 92.072 19 1832 1 chr3B.!!$F2 1813
8 TraesCS5B01G214900 chr3B 145900893 145901572 679 False 798 798 88.012 1901 2576 1 chr3B.!!$F1 675
9 TraesCS5B01G214900 chr2D 463864517 463865240 723 True 1168 1168 95.994 1900 2613 1 chr2D.!!$R1 713
10 TraesCS5B01G214900 chr3A 549417829 549418549 720 False 870 870 88.782 1900 2613 1 chr3A.!!$F2 713
11 TraesCS5B01G214900 chr3D 94843172 94843884 712 False 819 819 87.671 1900 2613 1 chr3D.!!$F1 713
12 TraesCS5B01G214900 chr2B 788440902 788441577 675 False 617 617 84.094 1 641 1 chr2B.!!$F1 640
13 TraesCS5B01G214900 chr1A 373587208 373587845 637 True 612 612 84.268 19 649 1 chr1A.!!$R1 630
14 TraesCS5B01G214900 chr5D 239195348 239195876 528 False 573 573 86.397 2 537 1 chr5D.!!$F1 535

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
121 133 0.640495 ACGAAGGATTAGGGGAGGGA 59.360 55.000 0.0 0.0 0.0 4.20 F
391 430 3.134458 GCCGTGCTGCTCTTTTATCTAT 58.866 45.455 0.0 0.0 0.0 1.98 F
1427 1503 0.880278 GCTCGACCTTTGTGTGCTCA 60.880 55.000 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1092 1.739562 GAGACACGAGCAGCAAGGG 60.740 63.158 0.0 0.0 0.0 3.95 R
1488 1564 2.154462 CACAAGGAACCGAGCAAGAAT 58.846 47.619 0.0 0.0 0.0 2.40 R
2315 2404 3.023832 GCTGAGCCCTGCCTTTAAAATA 58.976 45.455 0.0 0.0 0.0 1.40 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
74 82 1.846175 GTTGTTGTTGCTTTCGAGTGC 59.154 47.619 5.00 5.00 0.00 4.40
121 133 0.640495 ACGAAGGATTAGGGGAGGGA 59.360 55.000 0.00 0.00 0.00 4.20
301 323 7.968956 CGTGATGAACAAATAGTAGTAGACTGT 59.031 37.037 0.00 0.00 39.39 3.55
302 324 9.077674 GTGATGAACAAATAGTAGTAGACTGTG 57.922 37.037 0.00 0.00 39.39 3.66
391 430 3.134458 GCCGTGCTGCTCTTTTATCTAT 58.866 45.455 0.00 0.00 0.00 1.98
452 491 4.828925 GAGGCCGTGCTGCTCCTC 62.829 72.222 0.00 7.97 38.40 3.71
476 515 9.752961 CTCTCATCTATCTCAATTGCTATATGG 57.247 37.037 0.00 0.00 0.00 2.74
485 524 7.966812 TCTCAATTGCTATATGGAAAGCTCTA 58.033 34.615 0.00 0.00 39.53 2.43
537 576 9.372369 ACTAACTCTCATTTTCAAGCATAGTAC 57.628 33.333 0.00 0.00 0.00 2.73
538 577 9.593134 CTAACTCTCATTTTCAAGCATAGTACT 57.407 33.333 0.00 0.00 0.00 2.73
539 578 8.485976 AACTCTCATTTTCAAGCATAGTACTC 57.514 34.615 0.00 0.00 0.00 2.59
800 866 6.207928 TGCAAATAGTCACATTGTCTGTTTG 58.792 36.000 16.64 16.64 42.53 2.93
839 905 7.503521 TTCAGTACATGAATTTGTTGCACTA 57.496 32.000 0.00 0.00 43.09 2.74
1024 1092 1.590259 GACCGATCAGAAGCGAGGC 60.590 63.158 0.00 0.00 36.04 4.70
1119 1193 1.021968 GGCCGCCAAATAAGTACAGG 58.978 55.000 3.91 0.00 0.00 4.00
1427 1503 0.880278 GCTCGACCTTTGTGTGCTCA 60.880 55.000 0.00 0.00 0.00 4.26
1488 1564 9.787435 ATTTATGTTGTGTGTTTAGGTAGAAGA 57.213 29.630 0.00 0.00 0.00 2.87
1506 1582 2.704572 AGATTCTTGCTCGGTTCCTTG 58.295 47.619 0.00 0.00 0.00 3.61
1597 1673 5.127845 TCCTCTTCTAATCTGGCAAGTACTG 59.872 44.000 0.00 0.00 0.00 2.74
1665 1741 5.153513 GTGCACTGTTGGTTATGTTGTATG 58.846 41.667 10.32 0.00 0.00 2.39
1820 1901 2.947448 TGTCTCACGGATGACTGATG 57.053 50.000 0.00 0.00 34.57 3.07
1960 2042 6.043411 CCTACTTCCTTTCTCCAAATCTACG 58.957 44.000 0.00 0.00 0.00 3.51
1971 2053 6.216569 TCTCCAAATCTACGATTGCACTATC 58.783 40.000 0.00 0.00 0.00 2.08
2107 2189 8.355913 TGCATATGTATATAGAGCATGCTACTC 58.644 37.037 22.74 8.95 32.29 2.59
2202 2291 7.047460 ACAAAACTCTCATTGAATGAAAGCT 57.953 32.000 8.35 0.00 39.11 3.74
2203 2292 7.144000 ACAAAACTCTCATTGAATGAAAGCTC 58.856 34.615 8.35 0.00 39.11 4.09
2204 2293 7.014038 ACAAAACTCTCATTGAATGAAAGCTCT 59.986 33.333 8.35 0.00 39.11 4.09
2205 2294 7.521871 AAACTCTCATTGAATGAAAGCTCTT 57.478 32.000 8.35 0.00 39.11 2.85
2206 2295 7.521871 AACTCTCATTGAATGAAAGCTCTTT 57.478 32.000 8.35 0.00 39.11 2.52
2207 2296 7.521871 ACTCTCATTGAATGAAAGCTCTTTT 57.478 32.000 8.35 0.00 39.11 2.27
2208 2297 7.592051 ACTCTCATTGAATGAAAGCTCTTTTC 58.408 34.615 8.35 0.00 44.45 2.29
2219 2308 5.296780 TGAAAGCTCTTTTCGAATGTTCTGT 59.703 36.000 0.00 0.00 46.65 3.41
2230 2319 9.574458 TTTTCGAATGTTCTGTTGTTATTTTCA 57.426 25.926 0.00 0.00 0.00 2.69
2307 2396 6.927381 AGAAATGCCAAGAAAGAATTTGACAG 59.073 34.615 0.00 0.00 39.27 3.51
2353 2442 4.560128 CTCAGCAAGCAGTAGTTCAACTA 58.440 43.478 0.00 0.00 0.00 2.24
2605 2709 6.655003 GGAGACTCCTGAATTTTTCACATACA 59.345 38.462 14.72 0.00 35.46 2.29
2606 2710 7.361286 GGAGACTCCTGAATTTTTCACATACAC 60.361 40.741 14.72 0.00 35.46 2.90
2608 2712 7.173907 AGACTCCTGAATTTTTCACATACACTG 59.826 37.037 0.00 0.00 35.46 3.66
2610 2714 6.303054 TCCTGAATTTTTCACATACACTGGA 58.697 36.000 0.00 0.00 35.46 3.86
2612 2716 7.040478 TCCTGAATTTTTCACATACACTGGAAG 60.040 37.037 0.00 0.00 36.17 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 63 1.742831 AGCACTCGAAAGCAACAACAA 59.257 42.857 10.86 0.00 0.00 2.83
121 133 2.932234 CGAAGTCTCCACAGCCCGT 61.932 63.158 0.00 0.00 0.00 5.28
301 323 3.198635 CAGATAGGAGGAAAAGACCAGCA 59.801 47.826 0.00 0.00 0.00 4.41
302 324 3.452627 TCAGATAGGAGGAAAAGACCAGC 59.547 47.826 0.00 0.00 0.00 4.85
391 430 5.833406 TCTGAGTTGCACAAAATTCAGAA 57.167 34.783 15.44 0.00 31.17 3.02
476 515 7.163001 ACCTGATTGGAAATTTAGAGCTTTC 57.837 36.000 0.00 0.00 39.71 2.62
485 524 9.265862 TGGTGATATTTACCTGATTGGAAATTT 57.734 29.630 10.38 0.00 39.01 1.82
537 576 6.312426 CGCCTATTCTTTATATGCAGAAGGAG 59.688 42.308 0.00 6.02 32.53 3.69
538 577 6.166279 CGCCTATTCTTTATATGCAGAAGGA 58.834 40.000 0.00 0.00 32.53 3.36
539 578 5.934625 ACGCCTATTCTTTATATGCAGAAGG 59.065 40.000 0.00 0.00 32.53 3.46
559 601 3.057946 AGAGAAAATGAAAGAAGCACGCC 60.058 43.478 0.00 0.00 0.00 5.68
800 866 2.294979 ACTGAAAAACGACCCTCAACC 58.705 47.619 0.00 0.00 0.00 3.77
832 898 8.087136 TGCAAATTCTTTTACATGATAGTGCAA 58.913 29.630 0.00 0.00 33.23 4.08
839 905 8.697846 CATCAGTGCAAATTCTTTTACATGAT 57.302 30.769 0.00 0.00 0.00 2.45
1024 1092 1.739562 GAGACACGAGCAGCAAGGG 60.740 63.158 0.00 0.00 0.00 3.95
1059 1131 2.684843 GCTGGCAAGCTGAAGGTCG 61.685 63.158 5.60 0.00 46.60 4.79
1119 1193 3.181502 CGGACTTAGGTCTCTTCCGTAAC 60.182 52.174 4.85 0.00 43.46 2.50
1427 1503 6.183360 CGTGAGTCAACTAAGATTGCATGAAT 60.183 38.462 0.00 0.00 0.00 2.57
1488 1564 2.154462 CACAAGGAACCGAGCAAGAAT 58.846 47.619 0.00 0.00 0.00 2.40
1506 1582 3.881688 CTCATCTGGATCATCCCAAACAC 59.118 47.826 0.00 0.00 35.03 3.32
1550 1626 3.138304 TCTCATTGTGGTGGTTTCTTCG 58.862 45.455 0.00 0.00 0.00 3.79
1597 1673 3.973657 TGTTCGTCAGTCAAGTAGGAAC 58.026 45.455 0.00 0.00 38.09 3.62
1855 1937 6.421801 TGCGAAACCTACTAACTAAAGTTGTC 59.578 38.462 5.62 0.00 38.90 3.18
1939 2021 5.740290 TCGTAGATTTGGAGAAAGGAAGT 57.260 39.130 0.00 0.00 0.00 3.01
1960 2042 4.054671 GTGCTACCTCTGATAGTGCAATC 58.945 47.826 0.00 0.00 0.00 2.67
2015 2097 4.323417 TGTATGCACCGATTCAGTCTTTT 58.677 39.130 0.00 0.00 0.00 2.27
2169 2251 7.806409 TCAATGAGAGTTTTGTCAGAATTCA 57.194 32.000 8.44 0.00 29.18 2.57
2202 2291 9.796120 AAAATAACAACAGAACATTCGAAAAGA 57.204 25.926 0.00 0.00 0.00 2.52
2204 2293 9.574458 TGAAAATAACAACAGAACATTCGAAAA 57.426 25.926 0.00 0.00 0.00 2.29
2205 2294 9.743057 ATGAAAATAACAACAGAACATTCGAAA 57.257 25.926 0.00 0.00 0.00 3.46
2206 2295 9.179552 CATGAAAATAACAACAGAACATTCGAA 57.820 29.630 0.00 0.00 0.00 3.71
2207 2296 8.563732 TCATGAAAATAACAACAGAACATTCGA 58.436 29.630 0.00 0.00 0.00 3.71
2208 2297 8.726650 TCATGAAAATAACAACAGAACATTCG 57.273 30.769 0.00 0.00 0.00 3.34
2219 2308 6.990798 TGTTGCTGGATCATGAAAATAACAA 58.009 32.000 0.00 0.00 0.00 2.83
2230 2319 5.889853 ACATAACAAGATGTTGCTGGATCAT 59.110 36.000 1.83 0.00 41.30 2.45
2307 2396 6.049149 GCCCTGCCTTTAAAATAAGAATTCC 58.951 40.000 0.65 0.00 0.00 3.01
2315 2404 3.023832 GCTGAGCCCTGCCTTTAAAATA 58.976 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.