Multiple sequence alignment - TraesCS5D01G094900

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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 TraesCS5D01G094900 chr5D 100.000 2690 0 0 1 2690 104399361 104396672 0.000000e+00 4968.0
1 TraesCS5D01G094900 chr5D 92.767 871 49 8 895 1757 104447168 104446304 0.000000e+00 1247.0
2 TraesCS5D01G094900 chr5D 88.194 144 17 0 1 144 377264427 377264284 3.560000e-39 172.0
3 TraesCS5D01G094900 chr5B 94.455 1569 59 11 204 1763 113806569 113805020 0.000000e+00 2390.0
4 TraesCS5D01G094900 chr5B 94.888 939 30 7 1762 2690 113804974 113804044 0.000000e+00 1452.0
5 TraesCS5D01G094900 chr5B 92.537 871 51 9 895 1757 113823570 113822706 0.000000e+00 1236.0
6 TraesCS5D01G094900 chr5B 85.556 270 27 4 1 259 492007909 492007641 3.410000e-69 272.0
7 TraesCS5D01G094900 chr5B 96.377 138 5 0 1 138 113806908 113806771 7.490000e-56 228.0
8 TraesCS5D01G094900 chr5A 94.511 838 39 4 782 1619 93188244 93189074 0.000000e+00 1286.0
9 TraesCS5D01G094900 chr5A 92.512 868 55 5 895 1756 106855930 106855067 0.000000e+00 1234.0
10 TraesCS5D01G094900 chr5A 90.223 941 51 15 1762 2687 93189962 93190876 0.000000e+00 1190.0
11 TraesCS5D01G094900 chr5A 87.988 691 64 7 54 743 93186425 93187097 0.000000e+00 798.0
12 TraesCS5D01G094900 chr5A 94.737 152 5 1 1612 1763 93189768 93189916 1.610000e-57 233.0
13 TraesCS5D01G094900 chr1D 86.894 763 78 7 1 760 225692127 225692870 0.000000e+00 835.0
14 TraesCS5D01G094900 chr1D 84.367 774 91 7 1 758 223180328 223181087 0.000000e+00 732.0
15 TraesCS5D01G094900 chr1D 93.182 44 3 0 2647 2690 247514112 247514069 6.220000e-07 65.8
16 TraesCS5D01G094900 chr1D 95.238 42 0 1 2650 2689 456271764 456271723 6.220000e-07 65.8
17 TraesCS5D01G094900 chr4D 84.514 762 78 15 1 758 51606422 51605697 0.000000e+00 717.0
18 TraesCS5D01G094900 chr3D 84.273 763 89 13 1 759 460435332 460436067 0.000000e+00 715.0
19 TraesCS5D01G094900 chr3A 83.653 783 98 11 1 758 642614503 642615280 0.000000e+00 710.0
20 TraesCS5D01G094900 chr3A 85.156 128 18 1 2305 2431 681104623 681104496 2.170000e-26 130.0
21 TraesCS5D01G094900 chr1A 86.425 663 70 11 1 659 592760392 592759746 0.000000e+00 708.0
22 TraesCS5D01G094900 chr7D 83.681 766 87 24 1 758 504531689 504530954 0.000000e+00 688.0
23 TraesCS5D01G094900 chr7D 87.020 547 67 4 215 758 617981894 617982439 4.920000e-172 614.0
24 TraesCS5D01G094900 chr7D 85.098 255 19 4 1 255 539699852 539700087 2.680000e-60 243.0
25 TraesCS5D01G094900 chr7D 97.368 38 1 0 2653 2690 122961128 122961165 6.220000e-07 65.8
26 TraesCS5D01G094900 chr2A 83.289 754 113 3 1 753 136783364 136784105 0.000000e+00 682.0
27 TraesCS5D01G094900 chr2D 86.194 536 68 4 228 760 600152985 600153517 2.320000e-160 575.0
28 TraesCS5D01G094900 chr2D 85.584 548 72 5 217 760 587577000 587576456 3.890000e-158 568.0
29 TraesCS5D01G094900 chr2D 95.349 43 0 2 2650 2690 558961237 558961279 1.730000e-07 67.6
30 TraesCS5D01G094900 chr7A 84.505 555 78 7 209 758 8515459 8516010 2.360000e-150 542.0
31 TraesCS5D01G094900 chr1B 76.262 733 109 23 15 728 92884516 92883830 2.000000e-86 329.0
32 TraesCS5D01G094900 chr1B 100.000 35 0 0 2656 2690 57382456 57382422 6.220000e-07 65.8
33 TraesCS5D01G094900 chr6D 93.617 47 2 1 2644 2690 2919121 2919166 4.810000e-08 69.4
34 TraesCS5D01G094900 chr6D 95.349 43 2 0 2648 2690 313153072 313153030 4.810000e-08 69.4
35 TraesCS5D01G094900 chr4B 100.000 36 0 0 2655 2690 99970429 99970464 1.730000e-07 67.6


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 TraesCS5D01G094900 chr5D 104396672 104399361 2689 True 4968.000000 4968 100.00000 1 2690 1 chr5D.!!$R1 2689
1 TraesCS5D01G094900 chr5D 104446304 104447168 864 True 1247.000000 1247 92.76700 895 1757 1 chr5D.!!$R2 862
2 TraesCS5D01G094900 chr5B 113804044 113806908 2864 True 1356.666667 2390 95.24000 1 2690 3 chr5B.!!$R3 2689
3 TraesCS5D01G094900 chr5B 113822706 113823570 864 True 1236.000000 1236 92.53700 895 1757 1 chr5B.!!$R1 862
4 TraesCS5D01G094900 chr5A 106855067 106855930 863 True 1234.000000 1234 92.51200 895 1756 1 chr5A.!!$R1 861
5 TraesCS5D01G094900 chr5A 93186425 93190876 4451 False 876.750000 1286 91.86475 54 2687 4 chr5A.!!$F1 2633
6 TraesCS5D01G094900 chr1D 225692127 225692870 743 False 835.000000 835 86.89400 1 760 1 chr1D.!!$F2 759
7 TraesCS5D01G094900 chr1D 223180328 223181087 759 False 732.000000 732 84.36700 1 758 1 chr1D.!!$F1 757
8 TraesCS5D01G094900 chr4D 51605697 51606422 725 True 717.000000 717 84.51400 1 758 1 chr4D.!!$R1 757
9 TraesCS5D01G094900 chr3D 460435332 460436067 735 False 715.000000 715 84.27300 1 759 1 chr3D.!!$F1 758
10 TraesCS5D01G094900 chr3A 642614503 642615280 777 False 710.000000 710 83.65300 1 758 1 chr3A.!!$F1 757
11 TraesCS5D01G094900 chr1A 592759746 592760392 646 True 708.000000 708 86.42500 1 659 1 chr1A.!!$R1 658
12 TraesCS5D01G094900 chr7D 504530954 504531689 735 True 688.000000 688 83.68100 1 758 1 chr7D.!!$R1 757
13 TraesCS5D01G094900 chr7D 617981894 617982439 545 False 614.000000 614 87.02000 215 758 1 chr7D.!!$F3 543
14 TraesCS5D01G094900 chr2A 136783364 136784105 741 False 682.000000 682 83.28900 1 753 1 chr2A.!!$F1 752
15 TraesCS5D01G094900 chr2D 600152985 600153517 532 False 575.000000 575 86.19400 228 760 1 chr2D.!!$F2 532
16 TraesCS5D01G094900 chr2D 587576456 587577000 544 True 568.000000 568 85.58400 217 760 1 chr2D.!!$R1 543
17 TraesCS5D01G094900 chr7A 8515459 8516010 551 False 542.000000 542 84.50500 209 758 1 chr7A.!!$F1 549
18 TraesCS5D01G094900 chr1B 92883830 92884516 686 True 329.000000 329 76.26200 15 728 1 chr1B.!!$R2 713

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
555 733 0.340208 AGGAAGGGAGGTGAGGGTAG 59.660 60.000 0.0 0.0 0.00 3.18 F
675 854 0.383949 GCTCCACAAAAACAGCCGAA 59.616 50.000 0.0 0.0 0.00 4.30 F
1356 2646 2.432628 GCGTACAGCGTCAGCCTT 60.433 61.111 0.0 0.0 46.67 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 2646 0.598158 GCACGTTGAACCCGTCTACA 60.598 55.000 0.00 0.00 36.17 2.74 R
1600 2890 0.689080 ATGGACGACTGGCAGAGGAT 60.689 55.000 23.66 3.06 0.00 3.24 R
2581 4638 1.151413 ACCTCTAACCCCAGTCTCCAA 59.849 52.381 0.00 0.00 0.00 3.53 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
49 50 1.227999 CCGACAACGACAAGGTGCAT 61.228 55.000 0.00 0.00 42.61 3.96
315 492 2.618045 CCATGTGTTTAGTCCACTCCCC 60.618 54.545 0.00 0.00 33.92 4.81
328 505 2.619074 CCACTCCCCAACTCTTCAATCC 60.619 54.545 0.00 0.00 0.00 3.01
433 610 2.125753 GGAGGTCTGCAGTCGCTG 60.126 66.667 14.67 2.92 39.64 5.18
555 733 0.340208 AGGAAGGGAGGTGAGGGTAG 59.660 60.000 0.00 0.00 0.00 3.18
593 771 1.454276 GAAAACAACGCGACATCTCGA 59.546 47.619 15.93 0.00 43.06 4.04
669 848 1.398692 GGTCTGGCTCCACAAAAACA 58.601 50.000 0.00 0.00 0.00 2.83
675 854 0.383949 GCTCCACAAAAACAGCCGAA 59.616 50.000 0.00 0.00 0.00 4.30
682 861 4.047822 CACAAAAACAGCCGAATTAAGCA 58.952 39.130 2.34 0.00 0.00 3.91
705 884 4.749323 CTGGATGCAAGCCCAGAA 57.251 55.556 21.68 0.00 46.54 3.02
716 895 4.465660 TGCAAGCCCAGAAATGCTTTAATA 59.534 37.500 0.00 0.00 45.09 0.98
1356 2646 2.432628 GCGTACAGCGTCAGCCTT 60.433 61.111 0.00 0.00 46.67 4.35
1600 2890 2.066393 CCCGGGGAGCTCAAGATCA 61.066 63.158 14.71 0.00 30.87 2.92
1671 3662 2.516589 CGACATGGTCATCCGCACG 61.517 63.158 0.00 0.00 36.30 5.34
1740 3736 0.533491 TGCCGTACTTCTACGCCATT 59.467 50.000 0.00 0.00 43.82 3.16
1794 3837 9.410556 GTTGCAGTTAAATGTTTGTATTGAGAT 57.589 29.630 4.65 0.00 0.00 2.75
1817 3860 8.478877 AGATCTTAGGTTTCGTCATCTGTAATT 58.521 33.333 0.00 0.00 0.00 1.40
1819 3862 7.837863 TCTTAGGTTTCGTCATCTGTAATTCT 58.162 34.615 0.00 0.00 0.00 2.40
1997 4043 8.573035 TCACTTAGCTTAAAAATGGTAAACCTG 58.427 33.333 0.00 0.00 36.82 4.00
2106 4152 5.701224 TCCTACTGAAAACAGGGTTGATTT 58.299 37.500 0.00 0.00 32.69 2.17
2140 4186 2.936498 TGCTAGCGGTAGAAAATGAAGC 59.064 45.455 25.15 9.46 0.00 3.86
2257 4303 8.294577 GGTGTTTTTAAGGTGTATAGGTCTTTG 58.705 37.037 0.00 0.00 0.00 2.77
2259 4305 8.000127 TGTTTTTAAGGTGTATAGGTCTTTGGT 59.000 33.333 0.00 0.00 0.00 3.67
2260 4306 7.989416 TTTTAAGGTGTATAGGTCTTTGGTG 57.011 36.000 0.00 0.00 0.00 4.17
2496 4552 4.728772 AGGTGATCTGACCAATCAAAACA 58.271 39.130 5.11 0.00 38.63 2.83
2508 4564 6.275335 ACCAATCAAAACATGAACAGACAAG 58.725 36.000 0.00 0.00 42.54 3.16
2630 4687 1.580059 GGGTGATAAGGGTCACTGGA 58.420 55.000 6.94 0.00 46.02 3.86
2642 4699 1.302511 CACTGGAACGGAGGGGTTG 60.303 63.158 0.00 0.00 38.67 3.77
2643 4700 1.768888 ACTGGAACGGAGGGGTTGT 60.769 57.895 0.00 0.00 38.67 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
315 492 3.672808 AGAGCACAGGATTGAAGAGTTG 58.327 45.455 0.00 0.00 0.00 3.16
328 505 4.233789 GGCTAGATTCGATTAGAGCACAG 58.766 47.826 12.41 0.00 0.00 3.66
509 686 0.252927 CTCTCCCCTCTTCCCCACTT 60.253 60.000 0.00 0.00 0.00 3.16
574 752 1.455786 CTCGAGATGTCGCGTTGTTTT 59.544 47.619 6.58 0.00 46.39 2.43
593 771 4.969196 CACGCGTGGGTGCAGTCT 62.969 66.667 31.15 0.00 34.15 3.24
669 848 3.209410 CAGAGGAATGCTTAATTCGGCT 58.791 45.455 4.59 0.00 44.95 5.52
675 854 4.174704 TGCATCCAGAGGAATGCTTAAT 57.825 40.909 16.00 0.00 37.24 1.40
682 861 0.106318 GGGCTTGCATCCAGAGGAAT 60.106 55.000 7.68 0.00 34.34 3.01
705 884 6.969366 TGCATAGCACGAATATTAAAGCATT 58.031 32.000 0.00 0.00 31.71 3.56
716 895 0.178767 TGAGCCTGCATAGCACGAAT 59.821 50.000 11.08 0.00 33.79 3.34
769 2053 0.889994 TGTACCTTCTTAGCCGCGAA 59.110 50.000 8.23 0.00 0.00 4.70
770 2054 1.108776 ATGTACCTTCTTAGCCGCGA 58.891 50.000 8.23 0.00 0.00 5.87
776 2060 3.550437 AGGCTGCATGTACCTTCTTAG 57.450 47.619 0.50 0.00 0.00 2.18
777 2061 4.653801 TGATAGGCTGCATGTACCTTCTTA 59.346 41.667 0.50 0.00 34.92 2.10
778 2062 3.455910 TGATAGGCTGCATGTACCTTCTT 59.544 43.478 0.50 0.00 34.92 2.52
779 2063 3.041211 TGATAGGCTGCATGTACCTTCT 58.959 45.455 0.50 0.68 34.92 2.85
1075 2365 2.358737 CGGGCAGAGGTTGTGGAC 60.359 66.667 0.00 0.00 0.00 4.02
1263 2553 3.416382 GCGTCGCCCGTAAAGCAA 61.416 61.111 5.75 0.00 39.32 3.91
1299 2589 1.153823 GTCGTGGACCGTGATCTGG 60.154 63.158 3.35 3.35 37.94 3.86
1356 2646 0.598158 GCACGTTGAACCCGTCTACA 60.598 55.000 0.00 0.00 36.17 2.74
1434 2724 1.069090 GTCGCAGTTGAGGTCCACA 59.931 57.895 0.00 0.00 0.00 4.17
1498 2788 1.186917 TTCTTGAAGTACCCCGCGGA 61.187 55.000 30.73 2.89 0.00 5.54
1600 2890 0.689080 ATGGACGACTGGCAGAGGAT 60.689 55.000 23.66 3.06 0.00 3.24
1649 3640 3.272334 GGATGACCATGTCGGCGC 61.272 66.667 0.00 0.00 39.03 6.53
1794 3837 7.759886 CAGAATTACAGATGACGAAACCTAAGA 59.240 37.037 0.00 0.00 0.00 2.10
1817 3860 1.304630 TACCAGCTACACCGCCAGA 60.305 57.895 0.00 0.00 0.00 3.86
1819 3862 1.608336 AGTACCAGCTACACCGCCA 60.608 57.895 0.00 0.00 0.00 5.69
1997 4043 8.196771 TCAAATTGAATACTATCAATGCAACCC 58.803 33.333 3.52 0.00 46.57 4.11
2061 4107 6.377146 AGGAAAAACATGCGACCAACTATTAT 59.623 34.615 0.00 0.00 0.00 1.28
2106 4152 4.509616 ACCGCTAGCATATTGTTGTACAA 58.490 39.130 16.45 3.59 42.95 2.41
2140 4186 1.067495 AGGCTTCTTTCTTCGACTCCG 60.067 52.381 0.00 0.00 37.07 4.63
2337 4385 3.963129 TCTAAGCCCAGTTGGTTAATGG 58.037 45.455 0.00 0.00 36.04 3.16
2341 4389 2.872842 GCGTTCTAAGCCCAGTTGGTTA 60.873 50.000 0.00 0.00 36.04 2.85
2496 4552 3.813443 ACTTGTGAGCTTGTCTGTTCAT 58.187 40.909 0.00 0.00 30.43 2.57
2508 4564 1.536709 CCAGCAACCAAACTTGTGAGC 60.537 52.381 0.00 0.00 0.00 4.26
2541 4597 7.610305 CAGGGCTCCTCTATACAAAGTTAAAAA 59.390 37.037 0.00 0.00 0.00 1.94
2542 4598 7.037873 TCAGGGCTCCTCTATACAAAGTTAAAA 60.038 37.037 0.00 0.00 0.00 1.52
2543 4599 6.442564 TCAGGGCTCCTCTATACAAAGTTAAA 59.557 38.462 0.00 0.00 0.00 1.52
2544 4600 5.962031 TCAGGGCTCCTCTATACAAAGTTAA 59.038 40.000 0.00 0.00 0.00 2.01
2545 4601 5.525484 TCAGGGCTCCTCTATACAAAGTTA 58.475 41.667 0.00 0.00 0.00 2.24
2581 4638 1.151413 ACCTCTAACCCCAGTCTCCAA 59.849 52.381 0.00 0.00 0.00 3.53
2630 4687 1.420532 TTGCCTACAACCCCTCCGTT 61.421 55.000 0.00 0.00 0.00 4.44
2642 4699 3.945921 GGAGGGAGTAAAACATTGCCTAC 59.054 47.826 0.00 0.00 34.63 3.18
2643 4700 3.370103 CGGAGGGAGTAAAACATTGCCTA 60.370 47.826 0.00 0.00 34.63 3.93


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

AutoCloner maintained by Alex Coulton.