Multiple sequence alignment - TraesCS5D01G094200

Loading Multiple Alignment...

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 TraesCS5D01G094200 chr5D 100.000 2464 0 0 236 2699 103646885 103644422 0.000000e+00 4551.0
1 TraesCS5D01G094200 chr5D 88.867 1024 56 32 797 1794 103654966 103653975 0.000000e+00 1206.0
2 TraesCS5D01G094200 chr5D 100.000 29 0 0 1 29 103647120 103647092 1.000000e-03 54.7
3 TraesCS5D01G094200 chr5B 92.623 1464 53 15 797 2219 112587541 112586092 0.000000e+00 2054.0
4 TraesCS5D01G094200 chr5B 93.750 512 30 2 2190 2699 112586093 112585582 0.000000e+00 767.0
5 TraesCS5D01G094200 chr5B 94.382 89 4 1 2257 2345 382906812 382906899 4.690000e-28 135.0
6 TraesCS5D01G094200 chr5B 94.318 88 4 1 2257 2344 382906284 382906370 1.690000e-27 134.0
7 TraesCS5D01G094200 chr5B 93.258 89 5 1 2257 2345 382907341 382907428 2.180000e-26 130.0
8 TraesCS5D01G094200 chr5A 92.126 1016 48 11 797 1788 94741819 94742826 0.000000e+00 1404.0
9 TraesCS5D01G094200 chr5A 85.119 504 47 13 2202 2693 94743304 94743791 8.680000e-135 490.0
10 TraesCS5D01G094200 chr5A 80.147 408 21 30 1858 2210 94742852 94743254 1.600000e-62 250.0
11 TraesCS5D01G094200 chr6D 89.015 1147 81 25 861 1978 276902588 276903718 0.000000e+00 1378.0
12 TraesCS5D01G094200 chr6D 90.625 64 0 1 813 876 276902513 276902570 2.230000e-11 80.5
13 TraesCS5D01G094200 chr1D 94.444 558 11 7 236 774 50031090 50031646 0.000000e+00 841.0
14 TraesCS5D01G094200 chr1D 100.000 29 0 0 1 29 50030967 50030995 1.000000e-03 54.7
15 TraesCS5D01G094200 chr7D 88.172 558 38 11 239 774 93018354 93018905 8.150000e-180 640.0
16 TraesCS5D01G094200 chr2B 82.620 374 47 14 410 774 726601131 726601495 5.610000e-82 315.0
17 TraesCS5D01G094200 chr2B 95.062 81 4 0 2271 2351 76882582 76882502 7.840000e-26 128.0
18 TraesCS5D01G094200 chr2B 92.135 89 5 2 2257 2345 767472404 767472318 1.010000e-24 124.0
19 TraesCS5D01G094200 chr2B 83.099 142 12 4 273 413 726600831 726600961 4.720000e-23 119.0
20 TraesCS5D01G094200 chr2B 85.915 71 10 0 347 417 726601046 726601116 2.880000e-10 76.8
21 TraesCS5D01G094200 chr2A 98.667 75 1 0 2273 2347 537552253 537552179 1.690000e-27 134.0
22 TraesCS5D01G094200 chr7A 96.154 78 3 0 2271 2348 482324752 482324829 7.840000e-26 128.0
23 TraesCS5D01G094200 chr6A 90.244 82 3 2 2425 2503 338514956 338514877 4.750000e-18 102.0
24 TraesCS5D01G094200 chr3B 80.405 148 14 6 255 401 52883469 52883336 6.150000e-17 99.0
25 TraesCS5D01G094200 chr4A 91.045 67 6 0 708 774 729700986 729700920 1.030000e-14 91.6


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 TraesCS5D01G094200 chr5D 103644422 103647120 2698 True 2302.850000 4551 100.000000 1 2699 2 chr5D.!!$R2 2698
1 TraesCS5D01G094200 chr5D 103653975 103654966 991 True 1206.000000 1206 88.867000 797 1794 1 chr5D.!!$R1 997
2 TraesCS5D01G094200 chr5B 112585582 112587541 1959 True 1410.500000 2054 93.186500 797 2699 2 chr5B.!!$R1 1902
3 TraesCS5D01G094200 chr5A 94741819 94743791 1972 False 714.666667 1404 85.797333 797 2693 3 chr5A.!!$F1 1896
4 TraesCS5D01G094200 chr6D 276902513 276903718 1205 False 729.250000 1378 89.820000 813 1978 2 chr6D.!!$F1 1165
5 TraesCS5D01G094200 chr1D 50030967 50031646 679 False 447.850000 841 97.222000 1 774 2 chr1D.!!$F1 773
6 TraesCS5D01G094200 chr7D 93018354 93018905 551 False 640.000000 640 88.172000 239 774 1 chr7D.!!$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
788 830 0.103937 ATCTTCTGCTGACGCCTAGC 59.896 55.0 0.0 0.0 41.49 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 2802 2.092968 TCCAGGATAAGTGAAGCGCATT 60.093 45.455 11.47 0.0 0.0 3.56 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
284 285 2.274104 GCCAGGCCCCGAAACATA 59.726 61.111 0.00 0.00 0.00 2.29
409 410 1.137825 GGAGCTTCTCTGGTCGTCG 59.862 63.158 0.00 0.00 35.52 5.12
470 472 3.112709 GCTTGTCAGCCGACGGAC 61.113 66.667 20.50 7.75 45.80 4.79
574 576 3.270839 GAGCATCGCCTGAGCTGC 61.271 66.667 0.00 0.00 39.75 5.25
696 738 4.407621 ACGGTGTGGATGGAAATGATAGTA 59.592 41.667 0.00 0.00 0.00 1.82
775 817 2.906458 CCAGGCGGCTGATCTTCT 59.094 61.111 37.74 0.00 0.00 2.85
776 818 1.523258 CCAGGCGGCTGATCTTCTG 60.523 63.158 37.74 16.90 0.00 3.02
777 819 2.178890 CAGGCGGCTGATCTTCTGC 61.179 63.158 33.59 9.25 40.10 4.26
778 820 2.188994 GGCGGCTGATCTTCTGCT 59.811 61.111 0.00 0.00 40.57 4.24
779 821 2.178890 GGCGGCTGATCTTCTGCTG 61.179 63.158 0.00 9.95 46.44 4.41
780 822 1.153489 GCGGCTGATCTTCTGCTGA 60.153 57.895 16.45 0.00 46.58 4.26
781 823 1.427592 GCGGCTGATCTTCTGCTGAC 61.428 60.000 16.45 6.63 46.58 3.51
782 824 1.144565 CGGCTGATCTTCTGCTGACG 61.145 60.000 8.94 0.00 46.58 4.35
783 825 1.427592 GGCTGATCTTCTGCTGACGC 61.428 60.000 6.38 0.00 40.57 5.19
784 826 1.427592 GCTGATCTTCTGCTGACGCC 61.428 60.000 0.00 0.00 38.17 5.68
785 827 0.175302 CTGATCTTCTGCTGACGCCT 59.825 55.000 0.00 0.00 34.43 5.52
786 828 1.406898 CTGATCTTCTGCTGACGCCTA 59.593 52.381 0.00 0.00 34.43 3.93
787 829 1.406898 TGATCTTCTGCTGACGCCTAG 59.593 52.381 0.00 0.00 34.43 3.02
788 830 0.103937 ATCTTCTGCTGACGCCTAGC 59.896 55.000 0.00 0.00 41.49 3.42
806 848 1.202348 AGCAGCCGCCTTTGAAATTAC 59.798 47.619 0.00 0.00 39.83 1.89
834 876 3.206150 GTGGACTCACTTTGCTTTCTCA 58.794 45.455 0.00 0.00 40.58 3.27
925 1015 3.181522 GGAGACGACGTCGCCTATATAAG 60.182 52.174 34.66 8.03 46.43 1.73
939 1029 2.550830 TATAAGCAAGCTAGCCTGCC 57.449 50.000 30.09 15.27 34.23 4.85
962 1052 0.528033 TCCGTTGAACGTCGAAGCAA 60.528 50.000 17.05 0.00 40.58 3.91
1013 1110 0.471617 GAGACTATGGCTGGCATGGT 59.528 55.000 28.49 28.49 0.00 3.55
1014 1111 1.694150 GAGACTATGGCTGGCATGGTA 59.306 52.381 28.25 8.84 0.00 3.25
1535 1632 4.530857 GGTCGCGTGCTATGGGCT 62.531 66.667 5.77 0.00 42.39 5.19
1539 1636 2.822399 GCGTGCTATGGGCTACCT 59.178 61.111 0.00 0.00 42.39 3.08
1709 1830 2.258748 GAGAACTAGGTGGCTGGCCC 62.259 65.000 9.28 0.00 34.56 5.80
1735 1859 3.239941 GCGAGTGATGTTGATACACGTAC 59.760 47.826 0.00 0.00 37.03 3.67
2029 2189 2.804828 GAACAAGACAGAGGCCCCGG 62.805 65.000 0.00 0.00 0.00 5.73
2031 2191 2.203938 AAGACAGAGGCCCCGGAA 60.204 61.111 0.73 0.00 0.00 4.30
2038 2205 0.038310 AGAGGCCCCGGAAAAGAAAG 59.962 55.000 0.73 0.00 0.00 2.62
2236 2487 3.370104 TCTCTTCCCCAAAAACAAAGCA 58.630 40.909 0.00 0.00 0.00 3.91
2345 2596 3.282135 ACCATATGAGCTACATCCCCT 57.718 47.619 3.65 0.00 40.07 4.79
2354 2605 2.041620 AGCTACATCCCCTTTCTGCAAA 59.958 45.455 0.00 0.00 0.00 3.68
2396 2657 1.280998 GGAGGTGCCCTAAAAGTGCTA 59.719 52.381 0.00 0.00 31.76 3.49
2443 2704 3.535561 GTTCCATCTGTATCTGTGGGTG 58.464 50.000 0.00 0.00 32.58 4.61
2507 2768 4.898829 TCCCTATTTGCATTTCATGACG 57.101 40.909 0.00 0.00 0.00 4.35
2541 2802 0.610174 CCAGTAGCTTCAGGTGCTCA 59.390 55.000 0.00 0.00 41.46 4.26
2638 2900 1.265095 CTGTGCTTTGCATGTTCGACT 59.735 47.619 0.00 0.00 41.91 4.18
2639 2901 1.002576 TGTGCTTTGCATGTTCGACTG 60.003 47.619 0.00 0.00 41.91 3.51
2648 2910 2.030946 GCATGTTCGACTGCTTCATACC 59.969 50.000 6.56 0.00 35.49 2.73
2664 2926 5.165911 TCATACCAGTATTTCGAGACGAC 57.834 43.478 0.00 0.00 34.89 4.34
2665 2927 2.539346 ACCAGTATTTCGAGACGACG 57.461 50.000 0.00 0.00 34.89 5.12
2693 2955 1.568504 AGTGCCATACTCCTTCCGAA 58.431 50.000 0.00 0.00 33.17 4.30
2694 2956 1.482593 AGTGCCATACTCCTTCCGAAG 59.517 52.381 0.68 0.68 33.17 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
284 285 1.599047 CTCCACTGGAGCACCGATT 59.401 57.895 12.34 0.00 43.29 3.34
409 410 2.258897 GCGGCCTAGCGATACTCC 59.741 66.667 0.00 0.00 0.00 3.85
574 576 2.438434 GAACTGGTGATGCCCCGG 60.438 66.667 0.00 0.00 36.04 5.73
696 738 6.467677 CCGTTTGATTCCCTGATAGTATCAT 58.532 40.000 13.22 0.00 38.85 2.45
705 747 1.001393 GGGCCGTTTGATTCCCTGA 60.001 57.895 0.00 0.00 35.87 3.86
717 759 5.675684 AAATAGAATTTGATTTGGGCCGT 57.324 34.783 0.00 0.00 0.00 5.68
782 824 3.512516 CAAAGGCGGCTGCTAGGC 61.513 66.667 18.85 12.49 42.25 3.93
783 825 0.960364 TTTCAAAGGCGGCTGCTAGG 60.960 55.000 18.85 5.10 42.25 3.02
784 826 1.098050 ATTTCAAAGGCGGCTGCTAG 58.902 50.000 18.85 2.83 42.25 3.42
785 827 1.544724 AATTTCAAAGGCGGCTGCTA 58.455 45.000 18.85 0.00 42.25 3.49
786 828 1.202348 GTAATTTCAAAGGCGGCTGCT 59.798 47.619 18.85 0.00 42.25 4.24
787 829 1.629013 GTAATTTCAAAGGCGGCTGC 58.371 50.000 14.21 9.72 41.71 5.25
788 830 1.467374 CGGTAATTTCAAAGGCGGCTG 60.467 52.381 14.21 1.03 0.00 4.85
789 831 0.808755 CGGTAATTTCAAAGGCGGCT 59.191 50.000 5.25 5.25 0.00 5.52
790 832 0.179148 CCGGTAATTTCAAAGGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
791 833 1.135517 CACCGGTAATTTCAAAGGCGG 60.136 52.381 6.87 0.00 0.00 6.13
792 834 1.135517 CCACCGGTAATTTCAAAGGCG 60.136 52.381 6.87 0.00 0.00 5.52
793 835 1.203758 CCCACCGGTAATTTCAAAGGC 59.796 52.381 6.87 0.00 0.00 4.35
794 836 2.230266 CACCCACCGGTAATTTCAAAGG 59.770 50.000 6.87 0.00 42.04 3.11
795 837 2.230266 CCACCCACCGGTAATTTCAAAG 59.770 50.000 6.87 0.00 42.04 2.77
806 848 2.052047 AAAGTGAGTCCACCCACCGG 62.052 60.000 0.00 0.00 44.22 5.28
834 876 3.506398 CCTACTGTTCCCAAACCCAAAT 58.494 45.455 0.00 0.00 34.28 2.32
962 1052 2.281761 CTTGGCTTCGCAGGGTGT 60.282 61.111 0.00 0.00 0.00 4.16
971 1067 2.665794 GCGCTACTTGTTTCTTGGCTTC 60.666 50.000 0.00 0.00 0.00 3.86
1013 1110 2.543802 CCGATCACGAGGCGCTCTA 61.544 63.158 7.64 0.00 42.66 2.43
1014 1111 3.893763 CCGATCACGAGGCGCTCT 61.894 66.667 7.64 1.93 42.66 4.09
1071 1168 2.448542 AGGGTCAGTGTGGTGCCT 60.449 61.111 0.00 0.00 0.00 4.75
1080 1177 1.149174 CAGGTTGTGCAGGGTCAGT 59.851 57.895 0.00 0.00 0.00 3.41
1528 1625 2.326428 GAAGTAGCCAGGTAGCCCATA 58.674 52.381 0.00 0.00 0.00 2.74
1535 1632 1.066143 GCTGCTTGAAGTAGCCAGGTA 60.066 52.381 22.29 0.00 46.33 3.08
1709 1830 4.205181 CGTGTATCAACATCACTCGCTAAG 59.795 45.833 0.00 0.00 38.08 2.18
1735 1859 6.348540 GCCACTCTTATTTTCACTACACCTTG 60.349 42.308 0.00 0.00 0.00 3.61
2000 2160 4.702612 CCTCTGTCTTGTTCTAGCTACTCA 59.297 45.833 0.00 0.00 0.00 3.41
2271 2522 2.582436 GATTCCCCGCGTCTCCAA 59.418 61.111 4.92 0.00 0.00 3.53
2443 2704 6.750963 ACGAAGAATAATGAAAGACCGTCTAC 59.249 38.462 0.26 0.36 0.00 2.59
2507 2768 7.334421 TGAAGCTACTGGTTTACAAAGATGATC 59.666 37.037 0.00 0.00 33.64 2.92
2541 2802 2.092968 TCCAGGATAAGTGAAGCGCATT 60.093 45.455 11.47 0.00 0.00 3.56
2638 2900 5.348986 GTCTCGAAATACTGGTATGAAGCA 58.651 41.667 0.00 0.00 0.00 3.91
2639 2901 4.441415 CGTCTCGAAATACTGGTATGAAGC 59.559 45.833 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.