Multiple sequence alignment - TraesCS1D01G144300

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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 TraesCS1D01G144300 chr1D 100.000 2777 0 0 1 2777 199670814 199673590 0.000000e+00 5129.0
1 TraesCS1D01G144300 chr1D 84.040 401 51 10 1897 2292 413585379 413584987 9.390000e-100 374.0
2 TraesCS1D01G144300 chr1D 83.292 407 55 13 1891 2289 435171383 435170982 2.030000e-96 363.0
3 TraesCS1D01G144300 chr1A 95.065 1986 57 9 816 2777 251936080 251938048 0.000000e+00 3086.0
4 TraesCS1D01G144300 chr1A 86.152 686 58 13 1897 2549 15472298 15471617 0.000000e+00 706.0
5 TraesCS1D01G144300 chr1B 95.385 1105 27 3 805 1895 280209634 280210728 0.000000e+00 1736.0
6 TraesCS1D01G144300 chr6D 97.243 798 20 2 1 796 81109155 81109952 0.000000e+00 1351.0
7 TraesCS1D01G144300 chr6D 94.981 797 38 2 1 796 443752493 443753288 0.000000e+00 1249.0
8 TraesCS1D01G144300 chr2D 95.483 797 35 1 1 796 495103270 495104066 0.000000e+00 1271.0
9 TraesCS1D01G144300 chr2D 97.143 35 1 0 2570 2604 184124099 184124065 2.990000e-05 60.2
10 TraesCS1D01G144300 chr3D 95.232 797 37 1 1 796 368962531 368963327 0.000000e+00 1260.0
11 TraesCS1D01G144300 chr2B 93.392 802 40 5 1 800 8492529 8491739 0.000000e+00 1175.0
12 TraesCS1D01G144300 chr2B 85.766 822 77 23 1 796 180554115 180554922 0.000000e+00 833.0
13 TraesCS1D01G144300 chr2B 84.289 401 51 9 1897 2292 786863939 786863546 5.610000e-102 381.0
14 TraesCS1D01G144300 chr3A 92.965 796 37 6 1 796 700229552 700228776 0.000000e+00 1142.0
15 TraesCS1D01G144300 chr3A 92.857 798 37 6 1 796 700208468 700209247 0.000000e+00 1140.0
16 TraesCS1D01G144300 chr3A 79.208 404 66 13 2162 2551 545048620 545049019 5.900000e-67 265.0
17 TraesCS1D01G144300 chr2A 94.549 587 30 2 212 796 185714890 185714304 0.000000e+00 905.0
18 TraesCS1D01G144300 chr2A 86.772 824 76 17 2 796 774536445 774535626 0.000000e+00 887.0
19 TraesCS1D01G144300 chr2A 90.476 210 18 2 2343 2550 221083839 221083630 2.720000e-70 276.0
20 TraesCS1D01G144300 chr2A 79.703 404 60 18 2162 2549 258985108 258985505 3.520000e-69 272.0
21 TraesCS1D01G144300 chr6B 84.447 823 79 15 1 796 680133112 680133912 0.000000e+00 765.0
22 TraesCS1D01G144300 chr6A 85.449 701 64 10 1898 2565 62604295 62603600 0.000000e+00 695.0
23 TraesCS1D01G144300 chr4D 84.884 688 66 16 1897 2550 424577471 424576788 0.000000e+00 660.0
24 TraesCS1D01G144300 chr4D 83.333 402 55 9 1896 2292 452559981 452559587 7.310000e-96 361.0
25 TraesCS1D01G144300 chr4D 80.098 407 58 11 2162 2548 452559662 452559259 5.860000e-72 281.0
26 TraesCS1D01G144300 chr4D 100.000 31 0 0 2576 2606 3270907 3270877 1.070000e-04 58.4
27 TraesCS1D01G144300 chr7A 79.745 706 80 18 1897 2546 648749767 648749069 1.170000e-123 453.0
28 TraesCS1D01G144300 chr7A 97.143 35 1 0 2570 2604 54968069 54968103 2.990000e-05 60.2
29 TraesCS1D01G144300 chr7A 97.143 35 1 0 2570 2604 646669878 646669844 2.990000e-05 60.2
30 TraesCS1D01G144300 chr7D 83.763 388 51 9 1898 2280 614650565 614650945 9.460000e-95 357.0
31 TraesCS1D01G144300 chr5A 80.247 405 63 15 2162 2553 9208826 9208426 3.500000e-74 289.0
32 TraesCS1D01G144300 chr5A 80.144 418 50 19 2162 2549 445202263 445202677 5.860000e-72 281.0
33 TraesCS1D01G144300 chr5A 87.500 64 8 0 2570 2633 48897750 48897813 1.070000e-09 75.0
34 TraesCS1D01G144300 chr5B 97.143 35 1 0 2570 2604 554950910 554950944 2.990000e-05 60.2


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 TraesCS1D01G144300 chr1D 199670814 199673590 2776 False 5129 5129 100.0000 1 2777 1 chr1D.!!$F1 2776
1 TraesCS1D01G144300 chr1A 251936080 251938048 1968 False 3086 3086 95.0650 816 2777 1 chr1A.!!$F1 1961
2 TraesCS1D01G144300 chr1A 15471617 15472298 681 True 706 706 86.1520 1897 2549 1 chr1A.!!$R1 652
3 TraesCS1D01G144300 chr1B 280209634 280210728 1094 False 1736 1736 95.3850 805 1895 1 chr1B.!!$F1 1090
4 TraesCS1D01G144300 chr6D 81109155 81109952 797 False 1351 1351 97.2430 1 796 1 chr6D.!!$F1 795
5 TraesCS1D01G144300 chr6D 443752493 443753288 795 False 1249 1249 94.9810 1 796 1 chr6D.!!$F2 795
6 TraesCS1D01G144300 chr2D 495103270 495104066 796 False 1271 1271 95.4830 1 796 1 chr2D.!!$F1 795
7 TraesCS1D01G144300 chr3D 368962531 368963327 796 False 1260 1260 95.2320 1 796 1 chr3D.!!$F1 795
8 TraesCS1D01G144300 chr2B 8491739 8492529 790 True 1175 1175 93.3920 1 800 1 chr2B.!!$R1 799
9 TraesCS1D01G144300 chr2B 180554115 180554922 807 False 833 833 85.7660 1 796 1 chr2B.!!$F1 795
10 TraesCS1D01G144300 chr3A 700228776 700229552 776 True 1142 1142 92.9650 1 796 1 chr3A.!!$R1 795
11 TraesCS1D01G144300 chr3A 700208468 700209247 779 False 1140 1140 92.8570 1 796 1 chr3A.!!$F2 795
12 TraesCS1D01G144300 chr2A 185714304 185714890 586 True 905 905 94.5490 212 796 1 chr2A.!!$R1 584
13 TraesCS1D01G144300 chr2A 774535626 774536445 819 True 887 887 86.7720 2 796 1 chr2A.!!$R3 794
14 TraesCS1D01G144300 chr6B 680133112 680133912 800 False 765 765 84.4470 1 796 1 chr6B.!!$F1 795
15 TraesCS1D01G144300 chr6A 62603600 62604295 695 True 695 695 85.4490 1898 2565 1 chr6A.!!$R1 667
16 TraesCS1D01G144300 chr4D 424576788 424577471 683 True 660 660 84.8840 1897 2550 1 chr4D.!!$R2 653
17 TraesCS1D01G144300 chr4D 452559259 452559981 722 True 321 361 81.7155 1896 2548 2 chr4D.!!$R3 652
18 TraesCS1D01G144300 chr7A 648749069 648749767 698 True 453 453 79.7450 1897 2546 1 chr7A.!!$R2 649

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
651 685 0.761702 GTAGCAGGTTATCCCCGGGA 60.762 60.0 26.32 9.16 35.55 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2015 0.187117 TTGGGGATGCAAGTTGTCCA 59.813 50.0 13.05 7.19 33.62 4.02 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
251 255 7.043722 CGCACTTAAAAACAATTGTTCAGCTTA 60.044 33.333 23.47 14.95 37.25 3.09
601 633 7.623268 ATTCTAAAGTTCACGATTTTGTTGC 57.377 32.000 0.00 0.00 0.00 4.17
648 682 1.341531 CTGAGTAGCAGGTTATCCCCG 59.658 57.143 0.00 0.00 41.07 5.73
651 685 0.761702 GTAGCAGGTTATCCCCGGGA 60.762 60.000 26.32 9.16 35.55 5.14
672 708 4.706962 GGATTTTCTTATTCCCAGTGTGCT 59.293 41.667 0.00 0.00 0.00 4.40
764 800 5.116180 TCAGGGTTTGATTTAGCTATCGTG 58.884 41.667 0.00 0.00 0.00 4.35
796 832 6.525629 TCAAGGTTTGTTTTGGACTTTTTCA 58.474 32.000 0.00 0.00 0.00 2.69
800 836 8.073467 AGGTTTGTTTTGGACTTTTTCATAGA 57.927 30.769 0.00 0.00 0.00 1.98
801 837 8.704668 AGGTTTGTTTTGGACTTTTTCATAGAT 58.295 29.630 0.00 0.00 0.00 1.98
802 838 8.978539 GGTTTGTTTTGGACTTTTTCATAGATC 58.021 33.333 0.00 0.00 0.00 2.75
803 839 9.528018 GTTTGTTTTGGACTTTTTCATAGATCA 57.472 29.630 0.00 0.00 0.00 2.92
959 998 1.239347 GCTCCTAATCGCCCCATTTC 58.761 55.000 0.00 0.00 0.00 2.17
1086 1137 2.828549 GGGAACGGCATCGGCATT 60.829 61.111 0.00 0.00 43.71 3.56
1357 1408 3.014085 GCGGACGGGGAGTTCATGA 62.014 63.158 0.00 0.00 0.00 3.07
1964 2015 1.766496 TGGTCCCTCAACTTCGAAACT 59.234 47.619 0.00 0.00 0.00 2.66
1977 2028 2.571212 TCGAAACTGGACAACTTGCAT 58.429 42.857 0.00 0.00 0.00 3.96
2038 2089 1.134936 GGCTTTGAACGGTTTTGGTGT 60.135 47.619 0.00 0.00 0.00 4.16
2086 2137 9.635520 GGTGCTGACTTAAATACGTGTATATAT 57.364 33.333 0.00 0.00 0.00 0.86
2120 2171 7.377398 TCCGTGAATCATTTGAAATTCATGTT 58.623 30.769 13.36 0.00 43.01 2.71
2393 2520 5.514274 AATTTGAGTCAAAACACGGTCAT 57.486 34.783 21.57 0.00 36.90 3.06
2399 2526 4.562082 AGTCAAAACACGGTCATAATCGA 58.438 39.130 0.00 0.00 0.00 3.59
2404 2533 3.880047 ACACGGTCATAATCGAGGAAA 57.120 42.857 0.00 0.00 0.00 3.13
2431 2560 4.585162 ACATCAAAACCGGTCAAAACCATA 59.415 37.500 8.04 0.00 46.86 2.74
2498 2627 1.042229 TCCGGTTTCGAAGTTGAGGA 58.958 50.000 0.00 2.09 39.00 3.71
2501 2630 2.206750 CGGTTTCGAAGTTGAGGAACA 58.793 47.619 0.00 0.00 39.00 3.18
2569 2700 6.146601 TCTTGCATCAATGAGTTTTGTGAA 57.853 33.333 0.00 0.00 0.00 3.18
2632 2763 5.788450 TCAACAACAAACAACATCCAAAGT 58.212 33.333 0.00 0.00 0.00 2.66
2657 2788 2.014128 AGTTCAAGGTCCAAACACACG 58.986 47.619 0.00 0.00 0.00 4.49
2659 2790 1.010125 CAAGGTCCAAACACACGCG 60.010 57.895 3.53 3.53 0.00 6.01
2769 2900 0.895530 TGGACTCCATCAAGGACGTC 59.104 55.000 7.13 7.13 43.07 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 255 3.572255 TGAAGCGGGCTTTTATTTTCTGT 59.428 39.130 7.43 0.00 36.26 3.41
580 612 5.971202 ACAGCAACAAAATCGTGAACTTTAG 59.029 36.000 0.00 0.00 0.00 1.85
601 633 0.814010 GCCGGCCCACTATAACACAG 60.814 60.000 18.11 0.00 0.00 3.66
651 685 7.232534 TGTTTAGCACACTGGGAATAAGAAAAT 59.767 33.333 0.00 0.00 0.00 1.82
672 708 8.098912 GTCTATTTTGAACCCTAGACCTGTTTA 58.901 37.037 0.00 0.00 35.93 2.01
764 800 7.547722 AGTCCAAAACAAACCTTGAAATTGTAC 59.452 33.333 0.00 0.00 36.33 2.90
1206 1257 0.526524 GGAGAAGCAGGATGTCGTCG 60.527 60.000 0.00 0.00 39.31 5.12
1643 1694 2.335011 CCGTGCTGTCGTGTCTCA 59.665 61.111 0.00 0.00 0.00 3.27
1964 2015 0.187117 TTGGGGATGCAAGTTGTCCA 59.813 50.000 13.05 7.19 33.62 4.02
1977 2028 2.370849 GTCCAGTTTCAGTAGTTGGGGA 59.629 50.000 0.00 0.00 0.00 4.81
2038 2089 2.224597 GGTCAAAACCGGGGAGAGTTAA 60.225 50.000 6.32 0.00 35.36 2.01
2145 2198 8.000991 TGAATTTGAAATTTTTACGCGAACATG 58.999 29.630 15.93 0.00 0.00 3.21
2146 2199 8.001549 GTGAATTTGAAATTTTTACGCGAACAT 58.998 29.630 15.93 0.00 0.00 2.71
2147 2200 7.009265 TGTGAATTTGAAATTTTTACGCGAACA 59.991 29.630 15.93 0.00 0.00 3.18
2357 2484 5.235616 TGACTCAAATTCGCGTAGTTTCTTT 59.764 36.000 5.77 0.00 0.00 2.52
2364 2491 4.607235 GTGTTTTGACTCAAATTCGCGTAG 59.393 41.667 5.77 0.00 33.19 3.51
2399 2526 2.747446 CCGGTTTTGATGTCGATTTCCT 59.253 45.455 0.00 0.00 0.00 3.36
2404 2533 2.465860 TGACCGGTTTTGATGTCGAT 57.534 45.000 9.42 0.00 0.00 3.59
2431 2560 0.613777 GACAAGGTTCGTCCCTGGAT 59.386 55.000 0.00 0.00 34.19 3.41
2498 2627 5.855045 ACTCTTGACGGTCTAGATTTTGTT 58.145 37.500 19.80 1.93 28.61 2.83
2501 2630 6.097915 TCAACTCTTGACGGTCTAGATTTT 57.902 37.500 19.80 13.98 34.08 1.82
2632 2763 6.017770 CGTGTGTTTGGACCTTGAACTTTATA 60.018 38.462 0.00 0.00 0.00 0.98
2657 2788 2.826979 TATCTCTCGTGACTTGTCGC 57.173 50.000 4.41 4.41 0.00 5.19
2700 2831 7.956943 GCATTTGGAATTTCTTTTTCATTACCG 59.043 33.333 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.