Multiple sequence alignment - TraesCS5D01G069000

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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 TraesCS5D01G069000 chr5D 100.000 6827 0 0 1 6827 65977887 65971061 0 12608
1 TraesCS5D01G069000 chr5D 96.477 4286 115 20 1 4273 526658134 526653872 0 7046
2 TraesCS5D01G069000 chr5D 96.456 3527 94 18 1 3512 424149939 424146429 0 5792
3 TraesCS5D01G069000 chr6A 94.094 6858 328 52 1 6827 572216103 572222914 0 10349
4 TraesCS5D01G069000 chr7D 94.641 6513 246 59 366 6827 135392051 135385591 0 9998
5 TraesCS5D01G069000 chr4D 94.518 6531 243 61 366 6827 65863764 65870248 0 9971
6 TraesCS5D01G069000 chr4D 97.157 985 23 5 1 984 274216613 274215633 0 1659
7 TraesCS5D01G069000 chr1D 94.360 6560 251 64 338 6827 10791550 10798060 0 9954
8 TraesCS5D01G069000 chr1D 94.419 6522 242 61 366 6827 466333574 466340033 0 9915
9 TraesCS5D01G069000 chr1D 95.923 5568 176 26 1 5552 218969812 218964280 0 8977
10 TraesCS5D01G069000 chr3D 92.336 6850 428 56 1 6827 610719628 610712853 0 9651
11 TraesCS5D01G069000 chr3D 96.728 5073 133 19 1766 6827 500614392 500619442 0 8418
12 TraesCS5D01G069000 chr3D 96.680 1777 45 13 1 1772 500604053 500605820 0 2942
13 TraesCS5D01G069000 chr7B 92.775 6561 351 68 338 6827 709379663 709386171 0 9376
14 TraesCS5D01G069000 chr2D 94.267 6035 224 61 341 6306 536221166 536215185 0 9116
15 TraesCS5D01G069000 chr2D 96.889 3150 75 12 1 3140 594597475 594600611 0 5252
16 TraesCS5D01G069000 chr3A 94.273 5954 243 59 938 6827 32217477 32211558 0 9016
17 TraesCS5D01G069000 chr3B 93.541 6100 294 55 796 6827 755997663 756003730 0 8990
18 TraesCS5D01G069000 chr2B 93.450 6107 291 67 796 6827 747109264 747115336 0 8961
19 TraesCS5D01G069000 chr5A 91.991 3596 229 38 1 3582 484625141 484621591 0 4990
20 TraesCS5D01G069000 chr4A 85.266 1975 189 51 1 1941 527899355 527897449 0 1941


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 TraesCS5D01G069000 chr5D 65971061 65977887 6826 True 12608 12608 100.000 1 6827 1 chr5D.!!$R1 6826
1 TraesCS5D01G069000 chr5D 526653872 526658134 4262 True 7046 7046 96.477 1 4273 1 chr5D.!!$R3 4272
2 TraesCS5D01G069000 chr5D 424146429 424149939 3510 True 5792 5792 96.456 1 3512 1 chr5D.!!$R2 3511
3 TraesCS5D01G069000 chr6A 572216103 572222914 6811 False 10349 10349 94.094 1 6827 1 chr6A.!!$F1 6826
4 TraesCS5D01G069000 chr7D 135385591 135392051 6460 True 9998 9998 94.641 366 6827 1 chr7D.!!$R1 6461
5 TraesCS5D01G069000 chr4D 65863764 65870248 6484 False 9971 9971 94.518 366 6827 1 chr4D.!!$F1 6461
6 TraesCS5D01G069000 chr4D 274215633 274216613 980 True 1659 1659 97.157 1 984 1 chr4D.!!$R1 983
7 TraesCS5D01G069000 chr1D 10791550 10798060 6510 False 9954 9954 94.360 338 6827 1 chr1D.!!$F1 6489
8 TraesCS5D01G069000 chr1D 466333574 466340033 6459 False 9915 9915 94.419 366 6827 1 chr1D.!!$F2 6461
9 TraesCS5D01G069000 chr1D 218964280 218969812 5532 True 8977 8977 95.923 1 5552 1 chr1D.!!$R1 5551
10 TraesCS5D01G069000 chr3D 610712853 610719628 6775 True 9651 9651 92.336 1 6827 1 chr3D.!!$R1 6826
11 TraesCS5D01G069000 chr3D 500614392 500619442 5050 False 8418 8418 96.728 1766 6827 1 chr3D.!!$F2 5061
12 TraesCS5D01G069000 chr3D 500604053 500605820 1767 False 2942 2942 96.680 1 1772 1 chr3D.!!$F1 1771
13 TraesCS5D01G069000 chr7B 709379663 709386171 6508 False 9376 9376 92.775 338 6827 1 chr7B.!!$F1 6489
14 TraesCS5D01G069000 chr2D 536215185 536221166 5981 True 9116 9116 94.267 341 6306 1 chr2D.!!$R1 5965
15 TraesCS5D01G069000 chr2D 594597475 594600611 3136 False 5252 5252 96.889 1 3140 1 chr2D.!!$F1 3139
16 TraesCS5D01G069000 chr3A 32211558 32217477 5919 True 9016 9016 94.273 938 6827 1 chr3A.!!$R1 5889
17 TraesCS5D01G069000 chr3B 755997663 756003730 6067 False 8990 8990 93.541 796 6827 1 chr3B.!!$F1 6031
18 TraesCS5D01G069000 chr2B 747109264 747115336 6072 False 8961 8961 93.450 796 6827 1 chr2B.!!$F1 6031
19 TraesCS5D01G069000 chr5A 484621591 484625141 3550 True 4990 4990 91.991 1 3582 1 chr5A.!!$R1 3581
20 TraesCS5D01G069000 chr4A 527897449 527899355 1906 True 1941 1941 85.266 1 1941 1 chr4A.!!$R1 1940

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
59 60 0.332632 TAGCCAATCTGCCAGCCTTT 59.667 50.000 0.0 0.0 0.00 3.11 F
463 476 1.130749 TGGTTGTTCGTGTGTTTTCCG 59.869 47.619 0.0 0.0 0.00 4.30 F
1165 1369 1.080434 GGAAGTCAGTCGCTTCGCT 60.080 57.895 0.0 0.0 42.23 4.93 F
1488 1710 3.279116 GCAGCAGTTCGCACCACA 61.279 61.111 0.0 0.0 46.13 4.17 F
2814 3118 3.990959 TGGCTTTTCTTTTGTTGGGTT 57.009 38.095 0.0 0.0 0.00 4.11 F
4050 4398 1.269012 CCATCAATGCAAACTGGGGT 58.731 50.000 0.0 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1369 1.289066 CAGGACGCTTCGAGTTCCA 59.711 57.895 6.49 0.00 0.00 3.53 R
1462 1684 2.104144 GCGAACTGCTGCATAATTTCG 58.896 47.619 21.46 21.46 41.73 3.46 R
2660 2953 0.329261 TTGCTTCTCCTGGTCCATGG 59.671 55.000 4.97 4.97 0.00 3.66 R
3480 3805 3.804036 CCTGCGGATTGTAGGTTATTGA 58.196 45.455 0.00 0.00 44.80 2.57 R
4437 4822 1.746220 CGTCGTCTTCTTCCCTCTCAT 59.254 52.381 0.00 0.00 0.00 2.90 R
5866 6272 0.179004 ACAAATCACACCGGCTTCCA 60.179 50.000 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
59 60 0.332632 TAGCCAATCTGCCAGCCTTT 59.667 50.000 0.00 0.00 0.00 3.11
156 165 3.724732 ATGCTTGCCAATTTCCCAATT 57.275 38.095 0.00 0.00 32.36 2.32
168 177 7.419403 GCCAATTTCCCAATTTTCTCTATCCAT 60.419 37.037 0.00 0.00 29.41 3.41
239 249 4.383770 GCTATGTGCAACTAGGAACCCTTA 60.384 45.833 0.00 0.00 42.31 2.69
432 445 3.389002 ACTGATTTTTCTGCCAGCCTTTT 59.611 39.130 0.00 0.00 0.00 2.27
463 476 1.130749 TGGTTGTTCGTGTGTTTTCCG 59.869 47.619 0.00 0.00 0.00 4.30
762 903 7.119262 TGAGCTTGTTGCCTTTAGTTAACTATC 59.881 37.037 15.92 6.62 44.23 2.08
1023 1205 7.574021 AATGGTTATAATAGGAGGAGATGCA 57.426 36.000 0.00 0.00 0.00 3.96
1165 1369 1.080434 GGAAGTCAGTCGCTTCGCT 60.080 57.895 0.00 0.00 42.23 4.93
1462 1684 4.928661 TTCTCGCTTTTTAGATGCTGAC 57.071 40.909 0.00 0.00 0.00 3.51
1488 1710 3.279116 GCAGCAGTTCGCACCACA 61.279 61.111 0.00 0.00 46.13 4.17
1602 1868 4.574599 AGTTGACAAGTTGGCATCTTTC 57.425 40.909 13.36 9.74 33.90 2.62
2660 2953 4.156008 ACACATTAATGAAGCTTTCCGGAC 59.844 41.667 22.16 0.00 0.00 4.79
2814 3118 3.990959 TGGCTTTTCTTTTGTTGGGTT 57.009 38.095 0.00 0.00 0.00 4.11
3480 3805 2.358898 GCATTCGTGGCATCCAAGTTAT 59.641 45.455 0.00 0.00 34.18 1.89
3530 3855 8.413229 AGTGTTTTGCATACAGAAATTTGTACT 58.587 29.630 0.00 0.00 36.45 2.73
3567 3895 4.415596 TCTTTTGGCTGGGATGTATGTTT 58.584 39.130 0.00 0.00 0.00 2.83
4050 4398 1.269012 CCATCAATGCAAACTGGGGT 58.731 50.000 0.00 0.00 0.00 4.95
4145 4497 6.212187 TGAGTCAGAAGAAGATGAGGAAATGA 59.788 38.462 0.00 0.00 0.00 2.57
4437 4822 1.007502 GCGCAACAGTTGATGGCAA 60.008 52.632 17.99 0.00 0.00 4.52
4492 4880 5.871524 CGAGGATGGTTATGGTGATGATAAG 59.128 44.000 0.00 0.00 0.00 1.73
4634 5031 4.763793 AGCAGCAACAATTCATTGAGTAGT 59.236 37.500 6.53 0.00 40.14 2.73
4666 5063 7.588854 CACACTACAGATGTTGATTGACAAAAG 59.411 37.037 1.43 0.00 40.36 2.27
4866 5263 5.104776 AGCCTGTTCTTATCAAGTGATGCTA 60.105 40.000 4.00 0.00 36.05 3.49
5015 5415 0.250727 CAAACCCTCACGTGGTCCAT 60.251 55.000 17.00 0.00 34.15 3.41
5048 5448 6.413052 AGCAGCTTCAATGAAGAAGAATCTA 58.587 36.000 25.54 0.00 46.18 1.98
5388 5788 2.486982 CAGACTGGAAAGATGCCAACTG 59.513 50.000 0.00 0.00 35.35 3.16
5446 5846 1.740585 CGTGGTCACAGTCAAAACCAA 59.259 47.619 1.90 0.00 43.09 3.67
5588 5988 0.313043 GCACACAGCAGTCAAGCAAT 59.687 50.000 0.00 0.00 44.79 3.56
5605 6005 2.995283 CAATCCTGCATCACCAAGAGA 58.005 47.619 0.00 0.00 0.00 3.10
5866 6272 3.319135 CTCCAGCAGCAGAAACAGT 57.681 52.632 0.00 0.00 0.00 3.55
5931 6337 2.089201 CAGCTGTGAATGAAGGATGCA 58.911 47.619 5.25 0.00 0.00 3.96
6364 6774 8.123575 TCTGTTTTCAATTTCATGCACATTTTG 58.876 29.630 0.00 0.00 0.00 2.44
6365 6775 7.759465 TGTTTTCAATTTCATGCACATTTTGT 58.241 26.923 0.00 0.00 0.00 2.83
6366 6776 8.242053 TGTTTTCAATTTCATGCACATTTTGTT 58.758 25.926 0.00 0.00 0.00 2.83
6402 6813 4.282703 ACCCTTCGAGCTAACTTGTCTTTA 59.717 41.667 0.00 0.00 0.00 1.85
6403 6814 5.221581 ACCCTTCGAGCTAACTTGTCTTTAA 60.222 40.000 0.00 0.00 0.00 1.52
6456 6872 8.212259 AGATAATCAGGTATGGTGCTTTCTAT 57.788 34.615 0.00 0.00 0.00 1.98
6511 6927 2.029110 CCGGTTCAATGGCTGTCAAAAT 60.029 45.455 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.385347 ACCCAGGAGAACCACCACA 60.385 57.895 0.00 0.00 38.94 4.17
156 165 3.432749 GGCTGACAGCATGGATAGAGAAA 60.433 47.826 27.87 0.00 44.75 2.52
168 177 1.610038 CAATCACAAAGGCTGACAGCA 59.390 47.619 27.87 6.81 44.75 4.41
239 249 4.990426 GCATTGGTTCTAAACTGCACAAAT 59.010 37.500 0.00 0.00 0.00 2.32
432 445 1.877680 CGAACAACCAGATCCAGCACA 60.878 52.381 0.00 0.00 0.00 4.57
681 821 4.888326 AATGCATAGCCAACAGGAAAAA 57.112 36.364 0.00 0.00 0.00 1.94
711 851 4.032960 TGATAACTTGTGCAACTGGGAT 57.967 40.909 0.00 0.00 38.04 3.85
762 903 7.103641 TGTGGAAAGTAATAACTAGGCAGAAG 58.896 38.462 0.00 0.00 33.75 2.85
1023 1205 3.947612 ACATCTCCTTCATTGCCATCT 57.052 42.857 0.00 0.00 0.00 2.90
1111 1303 8.641499 TTAAGCAACCAAAAGTAAACATGAAG 57.359 30.769 0.00 0.00 0.00 3.02
1165 1369 1.289066 CAGGACGCTTCGAGTTCCA 59.711 57.895 6.49 0.00 0.00 3.53
1462 1684 2.104144 GCGAACTGCTGCATAATTTCG 58.896 47.619 21.46 21.46 41.73 3.46
1714 1985 6.029346 AGGTTTGCAAGGAACTATTCAATG 57.971 37.500 0.00 0.00 38.49 2.82
1910 2193 6.541934 TTCATAAAATGGATCATGCCAACA 57.458 33.333 0.00 0.00 42.16 3.33
2039 2329 2.594303 CACCGCTGGCCTGTTGAA 60.594 61.111 11.69 0.00 0.00 2.69
2296 2588 2.908796 GACACGGATCCTTCCCCC 59.091 66.667 10.75 0.00 39.01 5.40
2365 2657 7.283127 GGCATCCTTGTCAACTAAATATCTGAA 59.717 37.037 0.00 0.00 0.00 3.02
2660 2953 0.329261 TTGCTTCTCCTGGTCCATGG 59.671 55.000 4.97 4.97 0.00 3.66
2814 3118 6.524734 CATCAAGGTATAGTATCTGCACCAA 58.475 40.000 3.25 0.00 0.00 3.67
3371 3696 9.741647 AGCTGATGTAAAGAAAAAGAGAAAAAG 57.258 29.630 0.00 0.00 0.00 2.27
3379 3704 9.617975 CCTCTTTAAGCTGATGTAAAGAAAAAG 57.382 33.333 15.67 7.35 42.71 2.27
3381 3706 8.918202 TCCTCTTTAAGCTGATGTAAAGAAAA 57.082 30.769 15.67 7.31 42.71 2.29
3382 3707 8.157476 ACTCCTCTTTAAGCTGATGTAAAGAAA 58.843 33.333 15.67 8.80 42.71 2.52
3383 3708 7.680730 ACTCCTCTTTAAGCTGATGTAAAGAA 58.319 34.615 15.67 5.36 42.71 2.52
3384 3709 7.246171 ACTCCTCTTTAAGCTGATGTAAAGA 57.754 36.000 14.60 14.60 41.68 2.52
3480 3805 3.804036 CCTGCGGATTGTAGGTTATTGA 58.196 45.455 0.00 0.00 44.80 2.57
3530 3855 7.206687 CAGCCAAAAGAAAATGTTGGTAAGTA 58.793 34.615 3.79 0.00 43.17 2.24
3753 4087 8.045176 ACTAAAAACATGATTCTAGCCAACTC 57.955 34.615 0.00 0.00 0.00 3.01
3888 4232 3.118847 TGCCTTTTTCTGCATCAACACAA 60.119 39.130 0.00 0.00 31.31 3.33
3889 4233 2.429971 TGCCTTTTTCTGCATCAACACA 59.570 40.909 0.00 0.00 31.31 3.72
4050 4398 3.741830 TTTGGAGCACGGCGTGACA 62.742 57.895 40.94 30.47 35.23 3.58
4145 4497 5.035443 GTCGTCAACATCTATCGCTACTTT 58.965 41.667 0.00 0.00 0.00 2.66
4437 4822 1.746220 CGTCGTCTTCTTCCCTCTCAT 59.254 52.381 0.00 0.00 0.00 2.90
4555 4952 3.835790 TTGCCGCCTGTACCACCAC 62.836 63.158 0.00 0.00 0.00 4.16
4634 5031 4.086457 TCAACATCTGTAGTGTGCTCCTA 58.914 43.478 0.00 0.00 0.00 2.94
4666 5063 4.301628 CAAATCCTTGTCTTTCCAGCAAC 58.698 43.478 0.00 0.00 0.00 4.17
4866 5263 7.965718 TCCTCCATGTCAATTTGATTCTTTTT 58.034 30.769 1.78 0.00 0.00 1.94
5015 5415 4.000325 TCATTGAAGCTGCTTTACGCTTA 59.000 39.130 17.10 0.00 45.70 3.09
5029 5429 7.961827 GCAACTGTAGATTCTTCTTCATTGAAG 59.038 37.037 18.49 18.49 43.36 3.02
5388 5788 2.932614 CAGTTGGCACACTAGTATCTGC 59.067 50.000 9.78 9.78 39.29 4.26
5396 5796 2.103941 TGACACATCAGTTGGCACACTA 59.896 45.455 0.00 0.00 39.29 2.74
5446 5846 1.374190 CCTTCCTGAGCAGCTGTGT 59.626 57.895 16.64 2.54 0.00 3.72
5540 5940 1.298859 GGGACAGCACTTTGGTAGCG 61.299 60.000 0.00 0.00 0.00 4.26
5541 5941 0.960861 GGGGACAGCACTTTGGTAGC 60.961 60.000 0.00 0.00 0.00 3.58
5588 5988 2.093288 GTCATCTCTTGGTGATGCAGGA 60.093 50.000 0.00 0.00 40.59 3.86
5605 6005 5.301551 TGTGTTAATGGTTGCTGAAAGTCAT 59.698 36.000 0.00 0.00 35.30 3.06
5866 6272 0.179004 ACAAATCACACCGGCTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
5931 6337 2.750637 GCCAGCATCAGCAGCAGT 60.751 61.111 0.00 0.00 45.49 4.40
6364 6774 0.746659 AGGGTCACAGCAGCAAAAAC 59.253 50.000 0.00 0.00 0.00 2.43
6365 6775 1.408702 GAAGGGTCACAGCAGCAAAAA 59.591 47.619 0.00 0.00 0.00 1.94
6366 6776 1.032014 GAAGGGTCACAGCAGCAAAA 58.968 50.000 0.00 0.00 0.00 2.44
6511 6927 8.999431 GTGTAAGATTCCAGTCTCAATAACAAA 58.001 33.333 0.00 0.00 0.00 2.83
6799 7222 1.303074 ATGTGGGCACAGCACTCAG 60.303 57.895 0.00 0.00 45.48 3.35


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

AutoCloner maintained by Alex Coulton.