Multiple sequence alignment - TraesCS5A01G217400

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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 TraesCS5A01G217400 chr5A 100.000 2675 0 0 1 2675 435040029 435042703 0.000000e+00 4940.0
1 TraesCS5A01G217400 chr5A 85.185 567 59 12 1004 1568 686506677 686506134 2.330000e-155 558.0
2 TraesCS5A01G217400 chr5A 81.250 96 18 0 1277 1372 82306838 82306933 7.940000e-11 78.7
3 TraesCS5A01G217400 chr5B 92.405 2686 136 29 1 2675 389819856 389822484 0.000000e+00 3768.0
4 TraesCS5A01G217400 chr5B 86.301 73 10 0 1300 1372 94092999 94093071 2.210000e-11 80.5
5 TraesCS5A01G217400 chr5D 95.386 2059 55 15 622 2675 333382695 333384718 0.000000e+00 3240.0
6 TraesCS5A01G217400 chr5D 86.772 635 68 10 1 624 333377812 333378441 0.000000e+00 693.0
7 TraesCS5A01G217400 chr5D 81.250 96 18 0 1277 1372 88520309 88520404 7.940000e-11 78.7
8 TraesCS5A01G217400 chr2B 78.451 297 48 14 69 358 436987617 436987330 2.120000e-41 180.0
9 TraesCS5A01G217400 chr6B 80.851 141 20 7 240 376 496579296 496579433 1.310000e-18 104.0
10 TraesCS5A01G217400 chr4B 79.720 143 22 7 237 375 174146182 174146321 2.190000e-16 97.1
11 TraesCS5A01G217400 chr4B 76.761 142 28 5 237 375 382737285 382737146 1.030000e-09 75.0
12 TraesCS5A01G217400 chr7B 78.667 150 24 8 237 382 261230153 261230298 2.840000e-15 93.5
13 TraesCS5A01G217400 chr7B 78.000 150 25 8 237 382 177584719 177584574 1.320000e-13 87.9
14 TraesCS5A01G217400 chr7B 74.074 189 38 11 193 375 583187524 583187707 1.720000e-07 67.6
15 TraesCS5A01G217400 chr3B 78.767 146 25 6 237 378 437699586 437699729 2.840000e-15 93.5
16 TraesCS5A01G217400 chr6A 75.897 195 36 11 193 382 239901238 239901050 3.670000e-14 89.8
17 TraesCS5A01G217400 chr4A 73.016 189 42 9 192 375 164403548 164403732 1.030000e-04 58.4


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 TraesCS5A01G217400 chr5A 435040029 435042703 2674 False 4940 4940 100.000 1 2675 1 chr5A.!!$F2 2674
1 TraesCS5A01G217400 chr5A 686506134 686506677 543 True 558 558 85.185 1004 1568 1 chr5A.!!$R1 564
2 TraesCS5A01G217400 chr5B 389819856 389822484 2628 False 3768 3768 92.405 1 2675 1 chr5B.!!$F2 2674
3 TraesCS5A01G217400 chr5D 333382695 333384718 2023 False 3240 3240 95.386 622 2675 1 chr5D.!!$F3 2053
4 TraesCS5A01G217400 chr5D 333377812 333378441 629 False 693 693 86.772 1 624 1 chr5D.!!$F2 623

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
468 479 0.540133 ATAATGGCGCATGCATCCCA 60.54 50.0 19.57 19.8 45.35 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2163 0.038166 TTGCAACCTCCCCATCACTC 59.962 55.0 0.0 0.0 0.0 3.51 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
50 51 9.900710 TTGATTGTTGTGTTACATATTTGGTAC 57.099 29.630 0.00 0.00 0.00 3.34
64 65 4.554960 TTTGGTACCATCCATACAACGA 57.445 40.909 17.17 0.00 37.33 3.85
89 90 4.253685 CAATATCCACCCCTATGCTTACG 58.746 47.826 0.00 0.00 0.00 3.18
96 97 2.303600 ACCCCTATGCTTACGTTTCACA 59.696 45.455 0.00 0.00 0.00 3.58
117 118 8.445275 TCACACTATTGTTTGCTCTCTTTAAA 57.555 30.769 0.00 0.00 31.66 1.52
131 132 9.216117 TGCTCTCTTTAAATTACTTGTACTTCC 57.784 33.333 0.00 0.00 0.00 3.46
137 138 9.893305 CTTTAAATTACTTGTACTTCCCAACTG 57.107 33.333 0.00 0.00 0.00 3.16
139 140 1.878953 ACTTGTACTTCCCAACTGCG 58.121 50.000 0.00 0.00 0.00 5.18
140 141 1.414919 ACTTGTACTTCCCAACTGCGA 59.585 47.619 0.00 0.00 0.00 5.10
144 145 2.067013 GTACTTCCCAACTGCGAGTTC 58.933 52.381 0.00 0.00 36.03 3.01
192 194 3.871594 GCTACATACACCACTCCATTCAC 59.128 47.826 0.00 0.00 0.00 3.18
280 282 7.010923 TGACAATTCAATTGCCAAAGTTTACAC 59.989 33.333 10.21 0.00 43.98 2.90
337 339 4.447138 AGGGTTGAAATACTGTCCAACA 57.553 40.909 0.00 0.00 40.26 3.33
340 342 5.659079 AGGGTTGAAATACTGTCCAACAAAA 59.341 36.000 0.00 0.00 40.26 2.44
342 344 6.406512 GGGTTGAAATACTGTCCAACAAAAGT 60.407 38.462 0.00 0.00 40.26 2.66
360 362 4.862641 AAGTTGTTGTGCTCCCCTATAT 57.137 40.909 0.00 0.00 0.00 0.86
378 380 7.402054 CCCTATATTTTGTGGGCTATCACATA 58.598 38.462 8.40 2.85 45.63 2.29
389 391 7.123697 TGTGGGCTATCACATACTACCATATAC 59.876 40.741 4.47 0.00 42.05 1.47
394 396 8.957466 GCTATCACATACTACCATATACAGTGA 58.043 37.037 0.00 0.00 37.80 3.41
413 415 4.841246 AGTGAGAAGGTGATTTGTACTCCT 59.159 41.667 0.00 0.00 33.48 3.69
418 420 2.236395 AGGTGATTTGTACTCCTTCGGG 59.764 50.000 0.00 0.00 0.00 5.14
422 424 1.719529 TTTGTACTCCTTCGGGTCCA 58.280 50.000 0.00 0.00 36.28 4.02
426 428 2.438763 TGTACTCCTTCGGGTCCAAAAA 59.561 45.455 0.00 0.00 36.28 1.94
449 451 9.759473 AAAAAGGAATCCTTGATCTCTTTATCA 57.241 29.630 16.25 0.00 43.92 2.15
450 452 9.933240 AAAAGGAATCCTTGATCTCTTTATCAT 57.067 29.630 16.25 0.00 43.92 2.45
456 467 8.804912 ATCCTTGATCTCTTTATCATAATGGC 57.195 34.615 0.00 0.00 35.84 4.40
461 472 5.868043 TCTCTTTATCATAATGGCGCATG 57.132 39.130 10.83 4.11 0.00 4.06
468 479 0.540133 ATAATGGCGCATGCATCCCA 60.540 50.000 19.57 19.80 45.35 4.37
470 481 1.615165 AATGGCGCATGCATCCCAAA 61.615 50.000 21.11 6.43 45.35 3.28
474 485 1.670674 GGCGCATGCATCCCAAATATG 60.671 52.381 19.57 0.00 45.35 1.78
479 490 4.615223 CGCATGCATCCCAAATATGAAGAG 60.615 45.833 19.57 0.00 0.00 2.85
555 566 2.760092 AGAGTGAGCCTCATCTCTCAAC 59.240 50.000 16.29 0.00 43.12 3.18
599 611 6.268566 AGAATCAGAAACAAACACTCAAAGC 58.731 36.000 0.00 0.00 0.00 3.51
715 727 5.676744 CACGTGAAAATATTGCGGATACTTG 59.323 40.000 10.90 0.00 0.00 3.16
716 728 5.583061 ACGTGAAAATATTGCGGATACTTGA 59.417 36.000 0.00 0.00 0.00 3.02
717 729 6.129393 CGTGAAAATATTGCGGATACTTGAG 58.871 40.000 0.00 0.00 0.00 3.02
718 730 6.019075 CGTGAAAATATTGCGGATACTTGAGA 60.019 38.462 0.00 0.00 0.00 3.27
719 731 7.465379 CGTGAAAATATTGCGGATACTTGAGAA 60.465 37.037 0.00 0.00 0.00 2.87
720 732 8.181573 GTGAAAATATTGCGGATACTTGAGAAA 58.818 33.333 0.00 0.00 0.00 2.52
721 733 8.902806 TGAAAATATTGCGGATACTTGAGAAAT 58.097 29.630 0.00 0.00 0.00 2.17
762 774 1.456892 TGACGGTCAGACCAGTGGT 60.457 57.895 16.70 16.70 38.47 4.16
781 793 6.256321 CAGTGGTTGAACAATTCTTTCTTTGG 59.744 38.462 0.00 0.00 0.00 3.28
786 798 6.325919 TGAACAATTCTTTCTTTGGCGTAT 57.674 33.333 0.00 0.00 0.00 3.06
818 830 1.153349 GGTCCAAGATCCAGCGGAC 60.153 63.158 10.50 10.50 45.95 4.79
841 853 2.036098 CACCCCAATCTGCTGGCA 59.964 61.111 0.00 0.00 34.88 4.92
908 920 6.693315 TCTCTTGTCCTTTTCATCGTTTTT 57.307 33.333 0.00 0.00 0.00 1.94
925 937 4.024809 CGTTTTTCTCTTTCTCACCCTGAC 60.025 45.833 0.00 0.00 0.00 3.51
967 979 3.243941 TGCTCCTTAGAACAAGCGTACAA 60.244 43.478 0.00 0.00 37.57 2.41
968 980 3.933332 GCTCCTTAGAACAAGCGTACAAT 59.067 43.478 0.00 0.00 0.00 2.71
969 981 5.107133 GCTCCTTAGAACAAGCGTACAATA 58.893 41.667 0.00 0.00 0.00 1.90
970 982 5.753921 GCTCCTTAGAACAAGCGTACAATAT 59.246 40.000 0.00 0.00 0.00 1.28
1159 1171 1.890041 CCGTTCGCACCACCTTTGA 60.890 57.895 0.00 0.00 0.00 2.69
1706 1719 3.117512 TCTTCTCCCTTTCCTTTTGCTGT 60.118 43.478 0.00 0.00 0.00 4.40
1787 1801 5.636903 AGGCAAAGACATACTATGGTGAT 57.363 39.130 1.11 0.00 33.60 3.06
1816 1830 4.436515 CAGAATGGCCGCATACGA 57.563 55.556 0.00 0.00 43.93 3.43
1864 1878 9.461312 AAGTTACAAGGATGAAAACAGCATATA 57.539 29.630 0.00 0.00 32.24 0.86
1985 2004 4.892934 TCTTGTAAAGCAAATCTGTGGGTT 59.107 37.500 0.00 0.00 45.70 4.11
1986 2005 6.065374 TCTTGTAAAGCAAATCTGTGGGTTA 58.935 36.000 0.00 0.00 45.70 2.85
2214 2235 6.048732 AGAAAAGCTTGTGGAAAAGGAAAA 57.951 33.333 0.00 0.00 0.00 2.29
2215 2236 6.472016 AGAAAAGCTTGTGGAAAAGGAAAAA 58.528 32.000 0.00 0.00 0.00 1.94
2307 2328 5.989551 TTTTTGCAAAGCCAATTCTTCTC 57.010 34.783 12.41 0.00 0.00 2.87
2403 2426 2.446435 GGTGCACACATCCATAACCTT 58.554 47.619 20.43 0.00 0.00 3.50
2483 2506 4.635765 GCACTACAGGAAAATCACATGCTA 59.364 41.667 0.00 0.00 0.00 3.49
2561 2584 0.683504 AAGCCGAGTAGTGACCGGAT 60.684 55.000 9.46 0.00 40.07 4.18
2568 2591 4.458295 CCGAGTAGTGACCGGATAATACAT 59.542 45.833 9.46 0.73 40.07 2.29
2636 2659 1.265095 CACAAAACGCTCTCTGTGCAT 59.735 47.619 0.00 0.00 33.41 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.121463 GGATGGTACCAAATATGTAACACAACA 59.879 37.037 20.76 0.00 38.62 3.33
30 31 7.121463 TGGATGGTACCAAATATGTAACACAAC 59.879 37.037 20.76 0.00 38.62 3.32
33 34 7.817418 ATGGATGGTACCAAATATGTAACAC 57.183 36.000 20.76 0.00 43.47 3.32
50 51 2.411628 TTGGGTCGTTGTATGGATGG 57.588 50.000 0.00 0.00 0.00 3.51
64 65 1.710809 GCATAGGGGTGGATATTGGGT 59.289 52.381 0.00 0.00 0.00 4.51
89 90 6.305693 AGAGAGCAAACAATAGTGTGAAAC 57.694 37.500 0.00 0.00 38.27 2.78
117 118 4.000988 CGCAGTTGGGAAGTACAAGTAAT 58.999 43.478 0.00 0.00 30.73 1.89
159 161 7.338710 AGTGGTGTATGTAGCATCAAAGTAAT 58.661 34.615 0.00 0.00 0.00 1.89
221 223 4.816385 CACCTGAAAAGAGTACTTGCTCAA 59.184 41.667 0.00 0.00 37.94 3.02
234 236 5.043248 GTCAATTCAACCACACCTGAAAAG 58.957 41.667 0.00 0.00 35.31 2.27
235 237 4.464244 TGTCAATTCAACCACACCTGAAAA 59.536 37.500 0.00 0.00 35.31 2.29
265 267 5.761234 AGAGAATACGTGTAAACTTTGGCAA 59.239 36.000 0.00 0.00 0.00 4.52
274 276 4.082625 TGGAAGCGAGAGAATACGTGTAAA 60.083 41.667 0.00 0.00 0.00 2.01
280 282 3.355626 TGATGGAAGCGAGAGAATACG 57.644 47.619 0.00 0.00 0.00 3.06
337 339 2.159179 AGGGGAGCACAACAACTTTT 57.841 45.000 0.00 0.00 0.00 2.27
340 342 4.862641 AATATAGGGGAGCACAACAACT 57.137 40.909 0.00 0.00 0.00 3.16
342 344 5.184864 CACAAAATATAGGGGAGCACAACAA 59.815 40.000 0.00 0.00 0.00 2.83
353 355 5.630121 TGTGATAGCCCACAAAATATAGGG 58.370 41.667 2.22 0.00 43.32 3.53
378 380 6.432581 TCACCTTCTCACTGTATATGGTAGT 58.567 40.000 0.00 0.00 0.00 2.73
389 391 4.932200 GGAGTACAAATCACCTTCTCACTG 59.068 45.833 0.00 0.00 0.00 3.66
430 432 9.240734 GCCATTATGATAAAGAGATCAAGGATT 57.759 33.333 0.00 0.00 39.25 3.01
431 433 7.551974 CGCCATTATGATAAAGAGATCAAGGAT 59.448 37.037 0.00 0.00 39.25 3.24
434 436 6.148315 TGCGCCATTATGATAAAGAGATCAAG 59.852 38.462 4.18 0.00 39.25 3.02
436 438 5.550290 TGCGCCATTATGATAAAGAGATCA 58.450 37.500 4.18 0.00 40.08 2.92
439 441 4.154737 GCATGCGCCATTATGATAAAGAGA 59.845 41.667 4.18 0.00 0.00 3.10
442 444 4.163458 TGCATGCGCCATTATGATAAAG 57.837 40.909 14.09 0.00 37.32 1.85
443 445 4.380761 GGATGCATGCGCCATTATGATAAA 60.381 41.667 20.80 0.00 37.32 1.40
444 446 3.129113 GGATGCATGCGCCATTATGATAA 59.871 43.478 20.80 0.00 37.32 1.75
445 447 2.684374 GGATGCATGCGCCATTATGATA 59.316 45.455 20.80 0.00 37.32 2.15
446 448 1.475280 GGATGCATGCGCCATTATGAT 59.525 47.619 20.80 3.04 37.32 2.45
447 449 0.883153 GGATGCATGCGCCATTATGA 59.117 50.000 20.80 0.00 37.32 2.15
448 450 0.108992 GGGATGCATGCGCCATTATG 60.109 55.000 25.15 2.44 37.32 1.90
449 451 0.540133 TGGGATGCATGCGCCATTAT 60.540 50.000 25.15 8.50 37.32 1.28
450 452 0.754587 TTGGGATGCATGCGCCATTA 60.755 50.000 25.15 12.02 37.32 1.90
452 454 1.404479 ATTTGGGATGCATGCGCCAT 61.404 50.000 25.15 9.90 37.32 4.40
456 467 3.253921 TCTTCATATTTGGGATGCATGCG 59.746 43.478 14.09 0.00 0.00 4.73
461 472 6.058183 ACACTACTCTTCATATTTGGGATGC 58.942 40.000 0.00 0.00 0.00 3.91
468 479 8.588290 AGACTGAGACACTACTCTTCATATTT 57.412 34.615 0.00 0.00 37.73 1.40
470 481 9.116067 GTAAGACTGAGACACTACTCTTCATAT 57.884 37.037 0.00 0.00 37.73 1.78
474 485 6.804770 TGTAAGACTGAGACACTACTCTTC 57.195 41.667 0.00 0.00 37.73 2.87
479 490 6.074544 ACACTTGTAAGACTGAGACACTAC 57.925 41.667 0.00 0.00 0.00 2.73
535 546 2.479389 CGTTGAGAGATGAGGCTCACTC 60.479 54.545 26.16 26.16 46.78 3.51
653 665 8.844244 GCCACTCATCAATCAAATAGTTAGAAT 58.156 33.333 0.00 0.00 0.00 2.40
666 678 5.587844 AGAATTGTACAGCCACTCATCAATC 59.412 40.000 0.00 0.00 0.00 2.67
715 727 1.012841 CCGGAGCTTGCTCATTTCTC 58.987 55.000 21.97 4.90 0.00 2.87
716 728 0.393537 CCCGGAGCTTGCTCATTTCT 60.394 55.000 21.97 0.00 0.00 2.52
717 729 1.379642 CCCCGGAGCTTGCTCATTTC 61.380 60.000 21.97 5.87 0.00 2.17
718 730 1.379044 CCCCGGAGCTTGCTCATTT 60.379 57.895 21.97 0.00 0.00 2.32
719 731 2.273449 CCCCGGAGCTTGCTCATT 59.727 61.111 21.97 0.00 0.00 2.57
720 732 4.496336 GCCCCGGAGCTTGCTCAT 62.496 66.667 21.97 0.00 0.00 2.90
762 774 5.004922 ACGCCAAAGAAAGAATTGTTCAA 57.995 34.783 0.00 0.00 0.00 2.69
781 793 0.370273 CGAAAGCTGTGGACATACGC 59.630 55.000 0.00 0.00 0.00 4.42
786 798 1.070786 GGACCGAAAGCTGTGGACA 59.929 57.895 6.17 0.00 0.00 4.02
818 830 3.599584 CAGATTGGGGTGCTGCTG 58.400 61.111 0.00 0.00 0.00 4.41
824 836 1.601419 CTTGCCAGCAGATTGGGGTG 61.601 60.000 0.00 0.00 38.72 4.61
841 853 4.740934 GCCAGTAGACGAATAGGATTGCTT 60.741 45.833 0.00 0.00 0.00 3.91
908 920 3.244887 TCTGTCAGGGTGAGAAAGAGA 57.755 47.619 0.00 0.00 0.00 3.10
925 937 1.633561 CACGTACTGTGCAGGATCTG 58.366 55.000 4.11 0.00 42.70 2.90
967 979 8.386012 AGTAGGTGTACGAGGGTAGTATATAT 57.614 38.462 0.00 0.00 33.97 0.86
968 980 7.798710 AGTAGGTGTACGAGGGTAGTATATA 57.201 40.000 0.00 0.00 33.97 0.86
969 981 6.694445 AGTAGGTGTACGAGGGTAGTATAT 57.306 41.667 0.00 0.00 33.97 0.86
970 982 6.464465 GGAAGTAGGTGTACGAGGGTAGTATA 60.464 46.154 0.00 0.00 33.97 1.47
1750 1764 4.098349 TCTTTGCCTTGCTTATGCCTTATG 59.902 41.667 0.00 0.00 38.71 1.90
1751 1765 4.098501 GTCTTTGCCTTGCTTATGCCTTAT 59.901 41.667 0.00 0.00 38.71 1.73
1752 1766 3.443681 GTCTTTGCCTTGCTTATGCCTTA 59.556 43.478 0.00 0.00 38.71 2.69
1753 1767 2.232208 GTCTTTGCCTTGCTTATGCCTT 59.768 45.455 0.00 0.00 38.71 4.35
1754 1768 1.821136 GTCTTTGCCTTGCTTATGCCT 59.179 47.619 0.00 0.00 38.71 4.75
1755 1769 1.545582 TGTCTTTGCCTTGCTTATGCC 59.454 47.619 0.00 0.00 38.71 4.40
1756 1770 3.515330 ATGTCTTTGCCTTGCTTATGC 57.485 42.857 0.00 0.00 40.20 3.14
1787 1801 1.748244 GCCATTCTGGAGCAGTGCATA 60.748 52.381 19.20 1.65 40.96 3.14
1816 1830 6.946009 ACTTGGGCAGTAACTTTGTAACATAT 59.054 34.615 0.00 0.00 31.97 1.78
1864 1878 1.204941 GTGTCCATGTCTCGCCTAGTT 59.795 52.381 0.00 0.00 0.00 2.24
1985 2004 3.767673 GGACCACACACCTACAGAGAATA 59.232 47.826 0.00 0.00 0.00 1.75
1986 2005 2.567615 GGACCACACACCTACAGAGAAT 59.432 50.000 0.00 0.00 0.00 2.40
2144 2163 0.038166 TTGCAACCTCCCCATCACTC 59.962 55.000 0.00 0.00 0.00 3.51
2214 2235 3.711863 TGGGATTTTATTCCTGCTGCTT 58.288 40.909 0.00 0.00 35.97 3.91
2215 2236 3.386932 TGGGATTTTATTCCTGCTGCT 57.613 42.857 0.00 0.00 35.97 4.24
2350 2371 1.624336 GCCGGGTAAACCTCCTTTTT 58.376 50.000 2.18 0.00 36.97 1.94
2483 2506 3.731867 CGGCTTACACGTTAATACTCGGT 60.732 47.826 0.00 0.00 0.00 4.69
2623 2646 2.163390 CGGTCATGCACAGAGAGCG 61.163 63.158 14.42 14.42 44.93 5.03
2650 2673 4.087182 CCGAGTGCCTTTCCTCCTATATA 58.913 47.826 0.00 0.00 0.00 0.86
2654 2677 1.614241 GCCGAGTGCCTTTCCTCCTA 61.614 60.000 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.