Multiple sequence alignment - TraesCS5D01G077700

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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 TraesCS5D01G077700 chr5D 100.000 3658 0 0 1 3658 77581708 77585365 0.000000e+00 6756
1 TraesCS5D01G077700 chr5A 94.396 3676 147 24 1 3658 74482041 74485675 0.000000e+00 5592
2 TraesCS5D01G077700 chr5B 95.088 1934 83 5 1729 3658 87234959 87236884 0.000000e+00 3035
3 TraesCS5D01G077700 chr5B 95.194 1519 54 11 1 1508 87232898 87234408 0.000000e+00 2383
4 TraesCS5D01G077700 chr5B 90.344 611 39 11 1 607 672545120 672544526 0.000000e+00 784
5 TraesCS5D01G077700 chr5B 94.836 213 8 1 1492 1704 87234583 87234792 2.720000e-86 329
6 TraesCS5D01G077700 chr6B 88.853 619 38 11 1 596 599817491 599818101 0.000000e+00 732
7 TraesCS5D01G077700 chr2B 87.582 612 37 16 1 607 183538778 183538201 0.000000e+00 673


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 TraesCS5D01G077700 chr5D 77581708 77585365 3657 False 6756.000000 6756 100.000000 1 3658 1 chr5D.!!$F1 3657
1 TraesCS5D01G077700 chr5A 74482041 74485675 3634 False 5592.000000 5592 94.396000 1 3658 1 chr5A.!!$F1 3657
2 TraesCS5D01G077700 chr5B 87232898 87236884 3986 False 1915.666667 3035 95.039333 1 3658 3 chr5B.!!$F1 3657
3 TraesCS5D01G077700 chr5B 672544526 672545120 594 True 784.000000 784 90.344000 1 607 1 chr5B.!!$R1 606
4 TraesCS5D01G077700 chr6B 599817491 599818101 610 False 732.000000 732 88.853000 1 596 1 chr6B.!!$F1 595
5 TraesCS5D01G077700 chr2B 183538201 183538778 577 True 673.000000 673 87.582000 1 607 1 chr2B.!!$R1 606

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
423 452 1.415672 TTCCCTGTCCACAGTGGGTC 61.416 60.000 20.14 13.29 42.27 4.46 F
1785 2171 1.064060 GAGAAGTTTGTGCGCAGTGTT 59.936 47.619 12.22 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2495 1.15415 GTCGCTGCAGCAACCATTC 60.154 57.895 36.03 14.61 42.21 2.67 R
3542 3940 0.10230 AACAAGCCAACGCCTTGAAC 59.898 50.000 8.01 0.00 34.57 3.18 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
36 37 4.751060 AGCAGCAACATCACATTTTATGG 58.249 39.130 0.00 0.00 33.60 2.74
255 282 4.350368 TCACTCAGTTTGACAGCCATAA 57.650 40.909 0.00 0.00 0.00 1.90
407 434 9.901172 TCTCCCTAATTAATCAGTTTTACTTCC 57.099 33.333 0.00 0.00 0.00 3.46
423 452 1.415672 TTCCCTGTCCACAGTGGGTC 61.416 60.000 20.14 13.29 42.27 4.46
494 525 1.490490 TGGGTTCTCCATACAGCCATC 59.510 52.381 0.00 0.00 41.46 3.51
551 587 1.829849 CTGCTCAGAACATCCCTCTGA 59.170 52.381 2.78 2.78 45.50 3.27
760 796 9.897744 TTTTAGTGCTCAAAAGTCAAATCTATG 57.102 29.630 0.00 0.00 0.00 2.23
1192 1229 7.646446 AGTTTGTTAGTTTGTTGTTTTGGTC 57.354 32.000 0.00 0.00 0.00 4.02
1221 1258 3.197116 ACAACTTAGGTCCTGGGATAACG 59.803 47.826 0.00 0.00 0.00 3.18
1426 1466 7.552687 GTCTGGTTTTGTGAGACATGGATTATA 59.447 37.037 0.00 0.00 36.83 0.98
1476 1521 2.515429 AGTGGGTGGCATATCCTGAAAT 59.485 45.455 0.00 0.00 35.26 2.17
1478 1523 2.154462 GGGTGGCATATCCTGAAATCG 58.846 52.381 0.00 0.00 35.26 3.34
1556 1792 7.566760 TGAGAAGAAAACATGTTTGCTCTTA 57.433 32.000 28.30 19.97 37.46 2.10
1571 1807 9.730420 TGTTTGCTCTTAGTTTTCAGTAAAATC 57.270 29.630 0.00 0.00 36.96 2.17
1705 1944 9.670442 AATTACCTCTTTATCCTACCATGTAGA 57.330 33.333 2.88 0.00 0.00 2.59
1706 1945 8.707796 TTACCTCTTTATCCTACCATGTAGAG 57.292 38.462 2.88 0.00 0.00 2.43
1707 1946 6.684538 ACCTCTTTATCCTACCATGTAGAGT 58.315 40.000 2.88 0.00 0.00 3.24
1708 1947 7.823635 ACCTCTTTATCCTACCATGTAGAGTA 58.176 38.462 2.88 0.00 0.00 2.59
1785 2171 1.064060 GAGAAGTTTGTGCGCAGTGTT 59.936 47.619 12.22 0.00 0.00 3.32
2006 2392 2.740981 CAAGTGCTTGCGAGAAAGAGAT 59.259 45.455 4.70 0.00 33.45 2.75
2009 2395 5.521906 AGTGCTTGCGAGAAAGAGATATA 57.478 39.130 4.70 0.00 0.00 0.86
2143 2529 1.741993 CGACGGTTGCAAAACTTCAG 58.258 50.000 0.00 0.00 0.00 3.02
2187 2573 6.358178 TCCACACAAACCAAGTAAAGATACA 58.642 36.000 0.00 0.00 34.29 2.29
2188 2574 7.001674 TCCACACAAACCAAGTAAAGATACAT 58.998 34.615 0.00 0.00 34.29 2.29
2318 2705 3.126073 GTTCGGGTGAACGTAAGACTTT 58.874 45.455 0.00 0.00 44.55 2.66
2330 2717 3.005472 CGTAAGACTTTCACCAGGTCTCA 59.995 47.826 0.00 0.00 39.09 3.27
2340 2727 5.152623 TCACCAGGTCTCACTATTTCTTG 57.847 43.478 0.00 0.00 0.00 3.02
2394 2781 4.204012 AGGTGGAAGTCGACAAAATTGAA 58.796 39.130 19.50 0.00 0.00 2.69
2409 2796 6.654582 ACAAAATTGAACAAAATATCAGGCCC 59.345 34.615 0.00 0.00 0.00 5.80
2475 2869 5.163519 GGTTGATGGATTTCTGGTATGTTGG 60.164 44.000 0.00 0.00 0.00 3.77
2476 2870 3.953612 TGATGGATTTCTGGTATGTTGGC 59.046 43.478 0.00 0.00 0.00 4.52
2477 2871 3.448093 TGGATTTCTGGTATGTTGGCA 57.552 42.857 0.00 0.00 0.00 4.92
2478 2872 3.355378 TGGATTTCTGGTATGTTGGCAG 58.645 45.455 0.00 0.00 0.00 4.85
2479 2873 3.245229 TGGATTTCTGGTATGTTGGCAGT 60.245 43.478 0.00 0.00 0.00 4.40
2480 2874 3.763897 GGATTTCTGGTATGTTGGCAGTT 59.236 43.478 0.00 0.00 0.00 3.16
2481 2875 4.380867 GGATTTCTGGTATGTTGGCAGTTG 60.381 45.833 0.00 0.00 0.00 3.16
2585 2979 8.463930 TCAGATTCACCTGTTAAATCTTGTTT 57.536 30.769 0.00 0.00 37.59 2.83
2656 3050 9.833917 ATAGGTCATATCTCATATGCAAAGATG 57.166 33.333 13.18 7.51 41.82 2.90
2742 3136 3.053395 AGACATGGGGTGCTCATTACAAT 60.053 43.478 0.00 0.00 0.00 2.71
2901 3295 0.813184 AAGCAAGCCATCATCAACCG 59.187 50.000 0.00 0.00 0.00 4.44
3091 3485 5.254267 TGGGTCTTTTATGTAGGATTTCCCA 59.746 40.000 0.00 0.00 37.81 4.37
3102 3496 4.682021 AGGATTTCCCACTTCTTCCAAT 57.318 40.909 0.00 0.00 37.41 3.16
3119 3513 4.362677 TCCAATAGTCTTAGGCCTGAAGT 58.637 43.478 17.99 5.96 0.00 3.01
3177 3571 0.107459 GATTCACCACTCTGGAGGGC 60.107 60.000 2.58 0.00 40.96 5.19
3236 3631 5.722021 TTAAGCCTGAAATCCCTGTTTTC 57.278 39.130 0.00 0.00 34.40 2.29
3274 3669 3.923017 AACCAATGTTAGCAGCAGAAC 57.077 42.857 0.00 0.00 31.36 3.01
3290 3685 0.185175 GAACCCCCAGTTTGGTGAGT 59.815 55.000 0.00 0.00 39.40 3.41
3357 3752 3.054728 TCATCAGCGGAAGTTTATTCCCA 60.055 43.478 1.18 0.00 35.17 4.37
3370 3765 9.535878 GAAGTTTATTCCCAGTTATAGTGAGAG 57.464 37.037 0.00 0.00 0.00 3.20
3386 3783 5.719173 AGTGAGAGAACAGAATTAGAGCAC 58.281 41.667 0.00 0.00 0.00 4.40
3412 3809 8.154649 TGAAGTTTTCACTGAATCTTACTTCC 57.845 34.615 20.24 11.51 39.44 3.46
3414 3811 7.971183 AGTTTTCACTGAATCTTACTTCCTC 57.029 36.000 0.00 0.00 0.00 3.71
3457 3855 4.891756 CCTTCAGTCTGGATTATGCCAAAT 59.108 41.667 0.00 0.00 37.52 2.32
3523 3921 0.453390 GGAAAGCGCTCCATGGAAAG 59.547 55.000 17.00 13.44 35.36 2.62
3533 3931 3.181489 GCTCCATGGAAAGCTGAATTCAG 60.181 47.826 27.82 27.82 46.40 3.02
3542 3940 2.444421 AGCTGAATTCAGGAGCTTTGG 58.556 47.619 31.41 9.04 40.19 3.28
3585 3983 0.807496 GCTGGGAGCAGTTTGTCATC 59.193 55.000 0.00 0.00 41.89 2.92
3606 4004 3.504906 TCGACAACGAACTGGAACTAGAT 59.495 43.478 0.00 0.00 45.74 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.476295 AAATGTGATGTTGCTGCTACG 57.524 42.857 9.51 0.00 0.00 3.51
36 37 4.448395 TGCATCATTTTGTAAGTTGCTTGC 59.552 37.500 0.00 0.00 0.00 4.01
143 152 3.575687 AGGCATTTGTTCTGGGAAAAGAG 59.424 43.478 0.00 0.00 0.00 2.85
217 227 3.643792 GAGTGAACAGATAGGGTATGGCT 59.356 47.826 0.00 0.00 0.00 4.75
255 282 7.066284 CGACATACTTGGGAAGATTTTCTTGAT 59.934 37.037 0.00 0.00 36.73 2.57
348 375 3.759086 GGGAACTGAAAACCATCCTCTTC 59.241 47.826 0.00 0.00 0.00 2.87
443 473 1.666888 GCCGCATTCAACACTTCAAGG 60.667 52.381 0.00 0.00 0.00 3.61
494 525 6.097554 AGGTCACAGTCTCACAGATAAATAGG 59.902 42.308 0.00 0.00 0.00 2.57
551 587 0.899717 AATGCTGGTTGCCACGGATT 60.900 50.000 0.00 0.00 42.00 3.01
570 606 3.840666 AGATTACCAGGACTTCTGCAAGA 59.159 43.478 0.00 0.00 44.68 3.02
628 664 4.623167 GTGTAGTAGCAGATTGTGTCAGTG 59.377 45.833 0.00 0.00 0.00 3.66
703 739 9.388506 CAGAATCTACTGACATATTCCAGTTTT 57.611 33.333 10.88 5.02 42.86 2.43
760 796 3.441572 AGCATGACAAAGGTTGCTATGTC 59.558 43.478 0.00 0.00 38.88 3.06
762 798 4.445452 AAGCATGACAAAGGTTGCTATG 57.555 40.909 0.00 0.00 39.54 2.23
771 807 4.168922 TGCAGATGAAAGCATGACAAAG 57.831 40.909 0.00 0.00 35.51 2.77
1221 1258 7.923414 ACTAAGATGAGTAAACCATGAAACC 57.077 36.000 0.00 0.00 0.00 3.27
1426 1466 4.284234 AGTTTTTCAGGGCATGCTTTACAT 59.716 37.500 18.92 0.00 40.66 2.29
1476 1521 5.758296 CCTTATGCATAGTTTTAAGGAGCGA 59.242 40.000 15.74 0.00 42.10 4.93
1478 1523 5.763088 GCCTTATGCATAGTTTTAAGGAGC 58.237 41.667 22.38 8.40 42.10 4.70
1523 1759 9.903682 AAACATGTTTTCTTCTCAATACAGATG 57.096 29.630 18.13 0.00 0.00 2.90
1529 1765 8.169977 AGAGCAAACATGTTTTCTTCTCAATA 57.830 30.769 21.75 0.00 0.00 1.90
1556 1792 5.772825 TGCTGCTGATTTTACTGAAAACT 57.227 34.783 0.00 0.00 37.37 2.66
1571 1807 1.225855 TAACAAGGTCGTTGCTGCTG 58.774 50.000 5.19 0.00 40.15 4.41
1619 1855 7.849515 GCATTACACCGTTACTATTTTAAGAGC 59.150 37.037 0.00 0.00 0.00 4.09
1704 1943 4.041740 TGAACGCCATAGTCATGTACTC 57.958 45.455 0.00 0.00 39.80 2.59
1705 1944 4.672587 ATGAACGCCATAGTCATGTACT 57.327 40.909 0.00 0.00 42.62 2.73
1706 1945 5.926542 ACATATGAACGCCATAGTCATGTAC 59.073 40.000 10.38 0.00 40.75 2.90
1707 1946 6.096673 ACATATGAACGCCATAGTCATGTA 57.903 37.500 10.38 0.00 40.75 2.29
1708 1947 4.960938 ACATATGAACGCCATAGTCATGT 58.039 39.130 10.38 2.80 40.75 3.21
1717 1956 8.994429 AAAATAAATTTGACATATGAACGCCA 57.006 26.923 10.38 0.00 0.00 5.69
1785 2171 5.523588 ACTAGTTCAGAGATCATTCCTCCA 58.476 41.667 0.00 0.00 0.00 3.86
1821 2207 9.958180 TGAACATTATATGTATTACCATCTGGG 57.042 33.333 0.54 0.00 44.07 4.45
2006 2392 5.480205 TGTGGTTCATTACAACGCAGTATA 58.520 37.500 0.00 0.00 45.00 1.47
2095 2481 2.350522 ACCATTCTGACGCTTTGCTAG 58.649 47.619 0.00 0.00 0.00 3.42
2109 2495 1.154150 GTCGCTGCAGCAACCATTC 60.154 57.895 36.03 14.61 42.21 2.67
2128 2514 4.836125 TCATCTCTGAAGTTTTGCAACC 57.164 40.909 0.00 0.00 32.70 3.77
2143 2529 1.417145 AGAGCCTGCTGGATTCATCTC 59.583 52.381 14.77 8.99 34.57 2.75
2187 2573 7.343316 ACTGTGCTAGAACTAGGAGAAACATAT 59.657 37.037 1.64 0.00 34.15 1.78
2188 2574 6.663953 ACTGTGCTAGAACTAGGAGAAACATA 59.336 38.462 1.64 0.00 34.15 2.29
2309 2696 4.039366 AGTGAGACCTGGTGAAAGTCTTAC 59.961 45.833 2.82 0.70 43.64 2.34
2311 2698 3.041946 AGTGAGACCTGGTGAAAGTCTT 58.958 45.455 2.82 0.00 40.87 3.01
2318 2705 4.020218 CCAAGAAATAGTGAGACCTGGTGA 60.020 45.833 2.82 0.00 0.00 4.02
2330 2717 3.157087 CACCCTGTTGCCAAGAAATAGT 58.843 45.455 0.00 0.00 0.00 2.12
2340 2727 2.521708 AGGTTGCACCCTGTTGCC 60.522 61.111 0.04 0.00 42.25 4.52
2394 2781 3.864789 ATCTCGGGCCTGATATTTTGT 57.135 42.857 16.52 0.00 0.00 2.83
2409 2796 6.761242 TGGTTTTGACATATAGTGGAATCTCG 59.239 38.462 0.00 0.00 0.00 4.04
2481 2875 8.352201 TCATTAAGTATGGAATGCAAGTAATGC 58.648 33.333 0.00 0.00 43.90 3.56
2495 2889 7.268586 ACAGCTCAAGTAGTCATTAAGTATGG 58.731 38.462 0.00 0.00 34.85 2.74
2585 2979 3.925379 TCGATGAGTTCAGCAAAGCTTA 58.075 40.909 0.00 0.00 36.40 3.09
2641 3035 5.636543 TGATAGCGTCATCTTTGCATATGAG 59.363 40.000 6.97 0.00 32.93 2.90
2642 3036 5.540911 TGATAGCGTCATCTTTGCATATGA 58.459 37.500 6.97 0.00 0.00 2.15
2643 3037 5.851047 TGATAGCGTCATCTTTGCATATG 57.149 39.130 0.00 0.00 0.00 1.78
2644 3038 6.260714 TGTTTGATAGCGTCATCTTTGCATAT 59.739 34.615 0.00 0.00 36.54 1.78
2645 3039 5.584251 TGTTTGATAGCGTCATCTTTGCATA 59.416 36.000 0.00 0.00 36.54 3.14
2646 3040 4.395854 TGTTTGATAGCGTCATCTTTGCAT 59.604 37.500 0.00 0.00 36.54 3.96
2647 3041 3.750652 TGTTTGATAGCGTCATCTTTGCA 59.249 39.130 0.00 0.00 36.54 4.08
2656 3050 2.415512 GTGGAAGGTGTTTGATAGCGTC 59.584 50.000 0.00 0.00 0.00 5.19
2773 3167 1.244019 ACAAATCTCAACCAGCCGGC 61.244 55.000 21.89 21.89 34.57 6.13
2890 3284 2.036958 TTACCTGGCGGTTGATGATG 57.963 50.000 6.35 0.00 42.13 3.07
3091 3485 5.033522 AGGCCTAAGACTATTGGAAGAAGT 58.966 41.667 1.29 0.00 0.00 3.01
3102 3496 4.673968 TCTTGACTTCAGGCCTAAGACTA 58.326 43.478 21.60 14.20 0.00 2.59
3119 3513 4.974645 TCTTCAGGCCTAAAACTCTTGA 57.025 40.909 3.98 0.00 0.00 3.02
3177 3571 7.517614 TCTCATATACTTAGTCTTCAGCAGG 57.482 40.000 0.00 0.00 0.00 4.85
3236 3631 6.421377 TTGGTTTTCATCATGATAGACACG 57.579 37.500 8.15 0.00 0.00 4.49
3274 3669 0.537371 GTGACTCACCAAACTGGGGG 60.537 60.000 0.00 0.00 42.59 5.40
3290 3685 7.757941 TTGAATATGAACAAAGTGATGGTGA 57.242 32.000 0.00 0.00 0.00 4.02
3370 3765 6.793492 AACTTCAGTGCTCTAATTCTGTTC 57.207 37.500 0.00 0.00 0.00 3.18
3386 3783 8.286097 GGAAGTAAGATTCAGTGAAAACTTCAG 58.714 37.037 30.14 0.00 41.99 3.02
3523 3921 2.165998 ACCAAAGCTCCTGAATTCAGC 58.834 47.619 27.01 18.13 42.47 4.26
3533 3931 1.172812 ACGCCTTGAACCAAAGCTCC 61.173 55.000 0.00 0.00 29.60 4.70
3542 3940 0.102300 AACAAGCCAACGCCTTGAAC 59.898 50.000 8.01 0.00 34.57 3.18
3563 3961 0.538287 GACAAACTGCTCCCAGCCTT 60.538 55.000 0.00 0.00 43.02 4.35
3585 3983 3.278367 TCTAGTTCCAGTTCGTTGTCG 57.722 47.619 0.00 0.00 38.55 4.35


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

AutoCloner maintained by Alex Coulton.