Multiple sequence alignment - TraesCS2D01G265900

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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 TraesCS2D01G265900 chr2D 100.000 4277 0 0 1 4277 324594094 324598370 0.000000e+00 7899
1 TraesCS2D01G265900 chr2B 95.986 4310 79 31 1 4277 393464053 393468301 0.000000e+00 6914
2 TraesCS2D01G265900 chr2B 84.941 425 62 2 1 424 472899351 472899774 3.060000e-116 429
3 TraesCS2D01G265900 chr2A 95.145 3646 88 33 670 4277 394021163 394017569 0.000000e+00 5670
4 TraesCS2D01G265900 chr2A 94.783 575 16 4 1 563 394021949 394021377 0.000000e+00 883
5 TraesCS2D01G265900 chr2A 83.765 425 67 2 1 424 536624507 536624930 6.660000e-108 401
6 TraesCS2D01G265900 chr2A 98.413 63 1 0 556 618 394021356 394021294 1.260000e-20 111


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 TraesCS2D01G265900 chr2D 324594094 324598370 4276 False 7899.000000 7899 100.000000 1 4277 1 chr2D.!!$F1 4276
1 TraesCS2D01G265900 chr2B 393464053 393468301 4248 False 6914.000000 6914 95.986000 1 4277 1 chr2B.!!$F1 4276
2 TraesCS2D01G265900 chr2A 394017569 394021949 4380 True 2221.333333 5670 96.113667 1 4277 3 chr2A.!!$R1 4276

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
632 678 3.373439 TGCAATGTTCTGTTGTTTTTGGC 59.627 39.13 0.00 0.0 0.00 4.52 F
1910 2073 0.106719 CACCCACAACTGAACCACCT 60.107 55.00 0.00 0.0 0.00 4.00 F
2881 3046 0.322975 CTGGCTACAGTTCCAGTGCT 59.677 55.00 11.56 0.0 43.66 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2394 1.765904 TGGTGGTGCACTAAGAGTTGA 59.234 47.619 17.98 0.0 34.40 3.18 R
3048 3213 1.598130 GTCAAAGTGGCCGACTGCT 60.598 57.895 8.37 0.0 40.92 4.24 R
4042 4209 1.135489 AGATGTGCAAAATGCTCGCAG 60.135 47.619 3.78 0.0 45.31 5.18 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
511 524 3.829026 TGCCTGTGTGTTGCCATTATTTA 59.171 39.130 0.00 0.00 0.00 1.40
514 527 5.291614 GCCTGTGTGTTGCCATTATTTATTG 59.708 40.000 0.00 0.00 0.00 1.90
628 674 6.449635 TCTAGTGCAATGTTCTGTTGTTTT 57.550 33.333 0.00 0.00 0.00 2.43
629 675 6.862209 TCTAGTGCAATGTTCTGTTGTTTTT 58.138 32.000 0.00 0.00 0.00 1.94
630 676 5.783100 AGTGCAATGTTCTGTTGTTTTTG 57.217 34.783 0.00 0.00 0.00 2.44
631 677 4.630940 AGTGCAATGTTCTGTTGTTTTTGG 59.369 37.500 0.00 0.00 0.00 3.28
632 678 3.373439 TGCAATGTTCTGTTGTTTTTGGC 59.627 39.130 0.00 0.00 0.00 4.52
638 684 5.995055 TGTTCTGTTGTTTTTGGCTTTTTG 58.005 33.333 0.00 0.00 0.00 2.44
702 825 4.334759 CACTGCAGTAATGCAAGATTAGCT 59.665 41.667 21.20 0.00 44.88 3.32
1451 1602 1.670674 CGAAGGCTACGGTAAGCACAA 60.671 52.381 8.62 0.00 44.64 3.33
1471 1622 6.291955 GCACAAGAAACAATGTTCATTCACAG 60.292 38.462 0.00 0.00 0.00 3.66
1532 1692 8.796278 CAGCGAAAGAGTACTACAGTATAAAAC 58.204 37.037 0.00 0.00 32.54 2.43
1533 1693 8.517878 AGCGAAAGAGTACTACAGTATAAAACA 58.482 33.333 0.00 0.00 32.54 2.83
1534 1694 9.298774 GCGAAAGAGTACTACAGTATAAAACAT 57.701 33.333 0.00 0.00 32.54 2.71
1679 1842 2.287608 GCACCTCCACAAAGCTTGTAAC 60.288 50.000 0.00 0.00 43.23 2.50
1719 1882 5.309323 TCTATAGCCATTGTTTGTTGCAC 57.691 39.130 0.00 0.00 0.00 4.57
1723 1886 2.297033 AGCCATTGTTTGTTGCACCTAG 59.703 45.455 0.00 0.00 0.00 3.02
1873 2036 3.118482 TGCAAAGACTCCATCTCATCTCC 60.118 47.826 0.00 0.00 36.27 3.71
1874 2037 3.118482 GCAAAGACTCCATCTCATCTCCA 60.118 47.826 0.00 0.00 36.27 3.86
1875 2038 4.695396 CAAAGACTCCATCTCATCTCCAG 58.305 47.826 0.00 0.00 36.27 3.86
1876 2039 2.318908 AGACTCCATCTCATCTCCAGC 58.681 52.381 0.00 0.00 28.16 4.85
1877 2040 2.037901 GACTCCATCTCATCTCCAGCA 58.962 52.381 0.00 0.00 0.00 4.41
1910 2073 0.106719 CACCCACAACTGAACCACCT 60.107 55.000 0.00 0.00 0.00 4.00
1911 2074 0.629058 ACCCACAACTGAACCACCTT 59.371 50.000 0.00 0.00 0.00 3.50
2225 2390 7.730364 TTATTTCACCTCTTCAACTCAACTC 57.270 36.000 0.00 0.00 0.00 3.01
2226 2391 4.753516 TTCACCTCTTCAACTCAACTCA 57.246 40.909 0.00 0.00 0.00 3.41
2227 2392 4.753516 TCACCTCTTCAACTCAACTCAA 57.246 40.909 0.00 0.00 0.00 3.02
2228 2393 4.442706 TCACCTCTTCAACTCAACTCAAC 58.557 43.478 0.00 0.00 0.00 3.18
2229 2394 4.162320 TCACCTCTTCAACTCAACTCAACT 59.838 41.667 0.00 0.00 0.00 3.16
2253 2418 1.895798 CTCTTAGTGCACCACCAGAGA 59.104 52.381 20.00 11.60 41.24 3.10
2312 2477 6.310197 GCTCATTGTGTAGATTGACAAGTTC 58.690 40.000 0.00 0.00 35.60 3.01
2313 2478 6.621596 GCTCATTGTGTAGATTGACAAGTTCC 60.622 42.308 0.00 0.00 35.60 3.62
2350 2515 5.063204 TCAGGTCCAGAACAGTAAACATTG 58.937 41.667 0.00 0.00 0.00 2.82
2650 2815 8.794335 AACCCTCTTCTTACAAATCAGTATTC 57.206 34.615 0.00 0.00 0.00 1.75
2674 2839 1.226974 CAGGCAATGCAGCATCAGC 60.227 57.895 19.56 19.56 42.56 4.26
2694 2859 6.976088 TCAGCTAGCTACTCATATCTGTTTC 58.024 40.000 18.86 0.00 0.00 2.78
2741 2906 2.636830 CCCAAGTCAGTAATGAGGCTG 58.363 52.381 0.00 0.00 0.00 4.85
2881 3046 0.322975 CTGGCTACAGTTCCAGTGCT 59.677 55.000 11.56 0.00 43.66 4.40
3067 3232 1.891919 GCAGTCGGCCACTTTGACA 60.892 57.895 2.24 0.00 35.09 3.58
3342 3507 8.697507 TGAGCAATGAACTCTGTATCTCTATA 57.302 34.615 0.00 0.00 35.12 1.31
3445 3610 9.145865 CCGTATTTAAATGCAAGGTTGTAATTT 57.854 29.630 15.33 9.19 33.88 1.82
3570 3737 9.857957 AACAGAGCTACAAGTTACTTATAAGTC 57.142 33.333 21.25 8.65 40.37 3.01
3704 3871 3.904339 ACTACACATGAACTTCTGGAGGT 59.096 43.478 0.00 0.00 0.00 3.85
3759 3926 9.480053 TTCATTCAGGAAAGCAAAGAATTTAAG 57.520 29.630 0.00 0.00 35.03 1.85
3839 4006 1.535462 ACAAACTAGCGTGCATTGGTC 59.465 47.619 0.00 0.00 0.00 4.02
4042 4209 4.081420 TCTCCATCCTAGTTTTCTCAGCAC 60.081 45.833 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
511 524 4.952460 ACAGAAGACAATTTGCAAGCAAT 58.048 34.783 8.46 0.00 35.70 3.56
514 527 4.383948 GCTAACAGAAGACAATTTGCAAGC 59.616 41.667 0.00 0.00 0.00 4.01
553 566 3.261580 CTGTATTTCCATCACGCAGACA 58.738 45.455 0.00 0.00 0.00 3.41
554 567 3.262420 ACTGTATTTCCATCACGCAGAC 58.738 45.455 0.00 0.00 0.00 3.51
628 674 2.036475 ACACACACACACAAAAAGCCAA 59.964 40.909 0.00 0.00 0.00 4.52
629 675 1.615883 ACACACACACACAAAAAGCCA 59.384 42.857 0.00 0.00 0.00 4.75
630 676 1.991965 CACACACACACACAAAAAGCC 59.008 47.619 0.00 0.00 0.00 4.35
631 677 2.408032 CACACACACACACACAAAAAGC 59.592 45.455 0.00 0.00 0.00 3.51
632 678 3.424861 CACACACACACACACACAAAAAG 59.575 43.478 0.00 0.00 0.00 2.27
638 684 0.958382 ACCCACACACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
702 825 2.093235 CCCCTTTCACCAAACAAGCAAA 60.093 45.455 0.00 0.00 0.00 3.68
1080 1228 1.301479 GAACTTGAAGGACGCCGGT 60.301 57.895 1.90 0.00 0.00 5.28
1451 1602 6.064060 TCTCCTGTGAATGAACATTGTTTCT 58.936 36.000 3.08 0.00 0.00 2.52
1471 1622 9.530633 AAGAATGAAATACTACGTACAATCTCC 57.469 33.333 0.00 0.00 0.00 3.71
1532 1692 9.926158 ATATGTCTAGCTTAGTCTGAATGAATG 57.074 33.333 0.00 0.00 0.00 2.67
1697 1860 4.157656 GGTGCAACAAACAATGGCTATAGA 59.842 41.667 3.21 0.00 39.98 1.98
1719 1882 3.071312 AGAAGGATGCTTCATCTGCTAGG 59.929 47.826 26.36 0.00 40.39 3.02
1723 1886 2.613133 GTGAGAAGGATGCTTCATCTGC 59.387 50.000 26.36 14.09 40.39 4.26
1828 1991 3.753294 TCAGTGACCTGAAGTTCTTCC 57.247 47.619 4.17 0.00 44.67 3.46
2035 2198 3.773860 TGTCGACAATTTGCAAACTGT 57.226 38.095 24.87 24.87 0.00 3.55
2225 2390 3.248602 GTGGTGCACTAAGAGTTGAGTTG 59.751 47.826 17.98 0.00 0.00 3.16
2226 2391 3.467803 GTGGTGCACTAAGAGTTGAGTT 58.532 45.455 17.98 0.00 0.00 3.01
2227 2392 2.224305 GGTGGTGCACTAAGAGTTGAGT 60.224 50.000 17.98 0.00 34.40 3.41
2228 2393 2.224281 TGGTGGTGCACTAAGAGTTGAG 60.224 50.000 17.98 0.00 34.40 3.02
2229 2394 1.765904 TGGTGGTGCACTAAGAGTTGA 59.234 47.619 17.98 0.00 34.40 3.18
2488 2653 2.306805 ACATGAAGAGCCAATGACCTGA 59.693 45.455 0.00 0.00 0.00 3.86
2595 2760 2.088763 CCTGAGTACTGTGCGCACG 61.089 63.158 33.22 28.09 0.00 5.34
2672 2837 6.549364 AGTGAAACAGATATGAGTAGCTAGCT 59.451 38.462 23.12 23.12 41.43 3.32
2673 2838 6.640499 CAGTGAAACAGATATGAGTAGCTAGC 59.360 42.308 6.62 6.62 41.43 3.42
2674 2839 6.640499 GCAGTGAAACAGATATGAGTAGCTAG 59.360 42.308 0.00 0.00 41.43 3.42
2675 2840 6.096846 TGCAGTGAAACAGATATGAGTAGCTA 59.903 38.462 0.00 0.00 41.43 3.32
2694 2859 4.232221 GACAAAATCATGGAGTTGCAGTG 58.768 43.478 0.00 0.00 0.00 3.66
2741 2906 1.706287 GGTCGAAATCAGGCCGCTTC 61.706 60.000 0.00 0.00 0.00 3.86
3045 3210 3.553095 AAAGTGGCCGACTGCTCCC 62.553 63.158 8.37 0.00 40.92 4.30
3048 3213 1.598130 GTCAAAGTGGCCGACTGCT 60.598 57.895 8.37 0.00 40.92 4.24
3342 3507 2.353803 GGCTCGTCAACCACTTGTATCT 60.354 50.000 0.00 0.00 0.00 1.98
3445 3610 8.211116 TCATACTTTCCGTGAAACAGTAAAAA 57.789 30.769 3.75 0.00 35.74 1.94
3581 3748 5.644636 TCTCATAAAATTCCGGGTGTGTAAC 59.355 40.000 0.00 0.00 37.35 2.50
3592 3759 9.691362 TGCAAAGTTAGTTTCTCATAAAATTCC 57.309 29.630 0.00 0.00 0.00 3.01
3759 3926 5.593095 ACCTTTTCTCTTGGGTGAAGTTTAC 59.407 40.000 0.00 0.00 32.90 2.01
3898 4065 7.416664 GCATTGACCTTTTAATTAGCTCCATGA 60.417 37.037 0.00 0.00 0.00 3.07
3915 4082 3.512724 CCAGATCAAAAAGGCATTGACCT 59.487 43.478 0.00 0.00 43.91 3.85
4042 4209 1.135489 AGATGTGCAAAATGCTCGCAG 60.135 47.619 3.78 0.00 45.31 5.18


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

AutoCloner maintained by Alex Coulton.