Multiple sequence alignment - TraesCS3D01G229000

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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 TraesCS3D01G229000 chr3D 100.000 3893 0 0 1 3893 311669172 311665280 0.000000e+00 7190.0
1 TraesCS3D01G229000 chr3D 90.226 133 13 0 236 368 172356570 172356702 1.440000e-39 174.0
2 TraesCS3D01G229000 chr3A 97.386 3558 73 10 1 3543 420739128 420742680 0.000000e+00 6037.0
3 TraesCS3D01G229000 chr3A 94.118 170 8 2 3567 3735 420742803 420742971 1.390000e-64 257.0
4 TraesCS3D01G229000 chr3A 95.902 122 4 1 3773 3893 420742980 420743101 3.070000e-46 196.0
5 TraesCS3D01G229000 chr3A 91.791 134 10 1 245 378 621323865 621323733 6.640000e-43 185.0
6 TraesCS3D01G229000 chr3A 92.857 126 9 0 243 368 169855801 169855926 2.390000e-42 183.0
7 TraesCS3D01G229000 chr3A 90.441 136 13 0 236 371 137914543 137914408 3.090000e-41 180.0
8 TraesCS3D01G229000 chr3A 96.970 33 1 0 3768 3800 420742502 420742534 5.430000e-04 56.5
9 TraesCS3D01G229000 chr3B 96.289 3395 92 13 1 3386 409543699 409547068 0.000000e+00 5541.0
10 TraesCS3D01G229000 chr2B 91.852 135 10 1 244 378 572791182 572791049 1.850000e-43 187.0
11 TraesCS3D01G229000 chr2B 80.579 242 23 12 3456 3680 670168604 670168838 8.650000e-37 165.0
12 TraesCS3D01G229000 chr2A 91.111 135 11 1 244 378 632952429 632952296 8.590000e-42 182.0
13 TraesCS3D01G229000 chr6D 81.224 245 22 12 3453 3680 381358299 381358062 4.000000e-40 176.0
14 TraesCS3D01G229000 chr7A 87.582 153 16 3 225 375 627236795 627236946 1.440000e-39 174.0
15 TraesCS3D01G229000 chr7A 80.569 211 21 12 3476 3674 422822257 422822459 1.130000e-30 145.0
16 TraesCS3D01G229000 chr6A 82.075 212 19 9 3481 3680 522624118 522623914 3.110000e-36 163.0
17 TraesCS3D01G229000 chr6B 81.690 213 18 12 3480 3680 236400573 236400370 1.450000e-34 158.0
18 TraesCS3D01G229000 chr5A 79.339 242 24 12 3456 3680 98040617 98040849 3.130000e-31 147.0
19 TraesCS3D01G229000 chr2D 81.034 116 9 10 3577 3680 620544433 620544547 3.220000e-11 80.5


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 TraesCS3D01G229000 chr3D 311665280 311669172 3892 True 7190.000 7190 100.000 1 3893 1 chr3D.!!$R1 3892
1 TraesCS3D01G229000 chr3A 420739128 420743101 3973 False 1636.625 6037 96.094 1 3893 4 chr3A.!!$F2 3892
2 TraesCS3D01G229000 chr3B 409543699 409547068 3369 False 5541.000 5541 96.289 1 3386 1 chr3B.!!$F1 3385

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
601 602 0.109342 CTGCTCCTGGTTGTGGTCTT 59.891 55.000 0.0 0.0 0.0 3.01 F
1249 1250 2.155732 CGTTCACCAAGTTCATCTGACG 59.844 50.000 0.0 0.0 0.0 4.35 F
2073 2074 1.428912 AGGCATGGAGGTGGAAAAAGA 59.571 47.619 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2074 0.689055 TGCACTTCTCCTGCTGACAT 59.311 50.000 0.0 0.0 35.53 3.06 R
2487 2488 1.004044 CAGAAATCAGTGCTCCCCTGT 59.996 52.381 0.0 0.0 0.00 4.00 R
3460 3480 1.340502 TGAGTGTGCCACAAGTTCCAA 60.341 47.619 0.0 0.0 36.74 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
38 39 7.489113 GCTGGTATTCAAATAAACAACAGATGG 59.511 37.037 0.00 0.00 0.00 3.51
95 96 2.496679 ACACCTGGCCATCTATAGGT 57.503 50.000 5.51 5.98 44.05 3.08
118 119 3.008375 TCTGAGATTTGTTGTCCCCTCAG 59.992 47.826 0.00 0.00 45.24 3.35
195 196 8.901748 CACTTACAGATCAACAAATAAAAACGG 58.098 33.333 0.00 0.00 0.00 4.44
290 291 8.737175 ACTTGTCTTACATTTGTCTAGATACGA 58.263 33.333 0.00 0.00 0.00 3.43
527 528 3.804873 GGCACCGACAATTCTAAGATCTC 59.195 47.826 0.00 0.00 0.00 2.75
601 602 0.109342 CTGCTCCTGGTTGTGGTCTT 59.891 55.000 0.00 0.00 0.00 3.01
705 706 6.211584 TGAGCTTTGTAGTTGAGACTTCCTAT 59.788 38.462 0.00 0.00 37.33 2.57
706 707 6.402222 AGCTTTGTAGTTGAGACTTCCTATG 58.598 40.000 0.00 0.00 37.33 2.23
847 848 2.906354 ACATACTGGCGAGAAATGGAC 58.094 47.619 1.44 0.00 0.00 4.02
1062 1063 6.584954 CATCAACTCGTTAAACACTTCTCAG 58.415 40.000 0.00 0.00 0.00 3.35
1249 1250 2.155732 CGTTCACCAAGTTCATCTGACG 59.844 50.000 0.00 0.00 0.00 4.35
1381 1382 3.648339 ATGATGTTGCACACTTCCAAC 57.352 42.857 0.00 0.00 41.19 3.77
1779 1780 6.737346 GCAATCTTAACACTAAAACCTGCCAA 60.737 38.462 0.00 0.00 0.00 4.52
2073 2074 1.428912 AGGCATGGAGGTGGAAAAAGA 59.571 47.619 0.00 0.00 0.00 2.52
2487 2488 1.595109 CGGCTGTGTGAAGAGTGCA 60.595 57.895 0.00 0.00 0.00 4.57
2855 2856 0.850784 ACAGGCCCTGTTGGTAACTT 59.149 50.000 11.57 0.00 42.59 2.66
3126 3132 4.923281 GCCCTTGCTTTGTGTTTATTACAG 59.077 41.667 0.00 0.00 33.82 2.74
3190 3198 3.058708 TCATCTCTTCGCTGTTTGCTTTG 60.059 43.478 0.00 0.00 40.11 2.77
3253 3269 2.696526 TGGTGGGTAGAAGTCTGTCT 57.303 50.000 0.00 0.00 0.00 3.41
3409 3428 9.421399 TCTCTAGATTTAGTACCATGAATGTCA 57.579 33.333 0.00 0.00 0.00 3.58
3415 3434 9.383519 GATTTAGTACCATGAATGTCAAGAGAA 57.616 33.333 0.00 0.00 0.00 2.87
3428 3447 4.152938 TGTCAAGAGAAGAATGTTGATGCG 59.847 41.667 0.00 0.00 35.25 4.73
3504 3527 8.773645 TCAAATCAAGTACTTGTTACATCACTG 58.226 33.333 29.83 17.21 41.16 3.66
3538 3561 6.376018 AGCTAGGATAATCTACGAAGGATCAC 59.624 42.308 0.00 0.00 0.00 3.06
3539 3562 5.986501 AGGATAATCTACGAAGGATCACC 57.013 43.478 0.00 0.00 0.00 4.02
3540 3563 4.773149 AGGATAATCTACGAAGGATCACCC 59.227 45.833 0.00 0.00 36.73 4.61
3562 3585 4.164988 CCTCATCCTCCCAAGAAACTACAT 59.835 45.833 0.00 0.00 0.00 2.29
3563 3586 5.366768 CCTCATCCTCCCAAGAAACTACATA 59.633 44.000 0.00 0.00 0.00 2.29
3565 3588 6.650120 TCATCCTCCCAAGAAACTACATAAC 58.350 40.000 0.00 0.00 0.00 1.89
3568 3696 7.989947 TCCTCCCAAGAAACTACATAACTAT 57.010 36.000 0.00 0.00 0.00 2.12
3628 3756 4.601857 TGTTCCCCTAAGTGAGAGGAAAAT 59.398 41.667 0.00 0.00 38.30 1.82
3629 3757 5.788533 TGTTCCCCTAAGTGAGAGGAAAATA 59.211 40.000 0.00 0.00 38.30 1.40
3630 3758 5.952347 TCCCCTAAGTGAGAGGAAAATAC 57.048 43.478 0.00 0.00 35.99 1.89
3632 3760 4.141459 CCCCTAAGTGAGAGGAAAATACCC 60.141 50.000 0.00 0.00 35.99 3.69
3660 3788 9.899226 ATACTTTGAGCTAAATGAAAACACTTC 57.101 29.630 3.72 0.00 0.00 3.01
3709 3838 9.871238 GAAACTCTAGATTTAGTACCATGAACA 57.129 33.333 0.00 0.00 0.00 3.18
3735 3864 3.889538 AGAGATGAATGTTGATGCCCATG 59.110 43.478 0.00 0.00 0.00 3.66
3737 3866 3.635373 AGATGAATGTTGATGCCCATGTC 59.365 43.478 0.00 0.00 0.00 3.06
3738 3867 2.805194 TGAATGTTGATGCCCATGTCA 58.195 42.857 0.00 0.00 0.00 3.58
3739 3868 3.367321 TGAATGTTGATGCCCATGTCAT 58.633 40.909 0.00 0.00 0.00 3.06
3740 3869 3.770388 TGAATGTTGATGCCCATGTCATT 59.230 39.130 0.00 0.00 0.00 2.57
3741 3870 3.812156 ATGTTGATGCCCATGTCATTG 57.188 42.857 0.00 0.00 0.00 2.82
3742 3871 1.205179 TGTTGATGCCCATGTCATTGC 59.795 47.619 0.00 0.00 0.00 3.56
3743 3872 1.479323 GTTGATGCCCATGTCATTGCT 59.521 47.619 5.85 0.00 0.00 3.91
3744 3873 2.689471 GTTGATGCCCATGTCATTGCTA 59.311 45.455 5.85 0.00 0.00 3.49
3745 3874 2.578786 TGATGCCCATGTCATTGCTAG 58.421 47.619 5.85 0.00 0.00 3.42
3746 3875 2.173143 TGATGCCCATGTCATTGCTAGA 59.827 45.455 0.00 0.00 0.00 2.43
3747 3876 2.804986 TGCCCATGTCATTGCTAGAA 57.195 45.000 0.00 0.00 0.00 2.10
3748 3877 3.301794 TGCCCATGTCATTGCTAGAAT 57.698 42.857 0.00 0.00 0.00 2.40
3749 3878 3.634504 TGCCCATGTCATTGCTAGAATT 58.365 40.909 0.00 0.00 0.00 2.17
3750 3879 4.025360 TGCCCATGTCATTGCTAGAATTT 58.975 39.130 0.00 0.00 0.00 1.82
3751 3880 4.467082 TGCCCATGTCATTGCTAGAATTTT 59.533 37.500 0.00 0.00 0.00 1.82
3752 3881 5.045872 GCCCATGTCATTGCTAGAATTTTC 58.954 41.667 0.00 0.00 0.00 2.29
3753 3882 5.163478 GCCCATGTCATTGCTAGAATTTTCT 60.163 40.000 0.00 0.00 41.24 2.52
3754 3883 6.501781 CCCATGTCATTGCTAGAATTTTCTC 58.498 40.000 0.00 0.00 38.70 2.87
3755 3884 6.095860 CCCATGTCATTGCTAGAATTTTCTCA 59.904 38.462 0.00 0.00 38.70 3.27
3756 3885 7.363181 CCCATGTCATTGCTAGAATTTTCTCAA 60.363 37.037 0.00 0.00 38.70 3.02
3757 3886 7.487189 CCATGTCATTGCTAGAATTTTCTCAAC 59.513 37.037 0.00 0.00 38.70 3.18
3758 3887 7.509141 TGTCATTGCTAGAATTTTCTCAACA 57.491 32.000 0.00 0.00 38.70 3.33
3759 3888 7.939782 TGTCATTGCTAGAATTTTCTCAACAA 58.060 30.769 0.00 1.42 38.70 2.83
3760 3889 7.862372 TGTCATTGCTAGAATTTTCTCAACAAC 59.138 33.333 0.00 0.61 38.70 3.32
3761 3890 7.862372 GTCATTGCTAGAATTTTCTCAACAACA 59.138 33.333 0.00 0.00 38.70 3.33
3762 3891 8.412456 TCATTGCTAGAATTTTCTCAACAACAA 58.588 29.630 0.00 0.00 38.70 2.83
3763 3892 9.033481 CATTGCTAGAATTTTCTCAACAACAAA 57.967 29.630 0.00 0.00 38.70 2.83
3764 3893 8.994429 TTGCTAGAATTTTCTCAACAACAAAA 57.006 26.923 0.00 0.00 38.70 2.44
3765 3894 8.994429 TGCTAGAATTTTCTCAACAACAAAAA 57.006 26.923 0.00 0.00 38.70 1.94
3833 3963 1.749258 CTTTTGAGGCCCGGGCTAC 60.749 63.158 42.70 33.67 38.98 3.58
3873 4003 7.833682 TCATTGATCAATAAAGCTTGGGAGTTA 59.166 33.333 20.32 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 3.394274 TGAGGGGACAACAAATCTCAGAA 59.606 43.478 0.00 0.00 0.00 3.02
527 528 4.572909 TGTCCACTTCTGTCATGATCAAG 58.427 43.478 0.00 4.28 0.00 3.02
847 848 2.827800 AGCCAGATACATCATCACGG 57.172 50.000 0.00 0.00 35.96 4.94
1062 1063 3.746045 TGTTGGACTGAACTCTGGTAC 57.254 47.619 0.00 0.00 0.00 3.34
1381 1382 1.470098 CAAACCAGCAGAGGATTTCCG 59.530 52.381 0.00 0.00 42.08 4.30
2073 2074 0.689055 TGCACTTCTCCTGCTGACAT 59.311 50.000 0.00 0.00 35.53 3.06
2487 2488 1.004044 CAGAAATCAGTGCTCCCCTGT 59.996 52.381 0.00 0.00 0.00 4.00
2855 2856 4.069232 CAGAGGCGCCGTTCTCCA 62.069 66.667 23.20 0.00 0.00 3.86
3190 3198 5.154222 GCACTATTACCAGAAACACAAAGC 58.846 41.667 0.00 0.00 0.00 3.51
3307 3323 3.401033 TCTGATGACTCGGCAAAAAGA 57.599 42.857 0.00 0.00 0.00 2.52
3308 3324 5.801350 TTATCTGATGACTCGGCAAAAAG 57.199 39.130 0.00 0.00 0.00 2.27
3314 3330 4.876125 TGAGAATTATCTGATGACTCGGC 58.124 43.478 1.19 0.00 35.54 5.54
3315 3331 6.083098 ACTGAGAATTATCTGATGACTCGG 57.917 41.667 13.15 10.29 35.54 4.63
3405 3424 4.152938 CGCATCAACATTCTTCTCTTGACA 59.847 41.667 0.00 0.00 0.00 3.58
3409 3428 3.076621 TGCGCATCAACATTCTTCTCTT 58.923 40.909 5.66 0.00 0.00 2.85
3415 3434 5.458015 CAATGATATGCGCATCAACATTCT 58.542 37.500 29.11 13.13 38.39 2.40
3428 3447 8.861033 CTAGAGAGATTCTAGCAATGATATGC 57.139 38.462 0.00 0.00 46.54 3.14
3460 3480 1.340502 TGAGTGTGCCACAAGTTCCAA 60.341 47.619 0.00 0.00 36.74 3.53
3463 3483 3.066621 TGATTTGAGTGTGCCACAAGTTC 59.933 43.478 0.00 0.00 36.74 3.01
3467 3487 3.023119 ACTTGATTTGAGTGTGCCACAA 58.977 40.909 0.00 0.00 36.74 3.33
3504 3527 6.858993 CGTAGATTATCCTAGCTGAACTTGTC 59.141 42.308 0.00 0.00 0.00 3.18
3514 3537 6.404954 GGTGATCCTTCGTAGATTATCCTAGC 60.405 46.154 0.00 0.00 35.04 3.42
3538 3561 1.918957 AGTTTCTTGGGAGGATGAGGG 59.081 52.381 0.00 0.00 0.00 4.30
3539 3562 3.519510 TGTAGTTTCTTGGGAGGATGAGG 59.480 47.826 0.00 0.00 0.00 3.86
3540 3563 4.826274 TGTAGTTTCTTGGGAGGATGAG 57.174 45.455 0.00 0.00 0.00 2.90
3541 3564 6.443849 AGTTATGTAGTTTCTTGGGAGGATGA 59.556 38.462 0.00 0.00 0.00 2.92
3542 3565 6.653989 AGTTATGTAGTTTCTTGGGAGGATG 58.346 40.000 0.00 0.00 0.00 3.51
3543 3566 6.893020 AGTTATGTAGTTTCTTGGGAGGAT 57.107 37.500 0.00 0.00 0.00 3.24
3544 3567 7.989947 ATAGTTATGTAGTTTCTTGGGAGGA 57.010 36.000 0.00 0.00 0.00 3.71
3565 3588 9.323985 GCTTGCTAGGATTTCCTATGATTATAG 57.676 37.037 6.79 0.00 46.71 1.31
3568 3696 7.321717 AGCTTGCTAGGATTTCCTATGATTA 57.678 36.000 6.79 0.00 46.71 1.75
3580 3708 1.457346 GCACACAAGCTTGCTAGGAT 58.543 50.000 26.27 2.45 35.74 3.24
3628 3756 8.871629 TTTCATTTAGCTCAAAGTATTGGGTA 57.128 30.769 0.00 0.00 39.36 3.69
3629 3757 7.775053 TTTCATTTAGCTCAAAGTATTGGGT 57.225 32.000 0.00 0.00 39.36 4.51
3630 3758 8.087750 TGTTTTCATTTAGCTCAAAGTATTGGG 58.912 33.333 0.00 0.00 40.20 4.12
3632 3760 9.683069 AGTGTTTTCATTTAGCTCAAAGTATTG 57.317 29.630 0.00 0.00 37.92 1.90
3709 3838 4.583489 GGGCATCAACATTCATCTCTTGAT 59.417 41.667 0.00 0.00 34.37 2.57
3735 3864 7.862372 TGTTGTTGAGAAAATTCTAGCAATGAC 59.138 33.333 0.00 2.47 37.73 3.06
3737 3866 8.578308 TTGTTGTTGAGAAAATTCTAGCAATG 57.422 30.769 0.00 0.00 37.73 2.82
3738 3867 9.598517 TTTTGTTGTTGAGAAAATTCTAGCAAT 57.401 25.926 0.00 0.00 37.73 3.56
3739 3868 8.994429 TTTTGTTGTTGAGAAAATTCTAGCAA 57.006 26.923 0.00 0.16 37.73 3.91
3740 3869 8.994429 TTTTTGTTGTTGAGAAAATTCTAGCA 57.006 26.923 0.00 0.00 37.73 3.49
3763 3892 8.245701 CTAGAGAGTTTCTAGCAACGATTTTT 57.754 34.615 4.87 0.00 46.54 1.94
3764 3893 7.820044 CTAGAGAGTTTCTAGCAACGATTTT 57.180 36.000 4.87 0.00 46.54 1.82
3793 3922 1.412710 CATACATGGCGGTCTGGTACT 59.587 52.381 0.00 0.00 0.00 2.73
3819 3949 3.961225 TTACGTAGCCCGGGCCTCA 62.961 63.158 41.72 24.69 43.17 3.86


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

AutoCloner maintained by Alex Coulton.