Multiple sequence alignment - TraesCS2B01G286700

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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 TraesCS2B01G286700 chr2B 100.000 5664 0 0 1 5664 395545927 395540264 0.000000e+00 10460.0
1 TraesCS2B01G286700 chr2A 96.312 4989 128 17 1 4972 391869364 391874313 0.000000e+00 8142.0
2 TraesCS2B01G286700 chr2A 88.040 694 49 19 4971 5631 391874417 391875109 0.000000e+00 791.0
3 TraesCS2B01G286700 chr2A 96.610 59 2 0 3200 3258 391872475 391872533 1.300000e-16 99.0
4 TraesCS2B01G286700 chr2D 96.176 4053 119 20 1 4045 326221607 326217583 0.000000e+00 6593.0
5 TraesCS2B01G286700 chr2D 95.752 871 36 1 4040 4910 326217481 326216612 0.000000e+00 1402.0
6 TraesCS2B01G286700 chr2D 88.340 729 38 9 4983 5664 326215863 326215135 0.000000e+00 832.0
7 TraesCS2B01G286700 chr2D 86.157 549 65 7 4135 4676 643176718 643176174 2.940000e-162 582.0
8 TraesCS2B01G286700 chr2D 91.566 83 6 1 4915 4997 326216547 326216466 4.640000e-21 113.0
9 TraesCS2B01G286700 chr2D 94.915 59 3 0 3200 3258 326218465 326218407 6.040000e-15 93.5


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 TraesCS2B01G286700 chr2B 395540264 395545927 5663 True 10460.000000 10460 100.0000 1 5664 1 chr2B.!!$R1 5663
1 TraesCS2B01G286700 chr2A 391869364 391875109 5745 False 3010.666667 8142 93.6540 1 5631 3 chr2A.!!$F1 5630
2 TraesCS2B01G286700 chr2D 326215135 326221607 6472 True 1806.700000 6593 93.3498 1 5664 5 chr2D.!!$R2 5663
3 TraesCS2B01G286700 chr2D 643176174 643176718 544 True 582.000000 582 86.1570 4135 4676 1 chr2D.!!$R1 541

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
917 930 0.108329 TCTTACCGTTGCAGCTAGCC 60.108 55.000 12.13 0.0 44.83 3.93 F
1021 1034 0.521735 GGGGTTCAACACAGAATCGC 59.478 55.000 0.00 0.0 34.97 4.58 F
2697 2712 1.210478 ACTCACTGCAAGACACTGGTT 59.790 47.619 0.00 0.0 37.43 3.67 F
4160 4294 0.170339 GGTGGCCGAATAACAAGTGC 59.830 55.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2697 2712 0.323629 GGTTTGTCATCTCCGGGTCA 59.676 55.0 0.0 0.0 0.00 4.02 R
2898 2913 6.084925 GTGCATCTTTGAGTGAATTGAAGAG 58.915 40.0 0.0 0.0 30.72 2.85 R
4586 4720 0.752054 TTGGAAGCCTGCAAACAAGG 59.248 50.0 0.0 0.0 28.70 3.61 R
5326 6258 0.318762 ACCGCTCTCACAAAGACTCC 59.681 55.0 0.0 0.0 0.00 3.85 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
187 188 2.519302 ACCTGCTTGTTTGGCGCT 60.519 55.556 7.64 0.00 0.00 5.92
256 257 2.897969 TCCAGTAAGTTCCAGGTCTCAC 59.102 50.000 0.00 0.00 0.00 3.51
258 259 3.306364 CCAGTAAGTTCCAGGTCTCACAG 60.306 52.174 0.00 0.00 0.00 3.66
721 726 3.390639 AGAACCTCCAAGATATCTGCCTG 59.609 47.826 5.86 0.73 0.00 4.85
761 766 4.081309 TGTGGGTCCTACTTTTAATCTCGG 60.081 45.833 6.95 0.00 0.00 4.63
894 899 3.952508 TGGAAGCAAGCAGGCCGA 61.953 61.111 0.00 0.00 0.00 5.54
916 929 1.594862 CATCTTACCGTTGCAGCTAGC 59.405 52.381 6.62 6.62 45.96 3.42
917 930 0.108329 TCTTACCGTTGCAGCTAGCC 60.108 55.000 12.13 0.00 44.83 3.93
918 931 1.078708 TTACCGTTGCAGCTAGCCC 60.079 57.895 12.13 3.31 44.83 5.19
919 932 2.530958 TTACCGTTGCAGCTAGCCCC 62.531 60.000 12.13 2.89 44.83 5.80
920 933 4.101448 CCGTTGCAGCTAGCCCCT 62.101 66.667 12.13 0.00 44.83 4.79
921 934 2.512515 CGTTGCAGCTAGCCCCTC 60.513 66.667 12.13 0.00 44.83 4.30
922 935 2.993853 GTTGCAGCTAGCCCCTCT 59.006 61.111 12.13 0.00 44.83 3.69
923 936 1.451028 GTTGCAGCTAGCCCCTCTG 60.451 63.158 12.13 3.57 44.83 3.35
946 959 3.907260 TTCTGGCAGCTTGCTCCCG 62.907 63.158 10.34 0.00 44.28 5.14
1021 1034 0.521735 GGGGTTCAACACAGAATCGC 59.478 55.000 0.00 0.00 34.97 4.58
1353 1367 4.690748 TGACCAAAAACACGAGAGATCATC 59.309 41.667 0.00 0.00 0.00 2.92
1388 1402 6.202379 CAGCTGATAGTGACAACCAGATAATG 59.798 42.308 8.42 0.00 0.00 1.90
1677 1691 6.327279 AGGTGAGCTAAATTTACGCTTTTT 57.673 33.333 17.55 7.05 33.47 1.94
1716 1730 3.338249 TCTGGAACTTGCATAGCACTTC 58.662 45.455 0.00 0.00 38.71 3.01
2074 2089 1.318576 CTTTTGCGGGTTCCAGTTCT 58.681 50.000 0.00 0.00 0.00 3.01
2464 2479 3.197790 CCGCAGATGTTCTGGCCG 61.198 66.667 0.00 2.83 44.43 6.13
2697 2712 1.210478 ACTCACTGCAAGACACTGGTT 59.790 47.619 0.00 0.00 37.43 3.67
2790 2805 9.394767 ACATCAGTAATTAACATACAAGATGCA 57.605 29.630 20.80 0.00 39.29 3.96
2866 2881 1.284715 CACACATGTGGCAGCACTG 59.715 57.895 28.64 12.76 42.10 3.66
3058 3073 5.524284 CATATTCTTACTCACACCTCGAGG 58.476 45.833 30.11 30.11 42.17 4.63
3187 3202 8.715191 AACACAAATACAGAGAGAAGATCATC 57.285 34.615 0.00 0.00 0.00 2.92
3304 3319 2.484264 GGTGGTCGAGAATTTTCACCTG 59.516 50.000 14.36 0.00 40.84 4.00
3416 3431 6.405065 GGTCATACAATTCAAGACATGCACAT 60.405 38.462 0.00 0.00 0.00 3.21
3486 3501 1.074084 AGACCAAGACCGAGAGACAGA 59.926 52.381 0.00 0.00 0.00 3.41
3707 3723 4.394729 TGTTGTTCCTCCAAAGTGTATCC 58.605 43.478 0.00 0.00 0.00 2.59
3826 3842 6.036246 TGCTCATCGAATTCGTTTTCATAG 57.964 37.500 25.93 15.25 40.80 2.23
3856 3879 8.366401 AGTGAATTCTCATCATAGGACTATGTG 58.634 37.037 16.50 13.94 42.57 3.21
3950 3973 1.203149 AGAGTGGAACCCGTTAGGACT 60.203 52.381 0.00 0.00 41.02 3.85
4120 4254 1.869342 GCACCACACTTTTCCACATGC 60.869 52.381 0.00 0.00 0.00 4.06
4160 4294 0.170339 GGTGGCCGAATAACAAGTGC 59.830 55.000 0.00 0.00 0.00 4.40
4307 4441 5.779922 TCATTGAGGTCACTATATAACGCC 58.220 41.667 0.00 0.00 0.00 5.68
4389 4523 8.537728 AGAAATCATTTTGTGCCCAGATATTA 57.462 30.769 0.00 0.00 0.00 0.98
4416 4550 5.326200 AGGAGTATGACGTCTTTTTCGAT 57.674 39.130 17.92 2.21 0.00 3.59
4417 4551 5.103000 AGGAGTATGACGTCTTTTTCGATG 58.897 41.667 17.92 0.00 0.00 3.84
4503 4637 1.079127 GCTCTGGGCTCGCTTTGTA 60.079 57.895 0.00 0.00 38.06 2.41
4543 4677 3.452627 AGTTCCCTGGTAGCTAGAATGTG 59.547 47.826 0.00 0.00 0.00 3.21
4546 4680 2.501723 CCCTGGTAGCTAGAATGTGTGT 59.498 50.000 0.00 0.00 0.00 3.72
4584 4718 8.845413 ATGTTTCTAAGAATCTCATATCTGGC 57.155 34.615 0.00 0.00 0.00 4.85
4586 4720 5.065704 TCTAAGAATCTCATATCTGGCGC 57.934 43.478 0.00 0.00 0.00 6.53
4593 4727 2.092968 TCTCATATCTGGCGCCTTGTTT 60.093 45.455 29.70 14.07 0.00 2.83
4627 4761 4.978083 ATGTTCAAACCAGATGCAGATC 57.022 40.909 0.00 0.00 0.00 2.75
4736 4876 4.701651 CCCATTTCAATAAGAGTGTGCAGA 59.298 41.667 0.00 0.00 0.00 4.26
4737 4877 5.183713 CCCATTTCAATAAGAGTGTGCAGAA 59.816 40.000 0.00 0.00 0.00 3.02
4796 4939 2.360165 CTGAGATTTATGGCAACCCAGC 59.640 50.000 0.00 0.00 46.24 4.85
4837 4980 7.275920 ACAGAATATACTTTGATCACAGGACC 58.724 38.462 13.29 0.00 0.00 4.46
4861 5004 3.763360 TGAAATGCTATGGTGTGAAAGGG 59.237 43.478 0.00 0.00 0.00 3.95
4976 5179 8.603181 CAATTTCAAAACAACCAACCTAGAAAG 58.397 33.333 0.00 0.00 0.00 2.62
5002 5927 0.032815 TTCATGGACGTGACAGCGAA 59.967 50.000 0.00 0.00 35.59 4.70
5276 6208 7.719778 AAAGAAAGATGTGGCTTTTGAATTC 57.280 32.000 0.00 0.00 38.16 2.17
5283 6215 5.273674 TGTGGCTTTTGAATTCAACATCA 57.726 34.783 20.35 12.97 35.28 3.07
5284 6216 5.668471 TGTGGCTTTTGAATTCAACATCAA 58.332 33.333 20.35 11.02 35.28 2.57
5324 6256 1.715585 GTGATGGCACGGATTCACG 59.284 57.895 2.72 0.00 34.94 4.35
5335 6267 1.726791 CGGATTCACGTGGAGTCTTTG 59.273 52.381 17.00 3.05 33.09 2.77
5406 6343 3.195002 GCTGGCTGATAACGCGCA 61.195 61.111 5.73 0.00 0.00 6.09
5415 6352 2.139917 TGATAACGCGCAGTTTTCAGT 58.860 42.857 22.96 4.74 42.85 3.41
5455 6403 3.832527 ACAAGTGTTCCTACAAAGCCAT 58.167 40.909 0.00 0.00 35.69 4.40
5468 6416 4.593033 GCCATGTGCTCCCATCAT 57.407 55.556 0.00 0.00 36.87 2.45
5550 6523 4.819761 TCAGACCATCGGCTGCGC 62.820 66.667 0.00 0.00 30.75 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 4.866508 AACGACAAACAGATGAGAGGTA 57.133 40.909 0.00 0.00 0.00 3.08
258 259 5.269505 TGATTCTAGCTAGCAGAGGTTTC 57.730 43.478 18.83 11.13 37.09 2.78
387 392 2.456577 ACAGTTAATTGGCATGTCCCC 58.543 47.619 2.81 0.00 0.00 4.81
692 697 1.140312 TCTTGGAGGTTCTGCAGGTT 58.860 50.000 15.13 0.00 32.58 3.50
721 726 2.813100 CAAGAATTGCAACCACGGC 58.187 52.632 0.00 0.00 40.39 5.68
916 929 2.648059 CTGCCAGAAAATACAGAGGGG 58.352 52.381 0.00 0.00 31.67 4.79
917 930 2.019984 GCTGCCAGAAAATACAGAGGG 58.980 52.381 0.00 0.00 31.67 4.30
918 931 2.996631 AGCTGCCAGAAAATACAGAGG 58.003 47.619 0.00 0.00 31.67 3.69
919 932 3.427233 GCAAGCTGCCAGAAAATACAGAG 60.427 47.826 0.00 0.00 37.42 3.35
920 933 2.489329 GCAAGCTGCCAGAAAATACAGA 59.511 45.455 0.00 0.00 37.42 3.41
921 934 2.490903 AGCAAGCTGCCAGAAAATACAG 59.509 45.455 0.00 0.00 46.52 2.74
922 935 2.489329 GAGCAAGCTGCCAGAAAATACA 59.511 45.455 0.00 0.00 46.52 2.29
923 936 2.159324 GGAGCAAGCTGCCAGAAAATAC 60.159 50.000 0.00 0.00 46.52 1.89
1021 1034 0.601046 TCAGAACACAAGCCTCGCAG 60.601 55.000 0.00 0.00 0.00 5.18
1353 1367 2.032860 CTATCAGCTGGGTCCCCGTG 62.033 65.000 15.13 0.00 39.42 4.94
1636 1650 4.638421 TCACCTTGTACACCAAAGTTGAAG 59.362 41.667 0.00 0.00 31.20 3.02
1838 1852 2.093816 TGCATTTGCTGGTTGAACACAA 60.094 40.909 3.94 0.00 42.66 3.33
2074 2089 9.231297 CTTGGTTTCATTCTAGAAATGGAACTA 57.769 33.333 23.69 19.60 42.80 2.24
2117 2132 2.819608 GTTCCCTAAACAATGCTGCTGA 59.180 45.455 0.00 0.00 37.82 4.26
2697 2712 0.323629 GGTTTGTCATCTCCGGGTCA 59.676 55.000 0.00 0.00 0.00 4.02
2898 2913 6.084925 GTGCATCTTTGAGTGAATTGAAGAG 58.915 40.000 0.00 0.00 30.72 2.85
3058 3073 7.594015 CACTAAGAATTCAGCATAATCATTGGC 59.406 37.037 8.44 0.00 0.00 4.52
3108 3123 3.440173 ACGAGCAACTGTTTGGGATATTG 59.560 43.478 0.00 0.00 32.81 1.90
3187 3202 2.028112 TCGAAGAATCCAACCTCAGTGG 60.028 50.000 0.00 0.00 42.93 4.00
3304 3319 1.809547 GAAGCCTTCTTTGACTGAGGC 59.190 52.381 5.12 5.12 42.27 4.70
3486 3501 5.233083 TCATCCTGTCTTGAATCAGTTGT 57.767 39.130 0.00 0.00 0.00 3.32
3707 3723 1.674221 CCCACCTTCTCAGCTTTCTCG 60.674 57.143 0.00 0.00 0.00 4.04
3792 3808 8.223769 ACGAATTCGATGAGCATTATAATTCAC 58.776 33.333 33.05 0.00 43.02 3.18
3826 3842 7.385267 AGTCCTATGATGAGAATTCACTATGC 58.615 38.462 8.44 0.00 35.83 3.14
3920 3943 4.277423 ACGGGTTCCACTCTAATGTTTTTG 59.723 41.667 0.00 0.00 0.00 2.44
3926 3949 3.449737 TCCTAACGGGTTCCACTCTAATG 59.550 47.826 0.00 0.00 36.25 1.90
4106 4240 5.799681 AAAAACTTGCATGTGGAAAAGTG 57.200 34.783 5.94 0.00 33.30 3.16
4120 4254 7.584987 CCACCACACTATCTCTTAAAAACTTG 58.415 38.462 0.00 0.00 0.00 3.16
4160 4294 2.353889 GCTGCTTCAGTGACATGGTATG 59.646 50.000 0.00 0.00 33.43 2.39
4307 4441 2.076100 TGATGAAAACTAGTGCCTGCG 58.924 47.619 0.00 0.00 0.00 5.18
4389 4523 3.895232 AAGACGTCATACTCCTTGCAT 57.105 42.857 19.50 0.00 0.00 3.96
4461 4595 0.809241 CAGAACGATGCTCCAGCTCC 60.809 60.000 0.00 0.00 42.66 4.70
4503 4637 4.754114 GGAACTATGATACGTACCTCGACT 59.246 45.833 0.00 0.00 42.86 4.18
4543 4677 4.986659 AGAAACATACGTAACTGGTCACAC 59.013 41.667 0.00 0.00 0.00 3.82
4546 4680 7.218228 TCTTAGAAACATACGTAACTGGTCA 57.782 36.000 0.00 0.00 0.00 4.02
4586 4720 0.752054 TTGGAAGCCTGCAAACAAGG 59.248 50.000 0.00 0.00 28.70 3.61
4593 4727 1.702182 TGAACATTTGGAAGCCTGCA 58.298 45.000 0.00 0.00 0.00 4.41
4627 4761 1.588082 GTGCATCAGTGGGCAAAGG 59.412 57.895 11.21 0.00 42.45 3.11
4700 4840 2.026262 TGAAATGGGAACTGGACTAGCC 60.026 50.000 0.00 0.00 37.10 3.93
4736 4876 7.660112 TGTCTGCAATGAATAATGTTGTTCTT 58.340 30.769 4.31 0.00 30.69 2.52
4737 4877 7.218228 TGTCTGCAATGAATAATGTTGTTCT 57.782 32.000 4.31 0.00 30.69 3.01
4796 4939 4.661993 TTCTGTAACAGCATAAGCAACG 57.338 40.909 0.00 0.00 45.49 4.10
4837 4980 4.406069 CTTTCACACCATAGCATTTCACG 58.594 43.478 0.00 0.00 0.00 4.35
4861 5004 4.455533 TGAACTTCTGGTACACAATGCATC 59.544 41.667 0.00 0.00 0.00 3.91
4976 5179 4.260375 GCTGTCACGTCCATGAATGAATAC 60.260 45.833 0.00 0.00 0.00 1.89
5222 6154 9.491675 AATATTCAAAACTGAATCATTTGCACA 57.508 25.926 3.71 0.00 39.10 4.57
5260 6192 5.856156 TGATGTTGAATTCAAAAGCCACAT 58.144 33.333 22.07 19.22 37.63 3.21
5283 6215 6.534793 CACTGCGCCATCCTTATTTTAATTTT 59.465 34.615 4.18 0.00 0.00 1.82
5284 6216 6.042143 CACTGCGCCATCCTTATTTTAATTT 58.958 36.000 4.18 0.00 0.00 1.82
5324 6256 1.423395 CGCTCTCACAAAGACTCCAC 58.577 55.000 0.00 0.00 0.00 4.02
5326 6258 0.318762 ACCGCTCTCACAAAGACTCC 59.681 55.000 0.00 0.00 0.00 3.85
5406 6343 0.944386 AATGCACGCGACTGAAAACT 59.056 45.000 15.93 0.00 0.00 2.66
5415 6352 1.790090 TTGAAGCCAAATGCACGCGA 61.790 50.000 15.93 0.00 44.83 5.87
5455 6403 1.199615 TCGGTAATGATGGGAGCACA 58.800 50.000 0.00 0.00 0.00 4.57
5468 6416 1.747355 GGTGGAGAAGACGATCGGTAA 59.253 52.381 20.98 0.00 0.00 2.85
5589 6562 0.380378 TCAACTTCGGCAGCAACAAC 59.620 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.