Multiple sequence alignment - TraesCS2D01G321000

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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 TraesCS2D01G321000 chr2D 100.000 3695 0 0 1 3695 412331246 412334940 0 6824
1 TraesCS2D01G321000 chr2D 94.737 3724 159 16 1 3695 259243889 259240174 0 5757
2 TraesCS2D01G321000 chr2D 95.902 1025 42 0 2669 3693 258394914 258395938 0 1661
3 TraesCS2D01G321000 chr3D 95.702 3723 130 11 1 3695 323154461 323158181 0 5962
4 TraesCS2D01G321000 chr3D 94.440 3723 150 18 1 3695 395861730 395865423 0 5675
5 TraesCS2D01G321000 chr5D 95.700 3721 130 11 2 3695 190781136 190777419 0 5958
6 TraesCS2D01G321000 chr5D 93.568 3716 187 30 1 3695 108666118 108662434 0 5491
7 TraesCS2D01G321000 chr7D 94.792 3725 161 14 1 3695 291611954 291615675 0 5773
8 TraesCS2D01G321000 chr7D 94.012 3741 168 22 1 3695 298312684 298316414 0 5616
9 TraesCS2D01G321000 chr1D 94.769 3728 129 21 2 3695 371719920 371723615 0 5744
10 TraesCS2D01G321000 chr1D 94.023 3714 190 22 1 3695 88009183 88005483 0 5600
11 TraesCS2D01G321000 chr1D 93.172 3266 189 24 1 3246 78750937 78747686 0 4765
12 TraesCS2D01G321000 chr6D 94.333 3741 153 17 1 3695 256020688 256024415 0 5679
13 TraesCS2D01G321000 chr6D 88.237 3443 324 56 288 3695 229644626 229641230 0 4039
14 TraesCS2D01G321000 chr7A 94.280 3724 180 12 1 3695 265358191 265361910 0 5666
15 TraesCS2D01G321000 chr2A 92.999 3728 207 26 1 3695 160670694 160666988 0 5389
16 TraesCS2D01G321000 chr6A 88.352 3743 342 49 1 3695 343742118 343745814 0 4410
17 TraesCS2D01G321000 chr4B 89.913 3440 267 51 64 3463 279977929 279981328 0 4357
18 TraesCS2D01G321000 chr4D 96.021 1131 27 7 2579 3695 144576875 144575749 0 1823


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 TraesCS2D01G321000 chr2D 412331246 412334940 3694 False 6824 6824 100.000 1 3695 1 chr2D.!!$F2 3694
1 TraesCS2D01G321000 chr2D 259240174 259243889 3715 True 5757 5757 94.737 1 3695 1 chr2D.!!$R1 3694
2 TraesCS2D01G321000 chr2D 258394914 258395938 1024 False 1661 1661 95.902 2669 3693 1 chr2D.!!$F1 1024
3 TraesCS2D01G321000 chr3D 323154461 323158181 3720 False 5962 5962 95.702 1 3695 1 chr3D.!!$F1 3694
4 TraesCS2D01G321000 chr3D 395861730 395865423 3693 False 5675 5675 94.440 1 3695 1 chr3D.!!$F2 3694
5 TraesCS2D01G321000 chr5D 190777419 190781136 3717 True 5958 5958 95.700 2 3695 1 chr5D.!!$R2 3693
6 TraesCS2D01G321000 chr5D 108662434 108666118 3684 True 5491 5491 93.568 1 3695 1 chr5D.!!$R1 3694
7 TraesCS2D01G321000 chr7D 291611954 291615675 3721 False 5773 5773 94.792 1 3695 1 chr7D.!!$F1 3694
8 TraesCS2D01G321000 chr7D 298312684 298316414 3730 False 5616 5616 94.012 1 3695 1 chr7D.!!$F2 3694
9 TraesCS2D01G321000 chr1D 371719920 371723615 3695 False 5744 5744 94.769 2 3695 1 chr1D.!!$F1 3693
10 TraesCS2D01G321000 chr1D 88005483 88009183 3700 True 5600 5600 94.023 1 3695 1 chr1D.!!$R2 3694
11 TraesCS2D01G321000 chr1D 78747686 78750937 3251 True 4765 4765 93.172 1 3246 1 chr1D.!!$R1 3245
12 TraesCS2D01G321000 chr6D 256020688 256024415 3727 False 5679 5679 94.333 1 3695 1 chr6D.!!$F1 3694
13 TraesCS2D01G321000 chr6D 229641230 229644626 3396 True 4039 4039 88.237 288 3695 1 chr6D.!!$R1 3407
14 TraesCS2D01G321000 chr7A 265358191 265361910 3719 False 5666 5666 94.280 1 3695 1 chr7A.!!$F1 3694
15 TraesCS2D01G321000 chr2A 160666988 160670694 3706 True 5389 5389 92.999 1 3695 1 chr2A.!!$R1 3694
16 TraesCS2D01G321000 chr6A 343742118 343745814 3696 False 4410 4410 88.352 1 3695 1 chr6A.!!$F1 3694
17 TraesCS2D01G321000 chr4B 279977929 279981328 3399 False 4357 4357 89.913 64 3463 1 chr4B.!!$F1 3399
18 TraesCS2D01G321000 chr4D 144575749 144576875 1126 True 1823 1823 96.021 2579 3695 1 chr4D.!!$R1 1116

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
983 1050 0.401738 CTTCTCTCCCAAGCCCACAA 59.598 55.0 0.00 0.0 0.00 3.33 F
2214 2343 0.242017 GCAGCGCAAGTGGAAAGATT 59.758 50.0 11.47 0.0 41.68 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 2387 0.251916 CCGCTGTAGAATGGGTGGAA 59.748 55.0 0.00 0.0 0.0 3.53 R
3083 3271 5.562635 TGAAGCTTCCCGTTCCTTTTTATA 58.437 37.5 23.42 0.0 0.0 0.98 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
287 298 1.459972 ATCCCCCAACCCACCCAAAT 61.460 55.000 0.00 0.00 0.00 2.32
638 687 2.823747 AGCATACGTCACCTAACAGTGA 59.176 45.455 0.00 0.00 44.38 3.41
686 735 1.745087 CGTGCAAGTGGGATTTAGCAT 59.255 47.619 0.00 0.00 34.24 3.79
727 776 3.377346 AGACTAGTCAGTGCAACAGTG 57.623 47.619 24.44 0.00 41.43 3.66
907 971 1.849039 CCCCATTGTCTTCCATCTCCT 59.151 52.381 0.00 0.00 0.00 3.69
983 1050 0.401738 CTTCTCTCCCAAGCCCACAA 59.598 55.000 0.00 0.00 0.00 3.33
1164 1231 1.875813 GATCGTCTGCACCAGCGAG 60.876 63.158 13.76 0.00 46.23 5.03
1174 1241 2.210013 ACCAGCGAGCCAGACAAGA 61.210 57.895 0.00 0.00 0.00 3.02
1242 1309 1.272781 CGAGCTTCATCGGAGTTGAC 58.727 55.000 0.00 0.00 39.04 3.18
1394 1462 6.957984 TCTGTTGTACTAGTACTACTCACG 57.042 41.667 32.84 22.89 40.64 4.35
1508 1578 7.522073 GCATTTCTGAAACTGTGAAGTGGATTA 60.522 37.037 4.73 0.00 31.18 1.75
1511 1581 7.672983 TCTGAAACTGTGAAGTGGATTATTC 57.327 36.000 0.00 0.00 0.00 1.75
1949 2056 9.388506 CTAGTTTCTGAACTACATTCATCCATT 57.611 33.333 0.00 0.00 46.37 3.16
2001 2109 9.139174 CATGGATTATCACTTGTAAAACCAAAC 57.861 33.333 0.00 0.00 31.02 2.93
2003 2111 8.696374 TGGATTATCACTTGTAAAACCAAACAA 58.304 29.630 0.00 0.00 34.57 2.83
2119 2247 5.995282 AGGAGAAATTGTACACATTTGTCGA 59.005 36.000 20.85 0.00 37.15 4.20
2214 2343 0.242017 GCAGCGCAAGTGGAAAGATT 59.758 50.000 11.47 0.00 41.68 2.40
2215 2344 1.973138 CAGCGCAAGTGGAAAGATTG 58.027 50.000 11.47 0.00 41.68 2.67
2257 2387 1.973281 CCTTGGCCGATGTTGCAGT 60.973 57.895 0.00 0.00 0.00 4.40
2405 2546 4.213270 GTCATGGAAGACAATCGACAACAA 59.787 41.667 0.00 0.00 38.40 2.83
2427 2568 5.456921 ACATGACAGGTTGGGATATTTCT 57.543 39.130 0.00 0.00 0.00 2.52
2460 2601 1.895866 GCTGACCCCTACTACCACTGT 60.896 57.143 0.00 0.00 0.00 3.55
2545 2687 8.406297 GTCCTTAATCTTGTTGTTTCAGACTTT 58.594 33.333 0.00 0.00 0.00 2.66
2662 2804 3.840890 TGTCGTTCAACAAGTTTGCTT 57.159 38.095 0.00 0.00 34.82 3.91
2742 2919 4.391216 CAGCACTAGTCATGGAGAAACAAG 59.609 45.833 0.00 0.00 0.00 3.16
2846 3027 7.321153 ACGCTCAGTACAACTTAGACATTTAT 58.679 34.615 0.00 0.00 0.00 1.40
3113 3301 2.153913 CGGGAAGCTTCAGTTCACG 58.846 57.895 27.02 10.78 43.82 4.35
3275 3470 9.822185 GCCAAAACTAAATCAAAAGGATATCAT 57.178 29.630 4.83 0.00 34.28 2.45
3409 3607 6.906659 AGCACAATTGAAATCTCAGTACAAG 58.093 36.000 13.59 0.00 31.69 3.16
3539 3744 3.996150 ACAAACAACAGAAGCATCAGG 57.004 42.857 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 274 1.000359 GTGGGTTGGGGGATTGAGG 60.000 63.158 0.00 0.00 0.00 3.86
336 350 2.191641 GGCCTGACTGATCCTGCC 59.808 66.667 0.00 0.00 34.47 4.85
579 623 7.660617 TCCGTGTGGATGTTAAGTATTGTTTTA 59.339 33.333 0.00 0.00 40.17 1.52
638 687 2.236893 GGGTGGTGATGATGGCATTTTT 59.763 45.455 0.00 0.00 34.11 1.94
686 735 8.067751 AGTCTTGTCAAGCTGTACTTATGATA 57.932 34.615 7.78 0.00 36.04 2.15
727 776 2.034179 CCGTCCAAGTCAAAGGGTTTTC 59.966 50.000 0.00 0.00 0.00 2.29
907 971 2.054021 TGGTGGTTCTGTGAATGAGGA 58.946 47.619 0.00 0.00 0.00 3.71
1164 1231 1.444553 CTCGTCGGTCTTGTCTGGC 60.445 63.158 0.00 0.00 0.00 4.85
1242 1309 1.443872 GTCGCAGGTGTACTCCACG 60.444 63.158 16.03 17.22 45.52 4.94
1255 1322 1.067060 CTATGGAGGTTCATCGTCGCA 59.933 52.381 0.00 0.00 32.41 5.10
1293 1360 0.387929 AGAGTTCCTCGACGCACAAA 59.612 50.000 0.00 0.00 35.36 2.83
1360 1428 9.419297 GTACTAGTACAACAGATGAATGAACAA 57.581 33.333 25.02 0.00 36.15 2.83
1394 1462 9.157104 TGGGAAACAAGTTTAATGAAGTTTTTC 57.843 29.630 0.00 0.00 33.20 2.29
1836 1941 4.344679 TGCTTCACCAAATTCTTCACCAAT 59.655 37.500 0.00 0.00 0.00 3.16
2119 2247 4.082026 GCTTGTCACCTCCAATGCTAAAAT 60.082 41.667 0.00 0.00 0.00 1.82
2214 2343 5.048504 AGTCGTAGTATTTGTCGGTCTTTCA 60.049 40.000 0.00 0.00 0.00 2.69
2215 2344 5.397326 AGTCGTAGTATTTGTCGGTCTTTC 58.603 41.667 0.00 0.00 0.00 2.62
2257 2387 0.251916 CCGCTGTAGAATGGGTGGAA 59.748 55.000 0.00 0.00 0.00 3.53
2405 2546 5.456921 AGAAATATCCCAACCTGTCATGT 57.543 39.130 0.00 0.00 0.00 3.21
2545 2687 6.913673 GGTTCAACATAACGAAAGCAAACTAA 59.086 34.615 0.00 0.00 0.00 2.24
2662 2804 4.151121 TCAACTTCAAATGATGGGAAGCA 58.849 39.130 6.33 0.00 41.26 3.91
2742 2919 8.984891 TTTGTGAAAATATCCATGTGTGATTC 57.015 30.769 0.00 0.00 0.00 2.52
2846 3027 9.470399 TGATTTCTTAGTGTGATAGTACTACCA 57.530 33.333 4.31 0.00 0.00 3.25
2915 3096 6.665992 TGTTAGTAGTGAATGTTGTCCTCT 57.334 37.500 0.00 0.00 0.00 3.69
3083 3271 5.562635 TGAAGCTTCCCGTTCCTTTTTATA 58.437 37.500 23.42 0.00 0.00 0.98
3113 3301 8.564574 TCTTAGTGTGTCAATGTTTTATGGAAC 58.435 33.333 0.00 0.00 0.00 3.62
3178 3370 7.817641 TGATCATAGTACTTGCCTTATAGACG 58.182 38.462 0.00 0.00 0.00 4.18
3275 3470 6.537453 TGTGATTTTTCTCCTTGGTCAAAA 57.463 33.333 0.00 0.00 0.00 2.44
3409 3607 8.638685 TCATAGCACTTACCGAATAAACTAAC 57.361 34.615 0.00 0.00 0.00 2.34
3539 3744 6.743575 AATTACTTCACTAGTCAATGTGGC 57.256 37.500 0.00 0.00 38.33 5.01
3645 3857 8.020244 GCCAAATTTTTGTTTGAACTTCTTCAA 58.980 29.630 2.63 0.00 40.64 2.69
3646 3858 7.390162 AGCCAAATTTTTGTTTGAACTTCTTCA 59.610 29.630 2.63 0.00 40.64 3.02
3647 3859 7.751732 AGCCAAATTTTTGTTTGAACTTCTTC 58.248 30.769 2.63 0.00 40.64 2.87
3648 3860 7.607607 AGAGCCAAATTTTTGTTTGAACTTCTT 59.392 29.630 2.63 0.00 40.64 2.52
3649 3861 7.105588 AGAGCCAAATTTTTGTTTGAACTTCT 58.894 30.769 2.63 0.00 40.64 2.85
3650 3862 7.064490 TGAGAGCCAAATTTTTGTTTGAACTTC 59.936 33.333 2.63 0.00 40.64 3.01
3651 3863 6.878389 TGAGAGCCAAATTTTTGTTTGAACTT 59.122 30.769 2.63 0.00 40.64 2.66


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

AutoCloner maintained by Alex Coulton.