Multiple sequence alignment - TraesCS4D01G172400

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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 TraesCS4D01G172400 chr4D 100.000 7526 0 0 1 7526 299778747 299771222 0.000000e+00 13899
1 TraesCS4D01G172400 chr4B 98.027 7551 106 22 1 7526 372909606 372902074 0.000000e+00 13079
2 TraesCS4D01G172400 chr4A 97.255 7468 109 29 1 7444 183969612 183977007 0.000000e+00 12567
3 TraesCS4D01G172400 chr4A 79.463 969 133 26 5133 6058 94765911 94766856 1.780000e-175 627
4 TraesCS4D01G172400 chr5D 79.799 995 134 29 5130 6082 435152511 435153480 0.000000e+00 662
5 TraesCS4D01G172400 chr5D 77.007 735 104 31 5386 6082 159613325 159612618 2.000000e-95 361
6 TraesCS4D01G172400 chr6D 79.617 991 137 29 5133 6082 161151665 161152631 0.000000e+00 651
7 TraesCS4D01G172400 chr7A 79.293 990 133 34 5133 6080 8739568 8740527 1.780000e-175 627
8 TraesCS4D01G172400 chr6A 78.741 969 140 27 5133 6058 77892857 77893802 8.410000e-164 588
9 TraesCS4D01G172400 chr5A 78.463 989 146 28 5133 6080 154491835 154490873 1.090000e-162 584
10 TraesCS4D01G172400 chr3A 83.333 444 46 13 5512 5935 725058453 725058888 1.180000e-102 385
11 TraesCS4D01G172400 chrUn 83.108 444 47 13 5512 5935 45785436 45785871 5.510000e-101 379
12 TraesCS4D01G172400 chr3D 83.108 444 47 13 5512 5935 594480526 594480961 5.510000e-101 379


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 TraesCS4D01G172400 chr4D 299771222 299778747 7525 True 13899 13899 100.000 1 7526 1 chr4D.!!$R1 7525
1 TraesCS4D01G172400 chr4B 372902074 372909606 7532 True 13079 13079 98.027 1 7526 1 chr4B.!!$R1 7525
2 TraesCS4D01G172400 chr4A 183969612 183977007 7395 False 12567 12567 97.255 1 7444 1 chr4A.!!$F2 7443
3 TraesCS4D01G172400 chr4A 94765911 94766856 945 False 627 627 79.463 5133 6058 1 chr4A.!!$F1 925
4 TraesCS4D01G172400 chr5D 435152511 435153480 969 False 662 662 79.799 5130 6082 1 chr5D.!!$F1 952
5 TraesCS4D01G172400 chr5D 159612618 159613325 707 True 361 361 77.007 5386 6082 1 chr5D.!!$R1 696
6 TraesCS4D01G172400 chr6D 161151665 161152631 966 False 651 651 79.617 5133 6082 1 chr6D.!!$F1 949
7 TraesCS4D01G172400 chr7A 8739568 8740527 959 False 627 627 79.293 5133 6080 1 chr7A.!!$F1 947
8 TraesCS4D01G172400 chr6A 77892857 77893802 945 False 588 588 78.741 5133 6058 1 chr6A.!!$F1 925
9 TraesCS4D01G172400 chr5A 154490873 154491835 962 True 584 584 78.463 5133 6080 1 chr5A.!!$R1 947

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
148 154 0.107410 GAGTTCCCACACCACACACA 60.107 55.000 0.00 0.0 0.00 3.72 F
580 587 0.389948 CTAGCTCCGCGACCAAAGTT 60.390 55.000 8.23 0.0 0.00 2.66 F
1477 1494 2.620585 GAGCATGACCCAAGGCTAATTC 59.379 50.000 0.00 0.0 36.59 2.17 F
2586 2603 2.151202 GGTTCAAGATTTCAGTGCCGA 58.849 47.619 0.00 0.0 0.00 5.54 F
3825 3842 3.266772 TCAGTGAATGGCAGGAAAGGTAT 59.733 43.478 0.00 0.0 0.00 2.73 F
4528 4545 0.828762 ACACACCATGGCTGCACATT 60.829 50.000 13.04 0.0 0.00 2.71 F
5164 5184 2.151202 ACAATAACAAGCACCCAGTCG 58.849 47.619 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1846 1.544246 GAATTTTGACAACCTCCCCCG 59.456 52.381 0.00 0.00 0.00 5.73 R
2160 2177 0.325577 TCTCCTGGCCAGCATAGACA 60.326 55.000 28.39 3.80 0.00 3.41 R
3825 3842 1.644509 TGGAGGTGCTAGCTTCTTCA 58.355 50.000 17.23 14.56 0.00 3.02 R
3882 3899 2.996621 AGTCAAATCGCACTCTACAAGC 59.003 45.455 0.00 0.00 0.00 4.01 R
5068 5087 1.018910 CAATGCACGAGATGATGGCA 58.981 50.000 0.00 0.00 39.03 4.92 R
5931 6014 3.835478 AGCCCTGCCTCATATAGTCTA 57.165 47.619 0.00 0.00 0.00 2.59 R
7044 7135 2.609747 TCAGCCTCTTCTACAACCAGT 58.390 47.619 0.00 0.00 0.00 4.00 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
33 34 1.608336 CCTCCACCCGTCTACCACA 60.608 63.158 0.00 0.00 0.00 4.17
82 86 0.539438 CTCCTCTCCTCCCCGATCTG 60.539 65.000 0.00 0.00 0.00 2.90
83 87 2.206536 CCTCTCCTCCCCGATCTGC 61.207 68.421 0.00 0.00 0.00 4.26
84 88 1.456518 CTCTCCTCCCCGATCTGCA 60.457 63.158 0.00 0.00 0.00 4.41
148 154 0.107410 GAGTTCCCACACCACACACA 60.107 55.000 0.00 0.00 0.00 3.72
580 587 0.389948 CTAGCTCCGCGACCAAAGTT 60.390 55.000 8.23 0.00 0.00 2.66
811 823 7.811236 TCACAAAATCATGAGCTGAGAAAAATC 59.189 33.333 0.09 0.00 37.28 2.17
1381 1398 3.434739 GGTCGGAGTAGTATCTTCCTCCA 60.435 52.174 0.00 0.00 43.00 3.86
1477 1494 2.620585 GAGCATGACCCAAGGCTAATTC 59.379 50.000 0.00 0.00 36.59 2.17
1493 1510 4.516698 GCTAATTCACATCAATGATCCCGT 59.483 41.667 0.00 0.00 0.00 5.28
2160 2177 2.704065 AGAATGGATTATCGGGGTCGTT 59.296 45.455 0.00 0.00 37.69 3.85
2229 2246 2.413765 CCGTTCAAAGAGCAGCAATCTG 60.414 50.000 0.00 0.00 43.16 2.90
2586 2603 2.151202 GGTTCAAGATTTCAGTGCCGA 58.849 47.619 0.00 0.00 0.00 5.54
3825 3842 3.266772 TCAGTGAATGGCAGGAAAGGTAT 59.733 43.478 0.00 0.00 0.00 2.73
4347 4364 7.293073 AGTTAGCACTGATAATTGATGGGAAT 58.707 34.615 0.00 0.00 0.00 3.01
4456 4473 6.696411 TCTTTGTGTTCTGTTTCAATTGGTT 58.304 32.000 5.42 0.00 0.00 3.67
4528 4545 0.828762 ACACACCATGGCTGCACATT 60.829 50.000 13.04 0.00 0.00 2.71
4569 4587 6.862209 ACGTACAAAATACCGGTCATACTTA 58.138 36.000 12.40 0.00 0.00 2.24
4765 4783 7.729116 TCTGTATCTGATTCATGTTGCTATGA 58.271 34.615 0.00 0.00 35.38 2.15
4789 4807 9.573133 TGATGTTAGTGAGCATATCGTATATTG 57.427 33.333 0.00 0.00 0.00 1.90
4819 4837 8.259411 TCTTCCTTACGTATTAATTGGCTTGTA 58.741 33.333 0.00 0.00 0.00 2.41
5037 5055 6.071447 TGCACCTACGTTTTGTATCTTAGGTA 60.071 38.462 0.00 0.00 36.91 3.08
5164 5184 2.151202 ACAATAACAAGCACCCAGTCG 58.849 47.619 0.00 0.00 0.00 4.18
5190 5210 6.594788 TTAACCCGACAATTAGTACAGAGT 57.405 37.500 0.00 0.00 0.00 3.24
6717 6807 6.183360 GCATTACTTAACTGCAGTCGTTATGT 60.183 38.462 26.04 21.48 38.21 2.29
6858 6948 8.827677 GCTATTCGACAACTATTTCCAGTATTT 58.172 33.333 0.00 0.00 0.00 1.40
7044 7135 6.166279 CACAAGTTAGCAAGGACAAGAGATA 58.834 40.000 0.00 0.00 0.00 1.98
7349 7443 6.228995 GTTGAGGTTTTAGGTAGCTTAGTGT 58.771 40.000 0.00 0.00 0.00 3.55
7360 7454 3.113260 AGCTTAGTGTTGTGTCTGGTC 57.887 47.619 0.00 0.00 0.00 4.02
7401 7495 8.736097 AAAAGGGTACAGGATAAATTTTCCTT 57.264 30.769 15.22 11.13 41.78 3.36
7404 7498 6.890268 AGGGTACAGGATAAATTTTCCTTGTC 59.110 38.462 15.22 10.13 41.78 3.18
7418 7512 6.433847 TTTCCTTGTCAGATCCAGAACTTA 57.566 37.500 0.00 0.00 0.00 2.24
7422 7516 6.071108 TCCTTGTCAGATCCAGAACTTAAGAG 60.071 42.308 10.09 0.00 0.00 2.85
7471 7565 2.372172 ACAAGTCCTACAAAGGGTGGAG 59.628 50.000 0.00 0.00 43.84 3.86
7515 7611 4.159506 GTGGTTTATTGCTGAATTGCCCTA 59.840 41.667 0.00 0.00 0.00 3.53
7518 7614 4.630894 TTATTGCTGAATTGCCCTAACG 57.369 40.909 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 154 4.779733 ATGGAGGAGACGGCGGGT 62.780 66.667 13.24 0.00 0.00 5.28
280 286 4.508128 TTCCGCGGATCTGACGGC 62.508 66.667 31.56 7.55 46.49 5.68
282 288 2.956964 GCTTCCGCGGATCTGACG 60.957 66.667 31.56 13.93 0.00 4.35
488 495 0.665835 AAACAATCAACGCCGCTTCA 59.334 45.000 0.00 0.00 0.00 3.02
580 587 6.762187 TCAACAACTAATACGAAACAGACCAA 59.238 34.615 0.00 0.00 0.00 3.67
685 692 3.755378 AGCTTGACTTGAATGCAGGTAAG 59.245 43.478 0.00 0.00 34.10 2.34
811 823 4.967036 AGAAAAGAGAGAGTTGGAGTTGG 58.033 43.478 0.00 0.00 0.00 3.77
1381 1398 2.554564 GGGGTCGATTTGGTTTCTCCTT 60.555 50.000 0.00 0.00 37.07 3.36
1477 1494 3.183793 TCTGACGGGATCATTGATGTG 57.816 47.619 3.32 0.00 36.48 3.21
1493 1510 4.443913 TCATATCGGTCGTTTGTTCTGA 57.556 40.909 0.00 0.00 0.00 3.27
1829 1846 1.544246 GAATTTTGACAACCTCCCCCG 59.456 52.381 0.00 0.00 0.00 5.73
2160 2177 0.325577 TCTCCTGGCCAGCATAGACA 60.326 55.000 28.39 3.80 0.00 3.41
2229 2246 4.553330 TTCCCTGTTCATGTAACTCTCC 57.447 45.455 0.00 0.00 38.99 3.71
3825 3842 1.644509 TGGAGGTGCTAGCTTCTTCA 58.355 50.000 17.23 14.56 0.00 3.02
3882 3899 2.996621 AGTCAAATCGCACTCTACAAGC 59.003 45.455 0.00 0.00 0.00 4.01
4347 4364 9.488762 TCTTTCTCTAGAATATACACAAGGGAA 57.511 33.333 0.00 0.00 33.54 3.97
4569 4587 9.452287 AGTTGGCAAATATGAAATTATTGCTTT 57.548 25.926 0.00 0.00 42.62 3.51
4789 4807 7.924947 AGCCAATTAATACGTAAGGAAGACTAC 59.075 37.037 0.00 0.00 46.39 2.73
4802 4820 6.791303 ACCATTGTACAAGCCAATTAATACG 58.209 36.000 14.65 0.00 30.28 3.06
4967 4985 1.671979 ATCATTCGGCTGGTGATGTG 58.328 50.000 11.88 0.00 31.75 3.21
5064 5083 1.442526 GCACGAGATGATGGCAAGGG 61.443 60.000 0.00 0.00 0.00 3.95
5068 5087 1.018910 CAATGCACGAGATGATGGCA 58.981 50.000 0.00 0.00 39.03 4.92
5164 5184 4.506758 TGTACTAATTGTCGGGTTAAGCC 58.493 43.478 13.92 13.92 0.00 4.35
5190 5210 5.067544 TGCAACTGACAGAAATGATTTGTGA 59.932 36.000 20.07 0.00 37.37 3.58
5931 6014 3.835478 AGCCCTGCCTCATATAGTCTA 57.165 47.619 0.00 0.00 0.00 2.59
7044 7135 2.609747 TCAGCCTCTTCTACAACCAGT 58.390 47.619 0.00 0.00 0.00 4.00
7349 7443 3.495377 CGTAAAATTCCGACCAGACACAA 59.505 43.478 0.00 0.00 0.00 3.33
7360 7454 5.463286 ACCCTTTTAAAGCGTAAAATTCCG 58.537 37.500 0.00 0.00 0.00 4.30
7401 7495 7.487822 AATCTCTTAAGTTCTGGATCTGACA 57.512 36.000 1.63 0.00 0.00 3.58
7404 7498 8.040132 ACTCAAATCTCTTAAGTTCTGGATCTG 58.960 37.037 1.63 0.00 0.00 2.90
7499 7595 2.722094 TCGTTAGGGCAATTCAGCAAT 58.278 42.857 0.00 0.00 35.83 3.56


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

AutoCloner maintained by Alex Coulton.