Multiple sequence alignment - TraesCS5D01G102900

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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 TraesCS5D01G102900 chr5D 100.000 5162 0 0 1 5162 116175946 116170785 0.000000e+00 9533
1 TraesCS5D01G102900 chr5A 95.885 5030 154 24 158 5162 123713704 123708703 0.000000e+00 8093
2 TraesCS5D01G102900 chr5A 87.742 155 14 4 1 150 123713899 123713745 5.310000e-40 176
3 TraesCS5D01G102900 chr5B 95.498 4909 172 23 158 5028 128219946 128215049 0.000000e+00 7795
4 TraesCS5D01G102900 chr5B 88.660 97 5 5 5068 5162 128215051 128214959 4.220000e-21 113
5 TraesCS5D01G102900 chr4B 80.124 322 49 8 3156 3476 53449626 53449319 5.200000e-55 226
6 TraesCS5D01G102900 chr4B 79.385 325 49 10 3156 3476 53474643 53474333 4.050000e-51 213
7 TraesCS5D01G102900 chr4B 83.628 226 37 0 1436 1661 195464293 195464068 4.050000e-51 213
8 TraesCS5D01G102900 chr4B 83.621 116 19 0 2574 2689 195463262 195463147 5.460000e-20 110
9 TraesCS5D01G102900 chr4D 83.628 226 37 0 1436 1661 136187128 136186903 4.050000e-51 213
10 TraesCS5D01G102900 chr4D 83.621 116 19 0 2574 2689 136186098 136185983 5.460000e-20 110
11 TraesCS5D01G102900 chr4A 83.628 226 37 0 1436 1661 423155672 423155897 4.050000e-51 213
12 TraesCS5D01G102900 chr4A 73.858 394 83 16 2574 2960 423156566 423156946 6.970000e-29 139


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 TraesCS5D01G102900 chr5D 116170785 116175946 5161 True 9533.0 9533 100.0000 1 5162 1 chr5D.!!$R1 5161
1 TraesCS5D01G102900 chr5A 123708703 123713899 5196 True 4134.5 8093 91.8135 1 5162 2 chr5A.!!$R1 5161
2 TraesCS5D01G102900 chr5B 128214959 128219946 4987 True 3954.0 7795 92.0790 158 5162 2 chr5B.!!$R1 5004

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
293 332 0.107654 ACCGCCTTGTTCCTATCTGC 60.108 55.0 0.00 0.00 0.00 4.26 F
478 520 0.179150 AAGATCGAGCGCTGACACTC 60.179 55.0 18.48 7.68 0.00 3.51 F
907 986 0.536006 AGCAGCTTGCCTTCGTCTTT 60.536 50.0 0.00 0.00 46.52 2.52 F
2208 2295 0.756442 ACAAATGGGCATCGGATGGG 60.756 55.0 18.96 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1185 1.153745 GCCGTGCAACAACCAAACA 60.154 52.632 0.00 0.0 35.74 2.83 R
1780 1861 2.251371 GTGTGGAACGAAAGCGGC 59.749 61.111 0.00 0.0 42.39 6.53 R
2789 2877 0.527817 CTGGCCGTCTACGATTCCAC 60.528 60.000 3.65 0.0 43.02 4.02 R
4334 4424 0.539438 ATCAAGGACGCCAGCCAAAA 60.539 50.000 0.00 0.0 0.00 2.44 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 6.211986 ACATCCATGCATATTTTAGGGATTGG 59.788 38.462 9.20 0.00 31.59 3.16
47 48 8.428852 GCATATTTTAGGGATTGGGTTGTAATT 58.571 33.333 0.00 0.00 0.00 1.40
56 57 9.382307 AGGGATTGGGTTGTAATTTTAAGTTTA 57.618 29.630 0.00 0.00 0.00 2.01
107 108 3.166657 CGCTTTGACTTAATGCAGCTTC 58.833 45.455 0.00 0.00 38.87 3.86
108 109 3.505836 GCTTTGACTTAATGCAGCTTCC 58.494 45.455 0.00 0.00 38.80 3.46
109 110 3.192212 GCTTTGACTTAATGCAGCTTCCT 59.808 43.478 0.00 0.00 38.80 3.36
122 126 0.612174 GCTTCCTTTGGGACCCTTCC 60.612 60.000 13.00 0.00 42.05 3.46
124 128 1.146982 CTTCCTTTGGGACCCTTCCAA 59.853 52.381 13.00 0.00 44.98 3.53
130 134 2.785357 TGGGACCCTTCCAATTGTTT 57.215 45.000 13.00 0.00 44.98 2.83
132 136 3.773560 TGGGACCCTTCCAATTGTTTAG 58.226 45.455 13.00 0.00 44.98 1.85
240 279 9.076596 GTAGTTTATTATTTAGGACGACGTTGT 57.923 33.333 8.55 8.55 0.00 3.32
248 287 0.949105 GGACGACGTTGTGGCAAGAT 60.949 55.000 14.59 0.00 0.00 2.40
291 330 2.711542 CAAACCGCCTTGTTCCTATCT 58.288 47.619 0.00 0.00 0.00 1.98
293 332 0.107654 ACCGCCTTGTTCCTATCTGC 60.108 55.000 0.00 0.00 0.00 4.26
306 345 4.104086 TCCTATCTGCCTTTCTTTCTCCA 58.896 43.478 0.00 0.00 0.00 3.86
424 466 1.026584 TTCGTCAGACCTTGTCGTCA 58.973 50.000 0.00 0.00 39.02 4.35
439 481 1.822371 TCGTCAACCTCATCCGATGAA 59.178 47.619 12.16 0.00 39.11 2.57
441 483 2.673893 CGTCAACCTCATCCGATGAACA 60.674 50.000 12.16 0.00 39.11 3.18
478 520 0.179150 AAGATCGAGCGCTGACACTC 60.179 55.000 18.48 7.68 0.00 3.51
552 594 2.004583 TTAAAGAGCATGTCGTCGGG 57.995 50.000 0.00 0.00 0.00 5.14
608 668 1.893808 CACCACCGCCATATGAGCC 60.894 63.158 3.65 0.00 0.00 4.70
702 763 6.714810 TCCCAAGCGTAGATTTTGCATAATAT 59.285 34.615 2.12 2.39 27.80 1.28
803 864 3.750130 TCATCAAAACTTCAGCTCTGCTC 59.250 43.478 0.00 0.00 36.40 4.26
819 898 1.219124 CTCGGGCTGCTGCTTCTTA 59.781 57.895 15.64 0.00 39.59 2.10
907 986 0.536006 AGCAGCTTGCCTTCGTCTTT 60.536 50.000 0.00 0.00 46.52 2.52
1079 1159 2.815647 CCGCGAAGGTGCTCTTCC 60.816 66.667 8.23 6.73 46.93 3.46
1105 1185 1.282157 CTTCCTTCCCGGATTGGTTCT 59.718 52.381 0.73 0.00 42.70 3.01
1780 1861 2.882761 CAGGATTGATGTGGCATACCTG 59.117 50.000 3.96 3.96 36.19 4.00
1885 1971 4.443063 GTGGGTTTATTTGTCGCTTTCAAC 59.557 41.667 0.00 0.00 0.00 3.18
1984 2070 5.300792 TGGTGAAAGATGTTTAGTTGGAACC 59.699 40.000 0.00 0.00 0.00 3.62
2033 2119 8.686334 GGTCATATGTGATGTTTACCTTGAAAT 58.314 33.333 1.90 0.00 36.60 2.17
2083 2169 6.449635 TTTTGGTCTTGCGCATATTTAGAT 57.550 33.333 12.75 0.00 0.00 1.98
2084 2170 5.673337 TTGGTCTTGCGCATATTTAGATC 57.327 39.130 12.75 11.99 0.00 2.75
2208 2295 0.756442 ACAAATGGGCATCGGATGGG 60.756 55.000 18.96 0.00 0.00 4.00
2370 2457 1.939974 CACATCACGGAATGGACGAT 58.060 50.000 0.00 0.00 34.93 3.73
2386 2473 4.272504 TGGACGATGTCTTGTTGAGTTTTC 59.727 41.667 0.00 0.00 32.47 2.29
2969 3057 5.252547 TGTGTATTGCAGGTATGTTGACAT 58.747 37.500 1.84 1.84 40.22 3.06
3075 3164 3.547868 CGTAATGTCACAATCGAGACTGG 59.452 47.826 4.43 0.00 34.21 4.00
3149 3238 7.158697 TCATGTGCTGCTACTTTAGTAAAAGA 58.841 34.615 0.00 0.00 44.14 2.52
3151 3240 6.522054 TGTGCTGCTACTTTAGTAAAAGACT 58.478 36.000 0.00 0.00 44.14 3.24
3152 3241 6.990349 TGTGCTGCTACTTTAGTAAAAGACTT 59.010 34.615 0.00 0.00 44.14 3.01
3320 3409 8.265764 CCAGGAGCTAGTAAAAATAACCTACTT 58.734 37.037 0.00 0.00 0.00 2.24
4254 4343 1.227102 CATCGCCATCTTTCCCCCA 59.773 57.895 0.00 0.00 0.00 4.96
4255 4344 0.395586 CATCGCCATCTTTCCCCCAA 60.396 55.000 0.00 0.00 0.00 4.12
4334 4424 7.340232 TCAGCTTTGAGGCTCATAATACAAAAT 59.660 33.333 19.50 0.00 41.00 1.82
4642 4733 9.194972 TGGCTGTCAAATAAATTGGTATCAATA 57.805 29.630 0.58 0.00 42.29 1.90
4743 4834 3.123116 CGCAAGCTCATACTATCATGCTG 59.877 47.826 0.00 0.00 0.00 4.41
4923 5014 1.465689 CGCCTTTGCCAAGATTGTACG 60.466 52.381 0.00 0.00 30.57 3.67
4925 5016 1.539388 CCTTTGCCAAGATTGTACGCA 59.461 47.619 0.00 0.00 30.57 5.24
5091 5182 5.615925 ACAAGACAGTAGAAGGTTCTGTT 57.384 39.130 2.32 0.00 41.58 3.16
5096 5189 8.889717 CAAGACAGTAGAAGGTTCTGTTAAAAA 58.110 33.333 2.32 0.00 41.58 1.94
5144 5237 2.695147 CCTGGTTGGTTCAGAAAAAGCT 59.305 45.455 9.36 0.00 34.36 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.597637 GCATGGATGTCCGTAGACCG 60.598 60.000 0.00 0.00 42.81 4.79
13 14 6.211986 CCAATCCCTAAAATATGCATGGATGT 59.788 38.462 10.16 0.00 31.75 3.06
14 15 6.351541 CCCAATCCCTAAAATATGCATGGATG 60.352 42.308 10.16 6.07 31.75 3.51
15 16 5.722923 CCCAATCCCTAAAATATGCATGGAT 59.277 40.000 10.16 8.05 32.67 3.41
38 39 8.017373 GGACTCGGTAAACTTAAAATTACAACC 58.983 37.037 10.53 0.00 34.44 3.77
47 48 6.822676 TCACAAAAGGACTCGGTAAACTTAAA 59.177 34.615 0.00 0.00 0.00 1.52
52 53 4.374399 TCTCACAAAAGGACTCGGTAAAC 58.626 43.478 0.00 0.00 0.00 2.01
56 57 2.368875 ACATCTCACAAAAGGACTCGGT 59.631 45.455 0.00 0.00 0.00 4.69
69 70 2.611518 AGCGCTGAAAGTACATCTCAC 58.388 47.619 10.39 0.00 35.30 3.51
107 108 1.901833 CAATTGGAAGGGTCCCAAAGG 59.098 52.381 11.55 0.00 45.67 3.11
108 109 2.608623 ACAATTGGAAGGGTCCCAAAG 58.391 47.619 11.55 0.00 45.67 2.77
109 110 2.785357 ACAATTGGAAGGGTCCCAAA 57.215 45.000 11.55 0.00 45.67 3.28
147 151 9.976255 CGAGATAGAACTAACACTGCTATATAC 57.024 37.037 0.00 0.00 0.00 1.47
149 153 8.850007 TCGAGATAGAACTAACACTGCTATAT 57.150 34.615 0.00 0.00 0.00 0.86
152 156 5.007823 GCTCGAGATAGAACTAACACTGCTA 59.992 44.000 18.75 0.00 0.00 3.49
153 157 4.201970 GCTCGAGATAGAACTAACACTGCT 60.202 45.833 18.75 0.00 0.00 4.24
154 158 4.039032 GCTCGAGATAGAACTAACACTGC 58.961 47.826 18.75 0.00 0.00 4.40
166 205 5.048434 TCCTGTCACATAATGCTCGAGATAG 60.048 44.000 18.75 0.00 0.00 2.08
169 208 3.023832 TCCTGTCACATAATGCTCGAGA 58.976 45.455 18.75 1.31 0.00 4.04
235 274 0.734889 GGGATCATCTTGCCACAACG 59.265 55.000 0.00 0.00 0.00 4.10
240 279 0.396139 GCCAAGGGATCATCTTGCCA 60.396 55.000 17.50 0.00 40.00 4.92
248 287 2.203056 CGATGCGCCAAGGGATCA 60.203 61.111 4.18 0.00 0.00 2.92
291 330 4.019174 GGATTGATGGAGAAAGAAAGGCA 58.981 43.478 0.00 0.00 0.00 4.75
293 332 4.864726 AGGGATTGATGGAGAAAGAAAGG 58.135 43.478 0.00 0.00 0.00 3.11
424 466 3.535561 GTGATGTTCATCGGATGAGGTT 58.464 45.455 19.15 9.06 40.94 3.50
455 497 1.226802 TCAGCGCTCGATCTTGCTC 60.227 57.895 7.13 0.00 34.99 4.26
459 501 0.179150 GAGTGTCAGCGCTCGATCTT 60.179 55.000 7.13 0.00 41.62 2.40
478 520 1.261354 CTCTCGAGCTCAGAGACGATG 59.739 57.143 26.28 16.78 40.02 3.84
590 650 1.893808 GGCTCATATGGCGGTGGTG 60.894 63.158 2.13 0.00 0.00 4.17
597 657 2.670934 CCAGCGGGCTCATATGGC 60.671 66.667 2.13 5.30 0.00 4.40
608 668 2.047844 CTGACCAGTGACCAGCGG 60.048 66.667 0.00 0.00 0.00 5.52
656 716 4.571148 GGACTAGAAGAAAGAGGGAGGAGT 60.571 50.000 0.00 0.00 0.00 3.85
661 721 3.847042 TGGGACTAGAAGAAAGAGGGA 57.153 47.619 0.00 0.00 0.00 4.20
662 722 3.369997 GCTTGGGACTAGAAGAAAGAGGG 60.370 52.174 0.00 0.00 0.00 4.30
702 763 7.982761 AGGCATGAAAGAAAAATGCATAAAA 57.017 28.000 0.00 0.00 46.78 1.52
755 816 3.561725 GGTATGATACAGCTTGGCTTGTC 59.438 47.826 4.83 0.00 36.40 3.18
803 864 0.659957 GAATAAGAAGCAGCAGCCCG 59.340 55.000 0.00 0.00 43.56 6.13
819 898 3.111484 GGTGGGGAGAGAGAAGAAGAAT 58.889 50.000 0.00 0.00 0.00 2.40
1105 1185 1.153745 GCCGTGCAACAACCAAACA 60.154 52.632 0.00 0.00 35.74 2.83
1780 1861 2.251371 GTGTGGAACGAAAGCGGC 59.749 61.111 0.00 0.00 42.39 6.53
1885 1971 7.119699 TCCTAACAGTTCTCAATGTTAATGCAG 59.880 37.037 0.00 0.00 40.38 4.41
2370 2457 8.255206 TGTAGTAGAAGAAAACTCAACAAGACA 58.745 33.333 0.00 0.00 0.00 3.41
2777 2865 2.635915 ACGATTCCACTGTTCCCTGTAA 59.364 45.455 0.00 0.00 0.00 2.41
2789 2877 0.527817 CTGGCCGTCTACGATTCCAC 60.528 60.000 3.65 0.00 43.02 4.02
4334 4424 0.539438 ATCAAGGACGCCAGCCAAAA 60.539 50.000 0.00 0.00 0.00 2.44
4642 4733 0.186630 AAAACCGGCCTAACAACCCT 59.813 50.000 0.00 0.00 0.00 4.34
4743 4834 2.049627 TTGCACAAATGGCAACCCCC 62.050 55.000 0.00 0.00 45.57 5.40
4923 5014 1.187567 ATTGCCCTTGTTCCCAGTGC 61.188 55.000 0.00 0.00 0.00 4.40
4925 5016 0.482446 TGATTGCCCTTGTTCCCAGT 59.518 50.000 0.00 0.00 0.00 4.00
5144 5237 2.435663 CACCACATGGCCACCTCA 59.564 61.111 8.16 0.00 39.32 3.86


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

AutoCloner maintained by Alex Coulton.