Multiple sequence alignment - TraesCS1D01G259100

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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 TraesCS1D01G259100 chr1D 100.000 3471 0 0 1 3471 351544991 351541521 0.000000e+00 6410.0
1 TraesCS1D01G259100 chr1D 95.131 3163 129 9 1 3146 351917688 351914534 0.000000e+00 4964.0
2 TraesCS1D01G259100 chr1A 95.655 3452 100 16 49 3471 452455088 452451658 0.000000e+00 5498.0
3 TraesCS1D01G259100 chr1A 96.586 3163 84 9 1 3144 452296773 452293616 0.000000e+00 5221.0
4 TraesCS1D01G259100 chr1A 100.000 50 0 0 1 50 452455299 452455250 3.690000e-15 93.5
5 TraesCS1D01G259100 chr1B 94.817 3087 124 15 1 3058 474262194 474259115 0.000000e+00 4782.0
6 TraesCS1D01G259100 chr1B 91.991 437 25 2 3035 3471 474259109 474258683 3.830000e-169 604.0
7 TraesCS1D01G259100 chr3B 86.731 309 24 7 2613 2910 511819250 511818948 9.290000e-86 327.0
8 TraesCS1D01G259100 chr2B 85.437 309 30 6 2613 2910 535564910 535565214 1.210000e-79 307.0
9 TraesCS1D01G259100 chr5B 89.130 46 4 1 3134 3178 84265729 84265684 4.840000e-04 56.5


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 TraesCS1D01G259100 chr1D 351541521 351544991 3470 True 6410.00 6410 100.0000 1 3471 1 chr1D.!!$R1 3470
1 TraesCS1D01G259100 chr1D 351914534 351917688 3154 True 4964.00 4964 95.1310 1 3146 1 chr1D.!!$R2 3145
2 TraesCS1D01G259100 chr1A 452293616 452296773 3157 True 5221.00 5221 96.5860 1 3144 1 chr1A.!!$R1 3143
3 TraesCS1D01G259100 chr1A 452451658 452455299 3641 True 2795.75 5498 97.8275 1 3471 2 chr1A.!!$R2 3470
4 TraesCS1D01G259100 chr1B 474258683 474262194 3511 True 2693.00 4782 93.4040 1 3471 2 chr1B.!!$R1 3470

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
362 527 2.270205 CCTGCTCGGCATCCACTT 59.730 61.111 0.0 0.0 38.13 3.16 F
1163 1344 0.991920 ACTTGGAGGTACACATGGGG 59.008 55.000 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1944 0.179234 TCTGGTTGTCGAAGCACCAA 59.821 50.0 11.63 0.0 34.63 3.67 R
2608 2791 1.239968 CCAAGTCTGAAGCTGGCACC 61.240 60.0 0.00 0.0 0.00 5.01 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
115 279 5.600908 TGCGTAAAGATACCTCACAAAAC 57.399 39.130 0.00 0.00 0.00 2.43
362 527 2.270205 CCTGCTCGGCATCCACTT 59.730 61.111 0.00 0.00 38.13 3.16
426 607 3.917760 CGTCTCCCCAGGATCGCC 61.918 72.222 0.00 0.00 0.00 5.54
745 926 3.891366 CCTTTTCTGGGTGTTCAACAGAT 59.109 43.478 0.00 0.00 40.56 2.90
770 951 5.368145 TGCTCGCCTGATTACTATGAATTT 58.632 37.500 0.00 0.00 0.00 1.82
950 1131 7.791029 TGTGTGGCATGTTAGAGATTAATAGA 58.209 34.615 0.00 0.00 0.00 1.98
1163 1344 0.991920 ACTTGGAGGTACACATGGGG 59.008 55.000 0.00 0.00 0.00 4.96
1232 1413 2.099405 TGATAGTGCAGACGATGACCA 58.901 47.619 0.00 0.00 0.00 4.02
1425 1606 1.343465 CGTGACAGTTACAAGGTCCCT 59.657 52.381 0.00 0.00 0.00 4.20
1763 1944 4.141620 ACTGGAACTGAATTCTGACACAGT 60.142 41.667 18.13 20.39 43.92 3.55
1913 2094 9.760660 CACTTAGTGCTTATTATTTCACTGTTC 57.239 33.333 0.00 0.00 39.77 3.18
2042 2223 3.382865 TCAATCTCGGTGATCTCAAGGAG 59.617 47.826 0.00 0.00 33.57 3.69
2270 2452 3.454375 TGTCTCTTCCAGAACGTTGAAC 58.546 45.455 5.00 0.00 30.72 3.18
2279 2461 3.493503 CCAGAACGTTGAACTAGTTGGTC 59.506 47.826 14.14 6.73 0.00 4.02
2608 2791 8.969121 TGCATATATTCAATTTGGAAATAGCG 57.031 30.769 0.00 0.00 0.00 4.26
2731 2925 4.574674 TTGAGATAACATGCAAGGGAGT 57.425 40.909 0.00 0.00 0.00 3.85
2833 3039 1.833434 TACGGTTTTGGTCTTGCGCG 61.833 55.000 0.00 0.00 0.00 6.86
2891 3097 4.289410 TCTGTTTCCATGGAGAGGATCAAA 59.711 41.667 15.53 0.38 37.82 2.69
2910 3116 3.441500 AATCCAACCTCTGAAGGAACC 57.558 47.619 0.00 0.00 46.67 3.62
3013 3219 2.216898 GCAAGACACAAGCTCTGAAGT 58.783 47.619 0.00 0.00 0.00 3.01
3064 3300 6.584563 CCCATAATTTGTTGTTGAAGTTACCG 59.415 38.462 0.00 0.00 0.00 4.02
3069 3305 0.305313 TTGTTGAAGTTACCGCGTGC 59.695 50.000 4.92 0.00 0.00 5.34
3180 3417 9.740239 TCTGCGAAAACGTCTTATATTTAGTAT 57.260 29.630 0.00 0.00 0.00 2.12
3201 3438 7.061688 AGTATCAGAGGGTGTACTTTACTAGG 58.938 42.308 0.00 0.00 0.00 3.02
3205 3442 4.013050 GAGGGTGTACTTTACTAGGTCGT 58.987 47.826 0.00 0.00 0.00 4.34
3207 3444 3.505836 GGTGTACTTTACTAGGTCGTGC 58.494 50.000 0.00 0.00 0.00 5.34
3220 3457 1.332904 GGTCGTGCTCGTTCTGTTTTG 60.333 52.381 8.17 0.00 38.33 2.44
3228 3465 3.786048 GCTCGTTCTGTTTTGAACTGTTG 59.214 43.478 0.00 0.00 42.82 3.33
3229 3466 3.753842 TCGTTCTGTTTTGAACTGTTGC 58.246 40.909 0.00 0.00 42.82 4.17
3314 3551 4.458295 TGGGTCGTACTAGAAGTTCTTCAG 59.542 45.833 11.40 5.91 0.00 3.02
3315 3552 4.458642 GGGTCGTACTAGAAGTTCTTCAGT 59.541 45.833 11.40 11.75 0.00 3.41
3316 3553 5.391843 GGGTCGTACTAGAAGTTCTTCAGTC 60.392 48.000 11.40 3.60 0.00 3.51
3317 3554 5.412286 GGTCGTACTAGAAGTTCTTCAGTCT 59.588 44.000 11.40 0.00 0.00 3.24
3318 3555 6.402442 GGTCGTACTAGAAGTTCTTCAGTCTC 60.402 46.154 11.40 5.93 0.00 3.36
3319 3556 6.369615 GTCGTACTAGAAGTTCTTCAGTCTCT 59.630 42.308 11.40 0.00 0.00 3.10
3320 3557 6.935771 TCGTACTAGAAGTTCTTCAGTCTCTT 59.064 38.462 11.40 0.00 0.00 2.85
3321 3558 7.118101 TCGTACTAGAAGTTCTTCAGTCTCTTC 59.882 40.741 11.40 0.00 35.98 2.87
3322 3559 7.095144 CGTACTAGAAGTTCTTCAGTCTCTTCA 60.095 40.741 11.40 0.00 37.53 3.02
3335 3572 2.028930 GTCTCTTCAGTCGGGTGTCATT 60.029 50.000 0.00 0.00 0.00 2.57
3378 3615 0.735978 TGACTCTGCGGTAATGTGCG 60.736 55.000 0.00 0.00 0.00 5.34
3389 3626 1.659098 GTAATGTGCGAAAGGAGGACG 59.341 52.381 0.00 0.00 32.37 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
745 926 5.722021 TTCATAGTAATCAGGCGAGCATA 57.278 39.130 0.00 0.00 0.00 3.14
770 951 6.716173 TGAGAAATTTCACATCTCCACATGAA 59.284 34.615 19.99 0.00 39.04 2.57
858 1039 3.505480 ATTGGATGCATTCCTCCTCTC 57.495 47.619 1.51 0.00 45.68 3.20
1163 1344 4.712763 GAACATCAGTTCGGTCATTGAAC 58.287 43.478 0.00 0.00 44.11 3.18
1232 1413 9.950496 ACATATCAGTGAACTTAAGAAATCTGT 57.050 29.630 10.09 1.22 0.00 3.41
1663 1844 5.070313 AGCCTTCAATTTTTAGCACCTTGAA 59.930 36.000 0.00 0.00 35.29 2.69
1763 1944 0.179234 TCTGGTTGTCGAAGCACCAA 59.821 50.000 11.63 0.00 34.63 3.67
1888 2069 8.947115 GGAACAGTGAAATAATAAGCACTAAGT 58.053 33.333 0.00 0.00 39.40 2.24
1913 2094 3.328535 AGGCCCCCAAACATAATAAGG 57.671 47.619 0.00 0.00 0.00 2.69
2279 2461 2.028930 AGGAGCCAGTAAAGTCGAACAG 60.029 50.000 0.00 0.00 0.00 3.16
2608 2791 1.239968 CCAAGTCTGAAGCTGGCACC 61.240 60.000 0.00 0.00 0.00 5.01
2687 2881 5.500645 AGTCAACTAAAGGCAAACTGAAC 57.499 39.130 0.00 0.00 0.00 3.18
2731 2925 4.754618 ACAAACACGTTCATGCTCAGAATA 59.245 37.500 0.00 0.00 0.00 1.75
2791 2997 9.569167 CGTAGTCATAATTCTGAACTGAAGTAA 57.431 33.333 0.00 0.00 31.71 2.24
2833 3039 2.671963 GGGTGGCGAAGTTGACCC 60.672 66.667 0.00 0.00 41.43 4.46
2891 3097 2.307098 CTGGTTCCTTCAGAGGTTGGAT 59.693 50.000 0.00 0.00 43.97 3.41
2910 3116 3.423539 TCCTTCCAATGGTCTTGACTG 57.576 47.619 0.00 0.00 0.00 3.51
3013 3219 8.599792 GGATAACTTATGCCTGTATACCCTAAA 58.400 37.037 0.00 0.00 0.00 1.85
3064 3300 1.282875 GTTTTCCACAGGAGCACGC 59.717 57.895 0.00 0.00 31.21 5.34
3180 3417 5.259632 GACCTAGTAAAGTACACCCTCTGA 58.740 45.833 0.00 0.00 0.00 3.27
3201 3438 1.591158 TCAAAACAGAACGAGCACGAC 59.409 47.619 11.40 4.01 42.66 4.34
3220 3457 0.313672 TCAAATGGCGGCAACAGTTC 59.686 50.000 18.31 0.00 0.00 3.01
3228 3465 0.526954 CTGCATTCTCAAATGGCGGC 60.527 55.000 0.00 0.00 42.18 6.53
3229 3466 1.097232 TCTGCATTCTCAAATGGCGG 58.903 50.000 0.00 0.00 42.18 6.13
3314 3551 0.959553 TGACACCCGACTGAAGAGAC 59.040 55.000 0.00 0.00 0.00 3.36
3315 3552 1.924731 ATGACACCCGACTGAAGAGA 58.075 50.000 0.00 0.00 0.00 3.10
3316 3553 2.738846 CAAATGACACCCGACTGAAGAG 59.261 50.000 0.00 0.00 0.00 2.85
3317 3554 2.104111 ACAAATGACACCCGACTGAAGA 59.896 45.455 0.00 0.00 0.00 2.87
3318 3555 2.480419 GACAAATGACACCCGACTGAAG 59.520 50.000 0.00 0.00 0.00 3.02
3319 3556 2.158885 TGACAAATGACACCCGACTGAA 60.159 45.455 0.00 0.00 0.00 3.02
3320 3557 1.414550 TGACAAATGACACCCGACTGA 59.585 47.619 0.00 0.00 0.00 3.41
3321 3558 1.877637 TGACAAATGACACCCGACTG 58.122 50.000 0.00 0.00 0.00 3.51
3322 3559 2.158813 ACTTGACAAATGACACCCGACT 60.159 45.455 0.00 0.00 0.00 4.18
3335 3572 8.300286 TCAATGTAAACAAACTGAACTTGACAA 58.700 29.630 0.00 0.00 0.00 3.18
3378 3615 2.381725 AAACGGATCGTCCTCCTTTC 57.618 50.000 0.00 0.00 39.99 2.62
3389 3626 6.856135 AAAATATCTCGGGTTAAACGGATC 57.144 37.500 0.73 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.