Multiple sequence alignment - TraesCS3D01G257700

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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 TraesCS3D01G257700 chr3D 100.000 3630 0 0 1 3630 360039521 360043150 0.000000e+00 6704
1 TraesCS3D01G257700 chr3B 95.560 3649 134 16 1 3630 466099552 466103191 0.000000e+00 5816
2 TraesCS3D01G257700 chr3A 97.251 2692 48 8 1 2686 479473788 479476459 0.000000e+00 4538
3 TraesCS3D01G257700 chr3A 96.616 916 31 0 2715 3630 479476459 479477374 0.000000e+00 1520
4 TraesCS3D01G257700 chr3A 92.143 140 11 0 2737 2876 479471374 479471235 7.950000e-47 198


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 TraesCS3D01G257700 chr3D 360039521 360043150 3629 False 6704 6704 100.0000 1 3630 1 chr3D.!!$F1 3629
1 TraesCS3D01G257700 chr3B 466099552 466103191 3639 False 5816 5816 95.5600 1 3630 1 chr3B.!!$F1 3629
2 TraesCS3D01G257700 chr3A 479473788 479477374 3586 False 3029 4538 96.9335 1 3630 2 chr3A.!!$F1 3629

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
671 682 0.251165 CCCCCGCAAAGAAAGGAGAA 60.251 55.000 0.00 0.0 0.00 2.87 F
1706 1718 1.190984 CACGTACATGATCGATGCTGC 59.809 52.381 0.54 0.0 35.15 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2130 0.926846 GCAGAGTAGAAGCGCATGTC 59.073 55.000 11.47 3.56 0.00 3.06 R
3276 3332 1.069823 AGTTGGACACTCAGCAGTCTG 59.930 52.381 0.00 0.00 41.67 3.51 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
67 68 9.836864 ATTATGTACATTTATGTCAGAAGCTCA 57.163 29.630 14.77 0.00 41.97 4.26
111 112 3.130693 ACCTCTAAATCTTCCGGTCTTCG 59.869 47.826 0.00 0.00 38.88 3.79
156 158 2.106511 AGTTTTGCCTACAGCCTTCTCA 59.893 45.455 0.00 0.00 42.71 3.27
216 218 2.693591 GAGACATAGATGACCCGGAACA 59.306 50.000 0.73 2.36 0.00 3.18
231 233 2.618709 CGGAACAAAGTTCCTTCAGCTT 59.381 45.455 22.38 0.00 36.45 3.74
366 368 0.733150 GGCACTGCCTTTATTCCGAC 59.267 55.000 13.28 0.00 46.69 4.79
403 405 1.239347 GGAGGACCAACTTGCAAGAC 58.761 55.000 32.50 16.12 35.97 3.01
426 437 4.096984 CCAGAAGGTTGATAAGCCATTGTC 59.903 45.833 0.00 0.00 0.00 3.18
427 438 4.701651 CAGAAGGTTGATAAGCCATTGTCA 59.298 41.667 0.00 0.00 35.05 3.58
428 439 5.359009 CAGAAGGTTGATAAGCCATTGTCAT 59.641 40.000 0.00 0.00 36.56 3.06
429 440 5.954150 AGAAGGTTGATAAGCCATTGTCATT 59.046 36.000 0.00 0.00 36.56 2.57
430 441 6.438425 AGAAGGTTGATAAGCCATTGTCATTT 59.562 34.615 0.00 0.00 36.56 2.32
431 442 5.969423 AGGTTGATAAGCCATTGTCATTTG 58.031 37.500 0.00 0.00 36.56 2.32
432 443 4.567959 GGTTGATAAGCCATTGTCATTTGC 59.432 41.667 0.00 0.00 36.56 3.68
671 682 0.251165 CCCCCGCAAAGAAAGGAGAA 60.251 55.000 0.00 0.00 0.00 2.87
704 715 5.827797 GGGAATTCACAGTATAGCAAATCCA 59.172 40.000 7.93 0.00 0.00 3.41
1202 1214 2.423892 TCAAAGCTAGCCTCAGTACTCG 59.576 50.000 12.13 0.00 0.00 4.18
1234 1246 2.095263 CCAGCCACTAATGAAAACACCG 60.095 50.000 0.00 0.00 0.00 4.94
1706 1718 1.190984 CACGTACATGATCGATGCTGC 59.809 52.381 0.54 0.00 35.15 5.25
2036 2048 2.827921 AGAAAATGGACAATGAGCCACC 59.172 45.455 2.17 0.00 36.92 4.61
2112 2124 6.873076 TCAATTACCATGTCAAGGAATTTTGC 59.127 34.615 0.00 0.00 0.00 3.68
2117 2130 4.449743 CCATGTCAAGGAATTTTGCACTTG 59.550 41.667 6.22 6.22 41.14 3.16
2267 2290 8.464404 GTTCCTTTTAGTCTTTTACCAAACACT 58.536 33.333 0.00 0.00 0.00 3.55
2315 2338 6.529125 GTGATATGCATTGACACCTCAAAAAG 59.471 38.462 3.54 0.00 39.90 2.27
2322 2345 6.701400 GCATTGACACCTCAAAAAGTTACATT 59.299 34.615 0.00 0.00 39.90 2.71
2439 2465 3.300009 CCTTTTACGTTCAAGCAAGCTG 58.700 45.455 0.00 0.00 0.00 4.24
2768 2823 9.314321 CTTCCATATTACAAGTAGTCGAAACAT 57.686 33.333 0.00 0.00 0.00 2.71
2795 2850 4.897509 ATCACTGTTGATCTTGGAGTCA 57.102 40.909 0.00 0.00 38.08 3.41
2849 2904 6.751888 GTCATATTTCTTGTAATGTGGTTGGC 59.248 38.462 0.00 0.00 30.35 4.52
2884 2940 8.306761 CAGCTTCAGGGTTTCTTTACATATTTT 58.693 33.333 0.00 0.00 0.00 1.82
2938 2994 4.284746 GGATACAGGGAAGAACTGGATAGG 59.715 50.000 0.00 0.00 39.57 2.57
3005 3061 3.988819 AGAAAGAGACAGAGCTTGACAC 58.011 45.455 0.00 0.00 0.00 3.67
3082 3138 6.811665 TCTCACTTACTGTGTTATCCGAAATG 59.188 38.462 0.00 0.00 46.27 2.32
3085 3141 8.089597 TCACTTACTGTGTTATCCGAAATGTTA 58.910 33.333 0.00 0.00 46.27 2.41
3131 3187 7.636150 ACTGTAATGAAGCTCAAGCATATTT 57.364 32.000 4.59 0.00 45.16 1.40
3276 3332 7.232945 ACAATTTGTGCAACTTGTCATTTAC 57.767 32.000 12.73 0.00 39.09 2.01
3318 3374 3.258123 TCTTTTGCTAATTGGGAACTGGC 59.742 43.478 0.00 0.00 0.00 4.85
3569 3625 2.325484 TGGAGTCTTCAACAGTAGCCA 58.675 47.619 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.752101 AGACTGCGCCATGAATATCTTTAC 59.248 41.667 4.18 0.00 0.00 2.01
67 68 1.410153 CCAACTCCAAAGCAAGCAGTT 59.590 47.619 0.00 0.00 0.00 3.16
111 112 4.483476 ACAACTTCGTGCAGATTTTACC 57.517 40.909 0.00 0.00 0.00 2.85
156 158 2.634453 TGTATGGATCATGCGATCTGGT 59.366 45.455 0.00 0.00 46.30 4.00
231 233 0.392706 TGCCGACTGAAAGCTTCTCA 59.607 50.000 0.00 5.34 37.60 3.27
358 360 1.893137 CTGGGATGATCCGTCGGAATA 59.107 52.381 19.76 10.69 37.43 1.75
366 368 1.288439 CGCTCTCTGGGATGATCCG 59.712 63.158 5.22 0.00 37.43 4.18
403 405 4.019174 ACAATGGCTTATCAACCTTCTGG 58.981 43.478 0.00 0.00 39.83 3.86
426 437 2.610232 GCAGGTACCAAGTTGGCAAATG 60.610 50.000 22.25 15.92 42.67 2.32
427 438 1.618343 GCAGGTACCAAGTTGGCAAAT 59.382 47.619 22.25 4.85 42.67 2.32
428 439 1.036707 GCAGGTACCAAGTTGGCAAA 58.963 50.000 22.25 4.94 42.67 3.68
429 440 0.106469 TGCAGGTACCAAGTTGGCAA 60.106 50.000 22.25 7.66 42.67 4.52
430 441 0.821711 GTGCAGGTACCAAGTTGGCA 60.822 55.000 22.25 6.21 42.67 4.92
431 442 1.524008 GGTGCAGGTACCAAGTTGGC 61.524 60.000 22.25 6.39 42.67 4.52
432 443 2.641197 GGTGCAGGTACCAAGTTGG 58.359 57.895 20.76 20.76 45.02 3.77
671 682 2.443255 ACTGTGAATTCCCACCTCTTGT 59.557 45.455 2.27 0.00 36.26 3.16
1202 1214 0.106819 AGTGGCTGGAGGATGATTGC 60.107 55.000 0.00 0.00 0.00 3.56
1234 1246 4.698583 AAGTCGGCGTGGATACTATATC 57.301 45.455 6.85 0.00 37.61 1.63
1706 1718 5.133221 TCTTCCCTCTTGACCTTTTCTTTG 58.867 41.667 0.00 0.00 0.00 2.77
2036 2048 1.662629 CGTTATCAAGGTCTGCAGCAG 59.337 52.381 17.10 17.10 0.00 4.24
2112 2124 2.341257 AGTAGAAGCGCATGTCAAGTG 58.659 47.619 11.47 0.00 0.00 3.16
2117 2130 0.926846 GCAGAGTAGAAGCGCATGTC 59.073 55.000 11.47 3.56 0.00 3.06
2203 2221 4.634004 TCTTTGTCGTGCAAGAAGAAAGAA 59.366 37.500 23.79 14.04 38.47 2.52
2322 2345 6.759356 TGACGAACTGATGAAAAGTAACTTCA 59.241 34.615 0.00 0.00 37.22 3.02
2384 2407 7.652507 GCCCTGTAAGACATAGTAACATACTTC 59.347 40.741 0.00 0.00 36.69 3.01
2439 2465 4.084066 TCACACGTTAATCACATGTGAAGC 60.084 41.667 31.00 16.97 44.92 3.86
2702 2728 9.737427 TCACGTGTACATGTTTAAATTTTGATT 57.263 25.926 18.15 0.00 0.00 2.57
2703 2729 9.176181 GTCACGTGTACATGTTTAAATTTTGAT 57.824 29.630 18.15 0.00 0.00 2.57
2704 2730 7.644551 GGTCACGTGTACATGTTTAAATTTTGA 59.355 33.333 18.15 6.57 0.00 2.69
2705 2731 7.646130 AGGTCACGTGTACATGTTTAAATTTTG 59.354 33.333 18.15 4.29 0.00 2.44
2706 2732 7.708998 AGGTCACGTGTACATGTTTAAATTTT 58.291 30.769 18.15 0.00 0.00 1.82
2707 2733 7.266922 AGGTCACGTGTACATGTTTAAATTT 57.733 32.000 18.15 0.00 0.00 1.82
2708 2734 6.870971 AGGTCACGTGTACATGTTTAAATT 57.129 33.333 18.15 0.09 0.00 1.82
2709 2735 8.556213 AATAGGTCACGTGTACATGTTTAAAT 57.444 30.769 18.15 6.09 0.00 1.40
2710 2736 7.966246 AATAGGTCACGTGTACATGTTTAAA 57.034 32.000 18.15 4.04 0.00 1.52
2711 2737 7.966246 AAATAGGTCACGTGTACATGTTTAA 57.034 32.000 18.15 4.46 0.00 1.52
2712 2738 9.656040 ATTAAATAGGTCACGTGTACATGTTTA 57.344 29.630 18.15 18.65 0.00 2.01
2713 2739 7.966246 TTAAATAGGTCACGTGTACATGTTT 57.034 32.000 18.15 19.50 0.00 2.83
2768 2823 6.014242 ACTCCAAGATCAACAGTGATAGACAA 60.014 38.462 0.00 0.00 44.83 3.18
2884 2940 2.168458 TCCATACAATCCGGGTGAGA 57.832 50.000 12.37 1.49 0.00 3.27
2938 2994 3.936902 TTACACTGCACAAAACTCGTC 57.063 42.857 0.00 0.00 0.00 4.20
3005 3061 7.946237 GCAAACTACAAAACATTGAATTCATCG 59.054 33.333 9.40 6.04 0.00 3.84
3082 3138 6.819397 ACTAACTTTTCCAGGATTGCTAAC 57.181 37.500 0.00 0.00 0.00 2.34
3085 3141 6.431234 CAGTAACTAACTTTTCCAGGATTGCT 59.569 38.462 0.00 0.00 35.76 3.91
3160 3216 8.344831 TCACAAATGCACTAATATATGTTCTGC 58.655 33.333 0.00 7.47 0.00 4.26
3276 3332 1.069823 AGTTGGACACTCAGCAGTCTG 59.930 52.381 0.00 0.00 41.67 3.51
3465 3521 2.037687 TGGCTGGCCAATCCAAGG 59.962 61.111 20.70 2.83 46.01 3.61


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

AutoCloner maintained by Alex Coulton.