Multiple sequence alignment - TraesCS3D01G520700

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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 TraesCS3D01G520700 chr3D 100.000 3297 0 0 1 3297 602892535 602889239 0 6089
1 TraesCS3D01G520700 chr2D 98.626 1965 24 1 1336 3297 644701862 644703826 0 3476
2 TraesCS3D01G520700 chr2D 98.434 1341 11 3 1 1336 635070678 635069343 0 2351
3 TraesCS3D01G520700 chrUn 98.522 1962 28 1 1336 3297 45099394 45101354 0 3461
4 TraesCS3D01G520700 chrUn 98.472 1963 29 1 1336 3297 261514464 261512502 0 3458
5 TraesCS3D01G520700 chrUn 98.661 1344 10 2 1 1336 186160897 186162240 0 2375
6 TraesCS3D01G520700 chrUn 98.434 1341 12 5 1 1336 45097914 45099250 0 2351
7 TraesCS3D01G520700 chrUn 98.359 1341 15 4 1 1336 261515946 261514608 0 2348
8 TraesCS3D01G520700 chr5B 98.522 1962 28 1 1336 3297 130613503 130615463 0 3461
9 TraesCS3D01G520700 chr5B 98.219 1965 32 1 1336 3297 130570157 130568193 0 3432
10 TraesCS3D01G520700 chr5B 98.216 1962 34 1 1336 3297 130608479 130610439 0 3428
11 TraesCS3D01G520700 chr5B 98.735 1344 9 2 1 1336 130606992 130608335 0 2381
12 TraesCS3D01G520700 chr5B 98.581 1339 14 2 1 1334 130571641 130570303 0 2362
13 TraesCS3D01G520700 chr3A 98.420 1962 31 0 1336 3297 66031712 66029751 0 3452
14 TraesCS3D01G520700 chr3A 98.583 1341 11 4 1 1336 66033193 66031856 0 2364
15 TraesCS3D01G520700 chr7B 98.267 1962 34 0 1336 3297 743035099 743033138 0 3435
16 TraesCS3D01G520700 chr7B 98.287 1343 16 3 1 1336 743036585 743035243 0 2346
17 TraesCS3D01G520700 chr2A 98.114 1962 37 0 1336 3297 735224871 735222910 0 3419
18 TraesCS3D01G520700 chr1D 98.881 1340 9 4 1 1336 493801573 493802910 0 2386


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 TraesCS3D01G520700 chr3D 602889239 602892535 3296 True 6089.0 6089 100.0000 1 3297 1 chr3D.!!$R1 3296
1 TraesCS3D01G520700 chr2D 644701862 644703826 1964 False 3476.0 3476 98.6260 1336 3297 1 chr2D.!!$F1 1961
2 TraesCS3D01G520700 chr2D 635069343 635070678 1335 True 2351.0 2351 98.4340 1 1336 1 chr2D.!!$R1 1335
3 TraesCS3D01G520700 chrUn 45097914 45101354 3440 False 2906.0 3461 98.4780 1 3297 2 chrUn.!!$F2 3296
4 TraesCS3D01G520700 chrUn 261512502 261515946 3444 True 2903.0 3458 98.4155 1 3297 2 chrUn.!!$R1 3296
5 TraesCS3D01G520700 chrUn 186160897 186162240 1343 False 2375.0 2375 98.6610 1 1336 1 chrUn.!!$F1 1335
6 TraesCS3D01G520700 chr5B 130606992 130615463 8471 False 3090.0 3461 98.4910 1 3297 3 chr5B.!!$F1 3296
7 TraesCS3D01G520700 chr5B 130568193 130571641 3448 True 2897.0 3432 98.4000 1 3297 2 chr5B.!!$R1 3296
8 TraesCS3D01G520700 chr3A 66029751 66033193 3442 True 2908.0 3452 98.5015 1 3297 2 chr3A.!!$R1 3296
9 TraesCS3D01G520700 chr7B 743033138 743036585 3447 True 2890.5 3435 98.2770 1 3297 2 chr7B.!!$R1 3296
10 TraesCS3D01G520700 chr2A 735222910 735224871 1961 True 3419.0 3419 98.1140 1336 3297 1 chr2A.!!$R1 1961
11 TraesCS3D01G520700 chr1D 493801573 493802910 1337 False 2386.0 2386 98.8810 1 1336 1 chr1D.!!$F1 1335

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
616 629 0.107703 GACCGGCCTCATTCACATCA 60.108 55.0 0.0 0.0 0.00 3.07 F
1245 6288 1.638529 AGCTATTATCGCCCAGCTCT 58.361 50.0 0.0 0.0 40.25 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 6996 0.178953 AGTTTCCCTGCATGTGGCTT 60.179 50.0 0.0 0.0 45.15 4.35 R
3085 8278 1.187087 GGATAGGACGCCCCATCTAG 58.813 60.0 0.0 0.0 37.41 2.43 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
463 464 1.376037 GTTGCGAGCCTGCCTTACT 60.376 57.895 0.00 0.00 0.00 2.24
465 466 3.198489 GCGAGCCTGCCTTACTGC 61.198 66.667 0.00 0.00 0.00 4.40
466 467 2.512515 CGAGCCTGCCTTACTGCC 60.513 66.667 0.00 0.00 0.00 4.85
467 468 2.124529 GAGCCTGCCTTACTGCCC 60.125 66.667 0.00 0.00 0.00 5.36
468 469 3.705934 GAGCCTGCCTTACTGCCCC 62.706 68.421 0.00 0.00 0.00 5.80
469 470 4.822628 GCCTGCCTTACTGCCCCC 62.823 72.222 0.00 0.00 0.00 5.40
616 629 0.107703 GACCGGCCTCATTCACATCA 60.108 55.000 0.00 0.00 0.00 3.07
1186 6229 4.202631 TGGGTTGGCTTGGATTACTTAGTT 60.203 41.667 0.00 0.00 0.00 2.24
1245 6288 1.638529 AGCTATTATCGCCCAGCTCT 58.361 50.000 0.00 0.00 40.25 4.09
1342 6529 4.296690 GGCTAATCGTACGCAGAGTTAAT 58.703 43.478 11.24 0.00 0.00 1.40
1401 6588 5.955355 AGCTCTTTCGCTCTATAGGGATATT 59.045 40.000 2.98 0.00 43.51 1.28
1478 6671 6.956435 TGACTGATCCTGCCATAATATACTCT 59.044 38.462 0.00 0.00 0.00 3.24
1547 6740 1.668867 TTCATGCGTGAAGGGACGA 59.331 52.632 17.41 0.00 42.10 4.20
1558 6751 3.055747 GTGAAGGGACGAGAGGAAAGAAT 60.056 47.826 0.00 0.00 0.00 2.40
1582 6775 3.120649 GGCGGTAGATGATAATGCGAAAC 60.121 47.826 0.00 0.00 0.00 2.78
1803 6996 2.821378 TCCGAAGAAGTTATCACGGACA 59.179 45.455 12.50 0.00 46.38 4.02
1985 7178 9.485206 GCCAAATCCTTCTATTATTAAGTACGA 57.515 33.333 0.00 0.00 0.00 3.43
2074 7267 7.414222 TGTATTAATTCCACTTCCTACTCGT 57.586 36.000 0.00 0.00 0.00 4.18
2387 7580 0.461516 TGTCTCGATCTCCTACGCGT 60.462 55.000 19.17 19.17 0.00 6.01
2673 7866 1.210967 TCCTCCCGGAATTGCGTTATT 59.789 47.619 18.34 0.00 36.03 1.40
2848 8041 2.014857 CTCGACCAGATCTACCGAACA 58.985 52.381 12.31 0.00 0.00 3.18
2945 8138 2.484264 GCTTACTGCTCACGGAAACATT 59.516 45.455 0.00 0.00 38.95 2.71
2953 8146 2.139917 TCACGGAAACATTCGACCTTG 58.860 47.619 0.00 0.00 0.00 3.61
3085 8278 4.099573 TCAATATCTCGTTCTCTTGGTCCC 59.900 45.833 0.00 0.00 0.00 4.46
3169 8362 6.066032 AGGATTCTTCTTTTCGGTTAAACCA 58.934 36.000 0.00 0.00 38.47 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.990967 AGTCGGGTCGGCGGTTTA 60.991 61.111 7.21 0.00 36.23 2.01
342 343 5.456186 GCCCCATAAGCTATTCTTTCACCTA 60.456 44.000 0.00 0.00 36.25 3.08
616 629 2.884012 TGTGTTCATGTTGGCGATTTCT 59.116 40.909 0.00 0.00 0.00 2.52
1186 6229 4.467084 CCCTCCTAGGCGCGCAAA 62.467 66.667 34.42 19.02 32.73 3.68
1245 6288 1.044231 TCCGGCCGCATTAGGTTAGA 61.044 55.000 22.85 4.17 0.00 2.10
1342 6529 4.228567 TTGCAGCACGTCCGGTCA 62.229 61.111 0.00 0.00 0.00 4.02
1478 6671 1.013596 CGGTGCAATAGAATTGGCGA 58.986 50.000 0.00 0.00 0.00 5.54
1547 6740 1.486726 CTACCGCCCATTCTTTCCTCT 59.513 52.381 0.00 0.00 0.00 3.69
1558 6751 1.337728 CGCATTATCATCTACCGCCCA 60.338 52.381 0.00 0.00 0.00 5.36
1803 6996 0.178953 AGTTTCCCTGCATGTGGCTT 60.179 50.000 0.00 0.00 45.15 4.35
1985 7178 3.695830 ACACATCGAAATGGTACCAGT 57.304 42.857 21.41 15.91 37.19 4.00
2074 7267 4.081642 GCCGGGATCATTAAGAGCATACTA 60.082 45.833 2.18 0.00 33.23 1.82
2387 7580 4.277672 CCGTCTCCCGTATCTTATCTTTCA 59.722 45.833 0.00 0.00 33.66 2.69
2451 7644 3.733960 CACGCCGACTCTCCGTCA 61.734 66.667 0.00 0.00 42.98 4.35
2673 7866 1.382557 TATTCCTGGCTCGGCTCCA 60.383 57.895 0.00 0.00 0.00 3.86
2848 8041 4.717313 GACGGGGCGGCCTTCTTT 62.717 66.667 28.80 7.53 0.00 2.52
2953 8146 1.870055 TAGGCGGACGACTTGACCAC 61.870 60.000 5.00 0.00 34.01 4.16
3085 8278 1.187087 GGATAGGACGCCCCATCTAG 58.813 60.000 0.00 0.00 37.41 2.43
3169 8362 1.944024 TGAATCGCCGACTTGTGTTTT 59.056 42.857 0.00 0.00 0.00 2.43
3210 8403 2.370281 TCTAGCTTTGACCGCTCTTG 57.630 50.000 0.00 0.00 38.86 3.02


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

AutoCloner maintained by Alex Coulton.