Multiple sequence alignment - TraesCS3B01G488200

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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 TraesCS3B01G488200 chr3B 100.000 3246 0 0 1 3246 734220971 734224216 0.000000e+00 5995
1 TraesCS3B01G488200 chr7B 98.152 3247 59 1 1 3246 666622181 666618935 0.000000e+00 5662
2 TraesCS3B01G488200 chr7B 97.999 3249 60 4 1 3246 664946180 664949426 0.000000e+00 5635
3 TraesCS3B01G488200 chr7B 98.364 2384 36 3 1 2383 379917640 379915259 0.000000e+00 4183
4 TraesCS3B01G488200 chr5B 97.844 3247 51 2 1 3246 353924639 353927867 0.000000e+00 5590
5 TraesCS3B01G488200 chr5B 97.813 3247 52 2 1 3246 18190208 18186980 0.000000e+00 5585
6 TraesCS3B01G488200 chr5B 96.511 3267 69 13 1 3246 123793158 123789916 0.000000e+00 5360
7 TraesCS3B01G488200 chr5B 96.772 3222 82 4 1 3201 34299462 34296242 0.000000e+00 5354
8 TraesCS3B01G488200 chr5B 93.530 1221 36 4 2046 3246 514054862 514053665 0.000000e+00 1777
9 TraesCS3B01G488200 chr4B 97.747 2530 51 3 1 2524 522409967 522407438 0.000000e+00 4351
10 TraesCS3B01G488200 chr3D 93.463 2677 119 17 1 2649 581478759 581476111 0.000000e+00 3923
11 TraesCS3B01G488200 chr4A 95.392 586 27 0 2661 3246 692373579 692374164 0.000000e+00 933
12 TraesCS3B01G488200 chr4A 87.931 406 18 6 2121 2519 692372915 692373296 1.780000e-122 449
13 TraesCS3B01G488200 chr4A 93.284 134 9 0 2516 2649 692373353 692373486 7.100000e-47 198
14 TraesCS3B01G488200 chr6B 94.369 586 33 0 2661 3246 77324753 77325338 0.000000e+00 900


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 TraesCS3B01G488200 chr3B 734220971 734224216 3245 False 5995.000000 5995 100.000000 1 3246 1 chr3B.!!$F1 3245
1 TraesCS3B01G488200 chr7B 666618935 666622181 3246 True 5662.000000 5662 98.152000 1 3246 1 chr7B.!!$R2 3245
2 TraesCS3B01G488200 chr7B 664946180 664949426 3246 False 5635.000000 5635 97.999000 1 3246 1 chr7B.!!$F1 3245
3 TraesCS3B01G488200 chr7B 379915259 379917640 2381 True 4183.000000 4183 98.364000 1 2383 1 chr7B.!!$R1 2382
4 TraesCS3B01G488200 chr5B 353924639 353927867 3228 False 5590.000000 5590 97.844000 1 3246 1 chr5B.!!$F1 3245
5 TraesCS3B01G488200 chr5B 18186980 18190208 3228 True 5585.000000 5585 97.813000 1 3246 1 chr5B.!!$R1 3245
6 TraesCS3B01G488200 chr5B 123789916 123793158 3242 True 5360.000000 5360 96.511000 1 3246 1 chr5B.!!$R3 3245
7 TraesCS3B01G488200 chr5B 34296242 34299462 3220 True 5354.000000 5354 96.772000 1 3201 1 chr5B.!!$R2 3200
8 TraesCS3B01G488200 chr5B 514053665 514054862 1197 True 1777.000000 1777 93.530000 2046 3246 1 chr5B.!!$R4 1200
9 TraesCS3B01G488200 chr4B 522407438 522409967 2529 True 4351.000000 4351 97.747000 1 2524 1 chr4B.!!$R1 2523
10 TraesCS3B01G488200 chr3D 581476111 581478759 2648 True 3923.000000 3923 93.463000 1 2649 1 chr3D.!!$R1 2648
11 TraesCS3B01G488200 chr4A 692372915 692374164 1249 False 526.666667 933 92.202333 2121 3246 3 chr4A.!!$F1 1125
12 TraesCS3B01G488200 chr6B 77324753 77325338 585 False 900.000000 900 94.369000 2661 3246 1 chr6B.!!$F1 585

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
313 318 0.749454 GGCGATGATCAGTGGCCTTT 60.749 55.0 21.06 0.0 40.59 3.11 F
1436 1441 0.323178 CTTGGGCCATCAAGCACTCT 60.323 55.0 7.26 0.0 37.84 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2202 2.821366 GTGGGCTGTGATGGCTCG 60.821 66.667 0.0 0.0 31.94 5.03 R
2961 3217 0.674534 GATGCTACCTACCGACCCAG 59.325 60.000 0.0 0.0 0.00 4.45 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
30 31 6.079424 TGGTTATTACTTGTCAGTTTTGCC 57.921 37.500 0.00 0.0 34.06 4.52
31 32 5.830991 TGGTTATTACTTGTCAGTTTTGCCT 59.169 36.000 0.00 0.0 34.06 4.75
103 108 1.229820 AGGGGTCATAGTGCCCACA 60.230 57.895 0.00 0.0 46.59 4.17
313 318 0.749454 GGCGATGATCAGTGGCCTTT 60.749 55.000 21.06 0.0 40.59 3.11
430 435 2.807045 GCGAGCGTGACAGTGAGG 60.807 66.667 0.00 0.0 0.00 3.86
648 653 2.170607 GGGTTCAGGAGCACTAGCATAA 59.829 50.000 0.00 0.0 45.49 1.90
942 947 0.911769 CCTACTGTTGGGAGATGGCA 59.088 55.000 0.00 0.0 0.00 4.92
1033 1038 9.764363 CTCATAAGCAGGTAATGATAACTTACA 57.236 33.333 0.00 0.0 31.98 2.41
1041 1046 8.916654 CAGGTAATGATAACTTACATAAGAGCG 58.083 37.037 5.66 0.0 37.08 5.03
1436 1441 0.323178 CTTGGGCCATCAAGCACTCT 60.323 55.000 7.26 0.0 37.84 3.24
2031 2039 1.115467 GCTGGAGCTTCTACTAGCCA 58.885 55.000 0.00 0.0 42.20 4.75
2188 2202 1.364901 CCAAATGGATGATGCGCCC 59.635 57.895 4.18 0.0 37.39 6.13
2302 2339 6.810888 ATGTTTGATTCGTGAACTTTGTTG 57.189 33.333 0.00 0.0 0.00 3.33
2510 2674 4.878397 GCTTAGTGTTGCTGTCATCCTTAT 59.122 41.667 0.00 0.0 0.00 1.73
2886 3142 4.621460 CGAGTTCTTCTTGCGTGAATTCTA 59.379 41.667 7.05 0.0 0.00 2.10
2961 3217 1.450312 CATCTGGCACCGAGGAACC 60.450 63.158 0.00 0.0 0.00 3.62
3003 3259 4.398358 CGAGGAGCTTGGGTCGATATATAA 59.602 45.833 0.00 0.0 34.28 0.98
3136 3392 4.603946 GCCTGGGTCGGTATCGGC 62.604 72.222 0.00 0.0 40.80 5.54
3160 3416 4.025360 ACATAGCTTCATTGATTGCCCAA 58.975 39.130 0.00 0.0 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.613944 CATTGCATTATGGTTAGTGCCAG 58.386 43.478 0.00 0.00 42.47 4.85
31 32 3.181477 GCATTGCATTATGGTTAGTGCCA 60.181 43.478 3.15 0.00 39.58 4.92
313 318 4.460382 GGTCAAAGCTTCTCCATTGATTGA 59.540 41.667 0.00 0.00 34.62 2.57
430 435 2.416431 GGAGCCAATGATGCAACACTTC 60.416 50.000 0.00 0.00 0.00 3.01
942 947 2.154462 GAGCTGCCTGTGTACACATTT 58.846 47.619 28.03 10.71 41.01 2.32
1436 1441 4.777366 TGATTCCACAGACTTATCCACTCA 59.223 41.667 0.00 0.00 0.00 3.41
1761 1766 3.882102 ATGCAATAACTCCATGCCCTA 57.118 42.857 0.00 0.00 39.31 3.53
2188 2202 2.821366 GTGGGCTGTGATGGCTCG 60.821 66.667 0.00 0.00 31.94 5.03
2302 2339 9.173939 CACTTCTAAAGTTCATGAATCAAACAC 57.826 33.333 12.12 0.00 40.46 3.32
2510 2674 7.275341 CAGAAACTTCAACATAACAGCAAAACA 59.725 33.333 0.00 0.00 0.00 2.83
2915 3171 5.699458 CCAATGCAAGCAAGAAGAAGAAAAT 59.301 36.000 0.00 0.00 0.00 1.82
2961 3217 0.674534 GATGCTACCTACCGACCCAG 59.325 60.000 0.00 0.00 0.00 4.45
3136 3392 3.304257 GGGCAATCAATGAAGCTATGTCG 60.304 47.826 10.13 0.00 0.00 4.35
3160 3416 6.446110 TGAATAGGCCTGGATAGATCATTGAT 59.554 38.462 17.99 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.