Multiple sequence alignment - TraesCS3B01G207800

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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 TraesCS3B01G207800 chr3B 100.000 3390 0 0 1 3390 243254986 243258375 0.000000e+00 6261
1 TraesCS3B01G207800 chr3B 92.371 3395 244 12 1 3390 346450732 346447348 0.000000e+00 4820
2 TraesCS3B01G207800 chr2B 93.484 3407 197 13 1 3390 733617664 733621062 0.000000e+00 5038
3 TraesCS3B01G207800 chr2B 93.337 3407 202 13 1 3390 733607893 733611291 0.000000e+00 5011
4 TraesCS3B01G207800 chr7B 93.134 3408 210 9 1 3390 223740041 223743442 0.000000e+00 4975
5 TraesCS3B01G207800 chr7B 93.078 3395 224 7 1 3390 392666199 392662811 0.000000e+00 4957
6 TraesCS3B01G207800 chr7B 92.189 3367 245 8 28 3390 364459084 364462436 0.000000e+00 4745
7 TraesCS3B01G207800 chr6B 92.897 3407 220 13 1 3390 559290577 559293978 0.000000e+00 4931
8 TraesCS3B01G207800 chr6B 80.601 2995 514 47 439 3390 2934644 2937614 0.000000e+00 2250
9 TraesCS3B01G207800 chr4B 92.870 3408 221 10 1 3390 362276427 362273024 0.000000e+00 4927
10 TraesCS3B01G207800 chr4B 92.750 3407 219 14 1 3390 164916329 164912934 0.000000e+00 4898
11 TraesCS3B01G207800 chr1B 84.080 3436 464 50 1 3390 50396984 50393586 0.000000e+00 3238
12 TraesCS3B01G207800 chr4D 91.770 243 17 3 3138 3379 425257333 425257573 5.420000e-88 335
13 TraesCS3B01G207800 chr7D 90.800 250 19 4 3140 3389 271842657 271842412 7.010000e-87 331
14 TraesCS3B01G207800 chr3D 91.358 243 18 3 3138 3379 24796992 24797232 2.520000e-86 329


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 TraesCS3B01G207800 chr3B 243254986 243258375 3389 False 6261 6261 100.000 1 3390 1 chr3B.!!$F1 3389
1 TraesCS3B01G207800 chr3B 346447348 346450732 3384 True 4820 4820 92.371 1 3390 1 chr3B.!!$R1 3389
2 TraesCS3B01G207800 chr2B 733617664 733621062 3398 False 5038 5038 93.484 1 3390 1 chr2B.!!$F2 3389
3 TraesCS3B01G207800 chr2B 733607893 733611291 3398 False 5011 5011 93.337 1 3390 1 chr2B.!!$F1 3389
4 TraesCS3B01G207800 chr7B 223740041 223743442 3401 False 4975 4975 93.134 1 3390 1 chr7B.!!$F1 3389
5 TraesCS3B01G207800 chr7B 392662811 392666199 3388 True 4957 4957 93.078 1 3390 1 chr7B.!!$R1 3389
6 TraesCS3B01G207800 chr7B 364459084 364462436 3352 False 4745 4745 92.189 28 3390 1 chr7B.!!$F2 3362
7 TraesCS3B01G207800 chr6B 559290577 559293978 3401 False 4931 4931 92.897 1 3390 1 chr6B.!!$F2 3389
8 TraesCS3B01G207800 chr6B 2934644 2937614 2970 False 2250 2250 80.601 439 3390 1 chr6B.!!$F1 2951
9 TraesCS3B01G207800 chr4B 362273024 362276427 3403 True 4927 4927 92.870 1 3390 1 chr4B.!!$R2 3389
10 TraesCS3B01G207800 chr4B 164912934 164916329 3395 True 4898 4898 92.750 1 3390 1 chr4B.!!$R1 3389
11 TraesCS3B01G207800 chr1B 50393586 50396984 3398 True 3238 3238 84.080 1 3390 1 chr1B.!!$R1 3389

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
522 550 0.321298 CCTCCGACCCATTTTCGTGT 60.321 55.000 0.0 0.0 34.56 4.49 F
1254 1291 0.034380 CTGAGGAGGGTGAGGTCGTA 60.034 60.000 0.0 0.0 0.00 3.43 F
1598 1635 2.058001 TCCGTGGATGGCAGTCGAT 61.058 57.895 0.0 0.0 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1801 0.533755 CAAGAGATCCATGCCGGTCC 60.534 60.000 1.9 0.0 35.57 4.46 R
2254 2315 1.706287 GCTTGGATCGCCTTTCCGTC 61.706 60.000 0.0 0.0 35.94 4.79 R
2706 2778 1.723542 CGCCTCGTCATCATCATTAGC 59.276 52.381 0.0 0.0 0.00 3.09 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
94 95 4.017126 AGGCGATCGACTGGATTATATGA 58.983 43.478 25.76 0.0 34.82 2.15
467 494 2.930950 CTTCATCATTAGCCCCCGAAA 58.069 47.619 0.00 0.0 0.00 3.46
504 531 1.605753 GGGAAGGAGTTGAACACACC 58.394 55.000 0.00 0.0 36.40 4.16
522 550 0.321298 CCTCCGACCCATTTTCGTGT 60.321 55.000 0.00 0.0 34.56 4.49
564 594 3.309954 GGATCAATGAACTTAGGTGACGC 59.690 47.826 0.00 0.0 0.00 5.19
864 897 1.540267 GCCTACAAGTCAGTCACTCGA 59.460 52.381 0.00 0.0 32.30 4.04
883 916 7.341256 TCACTCGAAAGTAACCTCATATAAGGT 59.659 37.037 0.00 0.0 42.07 3.50
884 917 7.435488 CACTCGAAAGTAACCTCATATAAGGTG 59.565 40.741 0.00 0.0 40.45 4.00
968 1005 0.737367 CGTTCGCTTCCATCTCAGCA 60.737 55.000 0.00 0.0 35.60 4.41
1088 1125 2.584608 CAGTCGGGGCGGATCTTT 59.415 61.111 0.00 0.0 0.00 2.52
1171 1208 1.996798 AGAAGACCTTGACGACCTGA 58.003 50.000 0.00 0.0 0.00 3.86
1237 1274 4.079850 AGTCTGAGCCGCAGCCTG 62.080 66.667 0.00 0.0 44.52 4.85
1254 1291 0.034380 CTGAGGAGGGTGAGGTCGTA 60.034 60.000 0.00 0.0 0.00 3.43
1440 1477 3.509442 TCATTGGGGTCTTTTCAAGCAT 58.491 40.909 0.00 0.0 0.00 3.79
1598 1635 2.058001 TCCGTGGATGGCAGTCGAT 61.058 57.895 0.00 0.0 0.00 3.59
1660 1698 2.290960 ACCGGAATCCCTCCTTTTTCTG 60.291 50.000 9.46 0.0 42.85 3.02
2254 2315 2.034607 GGAAGTCGATCCTCCTCGG 58.965 63.158 0.00 0.0 39.13 4.63
2706 2778 5.032327 TCCTCCTCATGTCATTGATCTTG 57.968 43.478 0.00 0.0 0.00 3.02
2746 2818 2.841988 GCTGAGGCCGAGGAGGAT 60.842 66.667 0.00 0.0 45.00 3.24
2834 2906 2.894765 TGGTAACATCACTCGGACTTCA 59.105 45.455 0.00 0.0 46.17 3.02
3051 3123 1.000283 CTCTTCAGAGCAACGTCCAGT 60.000 52.381 0.00 0.0 35.13 4.00
3098 3172 9.482627 CTGTTAGGATATGGTATCTGAAAACTC 57.517 37.037 0.00 0.0 0.00 3.01
3171 3262 2.317992 TTTGGATTGGTGGGGGCACA 62.318 55.000 0.00 0.0 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 8.815565 ACTCATACTCATATAATCCAGTCGAT 57.184 34.615 0.00 0.00 0.00 3.59
94 95 1.480954 CGCACCCCTGTAACTCATACT 59.519 52.381 0.00 0.00 35.42 2.12
467 494 0.905357 CCCACTCAAACCTCGATCCT 59.095 55.000 0.00 0.00 0.00 3.24
504 531 0.796312 CACACGAAAATGGGTCGGAG 59.204 55.000 0.00 0.00 42.82 4.63
522 550 6.155049 TGATCCAGAACAAGACATACTCATCA 59.845 38.462 0.00 0.00 0.00 3.07
564 594 3.792124 GCGACTGAAAAAGAAGTTGGTGG 60.792 47.826 0.00 0.00 0.00 4.61
910 945 2.959421 AGAGGGGAGGAAATGAGAGT 57.041 50.000 0.00 0.00 0.00 3.24
1038 1075 3.723348 GCCTTCGCCGTCGCTTTT 61.723 61.111 0.00 0.00 35.26 2.27
1171 1208 1.216990 GGGATCAGTCCTCCATTGGT 58.783 55.000 1.86 0.00 44.44 3.67
1237 1274 0.034283 AGTACGACCTCACCCTCCTC 60.034 60.000 0.00 0.00 0.00 3.71
1254 1291 1.380302 GACATGGGTGGCCAAGAGT 59.620 57.895 7.24 1.42 0.00 3.24
1440 1477 1.626321 TGGGAGCGACAGGTGAAAATA 59.374 47.619 0.00 0.00 0.00 1.40
1598 1635 3.882888 CTGGTCTTTGCAGTAAAACCAGA 59.117 43.478 24.73 3.79 46.54 3.86
1634 1671 2.794028 GGAGGGATTCCGGTCGACC 61.794 68.421 25.28 25.28 35.91 4.79
1645 1682 2.041755 GGTCCACAGAAAAAGGAGGGAT 59.958 50.000 0.00 0.00 30.78 3.85
1660 1698 1.079750 GCTTCCTCACTCGGTCCAC 60.080 63.158 0.00 0.00 0.00 4.02
1763 1801 0.533755 CAAGAGATCCATGCCGGTCC 60.534 60.000 1.90 0.00 35.57 4.46
1857 1895 1.258445 GGTGGATCCGAGTGGTGTCT 61.258 60.000 7.39 0.00 36.30 3.41
2064 2103 8.190784 CCTAGAAGACAACAAACAAGACAAAAT 58.809 33.333 0.00 0.00 0.00 1.82
2254 2315 1.706287 GCTTGGATCGCCTTTCCGTC 61.706 60.000 0.00 0.00 35.94 4.79
2290 2351 3.044305 GCTTTGCCACGCTCGACT 61.044 61.111 0.00 0.00 0.00 4.18
2706 2778 1.723542 CGCCTCGTCATCATCATTAGC 59.276 52.381 0.00 0.00 0.00 3.09
2746 2818 2.435938 CAGCCGGCGCCTTTCTAA 60.436 61.111 26.68 0.00 34.57 2.10
2834 2906 1.893808 CGGCACAGCAAAGGACACT 60.894 57.895 0.00 0.00 0.00 3.55
3051 3123 2.335316 ACAAGCGGTGACCAACTAAA 57.665 45.000 1.11 0.00 0.00 1.85
3171 3262 3.941188 CCAGTGGGTGCACTCGGT 61.941 66.667 17.98 0.00 32.26 4.69


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

AutoCloner maintained by Alex Coulton.