Multiple sequence alignment - TraesCS2B01G255600

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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 TraesCS2B01G255600 chr2B 100.000 3368 0 0 1 3368 293242765 293246132 0 6220
1 TraesCS2B01G255600 chr2B 96.968 1880 52 3 1493 3368 317054190 317052312 0 3151
2 TraesCS2B01G255600 chr6B 96.771 3376 100 4 1 3368 42183844 42180470 0 5622
3 TraesCS2B01G255600 chr6B 96.358 3377 108 8 1 3368 536423347 536419977 0 5541
4 TraesCS2B01G255600 chr6B 94.826 1411 61 9 1 1404 85662840 85664245 0 2191
5 TraesCS2B01G255600 chr3B 96.179 3376 116 11 1 3368 649105556 649102186 0 5507
6 TraesCS2B01G255600 chr3B 96.394 3161 107 5 1 3156 572150994 572147836 0 5199
7 TraesCS2B01G255600 chr3B 96.638 2558 82 2 815 3368 664732515 664729958 0 4244
8 TraesCS2B01G255600 chr3B 94.444 1404 76 2 1 1404 545972556 545971155 0 2159
9 TraesCS2B01G255600 chr1B 95.878 3372 130 5 1 3368 84525611 84522245 0 5448
10 TraesCS2B01G255600 chr4B 95.375 3373 139 6 7 3368 211099979 211096613 0 5349
11 TraesCS2B01G255600 chr7B 96.862 1880 53 4 1493 3368 300043095 300044972 0 3140
12 TraesCS2B01G255600 chr7B 94.405 1412 70 7 1 1404 300041531 300042941 0 2161


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 TraesCS2B01G255600 chr2B 293242765 293246132 3367 False 6220.0 6220 100.0000 1 3368 1 chr2B.!!$F1 3367
1 TraesCS2B01G255600 chr2B 317052312 317054190 1878 True 3151.0 3151 96.9680 1493 3368 1 chr2B.!!$R1 1875
2 TraesCS2B01G255600 chr6B 42180470 42183844 3374 True 5622.0 5622 96.7710 1 3368 1 chr6B.!!$R1 3367
3 TraesCS2B01G255600 chr6B 536419977 536423347 3370 True 5541.0 5541 96.3580 1 3368 1 chr6B.!!$R2 3367
4 TraesCS2B01G255600 chr6B 85662840 85664245 1405 False 2191.0 2191 94.8260 1 1404 1 chr6B.!!$F1 1403
5 TraesCS2B01G255600 chr3B 649102186 649105556 3370 True 5507.0 5507 96.1790 1 3368 1 chr3B.!!$R3 3367
6 TraesCS2B01G255600 chr3B 572147836 572150994 3158 True 5199.0 5199 96.3940 1 3156 1 chr3B.!!$R2 3155
7 TraesCS2B01G255600 chr3B 664729958 664732515 2557 True 4244.0 4244 96.6380 815 3368 1 chr3B.!!$R4 2553
8 TraesCS2B01G255600 chr3B 545971155 545972556 1401 True 2159.0 2159 94.4440 1 1404 1 chr3B.!!$R1 1403
9 TraesCS2B01G255600 chr1B 84522245 84525611 3366 True 5448.0 5448 95.8780 1 3368 1 chr1B.!!$R1 3367
10 TraesCS2B01G255600 chr4B 211096613 211099979 3366 True 5349.0 5349 95.3750 7 3368 1 chr4B.!!$R1 3361
11 TraesCS2B01G255600 chr7B 300041531 300044972 3441 False 2650.5 3140 95.6335 1 3368 2 chr7B.!!$F1 3367

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
916 930 0.749649 CATCTCTCCCTCGTTCCCAG 59.250 60.000 0.0 0.0 0.0 4.45 F
1114 1128 1.335689 ACTACACCAGAACGCTCGAAC 60.336 52.381 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2363 2.494918 GGCGTACGCATCCAGTCT 59.505 61.111 37.99 0.0 44.11 3.24 R
2744 2869 2.547211 TCATAGTAGCGCTTACGGACTC 59.453 50.000 18.68 0.0 40.57 3.36 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
315 317 5.587844 CCAGTCCCAATTCAGAAAGACTATG 59.412 44.000 7.72 1.03 33.44 2.23
486 490 1.202348 CACCACACATAGTCTCGCTGA 59.798 52.381 0.00 0.00 0.00 4.26
522 526 5.132502 TCAATCACACTTCAATCACCAGTT 58.867 37.500 0.00 0.00 0.00 3.16
566 570 2.035237 GACCTCCACCAACACCGACA 62.035 60.000 0.00 0.00 0.00 4.35
660 664 1.126488 ATCATCACCACCGCAGAGAT 58.874 50.000 0.00 0.00 0.00 2.75
670 674 2.099831 GCAGAGATGCGCAAGTGC 59.900 61.111 17.11 17.20 41.68 4.40
719 723 5.972935 TGACAAGACTAGTCAGTTCAACAA 58.027 37.500 24.44 0.00 40.80 2.83
916 930 0.749649 CATCTCTCCCTCGTTCCCAG 59.250 60.000 0.00 0.00 0.00 4.45
1005 1019 2.124193 CGGATGAAGGCCATGGCA 60.124 61.111 36.56 18.14 44.11 4.92
1080 1094 2.165845 CCTCGTCGACATTAAAGTCCCT 59.834 50.000 17.16 0.00 35.07 4.20
1114 1128 1.335689 ACTACACCAGAACGCTCGAAC 60.336 52.381 0.00 0.00 0.00 3.95
1246 1260 3.509137 ATCGTCGGCGTTGGTGTGT 62.509 57.895 10.18 0.00 39.49 3.72
1313 1327 2.228103 AGTTGTGCATCGACGAACTCTA 59.772 45.455 0.00 0.00 35.69 2.43
1944 2062 4.074970 CAAAATGTCTCTACCCTTGCAGT 58.925 43.478 0.00 0.00 0.00 4.40
2077 2195 4.214119 CCAACAAGTTCATCGACATTCAGT 59.786 41.667 0.00 0.00 0.00 3.41
2245 2363 1.271379 ACAACCTCATCGAGTACGCAA 59.729 47.619 0.00 0.00 39.58 4.85
2297 2415 3.380320 TGGTTCATGATCGACTACGTCAT 59.620 43.478 0.00 0.00 39.12 3.06
2407 2525 2.166459 GCCTGCCTTCATTTTACTTCCC 59.834 50.000 0.00 0.00 0.00 3.97
2624 2747 2.548057 GCTTCTGAATGGAACGTTGTCA 59.452 45.455 5.00 4.24 0.00 3.58
2702 2825 4.058124 GCACAACTCAGTACACTTGATCA 58.942 43.478 0.00 0.00 0.00 2.92
2703 2826 4.511454 GCACAACTCAGTACACTTGATCAA 59.489 41.667 8.12 8.12 0.00 2.57
3080 3212 3.529341 ATCCGCACAACGCAGGACA 62.529 57.895 0.00 0.00 43.09 4.02
3084 3216 2.967076 CACAACGCAGGACACGCT 60.967 61.111 0.00 0.00 0.00 5.07
3122 3262 3.513438 GAGAGAGAGCGAGCGCCA 61.513 66.667 11.66 0.00 43.17 5.69
3172 3312 1.733399 GTTCGACTGGTGAGCGTCC 60.733 63.158 0.00 0.00 0.00 4.79
3280 3420 1.810606 CGCGGATGAGCTATCTGGGT 61.811 60.000 0.00 0.00 45.34 4.51
3338 3479 1.080329 ACCCCACCAAAATAAGCCCAT 59.920 47.619 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
486 490 7.389330 TGAAGTGTGATTGAACGTACCAATTAT 59.611 33.333 14.67 0.37 34.67 1.28
522 526 6.246163 TGAACTCCTCTACTGTCATACTCAA 58.754 40.000 0.00 0.00 0.00 3.02
566 570 1.523711 CCCACTTGCACGTGTCAGT 60.524 57.895 20.52 15.86 33.07 3.41
670 674 5.727791 GCTGTACTTATGACCTGCAAAATCG 60.728 44.000 0.00 0.00 0.00 3.34
916 930 0.318699 GAAGCGGCAAGGGTTGTTTC 60.319 55.000 1.45 0.00 0.00 2.78
1005 1019 1.604378 CTTGGCGGATGGTTCCTCT 59.396 57.895 0.00 0.00 40.17 3.69
1114 1128 2.825836 GCCATGGAGCTCAACCCG 60.826 66.667 18.40 0.00 0.00 5.28
1246 1260 6.350445 GGAGGTTAATCTTCGTTGGTGTAGTA 60.350 42.308 0.00 0.00 0.00 1.82
1572 1690 8.585018 TCACTACATCAAGTTCAGAAACATCTA 58.415 33.333 0.00 0.00 37.88 1.98
2053 2171 3.058293 TGAATGTCGATGAACTTGTTGGC 60.058 43.478 0.00 0.00 0.00 4.52
2245 2363 2.494918 GGCGTACGCATCCAGTCT 59.505 61.111 37.99 0.00 44.11 3.24
2297 2415 5.937540 TCTTTCGCAAATTCTGAACCATCTA 59.062 36.000 0.00 0.00 0.00 1.98
2375 2493 3.308401 TGAAGGCAGGCTCTGATGTATA 58.692 45.455 0.00 0.00 32.44 1.47
2407 2525 4.240096 CAAGATAAAAGGCAAGCACAAGG 58.760 43.478 0.00 0.00 0.00 3.61
2624 2747 9.482627 GCATCATAACTAGTACTTTAGAGCAAT 57.517 33.333 0.00 0.00 0.00 3.56
2744 2869 2.547211 TCATAGTAGCGCTTACGGACTC 59.453 50.000 18.68 0.00 40.57 3.36
2992 3124 4.020617 CTGCGCCTGACCTTGGGA 62.021 66.667 4.18 0.00 0.00 4.37
3084 3216 4.918360 ACCTGTGGGCCCTGGTCA 62.918 66.667 25.70 15.38 31.72 4.02
3122 3262 4.099573 ACACTTACCTGAGCGCTTATACAT 59.900 41.667 13.26 0.00 0.00 2.29
3280 3420 1.027792 GCTATTGGGCCGTTTTCCGA 61.028 55.000 0.00 0.00 39.56 4.55
3338 3479 2.420827 CCCGCCATCTGGTTTGTATACA 60.421 50.000 0.08 0.08 37.57 2.29


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

AutoCloner maintained by Alex Coulton.