Multiple sequence alignment - TraesCS2B01G166200

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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 TraesCS2B01G166200 chr2B 100.000 3470 0 0 1 3470 138994290 138990821 0.000000e+00 6408.0
1 TraesCS2B01G166200 chr2B 83.798 1901 269 23 638 2507 12421941 12423833 0.000000e+00 1768.0
2 TraesCS2B01G166200 chr2B 84.871 1778 234 26 827 2581 768807179 768805414 0.000000e+00 1760.0
3 TraesCS2B01G166200 chr2B 83.179 1938 285 23 638 2545 11518690 11516764 0.000000e+00 1735.0
4 TraesCS2B01G166200 chr2B 84.991 1739 218 18 828 2545 11445270 11446986 0.000000e+00 1725.0
5 TraesCS2B01G166200 chr2B 88.506 87 10 0 702 788 12996327 12996241 4.740000e-19 106.0
6 TraesCS2B01G166200 chr2B 84.211 95 15 0 683 777 13347775 13347681 3.690000e-15 93.5
7 TraesCS2B01G166200 chr2D 95.630 3364 98 10 1 3337 85930608 85927267 0.000000e+00 5352.0
8 TraesCS2B01G166200 chr2D 85.868 1861 225 22 683 2512 8695341 8697194 0.000000e+00 1945.0
9 TraesCS2B01G166200 chr2D 82.425 2128 308 37 427 2515 19586434 19588534 0.000000e+00 1797.0
10 TraesCS2B01G166200 chr2D 85.756 1706 205 20 828 2512 9665423 9663735 0.000000e+00 1770.0
11 TraesCS2B01G166200 chr2D 83.784 1850 270 19 681 2507 9604425 9606267 0.000000e+00 1727.0
12 TraesCS2B01G166200 chr2D 82.756 1531 225 18 995 2508 8670684 8672192 0.000000e+00 1328.0
13 TraesCS2B01G166200 chr2D 98.551 138 2 0 3333 3470 85927111 85926974 9.620000e-61 244.0
14 TraesCS2B01G166200 chr2A 91.131 1353 98 8 756 2105 86432355 86431022 0.000000e+00 1814.0
15 TraesCS2B01G166200 chr2A 83.426 1792 269 18 737 2507 8707129 8708913 0.000000e+00 1639.0
16 TraesCS2B01G166200 chr2A 82.835 1573 233 21 998 2554 9121997 9120446 0.000000e+00 1375.0
17 TraesCS2B01G166200 chr2A 82.293 1169 162 23 1377 2531 7514379 7513242 0.000000e+00 970.0
18 TraesCS2B01G166200 chr2A 92.184 499 25 8 2104 2595 86387305 86386814 0.000000e+00 693.0
19 TraesCS2B01G166200 chr2A 80.586 546 81 11 683 1211 9941530 9942067 6.980000e-107 398.0
20 TraesCS2B01G166200 chr2A 83.846 390 20 12 114 486 86432716 86432353 7.180000e-87 331.0
21 TraesCS2B01G166200 chr2A 76.923 429 65 20 3009 3415 8626211 8626627 2.710000e-51 213.0
22 TraesCS2B01G166200 chr7D 82.353 1921 255 50 692 2584 589391535 589389671 0.000000e+00 1592.0


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 TraesCS2B01G166200 chr2B 138990821 138994290 3469 True 6408.0 6408 100.0000 1 3470 1 chr2B.!!$R4 3469
1 TraesCS2B01G166200 chr2B 12421941 12423833 1892 False 1768.0 1768 83.7980 638 2507 1 chr2B.!!$F2 1869
2 TraesCS2B01G166200 chr2B 768805414 768807179 1765 True 1760.0 1760 84.8710 827 2581 1 chr2B.!!$R5 1754
3 TraesCS2B01G166200 chr2B 11516764 11518690 1926 True 1735.0 1735 83.1790 638 2545 1 chr2B.!!$R1 1907
4 TraesCS2B01G166200 chr2B 11445270 11446986 1716 False 1725.0 1725 84.9910 828 2545 1 chr2B.!!$F1 1717
5 TraesCS2B01G166200 chr2D 85926974 85930608 3634 True 2798.0 5352 97.0905 1 3470 2 chr2D.!!$R2 3469
6 TraesCS2B01G166200 chr2D 8695341 8697194 1853 False 1945.0 1945 85.8680 683 2512 1 chr2D.!!$F2 1829
7 TraesCS2B01G166200 chr2D 19586434 19588534 2100 False 1797.0 1797 82.4250 427 2515 1 chr2D.!!$F4 2088
8 TraesCS2B01G166200 chr2D 9663735 9665423 1688 True 1770.0 1770 85.7560 828 2512 1 chr2D.!!$R1 1684
9 TraesCS2B01G166200 chr2D 9604425 9606267 1842 False 1727.0 1727 83.7840 681 2507 1 chr2D.!!$F3 1826
10 TraesCS2B01G166200 chr2D 8670684 8672192 1508 False 1328.0 1328 82.7560 995 2508 1 chr2D.!!$F1 1513
11 TraesCS2B01G166200 chr2A 8707129 8708913 1784 False 1639.0 1639 83.4260 737 2507 1 chr2A.!!$F2 1770
12 TraesCS2B01G166200 chr2A 9120446 9121997 1551 True 1375.0 1375 82.8350 998 2554 1 chr2A.!!$R2 1556
13 TraesCS2B01G166200 chr2A 86431022 86432716 1694 True 1072.5 1814 87.4885 114 2105 2 chr2A.!!$R4 1991
14 TraesCS2B01G166200 chr2A 7513242 7514379 1137 True 970.0 970 82.2930 1377 2531 1 chr2A.!!$R1 1154
15 TraesCS2B01G166200 chr2A 9941530 9942067 537 False 398.0 398 80.5860 683 1211 1 chr2A.!!$F3 528
16 TraesCS2B01G166200 chr7D 589389671 589391535 1864 True 1592.0 1592 82.3530 692 2584 1 chr7D.!!$R1 1892

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
408 427 0.034863 TTTCGGGTACAATGCCCTCC 60.035 55.0 0.25 0.0 43.92 4.30 F
554 573 1.308998 AGCTCAAACAGTTTCCACCG 58.691 50.0 0.00 0.0 0.00 4.94 F
1277 1373 0.613777 AGCTACCGAAACCTCCAAGG 59.386 55.0 0.00 0.0 42.49 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1356 0.323629 TGCCTTGGAGGTTTCGGTAG 59.676 55.0 0.0 0.0 37.80 3.18 R
1953 2058 0.729116 CGAATGCCAGCGTCTTGAAT 59.271 50.0 0.0 0.0 0.00 2.57 R
3241 3371 0.407528 TAATGCTTTGCCCAGGTGGA 59.592 50.0 0.0 0.0 37.39 4.02 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
35 36 8.440771 AGTAAAATGGAGAAGAAAAAGGAGAGA 58.559 33.333 0.00 0.00 0.00 3.10
37 38 4.278975 TGGAGAAGAAAAAGGAGAGAGC 57.721 45.455 0.00 0.00 0.00 4.09
40 41 2.037772 AGAAGAAAAAGGAGAGAGCGCA 59.962 45.455 11.47 0.00 0.00 6.09
44 45 0.681733 AAAAGGAGAGAGCGCAGTGA 59.318 50.000 11.47 0.00 0.00 3.41
201 207 1.605232 TGCACACTGATTGCAACAGAG 59.395 47.619 25.72 21.67 46.90 3.35
263 276 4.689612 TTGTTTACTCTCTGCCTGACTT 57.310 40.909 0.00 0.00 0.00 3.01
298 317 3.671716 AGGACAACCGATAAAACTGACC 58.328 45.455 0.00 0.00 41.83 4.02
346 365 1.873591 GACGGTGATGACTTGCAAGTT 59.126 47.619 31.58 18.19 39.88 2.66
359 378 0.605589 GCAAGTTACGCCACCTCCTT 60.606 55.000 0.00 0.00 0.00 3.36
364 383 2.046009 TTACGCCACCTCCTTGCACA 62.046 55.000 0.00 0.00 0.00 4.57
408 427 0.034863 TTTCGGGTACAATGCCCTCC 60.035 55.000 0.25 0.00 43.92 4.30
433 452 9.499479 CCGGAAGATCACTACTACTAAAGTATA 57.501 37.037 0.00 0.00 39.96 1.47
554 573 1.308998 AGCTCAAACAGTTTCCACCG 58.691 50.000 0.00 0.00 0.00 4.94
634 655 7.040409 GGAGTCCAACACAAAAGAGAAATACAT 60.040 37.037 3.60 0.00 0.00 2.29
636 657 9.520515 AGTCCAACACAAAAGAGAAATACATAT 57.479 29.630 0.00 0.00 0.00 1.78
871 942 1.966451 CACCCACCCTTGAACTCGC 60.966 63.158 0.00 0.00 0.00 5.03
909 986 8.734386 GGAGACATTTCTACTGTTTGATGAATT 58.266 33.333 0.00 0.00 28.54 2.17
1186 1282 4.210328 CAGATGCGCGGTACATAACAAATA 59.790 41.667 8.83 0.00 0.00 1.40
1260 1356 3.660621 GTGCTGGACACCTTGAGC 58.339 61.111 0.00 0.00 44.02 4.26
1277 1373 0.613777 AGCTACCGAAACCTCCAAGG 59.386 55.000 0.00 0.00 42.49 3.61
1282 1378 0.955919 CCGAAACCTCCAAGGCAGTC 60.956 60.000 0.00 0.00 39.63 3.51
1953 2058 2.479566 ACGACGAGTTGAGGTACCTA 57.520 50.000 16.29 0.00 0.00 3.08
2571 2701 3.061322 TGGAGTTAAACGGATGTGTTCG 58.939 45.455 0.00 0.00 0.00 3.95
2890 3020 4.620589 ATTGTGTCAATTTGGATGCCAA 57.379 36.364 0.00 0.00 42.29 4.52
2979 3109 1.688735 CTAGGCATCAGGTCGGATCAA 59.311 52.381 0.00 0.00 0.00 2.57
3049 3179 6.128472 ACAGGTTTATTGAAATTACCGACGAC 60.128 38.462 0.00 0.00 34.09 4.34
3057 3187 2.068837 ATTACCGACGACTGCGAAAA 57.931 45.000 0.00 0.00 41.64 2.29
3157 3287 2.105128 CCCTTGAGGCGCTCGTAG 59.895 66.667 7.64 4.83 32.35 3.51
3158 3288 2.415608 CCCTTGAGGCGCTCGTAGA 61.416 63.158 7.64 0.00 32.35 2.59
3159 3289 1.226717 CCTTGAGGCGCTCGTAGAC 60.227 63.158 7.64 0.00 32.35 2.59
3200 3330 1.836166 TGCATCTCTTCCCTTCCTCTG 59.164 52.381 0.00 0.00 0.00 3.35
3242 3372 3.005539 TCCTGGGTGGAGCAGCTC 61.006 66.667 14.69 14.69 40.56 4.09
3325 3455 8.742777 TCTGCTTTTTCATGCATTAGTTTCTAT 58.257 29.630 0.00 0.00 38.59 1.98
3327 3457 9.709495 TGCTTTTTCATGCATTAGTTTCTATTT 57.291 25.926 0.00 0.00 33.94 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.391833 GCTCTCTCCTTTTTCTTCTCCATTTTA 59.608 37.037 0.00 0.00 0.00 1.52
20 21 2.414825 CTGCGCTCTCTCCTTTTTCTTC 59.585 50.000 9.73 0.00 0.00 2.87
35 36 1.376424 CATTGGAGGTCACTGCGCT 60.376 57.895 9.73 0.00 37.98 5.92
37 38 3.181367 GCATTGGAGGTCACTGCG 58.819 61.111 0.00 0.00 41.13 5.18
40 41 0.482446 TTTGGGCATTGGAGGTCACT 59.518 50.000 0.00 0.00 0.00 3.41
44 45 1.184970 CCGTTTTGGGCATTGGAGGT 61.185 55.000 0.00 0.00 0.00 3.85
196 202 3.771479 TCCACTTATGTGATCTGCTCTGT 59.229 43.478 10.20 0.00 46.55 3.41
201 207 5.049818 GTGCTAATCCACTTATGTGATCTGC 60.050 44.000 10.20 8.06 46.55 4.26
263 276 4.134563 GGTTGTCCTTCTAGCAAAAGACA 58.865 43.478 0.00 0.00 0.00 3.41
298 317 3.599285 TTCACGCCCGCCTTGTAGG 62.599 63.158 0.00 0.00 38.80 3.18
346 365 1.836999 ATGTGCAAGGAGGTGGCGTA 61.837 55.000 0.00 0.00 0.00 4.42
359 378 0.961857 CAAGCTACTGGCCATGTGCA 60.962 55.000 20.85 0.00 43.89 4.57
364 383 0.890683 GCAAACAAGCTACTGGCCAT 59.109 50.000 5.51 0.00 43.05 4.40
439 458 7.671398 ACCTTGGTCAGTGATGAGAATAATTTT 59.329 33.333 0.00 0.00 0.00 1.82
440 459 7.177878 ACCTTGGTCAGTGATGAGAATAATTT 58.822 34.615 0.00 0.00 0.00 1.82
554 573 5.652744 TTTCTACTCGAGCAAAGTTTGAC 57.347 39.130 19.82 10.38 0.00 3.18
871 942 4.763793 AGAAATGTCTCCAATTGACTGTGG 59.236 41.667 7.12 0.00 35.63 4.17
909 986 4.342862 AGCTTCTGCAAGTCTTACAGAA 57.657 40.909 21.73 21.73 45.56 3.02
1186 1282 0.178981 AGCTGCAACAACATCCCAGT 60.179 50.000 1.02 0.00 0.00 4.00
1260 1356 0.323629 TGCCTTGGAGGTTTCGGTAG 59.676 55.000 0.00 0.00 37.80 3.18
1277 1373 1.364626 CTCGTCAATGCCTGGACTGC 61.365 60.000 0.00 0.00 31.88 4.40
1282 1378 1.656652 CTAACCTCGTCAATGCCTGG 58.343 55.000 0.00 0.00 0.00 4.45
1845 1950 3.947612 ATGATGATCTTGCTTCCACCT 57.052 42.857 0.00 0.00 0.00 4.00
1899 2004 5.119694 CCTAGGAAAATAGGCTTCACAGAC 58.880 45.833 1.05 0.00 36.16 3.51
1953 2058 0.729116 CGAATGCCAGCGTCTTGAAT 59.271 50.000 0.00 0.00 0.00 2.57
2339 2453 4.889409 TCCTTGATTCCCATGCAATTAGAC 59.111 41.667 0.00 0.00 0.00 2.59
2522 2652 3.128589 ACATGAACACACCTGTTTGTCAC 59.871 43.478 0.00 0.00 40.93 3.67
2531 2661 2.618816 CCATAGCCACATGAACACACCT 60.619 50.000 0.00 0.00 0.00 4.00
2760 2890 7.856145 ACAAAATTTGAACCAAAACTATGCA 57.144 28.000 13.19 0.00 36.90 3.96
2793 2923 0.701731 TTGGATGGAACGGTTGGGAT 59.298 50.000 0.00 0.00 0.00 3.85
3000 3130 7.335924 TGTTTAGATACCGGAATCTCCAAAAAG 59.664 37.037 9.46 0.00 37.41 2.27
3006 3136 4.344390 ACCTGTTTAGATACCGGAATCTCC 59.656 45.833 9.46 0.00 37.41 3.71
3049 3179 1.205064 CGGTGCTCTGTTTTCGCAG 59.795 57.895 0.00 0.00 37.81 5.18
3057 3187 2.341543 CTGTGCTCGGTGCTCTGT 59.658 61.111 3.53 0.00 43.37 3.41
3200 3330 0.464036 TATCCCATCACACCTCGTGC 59.536 55.000 0.00 0.00 45.92 5.34
3241 3371 0.407528 TAATGCTTTGCCCAGGTGGA 59.592 50.000 0.00 0.00 37.39 4.02
3242 3372 1.137479 CATAATGCTTTGCCCAGGTGG 59.863 52.381 0.00 0.00 37.09 4.61
3243 3373 1.826720 ACATAATGCTTTGCCCAGGTG 59.173 47.619 0.00 0.00 0.00 4.00
3244 3374 2.236489 ACATAATGCTTTGCCCAGGT 57.764 45.000 0.00 0.00 0.00 4.00
3245 3375 3.890756 TGATACATAATGCTTTGCCCAGG 59.109 43.478 0.00 0.00 0.00 4.45
3246 3376 5.717078 ATGATACATAATGCTTTGCCCAG 57.283 39.130 0.00 0.00 0.00 4.45
3287 3417 7.676807 GCATGAAAAAGCAGACAAACAATTCAA 60.677 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.