Multiple sequence alignment - TraesCS3B01G354700

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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 TraesCS3B01G354700 chr3B 100.000 2450 0 0 1 2450 565179966 565182415 0 4525
1 TraesCS3B01G354700 chr3B 94.048 2453 128 14 1 2450 409840481 409838044 0 3705
2 TraesCS3B01G354700 chr3B 91.956 2474 173 11 1 2450 398773031 398775502 0 3443
3 TraesCS3B01G354700 chr3B 88.772 2476 204 41 1 2449 71908825 71911253 0 2964
4 TraesCS3B01G354700 chr3B 88.024 2480 250 26 1 2449 120083002 120080539 0 2891
5 TraesCS3B01G354700 chr3B 87.021 2481 239 54 1 2449 295072166 295069737 0 2721
6 TraesCS3B01G354700 chr3B 87.153 2343 243 39 1 2310 74830739 74828422 0 2606
7 TraesCS3B01G354700 chr3B 89.679 1182 90 18 1 1151 376502242 376503422 0 1478
8 TraesCS3B01G354700 chr3B 84.603 1247 154 23 1 1219 286885364 286884128 0 1205
9 TraesCS3B01G354700 chr3B 92.510 494 37 0 1 494 40495223 40495716 0 708
10 TraesCS3B01G354700 chr2B 94.130 2453 135 8 1 2448 550642976 550640528 0 3723
11 TraesCS3B01G354700 chr5B 93.071 2468 143 12 3 2448 316555857 316553396 0 3585
12 TraesCS3B01G354700 chrUn 91.754 2474 179 9 1 2450 59444602 59442130 0 3415
13 TraesCS3B01G354700 chrUn 90.505 1959 161 17 494 2450 79019530 79017595 0 2564
14 TraesCS3B01G354700 chr6B 88.535 2477 246 16 2 2449 144614275 144616742 0 2966
15 TraesCS3B01G354700 chr6B 85.882 2387 261 36 93 2449 371840573 371842913 0 2471
16 TraesCS3B01G354700 chr7B 91.624 1958 156 6 494 2449 476087354 476085403 0 2700


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 TraesCS3B01G354700 chr3B 565179966 565182415 2449 False 4525 4525 100.000 1 2450 1 chr3B.!!$F5 2449
1 TraesCS3B01G354700 chr3B 409838044 409840481 2437 True 3705 3705 94.048 1 2450 1 chr3B.!!$R5 2449
2 TraesCS3B01G354700 chr3B 398773031 398775502 2471 False 3443 3443 91.956 1 2450 1 chr3B.!!$F4 2449
3 TraesCS3B01G354700 chr3B 71908825 71911253 2428 False 2964 2964 88.772 1 2449 1 chr3B.!!$F2 2448
4 TraesCS3B01G354700 chr3B 120080539 120083002 2463 True 2891 2891 88.024 1 2449 1 chr3B.!!$R2 2448
5 TraesCS3B01G354700 chr3B 295069737 295072166 2429 True 2721 2721 87.021 1 2449 1 chr3B.!!$R4 2448
6 TraesCS3B01G354700 chr3B 74828422 74830739 2317 True 2606 2606 87.153 1 2310 1 chr3B.!!$R1 2309
7 TraesCS3B01G354700 chr3B 376502242 376503422 1180 False 1478 1478 89.679 1 1151 1 chr3B.!!$F3 1150
8 TraesCS3B01G354700 chr3B 286884128 286885364 1236 True 1205 1205 84.603 1 1219 1 chr3B.!!$R3 1218
9 TraesCS3B01G354700 chr2B 550640528 550642976 2448 True 3723 3723 94.130 1 2448 1 chr2B.!!$R1 2447
10 TraesCS3B01G354700 chr5B 316553396 316555857 2461 True 3585 3585 93.071 3 2448 1 chr5B.!!$R1 2445
11 TraesCS3B01G354700 chrUn 59442130 59444602 2472 True 3415 3415 91.754 1 2450 1 chrUn.!!$R1 2449
12 TraesCS3B01G354700 chrUn 79017595 79019530 1935 True 2564 2564 90.505 494 2450 1 chrUn.!!$R2 1956
13 TraesCS3B01G354700 chr6B 144614275 144616742 2467 False 2966 2966 88.535 2 2449 1 chr6B.!!$F1 2447
14 TraesCS3B01G354700 chr6B 371840573 371842913 2340 False 2471 2471 85.882 93 2449 1 chr6B.!!$F2 2356
15 TraesCS3B01G354700 chr7B 476085403 476087354 1951 True 2700 2700 91.624 494 2449 1 chr7B.!!$R1 1955

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
449 450 1.813513 CACCAGGAGATGTGTCCAAC 58.186 55.0 0.0 0.0 39.34 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2137 0.038166 ACCCGATTTCACATGCCACT 59.962 50.0 0.0 0.0 0.0 4.0 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
213 214 1.887198 CGTGGTTACTCTCACACTCCT 59.113 52.381 0.00 0.00 33.83 3.69
214 215 3.079578 CGTGGTTACTCTCACACTCCTA 58.920 50.000 0.00 0.00 33.83 2.94
354 355 7.042725 TCGTTTGCTTCTAGTAATCATATGCAC 60.043 37.037 0.00 0.00 0.00 4.57
449 450 1.813513 CACCAGGAGATGTGTCCAAC 58.186 55.000 0.00 0.00 39.34 3.77
542 573 2.738846 ACATAGACAAGCTCGCACTTTG 59.261 45.455 0.00 0.00 0.00 2.77
643 674 3.055094 TGGGAATGAGCTAGTGGAAGAAC 60.055 47.826 0.00 0.00 0.00 3.01
686 717 3.670625 TCAACGCTGGCAGTACTATTTT 58.329 40.909 17.16 0.00 0.00 1.82
799 830 3.181467 CCTTGAGCAAGAGATACCTCAGG 60.181 52.174 11.61 0.00 41.87 3.86
842 873 5.251764 AGACAAGGAACAAGATGATCAAGG 58.748 41.667 0.00 0.00 0.00 3.61
876 907 4.151335 CCAAGTGATCAAGTTGAAGACTCG 59.849 45.833 10.14 4.34 41.10 4.18
910 941 9.660180 CTACTCCTGAAGAAGTAAAATAAGCTT 57.340 33.333 3.48 3.48 0.00 3.74
976 1007 2.168326 ACATGAGCGTGATGTGTCAA 57.832 45.000 0.00 0.00 35.80 3.18
981 1012 2.942376 TGAGCGTGATGTGTCAAGTTTT 59.058 40.909 0.00 0.00 36.40 2.43
1154 1185 6.519679 TCATAGTTACTTTCCTCGTGCTAA 57.480 37.500 0.00 0.00 0.00 3.09
1253 1284 3.535561 ACCTTGCTGATTTCTACCATCG 58.464 45.455 0.00 0.00 0.00 3.84
1528 1567 3.117888 AGCAAAAGGAGAGGAGTCACAAA 60.118 43.478 0.00 0.00 0.00 2.83
1550 1589 2.417924 GCACGAGGATGTGAGAGTGATT 60.418 50.000 0.00 0.00 42.55 2.57
1562 1601 2.165437 GAGAGTGATTGAGCGAGACCTT 59.835 50.000 0.00 0.00 0.00 3.50
1568 1609 3.055891 TGATTGAGCGAGACCTTCATCAA 60.056 43.478 0.00 0.00 36.30 2.57
1662 1704 2.192664 TTTGGGTCGCTTGAGCAATA 57.807 45.000 3.65 0.00 41.93 1.90
1834 1876 9.924650 TCAAATCCTTAGTACACTAGAAAACTC 57.075 33.333 0.00 0.00 0.00 3.01
1887 1930 4.895224 AGATCACGACGTTTAGATGCTA 57.105 40.909 0.00 0.00 0.00 3.49
1996 2039 3.424703 ACCAAACATGGAGAAGTGATGG 58.575 45.455 1.10 0.00 34.42 3.51
1998 2041 3.441572 CCAAACATGGAGAAGTGATGGTC 59.558 47.826 0.00 0.00 0.00 4.02
2093 2137 1.134128 CATGTCATGTTCCCGGGATCA 60.134 52.381 31.49 31.49 0.00 2.92
2189 2233 1.304630 TGTTCTCGGGATCGGTGGA 60.305 57.895 0.00 0.00 36.95 4.02
2264 2319 4.038763 GTGTATACCATGTTCTCGGGATCA 59.961 45.833 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 3.257375 TCAAAAACTACTCCTCGCTGCTA 59.743 43.478 0.00 0.00 0.00 3.49
213 214 4.484236 CGAAGCTCATGCCAAAACAATTA 58.516 39.130 0.00 0.00 40.80 1.40
214 215 3.319755 CGAAGCTCATGCCAAAACAATT 58.680 40.909 0.00 0.00 40.80 2.32
354 355 5.565834 GCTCTCCTCTTCATACCTAAATCCG 60.566 48.000 0.00 0.00 0.00 4.18
542 573 1.887198 TCCAAGTGAACTCGAGACTCC 59.113 52.381 21.68 9.05 0.00 3.85
799 830 8.594881 TTGTCTTCTAGTTCATCTTCTTCAAC 57.405 34.615 0.00 0.00 0.00 3.18
842 873 1.135721 GATCACTTGGGAATTGCAGCC 59.864 52.381 0.00 0.00 0.00 4.85
876 907 8.508883 TTACTTCTTCAGGAGTAGTAGATGAC 57.491 38.462 0.00 0.00 38.81 3.06
904 935 8.298729 TCTTCATCTTCATCTACAGAAGCTTA 57.701 34.615 0.00 0.00 41.68 3.09
910 941 6.665248 TCAGGTTCTTCATCTTCATCTACAGA 59.335 38.462 0.00 0.00 0.00 3.41
976 1007 5.012893 GTCATCAAGAGGATTGGGAAAACT 58.987 41.667 0.00 0.00 32.57 2.66
981 1012 3.686405 GCATGTCATCAAGAGGATTGGGA 60.686 47.826 0.00 0.00 32.57 4.37
1069 1100 6.835819 ATCATCATATCCAAGCAAATGAGG 57.164 37.500 0.00 0.00 32.25 3.86
1528 1567 0.529833 CACTCTCACATCCTCGTGCT 59.470 55.000 0.00 0.00 36.80 4.40
1550 1589 3.616956 ATTTGATGAAGGTCTCGCTCA 57.383 42.857 0.00 0.00 0.00 4.26
1562 1601 2.917933 CTCACCGGGCTTATTTGATGA 58.082 47.619 6.32 0.00 0.00 2.92
1568 1609 3.118038 TGAAATAGCTCACCGGGCTTATT 60.118 43.478 6.32 3.72 40.74 1.40
1632 1674 1.130561 GCGACCCAAATAGCAGTTGAC 59.869 52.381 0.00 0.00 0.00 3.18
1662 1704 8.980481 AAATTCAGTGGGACGATATTTAAGAT 57.020 30.769 0.00 0.00 0.00 2.40
1834 1876 6.611381 TCGAGGTAAAAGCAGAAAATGATTG 58.389 36.000 0.00 0.00 37.65 2.67
1996 2039 4.226761 CGCATAAGAACAAAAACAGGGAC 58.773 43.478 0.00 0.00 0.00 4.46
1998 2041 4.237349 ACGCATAAGAACAAAAACAGGG 57.763 40.909 0.00 0.00 0.00 4.45
2059 2102 4.342378 ACATGACATGCTACTGTAGGTAGG 59.658 45.833 15.49 2.11 45.83 3.18
2093 2137 0.038166 ACCCGATTTCACATGCCACT 59.962 50.000 0.00 0.00 0.00 4.00
2170 2214 1.153628 CCACCGATCCCGAGAACAC 60.154 63.158 0.00 0.00 38.22 3.32
2264 2319 3.650942 TCTCACCAAAGGAACATACCACT 59.349 43.478 0.00 0.00 0.00 4.00
2380 2462 2.091541 GCATGATCCCGAGACCAAAAA 58.908 47.619 0.00 0.00 0.00 1.94
2386 2468 1.327303 AGAGAGCATGATCCCGAGAC 58.673 55.000 7.49 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.