Multiple sequence alignment - TraesCS4A01G382100

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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 TraesCS4A01G382100 chr4A 100.000 3351 0 0 1 3351 660000381 660003731 0 6189
1 TraesCS4A01G382100 chr4A 95.813 1624 48 6 1000 2605 672472400 672470779 0 2604
2 TraesCS4A01G382100 chr6B 96.253 2375 64 4 1000 3351 600466221 600463849 0 3869
3 TraesCS4A01G382100 chr6B 96.244 2183 58 3 1000 3159 116565633 116567814 0 3555
4 TraesCS4A01G382100 chr6B 96.743 1044 31 1 2 1042 600467267 600466224 0 1736
5 TraesCS4A01G382100 chr6B 95.989 1047 37 2 1 1042 20414121 20415167 0 1696
6 TraesCS4A01G382100 chr1B 96.042 2375 48 5 1000 3351 653201382 653203733 0 3823
7 TraesCS4A01G382100 chr1B 95.368 2375 57 4 1000 3351 392638180 392640524 0 3727
8 TraesCS4A01G382100 chr1B 97.225 1045 26 1 1 1042 653200335 653201379 0 1766
9 TraesCS4A01G382100 chr1B 96.938 1045 29 1 1 1042 392637133 392638177 0 1749
10 TraesCS4A01G382100 chr5B 94.194 2377 57 11 1000 3351 9022987 9025307 0 3550
11 TraesCS4A01G382100 chr5B 95.874 1624 48 2 1000 2605 682755773 682757395 0 2610
12 TraesCS4A01G382100 chr5B 93.337 1711 59 17 1684 3339 695584186 695582476 0 2477
13 TraesCS4A01G382100 chr5B 96.842 1045 30 1 1 1042 9021940 9022984 0 1744
14 TraesCS4A01G382100 chr2B 96.737 1839 34 5 1536 3351 514849096 514847261 0 3040
15 TraesCS4A01G382100 chr2B 96.147 1661 45 3 1000 2642 762871831 762873490 0 2695
16 TraesCS4A01G382100 chr2B 96.826 1607 50 1 1000 2605 87173121 87171515 0 2684
17 TraesCS4A01G382100 chr2B 94.596 1499 79 2 1000 2497 750605839 750607336 0 2318
18 TraesCS4A01G382100 chr2B 96.842 1045 30 1 1 1042 762870784 762871828 0 1744
19 TraesCS4A01G382100 chr2B 95.502 1045 23 5 1 1042 514850529 514849506 0 1648
20 TraesCS4A01G382100 chr7B 95.876 1867 51 5 1508 3351 14312435 14314298 0 2998
21 TraesCS4A01G382100 chr7B 95.769 1867 54 4 1508 3351 14328384 14330248 0 2987
22 TraesCS4A01G382100 chr7B 96.459 1045 34 1 1 1042 14311008 14312052 0 1722
23 TraesCS4A01G382100 chr7B 96.268 1045 36 1 1 1042 14326957 14328001 0 1711
24 TraesCS4A01G382100 chr4B 96.325 1687 43 2 1000 2668 23184886 23183201 0 2754
25 TraesCS4A01G382100 chr4B 97.077 992 25 2 1 989 6419483 6420473 0 1668
26 TraesCS4A01G382100 chr4B 96.875 576 18 0 2776 3351 6422066 6422641 0 965
27 TraesCS4A01G382100 chr3B 96.206 1687 45 2 1000 2668 306836056 306834371 0 2743
28 TraesCS4A01G382100 chr3B 95.706 1607 57 4 1000 2605 27360515 27358920 0 2575
29 TraesCS4A01G382100 chr3B 95.382 1624 53 5 1000 2605 713896007 713894388 0 2564


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 TraesCS4A01G382100 chr4A 660000381 660003731 3350 False 6189.0 6189 100.0000 1 3351 1 chr4A.!!$F1 3350
1 TraesCS4A01G382100 chr4A 672470779 672472400 1621 True 2604.0 2604 95.8130 1000 2605 1 chr4A.!!$R1 1605
2 TraesCS4A01G382100 chr6B 116565633 116567814 2181 False 3555.0 3555 96.2440 1000 3159 1 chr6B.!!$F2 2159
3 TraesCS4A01G382100 chr6B 600463849 600467267 3418 True 2802.5 3869 96.4980 2 3351 2 chr6B.!!$R1 3349
4 TraesCS4A01G382100 chr6B 20414121 20415167 1046 False 1696.0 1696 95.9890 1 1042 1 chr6B.!!$F1 1041
5 TraesCS4A01G382100 chr1B 653200335 653203733 3398 False 2794.5 3823 96.6335 1 3351 2 chr1B.!!$F2 3350
6 TraesCS4A01G382100 chr1B 392637133 392640524 3391 False 2738.0 3727 96.1530 1 3351 2 chr1B.!!$F1 3350
7 TraesCS4A01G382100 chr5B 9021940 9025307 3367 False 2647.0 3550 95.5180 1 3351 2 chr5B.!!$F2 3350
8 TraesCS4A01G382100 chr5B 682755773 682757395 1622 False 2610.0 2610 95.8740 1000 2605 1 chr5B.!!$F1 1605
9 TraesCS4A01G382100 chr5B 695582476 695584186 1710 True 2477.0 2477 93.3370 1684 3339 1 chr5B.!!$R1 1655
10 TraesCS4A01G382100 chr2B 87171515 87173121 1606 True 2684.0 2684 96.8260 1000 2605 1 chr2B.!!$R1 1605
11 TraesCS4A01G382100 chr2B 514847261 514850529 3268 True 2344.0 3040 96.1195 1 3351 2 chr2B.!!$R2 3350
12 TraesCS4A01G382100 chr2B 750605839 750607336 1497 False 2318.0 2318 94.5960 1000 2497 1 chr2B.!!$F1 1497
13 TraesCS4A01G382100 chr2B 762870784 762873490 2706 False 2219.5 2695 96.4945 1 2642 2 chr2B.!!$F2 2641
14 TraesCS4A01G382100 chr7B 14311008 14314298 3290 False 2360.0 2998 96.1675 1 3351 2 chr7B.!!$F1 3350
15 TraesCS4A01G382100 chr7B 14326957 14330248 3291 False 2349.0 2987 96.0185 1 3351 2 chr7B.!!$F2 3350
16 TraesCS4A01G382100 chr4B 23183201 23184886 1685 True 2754.0 2754 96.3250 1000 2668 1 chr4B.!!$R1 1668
17 TraesCS4A01G382100 chr4B 6419483 6422641 3158 False 1316.5 1668 96.9760 1 3351 2 chr4B.!!$F1 3350
18 TraesCS4A01G382100 chr3B 306834371 306836056 1685 True 2743.0 2743 96.2060 1000 2668 1 chr3B.!!$R2 1668
19 TraesCS4A01G382100 chr3B 27358920 27360515 1595 True 2575.0 2575 95.7060 1000 2605 1 chr3B.!!$R1 1605
20 TraesCS4A01G382100 chr3B 713894388 713896007 1619 True 2564.0 2564 95.3820 1000 2605 1 chr3B.!!$R3 1605

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
893 899 1.575788 TGCTCCATCTTCCTCCCTCTA 59.424 52.381 0.00 0.0 0.00 2.43 F
1311 1407 0.385849 CGCAAATTGCTGCAGTTCGA 60.386 50.000 16.64 0.0 42.25 3.71 F
2032 2350 2.291741 GCTGAAGTTGTCTGGTTTGGAG 59.708 50.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2441 0.768221 TAGGATGGGTGGATGAGGCC 60.768 60.000 0.00 0.0 0.00 5.19 R
2167 2485 3.393426 AGTAGGTGGTCCGAATTCCTA 57.607 47.619 0.00 0.0 39.05 2.94 R
3217 3570 3.831911 CCCAGTTGTGTATTCCCAATTGT 59.168 43.478 4.43 0.0 29.31 2.71 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
93 94 6.073003 GGGTTTATCGATGCTAAGGAGAATTG 60.073 42.308 8.54 0.00 0.00 2.32
273 274 5.779529 GGTACCTGCAAATTCATCATGAT 57.220 39.130 4.06 1.18 0.00 2.45
282 283 6.039605 TGCAAATTCATCATGATACGATGGTT 59.960 34.615 8.15 0.00 40.58 3.67
507 508 8.430801 AATGCATGCAAGTTTAAAGTAAAACA 57.569 26.923 26.68 0.00 40.97 2.83
511 512 9.715123 GCATGCAAGTTTAAAGTAAAACATTTT 57.285 25.926 14.21 0.00 40.97 1.82
658 659 9.148104 GTTTCGTCAGATATAGGTGTAGTTTTT 57.852 33.333 0.00 0.00 0.00 1.94
708 709 3.403038 CTGGACGTTTCAGAAACAGGAT 58.597 45.455 23.02 7.62 41.44 3.24
720 721 2.124983 CAGGATGGCCCACGTCTG 60.125 66.667 0.00 0.00 37.41 3.51
893 899 1.575788 TGCTCCATCTTCCTCCCTCTA 59.424 52.381 0.00 0.00 0.00 2.43
1277 1373 3.441163 GCGTTGATGTCGAGTATACCAA 58.559 45.455 0.00 0.00 0.00 3.67
1310 1406 1.339235 CCGCAAATTGCTGCAGTTCG 61.339 55.000 16.64 10.72 42.25 3.95
1311 1407 0.385849 CGCAAATTGCTGCAGTTCGA 60.386 50.000 16.64 0.00 42.25 3.71
1486 1582 9.396022 TCTGAAGTTATGAAGTTTCTGAAGTTT 57.604 29.630 0.00 0.00 0.00 2.66
1797 2039 9.772973 TTGTAGTTGTTGTGATCATTTAGTAGT 57.227 29.630 0.00 0.00 0.00 2.73
1891 2134 6.454795 TCAACTGAACCCATTTTAATTCTGC 58.545 36.000 0.00 0.00 0.00 4.26
1902 2145 7.656948 CCCATTTTAATTCTGCAGTTTCTGAAA 59.343 33.333 14.67 9.50 32.44 2.69
2032 2350 2.291741 GCTGAAGTTGTCTGGTTTGGAG 59.708 50.000 0.00 0.00 0.00 3.86
2167 2485 5.181009 TCAAACATGAAGCAGAAGATCGAT 58.819 37.500 0.00 0.00 0.00 3.59
2271 2589 2.678336 CCTACGAGGCATGGAAGAAAAC 59.322 50.000 0.00 0.00 0.00 2.43
2317 2635 3.393970 TGGCAAGAGGCGGAGGAG 61.394 66.667 0.00 0.00 46.16 3.69
2373 2691 5.332743 AGTTGTTTGTGGTATTGGGATGAT 58.667 37.500 0.00 0.00 0.00 2.45
2605 2923 9.842775 GCATGGAAGATATAATCATCCTTATGA 57.157 33.333 11.30 0.00 45.11 2.15
2663 3011 1.963515 ACTGCAAACATTTCCCCTGTC 59.036 47.619 0.00 0.00 0.00 3.51
2962 3315 5.076873 ACACACACCAGGCAGTTTTTATAT 58.923 37.500 0.00 0.00 0.00 0.86
3015 3368 3.189287 CAGGACAAGAAAAATCTCCACCG 59.811 47.826 0.00 0.00 0.00 4.94
3217 3570 5.546499 AGGGAAACATCAGTTAGACCACTAA 59.454 40.000 0.00 0.00 36.84 2.24
3254 3607 0.618458 CTGGGGCTAGGTTTGTGCTA 59.382 55.000 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 3.694566 CCAAGTGATTAGGCCCAACTTAC 59.305 47.826 0.00 0.00 0.00 2.34
270 271 3.704061 TCATGTCTCCAACCATCGTATCA 59.296 43.478 0.00 0.00 0.00 2.15
273 274 2.167693 GGTCATGTCTCCAACCATCGTA 59.832 50.000 0.00 0.00 0.00 3.43
282 283 2.655090 TTGCAAAGGTCATGTCTCCA 57.345 45.000 0.00 0.00 0.00 3.86
507 508 9.740710 AAGAGGAGTACTTGCATTAACTAAAAT 57.259 29.630 0.00 0.00 0.00 1.82
658 659 1.550130 CGTGGGCCCTCCTGTTTCTA 61.550 60.000 25.70 0.00 36.20 2.10
720 721 0.391793 CCTCGAAAACTCTGGAGGGC 60.392 60.000 2.58 0.00 41.87 5.19
893 899 1.849039 CAATGGAATGAGGAGGGAGGT 59.151 52.381 0.00 0.00 0.00 3.85
960 966 1.151810 TGGAGGCAGAGGGGAGTTT 60.152 57.895 0.00 0.00 0.00 2.66
1185 1281 1.738099 CTTGTCGGCTTCGTCTGGG 60.738 63.158 0.00 0.00 35.06 4.45
1277 1373 0.472471 TTGCGGAGGTTTGTCTTCCT 59.528 50.000 0.00 0.00 39.76 3.36
1310 1406 2.101582 AGATCCTCCACGCATAACTGTC 59.898 50.000 0.00 0.00 0.00 3.51
1311 1407 2.101582 GAGATCCTCCACGCATAACTGT 59.898 50.000 0.00 0.00 0.00 3.55
1440 1536 7.881775 TCAGAACTAGTATGCATCTACTTCA 57.118 36.000 0.19 0.00 33.96 3.02
1531 1627 7.750229 ATTGCATCTACTTCAGAAACTTCAA 57.250 32.000 0.00 0.00 36.67 2.69
1797 2039 9.114952 TCAGTTAAAACAGTATGATCACAACAA 57.885 29.630 0.00 0.00 39.69 2.83
1902 2145 9.932207 TGCATCAAATTCATCTACTTCAAAAAT 57.068 25.926 0.00 0.00 0.00 1.82
2000 2316 3.879892 GACAACTTCAGCTTCTCCTTGTT 59.120 43.478 0.00 0.00 0.00 2.83
2032 2350 1.067354 ACGTACTTGTCGGGGTTGATC 60.067 52.381 0.00 0.00 0.00 2.92
2056 2374 6.855907 GGAACTCTCCATTTGCACTGCAAC 62.856 50.000 16.18 0.97 43.97 4.17
2123 2441 0.768221 TAGGATGGGTGGATGAGGCC 60.768 60.000 0.00 0.00 0.00 5.19
2167 2485 3.393426 AGTAGGTGGTCCGAATTCCTA 57.607 47.619 0.00 0.00 39.05 2.94
2271 2589 4.298332 CAAACCTTCTTTGGTGATTTCGG 58.702 43.478 0.00 0.00 40.73 4.30
2605 2923 7.943079 TGGAAAGATCATGTGTCATTGTAAT 57.057 32.000 0.00 0.00 0.00 1.89
2663 3011 6.976088 TGGTTGGAATGTGTAACTACAATTG 58.024 36.000 3.24 3.24 38.04 2.32
3217 3570 3.831911 CCCAGTTGTGTATTCCCAATTGT 59.168 43.478 4.43 0.00 29.31 2.71
3266 3619 6.436261 CAATGCCTCTATATGCTCTGTTTTG 58.564 40.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.