Multiple sequence alignment - TraesCS2D01G237000

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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 TraesCS2D01G237000 chr2D 100.000 2548 0 0 1 2548 238958323 238960870 0 4706
1 TraesCS2D01G237000 chr2D 93.463 566 32 3 1 562 49711624 49711060 0 835
2 TraesCS2D01G237000 chr2D 93.298 567 34 2 1 563 196702754 196703320 0 833
3 TraesCS2D01G237000 chr5D 96.289 1994 55 11 563 2548 336262623 336264605 0 3254
4 TraesCS2D01G237000 chr5D 94.595 1998 82 16 564 2548 520497539 520495555 0 3068
5 TraesCS2D01G237000 chr6D 96.187 1993 61 7 562 2548 109963210 109965193 0 3245
6 TraesCS2D01G237000 chr6D 96.093 1971 62 8 583 2548 52521727 52519767 0 3199
7 TraesCS2D01G237000 chr6D 93.827 567 31 2 1 563 271269051 271269617 0 850
8 TraesCS2D01G237000 chr7D 95.884 1992 61 17 564 2548 574727118 574725141 0 3205
9 TraesCS2D01G237000 chr7D 93.286 566 35 2 1 563 222405653 222405088 0 832
10 TraesCS2D01G237000 chr1D 95.635 1993 73 7 561 2548 26486135 26488118 0 3186
11 TraesCS2D01G237000 chr1D 93.640 566 33 2 1 563 194977859 194978424 0 843
12 TraesCS2D01G237000 chr1D 93.750 560 32 2 1 557 163758785 163759344 0 837
13 TraesCS2D01G237000 chrUn 95.248 1999 74 18 564 2548 93726510 93724519 0 3145
14 TraesCS2D01G237000 chr2B 94.558 2003 85 14 559 2548 4739871 4741862 0 3073
15 TraesCS2D01G237000 chr7A 94.436 1995 96 12 564 2548 15645803 15647792 0 3055
16 TraesCS2D01G237000 chr3D 93.651 567 32 2 1 563 346880576 346880010 0 845
17 TraesCS2D01G237000 chr3D 93.274 565 33 3 1 561 135490216 135490779 0 828
18 TraesCS2D01G237000 chr3A 93.628 565 31 4 2 563 595694509 595693947 0 839


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 TraesCS2D01G237000 chr2D 238958323 238960870 2547 False 4706 4706 100.000 1 2548 1 chr2D.!!$F2 2547
1 TraesCS2D01G237000 chr2D 49711060 49711624 564 True 835 835 93.463 1 562 1 chr2D.!!$R1 561
2 TraesCS2D01G237000 chr2D 196702754 196703320 566 False 833 833 93.298 1 563 1 chr2D.!!$F1 562
3 TraesCS2D01G237000 chr5D 336262623 336264605 1982 False 3254 3254 96.289 563 2548 1 chr5D.!!$F1 1985
4 TraesCS2D01G237000 chr5D 520495555 520497539 1984 True 3068 3068 94.595 564 2548 1 chr5D.!!$R1 1984
5 TraesCS2D01G237000 chr6D 109963210 109965193 1983 False 3245 3245 96.187 562 2548 1 chr6D.!!$F1 1986
6 TraesCS2D01G237000 chr6D 52519767 52521727 1960 True 3199 3199 96.093 583 2548 1 chr6D.!!$R1 1965
7 TraesCS2D01G237000 chr6D 271269051 271269617 566 False 850 850 93.827 1 563 1 chr6D.!!$F2 562
8 TraesCS2D01G237000 chr7D 574725141 574727118 1977 True 3205 3205 95.884 564 2548 1 chr7D.!!$R2 1984
9 TraesCS2D01G237000 chr7D 222405088 222405653 565 True 832 832 93.286 1 563 1 chr7D.!!$R1 562
10 TraesCS2D01G237000 chr1D 26486135 26488118 1983 False 3186 3186 95.635 561 2548 1 chr1D.!!$F1 1987
11 TraesCS2D01G237000 chr1D 194977859 194978424 565 False 843 843 93.640 1 563 1 chr1D.!!$F3 562
12 TraesCS2D01G237000 chr1D 163758785 163759344 559 False 837 837 93.750 1 557 1 chr1D.!!$F2 556
13 TraesCS2D01G237000 chrUn 93724519 93726510 1991 True 3145 3145 95.248 564 2548 1 chrUn.!!$R1 1984
14 TraesCS2D01G237000 chr2B 4739871 4741862 1991 False 3073 3073 94.558 559 2548 1 chr2B.!!$F1 1989
15 TraesCS2D01G237000 chr7A 15645803 15647792 1989 False 3055 3055 94.436 564 2548 1 chr7A.!!$F1 1984
16 TraesCS2D01G237000 chr3D 346880010 346880576 566 True 845 845 93.651 1 563 1 chr3D.!!$R1 562
17 TraesCS2D01G237000 chr3D 135490216 135490779 563 False 828 828 93.274 1 561 1 chr3D.!!$F1 560
18 TraesCS2D01G237000 chr3A 595693947 595694509 562 True 839 839 93.628 2 563 1 chr3A.!!$R1 561

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
899 912 0.10412 CGGCGAGAGAGAGAGAGAGA 59.896 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1779 0.618458 TACGCTCTGAATTTGGCCCT 59.382 50.0 0.0 0.0 0.0 5.19 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
33 34 2.949451 ATCGTAGTGTCTCTTGGCTG 57.051 50.000 0.00 0.0 0.00 4.85
35 36 1.540267 TCGTAGTGTCTCTTGGCTGAC 59.460 52.381 0.00 0.0 0.00 3.51
62 63 4.628333 CCAAGTCTGGCTTTAATTTGCATG 59.372 41.667 0.00 0.0 35.39 4.06
63 64 5.232463 CAAGTCTGGCTTTAATTTGCATGT 58.768 37.500 0.00 0.0 34.69 3.21
187 188 2.417924 CCGTTCAGTCAAGCAGCTATCT 60.418 50.000 0.00 0.0 0.00 1.98
214 217 5.130350 GCACCTCCTATAGCCATTAAAACA 58.870 41.667 0.00 0.0 0.00 2.83
244 247 3.128589 GTGGCGTCACATGAATGGTTAAT 59.871 43.478 16.80 0.0 43.13 1.40
251 254 6.254804 CGTCACATGAATGGTTAATAGAACGA 59.745 38.462 0.00 0.0 0.00 3.85
252 255 7.515215 CGTCACATGAATGGTTAATAGAACGAG 60.515 40.741 0.00 0.0 0.00 4.18
268 271 4.092968 AGAACGAGCACGGTTTGAATTATC 59.907 41.667 8.74 0.0 40.51 1.75
336 341 2.677836 TGTTGGCTGTCATTATTCGAGC 59.322 45.455 0.00 0.0 0.00 5.03
365 370 6.476706 CCTTCTCTCAAAATGGACACAAAAAC 59.523 38.462 0.00 0.0 0.00 2.43
754 759 3.023832 CAGGGACGGCCAATTTTATTCT 58.976 45.455 11.00 0.0 35.15 2.40
767 772 2.442212 TTATTCTGACCGTTGCACGA 57.558 45.000 9.75 0.0 46.05 4.35
803 808 1.449246 GCAGAGAGCCGTTGAGCAT 60.449 57.895 0.00 0.0 37.23 3.79
808 813 1.678627 GAGAGCCGTTGAGCATAGAGA 59.321 52.381 0.00 0.0 34.23 3.10
896 909 0.742990 ACACGGCGAGAGAGAGAGAG 60.743 60.000 16.62 0.0 0.00 3.20
897 910 0.461163 CACGGCGAGAGAGAGAGAGA 60.461 60.000 16.62 0.0 0.00 3.10
898 911 0.179084 ACGGCGAGAGAGAGAGAGAG 60.179 60.000 16.62 0.0 0.00 3.20
899 912 0.104120 CGGCGAGAGAGAGAGAGAGA 59.896 60.000 0.00 0.0 0.00 3.10
900 913 1.869754 CGGCGAGAGAGAGAGAGAGAG 60.870 61.905 0.00 0.0 0.00 3.20
901 914 1.221414 GCGAGAGAGAGAGAGAGAGC 58.779 60.000 0.00 0.0 0.00 4.09
902 915 1.473257 GCGAGAGAGAGAGAGAGAGCA 60.473 57.143 0.00 0.0 0.00 4.26
903 916 2.905075 CGAGAGAGAGAGAGAGAGCAA 58.095 52.381 0.00 0.0 0.00 3.91
987 1000 1.351017 GTGGTGTTGAGATCCCCTTCA 59.649 52.381 0.00 0.0 0.00 3.02
1079 1092 0.038159 CCTTTCTTCGTCTGTCCGCT 60.038 55.000 0.00 0.0 0.00 5.52
1235 1249 3.004734 GGGTTGATCTGTTTGGTGTTCAG 59.995 47.826 0.00 0.0 0.00 3.02
1379 1393 0.105778 CCGGAAGAAGAGATGGAGGC 59.894 60.000 0.00 0.0 0.00 4.70
1380 1394 0.826715 CGGAAGAAGAGATGGAGGCA 59.173 55.000 0.00 0.0 0.00 4.75
1726 1744 3.014623 TCAATGAAATGCAGCTCTCTGG 58.985 45.455 0.00 0.0 40.65 3.86
1934 1957 5.625150 AGCTAATTGAATTATTCCGGAGCT 58.375 37.500 3.34 1.7 0.00 4.09
1938 1961 8.349983 GCTAATTGAATTATTCCGGAGCTAAAA 58.650 33.333 3.34 0.0 0.00 1.52
2278 2304 7.943447 GGAAGGAAGGTATACATAGTGAGACTA 59.057 40.741 5.01 0.0 34.82 2.59
2324 2355 0.316937 CGTGAATGTTTGCACACGCT 60.317 50.000 11.57 0.0 46.38 5.07
2328 2359 2.159324 TGAATGTTTGCACACGCTTGAA 60.159 40.909 0.00 0.0 39.64 2.69
2527 2569 2.610859 GGCTTCTCACCCCCTCCA 60.611 66.667 0.00 0.0 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.232463 ACATGCAAATTAAAGCCAGACTTG 58.768 37.500 0.00 0.00 39.09 3.16
62 63 2.471749 CGCAAACGGTTCAGATTACGAC 60.472 50.000 0.00 0.00 34.97 4.34
63 64 1.722464 CGCAAACGGTTCAGATTACGA 59.278 47.619 0.00 0.00 34.97 3.43
214 217 0.531974 ATGTGACGCCACGTGTCTTT 60.532 50.000 15.65 0.00 46.06 2.52
244 247 2.512485 TTCAAACCGTGCTCGTTCTA 57.488 45.000 7.47 0.00 35.01 2.10
251 254 4.614993 CGTTTGGATAATTCAAACCGTGCT 60.615 41.667 13.95 0.00 46.50 4.40
252 255 3.606346 CGTTTGGATAATTCAAACCGTGC 59.394 43.478 13.95 0.00 46.50 5.34
268 271 6.526674 GCCACTTTAATATCTCAAACGTTTGG 59.473 38.462 33.97 25.44 38.66 3.28
336 341 0.097674 CCATTTTGAGAGAAGGCGCG 59.902 55.000 0.00 0.00 0.00 6.86
365 370 0.740868 CACCCGACATGCTGTGGTAG 60.741 60.000 0.00 0.00 27.19 3.18
403 408 6.483307 ACTCGTCTGAAATTCATGAAACTTGA 59.517 34.615 13.09 2.65 0.00 3.02
488 493 5.245075 GGTAATGAATTTCAAACACCAGGGA 59.755 40.000 16.54 0.00 30.52 4.20
767 772 2.776526 TGGGTCCCACAAGCCACT 60.777 61.111 6.47 0.00 41.74 4.00
803 808 0.319555 GCACACCTGCAACGTCTCTA 60.320 55.000 0.00 0.00 43.62 2.43
808 813 2.691409 ATATAGCACACCTGCAACGT 57.309 45.000 0.00 0.00 46.97 3.99
877 884 0.742990 CTCTCTCTCTCTCGCCGTGT 60.743 60.000 0.00 0.00 0.00 4.49
971 984 1.556911 GAGCTGAAGGGGATCTCAACA 59.443 52.381 0.00 0.00 0.00 3.33
1063 1076 0.318699 CACAGCGGACAGACGAAGAA 60.319 55.000 0.00 0.00 35.47 2.52
1198 1212 3.765381 TCAACCCATTGCTCAAAGATCA 58.235 40.909 0.00 0.00 35.63 2.92
1235 1249 1.200948 GAAAGAAGCATGTCACCTGCC 59.799 52.381 0.81 0.00 40.56 4.85
1379 1393 0.234106 CTCTGTCAGTGCGTGCTTTG 59.766 55.000 0.00 0.00 0.00 2.77
1380 1394 0.104855 TCTCTGTCAGTGCGTGCTTT 59.895 50.000 0.00 0.00 0.00 3.51
1751 1772 2.511218 TCTGAATTTGGCCCTAGAGCAT 59.489 45.455 0.00 0.00 0.00 3.79
1758 1779 0.618458 TACGCTCTGAATTTGGCCCT 59.382 50.000 0.00 0.00 0.00 5.19
1834 1855 7.715686 AGAAAACAGAAAATACGGAAGAGAACT 59.284 33.333 0.00 0.00 0.00 3.01
1843 1864 6.954944 TCAGAACAGAAAACAGAAAATACGG 58.045 36.000 0.00 0.00 0.00 4.02
2295 2326 3.496884 GCAAACATTCACGGTCTCACTAA 59.503 43.478 0.00 0.00 0.00 2.24
2324 2355 5.707298 TGCAAAACAAAGGAAAACCATTCAA 59.293 32.000 0.00 0.00 0.00 2.69
2328 2359 4.635324 CAGTGCAAAACAAAGGAAAACCAT 59.365 37.500 0.00 0.00 0.00 3.55
2391 2424 2.460757 AACCAAAATCATGTGGCAGC 57.539 45.000 0.10 0.00 38.58 5.25


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

AutoCloner maintained by Alex Coulton.