Multiple sequence alignment - TraesCS2D01G460000

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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 TraesCS2D01G460000 chr2D 100.000 3718 0 0 1 3718 566832296 566836013 0.000000e+00 6866.0
1 TraesCS2D01G460000 chr2D 92.645 707 29 7 3013 3718 566979871 566980555 0.000000e+00 996.0
2 TraesCS2D01G460000 chr2D 95.833 192 8 0 1 192 295651927 295651736 1.000000e-80 311.0
3 TraesCS2D01G460000 chr2D 95.833 192 8 0 1 192 386463228 386463037 1.000000e-80 311.0
4 TraesCS2D01G460000 chr2A 89.699 1660 99 30 941 2569 706640852 706642470 0.000000e+00 2052.0
5 TraesCS2D01G460000 chr2A 95.298 957 27 7 2769 3718 706643638 706644583 0.000000e+00 1502.0
6 TraesCS2D01G460000 chr2A 92.201 718 31 6 3001 3718 706741343 706742035 0.000000e+00 992.0
7 TraesCS2D01G460000 chr2A 83.621 232 25 7 478 704 706640634 706640857 4.870000e-49 206.0
8 TraesCS2D01G460000 chr2A 93.548 124 3 4 2669 2787 706643493 706643616 2.950000e-41 180.0
9 TraesCS2D01G460000 chr2B 95.895 950 24 6 2769 3718 679815124 679816058 0.000000e+00 1524.0
10 TraesCS2D01G460000 chr2B 91.657 887 46 20 1923 2787 679814222 679815102 0.000000e+00 1203.0
11 TraesCS2D01G460000 chr2B 88.685 928 45 28 941 1822 679812574 679813487 0.000000e+00 1077.0
12 TraesCS2D01G460000 chr2B 92.618 718 28 6 3001 3718 679885210 679885902 0.000000e+00 1009.0
13 TraesCS2D01G460000 chr2B 82.913 515 53 15 190 704 679812100 679812579 7.380000e-117 431.0
14 TraesCS2D01G460000 chr2B 96.429 56 2 0 1832 1887 679814164 679814219 3.950000e-15 93.5
15 TraesCS2D01G460000 chr2B 86.667 60 7 1 572 631 441867583 441867525 8.620000e-07 65.8
16 TraesCS2D01G460000 chr7D 95.868 242 8 2 707 946 598519481 598519722 1.250000e-104 390.0
17 TraesCS2D01G460000 chr7D 93.004 243 15 2 705 946 257978311 257978552 1.640000e-93 353.0
18 TraesCS2D01G460000 chr7D 95.833 192 8 0 1 192 235830771 235830962 1.000000e-80 311.0
19 TraesCS2D01G460000 chr7D 80.442 317 41 13 1420 1727 60279478 60279782 4.830000e-54 222.0
20 TraesCS2D01G460000 chr4D 95.473 243 10 1 706 947 500495491 500495733 1.620000e-103 387.0
21 TraesCS2D01G460000 chr6D 95.021 241 11 1 710 949 55433166 55432926 9.750000e-101 377.0
22 TraesCS2D01G460000 chr6D 92.946 241 16 1 708 947 464734454 464734694 2.120000e-92 350.0
23 TraesCS2D01G460000 chr3D 93.878 245 14 1 706 949 23677559 23677315 5.870000e-98 368.0
24 TraesCS2D01G460000 chr3D 95.833 192 8 0 1 192 491080022 491079831 1.000000e-80 311.0
25 TraesCS2D01G460000 chr1B 93.548 248 13 3 705 949 520875299 520875052 2.110000e-97 366.0
26 TraesCS2D01G460000 chr5D 93.724 239 13 2 708 945 437126794 437126557 1.270000e-94 357.0
27 TraesCS2D01G460000 chr5D 95.833 192 8 0 1 192 391837416 391837225 1.000000e-80 311.0
28 TraesCS2D01G460000 chr5D 92.823 209 12 3 1 207 67045841 67045634 2.170000e-77 300.0
29 TraesCS2D01G460000 chr1D 92.623 244 18 0 706 949 309990573 309990330 5.910000e-93 351.0
30 TraesCS2D01G460000 chr1D 95.833 192 8 0 1 192 324772726 324772917 1.000000e-80 311.0
31 TraesCS2D01G460000 chr7B 77.797 581 89 27 1160 1727 2784438 2784991 4.630000e-84 322.0
32 TraesCS2D01G460000 chr1A 95.833 192 8 0 1 192 500608887 500608696 1.000000e-80 311.0
33 TraesCS2D01G460000 chr7A 92.925 212 13 2 1 210 507710907 507711118 1.300000e-79 307.0
34 TraesCS2D01G460000 chr7A 80.556 324 39 15 1416 1727 64608849 64609160 1.040000e-55 228.0
35 TraesCS2D01G460000 chr6B 97.561 41 0 1 583 623 712467470 712467431 6.660000e-08 69.4


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 TraesCS2D01G460000 chr2D 566832296 566836013 3717 False 6866.0 6866 100.0000 1 3718 1 chr2D.!!$F1 3717
1 TraesCS2D01G460000 chr2D 566979871 566980555 684 False 996.0 996 92.6450 3013 3718 1 chr2D.!!$F2 705
2 TraesCS2D01G460000 chr2A 706741343 706742035 692 False 992.0 992 92.2010 3001 3718 1 chr2A.!!$F1 717
3 TraesCS2D01G460000 chr2A 706640634 706644583 3949 False 985.0 2052 90.5415 478 3718 4 chr2A.!!$F2 3240
4 TraesCS2D01G460000 chr2B 679885210 679885902 692 False 1009.0 1009 92.6180 3001 3718 1 chr2B.!!$F1 717
5 TraesCS2D01G460000 chr2B 679812100 679816058 3958 False 865.7 1524 91.1158 190 3718 5 chr2B.!!$F2 3528
6 TraesCS2D01G460000 chr7B 2784438 2784991 553 False 322.0 322 77.7970 1160 1727 1 chr7B.!!$F1 567


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
456 458 0.034186 GACTGCATGGTGATGGGGAA 60.034 55.000 0.00 0.0 0.00 3.97 F
464 466 0.106967 GGTGATGGGGAAAGAGGAGC 60.107 60.000 0.00 0.0 0.00 4.70 F
1679 1737 0.110056 GTACGAGAACGAGAACCGCA 60.110 55.000 0.00 0.0 43.32 5.69 F
1767 1843 0.692419 TCCTCTTCCCTCCTCCATGC 60.692 60.000 0.00 0.0 0.00 4.06 F
1801 1882 1.067416 TGCATGATAGGCCGACGAC 59.933 57.895 0.00 0.0 0.00 4.34 F
2075 2823 1.134560 ACGATCTAGAGCAAACCGGTC 59.865 52.381 8.04 0.0 42.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 2649 0.039165 CCGCCTGCCTTTTTCTTCAC 60.039 55.000 0.00 0.00 0.00 3.18 R
2413 3170 0.676466 CCGTGCTCCATGGCAAGTTA 60.676 55.000 6.96 0.00 44.18 2.24 R
2490 3247 0.694444 ATAGGCTCCCCGAACCACAT 60.694 55.000 0.00 0.00 35.76 3.21 R
2668 3500 1.008424 ATCATGGCGCGTCGACTAG 60.008 57.895 14.70 8.35 35.04 2.57 R
2669 3501 1.299089 CATCATGGCGCGTCGACTA 60.299 57.895 14.70 0.00 35.04 2.59 R
2989 4735 1.301401 GGCCATCCACGCGCTTATA 60.301 57.895 5.73 0.00 0.00 0.98 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)



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AutoCloner maintained by Alex Coulton.