Multiple sequence alignment - TraesCS2D01G257900

Loading Multiple Alignment...

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 TraesCS2D01G257900 chr2D 100.000 2513 0 0 1 2513 314054812 314052300 0.000000e+00 4641.0
1 TraesCS2D01G257900 chr2D 89.081 1621 102 33 154 1739 314564644 314566224 0.000000e+00 1943.0
2 TraesCS2D01G257900 chr2D 93.610 1299 44 11 448 1739 314794617 314795883 0.000000e+00 1903.0
3 TraesCS2D01G257900 chr2D 92.361 144 10 1 1667 1809 314046342 314046199 1.180000e-48 204.0
4 TraesCS2D01G257900 chr2D 100.000 39 0 0 1765 1803 314566223 314566261 3.470000e-09 73.1
5 TraesCS2D01G257900 chr2D 100.000 39 0 0 1765 1803 314795882 314795920 3.470000e-09 73.1
6 TraesCS2D01G257900 chr2A 93.014 1002 44 13 317 1304 421061132 421060143 0.000000e+00 1439.0
7 TraesCS2D01G257900 chr2A 95.770 591 25 0 711 1301 422221561 422222151 0.000000e+00 953.0
8 TraesCS2D01G257900 chr2A 93.313 643 32 7 659 1301 422102822 422103453 0.000000e+00 939.0
9 TraesCS2D01G257900 chr2A 91.128 665 52 4 1150 1809 421060258 421059596 0.000000e+00 894.0
10 TraesCS2D01G257900 chr2A 90.440 659 56 4 1150 1803 422103341 422103997 0.000000e+00 861.0
11 TraesCS2D01G257900 chr2A 88.771 659 55 5 1150 1792 422222039 422222694 0.000000e+00 789.0
12 TraesCS2D01G257900 chr2A 86.460 709 43 32 12 696 422102147 422102826 0.000000e+00 728.0
13 TraesCS2D01G257900 chr2A 80.865 601 67 27 12 598 422220928 422221494 1.790000e-116 429.0
14 TraesCS2D01G257900 chr6D 97.529 688 14 3 1827 2513 329887529 329886844 0.000000e+00 1173.0
15 TraesCS2D01G257900 chr2B 85.269 1188 114 42 154 1301 382731279 382732445 0.000000e+00 1168.0
16 TraesCS2D01G257900 chr2B 93.960 596 31 2 709 1304 381914984 381914394 0.000000e+00 896.0
17 TraesCS2D01G257900 chr2B 89.724 652 46 6 1150 1783 382732333 382732981 0.000000e+00 813.0
18 TraesCS2D01G257900 chr2B 90.045 442 37 3 1153 1590 381914506 381914068 1.300000e-157 566.0
19 TraesCS2D01G257900 chr2B 93.939 198 6 3 1591 1783 381908858 381908662 6.800000e-76 294.0
20 TraesCS2D01G257900 chr1A 95.815 693 27 2 1821 2513 548460656 548461346 0.000000e+00 1118.0
21 TraesCS2D01G257900 chr1A 94.075 692 35 6 1824 2513 560370548 560369861 0.000000e+00 1046.0
22 TraesCS2D01G257900 chr7D 94.676 695 33 4 1820 2513 497569180 497569871 0.000000e+00 1075.0
23 TraesCS2D01G257900 chr5A 94.049 689 36 4 1826 2513 43566770 43567454 0.000000e+00 1040.0
24 TraesCS2D01G257900 chr7B 93.795 693 39 4 1822 2513 610224137 610224826 0.000000e+00 1038.0
25 TraesCS2D01G257900 chr5B 93.450 687 42 3 1826 2512 54552185 54551502 0.000000e+00 1016.0
26 TraesCS2D01G257900 chr4B 93.159 687 44 3 1827 2513 536847426 536848109 0.000000e+00 1005.0
27 TraesCS2D01G257900 chr3B 92.518 695 49 3 1819 2513 32726776 32727467 0.000000e+00 992.0


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 TraesCS2D01G257900 chr2D 314052300 314054812 2512 True 4641.000000 4641 100.000000 1 2513 1 chr2D.!!$R2 2512
1 TraesCS2D01G257900 chr2D 314564644 314566261 1617 False 1008.050000 1943 94.540500 154 1803 2 chr2D.!!$F1 1649
2 TraesCS2D01G257900 chr2D 314794617 314795920 1303 False 988.050000 1903 96.805000 448 1803 2 chr2D.!!$F2 1355
3 TraesCS2D01G257900 chr2A 421059596 421061132 1536 True 1166.500000 1439 92.071000 317 1809 2 chr2A.!!$R1 1492
4 TraesCS2D01G257900 chr2A 422102147 422103997 1850 False 842.666667 939 90.071000 12 1803 3 chr2A.!!$F1 1791
5 TraesCS2D01G257900 chr2A 422220928 422222694 1766 False 723.666667 953 88.468667 12 1792 3 chr2A.!!$F2 1780
6 TraesCS2D01G257900 chr6D 329886844 329887529 685 True 1173.000000 1173 97.529000 1827 2513 1 chr6D.!!$R1 686
7 TraesCS2D01G257900 chr2B 382731279 382732981 1702 False 990.500000 1168 87.496500 154 1783 2 chr2B.!!$F1 1629
8 TraesCS2D01G257900 chr2B 381914068 381914984 916 True 731.000000 896 92.002500 709 1590 2 chr2B.!!$R2 881
9 TraesCS2D01G257900 chr1A 548460656 548461346 690 False 1118.000000 1118 95.815000 1821 2513 1 chr1A.!!$F1 692
10 TraesCS2D01G257900 chr1A 560369861 560370548 687 True 1046.000000 1046 94.075000 1824 2513 1 chr1A.!!$R1 689
11 TraesCS2D01G257900 chr7D 497569180 497569871 691 False 1075.000000 1075 94.676000 1820 2513 1 chr7D.!!$F1 693
12 TraesCS2D01G257900 chr5A 43566770 43567454 684 False 1040.000000 1040 94.049000 1826 2513 1 chr5A.!!$F1 687
13 TraesCS2D01G257900 chr7B 610224137 610224826 689 False 1038.000000 1038 93.795000 1822 2513 1 chr7B.!!$F1 691
14 TraesCS2D01G257900 chr5B 54551502 54552185 683 True 1016.000000 1016 93.450000 1826 2512 1 chr5B.!!$R1 686
15 TraesCS2D01G257900 chr4B 536847426 536848109 683 False 1005.000000 1005 93.159000 1827 2513 1 chr4B.!!$F1 686
16 TraesCS2D01G257900 chr3B 32726776 32727467 691 False 992.000000 992 92.518000 1819 2513 1 chr3B.!!$F1 694

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
35 36 3.452474 TCCTTTTGTTTTGTTCGCATGG 58.548 40.909 0.00 0.00 0.0 3.66 F
565 631 3.945304 AAGTTTAGGGACGGCGCGG 62.945 63.158 14.03 14.03 0.0 6.46 F
1338 1607 3.596066 GAGCGCTGTCAAGAGGCCA 62.596 63.158 18.48 0.00 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1154 0.392461 GCAACGTAGAGATTGGGGCA 60.392 55.000 0.00 0.0 0.0 5.36 R
1396 1665 1.523258 CCTCCGGAGCAGCTTCATG 60.523 63.158 26.87 5.0 0.0 3.07 R
2207 2525 3.822192 CGACGACCAGATCCGGCA 61.822 66.667 0.00 0.0 32.4 5.69 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 3.452474 TCCTTTTGTTTTGTTCGCATGG 58.548 40.909 0.00 0.00 0.00 3.66
411 447 4.202010 ACAAATTTTGGACTCACGAACAGG 60.202 41.667 13.42 0.00 34.12 4.00
565 631 3.945304 AAGTTTAGGGACGGCGCGG 62.945 63.158 14.03 14.03 0.00 6.46
1041 1154 3.953775 CTGCCAACCCCACCGTCT 61.954 66.667 0.00 0.00 0.00 4.18
1338 1607 3.596066 GAGCGCTGTCAAGAGGCCA 62.596 63.158 18.48 0.00 0.00 5.36
1396 1665 4.452733 CCAAGGCTCCGGTCGACC 62.453 72.222 25.28 25.28 0.00 4.79
1398 1667 2.683933 AAGGCTCCGGTCGACCAT 60.684 61.111 32.80 9.27 35.14 3.55
1562 1845 3.773119 GGATTGGTCCCTTACTACAGTCA 59.227 47.826 0.00 0.00 38.69 3.41
1565 1848 4.055710 TGGTCCCTTACTACAGTCATCA 57.944 45.455 0.00 0.00 0.00 3.07
1709 2009 0.664761 GATGGGTGGCATGACAATCG 59.335 55.000 0.58 0.00 0.00 3.34
1754 2056 0.040204 CCCCTTGCAATCCTTCCTGT 59.960 55.000 0.00 0.00 0.00 4.00
1803 2112 5.953571 AGAAACCCAGTTTTAAGATCACCT 58.046 37.500 0.00 0.00 35.77 4.00
1805 2114 6.490381 AGAAACCCAGTTTTAAGATCACCTTC 59.510 38.462 0.00 0.00 35.77 3.46
1809 2118 5.479306 CCAGTTTTAAGATCACCTTCGAGA 58.521 41.667 0.00 0.00 36.34 4.04
1810 2119 5.932303 CCAGTTTTAAGATCACCTTCGAGAA 59.068 40.000 0.00 0.00 36.34 2.87
1811 2120 6.128526 CCAGTTTTAAGATCACCTTCGAGAAC 60.129 42.308 0.00 0.00 36.34 3.01
1812 2121 6.423905 CAGTTTTAAGATCACCTTCGAGAACA 59.576 38.462 0.00 0.00 36.34 3.18
1813 2122 6.424207 AGTTTTAAGATCACCTTCGAGAACAC 59.576 38.462 0.00 0.00 36.34 3.32
1814 2123 3.320673 AAGATCACCTTCGAGAACACC 57.679 47.619 0.00 0.00 0.00 4.16
1815 2124 1.550976 AGATCACCTTCGAGAACACCC 59.449 52.381 0.00 0.00 0.00 4.61
1816 2125 0.613777 ATCACCTTCGAGAACACCCC 59.386 55.000 0.00 0.00 0.00 4.95
1817 2126 0.471211 TCACCTTCGAGAACACCCCT 60.471 55.000 0.00 0.00 0.00 4.79
1818 2127 0.037232 CACCTTCGAGAACACCCCTC 60.037 60.000 0.00 0.00 0.00 4.30
2086 2403 2.203437 GTGGTGGCCCTCCGTTTT 60.203 61.111 0.00 0.00 34.14 2.43
2090 2407 1.072505 GTGGCCCTCCGTTTTCTCA 59.927 57.895 0.00 0.00 34.14 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.924475 TGCGAACAAAACAAAAGGAAAAA 57.076 30.435 0.00 0.0 0.00 1.94
257 283 7.324354 TGTTAGCGAGTTTTAAAAGGTTTCT 57.676 32.000 0.00 0.0 0.00 2.52
683 796 6.127451 TGCGTACATATCCTACAATGATAGGG 60.127 42.308 8.36 0.0 41.98 3.53
684 797 6.863275 TGCGTACATATCCTACAATGATAGG 58.137 40.000 0.00 0.0 42.91 2.57
686 799 6.436218 ACCTGCGTACATATCCTACAATGATA 59.564 38.462 0.00 0.0 0.00 2.15
687 800 5.246203 ACCTGCGTACATATCCTACAATGAT 59.754 40.000 0.00 0.0 0.00 2.45
688 801 4.587262 ACCTGCGTACATATCCTACAATGA 59.413 41.667 0.00 0.0 0.00 2.57
689 802 4.883083 ACCTGCGTACATATCCTACAATG 58.117 43.478 0.00 0.0 0.00 2.82
690 803 4.021368 GGACCTGCGTACATATCCTACAAT 60.021 45.833 0.00 0.0 30.42 2.71
691 804 3.319972 GGACCTGCGTACATATCCTACAA 59.680 47.826 0.00 0.0 30.42 2.41
692 805 2.889045 GGACCTGCGTACATATCCTACA 59.111 50.000 0.00 0.0 30.42 2.74
693 806 2.095364 CGGACCTGCGTACATATCCTAC 60.095 54.545 0.00 0.0 30.72 3.18
799 912 2.107546 CCGGGGTACGTATGTGGC 59.892 66.667 0.00 0.0 42.24 5.01
1041 1154 0.392461 GCAACGTAGAGATTGGGGCA 60.392 55.000 0.00 0.0 0.00 5.36
1359 1628 1.079503 GCTTCTTGTCACACCGATCC 58.920 55.000 0.00 0.0 0.00 3.36
1396 1665 1.523258 CCTCCGGAGCAGCTTCATG 60.523 63.158 26.87 5.0 0.00 3.07
1398 1667 4.087892 GCCTCCGGAGCAGCTTCA 62.088 66.667 26.87 0.0 0.00 3.02
1754 2056 4.777896 AGTAGAGGAAGTGGATGCAAACTA 59.222 41.667 0.00 0.0 0.00 2.24
1803 2112 1.916777 GGGGAGGGGTGTTCTCGAA 60.917 63.158 0.00 0.0 32.34 3.71
1805 2114 3.400054 GGGGGAGGGGTGTTCTCG 61.400 72.222 0.00 0.0 32.34 4.04
2207 2525 3.822192 CGACGACCAGATCCGGCA 61.822 66.667 0.00 0.0 32.40 5.69


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

AutoCloner maintained by Alex Coulton.