Multiple sequence alignment - TraesCS2A01G048300

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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 TraesCS2A01G048300 chr2A 100.000 2264 0 0 1 2264 18635576 18637839 0.000000e+00 4181
1 TraesCS2A01G048300 chr2A 91.140 1772 126 13 1 1767 18586007 18587752 0.000000e+00 2374
2 TraesCS2A01G048300 chr2D 95.825 2108 56 7 1 2104 17311935 17314014 0.000000e+00 3376
3 TraesCS2A01G048300 chr2D 97.019 1543 46 0 722 2264 17169522 17171064 0.000000e+00 2595
4 TraesCS2A01G048300 chr2D 95.897 658 18 4 1 658 17168874 17169522 0.000000e+00 1057
5 TraesCS2A01G048300 chr2D 90.323 248 22 2 1106 1352 17208272 17208518 7.800000e-85 324
6 TraesCS2A01G048300 chr2B 91.299 1609 119 11 1 1608 29992215 29990627 0.000000e+00 2176
7 TraesCS2A01G048300 chr2B 89.215 1771 140 23 1 1767 29045977 29047700 0.000000e+00 2165
8 TraesCS2A01G048300 chr2B 94.896 627 31 1 864 1490 28921248 28921873 0.000000e+00 979
9 TraesCS2A01G048300 chr2B 92.600 500 37 0 1765 2264 28922387 28922886 0.000000e+00 719
10 TraesCS2A01G048300 chr2B 95.720 257 11 0 1511 1767 28921864 28922120 4.500000e-112 414
11 TraesCS2A01G048300 chr2B 95.745 235 10 0 3 237 28920597 28920831 1.640000e-101 379
12 TraesCS2A01G048300 chr2B 93.750 240 15 0 230 469 28921014 28921253 5.940000e-96 361
13 TraesCS2A01G048300 chr6A 80.685 409 68 10 1813 2218 609579442 609579842 7.860000e-80 307
14 TraesCS2A01G048300 chr3D 80.344 407 69 9 1812 2214 54975145 54974746 4.730000e-77 298
15 TraesCS2A01G048300 chr3D 79.710 414 71 12 1808 2214 51045136 51045543 1.020000e-73 287
16 TraesCS2A01G048300 chr4D 80.392 408 65 14 1813 2218 375142651 375143045 1.700000e-76 296
17 TraesCS2A01G048300 chr5D 80.098 407 71 10 1813 2214 327629082 327629483 6.120000e-76 294
18 TraesCS2A01G048300 chr1D 80.098 407 71 10 1813 2214 17211523 17211924 6.120000e-76 294


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 TraesCS2A01G048300 chr2A 18635576 18637839 2263 False 4181.0 4181 100.0000 1 2264 1 chr2A.!!$F2 2263
1 TraesCS2A01G048300 chr2A 18586007 18587752 1745 False 2374.0 2374 91.1400 1 1767 1 chr2A.!!$F1 1766
2 TraesCS2A01G048300 chr2D 17311935 17314014 2079 False 3376.0 3376 95.8250 1 2104 1 chr2D.!!$F2 2103
3 TraesCS2A01G048300 chr2D 17168874 17171064 2190 False 1826.0 2595 96.4580 1 2264 2 chr2D.!!$F3 2263
4 TraesCS2A01G048300 chr2B 29990627 29992215 1588 True 2176.0 2176 91.2990 1 1608 1 chr2B.!!$R1 1607
5 TraesCS2A01G048300 chr2B 29045977 29047700 1723 False 2165.0 2165 89.2150 1 1767 1 chr2B.!!$F1 1766
6 TraesCS2A01G048300 chr2B 28920597 28922886 2289 False 570.4 979 94.5422 3 2264 5 chr2B.!!$F2 2261

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
892 1092 3.395941 GGTGGAGATTTCCCAGGTATGAT 59.604 47.826 0.0 0.0 43.33 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2712 0.951558 TGGCTCGAAGGCTTCAAAAC 59.048 50.0 25.66 13.61 41.96 2.43 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
69 70 7.530426 AGAAAGCCTTGACAAAATTACTGAT 57.470 32.000 0.00 0.00 0.00 2.90
198 200 4.175489 CATGTGCAGCGGCTGAGC 62.175 66.667 32.72 22.47 41.91 4.26
310 505 7.372260 AGAGCTCAATGACTCCACTAATATT 57.628 36.000 17.77 0.00 33.18 1.28
391 586 4.409187 AGCGGTTGGGTTAAAATTTAGGA 58.591 39.130 0.00 0.00 0.00 2.94
455 650 3.894288 CGCGTCGTCATAATAAAAGCATG 59.106 43.478 0.00 0.00 0.00 4.06
641 837 5.537300 TTTGGCTGCCATTTTTACTACAA 57.463 34.783 24.03 6.61 31.53 2.41
847 1047 8.624701 TCAAGAAACAGCACGTATAATACTAC 57.375 34.615 0.00 0.00 0.00 2.73
892 1092 3.395941 GGTGGAGATTTCCCAGGTATGAT 59.604 47.826 0.00 0.00 43.33 2.45
976 1177 4.094739 TCGTGAAATTCCTATGCATGTGTG 59.905 41.667 10.16 0.00 0.00 3.82
1352 1555 3.761481 GCCAGCAGCGCTAATATTG 57.239 52.632 10.99 4.15 36.40 1.90
1386 1589 4.336433 TGCCTACATGAAAATAAGCTGCTC 59.664 41.667 1.00 0.00 0.00 4.26
1540 1744 8.234546 GTGTAAGGAAACGTTCATGATTAACAT 58.765 33.333 0.00 0.00 40.17 2.71
1731 1935 5.687166 ACTTAATACCGGAAACTCCATCA 57.313 39.130 9.46 0.00 35.91 3.07
1877 2350 6.411376 ACCATTACCGATCACAAAACATCTA 58.589 36.000 0.00 0.00 0.00 1.98
2037 2510 0.102663 TATCGCCGCGTACCAATCAA 59.897 50.000 13.39 0.00 0.00 2.57
2239 2712 3.540367 AAACACCACTACCCGCCCG 62.540 63.158 0.00 0.00 0.00 6.13
2243 2716 2.032987 CCACTACCCGCCCGTTTT 59.967 61.111 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 5.289595 CGACCTTGTAGCTGCAGATAAATA 58.710 41.667 20.43 2.61 0.00 1.40
144 145 6.366340 CAGACTAGAGGGTCCAGAATAAGTA 58.634 44.000 0.00 0.00 36.95 2.24
146 147 4.038642 GCAGACTAGAGGGTCCAGAATAAG 59.961 50.000 0.00 0.00 36.95 1.73
198 200 2.573369 CATTTGGCTCTGGGATCTCAG 58.427 52.381 17.10 17.10 36.17 3.35
310 505 5.887598 TGTAAGCGTATAGGTAGAAGGACAA 59.112 40.000 0.00 0.00 0.00 3.18
349 544 3.863400 GCTTCAGTCGGGCACTAAAAGTA 60.863 47.826 0.00 0.00 32.87 2.24
641 837 2.239907 GCCTTTGGGACCAGTAGAATCT 59.760 50.000 0.00 0.00 33.58 2.40
789 989 1.048601 GTCAGGTCAGGTCAGGAACA 58.951 55.000 0.00 0.00 0.00 3.18
847 1047 5.392380 CCTTGAGATTCGATTGAAGTTTGGG 60.392 44.000 1.10 0.00 37.57 4.12
892 1092 7.865706 AGAAGAAACTAGCTTGAACAAAGAA 57.134 32.000 1.04 0.00 38.24 2.52
955 1156 5.124457 AGACACACATGCATAGGAATTTCAC 59.876 40.000 0.00 0.00 0.00 3.18
1386 1589 5.073311 TCTTCGACATTACTCTTCCCTTG 57.927 43.478 0.00 0.00 0.00 3.61
1540 1744 6.044046 GCATGAATTTTATTGATGACTGCCA 58.956 36.000 0.00 0.00 0.00 4.92
1877 2350 1.915489 TGATGTGCTATTCACCCCAGT 59.085 47.619 0.00 0.00 45.03 4.00
1959 2432 1.267574 ATCAGTGGCAGGTCATCCGT 61.268 55.000 0.00 0.00 39.05 4.69
1969 2442 2.125391 GAGAGCGCATCAGTGGCA 60.125 61.111 11.47 0.00 0.00 4.92
2118 2591 1.128200 TCAGATGTACCCATTCCCCG 58.872 55.000 0.00 0.00 0.00 5.73
2219 2692 1.239296 GGGCGGGTAGTGGTGTTTTC 61.239 60.000 0.00 0.00 0.00 2.29
2239 2712 0.951558 TGGCTCGAAGGCTTCAAAAC 59.048 50.000 25.66 13.61 41.96 2.43
2243 2716 2.046892 GCTGGCTCGAAGGCTTCA 60.047 61.111 25.66 12.54 41.96 3.02


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

AutoCloner maintained by Alex Coulton.