Multiple sequence alignment - TraesCS3A01G092600

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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 TraesCS3A01G092600 chr3A 100.000 2482 0 0 1 2482 58467054 58469535 0.000000e+00 4584.0
1 TraesCS3A01G092600 chr3A 93.061 2349 139 15 145 2482 58548920 58551255 0.000000e+00 3413.0
2 TraesCS3A01G092600 chr3A 96.921 1494 36 7 1 1487 58310841 58312331 0.000000e+00 2495.0
3 TraesCS3A01G092600 chr3A 95.173 808 31 4 1675 2481 58312330 58313130 0.000000e+00 1269.0
4 TraesCS3A01G092600 chr3A 89.865 148 13 2 1 147 58547582 58547728 3.260000e-44 189.0
5 TraesCS3A01G092600 chr3D 92.651 762 53 3 578 1338 46924906 46925665 0.000000e+00 1094.0
6 TraesCS3A01G092600 chr3D 92.190 717 54 2 578 1293 46636746 46637461 0.000000e+00 1013.0
7 TraesCS3A01G092600 chr3D 91.803 549 43 2 578 1126 46958749 46959295 0.000000e+00 763.0
8 TraesCS3A01G092600 chr3D 84.840 719 72 16 1356 2073 46926093 46926775 0.000000e+00 689.0
9 TraesCS3A01G092600 chr3D 84.085 710 76 17 1369 2076 46959720 46960394 0.000000e+00 651.0
10 TraesCS3A01G092600 chr3D 83.288 730 69 19 1349 2076 46637465 46638143 7.540000e-175 623.0
11 TraesCS3A01G092600 chr5A 80.000 100 19 1 426 524 494377524 494377623 3.420000e-09 73.1


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 TraesCS3A01G092600 chr3A 58467054 58469535 2481 False 4584.0 4584 100.0000 1 2482 1 chr3A.!!$F1 2481
1 TraesCS3A01G092600 chr3A 58310841 58313130 2289 False 1882.0 2495 96.0470 1 2481 2 chr3A.!!$F2 2480
2 TraesCS3A01G092600 chr3A 58547582 58551255 3673 False 1801.0 3413 91.4630 1 2482 2 chr3A.!!$F3 2481
3 TraesCS3A01G092600 chr3D 46924906 46926775 1869 False 891.5 1094 88.7455 578 2073 2 chr3D.!!$F2 1495
4 TraesCS3A01G092600 chr3D 46636746 46638143 1397 False 818.0 1013 87.7390 578 2076 2 chr3D.!!$F1 1498
5 TraesCS3A01G092600 chr3D 46958749 46960394 1645 False 707.0 763 87.9440 578 2076 2 chr3D.!!$F3 1498

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
134 135 0.652592 CGCCAATAAGTTCTCGCTGG 59.347 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 3663 0.038159 GCTCCGTGTTGCTGAGTAGT 60.038 55.0 0.0 0.0 32.01 2.73 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
25 26 2.853235 TGGATGCTGGCATATCAGAG 57.147 50.000 8.11 0.00 36.70 3.35
41 42 4.114015 TCAGAGTGGACTTTGGACTCTA 57.886 45.455 0.00 0.00 43.69 2.43
134 135 0.652592 CGCCAATAAGTTCTCGCTGG 59.347 55.000 0.00 0.00 0.00 4.85
214 1409 1.004277 GGGTGCAGGGTTTGTCTATCA 59.996 52.381 0.00 0.00 0.00 2.15
409 1605 5.072040 TCAAGCAAACGATCTATCTGTCA 57.928 39.130 0.00 0.00 0.00 3.58
576 1779 6.653740 ACGGGGCATCTAATAAAAACTATAGC 59.346 38.462 0.00 0.00 0.00 2.97
800 2004 6.372104 TGGGAGCATTCAATATGGTTATCAA 58.628 36.000 0.00 0.00 0.00 2.57
971 2175 5.630121 ACCAAAGATTGATCAACACACCTA 58.370 37.500 11.07 0.00 0.00 3.08
1007 2211 5.441718 TCTTCCACAAGAAAGATGGCTAT 57.558 39.130 0.00 0.00 35.57 2.97
1173 2377 1.308128 TCAGCATCCTGACCCCCAT 60.308 57.895 0.00 0.00 42.98 4.00
1235 2439 6.250711 TCCATGCTATATGCCAGAAATTCAT 58.749 36.000 0.00 0.00 42.00 2.57
1345 2549 5.586643 TGCGCAGGTGTGTTAATATGATTAA 59.413 36.000 5.66 0.00 0.00 1.40
1548 3162 6.155393 AGCACTTAGTCTAAGGCAGTCTTAAT 59.845 38.462 23.62 7.86 40.08 1.40
1553 3167 3.454812 GTCTAAGGCAGTCTTAATCCCCA 59.545 47.826 0.00 0.00 37.49 4.96
1554 3168 4.080526 GTCTAAGGCAGTCTTAATCCCCAA 60.081 45.833 0.00 0.00 37.49 4.12
1557 3171 3.701664 AGGCAGTCTTAATCCCCAAAAG 58.298 45.455 0.00 0.00 0.00 2.27
1576 3190 8.314021 CCCAAAAGAAAATAAGGCAGTCTTAAT 58.686 33.333 0.00 0.00 40.89 1.40
1603 3221 8.738645 AACAAAGGAAGAGTATGGTATTGATC 57.261 34.615 0.00 0.00 0.00 2.92
1792 3411 7.903995 AAATCAAAAGTCTTGAAAGCAAACA 57.096 28.000 0.00 0.00 32.73 2.83
1793 3412 8.496707 AAATCAAAAGTCTTGAAAGCAAACAT 57.503 26.923 0.00 0.00 32.73 2.71
1794 3413 9.598517 AAATCAAAAGTCTTGAAAGCAAACATA 57.401 25.926 0.00 0.00 32.73 2.29
1795 3414 9.768662 AATCAAAAGTCTTGAAAGCAAACATAT 57.231 25.926 0.00 0.00 32.73 1.78
1857 3476 9.429359 ACACTAATCAAAATTTTGTGTTTGTCA 57.571 25.926 25.98 8.62 37.72 3.58
1862 3481 5.121454 TCAAAATTTTGTGTTTGTCAGGTGC 59.879 36.000 25.98 0.00 39.18 5.01
1895 3514 7.528996 TTGCCAAGATCTATTTTATGGGATG 57.471 36.000 10.23 0.00 0.00 3.51
1914 3533 4.220602 GGATGTCAGCAAACCACCTATTTT 59.779 41.667 0.00 0.00 0.00 1.82
1957 3576 3.594134 AGCAAGCACTTGATAGAGTGTC 58.406 45.455 14.44 0.51 46.81 3.67
1976 3595 0.514691 CTTGTTTGCCGAGAGCTGTC 59.485 55.000 0.00 0.00 44.23 3.51
1986 3605 3.181516 GCCGAGAGCTGTCACAAAAATAG 60.182 47.826 11.90 0.00 38.99 1.73
2043 3662 2.428530 TGATGAGAGCTCGCAACATAGT 59.571 45.455 24.24 6.46 0.00 2.12
2044 3663 3.632145 TGATGAGAGCTCGCAACATAGTA 59.368 43.478 24.24 2.50 0.00 1.82
2045 3664 3.422417 TGAGAGCTCGCAACATAGTAC 57.578 47.619 18.45 0.00 0.00 2.73
2057 3676 5.168569 GCAACATAGTACTACTCAGCAACA 58.831 41.667 4.31 0.00 0.00 3.33
2087 3706 3.326521 TGGGGCAAGTATCCAGTGATAT 58.673 45.455 0.00 0.00 35.94 1.63
2259 3878 1.133982 CAGTCTCCACATCTGTCCTCG 59.866 57.143 0.00 0.00 0.00 4.63
2470 4090 5.942826 TGATGTATACAGCCACAACATTTCA 59.057 36.000 17.99 6.05 31.19 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.943993 GACGTAGAGTCCAAAGTCCAC 58.056 52.381 0.00 0.0 43.95 4.02
120 121 1.816835 TCACGACCAGCGAGAACTTAT 59.183 47.619 0.00 0.0 44.57 1.73
134 135 2.386661 ACCAGACCATTCATCACGAC 57.613 50.000 0.00 0.0 0.00 4.34
346 1542 6.127897 CCAAGATTTCTTTTTATGCTCCGACT 60.128 38.462 0.00 0.0 33.11 4.18
409 1605 5.610982 TGGCCCATATATAGACTTCTTTGGT 59.389 40.000 0.00 0.0 0.00 3.67
800 2004 2.592102 ATGGATGGCCTTGCGATATT 57.408 45.000 3.32 0.0 34.31 1.28
940 2144 7.384660 GTGTTGATCAATCTTTGGTTATGCAAA 59.615 33.333 12.12 0.0 0.00 3.68
971 2175 5.818678 TGTGGAAGATGTAAACACTAGGT 57.181 39.130 0.00 0.0 33.44 3.08
1007 2211 6.016610 GCAGAACACCCACATTACTTTAGAAA 60.017 38.462 0.00 0.0 0.00 2.52
1548 3162 4.488770 ACTGCCTTATTTTCTTTTGGGGA 58.511 39.130 0.00 0.0 0.00 4.81
1554 3168 9.914131 GTTCATTAAGACTGCCTTATTTTCTTT 57.086 29.630 0.00 0.0 37.22 2.52
1557 3171 9.691362 TTTGTTCATTAAGACTGCCTTATTTTC 57.309 29.630 0.00 0.0 37.22 2.29
1576 3190 7.685481 TCAATACCATACTCTTCCTTTGTTCA 58.315 34.615 0.00 0.0 0.00 3.18
1603 3221 2.173356 TGCAGAGGTCCCATGATAAAGG 59.827 50.000 0.00 0.0 0.00 3.11
1653 3271 5.016173 ACATGCAGGCAGTCCTTTTATTAA 58.984 37.500 0.00 0.0 41.93 1.40
1670 3288 5.003692 TGCTAAACACAAAGAAACATGCA 57.996 34.783 0.00 0.0 0.00 3.96
1857 3476 0.698238 TGGCAAAGACTATGGCACCT 59.302 50.000 0.00 0.0 46.85 4.00
1862 3481 7.814264 AAATAGATCTTGGCAAAGACTATGG 57.186 36.000 18.72 0.0 45.12 2.74
1895 3514 6.374333 TCTCATAAAATAGGTGGTTTGCTGAC 59.626 38.462 0.00 0.0 0.00 3.51
1914 3533 5.471556 TTTTACCGAGTGTGGTTCTCATA 57.528 39.130 0.00 0.0 43.56 2.15
1957 3576 0.514691 GACAGCTCTCGGCAAACAAG 59.485 55.000 0.00 0.0 44.79 3.16
1976 3595 3.320541 TGGGGTTGCTGACTATTTTTGTG 59.679 43.478 0.00 0.0 0.00 3.33
1986 3605 1.067060 GAGTGTTTTGGGGTTGCTGAC 59.933 52.381 0.00 0.0 0.00 3.51
2043 3662 1.201647 GCTCCGTGTTGCTGAGTAGTA 59.798 52.381 0.00 0.0 32.01 1.82
2044 3663 0.038159 GCTCCGTGTTGCTGAGTAGT 60.038 55.000 0.00 0.0 32.01 2.73
2045 3664 0.737715 GGCTCCGTGTTGCTGAGTAG 60.738 60.000 0.00 0.0 32.01 2.57
2074 3693 5.416013 TCTCATGGACGATATCACTGGATAC 59.584 44.000 3.12 0.0 38.76 2.24
2087 3706 3.306294 GCATGGTATCATCTCATGGACGA 60.306 47.826 0.00 0.0 38.80 4.20


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

AutoCloner maintained by Alex Coulton.