Multiple sequence alignment - TraesCS3A01G166700

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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 TraesCS3A01G166700 chr3A 100.000 2387 0 0 1 2387 171208686 171211072 0.000000e+00 4409.0
1 TraesCS3A01G166700 chr3D 92.703 1617 69 17 502 2099 157040887 157039301 0.000000e+00 2287.0
2 TraesCS3A01G166700 chr3D 91.165 498 26 8 1 490 157041429 157040942 0.000000e+00 660.0
3 TraesCS3A01G166700 chr3D 91.398 93 0 1 2303 2387 157038853 157038761 1.160000e-23 121.0
4 TraesCS3A01G166700 chr3B 92.365 1598 74 18 502 2087 228098386 228096825 0.000000e+00 2231.0
5 TraesCS3A01G166700 chr3B 91.313 495 31 9 1 490 228098928 228098441 0.000000e+00 665.0
6 TraesCS3A01G166700 chr3B 88.477 243 25 3 2108 2349 228093582 228093342 8.350000e-75 291.0
7 TraesCS3A01G166700 chr3B 100.000 45 0 0 2336 2380 228093339 228093295 1.520000e-12 84.2


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 TraesCS3A01G166700 chr3A 171208686 171211072 2386 False 4409.000000 4409 100.000000 1 2387 1 chr3A.!!$F1 2386
1 TraesCS3A01G166700 chr3D 157038761 157041429 2668 True 1022.666667 2287 91.755333 1 2387 3 chr3D.!!$R1 2386
2 TraesCS3A01G166700 chr3B 228093295 228098928 5633 True 817.800000 2231 93.038750 1 2380 4 chr3B.!!$R1 2379

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
984 1040 0.256177 CCTAAGCTTTCCCCCTCCAC 59.744 60.0 3.2 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2160 2.229792 TCAGATTTGGCTGTTGTGGAC 58.77 47.619 0.0 0.0 37.2 4.02 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
44 47 1.416772 CCCGTTATCTCCCCTTTCTCC 59.583 57.143 0.00 0.00 0.00 3.71
46 49 1.068741 CGTTATCTCCCCTTTCTCCGG 59.931 57.143 0.00 0.00 0.00 5.14
82 91 6.053005 TGCTTCTTTTACAGGGATTATACCG 58.947 40.000 0.00 0.00 0.00 4.02
118 127 4.180057 GACAGTAGCATCAACTTCTCCTG 58.820 47.826 0.00 0.00 0.00 3.86
151 161 0.602638 TCAACCTGCAGTACAAGCCG 60.603 55.000 13.81 0.00 0.00 5.52
283 294 6.790232 TGTGGACTACATGATCAATCAGTA 57.210 37.500 0.00 0.20 40.64 2.74
284 295 6.573434 TGTGGACTACATGATCAATCAGTAC 58.427 40.000 0.00 4.41 40.64 2.73
285 296 6.154363 TGTGGACTACATGATCAATCAGTACA 59.846 38.462 12.47 12.47 40.64 2.90
286 297 7.041721 GTGGACTACATGATCAATCAGTACAA 58.958 38.462 16.29 3.68 40.64 2.41
350 361 5.254339 ACTTACCGTATCTTTCTAACCGG 57.746 43.478 0.00 0.00 41.09 5.28
370 381 4.297510 CGGATCAACAATGCTTCAAAACA 58.702 39.130 0.00 0.00 0.00 2.83
385 396 5.947503 TCAAAACAAATTTCGTGCTTCTG 57.052 34.783 0.00 0.00 0.00 3.02
403 414 2.258286 GACCCATTTGCCGTGCAC 59.742 61.111 6.82 6.82 38.71 4.57
440 451 3.693085 ACATGCCTGCAGACATTAGAAAG 59.307 43.478 17.39 4.71 0.00 2.62
493 504 2.516460 CTGGAGGGAGCTGCATGC 60.516 66.667 11.82 11.82 43.29 4.06
568 622 2.158449 GGCAGACGTGTCAAATCTTCAG 59.842 50.000 0.00 0.00 0.00 3.02
609 663 3.068590 AGCCAATTGCCAAGAATATTCCG 59.931 43.478 11.92 3.85 42.71 4.30
612 666 2.435372 TTGCCAAGAATATTCCGCCT 57.565 45.000 11.92 0.00 0.00 5.52
661 715 1.340465 GTACGCACGCACAAGATCG 59.660 57.895 0.00 0.00 0.00 3.69
676 730 2.453773 GATCGCCATCGCAAGCATGG 62.454 60.000 14.92 14.92 43.46 3.66
834 889 3.955775 CATATGCATGCGCCGAGA 58.044 55.556 14.09 0.00 37.32 4.04
870 926 1.512926 CATTGCCGTCTAGCCCATAC 58.487 55.000 0.00 0.00 0.00 2.39
880 936 4.459685 CGTCTAGCCCATACTATAAGCACT 59.540 45.833 0.00 0.00 0.00 4.40
973 1029 1.296715 CTGCCACGACCCTAAGCTT 59.703 57.895 3.48 3.48 0.00 3.74
976 1032 1.025113 GCCACGACCCTAAGCTTTCC 61.025 60.000 3.20 0.00 0.00 3.13
984 1040 0.256177 CCTAAGCTTTCCCCCTCCAC 59.744 60.000 3.20 0.00 0.00 4.02
1009 1065 3.001514 CCACCACCATGGGGAGAG 58.998 66.667 18.14 0.26 46.22 3.20
1127 1183 4.452733 GCCGCCGCTGTCCTACTT 62.453 66.667 0.00 0.00 0.00 2.24
1169 1225 3.971702 GGTGTGCCTGGAGCCCTT 61.972 66.667 0.00 0.00 42.71 3.95
1182 1238 4.115199 CCCTTGAGCCCCGGGAAG 62.115 72.222 26.32 17.67 40.55 3.46
1224 1280 4.057428 GACACGGAGTCCAGCGCT 62.057 66.667 2.64 2.64 41.61 5.92
1491 1547 7.214381 CCATCATGCATGACCAAGAAATAAAT 58.786 34.615 30.92 8.13 40.03 1.40
1500 1556 5.059404 ACCAAGAAATAAATTCGGCAGTG 57.941 39.130 0.00 0.00 43.15 3.66
1614 1671 6.342338 AGGGTACAGATGATTTATACGTCC 57.658 41.667 0.00 0.00 0.00 4.79
1809 1872 8.428186 TGTATACCGAATAGTGGAAACATTTC 57.572 34.615 0.00 0.00 46.14 2.17
1856 1919 8.561738 AACAATCGATTCTGTGTATTTTACCT 57.438 30.769 7.92 0.00 0.00 3.08
1859 1922 7.948278 ATCGATTCTGTGTATTTTACCTAGC 57.052 36.000 0.00 0.00 0.00 3.42
1865 1928 9.686683 ATTCTGTGTATTTTACCTAGCTTGAAT 57.313 29.630 0.00 0.00 0.00 2.57
1932 1999 5.103687 TCGCATTATTTGTACGACTGCTTA 58.896 37.500 0.00 0.00 0.00 3.09
2080 2160 0.934901 CGTGACGTGTCTGTCCAGTG 60.935 60.000 0.00 0.00 38.11 3.66
2087 2800 1.134521 GTGTCTGTCCAGTGTCCACAA 60.135 52.381 0.00 0.00 0.00 3.33
2218 5521 1.339291 GCCAGAGCAAAATATCAGGGC 59.661 52.381 0.00 0.00 39.53 5.19
2246 5549 6.597562 AGCATAGGTGTATCCCGAATTTTAA 58.402 36.000 0.00 0.00 36.75 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.068741 CGGAGAAAGGGGAGATAACGG 59.931 57.143 0.00 0.00 0.00 4.44
54 57 9.289782 GTATAATCCCTGTAAAAGAAGCATCAT 57.710 33.333 0.00 0.00 0.00 2.45
65 68 5.931294 TGATTGCGGTATAATCCCTGTAAA 58.069 37.500 0.00 0.00 34.43 2.01
68 77 4.041567 TGATGATTGCGGTATAATCCCTGT 59.958 41.667 0.00 0.00 34.43 4.00
82 91 1.442769 ACTGTCCGTGTGATGATTGC 58.557 50.000 0.00 0.00 0.00 3.56
118 127 2.289002 CAGGTTGACTCACTTTGTCAGC 59.711 50.000 0.00 0.00 43.98 4.26
151 161 6.516739 AAGGAATTAGCTGAAGCCTTAAAC 57.483 37.500 11.90 0.00 43.38 2.01
334 345 5.345702 TGTTGATCCGGTTAGAAAGATACG 58.654 41.667 0.00 0.00 0.00 3.06
344 355 3.680490 TGAAGCATTGTTGATCCGGTTA 58.320 40.909 0.00 0.00 0.00 2.85
350 361 9.161684 GAAATTTGTTTTGAAGCATTGTTGATC 57.838 29.630 0.00 0.00 0.00 2.92
370 381 1.886542 GGGTCCAGAAGCACGAAATTT 59.113 47.619 0.00 0.00 0.00 1.82
385 396 2.988684 TGCACGGCAAATGGGTCC 60.989 61.111 0.00 0.00 34.76 4.46
403 414 2.287915 GGCATGTTACTTCGGTATGCAG 59.712 50.000 0.00 0.00 36.32 4.41
440 451 0.944386 TTGCGAGCACAAGGAAACTC 59.056 50.000 0.00 0.00 42.68 3.01
497 508 0.100503 AATAAAATCGTGGCGCCTGC 59.899 50.000 29.70 19.19 41.71 4.85
498 509 2.612212 AGTAATAAAATCGTGGCGCCTG 59.388 45.455 29.70 20.31 0.00 4.85
499 510 2.612212 CAGTAATAAAATCGTGGCGCCT 59.388 45.455 29.70 7.80 0.00 5.52
500 511 2.853281 GCAGTAATAAAATCGTGGCGCC 60.853 50.000 22.73 22.73 0.00 6.53
568 622 0.036732 TGCCTGGTCATTCACACTCC 59.963 55.000 0.00 0.00 0.00 3.85
661 715 1.285023 GATCCATGCTTGCGATGGC 59.715 57.895 14.69 0.00 40.35 4.40
676 730 4.433615 TCTCGTCCAACTTTAGCATGATC 58.566 43.478 0.00 0.00 0.00 2.92
683 737 2.231478 TCTGCCTCTCGTCCAACTTTAG 59.769 50.000 0.00 0.00 0.00 1.85
833 888 1.206831 GGCGAAAGTCAAAGGCGTC 59.793 57.895 0.00 0.00 34.40 5.19
834 889 1.525077 TGGCGAAAGTCAAAGGCGT 60.525 52.632 0.00 0.00 46.60 5.68
870 926 0.398318 GGGAGGGGCAGTGCTTATAG 59.602 60.000 16.11 0.00 0.00 1.31
880 936 2.887846 TTGTAGGGAGGGAGGGGCA 61.888 63.158 0.00 0.00 0.00 5.36
1168 1224 3.702048 CGTCTTCCCGGGGCTCAA 61.702 66.667 23.50 6.38 0.00 3.02
1207 1263 4.057428 AGCGCTGGACTCCGTGTC 62.057 66.667 10.39 0.00 44.63 3.67
1213 1269 2.813042 GTGCTCAGCGCTGGACTC 60.813 66.667 35.36 23.27 40.11 3.36
1223 1279 2.667536 AGTTGCCGCAGTGCTCAG 60.668 61.111 14.33 2.83 0.00 3.35
1224 1280 2.974148 CAGTTGCCGCAGTGCTCA 60.974 61.111 14.33 8.18 0.00 4.26
1306 1362 1.373497 ACTCGCCGCAGTTCTTCTG 60.373 57.895 0.00 0.00 46.12 3.02
1491 1547 3.364267 CGTAGTATATACGCACTGCCGAA 60.364 47.826 7.23 0.00 34.07 4.30
1500 1556 4.137849 TGCACTCACGTAGTATATACGC 57.862 45.455 7.23 4.19 41.61 4.42
1614 1671 4.500837 CGTAAATCATGAGACGAACAGAGG 59.499 45.833 17.96 0.00 37.50 3.69
1877 1942 7.742767 TGTACATGCCTACTAGTCTATACAGA 58.257 38.462 0.00 0.00 0.00 3.41
1932 1999 5.047802 CCAGTTCTATGAATTGGCAGTTTGT 60.048 40.000 8.51 0.00 0.00 2.83
2080 2160 2.229792 TCAGATTTGGCTGTTGTGGAC 58.770 47.619 0.00 0.00 37.20 4.02
2087 2800 9.331282 GAAATTACTAGTATCAGATTTGGCTGT 57.669 33.333 12.77 0.00 37.20 4.40
2171 5473 9.667107 CAAGATGATAAACCCTACAGTTTCTTA 57.333 33.333 0.00 0.00 40.38 2.10
2184 5486 2.620585 GCTCTGGCCAAGATGATAAACC 59.379 50.000 7.01 0.00 33.29 3.27
2218 5521 4.866508 TCGGGATACACCTATGCTAAAG 57.133 45.455 0.00 0.00 38.98 1.85
2246 5549 3.230743 GCGGGTGCATGTTTCTTAAAT 57.769 42.857 0.00 0.00 42.15 1.40


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

AutoCloner maintained by Alex Coulton.