Multiple sequence alignment - TraesCS3D01G335300

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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 TraesCS3D01G335300 chr3D 100.000 2678 0 0 631 3308 447132529 447129852 0.000000e+00 4946
1 TraesCS3D01G335300 chr3D 100.000 261 0 0 1 261 447133159 447132899 1.790000e-132 483
2 TraesCS3D01G335300 chr3A 96.945 2684 75 4 632 3308 588836406 588833723 0.000000e+00 4495
3 TraesCS3D01G335300 chr3A 94.064 219 13 0 41 259 588836626 588836408 1.900000e-87 333
4 TraesCS3D01G335300 chr3B 96.026 2265 87 1 631 2892 586518968 586516704 0.000000e+00 3681
5 TraesCS3D01G335300 chr3B 95.338 429 14 3 2883 3308 586516533 586516108 0.000000e+00 676
6 TraesCS3D01G335300 chr3B 88.168 262 15 3 1 261 586519213 586518967 6.940000e-77 298
7 TraesCS3D01G335300 chr6B 91.902 778 54 2 1135 1904 707361770 707362546 0.000000e+00 1079
8 TraesCS3D01G335300 chr6B 89.091 385 33 8 631 1012 707361393 707361771 1.390000e-128 470


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 TraesCS3D01G335300 chr3D 447129852 447133159 3307 True 2714.500000 4946 100.000000 1 3308 2 chr3D.!!$R1 3307
1 TraesCS3D01G335300 chr3A 588833723 588836626 2903 True 2414.000000 4495 95.504500 41 3308 2 chr3A.!!$R1 3267
2 TraesCS3D01G335300 chr3B 586516108 586519213 3105 True 1551.666667 3681 93.177333 1 3308 3 chr3B.!!$R1 3307
3 TraesCS3D01G335300 chr6B 707361393 707362546 1153 False 774.500000 1079 90.496500 631 1904 2 chr6B.!!$F1 1273

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
29 31 3.557898 GGCCCATATATATGATCAGCCGG 60.558 52.174 21.97 13.88 35.75 6.13 F
32 34 5.687441 GCCCATATATATGATCAGCCGGAAA 60.687 44.000 21.97 0.00 35.75 3.13 F
1399 1404 2.584064 CTGCAGTATGGCCGGACA 59.416 61.111 15.46 15.46 35.86 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1328 0.320421 GGTCAGCCGAGTAGTGCAAA 60.320 55.0 0.0 0.0 0.00 3.68 R
1673 1686 0.396435 TGTCATCTGGCGGAACAACT 59.604 50.0 0.0 0.0 0.00 3.16 R
2437 2453 1.061546 TTGGCGAAACCCTCTTACCT 58.938 50.0 0.0 0.0 37.83 3.08 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 27 3.982730 TGGGGGCCCATATATATGATCAG 59.017 47.826 26.86 9.98 41.89 2.90
29 31 3.557898 GGCCCATATATATGATCAGCCGG 60.558 52.174 21.97 13.88 35.75 6.13
32 34 5.687441 GCCCATATATATGATCAGCCGGAAA 60.687 44.000 21.97 0.00 35.75 3.13
34 36 6.408548 CCCATATATATGATCAGCCGGAAAGT 60.409 42.308 21.97 0.00 35.75 2.66
1398 1403 2.897350 GCTGCAGTATGGCCGGAC 60.897 66.667 16.64 0.56 35.86 4.79
1399 1404 2.584064 CTGCAGTATGGCCGGACA 59.416 61.111 15.46 15.46 35.86 4.02
1514 1519 2.823593 TCGCGATGGTGCAATGGG 60.824 61.111 3.71 0.00 34.15 4.00
1633 1638 6.510638 CGTGGCATCATGGAATATTATGATCG 60.511 42.308 9.75 7.68 40.93 3.69
1781 1794 3.559384 GGGTTTGTCGAAGAAGGGAGAAT 60.559 47.826 0.00 0.00 39.69 2.40
1783 1796 4.154375 GGTTTGTCGAAGAAGGGAGAATTC 59.846 45.833 0.00 0.00 39.69 2.17
1785 1798 4.891992 TGTCGAAGAAGGGAGAATTCTT 57.108 40.909 9.87 0.79 46.89 2.52
1823 1836 0.884704 GAGTTCAGTTTGGAGCCGCA 60.885 55.000 0.00 0.00 0.00 5.69
1843 1856 1.202463 AGATGGAGCACTACGCATGTC 60.202 52.381 0.00 0.00 46.13 3.06
1893 1906 0.984230 TGGATGAGGCGAGAAAGGTT 59.016 50.000 0.00 0.00 0.00 3.50
1926 1939 1.227380 GGATGTAGGAGCTGGTGCG 60.227 63.158 0.00 0.00 45.42 5.34
2109 2122 2.367202 GGGGGAGATGAGACGGCAA 61.367 63.158 0.00 0.00 0.00 4.52
2164 2180 3.172106 TGGGTGGAGGAAACGGCA 61.172 61.111 0.00 0.00 0.00 5.69
2169 2185 0.250338 GTGGAGGAAACGGCAAGAGT 60.250 55.000 0.00 0.00 0.00 3.24
2179 2195 1.414919 ACGGCAAGAGTGGAACAGTTA 59.585 47.619 0.00 0.00 45.14 2.24
2180 2196 2.038557 ACGGCAAGAGTGGAACAGTTAT 59.961 45.455 0.00 0.00 45.14 1.89
2223 2239 0.768221 AGGAACACCCTGAGGCTGAA 60.768 55.000 0.00 0.00 45.61 3.02
2247 2263 7.402811 AATGATTTATGAAATGCTGCATTCG 57.597 32.000 26.40 0.00 32.43 3.34
2433 2449 0.468226 AGAGCACCACCGAAACTTGA 59.532 50.000 0.00 0.00 0.00 3.02
2437 2453 1.384525 CACCACCGAAACTTGAACCA 58.615 50.000 0.00 0.00 0.00 3.67
2571 2587 2.370281 ATGTAGTTCTGTGGCACTCG 57.630 50.000 19.83 10.03 0.00 4.18
2934 3130 7.049754 TGAAGCTCATCTTAATTCATGTGCTA 58.950 34.615 16.06 5.38 44.91 3.49
2984 3180 8.547967 TTTTGATGGTAAGAATCAGACAGTAC 57.452 34.615 0.00 0.00 35.54 2.73
3008 3206 4.635223 TCTTATGACTATCATGGCAGCAC 58.365 43.478 1.49 0.00 37.70 4.40
3125 3323 3.484407 AGCCTATCAATGGATCAAGCAC 58.516 45.455 0.00 0.00 34.89 4.40
3171 3369 5.766150 TGTGTTGGTCATTTCCTTACAAG 57.234 39.130 0.00 0.00 0.00 3.16
3173 3371 6.358178 TGTGTTGGTCATTTCCTTACAAGTA 58.642 36.000 0.00 0.00 0.00 2.24
3203 3401 4.750098 AGATTTGCCGATAAAGATACACCG 59.250 41.667 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.557898 CGGCTGATCATATATATGGGCCC 60.558 52.174 25.53 17.59 34.95 5.80
11 12 7.495901 AGACTTTCCGGCTGATCATATATATG 58.504 38.462 15.47 15.47 35.04 1.78
29 31 3.387947 TCCGCCCGGGAGACTTTC 61.388 66.667 29.31 2.60 40.94 2.62
74 76 1.569479 GACTGGTGGCGCTTTCAGAC 61.569 60.000 23.30 16.50 0.00 3.51
121 123 0.967380 AGAGGGCCGCCATTTTTCTG 60.967 55.000 12.58 0.00 0.00 3.02
1323 1328 0.320421 GGTCAGCCGAGTAGTGCAAA 60.320 55.000 0.00 0.00 0.00 3.68
1673 1686 0.396435 TGTCATCTGGCGGAACAACT 59.604 50.000 0.00 0.00 0.00 3.16
1716 1729 0.610174 CTGCCAGCAGAGTTACCTCA 59.390 55.000 14.54 0.00 46.30 3.86
1755 1768 2.486548 CCCTTCTTCGACAAACCCAGAA 60.487 50.000 0.00 0.00 0.00 3.02
1781 1794 8.875168 ACTCCTCTTTCATTCTCTTAAGAAGAA 58.125 33.333 6.63 12.06 44.53 2.52
1783 1796 9.150348 GAACTCCTCTTTCATTCTCTTAAGAAG 57.850 37.037 6.63 0.00 44.53 2.85
1785 1798 8.195165 TGAACTCCTCTTTCATTCTCTTAAGA 57.805 34.615 4.81 4.81 0.00 2.10
1823 1836 0.826715 ACATGCGTAGTGCTCCATCT 59.173 50.000 0.00 0.00 46.63 2.90
1843 1856 1.642037 CGCCCAAGCATGTCAGTCAG 61.642 60.000 0.00 0.00 39.83 3.51
1893 1906 0.399091 CATCCCCTGCCTCCTCTACA 60.399 60.000 0.00 0.00 0.00 2.74
2002 2015 4.821589 CCCAGGCTCCTTCGTCGC 62.822 72.222 0.00 0.00 0.00 5.19
2143 2159 1.196104 CCGTTTCCTCCACCCACCTA 61.196 60.000 0.00 0.00 0.00 3.08
2164 2180 3.067106 CGTGCATAACTGTTCCACTCTT 58.933 45.455 0.00 0.00 0.00 2.85
2169 2185 1.890876 AAGCGTGCATAACTGTTCCA 58.109 45.000 0.00 0.00 0.00 3.53
2179 2195 1.335872 GCCACTAACAAAAGCGTGCAT 60.336 47.619 0.00 0.00 0.00 3.96
2180 2196 0.030101 GCCACTAACAAAAGCGTGCA 59.970 50.000 0.00 0.00 0.00 4.57
2214 2230 6.982141 GCATTTCATAAATCATTTCAGCCTCA 59.018 34.615 0.00 0.00 0.00 3.86
2215 2231 7.169308 CAGCATTTCATAAATCATTTCAGCCTC 59.831 37.037 0.00 0.00 0.00 4.70
2223 2239 6.982141 ACGAATGCAGCATTTCATAAATCATT 59.018 30.769 21.73 0.00 33.90 2.57
2247 2263 5.221126 GCAATCCCTCATCCAACTTATCAAC 60.221 44.000 0.00 0.00 0.00 3.18
2322 2338 8.792633 TCAGTGCTAGCTTGTAACAAAATAAAT 58.207 29.630 17.23 0.00 0.00 1.40
2323 2339 8.073768 GTCAGTGCTAGCTTGTAACAAAATAAA 58.926 33.333 17.23 0.00 0.00 1.40
2433 2449 1.271217 GCGAAACCCTCTTACCTGGTT 60.271 52.381 3.84 0.00 44.04 3.67
2437 2453 1.061546 TTGGCGAAACCCTCTTACCT 58.938 50.000 0.00 0.00 37.83 3.08
2806 2822 2.045708 GGTCGGCATCACATTGGCA 61.046 57.895 0.00 0.00 41.97 4.92
2946 3142 4.669700 ACCATCAAAAGGGTAAAGGGTAC 58.330 43.478 0.00 0.00 37.93 3.34
2984 3180 5.121925 GTGCTGCCATGATAGTCATAAGATG 59.878 44.000 0.00 0.00 34.28 2.90
3008 3206 2.005451 GTCAGCATGCTTGGTAGAGTG 58.995 52.381 19.98 4.27 34.76 3.51
3125 3323 2.791383 TTGGATGGAAAAGCACAACG 57.209 45.000 0.00 0.00 0.00 4.10
3157 3355 8.603898 TCTATCCACTACTTGTAAGGAAATGA 57.396 34.615 5.96 3.56 31.17 2.57
3171 3369 7.152645 TCTTTATCGGCAAATCTATCCACTAC 58.847 38.462 0.00 0.00 0.00 2.73
3173 3371 6.174720 TCTTTATCGGCAAATCTATCCACT 57.825 37.500 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.