Multiple sequence alignment - TraesCS4A01G033100

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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 TraesCS4A01G033100 chr4A 100.000 2716 0 0 1 2716 25201371 25204086 0.000000e+00 5016
1 TraesCS4A01G033100 chrUn 95.949 2691 74 22 32 2716 47721095 47718434 0.000000e+00 4333
2 TraesCS4A01G033100 chrUn 95.617 2692 81 25 32 2716 289579852 289582513 0.000000e+00 4283
3 TraesCS4A01G033100 chr7A 96.740 1319 37 4 32 1346 709871066 709872382 0.000000e+00 2193
4 TraesCS4A01G033100 chr7A 94.881 1348 39 17 1370 2716 709872378 709873696 0.000000e+00 2080
5 TraesCS4A01G033100 chr7A 80.210 1713 280 49 72 1750 522256244 522257931 0.000000e+00 1230
6 TraesCS4A01G033100 chr1A 93.715 1082 57 7 450 1522 497225905 497224826 0.000000e+00 1611
7 TraesCS4A01G033100 chr1A 94.393 428 20 2 1 424 497226788 497226361 0.000000e+00 654
8 TraesCS4A01G033100 chr3D 82.318 1691 243 40 72 1737 515700092 515698433 0.000000e+00 1415
9 TraesCS4A01G033100 chr3D 81.957 1707 253 41 71 1750 546581376 546579698 0.000000e+00 1395
10 TraesCS4A01G033100 chr3D 81.129 726 103 17 1996 2716 515698261 515697565 3.950000e-153 551
11 TraesCS4A01G033100 chr3D 79.804 510 71 15 1996 2502 546579541 546579061 2.590000e-90 342
12 TraesCS4A01G033100 chr7D 82.012 1690 250 40 72 1737 532956331 532957990 0.000000e+00 1387
13 TraesCS4A01G033100 chr7D 80.828 725 107 21 1996 2716 532958162 532958858 8.560000e-150 540
14 TraesCS4A01G033100 chr3B 82.911 316 54 0 1940 2255 615890565 615890250 4.430000e-73 285
15 TraesCS4A01G033100 chr3B 92.143 140 11 0 1597 1736 615890921 615890782 5.930000e-47 198


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 TraesCS4A01G033100 chr4A 25201371 25204086 2715 False 5016.0 5016 100.0000 1 2716 1 chr4A.!!$F1 2715
1 TraesCS4A01G033100 chrUn 47718434 47721095 2661 True 4333.0 4333 95.9490 32 2716 1 chrUn.!!$R1 2684
2 TraesCS4A01G033100 chrUn 289579852 289582513 2661 False 4283.0 4283 95.6170 32 2716 1 chrUn.!!$F1 2684
3 TraesCS4A01G033100 chr7A 709871066 709873696 2630 False 2136.5 2193 95.8105 32 2716 2 chr7A.!!$F2 2684
4 TraesCS4A01G033100 chr7A 522256244 522257931 1687 False 1230.0 1230 80.2100 72 1750 1 chr7A.!!$F1 1678
5 TraesCS4A01G033100 chr1A 497224826 497226788 1962 True 1132.5 1611 94.0540 1 1522 2 chr1A.!!$R1 1521
6 TraesCS4A01G033100 chr3D 515697565 515700092 2527 True 983.0 1415 81.7235 72 2716 2 chr3D.!!$R1 2644
7 TraesCS4A01G033100 chr3D 546579061 546581376 2315 True 868.5 1395 80.8805 71 2502 2 chr3D.!!$R2 2431
8 TraesCS4A01G033100 chr7D 532956331 532958858 2527 False 963.5 1387 81.4200 72 2716 2 chr7D.!!$F1 2644
9 TraesCS4A01G033100 chr3B 615890250 615890921 671 True 241.5 285 87.5270 1597 2255 2 chr3B.!!$R1 658

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
432 438 2.442413 CATGGGTTGTTGGTTCGGTAT 58.558 47.619 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2660 1.374252 GCTCCGTTCGGAAGCAAGA 60.374 57.895 21.2 0.39 33.41 3.02 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
109 115 4.589374 AGGTCAAGTGTCTGCTACTAGTTT 59.411 41.667 0.00 0.00 0.00 2.66
231 237 3.119849 CCAAAAACAGAGACCAATAGCCG 60.120 47.826 0.00 0.00 0.00 5.52
243 249 4.694339 ACCAATAGCCGAAGATTCTACAC 58.306 43.478 0.00 0.00 0.00 2.90
358 364 2.676076 GATCTTGTTTGGCGCAACAAT 58.324 42.857 21.79 11.49 0.00 2.71
390 396 2.619849 CCTGTGAAGATTGACCTGGCAT 60.620 50.000 0.00 0.00 0.00 4.40
432 438 2.442413 CATGGGTTGTTGGTTCGGTAT 58.558 47.619 0.00 0.00 0.00 2.73
468 904 4.697352 CAGAAAATGCGCTTAGGGCTATAT 59.303 41.667 21.33 4.89 42.10 0.86
1028 1476 9.620660 GGTACGACACTTATGAAATCAATTTTT 57.379 29.630 0.00 0.00 0.00 1.94
1626 2114 2.156917 CATCACACAGCAACCTCATGT 58.843 47.619 0.00 0.00 0.00 3.21
1787 2287 9.651913 TTTCCCTTATTTAAGAACATCATTTGC 57.348 29.630 0.00 0.00 35.33 3.68
1870 2373 8.250332 TGCACCTGAATAATTTTCTGGATTTAC 58.750 33.333 21.63 12.23 39.12 2.01
1899 2402 7.440856 ACTTTCATTACGGAAACAATTGCATTT 59.559 29.630 5.05 0.00 33.48 2.32
1900 2403 7.721286 TTCATTACGGAAACAATTGCATTTT 57.279 28.000 5.05 0.00 0.00 1.82
1955 2458 5.036117 TCACTAAGGCAGGGATACATTTC 57.964 43.478 0.00 0.00 29.05 2.17
2157 2660 5.360714 TCTTTCTTGAAAATGTTGGACTGCT 59.639 36.000 0.00 0.00 0.00 4.24
2235 2738 5.220662 CCGCAGATCGATCAATAGTTGTTTT 60.221 40.000 26.47 0.00 41.67 2.43
2236 2739 6.019075 CCGCAGATCGATCAATAGTTGTTTTA 60.019 38.462 26.47 0.00 41.67 1.52
2237 2740 7.059817 CGCAGATCGATCAATAGTTGTTTTAG 58.940 38.462 26.47 3.63 41.67 1.85
2238 2741 7.348201 GCAGATCGATCAATAGTTGTTTTAGG 58.652 38.462 26.47 0.00 0.00 2.69
2239 2742 7.224753 GCAGATCGATCAATAGTTGTTTTAGGA 59.775 37.037 26.47 0.00 0.00 2.94
2240 2743 9.098355 CAGATCGATCAATAGTTGTTTTAGGAA 57.902 33.333 26.47 0.00 0.00 3.36
2241 2744 9.838339 AGATCGATCAATAGTTGTTTTAGGAAT 57.162 29.630 26.47 0.00 0.00 3.01
2244 2747 9.443323 TCGATCAATAGTTGTTTTAGGAATTCA 57.557 29.630 7.93 0.00 0.00 2.57
2303 2806 0.647410 CATCGTGCCAAGCGTAGAAG 59.353 55.000 0.00 0.00 0.00 2.85
2378 2886 5.362430 AGACTCAAGCCCTCATAGTAAGAAG 59.638 44.000 0.00 0.00 0.00 2.85
2472 2980 2.592861 GAGATCCACATGGCCGCC 60.593 66.667 1.04 1.04 34.44 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 115 6.578439 GCTTCCATCCCTTTTCCTAGAAACTA 60.578 42.308 0.00 0.00 0.00 2.24
231 237 6.144724 GCGATGTCCATAAGTGTAGAATCTTC 59.855 42.308 0.00 0.00 0.00 2.87
243 249 2.064762 GCTGCTAGCGATGTCCATAAG 58.935 52.381 10.77 0.00 0.00 1.73
358 364 0.888619 CTTCACAGGTGCTCCGTCTA 59.111 55.000 0.00 0.00 39.05 2.59
390 396 1.073284 GTCCCTCCCAAAGTTGCACTA 59.927 52.381 0.00 0.00 0.00 2.74
945 1393 0.609131 CCTGAAACCCAGTGCGGATT 60.609 55.000 4.82 0.00 41.33 3.01
1028 1476 7.492524 TGTTTAGTGTTGACAAATTGCCATAA 58.507 30.769 0.00 0.00 0.00 1.90
1144 1595 4.406456 TGCTGGGTCTAACACAATGATTT 58.594 39.130 0.00 0.00 26.79 2.17
1193 1644 3.939837 CTCGTGCATGCTGACCCGT 62.940 63.158 20.33 0.00 0.00 5.28
1626 2114 1.933181 CATCCGCATCAGCTCGTAAAA 59.067 47.619 0.00 0.00 39.10 1.52
1787 2287 2.108168 TCTAGTTGGGGGAATGACTCG 58.892 52.381 0.00 0.00 0.00 4.18
1840 2342 6.267471 TCCAGAAAATTATTCAGGTGCAGTTT 59.733 34.615 0.00 0.00 0.00 2.66
1870 2373 4.839668 TTGTTTCCGTAATGAAAGTGGG 57.160 40.909 0.00 0.00 35.04 4.61
2157 2660 1.374252 GCTCCGTTCGGAAGCAAGA 60.374 57.895 21.20 0.39 33.41 3.02
2236 2739 9.300681 TGAAACAACTATTGAAGATGAATTCCT 57.699 29.630 2.27 0.00 32.17 3.36
2237 2740 9.565213 CTGAAACAACTATTGAAGATGAATTCC 57.435 33.333 2.27 0.00 32.17 3.01
2238 2741 9.565213 CCTGAAACAACTATTGAAGATGAATTC 57.435 33.333 0.00 0.00 32.52 2.17
2239 2742 9.300681 TCCTGAAACAACTATTGAAGATGAATT 57.699 29.630 0.00 0.00 32.52 2.17
2240 2743 8.868522 TCCTGAAACAACTATTGAAGATGAAT 57.131 30.769 0.00 0.00 32.52 2.57
2241 2744 8.690203 TTCCTGAAACAACTATTGAAGATGAA 57.310 30.769 0.00 0.00 32.52 2.57
2242 2745 8.868522 ATTCCTGAAACAACTATTGAAGATGA 57.131 30.769 0.00 0.00 32.52 2.92
2243 2746 9.565213 GAATTCCTGAAACAACTATTGAAGATG 57.435 33.333 0.00 0.00 34.29 2.90
2244 2747 9.300681 TGAATTCCTGAAACAACTATTGAAGAT 57.699 29.630 2.27 0.00 0.00 2.40
2245 2748 8.690203 TGAATTCCTGAAACAACTATTGAAGA 57.310 30.769 2.27 0.00 0.00 2.87
2246 2749 9.565213 GATGAATTCCTGAAACAACTATTGAAG 57.435 33.333 2.27 0.00 0.00 3.02
2247 2750 9.300681 AGATGAATTCCTGAAACAACTATTGAA 57.699 29.630 2.27 0.00 0.00 2.69
2248 2751 8.868522 AGATGAATTCCTGAAACAACTATTGA 57.131 30.769 2.27 0.00 0.00 2.57
2249 2752 9.565213 GAAGATGAATTCCTGAAACAACTATTG 57.435 33.333 2.27 0.00 0.00 1.90
2250 2753 9.300681 TGAAGATGAATTCCTGAAACAACTATT 57.699 29.630 2.27 0.00 0.00 1.73
2251 2754 8.868522 TGAAGATGAATTCCTGAAACAACTAT 57.131 30.769 2.27 0.00 0.00 2.12
2252 2755 8.690203 TTGAAGATGAATTCCTGAAACAACTA 57.310 30.769 2.27 0.00 0.00 2.24
2378 2886 7.124471 GGTTAGTGTTTCGAAAACTCTTCTTC 58.876 38.462 21.12 5.91 0.00 2.87


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

AutoCloner maintained by Alex Coulton.