Multiple sequence alignment - TraesCS5D01G288500

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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 TraesCS5D01G288500 chr5D 100.000 2987 0 0 1 2987 387707036 387704050 0.000000e+00 5517.0
1 TraesCS5D01G288500 chr5D 87.094 1263 130 17 24 1280 387713622 387712387 0.000000e+00 1399.0
2 TraesCS5D01G288500 chr5D 82.040 1186 186 18 304 1481 387693738 387692572 0.000000e+00 985.0
3 TraesCS5D01G288500 chr5D 80.422 853 125 28 1305 2123 387630832 387629988 1.970000e-171 612.0
4 TraesCS5D01G288500 chr5D 85.227 528 71 6 523 1048 387661696 387661174 1.220000e-148 536.0
5 TraesCS5D01G288500 chr5B 94.174 3021 128 25 1 2987 466173661 466170655 0.000000e+00 4560.0
6 TraesCS5D01G288500 chr5B 86.717 1724 181 25 24 1732 466222518 466220828 0.000000e+00 1871.0
7 TraesCS5D01G288500 chr5B 82.170 1189 181 22 815 1985 466004346 466003171 0.000000e+00 992.0
8 TraesCS5D01G288500 chr5B 75.588 1233 257 34 523 1738 466006667 466005462 1.200000e-158 569.0
9 TraesCS5D01G288500 chr5B 82.171 258 39 6 520 776 466004605 466004354 6.480000e-52 215.0
10 TraesCS5D01G288500 chr5B 86.364 66 3 4 2267 2327 625834400 625834336 1.920000e-07 67.6
11 TraesCS5D01G288500 chr5A 95.297 2658 88 17 1 2623 490595140 490592485 0.000000e+00 4181.0
12 TraesCS5D01G288500 chr5A 85.129 1903 239 24 288 2178 490652573 490650703 0.000000e+00 1906.0
13 TraesCS5D01G288500 chr5A 81.984 1482 224 29 523 1985 490321264 490319807 0.000000e+00 1218.0
14 TraesCS5D01G288500 chr5A 81.826 1183 188 18 304 1478 490419808 490418645 0.000000e+00 968.0
15 TraesCS5D01G288500 chr5A 75.588 1233 264 27 521 1738 490325559 490324349 2.580000e-160 575.0
16 TraesCS5D01G288500 chr5A 90.667 225 17 4 2615 2838 490592013 490591792 2.250000e-76 296.0
17 TraesCS5D01G288500 chr5A 92.344 209 14 2 2615 2823 490592339 490592133 2.250000e-76 296.0
18 TraesCS5D01G288500 chr7D 82.979 94 9 5 2271 2358 264746920 264746828 8.880000e-11 78.7
19 TraesCS5D01G288500 chr4B 92.000 50 3 1 2267 2316 98548146 98548194 5.340000e-08 69.4
20 TraesCS5D01G288500 chr4B 84.000 75 9 3 2271 2342 113393510 113393584 5.340000e-08 69.4
21 TraesCS5D01G288500 chr6B 86.154 65 3 4 2268 2327 71975751 71975814 6.910000e-07 65.8
22 TraesCS5D01G288500 chr2D 86.154 65 3 4 2268 2327 473492870 473492933 6.910000e-07 65.8
23 TraesCS5D01G288500 chr2D 85.938 64 4 4 2268 2327 244176240 244176178 2.490000e-06 63.9


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 TraesCS5D01G288500 chr5D 387704050 387707036 2986 True 5517.0 5517 100.000000 1 2987 1 chr5D.!!$R4 2986
1 TraesCS5D01G288500 chr5D 387712387 387713622 1235 True 1399.0 1399 87.094000 24 1280 1 chr5D.!!$R5 1256
2 TraesCS5D01G288500 chr5D 387692572 387693738 1166 True 985.0 985 82.040000 304 1481 1 chr5D.!!$R3 1177
3 TraesCS5D01G288500 chr5D 387629988 387630832 844 True 612.0 612 80.422000 1305 2123 1 chr5D.!!$R1 818
4 TraesCS5D01G288500 chr5D 387661174 387661696 522 True 536.0 536 85.227000 523 1048 1 chr5D.!!$R2 525
5 TraesCS5D01G288500 chr5B 466170655 466173661 3006 True 4560.0 4560 94.174000 1 2987 1 chr5B.!!$R1 2986
6 TraesCS5D01G288500 chr5B 466220828 466222518 1690 True 1871.0 1871 86.717000 24 1732 1 chr5B.!!$R2 1708
7 TraesCS5D01G288500 chr5B 466003171 466006667 3496 True 592.0 992 79.976333 520 1985 3 chr5B.!!$R4 1465
8 TraesCS5D01G288500 chr5A 490650703 490652573 1870 True 1906.0 1906 85.129000 288 2178 1 chr5A.!!$R2 1890
9 TraesCS5D01G288500 chr5A 490591792 490595140 3348 True 1591.0 4181 92.769333 1 2838 3 chr5A.!!$R4 2837
10 TraesCS5D01G288500 chr5A 490418645 490419808 1163 True 968.0 968 81.826000 304 1478 1 chr5A.!!$R1 1174
11 TraesCS5D01G288500 chr5A 490319807 490325559 5752 True 896.5 1218 78.786000 521 1985 2 chr5A.!!$R3 1464

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
911 4706 1.087771 GCTGCATTGGAGCATTTGGC 61.088 55.0 23.37 0.0 44.68 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 6243 0.316204 AAGGCAGCTGACAAATGCAC 59.684 50.0 24.55 0.0 41.78 4.57 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
747 4525 5.500645 ACTCGCTTTTATTTAATGGGAGC 57.499 39.130 12.31 3.69 46.32 4.70
778 4556 3.746045 TTCGGTATCTTGACATAGGCC 57.254 47.619 0.00 0.00 0.00 5.19
795 4573 1.371183 CCTCTGTGCCTTTCGTCCA 59.629 57.895 0.00 0.00 0.00 4.02
841 4627 4.996788 AGCTTGGCAATTTTATCTCTGG 57.003 40.909 0.00 0.00 0.00 3.86
911 4706 1.087771 GCTGCATTGGAGCATTTGGC 61.088 55.000 23.37 0.00 44.68 4.52
988 4784 2.516227 TAGGGTCCTGAGAGTGTCTG 57.484 55.000 0.00 0.00 0.00 3.51
1335 5143 0.458543 ACACCAACGCTATCTCGCAG 60.459 55.000 0.00 0.00 0.00 5.18
1675 5487 0.603707 CTCCGCAAAGAGCTTGGTCA 60.604 55.000 2.64 0.00 42.61 4.02
1809 5623 5.620738 TGTACTATACGGAGAGTGGTACT 57.379 43.478 4.84 0.00 36.53 2.73
1822 5636 2.043248 GTACTCTCGAGGGGGCCA 60.043 66.667 18.47 0.00 0.00 5.36
2013 5853 0.593518 TTGTTGCGCATGTTGAACCG 60.594 50.000 12.75 0.00 0.00 4.44
2219 6080 5.463061 CACGATTTTGTTGCTTCTCCATTTT 59.537 36.000 0.00 0.00 0.00 1.82
2244 6108 3.134458 GACAGATAGGCCAGCATGTTAC 58.866 50.000 5.01 0.00 0.00 2.50
2286 6150 8.258850 TCCAGAAATATTATACTCCCTTCGTT 57.741 34.615 0.00 0.00 0.00 3.85
2331 6195 6.715344 TGTATAAAGTACAAAGTTGAGGCG 57.285 37.500 0.00 0.00 0.00 5.52
2340 6204 5.699097 ACAAAGTTGAGGCGCTTATTTTA 57.301 34.783 7.64 0.00 0.00 1.52
2345 6209 5.246307 AGTTGAGGCGCTTATTTTAGAACT 58.754 37.500 7.64 0.46 0.00 3.01
2354 6218 6.719365 CGCTTATTTTAGAACTGAGGGAATG 58.281 40.000 0.00 0.00 0.00 2.67
2361 6225 9.920946 ATTTTAGAACTGAGGGAATGCTAATTA 57.079 29.630 0.00 0.00 0.00 1.40
2379 6243 3.710326 TTAGTGCTAGTGATAGTGCGG 57.290 47.619 0.00 0.00 0.00 5.69
2590 6456 4.775236 ACCAATCTCTCTTTGATACTGGC 58.225 43.478 0.00 0.00 29.44 4.85
2667 6686 6.765036 TGCTGAATTGCCATTTTACTCAAAAA 59.235 30.769 0.00 0.00 41.21 1.94
2801 7146 5.869888 ACGATCAACCTTTATTCACTCAGAC 59.130 40.000 0.00 0.00 0.00 3.51
2802 7147 5.004821 CGATCAACCTTTATTCACTCAGACG 59.995 44.000 0.00 0.00 0.00 4.18
2828 7173 6.642683 AGAAATTAGAACATACACGAACCG 57.357 37.500 0.00 0.00 0.00 4.44
2863 7210 8.990163 AATATAACCAAAAGTACATCCCGAAT 57.010 30.769 0.00 0.00 0.00 3.34
2865 7212 4.569719 ACCAAAAGTACATCCCGAATCT 57.430 40.909 0.00 0.00 0.00 2.40
2899 7246 3.678529 GCTTTTCCACAAAACTTCTGGCA 60.679 43.478 0.00 0.00 0.00 4.92
2940 7287 2.407562 ACCAATGCCAACCCTTCTTTT 58.592 42.857 0.00 0.00 0.00 2.27
2946 7293 2.316108 GCCAACCCTTCTTTTCTTCCA 58.684 47.619 0.00 0.00 0.00 3.53
2960 7307 7.437748 TCTTTTCTTCCAAACTTCAACAAACA 58.562 30.769 0.00 0.00 0.00 2.83
2976 7323 7.164803 TCAACAAACACTGGAATTTCCTTTTT 58.835 30.769 16.25 7.43 37.46 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
778 4556 0.868406 GTTGGACGAAAGGCACAGAG 59.132 55.000 0.00 0.00 45.40 3.35
911 4706 0.745845 CTCCGGGCAATTCAGGAGTG 60.746 60.000 0.00 0.00 43.82 3.51
1000 4796 3.066342 GCATTGCTGTCTATCACTTGCAT 59.934 43.478 0.16 0.00 35.90 3.96
1335 5143 4.508662 CAAGTACTTGAGGTGGAGGAATC 58.491 47.826 28.17 0.00 42.93 2.52
1675 5487 3.374220 CACAATGTGGCATGTCAACTT 57.626 42.857 0.00 0.00 0.00 2.66
1923 5743 2.033372 TCCACGACTTCTAACACCACA 58.967 47.619 0.00 0.00 0.00 4.17
2013 5853 6.418819 GCATCATAGACAATACAATTTGGCAC 59.581 38.462 0.78 0.00 37.06 5.01
2156 5997 6.237901 ACCTCATTTGTCTGCTGTAAACATA 58.762 36.000 0.00 0.00 0.00 2.29
2219 6080 0.325577 TGCTGGCCTATCTGTCTGGA 60.326 55.000 3.32 0.00 0.00 3.86
2282 6146 7.504924 AATTGAGACACTTATTTTGGAACGA 57.495 32.000 0.00 0.00 0.00 3.85
2329 6193 4.189231 TCCCTCAGTTCTAAAATAAGCGC 58.811 43.478 0.00 0.00 0.00 5.92
2331 6195 6.319911 AGCATTCCCTCAGTTCTAAAATAAGC 59.680 38.462 0.00 0.00 0.00 3.09
2340 6204 6.352516 CACTAATTAGCATTCCCTCAGTTCT 58.647 40.000 12.54 0.00 0.00 3.01
2345 6209 4.778213 AGCACTAATTAGCATTCCCTCA 57.222 40.909 12.54 0.00 0.00 3.86
2354 6218 5.343593 CGCACTATCACTAGCACTAATTAGC 59.656 44.000 12.54 0.32 0.00 3.09
2361 6225 1.135139 CACCGCACTATCACTAGCACT 59.865 52.381 0.00 0.00 0.00 4.40
2379 6243 0.316204 AAGGCAGCTGACAAATGCAC 59.684 50.000 24.55 0.00 41.78 4.57
2456 6320 2.560105 GGAGGCTTTGCTGTTCTCAAAT 59.440 45.455 0.00 0.00 33.54 2.32
2590 6456 6.702329 AGAGTATCACCTAAACTCTGGTTTG 58.298 40.000 3.55 0.00 46.25 2.93
2676 6695 4.101585 ACTCTCTTTGACTGTGGACATTGA 59.898 41.667 0.00 0.00 0.00 2.57
2677 6696 4.384056 ACTCTCTTTGACTGTGGACATTG 58.616 43.478 0.00 0.00 0.00 2.82
2744 6763 7.050377 TCATTTGCTTAAGTCTATCCAAGGAG 58.950 38.462 4.02 0.00 0.00 3.69
2758 7103 6.257630 TGATCGTTCGATGATCATTTGCTTAA 59.742 34.615 20.73 2.37 43.54 1.85
2801 7146 7.686938 GGTTCGTGTATGTTCTAATTTCTTTCG 59.313 37.037 0.00 0.00 0.00 3.46
2802 7147 7.686938 CGGTTCGTGTATGTTCTAATTTCTTTC 59.313 37.037 0.00 0.00 0.00 2.62
2863 7210 3.069586 TGGAAAAGCTGAGACTCGAAAGA 59.930 43.478 0.00 0.00 39.12 2.52
2865 7212 3.131396 GTGGAAAAGCTGAGACTCGAAA 58.869 45.455 0.00 0.00 0.00 3.46
2879 7226 4.543590 TTGCCAGAAGTTTTGTGGAAAA 57.456 36.364 8.96 0.53 46.44 2.29
2899 7246 4.645136 GGTTTGGTCTTCTCCAGTTCTTTT 59.355 41.667 0.00 0.00 38.80 2.27
2940 7287 5.336372 CCAGTGTTTGTTGAAGTTTGGAAGA 60.336 40.000 0.00 0.00 0.00 2.87
2946 7293 6.593770 GGAAATTCCAGTGTTTGTTGAAGTTT 59.406 34.615 7.23 0.00 36.28 2.66


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

AutoCloner maintained by Alex Coulton.