Multiple sequence alignment - TraesCS1D01G448500

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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 TraesCS1D01G448500 chr1D 100.000 2264 0 0 1 2264 490888673 490890936 0.000000e+00 4181
1 TraesCS1D01G448500 chr1D 92.587 688 27 11 635 1310 297551502 297550827 0.000000e+00 966
2 TraesCS1D01G448500 chr7D 95.466 1235 29 7 1 1211 21074615 21073384 0.000000e+00 1945
3 TraesCS1D01G448500 chr7D 92.693 958 63 6 1310 2262 16798360 16797405 0.000000e+00 1375
4 TraesCS1D01G448500 chr7D 95.820 622 20 4 689 1310 16799003 16798388 0.000000e+00 1000
5 TraesCS1D01G448500 chr7B 94.247 956 52 3 1310 2264 34280969 34280016 0.000000e+00 1458
6 TraesCS1D01G448500 chr7B 97.229 830 20 1 1 830 685201692 685202518 0.000000e+00 1402
7 TraesCS1D01G448500 chr7B 93.548 682 26 9 635 1310 34281666 34280997 0.000000e+00 1000
8 TraesCS1D01G448500 chr7B 91.870 369 27 3 1897 2264 34280240 34279874 1.550000e-141 512
9 TraesCS1D01G448500 chr7B 91.033 368 32 1 1897 2264 34280311 34279945 1.560000e-136 496
10 TraesCS1D01G448500 chr7A 93.305 956 59 5 1312 2264 595031685 595030732 0.000000e+00 1406
11 TraesCS1D01G448500 chr7A 95.788 546 22 1 1310 1854 130558512 130559057 0.000000e+00 880
12 TraesCS1D01G448500 chr7A 89.702 369 35 3 1897 2264 595030388 595030022 3.400000e-128 468
13 TraesCS1D01G448500 chr6B 92.372 957 69 4 1310 2264 425597329 425598283 0.000000e+00 1360
14 TraesCS1D01G448500 chr6B 96.140 829 23 6 1 823 578524175 578525000 0.000000e+00 1345
15 TraesCS1D01G448500 chr6B 93.695 682 31 7 635 1310 425588050 425588725 0.000000e+00 1011
16 TraesCS1D01G448500 chr5D 95.449 857 12 5 1 836 387840728 387839878 0.000000e+00 1341
17 TraesCS1D01G448500 chr5D 90.942 839 53 17 1 823 485079126 485078295 0.000000e+00 1107
18 TraesCS1D01G448500 chr5D 93.343 691 25 10 635 1310 313382838 313382154 0.000000e+00 1002
19 TraesCS1D01G448500 chr5D 92.636 679 26 11 644 1310 387840034 387839368 0.000000e+00 955
20 TraesCS1D01G448500 chr4B 95.823 838 17 2 1 823 598449022 598448188 0.000000e+00 1338
21 TraesCS1D01G448500 chr2D 96.043 834 9 5 1 813 524910416 524909586 0.000000e+00 1336
22 TraesCS1D01G448500 chr2B 95.995 824 29 3 1 823 138731671 138732491 0.000000e+00 1336
23 TraesCS1D01G448500 chr2B 94.035 855 47 4 1313 2165 47386443 47385591 0.000000e+00 1293
24 TraesCS1D01G448500 chr5B 95.704 838 17 3 1 823 16010498 16011331 0.000000e+00 1330
25 TraesCS1D01G448500 chr5B 95.644 551 23 1 1310 1859 35439402 35439952 0.000000e+00 883
26 TraesCS1D01G448500 chr5B 89.946 368 35 2 1897 2264 35440010 35440375 7.320000e-130 473
27 TraesCS1D01G448500 chr4A 92.603 730 51 3 1310 2038 514406286 514405559 0.000000e+00 1046
28 TraesCS1D01G448500 chr2A 93.006 672 29 11 645 1310 372743413 372744072 0.000000e+00 965
29 TraesCS1D01G448500 chr3A 92.229 682 35 9 635 1310 44773583 44772914 0.000000e+00 950
30 TraesCS1D01G448500 chr1A 94.872 546 27 1 1310 1854 480959469 480960014 0.000000e+00 852


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 TraesCS1D01G448500 chr1D 490888673 490890936 2263 False 4181.0 4181 100.0000 1 2264 1 chr1D.!!$F1 2263
1 TraesCS1D01G448500 chr1D 297550827 297551502 675 True 966.0 966 92.5870 635 1310 1 chr1D.!!$R1 675
2 TraesCS1D01G448500 chr7D 21073384 21074615 1231 True 1945.0 1945 95.4660 1 1211 1 chr7D.!!$R1 1210
3 TraesCS1D01G448500 chr7D 16797405 16799003 1598 True 1187.5 1375 94.2565 689 2262 2 chr7D.!!$R2 1573
4 TraesCS1D01G448500 chr7B 685201692 685202518 826 False 1402.0 1402 97.2290 1 830 1 chr7B.!!$F1 829
5 TraesCS1D01G448500 chr7B 34279874 34281666 1792 True 866.5 1458 92.6745 635 2264 4 chr7B.!!$R1 1629
6 TraesCS1D01G448500 chr7A 595030022 595031685 1663 True 937.0 1406 91.5035 1312 2264 2 chr7A.!!$R1 952
7 TraesCS1D01G448500 chr7A 130558512 130559057 545 False 880.0 880 95.7880 1310 1854 1 chr7A.!!$F1 544
8 TraesCS1D01G448500 chr6B 425597329 425598283 954 False 1360.0 1360 92.3720 1310 2264 1 chr6B.!!$F2 954
9 TraesCS1D01G448500 chr6B 578524175 578525000 825 False 1345.0 1345 96.1400 1 823 1 chr6B.!!$F3 822
10 TraesCS1D01G448500 chr6B 425588050 425588725 675 False 1011.0 1011 93.6950 635 1310 1 chr6B.!!$F1 675
11 TraesCS1D01G448500 chr5D 387839368 387840728 1360 True 1148.0 1341 94.0425 1 1310 2 chr5D.!!$R3 1309
12 TraesCS1D01G448500 chr5D 485078295 485079126 831 True 1107.0 1107 90.9420 1 823 1 chr5D.!!$R2 822
13 TraesCS1D01G448500 chr5D 313382154 313382838 684 True 1002.0 1002 93.3430 635 1310 1 chr5D.!!$R1 675
14 TraesCS1D01G448500 chr4B 598448188 598449022 834 True 1338.0 1338 95.8230 1 823 1 chr4B.!!$R1 822
15 TraesCS1D01G448500 chr2D 524909586 524910416 830 True 1336.0 1336 96.0430 1 813 1 chr2D.!!$R1 812
16 TraesCS1D01G448500 chr2B 138731671 138732491 820 False 1336.0 1336 95.9950 1 823 1 chr2B.!!$F1 822
17 TraesCS1D01G448500 chr2B 47385591 47386443 852 True 1293.0 1293 94.0350 1313 2165 1 chr2B.!!$R1 852
18 TraesCS1D01G448500 chr5B 16010498 16011331 833 False 1330.0 1330 95.7040 1 823 1 chr5B.!!$F1 822
19 TraesCS1D01G448500 chr5B 35439402 35440375 973 False 678.0 883 92.7950 1310 2264 2 chr5B.!!$F2 954
20 TraesCS1D01G448500 chr4A 514405559 514406286 727 True 1046.0 1046 92.6030 1310 2038 1 chr4A.!!$R1 728
21 TraesCS1D01G448500 chr2A 372743413 372744072 659 False 965.0 965 93.0060 645 1310 1 chr2A.!!$F1 665
22 TraesCS1D01G448500 chr3A 44772914 44773583 669 True 950.0 950 92.2290 635 1310 1 chr3A.!!$R1 675
23 TraesCS1D01G448500 chr1A 480959469 480960014 545 False 852.0 852 94.8720 1310 1854 1 chr1A.!!$F1 544

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
830 1023 0.470456 AGAGGTGGTGGTGGTCGTAA 60.47 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 3087 0.105453 TGCTCTCTGGATAGGGACCC 60.105 60.0 0.59 0.59 0.0 4.46 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
290 291 3.444703 TGTTTGTGATGGAAAAACCGG 57.555 42.857 0.00 0.00 42.61 5.28
405 406 3.728385 GGCCCTCATATTAAGCCAGAT 57.272 47.619 0.00 0.00 43.32 2.90
584 585 0.736636 CACAATGAGCGGACATGCAT 59.263 50.000 0.00 0.00 37.31 3.96
830 1023 0.470456 AGAGGTGGTGGTGGTCGTAA 60.470 55.000 0.00 0.00 0.00 3.18
1017 1210 0.749454 GCATGGCTTCATCCGGTTCT 60.749 55.000 0.00 0.00 0.00 3.01
1029 1222 2.050350 CGGTTCTAGGACGAGGCCA 61.050 63.158 5.01 0.00 0.00 5.36
1500 1721 2.555757 GCAAGAGAAGGCACACAAAGAT 59.444 45.455 0.00 0.00 0.00 2.40
1731 1952 4.877282 TGTCATTCGAGACATTGTGTGTA 58.123 39.130 3.54 0.00 43.18 2.90
1923 2165 1.427809 CATAGACCCTGGCATCTGGA 58.572 55.000 8.52 0.00 34.32 3.86
1958 2200 5.318630 AGAGCATTTTTGGAATTTGGCAAT 58.681 33.333 0.00 0.00 0.00 3.56
1959 2201 5.182380 AGAGCATTTTTGGAATTTGGCAATG 59.818 36.000 0.00 0.00 0.00 2.82
1960 2202 5.071370 AGCATTTTTGGAATTTGGCAATGA 58.929 33.333 0.00 0.00 0.00 2.57
1974 2713 1.536940 CAATGATGCACACCCAGACA 58.463 50.000 0.00 0.00 0.00 3.41
2083 2964 1.152139 GGCCCCTATCCAGAGAGCT 60.152 63.158 0.00 0.00 0.00 4.09
2135 3087 2.046892 CAAGGTCCCTGGCGTCTG 60.047 66.667 0.00 0.00 0.00 3.51
2159 3182 4.384940 GTCCCTATCCAGAGAGCATTTTC 58.615 47.826 0.00 0.00 0.00 2.29
2184 3207 1.697284 TTGCTAATGTGCACACCCAA 58.303 45.000 24.37 18.53 43.20 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 291 2.514824 GGACCTCTTGCATCCGCC 60.515 66.667 0.00 0.00 37.32 6.13
304 305 2.766828 ACCTAGTAGCTTCCACATGGAC 59.233 50.000 0.00 0.00 45.39 4.02
405 406 2.530701 GTCTCCACCTTCAGAAGAGGA 58.469 52.381 12.14 15.89 33.45 3.71
584 585 4.011023 TCCACGACTTGTTTTCCTTTTCA 58.989 39.130 0.00 0.00 0.00 2.69
830 1023 5.072741 CCGATCCATTATCAACCATTCCTT 58.927 41.667 0.00 0.00 33.87 3.36
1017 1210 3.449227 CACGCTGGCCTCGTCCTA 61.449 66.667 18.30 0.00 38.19 2.94
1487 1708 1.453155 CGCCTTATCTTTGTGTGCCT 58.547 50.000 0.00 0.00 0.00 4.75
1500 1721 0.108804 CTTCTTGACGAGCCGCCTTA 60.109 55.000 0.00 0.00 0.00 2.69
1724 1945 6.358118 GTCTCAATGACAAGTTTACACACA 57.642 37.500 0.00 0.00 44.73 3.72
1958 2200 1.073025 GGTGTCTGGGTGTGCATCA 59.927 57.895 0.00 0.00 0.00 3.07
1959 2201 0.537143 TTGGTGTCTGGGTGTGCATC 60.537 55.000 0.00 0.00 0.00 3.91
1960 2202 0.538057 CTTGGTGTCTGGGTGTGCAT 60.538 55.000 0.00 0.00 0.00 3.96
1974 2713 3.637273 GACGCCAGGGACCTTGGT 61.637 66.667 22.80 4.95 0.00 3.67
2018 2757 3.624326 GTGTGCACATAAGCAAACTGA 57.376 42.857 24.69 0.00 46.77 3.41
2028 2767 0.394216 GGCATCTGGGTGTGCACATA 60.394 55.000 24.69 11.74 43.00 2.29
2067 2948 3.941704 AAAAAGCTCTCTGGATAGGGG 57.058 47.619 0.00 0.00 0.00 4.79
2135 3087 0.105453 TGCTCTCTGGATAGGGACCC 60.105 60.000 0.59 0.59 0.00 4.46
2184 3207 4.660938 GCCAGGGACCTTGGCGTT 62.661 66.667 29.83 0.00 39.06 4.84


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

AutoCloner maintained by Alex Coulton.