Multiple sequence alignment - TraesCS3D01G221200

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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 TraesCS3D01G221200 chr3D 100.000 3563 0 0 1 3563 301740520 301736958 0.000000e+00 6580.0
1 TraesCS3D01G221200 chr2D 98.295 2698 38 2 874 3563 565531657 565534354 0.000000e+00 4721.0
2 TraesCS3D01G221200 chr2D 97.197 892 9 3 1 876 565529876 565530767 0.000000e+00 1495.0
3 TraesCS3D01G221200 chr2D 97.500 40 1 0 2872 2911 11510630 11510669 6.380000e-08 69.4
4 TraesCS3D01G221200 chr2A 98.182 1870 30 1 874 2739 182859562 182861431 0.000000e+00 3262.0
5 TraesCS3D01G221200 chr2A 95.721 888 26 2 1 876 182857785 182858672 0.000000e+00 1419.0
6 TraesCS3D01G221200 chr2A 91.877 357 4 2 3207 3563 182861426 182861757 3.220000e-130 475.0
7 TraesCS3D01G221200 chr2A 83.708 356 38 9 1228 1572 679012786 679013132 5.740000e-83 318.0
8 TraesCS3D01G221200 chr2A 94.545 110 6 0 3454 3563 304809202 304809093 1.700000e-38 171.0
9 TraesCS3D01G221200 chr2A 93.636 110 7 0 3454 3563 191964234 191964343 7.910000e-37 165.0
10 TraesCS3D01G221200 chr2A 89.431 123 12 1 1617 1739 679014604 679014725 1.710000e-33 154.0
11 TraesCS3D01G221200 chr2A 93.443 61 4 0 814 874 679001252 679001312 1.360000e-14 91.6
12 TraesCS3D01G221200 chr2A 91.525 59 5 0 1786 1844 424506885 424506827 8.200000e-12 82.4
13 TraesCS3D01G221200 chr2A 94.444 36 2 0 1749 1784 679014776 679014811 4.970000e-04 56.5
14 TraesCS3D01G221200 chr7A 97.972 1874 30 1 874 2739 577679295 577677422 0.000000e+00 3243.0
15 TraesCS3D01G221200 chr7A 95.833 888 25 5 1 876 499902032 499901145 0.000000e+00 1424.0
16 TraesCS3D01G221200 chr7A 95.833 888 25 2 1 876 577681072 577680185 0.000000e+00 1424.0
17 TraesCS3D01G221200 chr7A 98.104 791 13 1 874 1662 471965110 471964320 0.000000e+00 1376.0
18 TraesCS3D01G221200 chr7A 94.820 888 25 3 1 876 471966878 471966000 0.000000e+00 1365.0
19 TraesCS3D01G221200 chr7A 96.638 803 13 1 874 1662 499900255 499899453 0.000000e+00 1321.0
20 TraesCS3D01G221200 chr7A 94.620 632 22 7 257 876 499853417 499852786 0.000000e+00 968.0
21 TraesCS3D01G221200 chr7A 96.429 392 10 1 930 1317 499847821 499847430 0.000000e+00 643.0
22 TraesCS3D01G221200 chr7A 97.938 291 6 0 1372 1662 499847431 499847141 4.110000e-139 505.0
23 TraesCS3D01G221200 chr7A 92.157 357 3 2 3207 3563 577677427 577677096 6.920000e-132 481.0
24 TraesCS3D01G221200 chr7A 96.610 59 2 0 874 932 499851896 499851838 8.140000e-17 99.0
25 TraesCS3D01G221200 chr1A 97.215 1867 45 6 874 2739 450979046 450980906 0.000000e+00 3153.0
26 TraesCS3D01G221200 chr1A 94.482 888 37 2 1 876 450977319 450978206 0.000000e+00 1358.0
27 TraesCS3D01G221200 chr1A 91.620 358 5 2 3207 3563 450980901 450981234 4.160000e-129 472.0
28 TraesCS3D01G221200 chr4A 94.961 1151 35 7 1800 2938 702700276 702701415 0.000000e+00 1783.0
29 TraesCS3D01G221200 chr4A 96.519 747 16 1 874 1610 702698766 702699512 0.000000e+00 1227.0
30 TraesCS3D01G221200 chr4A 94.969 636 25 4 2934 3563 702702502 702703136 0.000000e+00 990.0
31 TraesCS3D01G221200 chr4A 90.237 379 27 4 1786 2155 298169535 298169158 1.490000e-133 486.0
32 TraesCS3D01G221200 chr3A 94.570 884 40 7 1 876 493273919 493274802 0.000000e+00 1360.0
33 TraesCS3D01G221200 chr3A 97.592 789 19 0 874 1662 493275688 493276476 0.000000e+00 1352.0
34 TraesCS3D01G221200 chr3A 95.385 325 14 1 3129 3453 56089809 56090132 1.900000e-142 516.0
35 TraesCS3D01G221200 chr3A 95.349 43 2 0 2872 2914 597967856 597967814 6.380000e-08 69.4
36 TraesCS3D01G221200 chr3B 89.279 1026 91 6 1831 2838 706921544 706920520 0.000000e+00 1267.0
37 TraesCS3D01G221200 chr3B 87.283 173 16 5 2963 3133 706920434 706920266 3.630000e-45 193.0
38 TraesCS3D01G221200 chr3B 93.617 47 3 0 2872 2918 687465909 687465863 1.770000e-08 71.3
39 TraesCS3D01G221200 chr5D 85.988 1042 102 23 1829 2833 521483874 521484908 0.000000e+00 1075.0
40 TraesCS3D01G221200 chr5D 87.245 196 19 4 2941 3133 108541606 108541414 5.990000e-53 219.0
41 TraesCS3D01G221200 chr5D 90.741 54 4 1 2872 2924 2788074 2788127 1.770000e-08 71.3
42 TraesCS3D01G221200 chr5B 88.600 886 70 13 10 876 166677603 166676730 0.000000e+00 1048.0
43 TraesCS3D01G221200 chr5B 83.974 1067 107 29 1806 2833 657729777 657730818 0.000000e+00 965.0
44 TraesCS3D01G221200 chr5B 86.207 783 86 13 2068 2833 657880140 657880917 0.000000e+00 828.0
45 TraesCS3D01G221200 chr6D 90.418 574 46 7 17 583 337760904 337761475 0.000000e+00 747.0
46 TraesCS3D01G221200 chr6D 87.179 273 30 4 3129 3398 430832934 430833204 4.470000e-79 305.0
47 TraesCS3D01G221200 chr6D 87.245 196 19 4 2941 3133 291688096 291688288 5.990000e-53 219.0
48 TraesCS3D01G221200 chr5A 83.914 833 72 21 2018 2833 649806475 649807262 0.000000e+00 739.0
49 TraesCS3D01G221200 chr5A 85.204 196 23 5 2941 3133 294614884 294615076 2.810000e-46 196.0
50 TraesCS3D01G221200 chr7D 90.780 282 14 6 1819 2089 336236021 336236301 2.020000e-97 366.0
51 TraesCS3D01G221200 chr7D 96.296 54 2 0 3400 3453 584104953 584104900 4.900000e-14 89.8
52 TraesCS3D01G221200 chr2B 90.594 202 13 4 1596 1792 46418814 46418614 2.730000e-66 263.0
53 TraesCS3D01G221200 chr2B 97.561 41 1 0 2872 2912 556204387 556204347 1.770000e-08 71.3
54 TraesCS3D01G221200 chr1D 87.895 190 17 5 2944 3133 428193165 428192982 5.990000e-53 219.0
55 TraesCS3D01G221200 chr4D 86.735 196 20 4 2941 3133 24096903 24097095 2.790000e-51 213.0
56 TraesCS3D01G221200 chr4D 86.224 196 21 4 2941 3133 215176482 215176290 1.300000e-49 207.0
57 TraesCS3D01G221200 chr4D 97.500 40 1 0 2872 2911 488960923 488960962 6.380000e-08 69.4
58 TraesCS3D01G221200 chr6A 96.296 54 2 0 3400 3453 577717582 577717635 4.900000e-14 89.8
59 TraesCS3D01G221200 chr6A 96.296 54 2 0 3400 3453 577718386 577718439 4.900000e-14 89.8
60 TraesCS3D01G221200 chr4B 95.455 44 1 1 2872 2914 136321585 136321628 6.380000e-08 69.4
61 TraesCS3D01G221200 chr6B 100.000 29 0 0 2853 2881 579542403 579542431 2.000000e-03 54.7
62 TraesCS3D01G221200 chr6B 100.000 28 0 0 2851 2878 21036511 21036484 6.000000e-03 52.8


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 TraesCS3D01G221200 chr3D 301736958 301740520 3562 True 6580.000000 6580 100.000000 1 3563 1 chr3D.!!$R1 3562
1 TraesCS3D01G221200 chr2D 565529876 565534354 4478 False 3108.000000 4721 97.746000 1 3563 2 chr2D.!!$F2 3562
2 TraesCS3D01G221200 chr2A 182857785 182861757 3972 False 1718.666667 3262 95.260000 1 3563 3 chr2A.!!$F3 3562
3 TraesCS3D01G221200 chr7A 577677096 577681072 3976 True 1716.000000 3243 95.320667 1 3563 3 chr7A.!!$R5 3562
4 TraesCS3D01G221200 chr7A 499899453 499902032 2579 True 1372.500000 1424 96.235500 1 1662 2 chr7A.!!$R4 1661
5 TraesCS3D01G221200 chr7A 471964320 471966878 2558 True 1370.500000 1376 96.462000 1 1662 2 chr7A.!!$R1 1661
6 TraesCS3D01G221200 chr7A 499847141 499847821 680 True 574.000000 643 97.183500 930 1662 2 chr7A.!!$R2 732
7 TraesCS3D01G221200 chr7A 499851838 499853417 1579 True 533.500000 968 95.615000 257 932 2 chr7A.!!$R3 675
8 TraesCS3D01G221200 chr1A 450977319 450981234 3915 False 1661.000000 3153 94.439000 1 3563 3 chr1A.!!$F1 3562
9 TraesCS3D01G221200 chr4A 702698766 702703136 4370 False 1333.333333 1783 95.483000 874 3563 3 chr4A.!!$F1 2689
10 TraesCS3D01G221200 chr3A 493273919 493276476 2557 False 1356.000000 1360 96.081000 1 1662 2 chr3A.!!$F2 1661
11 TraesCS3D01G221200 chr3B 706920266 706921544 1278 True 730.000000 1267 88.281000 1831 3133 2 chr3B.!!$R2 1302
12 TraesCS3D01G221200 chr5D 521483874 521484908 1034 False 1075.000000 1075 85.988000 1829 2833 1 chr5D.!!$F2 1004
13 TraesCS3D01G221200 chr5B 166676730 166677603 873 True 1048.000000 1048 88.600000 10 876 1 chr5B.!!$R1 866
14 TraesCS3D01G221200 chr5B 657729777 657730818 1041 False 965.000000 965 83.974000 1806 2833 1 chr5B.!!$F1 1027
15 TraesCS3D01G221200 chr5B 657880140 657880917 777 False 828.000000 828 86.207000 2068 2833 1 chr5B.!!$F2 765
16 TraesCS3D01G221200 chr6D 337760904 337761475 571 False 747.000000 747 90.418000 17 583 1 chr6D.!!$F2 566
17 TraesCS3D01G221200 chr5A 649806475 649807262 787 False 739.000000 739 83.914000 2018 2833 1 chr5A.!!$F2 815

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
729 746 2.393768 CGCGCTGGTTGATGAAGCT 61.394 57.895 5.56 0.0 34.72 3.74 F
2171 3826 1.480219 GAAGATGTCGCGTTAGCCCG 61.480 60.000 5.77 0.0 41.18 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 3941 1.336517 TGCTTACTTCGGGACTTCGTG 60.337 52.381 0.0 0.0 0.00 4.35 R
2995 5863 0.536724 TCCTGTCCACGATGTCATGG 59.463 55.000 0.0 0.0 37.32 3.66 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
552 564 5.774690 TGCTTATCCCTTTTCTGTTTGTGAT 59.225 36.000 0.00 0.0 0.00 3.06
729 746 2.393768 CGCGCTGGTTGATGAAGCT 61.394 57.895 5.56 0.0 34.72 3.74
1007 1958 6.482973 TGTGTGATGCAATGACGTATGAATAT 59.517 34.615 0.00 0.0 30.91 1.28
1389 2340 4.775780 TCCTACTTATAGGCCGTATTGCAT 59.224 41.667 0.00 0.0 46.97 3.96
1535 2486 3.181443 CCCTAGATTTCACCCCATACCAC 60.181 52.174 0.00 0.0 0.00 4.16
1735 3368 6.014156 CCTCCAAGAGTTCTCCGGATATAATT 60.014 42.308 3.57 0.0 30.14 1.40
1833 3466 4.207165 TGGCTGAAATGAAGCTAATACCC 58.793 43.478 0.00 0.0 40.64 3.69
2171 3826 1.480219 GAAGATGTCGCGTTAGCCCG 61.480 60.000 5.77 0.0 41.18 6.13
2278 3941 3.217743 CGGAGCTCTACCCCGACC 61.218 72.222 14.64 0.0 45.58 4.79
2879 4619 0.822164 CGGACGGAGGGAGTACAAAT 59.178 55.000 0.00 0.0 0.00 2.32
2902 4642 3.013921 TGGGTCATCTATTTTGGAACGC 58.986 45.455 0.00 0.0 0.00 4.84
2954 5786 8.832521 CATTTTTACCTGTTCAGTACACTTACA 58.167 33.333 0.00 0.0 32.10 2.41
3473 6349 3.288092 GAACTCTTCCCAACCAAACAGT 58.712 45.455 0.00 0.0 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 384 2.435059 GACGGCAACTGGAGCTCC 60.435 66.667 26.78 26.78 0.00 4.70
552 564 6.414408 ACAACAAACGCAATCAATTCAAAA 57.586 29.167 0.00 0.00 0.00 2.44
805 834 1.001120 TACAGATCCGGCCAGACCA 59.999 57.895 2.24 0.00 39.03 4.02
1007 1958 4.081142 TCCTCAGGCATATTTTTCTGTCGA 60.081 41.667 0.00 0.00 0.00 4.20
1389 2340 7.012799 TGTTCAGTAAAACATGAGTACATTGCA 59.987 33.333 0.00 0.00 34.31 4.08
1526 2477 7.428020 CATTTGTATCTCAATTGTGGTATGGG 58.572 38.462 5.13 0.00 35.84 4.00
1535 2486 4.637483 ACGCCCATTTGTATCTCAATTG 57.363 40.909 0.00 0.00 37.24 2.32
1626 3259 6.313744 AGTAGTGAATCCGAAACTTTTTGG 57.686 37.500 1.87 1.87 42.11 3.28
1833 3466 4.753610 CCACTGCAGGATATTCAGTACATG 59.246 45.833 19.93 1.30 38.85 3.21
2171 3826 3.561503 GGGTTTTCAAACAGCGTGATAC 58.438 45.455 4.85 0.00 40.63 2.24
2278 3941 1.336517 TGCTTACTTCGGGACTTCGTG 60.337 52.381 0.00 0.00 0.00 4.35
2849 4589 0.388134 CTCCGTCCGAAAAAGCTCGA 60.388 55.000 0.00 0.00 41.44 4.04
2879 4619 4.082463 GCGTTCCAAAATAGATGACCCAAA 60.082 41.667 0.00 0.00 0.00 3.28
2902 4642 9.411189 GAGGTATAGATAAGGTAATACTCCCTG 57.589 40.741 0.00 0.00 0.00 4.45
2995 5863 0.536724 TCCTGTCCACGATGTCATGG 59.463 55.000 0.00 0.00 37.32 3.66
3473 6349 8.754991 TTTTGGGAGTTTTTACAGATAGTTGA 57.245 30.769 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.