Multiple sequence alignment - TraesCS2D01G231200

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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 TraesCS2D01G231200 chr2D 100.000 2149 0 0 836 2984 202564838 202566986 0.000000e+00 3969.0
1 TraesCS2D01G231200 chr2D 100.000 568 0 0 1 568 202564003 202564570 0.000000e+00 1050.0
2 TraesCS2D01G231200 chr2D 80.788 203 28 9 2501 2699 152017230 152017035 6.660000e-32 148.0
3 TraesCS2D01G231200 chr2D 84.397 141 20 2 2844 2984 152016923 152016785 1.440000e-28 137.0
4 TraesCS2D01G231200 chr2D 92.754 69 4 1 2134 2202 443480565 443480632 6.810000e-17 99.0
5 TraesCS2D01G231200 chr2D 94.444 36 1 1 1976 2010 76820552 76820517 1.000000e-03 54.7
6 TraesCS2D01G231200 chr2B 94.432 1347 33 13 836 2140 256326549 256327895 0.000000e+00 2034.0
7 TraesCS2D01G231200 chr2B 93.298 567 26 6 2 568 256325951 256326505 0.000000e+00 826.0
8 TraesCS2D01G231200 chr2B 89.855 69 3 2 2140 2205 753116750 753116683 5.300000e-13 86.1
9 TraesCS2D01G231200 chr2A 94.113 1155 34 18 836 1971 229672213 229673352 0.000000e+00 1725.0
10 TraesCS2D01G231200 chr2A 88.648 599 29 16 1 568 229671319 229671909 0.000000e+00 693.0
11 TraesCS2D01G231200 chr2A 81.154 520 31 18 2500 2979 767585920 767586412 3.660000e-94 355.0
12 TraesCS2D01G231200 chr2A 80.962 520 32 18 2500 2979 684464272 684464764 1.700000e-92 350.0
13 TraesCS2D01G231200 chr2A 97.087 206 6 0 363 568 229671964 229672169 6.120000e-92 348.0
14 TraesCS2D01G231200 chr2A 88.593 263 25 2 1 263 229669951 229670208 6.210000e-82 315.0
15 TraesCS2D01G231200 chr2A 86.207 58 6 1 2039 2094 229673373 229673430 8.930000e-06 62.1
16 TraesCS2D01G231200 chr3D 99.057 848 5 3 2138 2984 29414459 29413614 0.000000e+00 1519.0
17 TraesCS2D01G231200 chr5D 98.927 839 7 2 2147 2984 561491928 561492765 0.000000e+00 1498.0
18 TraesCS2D01G231200 chr5D 100.000 30 0 0 1976 2005 366497767 366497796 4.160000e-04 56.5
19 TraesCS2D01G231200 chr5D 100.000 29 0 0 1977 2005 387703527 387703555 1.000000e-03 54.7
20 TraesCS2D01G231200 chr5D 100.000 28 0 0 1976 2003 297053753 297053726 5.000000e-03 52.8
21 TraesCS2D01G231200 chr3B 88.090 890 39 14 2138 2979 560590869 560591739 0.000000e+00 994.0
22 TraesCS2D01G231200 chr3B 100.000 32 0 0 1976 2007 691481801 691481770 3.210000e-05 60.2
23 TraesCS2D01G231200 chr6B 77.983 922 90 45 2138 2979 683263476 683262588 9.680000e-130 473.0
24 TraesCS2D01G231200 chr6B 78.676 680 79 34 2334 2979 683265021 683264374 2.790000e-105 392.0
25 TraesCS2D01G231200 chr6B 86.007 293 29 6 2697 2979 683259300 683259010 1.340000e-78 303.0
26 TraesCS2D01G231200 chr6B 87.786 131 15 1 2138 2268 683259898 683259769 5.150000e-33 152.0
27 TraesCS2D01G231200 chr7A 80.732 519 34 17 2500 2979 67229545 67229054 7.920000e-91 344.0
28 TraesCS2D01G231200 chr7A 80.276 507 33 19 2513 2979 67206401 67205922 1.330000e-83 320.0
29 TraesCS2D01G231200 chr7A 80.549 437 26 21 2513 2910 66950944 66950528 6.300000e-72 281.0
30 TraesCS2D01G231200 chr7A 100.000 29 0 0 1973 2001 454049756 454049728 1.000000e-03 54.7
31 TraesCS2D01G231200 chr6D 87.713 293 24 6 2697 2979 95350133 95349843 6.170000e-87 331.0
32 TraesCS2D01G231200 chr3A 80.276 507 32 31 2513 2979 690734838 690734360 1.330000e-83 320.0
33 TraesCS2D01G231200 chr3A 79.423 520 40 19 2500 2979 723499776 723499284 3.740000e-79 305.0
34 TraesCS2D01G231200 chr5B 83.158 380 32 14 2334 2699 550915796 550915435 4.800000e-83 318.0
35 TraesCS2D01G231200 chr6A 77.308 520 41 22 2500 2979 477921405 477920923 4.970000e-58 235.0
36 TraesCS2D01G231200 chr7B 87.023 131 15 2 2139 2268 41065340 41065211 2.400000e-31 147.0
37 TraesCS2D01G231200 chr7B 93.651 63 2 2 2138 2200 138151036 138150976 3.170000e-15 93.5
38 TraesCS2D01G231200 chr1A 93.548 62 3 1 2139 2200 398111079 398111139 1.140000e-14 91.6
39 TraesCS2D01G231200 chr4B 92.105 38 3 0 1966 2003 12499250 12499287 1.000000e-03 54.7
40 TraesCS2D01G231200 chr4D 100.000 28 0 0 1977 2004 468592251 468592224 5.000000e-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 TraesCS2D01G231200 chr2D 202564003 202566986 2983 False 2509.50 3969 100.0000 1 2984 2 chr2D.!!$F2 2983
1 TraesCS2D01G231200 chr2B 256325951 256327895 1944 False 1430.00 2034 93.8650 2 2140 2 chr2B.!!$F1 2138
2 TraesCS2D01G231200 chr2A 229669951 229673430 3479 False 628.62 1725 90.9296 1 2094 5 chr2A.!!$F3 2093
3 TraesCS2D01G231200 chr3D 29413614 29414459 845 True 1519.00 1519 99.0570 2138 2984 1 chr3D.!!$R1 846
4 TraesCS2D01G231200 chr5D 561491928 561492765 837 False 1498.00 1498 98.9270 2147 2984 1 chr5D.!!$F3 837
5 TraesCS2D01G231200 chr3B 560590869 560591739 870 False 994.00 994 88.0900 2138 2979 1 chr3B.!!$F1 841
6 TraesCS2D01G231200 chr6B 683259010 683265021 6011 True 330.00 473 82.6130 2138 2979 4 chr6B.!!$R1 841

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
396 2053 0.541863 ATTAACCCTGTCTCTGCCCG 59.458 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 3915 0.534203 GGTGGCCGAAACAAGTGAGA 60.534 55.0 0.0 0.0 0.0 3.27 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
64 65 5.973565 GCTTGCTAAATATGACCACATGTTC 59.026 40.000 0.00 0.00 36.96 3.18
146 147 9.142014 TGATCGTGGATATTTATTTTTCCCAAT 57.858 29.630 0.00 0.00 0.00 3.16
149 150 9.196139 TCGTGGATATTTATTTTTCCCAATCTT 57.804 29.630 0.00 0.00 0.00 2.40
203 204 4.706035 TCTTTAGCCGGCCGAATTTAATA 58.294 39.130 30.73 1.76 0.00 0.98
204 205 5.124645 TCTTTAGCCGGCCGAATTTAATAA 58.875 37.500 30.73 8.98 0.00 1.40
396 2053 0.541863 ATTAACCCTGTCTCTGCCCG 59.458 55.000 0.00 0.00 0.00 6.13
437 2094 1.337354 CCCGGCCATAACAACAAAACC 60.337 52.381 2.24 0.00 0.00 3.27
544 2201 1.622442 CCCAAATCCTCCCCTCCCA 60.622 63.158 0.00 0.00 0.00 4.37
967 2624 1.072965 CTTGTGGAGCTCCCTCTGTTT 59.927 52.381 29.95 0.00 38.21 2.83
1613 3270 1.672356 TGAAGCCTTTCGCCTCTGC 60.672 57.895 0.00 0.00 38.78 4.26
1670 3329 6.734281 AGGGTAGTGGACTAAACCTTCTTATT 59.266 38.462 5.79 0.00 35.70 1.40
1671 3330 6.822170 GGGTAGTGGACTAAACCTTCTTATTG 59.178 42.308 0.00 0.00 0.00 1.90
1698 3357 3.726291 TTCGCCTTTTTCCTTTCCTTG 57.274 42.857 0.00 0.00 0.00 3.61
1726 3385 5.022787 TGCAAGGGTAGGCTTTATTTCAAT 58.977 37.500 0.00 0.00 0.00 2.57
1751 3410 5.793457 GTGGTAGCATTTTAGCGTGTAAAAG 59.207 40.000 0.00 5.03 40.15 2.27
1767 3426 7.837923 GCGTGTAAAAGTGTACGTATAATTCAG 59.162 37.037 5.49 0.00 38.67 3.02
1867 3546 6.142139 GCAATGCATGCGTATTTACTCATTA 58.858 36.000 13.96 0.00 46.87 1.90
1893 3572 2.928731 GCTCTTGAGTGTAGACTGCCAC 60.929 54.545 0.00 0.16 30.16 5.01
1991 3670 3.491766 AAAGGTACTCCCTCTGATCCA 57.508 47.619 0.00 0.00 45.47 3.41
2036 3715 4.940463 AGTTCTACTAAGTGTGCGTCAAA 58.060 39.130 0.00 0.00 0.00 2.69
2037 3716 4.982916 AGTTCTACTAAGTGTGCGTCAAAG 59.017 41.667 0.00 0.00 0.00 2.77
2090 3791 2.159327 TCATCAGCTGTGTCTGTGTG 57.841 50.000 14.67 1.86 35.63 3.82
2094 3795 0.179076 CAGCTGTGTCTGTGTGACCA 60.179 55.000 5.25 0.00 44.75 4.02
2096 3797 1.970640 AGCTGTGTCTGTGTGACCATA 59.029 47.619 0.00 0.00 44.75 2.74
2097 3798 2.069273 GCTGTGTCTGTGTGACCATAC 58.931 52.381 0.00 0.00 44.75 2.39
2098 3799 2.547855 GCTGTGTCTGTGTGACCATACA 60.548 50.000 0.00 0.00 44.75 2.29
2099 3800 3.866066 GCTGTGTCTGTGTGACCATACAT 60.866 47.826 0.20 0.00 44.75 2.29
2100 3801 4.620567 GCTGTGTCTGTGTGACCATACATA 60.621 45.833 0.20 0.00 44.75 2.29
2101 3802 5.664457 CTGTGTCTGTGTGACCATACATAT 58.336 41.667 0.20 0.00 44.75 1.78
2110 3817 8.429237 TGTGTGACCATACATATATACATCCA 57.571 34.615 0.00 0.00 32.43 3.41
2129 3836 5.078411 TCCATCTGTTTAGCACTCTCTTC 57.922 43.478 0.00 0.00 0.00 2.87
2130 3837 3.862267 CCATCTGTTTAGCACTCTCTTCG 59.138 47.826 0.00 0.00 0.00 3.79
2146 3853 7.012894 CACTCTCTTCGTTCCATAATCTCTACT 59.987 40.741 0.00 0.00 0.00 2.57
2147 3854 8.212312 ACTCTCTTCGTTCCATAATCTCTACTA 58.788 37.037 0.00 0.00 0.00 1.82
2149 3856 9.221933 TCTCTTCGTTCCATAATCTCTACTATC 57.778 37.037 0.00 0.00 0.00 2.08
2207 3915 1.652124 CGTTCGTTTCGTCGATCCATT 59.348 47.619 0.00 0.00 39.57 3.16
2307 4035 3.760035 CGCACGCACCCTCCTAGT 61.760 66.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.986817 GCATTCTCTTAGCAATAAGTGAGGTA 59.013 38.462 0.00 0.00 33.08 3.08
21 22 2.158842 AGCTCCGCATTCTCTTAGCAAT 60.159 45.455 0.00 0.00 32.42 3.56
23 24 0.826715 AGCTCCGCATTCTCTTAGCA 59.173 50.000 0.00 0.00 32.42 3.49
35 36 2.224314 GGTCATATTTAGCAAGCTCCGC 59.776 50.000 0.00 0.00 0.00 5.54
64 65 8.915057 ATTTATTATCCACTCCTCACTTCATG 57.085 34.615 0.00 0.00 0.00 3.07
164 165 6.479990 GGCTAAAGATGGCAATGGATTAAAAC 59.520 38.462 0.00 0.00 34.13 2.43
221 222 6.847956 TTTTGAGAAAATGCTTTGACATGG 57.152 33.333 0.00 0.00 0.00 3.66
268 269 9.406828 GACACCGCTTTCTTTTCTTTTTATTAT 57.593 29.630 0.00 0.00 0.00 1.28
270 271 6.700081 GGACACCGCTTTCTTTTCTTTTTATT 59.300 34.615 0.00 0.00 0.00 1.40
279 1676 3.505835 TGGGACACCGCTTTCTTTT 57.494 47.368 0.00 0.00 40.75 2.27
396 2053 1.278413 GAAGAAGGGTGTGGGGTCTAC 59.722 57.143 0.00 0.00 0.00 2.59
437 2094 1.619704 GGGGGAGGTGATTTTTCAGGG 60.620 57.143 0.00 0.00 0.00 4.45
504 2161 2.203126 GAGAGCCATTGGGGAGCG 60.203 66.667 4.53 0.00 40.01 5.03
505 2162 2.194326 GGAGAGCCATTGGGGAGC 59.806 66.667 4.53 0.00 40.01 4.70
1670 3329 2.693074 AGGAAAAAGGCGAAAAAGAGCA 59.307 40.909 0.00 0.00 34.54 4.26
1671 3330 3.371102 AGGAAAAAGGCGAAAAAGAGC 57.629 42.857 0.00 0.00 0.00 4.09
1698 3357 6.465439 AATAAAGCCTACCCTTGCAATTAC 57.535 37.500 0.00 0.00 0.00 1.89
1726 3385 2.773487 ACACGCTAAAATGCTACCACA 58.227 42.857 0.00 0.00 0.00 4.17
1767 3426 7.061789 CGCATTTTCCTTTTGAGTTAATACACC 59.938 37.037 0.00 0.00 0.00 4.16
1785 3449 2.201732 TCGTCATAGCTCCGCATTTTC 58.798 47.619 0.00 0.00 0.00 2.29
1867 3546 3.505680 CAGTCTACACTCAAGAGCTGACT 59.494 47.826 0.00 3.62 30.35 3.41
1893 3572 7.017645 CAGACAACGTAATTCCAATTGAGAAG 58.982 38.462 7.12 0.49 0.00 2.85
1985 3664 8.190122 GCAAAGTGTGTCAATTAATATGGATCA 58.810 33.333 0.00 0.00 0.00 2.92
1986 3665 8.190122 TGCAAAGTGTGTCAATTAATATGGATC 58.810 33.333 0.00 0.00 0.00 3.36
2036 3715 6.218019 TGCTAAAGTATTCGTACAACACACT 58.782 36.000 0.00 0.00 0.00 3.55
2037 3716 6.400727 CCTGCTAAAGTATTCGTACAACACAC 60.401 42.308 0.00 0.00 0.00 3.82
2096 3797 9.658799 GTGCTAAACAGATGGATGTATATATGT 57.341 33.333 0.00 0.00 31.70 2.29
2097 3798 9.881649 AGTGCTAAACAGATGGATGTATATATG 57.118 33.333 0.00 0.00 31.70 1.78
2099 3800 9.314133 AGAGTGCTAAACAGATGGATGTATATA 57.686 33.333 0.00 0.00 31.70 0.86
2100 3801 8.200024 AGAGTGCTAAACAGATGGATGTATAT 57.800 34.615 0.00 0.00 31.70 0.86
2101 3802 7.507277 AGAGAGTGCTAAACAGATGGATGTATA 59.493 37.037 0.00 0.00 31.70 1.47
2110 3817 4.792521 ACGAAGAGAGTGCTAAACAGAT 57.207 40.909 0.00 0.00 0.00 2.90
2207 3915 0.534203 GGTGGCCGAAACAAGTGAGA 60.534 55.000 0.00 0.00 0.00 3.27
2307 4035 0.965866 CCTAGATCGCGGGGATAGCA 60.966 60.000 6.13 0.00 34.82 3.49


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

AutoCloner maintained by Alex Coulton.