Multiple sequence alignment - TraesCS2D01G454000

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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 TraesCS2D01G454000 chr2D 100.000 2291 0 0 1 2291 562734113 562736403 0.000000e+00 4231.0
1 TraesCS2D01G454000 chr2D 96.307 677 8 7 935 1594 562785521 562786197 0.000000e+00 1096.0
2 TraesCS2D01G454000 chr2D 96.195 657 16 4 1641 2291 562786198 562786851 0.000000e+00 1066.0
3 TraesCS2D01G454000 chr2D 85.535 954 53 28 6 938 562784600 562785489 0.000000e+00 918.0
4 TraesCS2D01G454000 chr2D 89.135 497 44 7 935 1426 562839607 562840098 5.410000e-171 610.0
5 TraesCS2D01G454000 chr2D 89.562 479 44 6 957 1432 562684968 562685443 9.050000e-169 603.0
6 TraesCS2D01G454000 chr2D 91.031 446 36 2 931 1373 562754030 562754474 1.170000e-167 599.0
7 TraesCS2D01G454000 chr2D 89.011 455 41 5 935 1381 562807847 562808300 2.570000e-154 555.0
8 TraesCS2D01G454000 chr2D 86.623 456 35 11 990 1424 562845353 562845803 4.430000e-132 481.0
9 TraesCS2D01G454000 chr2D 90.343 321 28 2 409 728 562684215 562684533 3.520000e-113 418.0
10 TraesCS2D01G454000 chr2D 82.609 414 51 11 1459 1858 562588454 562588860 1.680000e-91 346.0
11 TraesCS2D01G454000 chr2D 81.087 423 23 20 44 450 562804458 562804839 3.730000e-73 285.0
12 TraesCS2D01G454000 chr2D 88.288 222 19 7 512 728 562585106 562585325 2.260000e-65 259.0
13 TraesCS2D01G454000 chr2D 78.816 321 37 20 416 728 562849744 562850041 1.080000e-43 187.0
14 TraesCS2D01G454000 chr2D 83.412 211 24 7 1639 1846 562685752 562685954 3.890000e-43 185.0
15 TraesCS2D01G454000 chr2D 84.239 184 17 7 1 182 562683846 562684019 3.910000e-38 169.0
16 TraesCS2D01G454000 chr2D 79.182 269 16 16 709 938 562807539 562807806 1.420000e-32 150.0
17 TraesCS2D01G454000 chr2D 91.667 72 5 1 813 884 562684738 562684808 5.210000e-17 99.0
18 TraesCS2D01G454000 chr2A 90.690 1826 85 32 526 2291 703290770 703292570 0.000000e+00 2351.0
19 TraesCS2D01G454000 chr2A 90.508 453 28 6 892 1336 703337484 703337929 3.280000e-163 584.0
20 TraesCS2D01G454000 chr2A 86.331 278 20 3 591 865 703282018 703282280 1.040000e-73 287.0
21 TraesCS2D01G454000 chr2A 90.722 194 18 0 1 194 703288804 703288997 2.260000e-65 259.0
22 TraesCS2D01G454000 chr2A 81.009 337 42 11 1588 1909 703208789 703209118 4.890000e-62 248.0
23 TraesCS2D01G454000 chr2A 96.528 144 5 0 244 387 703281796 703281939 2.940000e-59 239.0
24 TraesCS2D01G454000 chr2A 91.279 172 13 2 666 835 703337222 703337393 1.370000e-57 233.0
25 TraesCS2D01G454000 chr2A 83.453 278 15 11 419 687 703206580 703206835 1.770000e-56 230.0
26 TraesCS2D01G454000 chr2A 78.042 378 37 19 1 369 703333397 703333737 1.800000e-46 196.0
27 TraesCS2D01G454000 chr2A 90.076 131 13 0 64 194 703281655 703281785 1.090000e-38 171.0
28 TraesCS2D01G454000 chr2A 89.474 76 6 2 813 887 703207356 703207430 6.740000e-16 95.3
29 TraesCS2D01G454000 chr2A 100.000 29 0 0 1404 1432 703208606 703208634 1.000000e-03 54.7
30 TraesCS2D01G454000 chr2B 89.882 425 35 3 957 1373 672646529 672646953 7.200000e-150 540.0
31 TraesCS2D01G454000 chr2B 88.631 431 35 5 957 1373 673050886 673051316 1.570000e-141 512.0
32 TraesCS2D01G454000 chr2B 88.952 353 31 2 957 1301 673003667 673004019 1.630000e-116 429.0
33 TraesCS2D01G454000 chr2B 83.579 475 41 17 416 884 673050280 673050723 5.890000e-111 411.0
34 TraesCS2D01G454000 chr2B 86.139 404 17 16 543 937 673092533 673092906 1.280000e-107 399.0
35 TraesCS2D01G454000 chr2B 82.200 500 48 21 239 714 672797965 672797483 2.130000e-105 392.0
36 TraesCS2D01G454000 chr2B 88.199 322 20 6 416 728 672645768 672646080 3.600000e-98 368.0
37 TraesCS2D01G454000 chr2B 87.676 284 28 6 604 884 672666757 672667036 7.890000e-85 324.0
38 TraesCS2D01G454000 chr2B 83.289 377 30 14 1 377 672645308 672645651 1.320000e-82 316.0
39 TraesCS2D01G454000 chr2B 82.972 323 35 16 416 728 672828551 672828239 8.060000e-70 274.0
40 TraesCS2D01G454000 chr2B 89.950 199 11 4 416 614 673002197 673002386 4.890000e-62 248.0
41 TraesCS2D01G454000 chr2B 91.279 172 13 2 1 172 672798146 672797977 1.370000e-57 233.0
42 TraesCS2D01G454000 chr2B 86.243 189 16 5 1 184 673049860 673050043 1.800000e-46 196.0
43 TraesCS2D01G454000 chr2B 84.536 194 24 3 2047 2236 672823665 672823474 1.080000e-43 187.0
44 TraesCS2D01G454000 chr2B 82.857 210 31 4 1668 1875 673051573 673051779 1.400000e-42 183.0
45 TraesCS2D01G454000 chr2B 83.770 191 23 4 1 184 672626542 672626731 8.410000e-40 174.0
46 TraesCS2D01G454000 chr2B 81.818 143 8 7 221 363 673001952 673002076 1.120000e-18 104.0
47 TraesCS2D01G454000 chr2B 93.333 45 3 0 375 419 672645701 672645745 1.470000e-07 67.6
48 TraesCS2D01G454000 chr2B 100.000 36 0 0 416 451 672777421 672777386 1.470000e-07 67.6
49 TraesCS2D01G454000 chr2B 100.000 29 0 0 1404 1432 673051320 673051348 1.000000e-03 54.7


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 TraesCS2D01G454000 chr2D 562734113 562736403 2290 False 4231.000000 4231 100.000000 1 2291 1 chr2D.!!$F1 2290
1 TraesCS2D01G454000 chr2D 562784600 562786851 2251 False 1026.666667 1096 92.679000 6 2291 3 chr2D.!!$F6 2285
2 TraesCS2D01G454000 chr2D 562845353 562850041 4688 False 334.000000 481 82.719500 416 1424 2 chr2D.!!$F8 1008
3 TraesCS2D01G454000 chr2D 562804458 562808300 3842 False 330.000000 555 83.093333 44 1381 3 chr2D.!!$F7 1337
4 TraesCS2D01G454000 chr2D 562585106 562588860 3754 False 302.500000 346 85.448500 512 1858 2 chr2D.!!$F4 1346
5 TraesCS2D01G454000 chr2D 562683846 562685954 2108 False 294.800000 603 87.844600 1 1846 5 chr2D.!!$F5 1845
6 TraesCS2D01G454000 chr2A 703288804 703292570 3766 False 1305.000000 2351 90.706000 1 2291 2 chr2A.!!$F3 2290
7 TraesCS2D01G454000 chr2A 703333397 703337929 4532 False 337.666667 584 86.609667 1 1336 3 chr2A.!!$F4 1335
8 TraesCS2D01G454000 chr2A 703281655 703282280 625 False 232.333333 287 90.978333 64 865 3 chr2A.!!$F2 801
9 TraesCS2D01G454000 chr2B 672645308 672646953 1645 False 322.900000 540 88.675750 1 1373 4 chr2B.!!$F4 1372
10 TraesCS2D01G454000 chr2B 672797483 672798146 663 True 312.500000 392 86.739500 1 714 2 chr2B.!!$R4 713
11 TraesCS2D01G454000 chr2B 673049860 673051779 1919 False 271.340000 512 88.262000 1 1875 5 chr2B.!!$F6 1874
12 TraesCS2D01G454000 chr2B 673001952 673004019 2067 False 260.333333 429 86.906667 221 1301 3 chr2B.!!$F5 1080

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
806 11025 0.529378 ACTTACATCACCCGGACGTC 59.471 55.0 7.13 7.13 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 14294 1.281899 CTGAGTTAGCTACTTGCCGC 58.718 55.0 0.0 0.0 44.23 6.53 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
26 27 2.084681 CCGACGCGTCAGTGTTACC 61.085 63.158 35.71 9.36 41.83 2.85
40 44 1.607178 TTACCGGTCGAGGAAGCCA 60.607 57.895 12.40 0.00 34.73 4.75
156 184 4.159135 GTGAGTGCCAATGGAATCTTTGAT 59.841 41.667 2.05 0.00 31.89 2.57
197 225 3.121934 CAACACCAGCTGCAGCAA 58.878 55.556 38.24 0.00 45.16 3.91
198 226 1.007734 CAACACCAGCTGCAGCAAG 60.008 57.895 38.24 29.69 45.16 4.01
199 227 2.853290 AACACCAGCTGCAGCAAGC 61.853 57.895 38.24 14.86 45.16 4.01
200 228 4.052229 CACCAGCTGCAGCAAGCC 62.052 66.667 38.24 10.93 44.68 4.35
201 229 4.281527 ACCAGCTGCAGCAAGCCT 62.282 61.111 38.24 16.73 44.68 4.58
202 230 3.749064 CCAGCTGCAGCAAGCCTG 61.749 66.667 38.24 26.49 44.68 4.85
249 286 2.776072 GAAACGTGCACGATCCCG 59.224 61.111 42.94 18.44 43.02 5.14
311 350 8.125448 GGCTAGTTAAACAGCTCAATAATCTTG 58.875 37.037 8.89 0.00 37.91 3.02
312 351 8.669243 GCTAGTTAAACAGCTCAATAATCTTGT 58.331 33.333 2.96 0.00 34.86 3.16
453 2269 3.112263 TCAAGATTTCCCTCCCGTATGT 58.888 45.455 0.00 0.00 0.00 2.29
459 2275 2.759839 TCCCTCCCGTATGTGTATGA 57.240 50.000 0.00 0.00 0.00 2.15
648 7890 2.046285 AAAAAGCCTGGCGCGCTAT 61.046 52.632 32.29 7.24 44.76 2.97
738 10895 9.787435 ACAGCCGGAATATATTTCAAGTATTTA 57.213 29.630 5.05 0.00 0.00 1.40
766 10935 6.148976 AGAGTTTTCAAATACGGCTACTTTCC 59.851 38.462 0.00 0.00 0.00 3.13
806 11025 0.529378 ACTTACATCACCCGGACGTC 59.471 55.000 7.13 7.13 0.00 4.34
843 11076 2.777972 CGACCTCGCCCGGACATAA 61.778 63.158 0.73 0.00 0.00 1.90
1559 12151 2.280119 TGTCTGTGCTGTGCCGAC 60.280 61.111 0.00 0.00 0.00 4.79
1570 12163 2.095213 GCTGTGCCGACGAATTGATTTA 59.905 45.455 0.00 0.00 0.00 1.40
1594 12201 3.691575 TCAAACGAAATGGCCAAGGATA 58.308 40.909 10.96 0.00 0.00 2.59
1621 12228 5.543714 AGAAAGCAATCAAACATGATGCAA 58.456 33.333 0.00 0.00 0.00 4.08
1692 12387 6.206829 CCTCTCTCGTTTTGTTTCCCTTAATT 59.793 38.462 0.00 0.00 0.00 1.40
1721 12421 3.070302 TCCTGTTTGGTTTTGGTAATGCC 59.930 43.478 0.00 0.00 37.07 4.40
1763 12464 5.626543 CACTGTCACTGTAAAAACATCATGC 59.373 40.000 0.00 0.00 0.00 4.06
1813 12514 6.871492 CCCTAAATTTTGTTATGCTTTTCGGT 59.129 34.615 0.00 0.00 0.00 4.69
2079 14122 5.242838 TCAAACTTACCTAATTTGGGTGCAG 59.757 40.000 14.21 11.74 37.65 4.41
2203 14250 1.347707 ACCAAGAACCGCTTCTCATCA 59.652 47.619 0.00 0.00 35.52 3.07
2247 14294 6.728200 ACATGTGTTGTCAAAACATCTACAG 58.272 36.000 17.05 9.33 34.73 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.018542 TTTTATGGCTTCCTCGACCG 57.981 50.000 0.00 0.00 0.00 4.79
40 44 6.158598 AGATCTGCGTGCAATTTGTTTTTAT 58.841 32.000 0.00 0.00 0.00 1.40
197 225 2.856000 ACCTCCCAGTTGCAGGCT 60.856 61.111 0.00 0.00 0.00 4.58
198 226 2.674380 CACCTCCCAGTTGCAGGC 60.674 66.667 0.00 0.00 0.00 4.85
199 227 2.034687 CCACCTCCCAGTTGCAGG 59.965 66.667 0.00 0.00 0.00 4.85
200 228 0.890996 GAACCACCTCCCAGTTGCAG 60.891 60.000 0.00 0.00 0.00 4.41
201 229 1.150536 GAACCACCTCCCAGTTGCA 59.849 57.895 0.00 0.00 0.00 4.08
202 230 1.603739 GGAACCACCTCCCAGTTGC 60.604 63.158 0.00 0.00 35.41 4.17
203 231 4.821935 GGAACCACCTCCCAGTTG 57.178 61.111 0.00 0.00 35.41 3.16
224 260 1.915350 TCGTGCACGTTTCGTATCATC 59.085 47.619 35.74 0.00 38.32 2.92
249 286 3.010420 CCAGGTTTGTTTAGCTAGCTCC 58.990 50.000 23.26 14.42 0.00 4.70
453 2269 6.464222 CCTCCTTCAAGTTAAGTGTCATACA 58.536 40.000 0.00 0.00 0.00 2.29
459 2275 3.072622 GTCCCCTCCTTCAAGTTAAGTGT 59.927 47.826 0.00 0.00 0.00 3.55
515 4815 8.455903 TTTCTCAGACACAAGATGAAGAAAAT 57.544 30.769 0.00 0.00 30.61 1.82
648 7890 4.201744 GCGCTAAGTTTTAGTGCCGATAAA 60.202 41.667 18.73 0.00 43.17 1.40
738 10895 6.407202 AGTAGCCGTATTTGAAAACTCTCAT 58.593 36.000 0.00 0.00 0.00 2.90
766 10935 4.082787 AGTTGTGATATTTTGTGAAGGCCG 60.083 41.667 0.00 0.00 0.00 6.13
806 11025 1.540363 CGACCAGGTCCCGAATAATGG 60.540 57.143 14.46 0.00 0.00 3.16
902 11231 3.039011 GGAGTGGAAGGCTCAGGTATAA 58.961 50.000 0.00 0.00 34.83 0.98
1559 12151 8.365210 CCATTTCGTTTGAACTAAATCAATTCG 58.635 33.333 4.08 0.00 38.98 3.34
1570 12163 2.035832 CCTTGGCCATTTCGTTTGAACT 59.964 45.455 6.09 0.00 32.71 3.01
1594 12201 6.312918 GCATCATGTTTGATTGCTTTCTTCAT 59.687 34.615 0.00 0.00 40.70 2.57
1692 12387 5.151454 ACCAAAACCAAACAGGATCCAATA 58.849 37.500 15.82 0.00 41.22 1.90
1763 12464 4.444388 CACGATAATGTGTAGGTCGATTGG 59.556 45.833 0.00 0.00 36.28 3.16
1813 12514 8.038944 ACTGGAAACATTAGAGACGCTATAAAA 58.961 33.333 0.00 0.00 41.51 1.52
2247 14294 1.281899 CTGAGTTAGCTACTTGCCGC 58.718 55.000 0.00 0.00 44.23 6.53


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

AutoCloner maintained by Alex Coulton.