Multiple sequence alignment - TraesCS4D01G341100

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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 TraesCS4D01G341100 chr4D 100.000 2486 0 0 1 2486 497998373 498000858 0.000000e+00 4591.0
1 TraesCS4D01G341100 chr4D 93.617 752 43 2 1735 2486 352496892 352497638 0.000000e+00 1118.0
2 TraesCS4D01G341100 chr4D 97.174 637 16 2 1 635 342746638 342747274 0.000000e+00 1075.0
3 TraesCS4D01G341100 chr4D 91.291 333 29 0 1157 1489 352487601 352487933 2.910000e-124 455.0
4 TraesCS4D01G341100 chr4D 95.312 128 6 0 1026 1153 497999362 497999489 1.170000e-48 204.0
5 TraesCS4D01G341100 chr4D 95.312 128 6 0 990 1117 497999398 497999525 1.170000e-48 204.0
6 TraesCS4D01G341100 chr4D 88.060 67 5 3 1536 1602 352487945 352488008 2.650000e-10 76.8
7 TraesCS4D01G341100 chr7B 98.290 1871 21 3 626 2486 461211674 461209805 0.000000e+00 3267.0
8 TraesCS4D01G341100 chr7B 96.268 777 28 1 1707 2483 622461892 622462667 0.000000e+00 1273.0
9 TraesCS4D01G341100 chr7B 86.519 586 68 9 990 1574 622460988 622461563 3.490000e-178 634.0
10 TraesCS4D01G341100 chr7B 96.032 126 5 0 995 1120 461211269 461211144 3.240000e-49 206.0
11 TraesCS4D01G341100 chr7B 93.130 131 9 0 1026 1156 461211310 461211180 2.520000e-45 193.0
12 TraesCS4D01G341100 chr6D 97.678 1507 24 2 990 2486 87582113 87580608 0.000000e+00 2579.0
13 TraesCS4D01G341100 chr6D 97.714 525 11 1 633 1156 87582507 87581983 0.000000e+00 902.0
14 TraesCS4D01G341100 chr6D 91.549 142 8 3 1026 1167 87582149 87582012 2.520000e-45 193.0
15 TraesCS4D01G341100 chr2D 95.897 780 31 1 1707 2486 177443021 177442243 0.000000e+00 1262.0
16 TraesCS4D01G341100 chr2D 83.989 712 73 26 997 1677 177443809 177443108 0.000000e+00 645.0
17 TraesCS4D01G341100 chr6A 95.256 780 36 1 1707 2486 480460938 480461716 0.000000e+00 1234.0
18 TraesCS4D01G341100 chr6A 99.696 329 1 0 633 961 117400836 117401164 9.840000e-169 603.0
19 TraesCS4D01G341100 chr6A 82.865 712 81 26 997 1677 480459994 480460695 3.540000e-168 601.0
20 TraesCS4D01G341100 chr7D 94.615 780 39 3 1707 2486 318859102 318859878 0.000000e+00 1205.0
21 TraesCS4D01G341100 chr7D 97.956 636 12 1 1 635 209855076 209855711 0.000000e+00 1101.0
22 TraesCS4D01G341100 chr7D 97.327 636 16 1 1 635 91670798 91671433 0.000000e+00 1079.0
23 TraesCS4D01G341100 chr7D 97.327 636 15 2 1 635 160335692 160335058 0.000000e+00 1079.0
24 TraesCS4D01G341100 chr7D 97.327 636 16 1 1 635 586845482 586844847 0.000000e+00 1079.0
25 TraesCS4D01G341100 chr7D 97.327 636 14 3 1 635 390199996 390200629 0.000000e+00 1077.0
26 TraesCS4D01G341100 chr7D 97.327 636 13 4 1 635 587781508 587780876 0.000000e+00 1077.0
27 TraesCS4D01G341100 chr7D 86.034 580 68 6 997 1574 318858165 318858733 5.880000e-171 610.0
28 TraesCS4D01G341100 chr7D 87.719 114 4 1 1553 1666 318858752 318858855 9.340000e-25 124.0
29 TraesCS4D01G341100 chr7D 88.043 92 2 1 1675 1757 318858985 318859076 1.570000e-17 100.0
30 TraesCS4D01G341100 chr5D 97.488 637 13 3 1 635 539160134 539159499 0.000000e+00 1085.0
31 TraesCS4D01G341100 chr5D 90.360 695 54 10 1752 2437 268493302 268492612 0.000000e+00 900.0
32 TraesCS4D01G341100 chr1D 97.174 637 16 2 1 635 246633678 246634314 0.000000e+00 1075.0
33 TraesCS4D01G341100 chr1D 89.928 695 57 11 1752 2437 90297210 90296520 0.000000e+00 883.0
34 TraesCS4D01G341100 chr1A 90.360 695 54 11 1752 2437 369353036 369352346 0.000000e+00 900.0
35 TraesCS4D01G341100 chr4A 95.740 493 20 1 1707 2198 500091774 500092266 0.000000e+00 793.0
36 TraesCS4D01G341100 chr4A 88.225 586 58 9 990 1574 500090922 500091497 0.000000e+00 689.0
37 TraesCS4D01G341100 chr4A 92.806 139 10 0 1015 1153 500090875 500091013 4.190000e-48 202.0
38 TraesCS4D01G341100 chr4A 88.288 111 3 4 1553 1663 500091516 500091616 9.340000e-25 124.0
39 TraesCS4D01G341100 chr4A 100.000 51 0 0 1707 1757 500091698 500091748 7.320000e-16 95.3
40 TraesCS4D01G341100 chr7A 99.110 337 2 1 626 961 611911843 611912179 2.730000e-169 604.0
41 TraesCS4D01G341100 chr7A 94.561 239 3 1 1680 1908 611912172 611912410 6.540000e-96 361.0
42 TraesCS4D01G341100 chr6B 99.695 328 1 0 634 961 6474216 6473889 3.540000e-168 601.0
43 TraesCS4D01G341100 chr1B 99.396 331 2 0 631 961 22114927 22115257 3.540000e-168 601.0
44 TraesCS4D01G341100 chr1B 94.561 239 3 1 1680 1908 22115250 22115488 6.540000e-96 361.0
45 TraesCS4D01G341100 chr3B 99.392 329 1 1 633 961 662510585 662510912 1.650000e-166 595.0
46 TraesCS4D01G341100 chr3B 94.979 239 2 1 1680 1908 662510905 662511143 1.400000e-97 366.0


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 TraesCS4D01G341100 chr4D 497998373 498000858 2485 False 1666.333333 4591 96.874667 1 2486 3 chr4D.!!$F4 2485
1 TraesCS4D01G341100 chr4D 352496892 352497638 746 False 1118.000000 1118 93.617000 1735 2486 1 chr4D.!!$F2 751
2 TraesCS4D01G341100 chr4D 342746638 342747274 636 False 1075.000000 1075 97.174000 1 635 1 chr4D.!!$F1 634
3 TraesCS4D01G341100 chr7B 461209805 461211674 1869 True 1222.000000 3267 95.817333 626 2486 3 chr7B.!!$R1 1860
4 TraesCS4D01G341100 chr7B 622460988 622462667 1679 False 953.500000 1273 91.393500 990 2483 2 chr7B.!!$F1 1493
5 TraesCS4D01G341100 chr6D 87580608 87582507 1899 True 1224.666667 2579 95.647000 633 2486 3 chr6D.!!$R1 1853
6 TraesCS4D01G341100 chr2D 177442243 177443809 1566 True 953.500000 1262 89.943000 997 2486 2 chr2D.!!$R1 1489
7 TraesCS4D01G341100 chr6A 480459994 480461716 1722 False 917.500000 1234 89.060500 997 2486 2 chr6A.!!$F2 1489
8 TraesCS4D01G341100 chr7D 209855076 209855711 635 False 1101.000000 1101 97.956000 1 635 1 chr7D.!!$F2 634
9 TraesCS4D01G341100 chr7D 91670798 91671433 635 False 1079.000000 1079 97.327000 1 635 1 chr7D.!!$F1 634
10 TraesCS4D01G341100 chr7D 160335058 160335692 634 True 1079.000000 1079 97.327000 1 635 1 chr7D.!!$R1 634
11 TraesCS4D01G341100 chr7D 586844847 586845482 635 True 1079.000000 1079 97.327000 1 635 1 chr7D.!!$R2 634
12 TraesCS4D01G341100 chr7D 390199996 390200629 633 False 1077.000000 1077 97.327000 1 635 1 chr7D.!!$F3 634
13 TraesCS4D01G341100 chr7D 587780876 587781508 632 True 1077.000000 1077 97.327000 1 635 1 chr7D.!!$R3 634
14 TraesCS4D01G341100 chr7D 318858165 318859878 1713 False 509.750000 1205 89.102750 997 2486 4 chr7D.!!$F4 1489
15 TraesCS4D01G341100 chr5D 539159499 539160134 635 True 1085.000000 1085 97.488000 1 635 1 chr5D.!!$R2 634
16 TraesCS4D01G341100 chr5D 268492612 268493302 690 True 900.000000 900 90.360000 1752 2437 1 chr5D.!!$R1 685
17 TraesCS4D01G341100 chr1D 246633678 246634314 636 False 1075.000000 1075 97.174000 1 635 1 chr1D.!!$F1 634
18 TraesCS4D01G341100 chr1D 90296520 90297210 690 True 883.000000 883 89.928000 1752 2437 1 chr1D.!!$R1 685
19 TraesCS4D01G341100 chr1A 369352346 369353036 690 True 900.000000 900 90.360000 1752 2437 1 chr1A.!!$R1 685
20 TraesCS4D01G341100 chr4A 500090875 500092266 1391 False 380.660000 793 93.011800 990 2198 5 chr4A.!!$F1 1208
21 TraesCS4D01G341100 chr7A 611911843 611912410 567 False 482.500000 604 96.835500 626 1908 2 chr7A.!!$F1 1282
22 TraesCS4D01G341100 chr1B 22114927 22115488 561 False 481.000000 601 96.978500 631 1908 2 chr1B.!!$F1 1277
23 TraesCS4D01G341100 chr3B 662510585 662511143 558 False 480.500000 595 97.185500 633 1908 2 chr3B.!!$F1 1275

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
450 455 1.202582 CCTCTGGATCACGTTCGTTCT 59.797 52.381 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2380 2.490903 CCCATCAAAAGCTCAACAGGAG 59.509 50.0 0.0 0.0 46.93 3.69 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
28 29 5.180492 ACCGCAAAAGAAGATTACATCGAAA 59.820 36.000 0.00 0.00 0.00 3.46
281 282 2.304761 AGGTTTTTGGCTCCGTATCTGA 59.695 45.455 0.00 0.00 0.00 3.27
450 455 1.202582 CCTCTGGATCACGTTCGTTCT 59.797 52.381 0.00 0.00 0.00 3.01
1200 1270 1.426751 AAACCTACTCCAACCCGACA 58.573 50.000 0.00 0.00 0.00 4.35
1293 1363 1.774894 TTTGCTCGGGGTGTAGGCTT 61.775 55.000 0.00 0.00 0.00 4.35
1804 2252 6.856135 TGCTTGCTCAACATATTCTAGATG 57.144 37.500 0.00 0.00 0.00 2.90
1932 2380 2.346847 CACGCTTGATGACTCAACTAGC 59.653 50.000 11.16 11.16 36.46 3.42
2374 2835 4.617593 AGTATTCCCGACTTTTCTCCCTA 58.382 43.478 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1200 1270 2.346766 TGCACACCTCACAAGTTGAT 57.653 45.000 10.54 0.0 32.17 2.57
1293 1363 3.742385 ACGTAAATCTTTTGGAACCGGA 58.258 40.909 9.46 0.0 0.00 5.14
1932 2380 2.490903 CCCATCAAAAGCTCAACAGGAG 59.509 50.000 0.00 0.0 46.93 3.69
2458 2919 7.869429 TGTTACTACTCCTACTTTGTGCTAAAC 59.131 37.037 0.00 0.0 0.00 2.01


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

AutoCloner maintained by Alex Coulton.