Multiple sequence alignment - TraesCS4A01G168200

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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 TraesCS4A01G168200 chr4A 100.000 2261 0 0 1 2261 420015955 420018215 0.000000e+00 4176.0
1 TraesCS4A01G168200 chr1A 98.000 1500 27 3 764 2261 558016883 558015385 0.000000e+00 2601.0
2 TraesCS4A01G168200 chr1A 92.373 944 45 11 483 1403 490470942 490470003 0.000000e+00 1319.0
3 TraesCS4A01G168200 chr1A 97.584 745 15 3 1 743 558017969 558017226 0.000000e+00 1273.0
4 TraesCS4A01G168200 chr1A 94.444 306 16 1 156 461 490473022 490472718 9.450000e-129 470.0
5 TraesCS4A01G168200 chr1A 95.031 161 8 0 1 161 490473302 490473142 1.040000e-63 254.0
6 TraesCS4A01G168200 chr1A 100.000 46 0 0 732 777 558017221 558017176 4.000000e-13 86.1
7 TraesCS4A01G168200 chr7D 93.487 1428 41 7 1 1403 221992214 221990814 0.000000e+00 2074.0
8 TraesCS4A01G168200 chr5B 90.412 1262 57 23 164 1403 166590937 166592156 0.000000e+00 1602.0
9 TraesCS4A01G168200 chr5B 93.473 858 31 8 1404 2261 634119252 634120084 0.000000e+00 1251.0
10 TraesCS4A01G168200 chr5B 95.000 320 14 2 164 482 166586182 166586500 3.350000e-138 501.0
11 TraesCS4A01G168200 chr5B 96.532 173 6 0 1 173 166585340 166585512 1.020000e-73 287.0
12 TraesCS4A01G168200 chr5B 96.491 171 6 0 1 171 166590107 166590277 1.320000e-72 283.0
13 TraesCS4A01G168200 chr2D 96.154 858 29 4 1404 2261 52286635 52285782 0.000000e+00 1399.0
14 TraesCS4A01G168200 chr2D 86.410 493 53 10 4 486 610357226 610357714 5.530000e-146 527.0
15 TraesCS4A01G168200 chr2D 84.190 253 22 9 740 978 610357932 610358180 1.750000e-56 230.0
16 TraesCS4A01G168200 chr5D 84.318 1422 155 37 4 1394 196319174 196320558 0.000000e+00 1328.0
17 TraesCS4A01G168200 chr5D 86.640 494 52 9 4 487 527081313 527080824 3.310000e-148 534.0
18 TraesCS4A01G168200 chr5D 95.082 61 3 0 660 720 196319790 196319850 1.850000e-16 97.1
19 TraesCS4A01G168200 chr7A 95.442 746 29 5 1404 2146 299414532 299415275 0.000000e+00 1184.0
20 TraesCS4A01G168200 chr7A 85.824 522 49 11 732 1233 123205711 123206227 4.280000e-147 531.0
21 TraesCS4A01G168200 chr7A 97.619 126 3 0 2136 2261 299429489 299429614 1.360000e-52 217.0
22 TraesCS4A01G168200 chr3D 95.184 706 29 3 1404 2105 30973554 30972850 0.000000e+00 1110.0
23 TraesCS4A01G168200 chr3D 92.131 610 41 6 1404 2008 412105397 412104790 0.000000e+00 854.0
24 TraesCS4A01G168200 chr3D 96.015 527 18 2 1735 2261 477611554 477612077 0.000000e+00 854.0
25 TraesCS4A01G168200 chr3D 87.984 491 47 6 4 486 593315335 593315821 9.060000e-159 569.0
26 TraesCS4A01G168200 chr3D 96.450 338 10 2 1404 1740 477570929 477571265 7.050000e-155 556.0
27 TraesCS4A01G168200 chr3D 94.203 207 12 0 2052 2258 412104792 412104586 1.300000e-82 316.0
28 TraesCS4A01G168200 chr3D 98.113 159 3 0 2101 2259 30972034 30971876 6.150000e-71 278.0
29 TraesCS4A01G168200 chr2B 85.009 1054 117 23 374 1403 15466160 15465124 0.000000e+00 1033.0
30 TraesCS4A01G168200 chr2B 85.057 522 53 11 732 1233 17851056 17850540 2.000000e-140 508.0
31 TraesCS4A01G168200 chr2B 83.636 110 12 5 1593 1701 583417171 583417067 5.140000e-17 99.0
32 TraesCS4A01G168200 chr2A 95.008 601 30 0 1661 2261 315764602 315764002 0.000000e+00 944.0
33 TraesCS4A01G168200 chr6D 92.084 619 41 5 1648 2259 169716392 169715775 0.000000e+00 865.0
34 TraesCS4A01G168200 chr6D 90.506 158 12 2 1405 1559 169716902 169716745 2.940000e-49 206.0
35 TraesCS4A01G168200 chr3B 89.897 584 43 11 1603 2182 726178471 726179042 0.000000e+00 737.0
36 TraesCS4A01G168200 chr3B 91.534 189 14 1 1404 1590 726178213 726178401 2.230000e-65 259.0
37 TraesCS4A01G168200 chr3B 86.735 98 11 2 1595 1691 242876368 242876272 8.540000e-20 108.0
38 TraesCS4A01G168200 chr1B 85.441 522 51 11 732 1233 62430318 62429802 9.260000e-144 520.0
39 TraesCS4A01G168200 chr1B 85.249 522 52 12 732 1233 229526224 229525708 4.310000e-142 514.0
40 TraesCS4A01G168200 chr1B 79.570 93 14 4 1315 1403 469209007 469208916 6.740000e-06 62.1
41 TraesCS4A01G168200 chr1B 85.965 57 6 2 1349 1403 469195068 469195012 2.430000e-05 60.2


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 TraesCS4A01G168200 chr4A 420015955 420018215 2260 False 4176.000000 4176 100.000000 1 2261 1 chr4A.!!$F1 2260
1 TraesCS4A01G168200 chr1A 558015385 558017969 2584 True 1320.033333 2601 98.528000 1 2261 3 chr1A.!!$R2 2260
2 TraesCS4A01G168200 chr1A 490470003 490473302 3299 True 681.000000 1319 93.949333 1 1403 3 chr1A.!!$R1 1402
3 TraesCS4A01G168200 chr7D 221990814 221992214 1400 True 2074.000000 2074 93.487000 1 1403 1 chr7D.!!$R1 1402
4 TraesCS4A01G168200 chr5B 634119252 634120084 832 False 1251.000000 1251 93.473000 1404 2261 1 chr5B.!!$F1 857
5 TraesCS4A01G168200 chr5B 166585340 166592156 6816 False 668.250000 1602 94.608750 1 1403 4 chr5B.!!$F2 1402
6 TraesCS4A01G168200 chr2D 52285782 52286635 853 True 1399.000000 1399 96.154000 1404 2261 1 chr2D.!!$R1 857
7 TraesCS4A01G168200 chr2D 610357226 610358180 954 False 378.500000 527 85.300000 4 978 2 chr2D.!!$F1 974
8 TraesCS4A01G168200 chr5D 196319174 196320558 1384 False 712.550000 1328 89.700000 4 1394 2 chr5D.!!$F1 1390
9 TraesCS4A01G168200 chr7A 299414532 299415275 743 False 1184.000000 1184 95.442000 1404 2146 1 chr7A.!!$F2 742
10 TraesCS4A01G168200 chr7A 123205711 123206227 516 False 531.000000 531 85.824000 732 1233 1 chr7A.!!$F1 501
11 TraesCS4A01G168200 chr3D 477611554 477612077 523 False 854.000000 854 96.015000 1735 2261 1 chr3D.!!$F2 526
12 TraesCS4A01G168200 chr3D 30971876 30973554 1678 True 694.000000 1110 96.648500 1404 2259 2 chr3D.!!$R1 855
13 TraesCS4A01G168200 chr3D 412104586 412105397 811 True 585.000000 854 93.167000 1404 2258 2 chr3D.!!$R2 854
14 TraesCS4A01G168200 chr2B 15465124 15466160 1036 True 1033.000000 1033 85.009000 374 1403 1 chr2B.!!$R1 1029
15 TraesCS4A01G168200 chr2B 17850540 17851056 516 True 508.000000 508 85.057000 732 1233 1 chr2B.!!$R2 501
16 TraesCS4A01G168200 chr2A 315764002 315764602 600 True 944.000000 944 95.008000 1661 2261 1 chr2A.!!$R1 600
17 TraesCS4A01G168200 chr6D 169715775 169716902 1127 True 535.500000 865 91.295000 1405 2259 2 chr6D.!!$R1 854
18 TraesCS4A01G168200 chr3B 726178213 726179042 829 False 498.000000 737 90.715500 1404 2182 2 chr3B.!!$F1 778
19 TraesCS4A01G168200 chr1B 62429802 62430318 516 True 520.000000 520 85.441000 732 1233 1 chr1B.!!$R1 501
20 TraesCS4A01G168200 chr1B 229525708 229526224 516 True 514.000000 514 85.249000 732 1233 1 chr1B.!!$R2 501

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
807 8524 0.817634 CGTCTGCCTCCTCTCGATCT 60.818 60.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 10173 4.56358 GGACACTCTTGCTTGATACAAGGA 60.564 45.833 12.36 7.49 43.79 3.36 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
250 1060 1.198759 ACACCGGCCTACTTGACCAT 61.199 55.000 0.00 0.0 0.00 3.55
487 7813 5.105675 TGCTAACCGAATTCCCAAATTAACC 60.106 40.000 0.00 0.0 35.21 2.85
807 8524 0.817634 CGTCTGCCTCCTCTCGATCT 60.818 60.000 0.00 0.0 0.00 2.75
1016 8739 3.204827 CATGGCCGCCTCCTTTCG 61.205 66.667 11.61 0.0 0.00 3.46
1101 8825 1.528824 CATCCACGATGCTCCCCTT 59.471 57.895 0.00 0.0 33.17 3.95
1208 8933 2.517553 TCTCCATGTCTCCTCCATCTCT 59.482 50.000 0.00 0.0 0.00 3.10
1294 9023 2.514458 AGGATTGCGGGTTGAAGAAT 57.486 45.000 0.00 0.0 0.00 2.40
1775 9873 3.008049 ACCAAACAGCCCTGACTACTAAG 59.992 47.826 1.69 0.0 0.00 2.18
2069 10173 5.348986 GGTCAGTGTACGACATGTTCATAT 58.651 41.667 0.00 0.0 34.97 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 1060 1.303806 GTGGGCCGGCTAAAAAGGA 60.304 57.895 28.56 0.00 0.00 3.36
323 1133 7.881232 TCTTTGGTTCTCGGTTTTTATACTCAT 59.119 33.333 0.00 0.00 0.00 2.90
487 7813 6.036300 TGGCCGACTTTAATTACTGTATTTCG 59.964 38.462 0.00 0.00 0.00 3.46
564 7891 1.064017 TGTGGCTGAGAAAAAGGGTGT 60.064 47.619 0.00 0.00 0.00 4.16
807 8524 2.750637 GCGAGGTGAGGTCGAGGA 60.751 66.667 0.00 0.00 39.92 3.71
1101 8825 2.418746 GGGATAGCAAGAAGACGAGCAA 60.419 50.000 0.00 0.00 0.00 3.91
2069 10173 4.563580 GGACACTCTTGCTTGATACAAGGA 60.564 45.833 12.36 7.49 43.79 3.36


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

AutoCloner maintained by Alex Coulton.