Multiple sequence alignment - TraesCS4D01G188900

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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 TraesCS4D01G188900 chr4D 100.000 2147 0 0 1 2147 328704948 328702802 0.000000e+00 3965
1 TraesCS4D01G188900 chr1D 98.409 817 13 0 1331 2147 479615212 479616028 0.000000e+00 1437
2 TraesCS4D01G188900 chr1D 97.677 818 18 1 1331 2147 464291269 464290452 0.000000e+00 1404
3 TraesCS4D01G188900 chr1D 97.674 817 16 1 1331 2147 43190041 43189228 0.000000e+00 1400
4 TraesCS4D01G188900 chr1D 97.294 813 19 2 1 810 440707454 440708266 0.000000e+00 1376
5 TraesCS4D01G188900 chr1D 97.284 810 20 2 1 809 401598477 401599285 0.000000e+00 1373
6 TraesCS4D01G188900 chrUn 97.805 820 18 0 1328 2147 94833486 94834305 0.000000e+00 1415
7 TraesCS4D01G188900 chrUn 97.649 808 14 2 1 808 230383825 230383023 0.000000e+00 1382
8 TraesCS4D01G188900 chrUn 97.649 808 14 2 1 808 380710028 380709226 0.000000e+00 1382
9 TraesCS4D01G188900 chrUn 97.525 808 15 2 1 808 380683523 380682721 0.000000e+00 1376
10 TraesCS4D01G188900 chr7D 97.694 824 18 1 1324 2147 389455154 389455976 0.000000e+00 1415
11 TraesCS4D01G188900 chr7D 98.144 808 15 0 1340 2147 563844109 563843302 0.000000e+00 1410
12 TraesCS4D01G188900 chr7D 97.552 817 20 0 1331 2147 80294438 80293622 0.000000e+00 1399
13 TraesCS4D01G188900 chr7D 97.528 809 20 0 1 809 250991777 250990969 0.000000e+00 1384
14 TraesCS4D01G188900 chr7D 93.716 366 17 3 812 1176 475101114 475100754 5.210000e-151 544
15 TraesCS4D01G188900 chr6D 97.922 818 14 3 1331 2147 1555720 1556535 0.000000e+00 1413
16 TraesCS4D01G188900 chr6D 91.281 367 25 3 812 1173 69198009 69197645 5.320000e-136 494
17 TraesCS4D01G188900 chr5D 98.020 808 16 0 1 808 96981691 96980884 0.000000e+00 1404
18 TraesCS4D01G188900 chr5D 97.772 808 17 1 1 808 442157738 442158544 0.000000e+00 1391
19 TraesCS4D01G188900 chr5D 97.055 815 21 3 1 813 480661954 480662767 0.000000e+00 1369
20 TraesCS4D01G188900 chr7B 97.062 817 23 1 1331 2147 537833777 537832962 0.000000e+00 1375
21 TraesCS4D01G188900 chr2D 95.781 640 16 4 544 1173 407453227 407453865 0.000000e+00 1022
22 TraesCS4D01G188900 chr2D 99.363 157 1 0 1174 1330 407453941 407454097 3.490000e-73 285
23 TraesCS4D01G188900 chr2D 95.541 157 7 0 1174 1330 622711991 622712147 3.540000e-63 252
24 TraesCS4D01G188900 chr4A 94.780 364 19 0 809 1172 407814874 407815237 3.090000e-158 568
25 TraesCS4D01G188900 chr4A 96.178 157 6 0 1174 1330 407815314 407815470 7.600000e-65 257
26 TraesCS4D01G188900 chr4A 94.904 157 8 0 1174 1330 657666311 657666155 1.650000e-61 246
27 TraesCS4D01G188900 chr6A 94.490 363 20 0 809 1171 360194607 360194969 5.170000e-156 560
28 TraesCS4D01G188900 chr6A 88.556 367 32 6 812 1173 87298781 87298420 9.100000e-119 436
29 TraesCS4D01G188900 chr2A 94.247 365 21 0 809 1173 762023882 762024246 1.860000e-155 558
30 TraesCS4D01G188900 chr2A 96.552 145 5 0 1174 1318 121688474 121688618 7.660000e-60 241
31 TraesCS4D01G188900 chr2A 95.862 145 6 0 1174 1318 736664791 736664935 3.560000e-58 235
32 TraesCS4D01G188900 chr2A 93.671 158 8 2 1174 1330 762078978 762079134 3.560000e-58 235
33 TraesCS4D01G188900 chr2B 93.699 365 23 0 809 1173 795408321 795408685 4.030000e-152 547
34 TraesCS4D01G188900 chr2B 94.304 158 7 2 1174 1330 795318405 795318249 7.660000e-60 241
35 TraesCS4D01G188900 chr3A 95.960 297 12 0 877 1173 152000825 152000529 1.150000e-132 483
36 TraesCS4D01G188900 chr3A 96.178 157 6 0 1174 1330 152000453 152000297 7.600000e-65 257


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 TraesCS4D01G188900 chr4D 328702802 328704948 2146 True 3965.0 3965 100.000 1 2147 1 chr4D.!!$R1 2146
1 TraesCS4D01G188900 chr1D 479615212 479616028 816 False 1437.0 1437 98.409 1331 2147 1 chr1D.!!$F3 816
2 TraesCS4D01G188900 chr1D 464290452 464291269 817 True 1404.0 1404 97.677 1331 2147 1 chr1D.!!$R2 816
3 TraesCS4D01G188900 chr1D 43189228 43190041 813 True 1400.0 1400 97.674 1331 2147 1 chr1D.!!$R1 816
4 TraesCS4D01G188900 chr1D 440707454 440708266 812 False 1376.0 1376 97.294 1 810 1 chr1D.!!$F2 809
5 TraesCS4D01G188900 chr1D 401598477 401599285 808 False 1373.0 1373 97.284 1 809 1 chr1D.!!$F1 808
6 TraesCS4D01G188900 chrUn 94833486 94834305 819 False 1415.0 1415 97.805 1328 2147 1 chrUn.!!$F1 819
7 TraesCS4D01G188900 chrUn 230383023 230383825 802 True 1382.0 1382 97.649 1 808 1 chrUn.!!$R1 807
8 TraesCS4D01G188900 chrUn 380709226 380710028 802 True 1382.0 1382 97.649 1 808 1 chrUn.!!$R3 807
9 TraesCS4D01G188900 chrUn 380682721 380683523 802 True 1376.0 1376 97.525 1 808 1 chrUn.!!$R2 807
10 TraesCS4D01G188900 chr7D 389455154 389455976 822 False 1415.0 1415 97.694 1324 2147 1 chr7D.!!$F1 823
11 TraesCS4D01G188900 chr7D 563843302 563844109 807 True 1410.0 1410 98.144 1340 2147 1 chr7D.!!$R4 807
12 TraesCS4D01G188900 chr7D 80293622 80294438 816 True 1399.0 1399 97.552 1331 2147 1 chr7D.!!$R1 816
13 TraesCS4D01G188900 chr7D 250990969 250991777 808 True 1384.0 1384 97.528 1 809 1 chr7D.!!$R2 808
14 TraesCS4D01G188900 chr6D 1555720 1556535 815 False 1413.0 1413 97.922 1331 2147 1 chr6D.!!$F1 816
15 TraesCS4D01G188900 chr5D 96980884 96981691 807 True 1404.0 1404 98.020 1 808 1 chr5D.!!$R1 807
16 TraesCS4D01G188900 chr5D 442157738 442158544 806 False 1391.0 1391 97.772 1 808 1 chr5D.!!$F1 807
17 TraesCS4D01G188900 chr5D 480661954 480662767 813 False 1369.0 1369 97.055 1 813 1 chr5D.!!$F2 812
18 TraesCS4D01G188900 chr7B 537832962 537833777 815 True 1375.0 1375 97.062 1331 2147 1 chr7B.!!$R1 816
19 TraesCS4D01G188900 chr2D 407453227 407454097 870 False 653.5 1022 97.572 544 1330 2 chr2D.!!$F2 786
20 TraesCS4D01G188900 chr4A 407814874 407815470 596 False 412.5 568 95.479 809 1330 2 chr4A.!!$F1 521
21 TraesCS4D01G188900 chr3A 152000297 152000825 528 True 370.0 483 96.069 877 1330 2 chr3A.!!$R1 453

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
445 446 2.607282 CGACGTGCAGAAGACCTAAAGT 60.607 50.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1640 0.736053 GAGTTTGTGGGTGTTTGCGA 59.264 50.0 0.0 0.0 0.0 5.1 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
92 93 4.865925 CGGATGACGTTATAAAACCAGTCA 59.134 41.667 0.00 9.69 39.05 3.41
115 116 5.583854 CAGTCATTTCTGAATCGATCAAGGT 59.416 40.000 0.00 0.00 37.67 3.50
317 318 3.963428 TGTCCTAGAAGCAAAGAGGTC 57.037 47.619 0.00 0.00 0.00 3.85
445 446 2.607282 CGACGTGCAGAAGACCTAAAGT 60.607 50.000 0.00 0.00 0.00 2.66
737 740 2.720578 CTCGTAAAACTCGTGCGTACAA 59.279 45.455 4.09 0.00 0.00 2.41
769 772 4.037927 AGCTAGGACCTTGCCTTTACATA 58.962 43.478 22.23 0.00 39.50 2.29
921 934 2.890945 GGCTAGGTGTTTGTGGAATTGT 59.109 45.455 0.00 0.00 0.00 2.71
1206 1294 5.883115 TGATTACCCTATCTGCTCTCTATCG 59.117 44.000 0.00 0.00 0.00 2.92
1345 1433 5.931724 TCAGTTATCTTTTGAGCATGAACGA 59.068 36.000 0.00 0.00 0.00 3.85
1349 1437 3.727726 TCTTTTGAGCATGAACGACAGA 58.272 40.909 0.00 0.00 0.00 3.41
1884 1974 3.007920 AGCCTCTCCCACCTGCAG 61.008 66.667 6.78 6.78 0.00 4.41
1978 2068 0.761187 GAGGCTCATCTGCACCCATA 59.239 55.000 10.25 0.00 34.04 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 5.583854 CACCTTGATCGATTCAGAAATGACT 59.416 40.000 0.00 0.00 35.27 3.41
115 116 1.202486 ACTTCGGCTTCGTTTCAGTCA 60.202 47.619 0.00 0.00 35.06 3.41
317 318 2.973406 GGTCCCCTCTATTTACTCCTGG 59.027 54.545 0.00 0.00 0.00 4.45
445 446 2.661537 CGTTGCTGTGCGGAGTGA 60.662 61.111 0.00 0.00 0.00 3.41
673 676 0.896940 AACAGCCCTACGTCTCGGAA 60.897 55.000 0.00 0.00 0.00 4.30
737 740 3.964031 CAAGGTCCTAGCTATGGAGAAGT 59.036 47.826 10.98 0.00 33.78 3.01
769 772 2.045326 TGACAGTAGAATGGGGGTAGGT 59.955 50.000 0.00 0.00 0.00 3.08
921 934 1.174712 GCAGTTGCAAAGGAGGCAGA 61.175 55.000 0.00 0.00 43.05 4.26
959 972 2.159000 GCCTAGCCTTAGCGTTCCTTAA 60.159 50.000 0.00 0.00 46.67 1.85
1206 1294 3.000078 CACATAGTCGGCGTGTATTTCAC 60.000 47.826 6.85 0.00 43.03 3.18
1550 1640 0.736053 GAGTTTGTGGGTGTTTGCGA 59.264 50.000 0.00 0.00 0.00 5.10
1884 1974 3.843240 CGAGCTCGCCGCAAGTTC 61.843 66.667 25.07 0.00 42.61 3.01
1904 1994 1.725706 CGAAGAGCTTGCTCTCACTTG 59.274 52.381 23.17 9.93 35.59 3.16
1905 1995 1.615883 TCGAAGAGCTTGCTCTCACTT 59.384 47.619 23.17 9.59 35.59 3.16


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

AutoCloner maintained by Alex Coulton.