Multiple sequence alignment - TraesCS6A01G387700

Loading Multiple Alignment...

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 TraesCS6A01G387700 chr6A 100.000 2300 0 0 1 2300 604196212 604198511 0.000000e+00 4248.0
1 TraesCS6A01G387700 chr6A 92.553 188 13 1 375 562 25623554 25623368 3.770000e-68 268.0
2 TraesCS6A01G387700 chr6A 90.476 189 15 2 374 562 501926586 501926401 1.760000e-61 246.0
3 TraesCS6A01G387700 chr5A 96.470 2323 56 9 1 2300 531398035 531395716 0.000000e+00 3812.0
4 TraesCS6A01G387700 chr5A 91.398 186 14 2 375 559 33132176 33131992 1.050000e-63 254.0
5 TraesCS6A01G387700 chr6B 89.766 811 61 14 977 1776 695834260 695835059 0.000000e+00 1018.0
6 TraesCS6A01G387700 chr6B 86.157 549 70 6 1554 2100 649107900 649108444 2.550000e-164 588.0
7 TraesCS6A01G387700 chr6B 94.985 339 15 1 1773 2109 695840337 695840675 4.350000e-147 531.0
8 TraesCS6A01G387700 chr6B 84.919 431 42 8 572 979 695821021 695821451 4.570000e-112 414.0
9 TraesCS6A01G387700 chr6B 98.131 107 2 0 2194 2300 695840677 695840783 1.080000e-43 187.0
10 TraesCS6A01G387700 chr6B 98.876 89 1 0 2106 2194 58626899 58626811 2.370000e-35 159.0
11 TraesCS6A01G387700 chr6B 89.286 84 9 0 291 374 695820946 695821029 3.130000e-19 106.0
12 TraesCS6A01G387700 chr6D 84.258 559 63 16 1554 2111 430706334 430706868 2.620000e-144 521.0
13 TraesCS6A01G387700 chr6D 94.444 342 12 2 1777 2111 457265074 457265415 9.420000e-144 520.0
14 TraesCS6A01G387700 chr6D 93.243 222 9 1 572 793 457260266 457260481 2.850000e-84 322.0
15 TraesCS6A01G387700 chr6D 99.083 109 1 0 2192 2300 457265413 457265521 1.800000e-46 196.0
16 TraesCS6A01G387700 chr6D 98.837 86 1 0 2109 2194 326981633 326981548 1.100000e-33 154.0
17 TraesCS6A01G387700 chr6D 88.991 109 10 1 2192 2298 430706866 430706974 1.430000e-27 134.0
18 TraesCS6A01G387700 chr3A 91.848 184 15 0 375 558 290712318 290712501 8.150000e-65 257.0
19 TraesCS6A01G387700 chr1A 91.351 185 16 0 375 559 402617218 402617402 1.050000e-63 254.0
20 TraesCS6A01G387700 chr1A 98.864 88 1 0 2107 2194 14584509 14584422 8.510000e-35 158.0
21 TraesCS6A01G387700 chr4A 90.860 186 17 0 374 559 609797875 609798060 1.360000e-62 250.0
22 TraesCS6A01G387700 chr4A 90.811 185 17 0 375 559 604639722 604639538 4.910000e-62 248.0
23 TraesCS6A01G387700 chrUn 91.257 183 15 1 380 562 63263791 63263610 4.910000e-62 248.0
24 TraesCS6A01G387700 chr3D 97.778 90 2 0 2105 2194 336539268 336539179 3.060000e-34 156.0
25 TraesCS6A01G387700 chr3D 94.286 35 2 0 943 977 596080945 596080911 1.000000e-03 54.7
26 TraesCS6A01G387700 chr7B 97.753 89 2 0 2106 2194 700274410 700274498 1.100000e-33 154.0
27 TraesCS6A01G387700 chr4B 97.778 90 1 1 2105 2193 342857070 342857159 1.100000e-33 154.0
28 TraesCS6A01G387700 chr2D 96.739 92 3 0 2105 2196 441852483 441852574 1.100000e-33 154.0
29 TraesCS6A01G387700 chr2A 94.792 96 5 0 2098 2193 36742313 36742408 1.420000e-32 150.0


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 TraesCS6A01G387700 chr6A 604196212 604198511 2299 False 4248.0 4248 100.0000 1 2300 1 chr6A.!!$F1 2299
1 TraesCS6A01G387700 chr5A 531395716 531398035 2319 True 3812.0 3812 96.4700 1 2300 1 chr5A.!!$R2 2299
2 TraesCS6A01G387700 chr6B 695834260 695835059 799 False 1018.0 1018 89.7660 977 1776 1 chr6B.!!$F2 799
3 TraesCS6A01G387700 chr6B 649107900 649108444 544 False 588.0 588 86.1570 1554 2100 1 chr6B.!!$F1 546
4 TraesCS6A01G387700 chr6B 695820946 695821451 505 False 260.0 414 87.1025 291 979 2 chr6B.!!$F3 688
5 TraesCS6A01G387700 chr6D 430706334 430706974 640 False 327.5 521 86.6245 1554 2298 2 chr6D.!!$F2 744

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
193 194 0.107361 TCTCTGTGCCGTCCGATCTA 60.107 55.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1864 0.333993 ACCATTGCAGGAGAAGCCAT 59.666 50.0 0.0 0.0 40.02 4.4 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
38 39 9.627395 GGAACTTTTAAGCTAGGATTTTTCTTC 57.373 33.333 0.00 0.00 0.00 2.87
99 100 1.771255 CAGAATTCCCACCTCCTAGGG 59.229 57.143 9.46 0.00 46.90 3.53
107 108 2.309504 ACCTCCTAGGGGGCTTTGC 61.310 63.158 29.09 0.00 40.58 3.68
131 132 3.512516 GAGTGCCGCCCTTCATGC 61.513 66.667 0.00 0.00 0.00 4.06
193 194 0.107361 TCTCTGTGCCGTCCGATCTA 60.107 55.000 0.00 0.00 0.00 1.98
275 276 2.678580 TCGGGACCATCAGCACGA 60.679 61.111 0.00 0.00 0.00 4.35
319 320 2.255252 CCCTTTCGTTTGCTGCCG 59.745 61.111 0.00 0.00 0.00 5.69
343 344 2.545526 CGCACAACAATTCAGTCAGACT 59.454 45.455 0.00 0.00 0.00 3.24
385 388 1.389609 GCGTCGGGGGATGAGACTTA 61.390 60.000 0.00 0.00 33.10 2.24
414 417 2.463620 CGTCGTGTGCCCATCCATG 61.464 63.158 0.00 0.00 0.00 3.66
446 449 5.138125 ACGTGGCTTGATTTGATTGAAAT 57.862 34.783 0.00 0.00 36.94 2.17
466 469 0.634465 AAAATAAGGTCCGGCCCCAT 59.366 50.000 0.00 0.00 38.26 4.00
469 472 2.638025 ATAAGGTCCGGCCCCATCCT 62.638 60.000 0.00 0.00 38.26 3.24
480 483 3.225940 GGCCCCATCCTCTTAAAATCAG 58.774 50.000 0.00 0.00 0.00 2.90
482 485 3.117512 GCCCCATCCTCTTAAAATCAGGA 60.118 47.826 0.00 0.00 40.70 3.86
495 498 9.003145 TCTTAAAATCAGGAGGGAGATGATTAA 57.997 33.333 0.49 0.00 41.56 1.40
552 555 0.824109 TAAGTGGGAGCACGGATGAG 59.176 55.000 0.00 0.00 0.00 2.90
565 581 1.299014 GATGAGAGCACGAGAGCCG 60.299 63.158 0.00 0.00 45.44 5.52
1056 1095 2.653115 GCCAACAAGCTTGAGCCC 59.347 61.111 32.50 13.71 43.38 5.19
1082 1121 0.241213 CGCTACGACGGGATGATGAT 59.759 55.000 0.00 0.00 0.00 2.45
1448 1502 3.441222 TCCATATATACCCACGCGTACAG 59.559 47.826 13.44 6.06 0.00 2.74
1807 1864 4.113617 CGGAGGAGGAGTTGTGGA 57.886 61.111 0.00 0.00 0.00 4.02
1944 2002 2.364186 TCGAGCCTGAGCCATGGA 60.364 61.111 18.40 0.00 41.25 3.41
2119 2177 1.264295 GTGGAAACTACTCCCTCCGT 58.736 55.000 0.00 0.00 34.22 4.69
2181 2239 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 3.752339 CTCTTGCCCGCAAAGCCC 61.752 66.667 3.37 0.00 35.33 5.19
131 132 1.883021 GCAACCTGGAAATGGACGG 59.117 57.895 0.00 0.00 0.00 4.79
156 157 3.186656 AACCCCCGAAAGACCCACG 62.187 63.158 0.00 0.00 0.00 4.94
193 194 2.809601 GTTGCGCATCGTCGAGGT 60.810 61.111 12.75 0.00 0.00 3.85
319 320 1.268488 TGACTGAATTGTTGTGCGCAC 60.268 47.619 33.11 33.11 0.00 5.34
377 380 0.617820 GGGGGAGCAGGTAAGTCTCA 60.618 60.000 0.00 0.00 0.00 3.27
446 449 1.296984 TGGGGCCGGACCTTATTTTA 58.703 50.000 29.76 0.75 39.10 1.52
458 461 2.230660 GATTTTAAGAGGATGGGGCCG 58.769 52.381 0.00 0.00 0.00 6.13
469 472 7.457380 AATCATCTCCCTCCTGATTTTAAGA 57.543 36.000 0.00 0.00 36.47 2.10
480 483 9.853177 TTCTTTCTAATTTAATCATCTCCCTCC 57.147 33.333 0.00 0.00 0.00 4.30
513 516 5.936372 ACTTAATCCTACGGTTGTCCTTTTC 59.064 40.000 0.00 0.00 0.00 2.29
519 522 3.196254 TCCCACTTAATCCTACGGTTGTC 59.804 47.826 0.00 0.00 0.00 3.18
534 537 0.904865 TCTCATCCGTGCTCCCACTT 60.905 55.000 0.00 0.00 39.86 3.16
539 542 1.520342 GTGCTCTCATCCGTGCTCC 60.520 63.158 0.00 0.00 0.00 4.70
540 543 1.875813 CGTGCTCTCATCCGTGCTC 60.876 63.158 0.00 0.00 0.00 4.26
552 555 2.026879 GATCCGGCTCTCGTGCTC 59.973 66.667 0.00 0.00 37.11 4.26
565 581 2.029666 CATCCCGACGCAGGATCC 59.970 66.667 2.48 2.48 42.41 3.36
801 840 1.745489 GTCAGAACCATGGACGGCC 60.745 63.158 21.47 0.00 0.00 6.13
1056 1095 2.579787 CCGTCGTAGCGCTCCTTG 60.580 66.667 16.34 1.84 0.00 3.61
1082 1121 0.616395 TTCCGCCTCATACACCTCCA 60.616 55.000 0.00 0.00 0.00 3.86
1448 1502 2.092914 AGGAACTCGTGGATGATTTCCC 60.093 50.000 12.20 0.00 44.51 3.97
1552 1608 2.612567 TTGCGGGCGCTACAACAAG 61.613 57.895 7.64 0.00 42.51 3.16
1807 1864 0.333993 ACCATTGCAGGAGAAGCCAT 59.666 50.000 0.00 0.00 40.02 4.40
1857 1915 2.753966 GCTACGCCCAGTGCACATG 61.754 63.158 21.04 13.83 41.33 3.21
2100 2158 1.204231 GACGGAGGGAGTAGTTTCCAC 59.796 57.143 0.00 0.00 39.09 4.02
2119 2177 7.601886 TGTCAAAAACGTTCTTATATTACGGGA 59.398 33.333 0.00 0.00 39.45 5.14
2177 2235 2.243888 AGGTACTCCCTCCGTCCCA 61.244 63.158 0.00 0.00 40.71 4.37
2181 2239 1.217057 TACCCAGGTACTCCCTCCGT 61.217 60.000 0.00 0.00 43.86 4.69


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

AutoCloner maintained by Alex Coulton.