Multiple sequence alignment - TraesCS4A01G144900

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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 TraesCS4A01G144900 chr4A 100.000 2438 0 0 1 2438 246657023 246659460 0 4503
1 TraesCS4A01G144900 chr7D 98.444 2442 32 5 1 2438 381925604 381923165 0 4294
2 TraesCS4A01G144900 chr7D 98.159 2444 33 6 1 2438 382051682 382049245 0 4253
3 TraesCS4A01G144900 chr7D 98.077 2444 36 7 1 2438 203501602 203499164 0 4242
4 TraesCS4A01G144900 chr6D 98.198 2442 36 5 1 2438 124519125 124516688 0 4259
5 TraesCS4A01G144900 chr5A 98.040 2449 33 7 1 2438 19247240 19249684 0 4242
6 TraesCS4A01G144900 chr5A 97.834 2447 44 4 1 2438 238821205 238823651 0 4217
7 TraesCS4A01G144900 chr7B 97.913 2444 40 6 1 2438 716877178 716879616 0 4220
8 TraesCS4A01G144900 chr7B 97.831 2444 45 6 1 2438 742991048 742988607 0 4213
9 TraesCS4A01G144900 chrUn 97.791 2445 45 7 1 2438 186206818 186209260 0 4207


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 TraesCS4A01G144900 chr4A 246657023 246659460 2437 False 4503 4503 100.000 1 2438 1 chr4A.!!$F1 2437
1 TraesCS4A01G144900 chr7D 381923165 381925604 2439 True 4294 4294 98.444 1 2438 1 chr7D.!!$R2 2437
2 TraesCS4A01G144900 chr7D 382049245 382051682 2437 True 4253 4253 98.159 1 2438 1 chr7D.!!$R3 2437
3 TraesCS4A01G144900 chr7D 203499164 203501602 2438 True 4242 4242 98.077 1 2438 1 chr7D.!!$R1 2437
4 TraesCS4A01G144900 chr6D 124516688 124519125 2437 True 4259 4259 98.198 1 2438 1 chr6D.!!$R1 2437
5 TraesCS4A01G144900 chr5A 19247240 19249684 2444 False 4242 4242 98.040 1 2438 1 chr5A.!!$F1 2437
6 TraesCS4A01G144900 chr5A 238821205 238823651 2446 False 4217 4217 97.834 1 2438 1 chr5A.!!$F2 2437
7 TraesCS4A01G144900 chr7B 716877178 716879616 2438 False 4220 4220 97.913 1 2438 1 chr7B.!!$F1 2437
8 TraesCS4A01G144900 chr7B 742988607 742991048 2441 True 4213 4213 97.831 1 2438 1 chr7B.!!$R1 2437
9 TraesCS4A01G144900 chrUn 186206818 186209260 2442 False 4207 4207 97.791 1 2438 1 chrUn.!!$F1 2437

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
287 288 0.036199 ACGGGTTTGCCGTAATGCTA 60.036 50.0 0.0 0.0 42.28 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1545 2.590092 CCTCGCCCCTTCCGAATT 59.41 61.111 0.0 0.0 33.92 2.17 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
217 218 4.322080 TGTAATGGAGAAGGTCATAGCG 57.678 45.455 0.00 0.00 0.00 4.26
218 219 3.958147 TGTAATGGAGAAGGTCATAGCGA 59.042 43.478 0.00 0.00 0.00 4.93
287 288 0.036199 ACGGGTTTGCCGTAATGCTA 60.036 50.000 0.00 0.00 42.28 3.49
395 396 9.261180 CACATGAGAAACCAGTACGAATATAAT 57.739 33.333 0.00 0.00 0.00 1.28
488 489 5.996513 CCTAAGATCATAGAAGCAATGCTGT 59.003 40.000 9.14 1.52 39.62 4.40
592 593 1.405105 GGCGCAATAGAAAGGAATGCA 59.595 47.619 10.83 0.00 36.84 3.96
599 600 2.957402 AGAAAGGAATGCAGTCACCA 57.043 45.000 16.99 0.00 0.00 4.17
847 849 2.174363 TCACGTAACTCCACTCTCGA 57.826 50.000 0.00 0.00 0.00 4.04
961 963 2.034687 ATGCCGAACCTGCTGCTT 59.965 55.556 0.00 0.00 0.00 3.91
972 974 4.410400 GCTGCTTAGTGGGCGGGT 62.410 66.667 0.00 0.00 36.65 5.28
1185 1188 1.292223 CCTTCGTCGAGCCTTTCCA 59.708 57.895 0.00 0.00 0.00 3.53
1406 1412 3.394719 GACAAAGGAGAAGACGCTCTTT 58.605 45.455 0.00 0.00 36.73 2.52
1424 1430 5.762711 GCTCTTTGACTTTCTTTCTTCCTCT 59.237 40.000 0.00 0.00 0.00 3.69
1539 1545 4.335874 CGAGAACTTTAGGATCGGAGAAGA 59.664 45.833 4.44 0.00 43.58 2.87
1570 1576 1.365699 GCGAGGCCTTCATTTCGTTA 58.634 50.000 6.77 0.00 35.61 3.18
2050 2071 1.466558 GCAGGCTTCTTTCAGTAGCAC 59.533 52.381 4.96 0.00 39.95 4.40
2174 2195 0.037590 CCGGAAAGGTCATTGGGTCA 59.962 55.000 0.00 0.00 34.51 4.02
2192 2213 2.884639 GTCACCTTTGGAAGCTAAAGCA 59.115 45.455 4.54 0.00 45.16 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 7.624549 ACAATGTTCTCATACACAGGAATACT 58.375 34.615 0.00 0.0 33.49 2.12
183 184 7.770433 CCTTCTCCATTACAATGTTCTCATACA 59.230 37.037 0.00 0.0 34.60 2.29
217 218 7.316544 TCTAGCCAAAACGAATCCTATTTTC 57.683 36.000 0.00 0.0 0.00 2.29
218 219 6.183360 GCTCTAGCCAAAACGAATCCTATTTT 60.183 38.462 0.00 0.0 34.31 1.82
287 288 3.482156 AGATGCATTCGCCATAGTTCT 57.518 42.857 0.00 0.0 37.32 3.01
395 396 6.709018 TCATAGTTCGATTGGACATGTAGA 57.291 37.500 0.00 0.0 0.00 2.59
972 974 1.078214 GGTCCATGTAGCTGCTGCA 60.078 57.895 22.30 22.3 42.74 4.41
1185 1188 4.913968 AGGTGCATATCCCTTACCACTAAT 59.086 41.667 0.00 0.0 33.88 1.73
1406 1412 3.654414 GCGAGAGGAAGAAAGAAAGTCA 58.346 45.455 0.00 0.0 0.00 3.41
1525 1531 3.828921 TCCGAATTCTTCTCCGATCCTA 58.171 45.455 3.52 0.0 0.00 2.94
1539 1545 2.590092 CCTCGCCCCTTCCGAATT 59.410 61.111 0.00 0.0 33.92 2.17
1570 1576 2.867624 TGGATTGTTTCTGCTTCTGCT 58.132 42.857 0.00 0.0 40.48 4.24
1855 1869 3.996150 AGTCCGTGACGAAGAACTTTA 57.004 42.857 6.54 0.0 37.67 1.85
1860 1874 3.788937 AGAAAAAGTCCGTGACGAAGAA 58.211 40.909 6.54 0.0 37.67 2.52
2050 2071 3.381272 AGCCCGGTGAAAATGAATATGTG 59.619 43.478 0.00 0.0 0.00 3.21
2174 2195 4.405680 ACTTTTGCTTTAGCTTCCAAAGGT 59.594 37.500 9.04 8.9 42.66 3.50
2192 2213 3.146847 CTCCCGGCTTTCTACAACTTTT 58.853 45.455 0.00 0.0 0.00 2.27


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

AutoCloner maintained by Alex Coulton.