Multiple sequence alignment - TraesCS6D01G374700

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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 TraesCS6D01G374700 chr6D 100.000 2594 0 0 1 2594 458898149 458900742 0 4791
1 TraesCS6D01G374700 chr6D 98.651 2595 34 1 1 2594 124517488 124520082 0 4597
2 TraesCS6D01G374700 chr7D 98.767 2595 31 1 1 2594 381923967 381926561 0 4614
3 TraesCS6D01G374700 chr7D 98.690 2596 32 1 1 2594 382050044 382052639 0 4604
4 TraesCS6D01G374700 chr7D 98.690 2595 33 1 1 2594 203499965 203502559 0 4602
5 TraesCS6D01G374700 chr4D 98.381 2594 41 1 1 2594 123335439 123338031 0 4556
6 TraesCS6D01G374700 chr1A 98.266 2595 39 2 1 2594 498691261 498688672 0 4538
7 TraesCS6D01G374700 chr1D 98.225 2592 43 3 1 2591 269406768 269409357 0 4529
8 TraesCS6D01G374700 chrUn 98.073 2595 44 2 1 2594 186208455 186205866 0 4510


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 TraesCS6D01G374700 chr6D 458898149 458900742 2593 False 4791 4791 100.000 1 2594 1 chr6D.!!$F2 2593
1 TraesCS6D01G374700 chr6D 124517488 124520082 2594 False 4597 4597 98.651 1 2594 1 chr6D.!!$F1 2593
2 TraesCS6D01G374700 chr7D 381923967 381926561 2594 False 4614 4614 98.767 1 2594 1 chr7D.!!$F2 2593
3 TraesCS6D01G374700 chr7D 382050044 382052639 2595 False 4604 4604 98.690 1 2594 1 chr7D.!!$F3 2593
4 TraesCS6D01G374700 chr7D 203499965 203502559 2594 False 4602 4602 98.690 1 2594 1 chr7D.!!$F1 2593
5 TraesCS6D01G374700 chr4D 123335439 123338031 2592 False 4556 4556 98.381 1 2594 1 chr4D.!!$F1 2593
6 TraesCS6D01G374700 chr1A 498688672 498691261 2589 True 4538 4538 98.266 1 2594 1 chr1A.!!$R1 2593
7 TraesCS6D01G374700 chr1D 269406768 269409357 2589 False 4529 4529 98.225 1 2591 1 chr1D.!!$F1 2590
8 TraesCS6D01G374700 chrUn 186205866 186208455 2589 True 4510 4510 98.073 1 2594 1 chrUn.!!$R1 2593

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
50 51 0.178992 GCCCCGAATGGATTGGATCA 60.179 55.000 0.0 0.0 37.49 2.92 F
824 828 1.197721 GTGAACAGCCGTTTGATGGAG 59.802 52.381 0.0 0.0 34.75 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1187 0.178975 ACTTTCGTTTGGGCCATGGA 60.179 50.0 18.4 1.75 0.00 3.41 R
1995 1999 2.552585 TTCGGATGGACTTCGCCGTC 62.553 60.0 0.0 0.00 43.92 4.79 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
50 51 0.178992 GCCCCGAATGGATTGGATCA 60.179 55.000 0.00 0.00 37.49 2.92
65 66 1.680207 GGATCATTTCTGCTTCTGCCC 59.320 52.381 0.00 0.00 38.71 5.36
154 155 1.941820 AGCTCCCCCTCCCTCTGTA 60.942 63.158 0.00 0.00 0.00 2.74
232 233 4.345547 AGGAGGAAGAAAGAAAGTCGAAGT 59.654 41.667 0.00 0.00 0.00 3.01
602 606 6.183360 CCTGCCGACGTTCTAATAAAGAATTT 60.183 38.462 0.00 0.00 45.84 1.82
609 613 6.592607 ACGTTCTAATAAAGAATTTCGGCTCA 59.407 34.615 0.00 0.00 45.84 4.26
816 820 1.494824 GAGTTACGTGAACAGCCGTT 58.505 50.000 0.00 0.00 40.86 4.44
824 828 1.197721 GTGAACAGCCGTTTGATGGAG 59.802 52.381 0.00 0.00 34.75 3.86
1172 1176 5.699915 GCAGCATTGCTTCTATGATCTTAGA 59.300 40.000 8.83 12.98 46.95 2.10
1183 1187 2.191400 TGATCTTAGAAGCACTGGCCT 58.809 47.619 3.32 0.00 42.56 5.19
1437 1441 1.964223 TCGGCTATGACCTTCTCCATC 59.036 52.381 0.00 0.00 0.00 3.51
1695 1699 1.629043 TGCTACGAAAGACAGGGTCT 58.371 50.000 0.00 0.00 45.64 3.85
1712 1716 5.596361 CAGGGTCTAGTCTGATACATCAACT 59.404 44.000 10.06 10.06 36.18 3.16
1995 1999 4.329462 TTTCCATTTTCGTTGGGAAAGG 57.671 40.909 0.00 0.00 44.95 3.11
2372 2376 0.460987 CGAAGCACTGGAGTGATCCC 60.461 60.000 11.06 0.00 44.74 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.519771 TCATGGGCAGAAGCAGAAAT 57.480 45.000 0.00 0.00 44.61 2.17
65 66 0.383231 GGCGAGGCCTTCATTTCATG 59.617 55.000 6.77 0.00 46.69 3.07
154 155 5.410924 GGAAGATTAGCAAAGCGGAAAAAT 58.589 37.500 0.00 0.00 0.00 1.82
209 210 4.345547 ACTTCGACTTTCTTTCTTCCTCCT 59.654 41.667 0.00 0.00 0.00 3.69
232 233 1.048601 AGGACAAAGGAGAAGACGCA 58.951 50.000 0.00 0.00 0.00 5.24
816 820 4.196193 ACGTGAAAGTTGTTCTCCATCAA 58.804 39.130 0.00 0.00 0.00 2.57
824 828 3.181518 TGAACCGAACGTGAAAGTTGTTC 60.182 43.478 0.00 0.00 37.45 3.18
1172 1176 2.357836 CCATGGAGGCCAGTGCTT 59.642 61.111 5.56 0.00 36.75 3.91
1183 1187 0.178975 ACTTTCGTTTGGGCCATGGA 60.179 50.000 18.40 1.75 0.00 3.41
1325 1329 4.541973 ACTATGGCGAATGCATCTATCA 57.458 40.909 0.00 0.00 45.35 2.15
1437 1441 3.261580 TCCTGCGTATGAGAACATTGTG 58.738 45.455 0.00 0.00 37.87 3.33
1497 1501 1.104577 AACCCAAAGCGGCGAAGAAA 61.105 50.000 12.98 0.00 0.00 2.52
1695 1699 5.880887 AGTCGACAGTTGATGTATCAGACTA 59.119 40.000 19.50 0.00 44.17 2.59
1712 1716 3.314357 CGTACAAGGATATGGAGTCGACA 59.686 47.826 19.50 0.00 0.00 4.35
1995 1999 2.552585 TTCGGATGGACTTCGCCGTC 62.553 60.000 0.00 0.00 43.92 4.79
2060 2064 3.126879 CCTTCCGCATGCGCTTCA 61.127 61.111 34.00 14.42 38.24 3.02
2218 2222 8.774546 TTAGATATCTGGATAGATGGATGGAC 57.225 38.462 15.79 0.00 43.41 4.02


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

AutoCloner maintained by Alex Coulton.