Multiple sequence alignment - TraesCS4A01G069800

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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 TraesCS4A01G069800 chr4A 100.000 2816 0 0 1 2816 67568127 67565312 0 5201
1 TraesCS4A01G069800 chr6A 98.545 2818 39 2 1 2816 608874687 608871870 0 4975
2 TraesCS4A01G069800 chr5A 97.835 2817 51 5 1 2816 492847660 492850467 0 4855
3 TraesCS4A01G069800 chr7A 97.764 2817 59 2 1 2816 46410809 46413622 0 4850
4 TraesCS4A01G069800 chr1A 98.476 2100 30 2 1 2098 238117485 238119584 0 3699
5 TraesCS4A01G069800 chr1A 98.332 2098 35 0 1 2098 238121408 238123505 0 3681
6 TraesCS4A01G069800 chr1A 98.217 729 13 0 2088 2816 238124845 238125573 0 1275
7 TraesCS4A01G069800 chrUn 98.427 2098 33 0 1 2098 86449117 86451214 0 3692
8 TraesCS4A01G069800 chrUn 98.428 2099 32 1 1 2098 222680160 222678062 0 3692
9 TraesCS4A01G069800 chrUn 98.765 729 8 1 2088 2816 86458553 86459280 0 1295
10 TraesCS4A01G069800 chrUn 98.354 729 12 0 2088 2816 222676722 222675994 0 1280
11 TraesCS4A01G069800 chrUn 98.352 728 11 1 2089 2816 86452554 86453280 0 1277
12 TraesCS4A01G069800 chr5B 98.380 2099 33 1 1 2098 533066664 533068762 0 3687
13 TraesCS4A01G069800 chr7B 98.333 2100 33 2 1 2098 742925241 742927340 0 3683
14 TraesCS4A01G069800 chr6B 98.764 728 8 1 2089 2816 596632282 596633008 0 1293
15 TraesCS4A01G069800 chr2D 98.354 729 12 0 2088 2816 322914602 322915330 0 1280


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 TraesCS4A01G069800 chr4A 67565312 67568127 2815 True 5201.0 5201 100.000000 1 2816 1 chr4A.!!$R1 2815
1 TraesCS4A01G069800 chr6A 608871870 608874687 2817 True 4975.0 4975 98.545000 1 2816 1 chr6A.!!$R1 2815
2 TraesCS4A01G069800 chr5A 492847660 492850467 2807 False 4855.0 4855 97.835000 1 2816 1 chr5A.!!$F1 2815
3 TraesCS4A01G069800 chr7A 46410809 46413622 2813 False 4850.0 4850 97.764000 1 2816 1 chr7A.!!$F1 2815
4 TraesCS4A01G069800 chr1A 238117485 238125573 8088 False 2885.0 3699 98.341667 1 2816 3 chr1A.!!$F1 2815
5 TraesCS4A01G069800 chrUn 222675994 222680160 4166 True 2486.0 3692 98.391000 1 2816 2 chrUn.!!$R1 2815
6 TraesCS4A01G069800 chrUn 86449117 86453280 4163 False 2484.5 3692 98.389500 1 2816 2 chrUn.!!$F2 2815
7 TraesCS4A01G069800 chrUn 86458553 86459280 727 False 1295.0 1295 98.765000 2088 2816 1 chrUn.!!$F1 728
8 TraesCS4A01G069800 chr5B 533066664 533068762 2098 False 3687.0 3687 98.380000 1 2098 1 chr5B.!!$F1 2097
9 TraesCS4A01G069800 chr7B 742925241 742927340 2099 False 3683.0 3683 98.333000 1 2098 1 chr7B.!!$F1 2097
10 TraesCS4A01G069800 chr6B 596632282 596633008 726 False 1293.0 1293 98.764000 2089 2816 1 chr6B.!!$F1 727
11 TraesCS4A01G069800 chr2D 322914602 322915330 728 False 1280.0 1280 98.354000 2088 2816 1 chr2D.!!$F1 728

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
493 495 0.101399 CGAGTCCCGAGAAGGTGATG 59.899 60.0 0.0 0.0 41.76 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 8855 1.30593 GCGAAAGAAGCCCACGGAAT 61.306 55.0 0.0 0.0 0.0 3.01 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
148 150 4.657013 GAGATGAAAACCCTTTGTCCTCT 58.343 43.478 0.00 0.00 0.00 3.69
386 388 6.275335 GTCACCTTAAAAACCCCAAAAGTAC 58.725 40.000 0.00 0.00 0.00 2.73
423 425 4.193826 TCTTTAGTGCTGCTCTTCGATT 57.806 40.909 9.71 0.00 0.00 3.34
493 495 0.101399 CGAGTCCCGAGAAGGTGATG 59.899 60.000 0.00 0.00 41.76 3.07
699 701 4.378356 CGAACCTTCAAAATGAGCGAATCA 60.378 41.667 0.00 0.00 43.70 2.57
754 757 2.214376 ACGAATCCAGGGCAATCAAA 57.786 45.000 0.00 0.00 0.00 2.69
784 787 3.673543 AAAACCCAGGTTGGACAACTA 57.326 42.857 14.14 0.00 40.96 2.24
812 815 2.449345 GGGGGATTAGCAGGGGATTTTA 59.551 50.000 0.00 0.00 0.00 1.52
860 863 2.551938 AGGGACTTCAAAGCTCAGAAGC 60.552 50.000 21.50 15.77 43.43 3.86
1126 1129 4.035909 GTCTTGGTTTGACATGGTTTACGT 59.964 41.667 0.00 0.00 34.80 3.57
1205 1208 7.388500 CCTACCTTTGGACTCGTATTTTGTTTA 59.612 37.037 0.00 0.00 0.00 2.01
1324 1329 3.644966 TTTCGATCCCCAGTTGCTATT 57.355 42.857 0.00 0.00 0.00 1.73
1389 1394 2.803956 TCTCGCTTCTCCTTGTTCCTA 58.196 47.619 0.00 0.00 0.00 2.94
1561 1566 2.916934 TGCTCCCAGGTACCTGTAATTT 59.083 45.455 34.49 1.09 42.15 1.82
1607 1612 4.145052 GGTCTTTCTGTGGAAACCTTCAT 58.855 43.478 0.00 0.00 36.63 2.57
1857 5783 9.903682 ACTTCAAAAGTCACTATCAATGAATTG 57.096 29.630 0.00 0.00 37.02 2.32
1882 5808 7.445707 TGCCGAGCAATTATAAACCAACATATA 59.554 33.333 0.00 0.00 34.76 0.86
2022 5948 4.042311 TGTTGCCCTAACTGAGTCCATTAA 59.958 41.667 0.00 0.00 40.05 1.40
2231 8855 4.985538 AGTCAGGAAAAATAACTGCTCCA 58.014 39.130 0.00 0.00 32.42 3.86
2257 8881 0.108138 GGGCTTCTTTCGCAGCTCTA 60.108 55.000 0.00 0.00 33.28 2.43
2750 9374 3.708631 ACTGGAATCGATCTGAATGAGGT 59.291 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 169 2.907634 GGGCTAGTAGCACTTTTCTCC 58.092 52.381 23.24 9.02 42.59 3.71
315 317 2.504175 GGCCCATCCTTAGTACTTGACA 59.496 50.000 0.00 0.00 0.00 3.58
386 388 1.983972 AAGAAGCACGCTAGACTTCG 58.016 50.000 0.00 0.00 43.61 3.79
423 425 5.111989 CCTCGTTCAATGAGAAAGCATCTA 58.888 41.667 8.32 0.00 38.96 1.98
493 495 5.349543 GCCAACTTCATGATCAAAATCAACC 59.650 40.000 0.00 0.00 44.85 3.77
754 757 5.073965 TCCAACCTGGGTTTTTAGATAGTGT 59.926 40.000 1.81 0.00 38.32 3.55
784 787 2.257409 CTGCTAATCCCCCAGCACGT 62.257 60.000 0.00 0.00 42.68 4.49
860 863 1.065701 CTGATAGAAGTGGGACCGTCG 59.934 57.143 0.00 0.00 0.00 5.12
1205 1208 1.408266 GGGCCTCCGTTGATTGTGTAT 60.408 52.381 0.84 0.00 0.00 2.29
1324 1329 3.838565 TGTATTTCTGCCTTTGTTCCCA 58.161 40.909 0.00 0.00 0.00 4.37
1389 1394 1.310373 CCGGGGAGGAGTTAGGAGT 59.690 63.158 0.00 0.00 45.00 3.85
1513 1518 6.094881 ACCGATGGAATGAACAAAATACGAAT 59.905 34.615 0.00 0.00 0.00 3.34
1687 5613 5.424252 TCGAATATATAAGGAAAGGGGCGAT 59.576 40.000 0.00 0.00 0.00 4.58
1857 5783 4.364415 TGTTGGTTTATAATTGCTCGGC 57.636 40.909 0.00 0.00 0.00 5.54
2022 5948 2.644798 ACCATAGAAGGGCAACAAGAGT 59.355 45.455 0.00 0.00 39.74 3.24
2093 7370 6.538263 AGACCATAAGCCATCCTTTATCTTC 58.462 40.000 0.00 0.00 34.95 2.87
2231 8855 1.305930 GCGAAAGAAGCCCACGGAAT 61.306 55.000 0.00 0.00 0.00 3.01
2257 8881 3.411808 TCGTAAAGCGAGCGTGAAT 57.588 47.368 0.00 0.00 45.68 2.57


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

AutoCloner maintained by Alex Coulton.