Multiple sequence alignment - TraesCS1D01G298700

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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 TraesCS1D01G298700 chr1D 100.000 2162 0 0 1 2162 397089444 397087283 0 3993
1 TraesCS1D01G298700 chr5D 96.610 2183 53 10 1 2162 503217703 503219885 0 3602
2 TraesCS1D01G298700 chr5D 96.290 2183 60 9 1 2162 503278741 503276559 0 3563
3 TraesCS1D01G298700 chr5D 96.116 1210 30 6 970 2162 446174242 446175451 0 1958
4 TraesCS1D01G298700 chr1A 96.564 2183 54 10 1 2162 554511733 554513915 0 3596
5 TraesCS1D01G298700 chr3B 96.519 2183 55 10 1 2162 201526509 201528691 0 3591
6 TraesCS1D01G298700 chr3B 96.138 958 21 5 1221 2162 101911885 101912842 0 1550
7 TraesCS1D01G298700 chr6D 96.381 2183 58 10 1 2162 168254411 168256593 0 3574
8 TraesCS1D01G298700 chr3D 96.290 2183 57 12 1 2162 589280057 589277878 0 3561
9 TraesCS1D01G298700 chr3A 96.150 2182 63 10 1 2162 672910522 672908342 0 3544
10 TraesCS1D01G298700 chr3A 95.923 2183 68 14 1 2162 594900139 594897957 0 3518
11 TraesCS1D01G298700 chrUn 96.104 2182 65 9 1 2162 216519117 216516936 0 3541
12 TraesCS1D01G298700 chrUn 96.446 2026 50 12 1 2005 93410146 93408122 0 3323
13 TraesCS1D01G298700 chrUn 96.315 2008 54 8 175 2162 346596834 346594827 0 3280
14 TraesCS1D01G298700 chr2D 95.465 2183 58 11 1 2162 272794408 272792246 0 3445
15 TraesCS1D01G298700 chr2D 95.931 1278 35 6 902 2162 272564345 272565622 0 2056


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 TraesCS1D01G298700 chr1D 397087283 397089444 2161 True 3993 3993 100.000 1 2162 1 chr1D.!!$R1 2161
1 TraesCS1D01G298700 chr5D 503217703 503219885 2182 False 3602 3602 96.610 1 2162 1 chr5D.!!$F2 2161
2 TraesCS1D01G298700 chr5D 503276559 503278741 2182 True 3563 3563 96.290 1 2162 1 chr5D.!!$R1 2161
3 TraesCS1D01G298700 chr5D 446174242 446175451 1209 False 1958 1958 96.116 970 2162 1 chr5D.!!$F1 1192
4 TraesCS1D01G298700 chr1A 554511733 554513915 2182 False 3596 3596 96.564 1 2162 1 chr1A.!!$F1 2161
5 TraesCS1D01G298700 chr3B 201526509 201528691 2182 False 3591 3591 96.519 1 2162 1 chr3B.!!$F2 2161
6 TraesCS1D01G298700 chr3B 101911885 101912842 957 False 1550 1550 96.138 1221 2162 1 chr3B.!!$F1 941
7 TraesCS1D01G298700 chr6D 168254411 168256593 2182 False 3574 3574 96.381 1 2162 1 chr6D.!!$F1 2161
8 TraesCS1D01G298700 chr3D 589277878 589280057 2179 True 3561 3561 96.290 1 2162 1 chr3D.!!$R1 2161
9 TraesCS1D01G298700 chr3A 672908342 672910522 2180 True 3544 3544 96.150 1 2162 1 chr3A.!!$R2 2161
10 TraesCS1D01G298700 chr3A 594897957 594900139 2182 True 3518 3518 95.923 1 2162 1 chr3A.!!$R1 2161
11 TraesCS1D01G298700 chrUn 216516936 216519117 2181 True 3541 3541 96.104 1 2162 1 chrUn.!!$R2 2161
12 TraesCS1D01G298700 chrUn 93408122 93410146 2024 True 3323 3323 96.446 1 2005 1 chrUn.!!$R1 2004
13 TraesCS1D01G298700 chrUn 346594827 346596834 2007 True 3280 3280 96.315 175 2162 1 chrUn.!!$R3 1987
14 TraesCS1D01G298700 chr2D 272792246 272794408 2162 True 3445 3445 95.465 1 2162 1 chr2D.!!$R1 2161
15 TraesCS1D01G298700 chr2D 272564345 272565622 1277 False 2056 2056 95.931 902 2162 1 chr2D.!!$F1 1260

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
527 530 2.665185 GCGCTTCCGGTTCTGTGT 60.665 61.111 0.0 0.0 34.32 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1662 0.606096 AATGGTTAAAGCGCCCAACC 59.394 50.0 22.08 22.08 41.75 3.77 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
177 179 6.477033 GCATACGGCTTTCTAGATGTATATGG 59.523 42.308 0.00 0.0 40.25 2.74
339 341 5.528690 TGGCTTATGTTCTTCATGTAGCATC 59.471 40.000 13.97 0.0 42.20 3.91
357 359 4.022416 AGCATCCAGATCGAATGACTCTAC 60.022 45.833 8.60 0.0 0.00 2.59
527 530 2.665185 GCGCTTCCGGTTCTGTGT 60.665 61.111 0.00 0.0 34.32 3.72
545 548 6.625362 TCTGTGTGTGCTTCAAACAATTTTA 58.375 32.000 6.85 0.0 42.85 1.52
636 639 3.488553 GCTGCCGTTACTCAACAGTTTTT 60.489 43.478 0.00 0.0 34.05 1.94
896 903 6.959639 AATGTATGCATTTCGATTAGGGTT 57.040 33.333 3.54 0.0 42.19 4.11
912 919 8.145767 CGATTAGGGTTGTATTCTATGGTTACA 58.854 37.037 0.00 0.0 0.00 2.41
1009 1016 2.024414 GCCTTGCGGTAATGATTCCTT 58.976 47.619 0.00 0.0 0.00 3.36
1093 1100 1.414919 TCACTTGCCTGTCTACGGTTT 59.585 47.619 0.00 0.0 0.00 3.27
1206 1214 7.556275 GTGGAATAGAATAACATGGTTGAAGGA 59.444 37.037 0.00 0.0 0.00 3.36
1291 1299 4.660303 TCCAGGTAGTCAATGGCTATTCAT 59.340 41.667 0.00 0.0 33.92 2.57
1461 1484 5.211973 TCCTATGCTCTGAGTTCCAGTATT 58.788 41.667 6.53 0.0 43.38 1.89
1694 1717 5.739070 GCTTAACAGGGATCATCGTACATCA 60.739 44.000 0.00 0.0 0.00 3.07
1769 1793 8.023128 CGAAATATTCCGAGATGGCAAATATTT 58.977 33.333 18.30 18.3 43.23 1.40
1978 2002 6.299141 ACTTATGATACCTAGTTGGCATTGG 58.701 40.000 0.00 0.0 40.22 3.16
2056 2080 8.535335 ACGTATATTCCTTGCTCATTATCAGAT 58.465 33.333 0.00 0.0 0.00 2.90
2097 2121 5.046159 ACCTCGTGTGGGACTAATCATTTTA 60.046 40.000 0.00 0.0 0.00 1.52
2144 2168 0.387929 CGTTCCGCTTAGCCCTATCA 59.612 55.000 0.00 0.0 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 179 4.009675 AGATCCATCTGTCTAGAGATCGC 58.990 47.826 10.21 0.00 38.60 4.58
339 341 4.553756 TTCGTAGAGTCATTCGATCTGG 57.446 45.455 0.00 0.00 38.43 3.86
357 359 6.822073 TGTGGAAGTATCGATGTAATTTCG 57.178 37.500 8.54 0.00 37.94 3.46
417 419 2.025699 GCAGTGGTAATTAAGACCCCCA 60.026 50.000 6.83 0.00 35.99 4.96
527 530 7.867403 GGAGAAGATAAAATTGTTTGAAGCACA 59.133 33.333 0.00 0.00 0.00 4.57
636 639 3.952323 CTCTACGGGATAGACCTCAACAA 59.048 47.826 0.00 0.00 34.80 2.83
843 850 3.397527 ACACTATGGGGATGGTGAGAAT 58.602 45.455 5.65 0.00 36.65 2.40
939 946 9.385902 CTATACCGTAAAATAGATTTTCGACGA 57.614 33.333 18.09 0.00 40.98 4.20
1009 1016 4.970711 TGTGGTAAAGGTCGTAATTCCAA 58.029 39.130 0.00 0.00 0.00 3.53
1093 1100 4.680237 CCCGAGCACACGCAAGGA 62.680 66.667 0.00 0.00 46.39 3.36
1195 1203 7.453393 ACGTATGATCATTATCCTTCAACCAT 58.547 34.615 14.65 0.00 0.00 3.55
1196 1204 6.826668 ACGTATGATCATTATCCTTCAACCA 58.173 36.000 14.65 0.00 0.00 3.67
1206 1214 9.440773 AATGCATTACAGACGTATGATCATTAT 57.559 29.630 18.55 0.00 0.00 1.28
1291 1299 4.161876 TCTTGGTGTTAAGGTGGTAGCTA 58.838 43.478 0.00 0.00 0.00 3.32
1522 1545 7.932491 GGAATCTCATCCATCATCCATACATAG 59.068 40.741 0.00 0.00 39.42 2.23
1639 1662 0.606096 AATGGTTAAAGCGCCCAACC 59.394 50.000 22.08 22.08 41.75 3.77
1739 1762 4.690748 TGCCATCTCGGAATATTTCGATTC 59.309 41.667 18.93 7.56 36.56 2.52
1769 1793 7.786943 AGAGAGGTATTTTCATAGTCATCTCCA 59.213 37.037 0.00 0.00 31.90 3.86
1787 1811 3.885976 ATTCGAGGATCCAGAGAGGTA 57.114 47.619 15.82 0.00 39.02 3.08
2056 2080 5.878116 CACGAGGTTTGGGAATAAGTGATTA 59.122 40.000 0.00 0.00 0.00 1.75
2097 2121 6.263754 AGGGTTTTCCATGAGATGGTAAATT 58.736 36.000 9.71 0.00 46.61 1.82


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

AutoCloner maintained by Alex Coulton.