Multiple sequence alignment - TraesCS1D01G134000

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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 TraesCS1D01G134000 chr1D 100.000 2877 0 0 1 2877 165202036 165204912 0.000000e+00 5313
1 TraesCS1D01G134000 chr1B 96.438 2892 75 10 1 2877 246770234 246767356 0.000000e+00 4745
2 TraesCS1D01G134000 chr1A 97.598 1665 27 4 628 2285 216416427 216414769 0.000000e+00 2841
3 TraesCS1D01G134000 chr1A 96.688 634 13 3 1 630 216419450 216418821 0.000000e+00 1048
4 TraesCS1D01G134000 chr1A 96.796 593 19 0 2285 2877 216401729 216401137 0.000000e+00 990
5 TraesCS1D01G134000 chr3D 87.940 398 48 0 1008 1405 137486547 137486150 1.210000e-128 470
6 TraesCS1D01G134000 chr3D 79.250 400 70 10 2441 2837 548531415 548531026 1.700000e-67 267
7 TraesCS1D01G134000 chr3A 87.186 398 51 0 1008 1405 155430075 155429678 1.220000e-123 453
8 TraesCS1D01G134000 chr3A 85.220 318 47 0 1515 1832 155429516 155429199 7.690000e-86 327
9 TraesCS1D01G134000 chr3A 79.000 400 71 10 2441 2837 686120782 686120393 7.910000e-66 261
10 TraesCS1D01G134000 chr3B 86.111 324 44 1 1509 1832 200873675 200873353 5.900000e-92 348
11 TraesCS1D01G134000 chr7A 81.796 412 71 3 996 1405 486144938 486145347 2.740000e-90 342
12 TraesCS1D01G134000 chr7D 81.436 404 71 3 1004 1405 436737831 436737430 7.690000e-86 327
13 TraesCS1D01G134000 chr7B 81.658 398 69 3 1010 1405 453150480 453150085 7.690000e-86 327


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 TraesCS1D01G134000 chr1D 165202036 165204912 2876 False 5313.0 5313 100.000 1 2877 1 chr1D.!!$F1 2876
1 TraesCS1D01G134000 chr1B 246767356 246770234 2878 True 4745.0 4745 96.438 1 2877 1 chr1B.!!$R1 2876
2 TraesCS1D01G134000 chr1A 216414769 216419450 4681 True 1944.5 2841 97.143 1 2285 2 chr1A.!!$R2 2284
3 TraesCS1D01G134000 chr1A 216401137 216401729 592 True 990.0 990 96.796 2285 2877 1 chr1A.!!$R1 592
4 TraesCS1D01G134000 chr3A 155429199 155430075 876 True 390.0 453 86.203 1008 1832 2 chr3A.!!$R2 824

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
102 103 0.183492 TCTCTGTGCCTTTGCCTGTT 59.817 50.0 0.0 0.0 36.33 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 4430 3.068165 GTGGATAAATAACAAGCCCAGCC 59.932 47.826 0.0 0.0 0.0 4.85 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
90 91 1.534595 GCAGCCTGAGTTTTCTCTGTG 59.465 52.381 0.00 0.00 46.30 3.66
102 103 0.183492 TCTCTGTGCCTTTGCCTGTT 59.817 50.000 0.00 0.00 36.33 3.16
514 517 9.710900 AACTCTCAACATGGAATTTTTAATTCC 57.289 29.630 19.50 19.50 45.89 3.01
1329 3730 1.154205 AAGTCGATATGCACAGCGGC 61.154 55.000 0.00 0.00 0.00 6.53
1911 4430 0.984109 GCGATGAAAATGGTTGTGCG 59.016 50.000 0.00 0.00 0.00 5.34
1913 4432 1.349234 GATGAAAATGGTTGTGCGGC 58.651 50.000 0.00 0.00 0.00 6.53
1914 4433 0.968405 ATGAAAATGGTTGTGCGGCT 59.032 45.000 0.00 0.00 0.00 5.52
1915 4434 0.031857 TGAAAATGGTTGTGCGGCTG 59.968 50.000 0.00 0.00 0.00 4.85
2109 4635 5.941555 TTTAGAGGAAAAGGGCACAAAAA 57.058 34.783 0.00 0.00 0.00 1.94
2148 4674 1.334869 AGCAAAGAAAACCAGCGTCTG 59.665 47.619 0.52 0.52 0.00 3.51
2186 4712 2.202756 GCGGAGGACAGCTAACCG 60.203 66.667 0.00 0.00 45.26 4.44
2233 4759 7.713073 AGAAGAAAACACAAAGAAAACCAAACA 59.287 29.630 0.00 0.00 0.00 2.83
2294 4820 5.186198 AGGTTCCTAAACATGCTGATACAC 58.814 41.667 0.00 0.00 37.10 2.90
2402 4928 2.740055 CAGCTCCCACTGCGTCAC 60.740 66.667 0.00 0.00 35.28 3.67
2758 5284 6.688073 TGATCTCTCCTCTAAAACCAGTTT 57.312 37.500 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 3.006217 AGAATTGAGAAACAGGCAAAGGC 59.994 43.478 0.00 0.00 40.13 4.35
241 244 1.406341 GGGTGATGGTTACTAGCGCAA 60.406 52.381 11.47 0.00 0.00 4.85
242 245 0.177141 GGGTGATGGTTACTAGCGCA 59.823 55.000 11.47 0.00 0.00 6.09
243 246 0.464452 AGGGTGATGGTTACTAGCGC 59.536 55.000 0.00 0.00 0.00 5.92
514 517 5.033507 TCAATGTGTGACATGAAAAACACG 58.966 37.500 0.00 0.00 44.62 4.49
686 3087 6.483640 ACAGAAGTTGAACTGAGAAATACCAC 59.516 38.462 0.00 0.00 37.54 4.16
722 3123 7.446106 TTTTTATCTGGCTAGGACCATAGAA 57.554 36.000 0.00 0.00 39.54 2.10
753 3154 7.275999 GCCTTCACTAACTCAACAATAGAGTAC 59.724 40.741 0.00 0.00 45.11 2.73
982 3383 7.365741 AGAAACATCAAAGTGCTAACAATCAG 58.634 34.615 0.00 0.00 0.00 2.90
1329 3730 4.811024 ACATATCTATGGTTGAACGTGCAG 59.189 41.667 0.00 0.00 38.00 4.41
1453 3972 3.463048 AAGCATCCCAAACCTCAGATT 57.537 42.857 0.00 0.00 0.00 2.40
1911 4430 3.068165 GTGGATAAATAACAAGCCCAGCC 59.932 47.826 0.00 0.00 0.00 4.85
1913 4432 5.066505 GTCAGTGGATAAATAACAAGCCCAG 59.933 44.000 0.00 0.00 0.00 4.45
1914 4433 4.947388 GTCAGTGGATAAATAACAAGCCCA 59.053 41.667 0.00 0.00 0.00 5.36
1915 4434 4.947388 TGTCAGTGGATAAATAACAAGCCC 59.053 41.667 0.00 0.00 0.00 5.19
2109 4635 0.630673 TATGCAAATGGAGCTGGGGT 59.369 50.000 0.00 0.00 0.00 4.95
2148 4674 2.095853 CGTGCTGGAATTGGTGTATGTC 59.904 50.000 0.00 0.00 0.00 3.06
2233 4759 0.251474 ACCCATGCATGCAGACTGTT 60.251 50.000 26.69 4.78 0.00 3.16
2294 4820 1.871772 CTCGCCTTTCTGCCACTTG 59.128 57.895 0.00 0.00 0.00 3.16
2362 4888 0.396435 TTTGCTGGAGACGTCCACAT 59.604 50.000 13.01 0.00 46.77 3.21
2437 4963 2.434331 CCGGACCCAGGCTGAAAA 59.566 61.111 17.94 0.00 0.00 2.29
2758 5284 2.703536 TCTGGAGAACTGTTGCCAAGTA 59.296 45.455 11.46 0.98 0.00 2.24
2791 5317 6.462207 CCACCATCTATTTTTGGTTGTGTTGA 60.462 38.462 0.00 0.00 43.73 3.18


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

AutoCloner maintained by Alex Coulton.