Multiple sequence alignment - TraesCS5D01G327500

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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 TraesCS5D01G327500 chr5D 100.000 4027 0 0 1 4027 420310682 420306656 0.000000e+00 7437
1 TraesCS5D01G327500 chr5D 98.374 2029 22 8 1 2024 30634481 30632459 0.000000e+00 3554
2 TraesCS5D01G327500 chr5D 98.492 1990 21 7 2040 4027 30632474 30630492 0.000000e+00 3500
3 TraesCS5D01G327500 chr7D 98.228 2032 26 8 1 2024 108265487 108263458 0.000000e+00 3544
4 TraesCS5D01G327500 chr7D 98.176 2029 27 9 1 2024 108302407 108300384 0.000000e+00 3533
5 TraesCS5D01G327500 chr7D 97.730 2026 36 9 1 2024 21682204 21680187 0.000000e+00 3478
6 TraesCS5D01G327500 chr7D 98.291 1989 20 8 2040 4027 108300399 108298424 0.000000e+00 3472
7 TraesCS5D01G327500 chr7D 98.241 1990 23 9 2040 4027 108263473 108261494 0.000000e+00 3470
8 TraesCS5D01G327500 chr7D 97.587 1989 27 11 2040 4027 21680202 21678234 0.000000e+00 3387
9 TraesCS5D01G327500 chr1D 98.179 2032 27 8 1 2024 66200714 66198685 0.000000e+00 3539
10 TraesCS5D01G327500 chr1D 98.856 1399 11 3 2040 3438 66198700 66197307 0.000000e+00 2490
11 TraesCS5D01G327500 chr1D 96.918 649 7 4 3379 4027 66197308 66196673 0.000000e+00 1075
12 TraesCS5D01G327500 chr2D 97.734 2030 34 10 1 2024 343143642 343141619 0.000000e+00 3483
13 TraesCS5D01G327500 chr2D 97.841 1992 28 10 2040 4027 343141634 343139654 0.000000e+00 3426
14 TraesCS5D01G327500 chr6A 91.182 1633 95 33 2040 3641 615411471 615409857 0.000000e+00 2172
15 TraesCS5D01G327500 chr6A 94.226 1351 68 10 680 2024 615412802 615411456 0.000000e+00 2054
16 TraesCS5D01G327500 chr6A 91.335 704 38 16 1 689 615413625 615412930 0.000000e+00 941
17 TraesCS5D01G327500 chr6A 93.651 126 8 0 3822 3947 615409750 615409625 5.310000e-44 189
18 TraesCS5D01G327500 chr4B 85.910 2044 185 63 2040 4027 638492315 638490319 0.000000e+00 2084
19 TraesCS5D01G327500 chr4B 86.364 880 101 15 1156 2021 638493177 638492303 0.000000e+00 942
20 TraesCS5D01G327500 chr3A 94.370 1350 68 7 680 2024 735465089 735466435 0.000000e+00 2065
21 TraesCS5D01G327500 chr3A 88.889 1026 85 20 2622 3634 735466937 735467946 0.000000e+00 1236
22 TraesCS5D01G327500 chr3A 92.704 699 29 15 2 689 735464263 735464950 0.000000e+00 989
23 TraesCS5D01G327500 chr3A 94.847 524 20 7 2040 2559 735466420 735466940 0.000000e+00 811
24 TraesCS5D01G327500 chr3A 86.893 206 14 6 3822 4027 735468061 735468253 6.780000e-53 219
25 TraesCS5D01G327500 chr7B 85.581 2039 204 61 2040 4025 712609085 712611086 0.000000e+00 2054
26 TraesCS5D01G327500 chr7B 83.769 1836 191 70 2040 3821 733216676 733214894 0.000000e+00 1640
27 TraesCS5D01G327500 chr7B 86.792 371 43 6 680 1047 712607804 712608171 3.750000e-110 409
28 TraesCS5D01G327500 chr7B 80.594 505 56 23 100 599 712607088 712607555 6.400000e-93 351
29 TraesCS5D01G327500 chr3B 84.229 577 64 16 2040 2594 18006668 18006097 1.650000e-148 536


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 TraesCS5D01G327500 chr5D 420306656 420310682 4026 True 7437.0 7437 100.000000 1 4027 1 chr5D.!!$R1 4026
1 TraesCS5D01G327500 chr5D 30630492 30634481 3989 True 3527.0 3554 98.433000 1 4027 2 chr5D.!!$R2 4026
2 TraesCS5D01G327500 chr7D 108261494 108265487 3993 True 3507.0 3544 98.234500 1 4027 2 chr7D.!!$R2 4026
3 TraesCS5D01G327500 chr7D 108298424 108302407 3983 True 3502.5 3533 98.233500 1 4027 2 chr7D.!!$R3 4026
4 TraesCS5D01G327500 chr7D 21678234 21682204 3970 True 3432.5 3478 97.658500 1 4027 2 chr7D.!!$R1 4026
5 TraesCS5D01G327500 chr1D 66196673 66200714 4041 True 2368.0 3539 97.984333 1 4027 3 chr1D.!!$R1 4026
6 TraesCS5D01G327500 chr2D 343139654 343143642 3988 True 3454.5 3483 97.787500 1 4027 2 chr2D.!!$R1 4026
7 TraesCS5D01G327500 chr6A 615409625 615413625 4000 True 1339.0 2172 92.598500 1 3947 4 chr6A.!!$R1 3946
8 TraesCS5D01G327500 chr4B 638490319 638493177 2858 True 1513.0 2084 86.137000 1156 4027 2 chr4B.!!$R1 2871
9 TraesCS5D01G327500 chr3A 735464263 735468253 3990 False 1064.0 2065 91.540600 2 4027 5 chr3A.!!$F1 4025
10 TraesCS5D01G327500 chr7B 733214894 733216676 1782 True 1640.0 1640 83.769000 2040 3821 1 chr7B.!!$R1 1781
11 TraesCS5D01G327500 chr7B 712607088 712611086 3998 False 938.0 2054 84.322333 100 4025 3 chr7B.!!$F1 3925
12 TraesCS5D01G327500 chr3B 18006097 18006668 571 True 536.0 536 84.229000 2040 2594 1 chr3B.!!$R1 554

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
939 1150 1.028330 CCAGACATCGCCTGTTGCAT 61.028 55.000 0.0 0.0 38.54 3.96 F
2498 2779 2.513753 GGAACACACCATTCCACATCA 58.486 47.619 0.0 0.0 44.42 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2897 3211 0.108186 TGAACTGTCGCTGCATAGGG 60.108 55.000 0.0 0.0 38.16 3.53 R
3451 3845 5.885449 TGGGACATTCCAAATTGTTTTCT 57.115 34.783 0.0 0.0 38.64 2.52 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
149 157 4.979943 TGTTTCAGATCAAAACACTGCA 57.020 36.364 17.57 0.00 40.64 4.41
298 307 2.430481 TGCATGCTTTTGCTGGCAGTA 61.430 47.619 20.33 9.18 45.10 2.74
939 1150 1.028330 CCAGACATCGCCTGTTGCAT 61.028 55.000 0.00 0.00 38.54 3.96
1049 1260 7.472334 AAAGCACAAGAAGGTATCATCATTT 57.528 32.000 0.00 0.00 0.00 2.32
1050 1261 6.690194 AGCACAAGAAGGTATCATCATTTC 57.310 37.500 0.00 0.00 0.00 2.17
1070 1281 8.924691 TCATTTCTTTTGTTATGTTGCTTATGC 58.075 29.630 0.00 0.00 40.20 3.14
2008 2252 7.226441 TCTTCACTACACTAGGTGTAAGTACA 58.774 38.462 10.96 0.00 46.35 2.90
2009 2253 7.720957 TCTTCACTACACTAGGTGTAAGTACAA 59.279 37.037 10.96 7.39 46.35 2.41
2010 2254 7.822161 TCACTACACTAGGTGTAAGTACAAA 57.178 36.000 10.96 0.00 46.35 2.83
2011 2255 7.879070 TCACTACACTAGGTGTAAGTACAAAG 58.121 38.462 10.96 2.75 46.35 2.77
2012 2256 7.720957 TCACTACACTAGGTGTAAGTACAAAGA 59.279 37.037 10.96 4.03 46.35 2.52
2013 2257 8.355169 CACTACACTAGGTGTAAGTACAAAGAA 58.645 37.037 10.96 0.00 46.35 2.52
2014 2258 8.917088 ACTACACTAGGTGTAAGTACAAAGAAA 58.083 33.333 10.96 0.00 46.35 2.52
2015 2259 9.924650 CTACACTAGGTGTAAGTACAAAGAAAT 57.075 33.333 10.96 0.00 46.35 2.17
2017 2261 9.623000 ACACTAGGTGTAAGTACAAAGAAATTT 57.377 29.630 1.18 0.00 45.56 1.82
2019 2263 9.841295 ACTAGGTGTAAGTACAAAGAAATTTCA 57.159 29.630 19.99 0.00 38.04 2.69
2117 2363 6.229936 TGTACAACACTTTACTGGACTTCT 57.770 37.500 0.00 0.00 0.00 2.85
2498 2779 2.513753 GGAACACACCATTCCACATCA 58.486 47.619 0.00 0.00 44.42 3.07
2526 2809 8.868522 ATCAGAGATTTGATGGTTAAAACAGA 57.131 30.769 0.00 0.00 36.48 3.41
2897 3211 0.030235 AAACTTGGGCTTCGCGAAAC 59.970 50.000 23.54 18.55 0.00 2.78
3517 3913 6.215121 TCGAAACATCGGTTTTAGAGTGTTA 58.785 36.000 0.00 0.00 46.84 2.41
3649 4055 7.329471 GCCCTTGTTCTTTTGTTTCTATCATTC 59.671 37.037 0.00 0.00 0.00 2.67
3956 4375 3.070748 GGCACAACAAACAACCAAAACT 58.929 40.909 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 157 7.189512 GCTTCTTGTAATCGCTGACATTATTT 58.810 34.615 0.00 0.00 0.00 1.40
298 307 7.628769 AAAGGCACAAAACAATGAGAAAATT 57.371 28.000 0.00 0.00 0.00 1.82
673 727 3.255149 CACTTCTTGCTCATCCTTGCTTT 59.745 43.478 0.00 0.00 0.00 3.51
920 1131 3.181367 GCAACAGGCGATGTCTGG 58.819 61.111 3.23 0.00 43.00 3.86
939 1150 0.182299 TCCCAAGTGTGTGACATGCA 59.818 50.000 0.00 0.00 0.00 3.96
1049 1260 7.452880 AGAGCATAAGCAACATAACAAAAGA 57.547 32.000 0.00 0.00 45.49 2.52
1050 1261 9.793252 ATAAGAGCATAAGCAACATAACAAAAG 57.207 29.630 0.00 0.00 45.49 2.27
1664 1901 3.573538 CCTGTGTAGCTCTATCTCATGCT 59.426 47.826 0.00 0.00 39.30 3.79
1665 1902 3.305950 CCCTGTGTAGCTCTATCTCATGC 60.306 52.174 0.00 0.00 0.00 4.06
1788 2029 5.003804 ACCAGTATTGTTAGTGAAGGCAAG 58.996 41.667 0.00 0.00 31.43 4.01
2037 2281 9.558396 TTGTGCTTGGATATGAAATTTCTTTTT 57.442 25.926 18.64 4.68 0.00 1.94
2038 2282 8.992073 GTTGTGCTTGGATATGAAATTTCTTTT 58.008 29.630 18.64 8.07 0.00 2.27
2498 2779 7.890127 TGTTTTAACCATCAAATCTCTGATCCT 59.110 33.333 0.00 0.00 33.66 3.24
2897 3211 0.108186 TGAACTGTCGCTGCATAGGG 60.108 55.000 0.00 0.00 38.16 3.53
3191 3522 8.549338 AGAACTAGTTAGTAACCTGAAAATGC 57.451 34.615 8.42 0.00 34.99 3.56
3449 3843 6.657875 TGGGACATTCCAAATTGTTTTCTTT 58.342 32.000 0.00 0.00 38.64 2.52
3450 3844 6.245890 TGGGACATTCCAAATTGTTTTCTT 57.754 33.333 0.00 0.00 38.64 2.52
3451 3845 5.885449 TGGGACATTCCAAATTGTTTTCT 57.115 34.783 0.00 0.00 38.64 2.52
3956 4375 7.271511 ACTGGAAAAATGTAAATGCACTCAAA 58.728 30.769 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.