Multiple sequence alignment - TraesCS5D01G275700

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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 TraesCS5D01G275700 chr5D 100.000 2426 0 0 1 2426 378151182 378153607 0.000000e+00 4481.0
1 TraesCS5D01G275700 chr5B 97.789 2397 44 5 34 2426 451532131 451529740 0.000000e+00 4124.0
2 TraesCS5D01G275700 chr5B 94.155 787 45 1 1 787 642595492 642594707 0.000000e+00 1197.0
3 TraesCS5D01G275700 chr5B 98.219 393 5 1 2036 2426 453235857 453236249 0.000000e+00 686.0
4 TraesCS5D01G275700 chr5B 80.441 680 80 27 886 1531 453673871 453673211 1.020000e-128 470.0
5 TraesCS5D01G275700 chr5B 79.643 560 78 15 887 1436 453723512 453722979 1.060000e-98 370.0
6 TraesCS5D01G275700 chr5B 94.444 108 5 1 1884 1991 453235744 453235850 5.370000e-37 165.0
7 TraesCS5D01G275700 chr7B 94.670 788 40 2 1 788 407386998 407387783 0.000000e+00 1221.0
8 TraesCS5D01G275700 chr2B 94.451 793 40 4 1 793 310898308 310899096 0.000000e+00 1218.0
9 TraesCS5D01G275700 chr1B 94.354 797 40 4 1 797 57111110 57110319 0.000000e+00 1218.0
10 TraesCS5D01G275700 chr2A 94.409 787 41 3 1 787 348050488 348051271 0.000000e+00 1206.0
11 TraesCS5D01G275700 chr2A 94.409 787 40 4 1 786 550182333 550183116 0.000000e+00 1206.0
12 TraesCS5D01G275700 chr1D 94.066 792 43 4 1 791 142663438 142664226 0.000000e+00 1199.0
13 TraesCS5D01G275700 chr6A 93.893 786 44 4 1 786 155746807 155746026 0.000000e+00 1182.0
14 TraesCS5D01G275700 chr5A 85.881 772 80 16 786 1531 478892602 478893370 0.000000e+00 795.0
15 TraesCS5D01G275700 chr5A 84.194 639 76 16 821 1444 478895111 478895739 4.460000e-167 597.0
16 TraesCS5D01G275700 chr5A 80.832 673 77 27 886 1532 478858982 478859628 4.690000e-132 481.0
17 TraesCS5D01G275700 chrUn 82.857 560 68 11 886 1429 171237422 171237969 6.070000e-131 477.0
18 TraesCS5D01G275700 chrUn 82.373 573 71 13 886 1440 67042055 67041495 2.820000e-129 472.0
19 TraesCS5D01G275700 chrUn 84.532 459 54 5 987 1440 342519087 342518641 2.860000e-119 438.0
20 TraesCS5D01G275700 chr3A 96.774 31 1 0 1997 2027 605239743 605239713 4.000000e-03 52.8


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 TraesCS5D01G275700 chr5D 378151182 378153607 2425 False 4481.0 4481 100.0000 1 2426 1 chr5D.!!$F1 2425
1 TraesCS5D01G275700 chr5B 451529740 451532131 2391 True 4124.0 4124 97.7890 34 2426 1 chr5B.!!$R1 2392
2 TraesCS5D01G275700 chr5B 642594707 642595492 785 True 1197.0 1197 94.1550 1 787 1 chr5B.!!$R4 786
3 TraesCS5D01G275700 chr5B 453673211 453673871 660 True 470.0 470 80.4410 886 1531 1 chr5B.!!$R2 645
4 TraesCS5D01G275700 chr5B 453235744 453236249 505 False 425.5 686 96.3315 1884 2426 2 chr5B.!!$F1 542
5 TraesCS5D01G275700 chr5B 453722979 453723512 533 True 370.0 370 79.6430 887 1436 1 chr5B.!!$R3 549
6 TraesCS5D01G275700 chr7B 407386998 407387783 785 False 1221.0 1221 94.6700 1 788 1 chr7B.!!$F1 787
7 TraesCS5D01G275700 chr2B 310898308 310899096 788 False 1218.0 1218 94.4510 1 793 1 chr2B.!!$F1 792
8 TraesCS5D01G275700 chr1B 57110319 57111110 791 True 1218.0 1218 94.3540 1 797 1 chr1B.!!$R1 796
9 TraesCS5D01G275700 chr2A 348050488 348051271 783 False 1206.0 1206 94.4090 1 787 1 chr2A.!!$F1 786
10 TraesCS5D01G275700 chr2A 550182333 550183116 783 False 1206.0 1206 94.4090 1 786 1 chr2A.!!$F2 785
11 TraesCS5D01G275700 chr1D 142663438 142664226 788 False 1199.0 1199 94.0660 1 791 1 chr1D.!!$F1 790
12 TraesCS5D01G275700 chr6A 155746026 155746807 781 True 1182.0 1182 93.8930 1 786 1 chr6A.!!$R1 785
13 TraesCS5D01G275700 chr5A 478892602 478895739 3137 False 696.0 795 85.0375 786 1531 2 chr5A.!!$F2 745
14 TraesCS5D01G275700 chr5A 478858982 478859628 646 False 481.0 481 80.8320 886 1532 1 chr5A.!!$F1 646
15 TraesCS5D01G275700 chrUn 171237422 171237969 547 False 477.0 477 82.8570 886 1429 1 chrUn.!!$F1 543
16 TraesCS5D01G275700 chrUn 67041495 67042055 560 True 472.0 472 82.3730 886 1440 1 chrUn.!!$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
409 410 0.326264 ACTGGAGGATTGACTGGTGC 59.674 55.0 0.0 0.0 0.0 5.01 F
742 744 5.657302 ACCTCTTCTTATGGACGATGTAACT 59.343 40.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1255 0.033503 TCGGTGGCATAGGAGACAGA 60.034 55.000 0.0 0.0 0.0 3.41 R
1828 2295 1.691434 CTTAGCACCTCCCTCTGATCC 59.309 57.143 0.0 0.0 0.0 3.36 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
25 26 6.205464 CCATAAAGTCTGTGTTGTTGATCACT 59.795 38.462 0.00 0.0 35.82 3.41
26 27 5.490139 AAAGTCTGTGTTGTTGATCACTG 57.510 39.130 0.00 0.0 35.82 3.66
27 28 4.406648 AGTCTGTGTTGTTGATCACTGA 57.593 40.909 0.00 0.0 39.12 3.41
219 220 0.577269 GCTCGTGCTATAACGGCAAG 59.423 55.000 1.41 0.0 43.73 4.01
409 410 0.326264 ACTGGAGGATTGACTGGTGC 59.674 55.000 0.00 0.0 0.00 5.01
529 531 6.994496 ACATGGAAGTGATCGACATAATGAAT 59.006 34.615 0.00 0.0 0.00 2.57
742 744 5.657302 ACCTCTTCTTATGGACGATGTAACT 59.343 40.000 0.00 0.0 0.00 2.24
1219 1255 4.070716 CACCTTCAAGAAGATCAAGCAGT 58.929 43.478 11.25 0.0 40.79 4.40
1254 1290 1.084370 CCGAGGTGACCGCTTTCATC 61.084 60.000 3.39 0.0 0.00 2.92
1485 1541 4.503007 CGGCACTATGTTCACATGTAGTAC 59.497 45.833 0.00 0.0 37.15 2.73
1722 1987 4.668289 AGGTAAAAGTTGTTTGAGCGTTG 58.332 39.130 0.00 0.0 30.69 4.10
1763 2187 9.326413 AGGATAGGTTTCAGATAACATAAAACG 57.674 33.333 0.00 0.0 32.06 3.60
1828 2295 7.920151 TGCCGAAATTTGGAAGTTGATAATATG 59.080 33.333 2.82 0.0 0.00 1.78
2019 2486 9.783256 ATTCCTTTGTAAACAAATATAAGACGC 57.217 29.630 8.62 0.0 43.92 5.19
2127 2911 7.912250 CAGATAATTCCTTGAATTTCAGGTTCG 59.088 37.037 7.31 0.0 41.64 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.494924 CCCTCAGTGATCAACAACACAGA 60.495 47.826 0.00 0.00 39.18 3.41
25 26 3.296842 TAGCACCGCCTCTCCCTCA 62.297 63.158 0.00 0.00 0.00 3.86
26 27 2.442272 TAGCACCGCCTCTCCCTC 60.442 66.667 0.00 0.00 0.00 4.30
27 28 2.443016 CTAGCACCGCCTCTCCCT 60.443 66.667 0.00 0.00 0.00 4.20
219 220 3.077359 GGGGAGTATGCATTGACATAGC 58.923 50.000 3.54 0.00 33.27 2.97
436 437 8.687242 GCTAGGAATAAACCAAATTTAAGAGCT 58.313 33.333 0.00 0.00 36.35 4.09
529 531 1.672854 CCGCCGAGTGTCCTCCATTA 61.673 60.000 0.00 0.00 33.93 1.90
628 630 1.354031 TGGGCCACTCTATTTGCTTCA 59.646 47.619 0.00 0.00 0.00 3.02
782 784 7.873505 AGTCCACAATAGAACACTAGAGTTTTC 59.126 37.037 7.01 1.11 35.56 2.29
799 801 5.505181 AATACCACTCTGAAGTCCACAAT 57.495 39.130 0.00 0.00 31.71 2.71
800 802 4.974645 AATACCACTCTGAAGTCCACAA 57.025 40.909 0.00 0.00 31.71 3.33
825 827 9.277783 CTTCTTTCAGATACTTCTTTTTCTGGA 57.722 33.333 0.00 0.00 36.95 3.86
826 828 9.277783 TCTTCTTTCAGATACTTCTTTTTCTGG 57.722 33.333 0.00 0.00 36.95 3.86
1219 1255 0.033503 TCGGTGGCATAGGAGACAGA 60.034 55.000 0.00 0.00 0.00 3.41
1254 1290 3.873952 CCTTCTTTATCTTGCCCTTCTCG 59.126 47.826 0.00 0.00 0.00 4.04
1485 1541 5.744490 AGATTACAAGAAAACGGAAACACG 58.256 37.500 0.00 0.00 40.31 4.49
1722 1987 8.457238 AAACCTATCCTTTAGAGATGAAATGC 57.543 34.615 0.00 0.00 0.00 3.56
1763 2187 3.679980 TCGTAGCATGAGAAGTTCTTTGC 59.320 43.478 23.87 23.87 36.66 3.68
1828 2295 1.691434 CTTAGCACCTCCCTCTGATCC 59.309 57.143 0.00 0.00 0.00 3.36
1876 2343 4.099419 CCAAAGCTTTTGTACTCCCTTTGT 59.901 41.667 9.53 0.00 38.15 2.83
1877 2344 4.340950 TCCAAAGCTTTTGTACTCCCTTTG 59.659 41.667 9.53 13.25 39.02 2.77
1878 2345 4.542697 TCCAAAGCTTTTGTACTCCCTTT 58.457 39.130 9.53 0.00 0.00 3.11
2127 2911 3.010420 GGAGAGGTGTTGTTAAGGATGC 58.990 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.