Multiple sequence alignment - TraesCS5D01G538100

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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 TraesCS5D01G538100 chr5D 100.000 4583 0 0 1 4583 550419947 550415365 0.000000e+00 8464
1 TraesCS5D01G538100 chr7D 97.996 4590 76 4 1 4583 4416627 4421207 0.000000e+00 7952
2 TraesCS5D01G538100 chr3B 97.464 4613 75 14 1 4583 768505304 768509904 0.000000e+00 7832
3 TraesCS5D01G538100 chr4A 97.334 4614 80 15 1 4583 481088403 481093004 0.000000e+00 7799
4 TraesCS5D01G538100 chr4A 87.421 3021 286 39 897 3865 90394584 90391606 0.000000e+00 3387
5 TraesCS5D01G538100 chr1A 97.182 4613 84 16 1 4583 146608825 146613421 0.000000e+00 7757
6 TraesCS5D01G538100 chr1A 97.485 3897 56 14 717 4583 482818549 482822433 0.000000e+00 6615
7 TraesCS5D01G538100 chr1A 84.683 2729 360 43 990 3688 555296116 555298816 0.000000e+00 2671
8 TraesCS5D01G538100 chr1A 96.260 722 17 5 1 722 482816851 482817562 0.000000e+00 1175
9 TraesCS5D01G538100 chr5A 97.520 4234 82 6 181 4403 612386598 612382377 0.000000e+00 7215
10 TraesCS5D01G538100 chr5A 99.200 125 1 0 4459 4583 612382376 612382252 4.610000e-55 226
11 TraesCS5D01G538100 chrUn 97.241 2791 43 13 1825 4583 62686915 62689703 0.000000e+00 4697
12 TraesCS5D01G538100 chrUn 97.929 1835 27 3 1 1834 62671821 62673645 0.000000e+00 3168
13 TraesCS5D01G538100 chr3D 88.635 3018 270 39 897 3865 41716731 41719724 0.000000e+00 3605
14 TraesCS5D01G538100 chr4D 88.553 3014 276 36 897 3865 40415643 40412654 0.000000e+00 3591
15 TraesCS5D01G538100 chr4D 80.519 154 22 5 4301 4447 40412377 40412225 1.350000e-20 111
16 TraesCS5D01G538100 chr7A 87.889 3022 292 40 897 3865 727630581 727627581 0.000000e+00 3485
17 TraesCS5D01G538100 chr1D 98.420 1329 19 1 3255 4583 334045201 334043875 0.000000e+00 2337
18 TraesCS5D01G538100 chr1D 97.905 907 19 0 1 907 334046126 334045220 0.000000e+00 1570
19 TraesCS5D01G538100 chr6B 94.225 1091 37 7 3508 4583 279329654 279328575 0.000000e+00 1642
20 TraesCS5D01G538100 chr6B 96.774 868 26 1 1 868 279330524 279329659 0.000000e+00 1447
21 TraesCS5D01G538100 chr6D 95.556 630 25 3 1 627 109881738 109882367 0.000000e+00 1005


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 TraesCS5D01G538100 chr5D 550415365 550419947 4582 True 8464.0 8464 100.0000 1 4583 1 chr5D.!!$R1 4582
1 TraesCS5D01G538100 chr7D 4416627 4421207 4580 False 7952.0 7952 97.9960 1 4583 1 chr7D.!!$F1 4582
2 TraesCS5D01G538100 chr3B 768505304 768509904 4600 False 7832.0 7832 97.4640 1 4583 1 chr3B.!!$F1 4582
3 TraesCS5D01G538100 chr4A 481088403 481093004 4601 False 7799.0 7799 97.3340 1 4583 1 chr4A.!!$F1 4582
4 TraesCS5D01G538100 chr4A 90391606 90394584 2978 True 3387.0 3387 87.4210 897 3865 1 chr4A.!!$R1 2968
5 TraesCS5D01G538100 chr1A 146608825 146613421 4596 False 7757.0 7757 97.1820 1 4583 1 chr1A.!!$F1 4582
6 TraesCS5D01G538100 chr1A 482816851 482822433 5582 False 3895.0 6615 96.8725 1 4583 2 chr1A.!!$F3 4582
7 TraesCS5D01G538100 chr1A 555296116 555298816 2700 False 2671.0 2671 84.6830 990 3688 1 chr1A.!!$F2 2698
8 TraesCS5D01G538100 chr5A 612382252 612386598 4346 True 3720.5 7215 98.3600 181 4583 2 chr5A.!!$R1 4402
9 TraesCS5D01G538100 chrUn 62686915 62689703 2788 False 4697.0 4697 97.2410 1825 4583 1 chrUn.!!$F2 2758
10 TraesCS5D01G538100 chrUn 62671821 62673645 1824 False 3168.0 3168 97.9290 1 1834 1 chrUn.!!$F1 1833
11 TraesCS5D01G538100 chr3D 41716731 41719724 2993 False 3605.0 3605 88.6350 897 3865 1 chr3D.!!$F1 2968
12 TraesCS5D01G538100 chr4D 40412225 40415643 3418 True 1851.0 3591 84.5360 897 4447 2 chr4D.!!$R1 3550
13 TraesCS5D01G538100 chr7A 727627581 727630581 3000 True 3485.0 3485 87.8890 897 3865 1 chr7A.!!$R1 2968
14 TraesCS5D01G538100 chr1D 334043875 334046126 2251 True 1953.5 2337 98.1625 1 4583 2 chr1D.!!$R1 4582
15 TraesCS5D01G538100 chr6B 279328575 279330524 1949 True 1544.5 1642 95.4995 1 4583 2 chr6B.!!$R1 4582
16 TraesCS5D01G538100 chr6D 109881738 109882367 629 False 1005.0 1005 95.5560 1 627 1 chr6D.!!$F1 626

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
874 1870 2.349060 CCATTTGTGTACAACGACCACG 60.349 50.00 0.00 0.0 45.75 4.94 F
1551 2554 3.765511 AGCAAAGGAAAAGATGCTGCATA 59.234 39.13 16.23 0.0 46.66 3.14 F
3096 4130 0.963962 AAACCTCATGTGCAGGCAAG 59.036 50.00 0.00 0.0 33.84 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2869 3902 6.545666 TGCCATTACATTTTGAGACGGATAAT 59.454 34.615 0.0 0.0 0.00 1.28 R
3417 4451 0.523072 CTTGTGTTTCCCCATGCTCG 59.477 55.000 0.0 0.0 0.00 5.03 R
4057 5150 7.397221 TCTTTCTTTCATGGTCTGTATCATGT 58.603 34.615 0.0 0.0 43.56 3.21 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
143 144 4.458397 CCATCTTCAATAGGACTGCACAT 58.542 43.478 0.00 0.00 0.00 3.21
179 183 7.054491 TCTTGTTATCATCATCATCTTCCGA 57.946 36.000 0.00 0.00 0.00 4.55
189 193 5.225642 TCATCATCTTCCGATCTTCAATCG 58.774 41.667 0.58 0.58 40.86 3.34
874 1870 2.349060 CCATTTGTGTACAACGACCACG 60.349 50.000 0.00 0.00 45.75 4.94
1344 2345 5.072741 TCAGAAGAAATTTGGGAGGAACTG 58.927 41.667 0.00 0.00 41.55 3.16
1551 2554 3.765511 AGCAAAGGAAAAGATGCTGCATA 59.234 39.130 16.23 0.00 46.66 3.14
1622 2625 7.894013 CATGAGATTGATTCTGATGAAAACG 57.106 36.000 0.00 0.00 45.79 3.60
1626 2629 9.551734 TGAGATTGATTCTGATGAAAACGATAT 57.448 29.630 0.00 0.00 35.63 1.63
2868 3901 6.458888 GCAAACTCCTTACAGAAATAGGCATC 60.459 42.308 0.00 0.00 0.00 3.91
2869 3902 5.957771 ACTCCTTACAGAAATAGGCATCA 57.042 39.130 0.00 0.00 0.00 3.07
2970 4003 2.541762 GCATCGGATCAAGCTGTTCTAC 59.458 50.000 0.00 0.00 0.00 2.59
3096 4130 0.963962 AAACCTCATGTGCAGGCAAG 59.036 50.000 0.00 0.00 33.84 4.01
3151 4185 7.450323 ACTCCAAAATTTATTGCCCCATATT 57.550 32.000 0.00 0.00 0.00 1.28
3358 4392 7.117667 CCCAAGTTAAAATTGTTATGGCTTGTC 59.882 37.037 0.00 0.00 31.73 3.18
3417 4451 5.693814 CCTGATGAGTTGTTTGAGCTTTAC 58.306 41.667 0.00 0.00 0.00 2.01
3826 4900 9.135843 TGTTCTTATGTAACATAAGAGTGTTCG 57.864 33.333 18.65 0.00 41.18 3.95
4057 5150 5.992829 TGAAGTATTTTTCTGTCGGCAAGTA 59.007 36.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 3.954258 TGATAACAAGAGCTCGATGGAGA 59.046 43.478 21.57 10.18 43.27 3.71
179 183 2.838736 CCACGAATCCCGATTGAAGAT 58.161 47.619 0.00 0.00 41.76 2.40
189 193 1.749258 GGGTGAAGCCACGAATCCC 60.749 63.158 0.00 0.00 44.09 3.85
279 283 9.013229 AGAATTAATTCAATGAACAGTAGCACA 57.987 29.630 26.02 0.00 39.23 4.57
467 471 6.848451 ACAATATTATTGTGGTTCGGTGTTC 58.152 36.000 18.86 0.00 0.00 3.18
842 1838 4.841813 TGTACACAAATGGGAGTCTAGGAA 59.158 41.667 0.00 0.00 0.00 3.36
1344 2345 7.208080 TCTACTCGCAAATCCTTACCTTAATC 58.792 38.462 0.00 0.00 0.00 1.75
1551 2554 7.692460 TCAATCTGTGAAGATTTGCTTGTAT 57.308 32.000 0.00 0.00 36.48 2.29
1622 2625 4.503714 TGAAGACACCAGGGGAAATATC 57.496 45.455 0.00 0.00 0.00 1.63
1626 2629 2.061848 TCATGAAGACACCAGGGGAAA 58.938 47.619 0.00 0.00 0.00 3.13
1855 2858 9.303116 TCTTTGGGATCTAGATTACTCATACTC 57.697 37.037 6.70 0.00 0.00 2.59
2868 3901 6.857964 GCCATTACATTTTGAGACGGATAATG 59.142 38.462 0.00 0.00 33.55 1.90
2869 3902 6.545666 TGCCATTACATTTTGAGACGGATAAT 59.454 34.615 0.00 0.00 0.00 1.28
2970 4003 1.202533 CCCACTAGTAACAGCCCATCG 60.203 57.143 0.00 0.00 0.00 3.84
3096 4130 7.433425 GCATAGCCTGAATCAACAAGATAAAAC 59.567 37.037 0.00 0.00 35.39 2.43
3245 4279 3.208747 AGGTTCGTTCCACAATGTTCT 57.791 42.857 0.00 0.00 0.00 3.01
3358 4392 4.260907 CCTTATGAAGTTGTGGATGATGCG 60.261 45.833 0.00 0.00 0.00 4.73
3417 4451 0.523072 CTTGTGTTTCCCCATGCTCG 59.477 55.000 0.00 0.00 0.00 5.03
4057 5150 7.397221 TCTTTCTTTCATGGTCTGTATCATGT 58.603 34.615 0.00 0.00 43.56 3.21
4126 5241 9.598517 TGATTTTTCTTTTTGCAAACTCTGTAT 57.401 25.926 12.39 0.65 0.00 2.29


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

AutoCloner maintained by Alex Coulton.