Multiple sequence alignment - TraesCS4A01G480000

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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 TraesCS4A01G480000 chr4A 100.000 4610 0 0 1 4610 736571006 736575615 0.000000e+00 8514
1 TraesCS4A01G480000 chr4A 98.382 4634 50 8 1 4610 734730929 734735561 0.000000e+00 8118
2 TraesCS4A01G480000 chr4A 84.879 3677 499 43 1 3647 735316582 735320231 0.000000e+00 3657
3 TraesCS4A01G480000 chr4A 84.489 3720 516 35 1 3683 735562438 735558743 0.000000e+00 3616
4 TraesCS4A01G480000 chr4A 84.023 3699 523 48 1 3670 736147558 736151217 0.000000e+00 3494
5 TraesCS4A01G480000 chr4A 83.024 3929 585 54 1 3881 736470427 736466533 0.000000e+00 3485
6 TraesCS4A01G480000 chr4A 83.119 3886 577 51 1 3846 734385450 734389296 0.000000e+00 3469
7 TraesCS4A01G480000 chr4A 83.898 3689 536 45 2 3667 736756597 736760250 0.000000e+00 3469
8 TraesCS4A01G480000 chr4A 83.066 3809 590 45 6 3782 735747411 735751196 0.000000e+00 3410
9 TraesCS4A01G480000 chr4A 82.788 3817 586 51 1 3782 734585410 734589190 0.000000e+00 3343
10 TraesCS4A01G480000 chr4A 82.572 3764 571 54 19 3739 736413010 736409289 0.000000e+00 3238
11 TraesCS4A01G480000 chr4A 82.754 3537 549 47 180 3684 735689506 735693013 0.000000e+00 3096
12 TraesCS4A01G480000 chr4A 81.528 3546 565 60 222 3737 735662557 735659072 0.000000e+00 2837
13 TraesCS4A01G480000 chr4A 86.620 142 19 0 1 142 735662754 735662613 1.720000e-34 158
14 TraesCS4A01G480000 chr7D 96.127 4570 141 15 66 4610 5486535 5481977 0.000000e+00 7426
15 TraesCS4A01G480000 chr7D 83.211 3818 569 55 1 3782 5649114 5645333 0.000000e+00 3434


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 TraesCS4A01G480000 chr4A 736571006 736575615 4609 False 8514.0 8514 100.000 1 4610 1 chr4A.!!$F8 4609
1 TraesCS4A01G480000 chr4A 734730929 734735561 4632 False 8118.0 8118 98.382 1 4610 1 chr4A.!!$F3 4609
2 TraesCS4A01G480000 chr4A 735316582 735320231 3649 False 3657.0 3657 84.879 1 3647 1 chr4A.!!$F4 3646
3 TraesCS4A01G480000 chr4A 735558743 735562438 3695 True 3616.0 3616 84.489 1 3683 1 chr4A.!!$R1 3682
4 TraesCS4A01G480000 chr4A 736147558 736151217 3659 False 3494.0 3494 84.023 1 3670 1 chr4A.!!$F7 3669
5 TraesCS4A01G480000 chr4A 736466533 736470427 3894 True 3485.0 3485 83.024 1 3881 1 chr4A.!!$R3 3880
6 TraesCS4A01G480000 chr4A 734385450 734389296 3846 False 3469.0 3469 83.119 1 3846 1 chr4A.!!$F1 3845
7 TraesCS4A01G480000 chr4A 736756597 736760250 3653 False 3469.0 3469 83.898 2 3667 1 chr4A.!!$F9 3665
8 TraesCS4A01G480000 chr4A 735747411 735751196 3785 False 3410.0 3410 83.066 6 3782 1 chr4A.!!$F6 3776
9 TraesCS4A01G480000 chr4A 734585410 734589190 3780 False 3343.0 3343 82.788 1 3782 1 chr4A.!!$F2 3781
10 TraesCS4A01G480000 chr4A 736409289 736413010 3721 True 3238.0 3238 82.572 19 3739 1 chr4A.!!$R2 3720
11 TraesCS4A01G480000 chr4A 735689506 735693013 3507 False 3096.0 3096 82.754 180 3684 1 chr4A.!!$F5 3504
12 TraesCS4A01G480000 chr4A 735659072 735662754 3682 True 1497.5 2837 84.074 1 3737 2 chr4A.!!$R4 3736
13 TraesCS4A01G480000 chr7D 5481977 5486535 4558 True 7426.0 7426 96.127 66 4610 1 chr7D.!!$R1 4544
14 TraesCS4A01G480000 chr7D 5645333 5649114 3781 True 3434.0 3434 83.211 1 3782 1 chr7D.!!$R2 3781

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
248 255 0.983378 AGAGAGCCCCACCATACCAC 60.983 60.000 0.00 0.0 0.00 4.16 F
1124 1159 7.504924 TTCCAAAAGGTCACAAGTATGTTAG 57.495 36.000 0.00 0.0 37.82 2.34 F
2266 2354 2.187958 ACCTGCAGATGCTACCTTGTA 58.812 47.619 17.39 0.0 42.66 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 1159 3.507622 CCAAAGAAGAACCAACTCATCCC 59.492 47.826 0.0 0.0 0.00 3.85 R
2926 3014 2.547218 GGCATAATGGCAAGCATTCTGG 60.547 50.000 0.0 0.0 43.14 3.86 R
3642 3741 0.251077 AAGGTGGCTGAGGAAAGCTG 60.251 55.000 0.0 0.0 43.06 4.24 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
248 255 0.983378 AGAGAGCCCCACCATACCAC 60.983 60.000 0.00 0.00 0.00 4.16
1124 1159 7.504924 TTCCAAAAGGTCACAAGTATGTTAG 57.495 36.000 0.00 0.00 37.82 2.34
2266 2354 2.187958 ACCTGCAGATGCTACCTTGTA 58.812 47.619 17.39 0.00 42.66 2.41
2688 2776 8.803201 TCACTCTTTCTTCATGCTATATTACG 57.197 34.615 0.00 0.00 0.00 3.18
2926 3014 4.207891 TCTTTAGAGTTGGCAGATGGAC 57.792 45.455 0.00 0.00 0.00 4.02
3094 3182 3.056821 CACCTCCGTTGAATCACTCTACA 60.057 47.826 0.00 0.00 30.94 2.74
3680 3779 6.204301 CCACCTTTGCACTCTCAATAGATATG 59.796 42.308 0.00 0.00 0.00 1.78
3898 4007 1.280421 GTGCTGATTGGTCCTCCTTCT 59.720 52.381 0.00 0.00 34.23 2.85
3955 4064 4.161754 GGCCTTAAGAGTTGGAAGCTACTA 59.838 45.833 3.36 0.00 0.00 1.82
4052 4161 6.543831 GCACTTTAATGTATTCATCCTCCAGT 59.456 38.462 0.00 0.00 32.56 4.00
4178 4287 2.677037 GCAAGTAGCGGTACCATGACTT 60.677 50.000 24.18 13.71 0.00 3.01
4179 4288 2.930040 CAAGTAGCGGTACCATGACTTG 59.070 50.000 24.32 24.32 38.23 3.16
4180 4289 1.134788 AGTAGCGGTACCATGACTTGC 60.135 52.381 20.54 5.09 0.00 4.01
4181 4290 1.134788 GTAGCGGTACCATGACTTGCT 60.135 52.381 13.80 12.67 35.89 3.91
4182 4291 0.108138 AGCGGTACCATGACTTGCTC 60.108 55.000 13.54 0.00 0.00 4.26
4183 4292 1.421410 GCGGTACCATGACTTGCTCG 61.421 60.000 13.54 0.00 0.00 5.03
4421 4552 3.812609 TGGCTAAGTTGTGTGTATGTGTG 59.187 43.478 0.00 0.00 0.00 3.82
4425 4556 4.614555 AAGTTGTGTGTATGTGTGTGTG 57.385 40.909 0.00 0.00 0.00 3.82
4427 4558 3.373748 AGTTGTGTGTATGTGTGTGTGTG 59.626 43.478 0.00 0.00 0.00 3.82
4455 4586 3.007506 TCAAGAGAAAAGGCATACGACCA 59.992 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 255 1.815003 GGCCTCAAGAACATCAACTGG 59.185 52.381 0.00 0.00 0.00 4.00
1124 1159 3.507622 CCAAAGAAGAACCAACTCATCCC 59.492 47.826 0.00 0.00 0.00 3.85
2926 3014 2.547218 GGCATAATGGCAAGCATTCTGG 60.547 50.000 0.00 0.00 43.14 3.86
3094 3182 8.870116 TGTACATAGATCTGGCAAGTAATACAT 58.130 33.333 5.18 0.00 0.00 2.29
3642 3741 0.251077 AAGGTGGCTGAGGAAAGCTG 60.251 55.000 0.00 0.00 43.06 4.24
3886 3995 1.065410 TGGCCAAAGAAGGAGGACCA 61.065 55.000 0.61 0.00 38.94 4.02
3955 4064 2.629617 GCATAATTACCAGCCTTGCCAT 59.370 45.455 0.00 0.00 0.00 4.40
4052 4161 9.555727 AGAAAACAGCTAAACAACAGTTATCTA 57.444 29.630 0.00 0.00 0.00 1.98
4104 4213 1.268539 CCAGCAAAACAGAACACGGAC 60.269 52.381 0.00 0.00 0.00 4.79
4111 4220 1.953686 GGTAGCACCAGCAAAACAGAA 59.046 47.619 1.01 0.00 45.49 3.02
4239 4370 4.104383 ACAAACTCTGGGATGACAACAT 57.896 40.909 0.00 0.00 39.67 2.71
4241 4372 4.084013 CGTAACAAACTCTGGGATGACAAC 60.084 45.833 0.00 0.00 0.00 3.32
4421 4552 6.030228 CCTTTTCTCTTGAGAAAACACACAC 58.970 40.000 25.59 0.00 41.24 3.82
4425 4556 5.248870 TGCCTTTTCTCTTGAGAAAACAC 57.751 39.130 25.59 21.15 41.24 3.32
4427 4558 6.073222 TCGTATGCCTTTTCTCTTGAGAAAAC 60.073 38.462 25.59 19.61 41.24 2.43
4502 4633 1.202746 GGCAGGCTCCATTTCTCCTAG 60.203 57.143 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.