Multiple sequence alignment - TraesCS4A01G477200

Loading Multiple Alignment...

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 TraesCS4A01G477200 chr4A 100.000 4608 0 0 1 4608 735300112 735295505 0 8510
1 TraesCS4A01G477200 chr5B 98.873 4615 34 5 9 4606 436483934 436479321 0 8218
2 TraesCS4A01G477200 chr5B 98.424 4252 36 7 384 4606 281825796 281830045 0 7452
3 TraesCS4A01G477200 chr1B 98.658 4620 44 5 3 4606 302765053 302769670 0 8172
4 TraesCS4A01G477200 chr1B 97.531 3888 61 7 747 4606 649294691 649298571 0 6615
5 TraesCS4A01G477200 chr3A 98.397 4616 47 7 6 4606 237060124 237055521 0 8089
6 TraesCS4A01G477200 chr3A 98.323 3996 48 5 6 3983 69954989 69950995 0 6990
7 TraesCS4A01G477200 chr2B 98.295 4634 46 9 3 4606 364330656 364335286 0 8089
8 TraesCS4A01G477200 chr2B 98.139 4621 49 9 6 4606 770078141 770082744 0 8022
9 TraesCS4A01G477200 chr4B 98.246 4619 38 7 6 4606 655798251 655793658 0 8041
10 TraesCS4A01G477200 chr4B 97.076 1402 30 10 6 1401 649627928 649626532 0 2351
11 TraesCS4A01G477200 chr7A 97.692 4637 56 9 3 4606 16012315 16007697 0 7923
12 TraesCS4A01G477200 chr7A 97.557 3888 60 7 747 4606 497712883 497716763 0 6621
13 TraesCS4A01G477200 chr7A 98.208 2065 21 3 2555 4606 121917472 121919533 0 3594
14 TraesCS4A01G477200 chr2A 97.648 4635 59 16 6 4606 148608101 148612719 0 7910
15 TraesCS4A01G477200 chr3B 97.264 4641 52 15 6 4606 798605217 798609822 0 7797
16 TraesCS4A01G477200 chr6A 97.655 4264 50 9 377 4606 466685838 466681591 0 7275
17 TraesCS4A01G477200 chr7B 98.651 3557 30 8 5 3545 133423914 133427468 0 6287
18 TraesCS4A01G477200 chrUn 97.750 1600 11 2 2886 4484 387866504 387868079 0 2732


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 TraesCS4A01G477200 chr4A 735295505 735300112 4607 True 8510 8510 100.000 1 4608 1 chr4A.!!$R1 4607
1 TraesCS4A01G477200 chr5B 436479321 436483934 4613 True 8218 8218 98.873 9 4606 1 chr5B.!!$R1 4597
2 TraesCS4A01G477200 chr5B 281825796 281830045 4249 False 7452 7452 98.424 384 4606 1 chr5B.!!$F1 4222
3 TraesCS4A01G477200 chr1B 302765053 302769670 4617 False 8172 8172 98.658 3 4606 1 chr1B.!!$F1 4603
4 TraesCS4A01G477200 chr1B 649294691 649298571 3880 False 6615 6615 97.531 747 4606 1 chr1B.!!$F2 3859
5 TraesCS4A01G477200 chr3A 237055521 237060124 4603 True 8089 8089 98.397 6 4606 1 chr3A.!!$R2 4600
6 TraesCS4A01G477200 chr3A 69950995 69954989 3994 True 6990 6990 98.323 6 3983 1 chr3A.!!$R1 3977
7 TraesCS4A01G477200 chr2B 364330656 364335286 4630 False 8089 8089 98.295 3 4606 1 chr2B.!!$F1 4603
8 TraesCS4A01G477200 chr2B 770078141 770082744 4603 False 8022 8022 98.139 6 4606 1 chr2B.!!$F2 4600
9 TraesCS4A01G477200 chr4B 655793658 655798251 4593 True 8041 8041 98.246 6 4606 1 chr4B.!!$R2 4600
10 TraesCS4A01G477200 chr4B 649626532 649627928 1396 True 2351 2351 97.076 6 1401 1 chr4B.!!$R1 1395
11 TraesCS4A01G477200 chr7A 16007697 16012315 4618 True 7923 7923 97.692 3 4606 1 chr7A.!!$R1 4603
12 TraesCS4A01G477200 chr7A 497712883 497716763 3880 False 6621 6621 97.557 747 4606 1 chr7A.!!$F2 3859
13 TraesCS4A01G477200 chr7A 121917472 121919533 2061 False 3594 3594 98.208 2555 4606 1 chr7A.!!$F1 2051
14 TraesCS4A01G477200 chr2A 148608101 148612719 4618 False 7910 7910 97.648 6 4606 1 chr2A.!!$F1 4600
15 TraesCS4A01G477200 chr3B 798605217 798609822 4605 False 7797 7797 97.264 6 4606 1 chr3B.!!$F1 4600
16 TraesCS4A01G477200 chr6A 466681591 466685838 4247 True 7275 7275 97.655 377 4606 1 chr6A.!!$R1 4229
17 TraesCS4A01G477200 chr7B 133423914 133427468 3554 False 6287 6287 98.651 5 3545 1 chr7B.!!$F1 3540
18 TraesCS4A01G477200 chrUn 387866504 387868079 1575 False 2732 2732 97.750 2886 4484 1 chrUn.!!$F1 1598

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
196 198 1.287815 CCGTTGACCTGCTGACGTA 59.712 57.895 0.0 0.00 33.95 3.57 F
392 397 2.611518 CTCAAACTCACAGATCGGACC 58.388 52.381 0.0 0.00 0.00 4.46 F
1970 2013 1.753903 TTGAAGAACCCCCTCATGGA 58.246 50.000 0.0 0.00 35.39 3.41 F
2729 2772 1.353358 TGTCTGAAGACCCGGAGACTA 59.647 52.381 16.9 4.29 44.15 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1933 2.618045 CGGATAGGCTCCAAACAAACCT 60.618 50.000 0.0 0.0 45.24 3.50 R
2222 2265 5.505181 AGTCACAATCTTCCACATAAGGT 57.495 39.130 0.0 0.0 0.00 3.50 R
2913 2956 1.233950 TTGGCATCGTTGACGCACAT 61.234 50.000 0.0 0.0 39.60 3.21 R
3865 4052 2.759973 CTGGCGTCTGGCTCCCTA 60.760 66.667 0.0 0.0 42.94 3.53 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
196 198 1.287815 CCGTTGACCTGCTGACGTA 59.712 57.895 0.00 0.00 33.95 3.57
392 397 2.611518 CTCAAACTCACAGATCGGACC 58.388 52.381 0.00 0.00 0.00 4.46
619 628 8.952278 GTTTTGTGTATATGTTGTCCATAGGAA 58.048 33.333 0.00 0.00 39.36 3.36
1970 2013 1.753903 TTGAAGAACCCCCTCATGGA 58.246 50.000 0.00 0.00 35.39 3.41
2219 2262 5.359576 TCTCTTTGTTTTGCAGGTACATTGT 59.640 36.000 0.00 0.00 0.00 2.71
2222 2265 7.548097 TCTTTGTTTTGCAGGTACATTGTTTA 58.452 30.769 0.00 0.00 0.00 2.01
2238 2281 8.650143 ACATTGTTTACCTTATGTGGAAGATT 57.350 30.769 0.00 0.00 30.51 2.40
2729 2772 1.353358 TGTCTGAAGACCCGGAGACTA 59.647 52.381 16.90 4.29 44.15 2.59
2913 2956 0.036010 GCAGGGCAGAGAGTTGCTTA 60.036 55.000 0.00 0.00 43.57 3.09
3478 3521 3.900971 TCCTCATCAATTTATGCCTGCA 58.099 40.909 0.00 0.00 0.00 4.41
3576 3667 3.107402 AGAGGAGGAGCATACACTTGA 57.893 47.619 0.00 0.00 0.00 3.02
3932 4125 1.987855 CCAGACGCCAGGGTCCTTA 60.988 63.158 10.87 0.00 37.66 2.69
4052 4245 1.077805 TCCTTGGCGTCTGGTCCTA 59.922 57.895 0.00 0.00 0.00 2.94
4338 4547 7.264947 ACGACATGAACATCACATATAACTCA 58.735 34.615 0.00 0.00 0.00 3.41
4526 4735 8.077991 TGCTTCAACATGAATTTAGTCTTCAAG 58.922 33.333 0.00 0.00 35.59 3.02
4532 4741 8.114331 ACATGAATTTAGTCTTCAAGCAATCA 57.886 30.769 0.00 0.00 36.30 2.57
4606 4815 2.356665 TGAACAACAGGGCTAAGCAA 57.643 45.000 0.00 0.00 0.00 3.91
4607 4816 1.953686 TGAACAACAGGGCTAAGCAAC 59.046 47.619 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.190535 CAGAACAGTAATTTTGTCCCCCG 59.809 47.826 0.00 0.00 0.00 5.73
231 233 0.835276 GTTATCCACTTACCGGGGCT 59.165 55.000 6.32 0.00 0.00 5.19
441 448 3.390175 TCCAACCAAAGAGGGAAAACA 57.610 42.857 0.00 0.00 43.89 2.83
442 449 3.554960 GCATCCAACCAAAGAGGGAAAAC 60.555 47.826 0.00 0.00 43.89 2.43
446 453 0.776810 TGCATCCAACCAAAGAGGGA 59.223 50.000 0.00 0.00 43.89 4.20
1626 1668 6.042897 GGTTAGTACATACCAAAGATAGGCCT 59.957 42.308 11.78 11.78 34.48 5.19
1891 1933 2.618045 CGGATAGGCTCCAAACAAACCT 60.618 50.000 0.00 0.00 45.24 3.50
2219 2262 7.458397 AGTCACAATCTTCCACATAAGGTAAA 58.542 34.615 0.00 0.00 0.00 2.01
2222 2265 5.505181 AGTCACAATCTTCCACATAAGGT 57.495 39.130 0.00 0.00 0.00 3.50
2238 2281 7.148356 GCACATCTCATTAAGATCAAAGTCACA 60.148 37.037 0.00 0.00 43.13 3.58
2913 2956 1.233950 TTGGCATCGTTGACGCACAT 61.234 50.000 0.00 0.00 39.60 3.21
3478 3521 7.047891 TGTTCGACTTATATCTTTGCATTCCT 58.952 34.615 0.00 0.00 0.00 3.36
3554 3621 3.840666 TCAAGTGTATGCTCCTCCTCTTT 59.159 43.478 0.00 0.00 0.00 2.52
3576 3667 5.450453 TCCTTCCTCTCTTCACGATATCTT 58.550 41.667 0.34 0.00 0.00 2.40
3865 4052 2.759973 CTGGCGTCTGGCTCCCTA 60.760 66.667 0.00 0.00 42.94 3.53
4338 4547 3.490348 ACTTGCATTGCTACAGGAAACT 58.510 40.909 10.49 0.00 46.44 2.66
4526 4735 3.288809 GTGGACCTCACTTTTGATTGC 57.711 47.619 0.00 0.00 42.86 3.56


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

AutoCloner maintained by Alex Coulton.