Multiple sequence alignment - TraesCS6A01G361300

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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 TraesCS6A01G361300 chr6A 100.000 4267 0 0 1 4267 591833233 591837499 0 7880
1 TraesCS6A01G361300 chr6A 98.878 4278 37 8 1 4267 87933837 87938114 0 7624
2 TraesCS6A01G361300 chr6A 98.876 4270 35 5 1 4267 570883178 570887437 0 7607
3 TraesCS6A01G361300 chr6A 98.645 4281 40 14 1 4267 480630564 480634840 0 7568
4 TraesCS6A01G361300 chr6A 100.000 2511 0 0 4699 7209 591837931 591840441 0 4638
5 TraesCS6A01G361300 chr6A 98.686 2511 33 0 4699 7209 12696421 12693911 0 4455
6 TraesCS6A01G361300 chr6A 98.447 2512 38 1 4699 7209 480634841 480637352 0 4421
7 TraesCS6A01G361300 chr7A 99.134 4273 30 5 1 4267 624766395 624762124 0 7679
8 TraesCS6A01G361300 chr7A 98.666 4273 48 7 1 4267 634123097 634127366 0 7566
9 TraesCS6A01G361300 chr7A 98.726 2511 31 1 4699 7209 624762120 624759611 0 4458
10 TraesCS6A01G361300 chr1B 98.970 4270 35 5 1 4267 637607134 637611397 0 7633
11 TraesCS6A01G361300 chr1B 98.448 2513 37 2 4699 7209 637611398 637613910 0 4423
12 TraesCS6A01G361300 chr7B 98.877 4276 38 7 1 4267 666533823 666529549 0 7622
13 TraesCS6A01G361300 chr7B 98.575 4280 46 13 1 4267 194120439 194124716 0 7552
14 TraesCS6A01G361300 chr7B 98.288 2511 41 2 4699 7209 194124714 194127222 0 4397
15 TraesCS6A01G361300 chr5A 98.900 4272 37 7 1 4264 396395848 396400117 0 7620
16 TraesCS6A01G361300 chr6B 98.726 2511 32 0 4699 7209 21367525 21365015 0 4460
17 TraesCS6A01G361300 chr2B 98.368 2512 40 1 4699 7209 99562386 99564897 0 4410
18 TraesCS6A01G361300 chr2A 98.169 2512 45 1 4699 7209 687275263 687272752 0 4383
19 TraesCS6A01G361300 chr4B 98.131 2515 43 3 4699 7209 14714822 14712308 0 4381


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 TraesCS6A01G361300 chr6A 591833233 591840441 7208 False 6259.0 7880 100.0000 1 7209 2 chr6A.!!$F4 7208
1 TraesCS6A01G361300 chr6A 87933837 87938114 4277 False 7624.0 7624 98.8780 1 4267 1 chr6A.!!$F1 4266
2 TraesCS6A01G361300 chr6A 570883178 570887437 4259 False 7607.0 7607 98.8760 1 4267 1 chr6A.!!$F2 4266
3 TraesCS6A01G361300 chr6A 480630564 480637352 6788 False 5994.5 7568 98.5460 1 7209 2 chr6A.!!$F3 7208
4 TraesCS6A01G361300 chr6A 12693911 12696421 2510 True 4455.0 4455 98.6860 4699 7209 1 chr6A.!!$R1 2510
5 TraesCS6A01G361300 chr7A 634123097 634127366 4269 False 7566.0 7566 98.6660 1 4267 1 chr7A.!!$F1 4266
6 TraesCS6A01G361300 chr7A 624759611 624766395 6784 True 6068.5 7679 98.9300 1 7209 2 chr7A.!!$R1 7208
7 TraesCS6A01G361300 chr1B 637607134 637613910 6776 False 6028.0 7633 98.7090 1 7209 2 chr1B.!!$F1 7208
8 TraesCS6A01G361300 chr7B 666529549 666533823 4274 True 7622.0 7622 98.8770 1 4267 1 chr7B.!!$R1 4266
9 TraesCS6A01G361300 chr7B 194120439 194127222 6783 False 5974.5 7552 98.4315 1 7209 2 chr7B.!!$F1 7208
10 TraesCS6A01G361300 chr5A 396395848 396400117 4269 False 7620.0 7620 98.9000 1 4264 1 chr5A.!!$F1 4263
11 TraesCS6A01G361300 chr6B 21365015 21367525 2510 True 4460.0 4460 98.7260 4699 7209 1 chr6B.!!$R1 2510
12 TraesCS6A01G361300 chr2B 99562386 99564897 2511 False 4410.0 4410 98.3680 4699 7209 1 chr2B.!!$F1 2510
13 TraesCS6A01G361300 chr2A 687272752 687275263 2511 True 4383.0 4383 98.1690 4699 7209 1 chr2A.!!$R1 2510
14 TraesCS6A01G361300 chr4B 14712308 14714822 2514 True 4381.0 4381 98.1310 4699 7209 1 chr4B.!!$R1 2510

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
664 672 5.799936 CCCTTGATTTGTGCAAATTAGTACG 59.200 40.000 10.94 0.0 40.77 3.67 F
1642 1675 5.835257 AGTTGACATCAGTGGTCATTTTTG 58.165 37.500 3.45 0.0 44.11 2.44 F
2142 2179 2.952978 CGCCTCTCTAACTCCACTACAT 59.047 50.000 0.00 0.0 0.00 2.29 F
2945 2984 4.096532 TGTGTTCGGCAAATTACAAGTGAA 59.903 37.500 0.00 0.0 0.00 3.18 F
3927 3975 2.025981 TGGTCAATGAGCTATGCAAGGT 60.026 45.455 13.84 0.0 39.11 3.50 F
5735 5790 0.035534 AGAGACGAGAGAGAGCTGCA 60.036 55.000 1.02 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2179 5.448768 CGACCTCGAAACTAGCTCTGATTTA 60.449 44.000 0.0 0.0 43.02 1.40 R
2495 2532 5.801531 TGGTGCTAGAAAAGTACTGAAGA 57.198 39.130 0.0 0.0 40.41 2.87 R
3927 3975 2.685897 GTGCCAACCTGTTCAGTTACAA 59.314 45.455 0.0 0.0 0.00 2.41 R
4831 4885 1.141657 TGCTGCACCTTTGTCTTCTCT 59.858 47.619 0.0 0.0 0.00 3.10 R
5873 5928 1.150536 GTGGTGCCTTCCTGACCAA 59.849 57.895 0.0 0.0 41.43 3.67 R
6750 6807 1.301716 GCTCGAAGGGTCACAGCAA 60.302 57.895 0.0 0.0 32.01 3.91 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
664 672 5.799936 CCCTTGATTTGTGCAAATTAGTACG 59.200 40.000 10.94 0.00 40.77 3.67
1478 1506 7.812690 AGATAGTGATGAAATTATGCAGCAA 57.187 32.000 0.00 0.00 31.67 3.91
1642 1675 5.835257 AGTTGACATCAGTGGTCATTTTTG 58.165 37.500 3.45 0.00 44.11 2.44
2142 2179 2.952978 CGCCTCTCTAACTCCACTACAT 59.047 50.000 0.00 0.00 0.00 2.29
2945 2984 4.096532 TGTGTTCGGCAAATTACAAGTGAA 59.903 37.500 0.00 0.00 0.00 3.18
3294 3338 6.710295 TCAGTATCTTGTTTGTAGTTGCACAT 59.290 34.615 0.00 0.00 0.00 3.21
3502 3550 8.079203 CAGGTTAGTGTTTTGCATACATAAACA 58.921 33.333 19.65 15.68 35.92 2.83
3927 3975 2.025981 TGGTCAATGAGCTATGCAAGGT 60.026 45.455 13.84 0.00 39.11 3.50
4736 4787 2.903135 ACAAAGGAGAGGAGGAGAACAG 59.097 50.000 0.00 0.00 0.00 3.16
4831 4885 1.277273 CAGTTGATGGCAGTGAGAGGA 59.723 52.381 0.00 0.00 0.00 3.71
4878 4932 1.836802 GGCAGTGAGAGGGAAGAAGAT 59.163 52.381 0.00 0.00 0.00 2.40
5027 5081 0.972983 AGGACTAGCACTCACGCCAT 60.973 55.000 0.00 0.00 0.00 4.40
5224 5278 1.675310 CCCGTGCCAGATTTCAGCA 60.675 57.895 0.00 0.00 0.00 4.41
5291 5345 4.394300 CCTGTTCTTATCAACTGAAGCTGG 59.606 45.833 0.00 0.00 0.00 4.85
5439 5494 0.464735 CAAACCCTCACGTGGTCCAA 60.465 55.000 17.00 0.00 34.15 3.53
5472 5527 8.627208 AAGCAGTTTCAATGAAGAAGAATCTA 57.373 30.769 0.00 0.00 33.77 1.98
5490 5545 3.892284 TCTACAGTTGCCTCAAACCAAA 58.108 40.909 0.00 0.00 0.00 3.28
5671 5726 6.547510 ACCTAAGCAGAAGATTGTCAAGTTTT 59.452 34.615 0.00 0.00 0.00 2.43
5735 5790 0.035534 AGAGACGAGAGAGAGCTGCA 60.036 55.000 1.02 0.00 0.00 4.41
5873 5928 2.091541 CACAGTCAAAACCACCACAGT 58.908 47.619 0.00 0.00 0.00 3.55
6145 6200 1.923148 CCCTGGTCCTTGAACCCTTAT 59.077 52.381 0.00 0.00 38.65 1.73
6422 6477 0.947244 CTTGGCACGAGCAGTTCTTT 59.053 50.000 7.26 0.00 44.61 2.52
7059 7117 1.221021 GGGAGGCCTTTCACCTACG 59.779 63.158 6.77 0.00 39.27 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
664 672 5.632244 AAATGGAAAATTGGCAAGCATTC 57.368 34.783 5.96 9.61 0.00 2.67
2142 2179 5.448768 CGACCTCGAAACTAGCTCTGATTTA 60.449 44.000 0.00 0.00 43.02 1.40
2495 2532 5.801531 TGGTGCTAGAAAAGTACTGAAGA 57.198 39.130 0.00 0.00 40.41 2.87
3269 3313 6.052360 TGTGCAACTACAAACAAGATACTGA 58.948 36.000 0.00 0.00 38.04 3.41
3294 3338 6.456795 TGAATGAAACCACACATTACAACA 57.543 33.333 0.00 0.00 36.94 3.33
3927 3975 2.685897 GTGCCAACCTGTTCAGTTACAA 59.314 45.455 0.00 0.00 0.00 2.41
4043 4091 3.139077 GCCGTCTCTTTCTTTTTGGAGA 58.861 45.455 0.00 0.00 33.19 3.71
4736 4787 4.502950 CCTCTGCATCACTATCTTCTTCCC 60.503 50.000 0.00 0.00 0.00 3.97
4831 4885 1.141657 TGCTGCACCTTTGTCTTCTCT 59.858 47.619 0.00 0.00 0.00 3.10
4878 4932 3.087370 TCCTCGTCTTCTTCATCCTCA 57.913 47.619 0.00 0.00 0.00 3.86
5224 5278 8.725148 GTTGATCTTCTCACACATATCTTTGTT 58.275 33.333 0.00 0.00 32.17 2.83
5291 5345 7.161773 TCCTCCATGTCAATTTGATTCTTTC 57.838 36.000 1.78 0.00 0.00 2.62
5439 5494 7.771183 TCTTCATTGAAACTGCTTTACACTTT 58.229 30.769 0.01 0.00 0.00 2.66
5490 5545 4.802248 GCAACTTCACTCACCATCTTCTCT 60.802 45.833 0.00 0.00 0.00 3.10
5735 5790 3.072486 GCATCAATGGCTGCGGCTT 62.072 57.895 18.85 1.05 38.73 4.35
5873 5928 1.150536 GTGGTGCCTTCCTGACCAA 59.849 57.895 0.00 0.00 41.43 3.67
6145 6200 7.550551 GTCACCATGATAAGAGTTTGATCTTCA 59.449 37.037 0.00 0.00 40.08 3.02
6233 6288 2.293677 GCTTCCGCTGTATCTACTGCTA 59.706 50.000 14.63 3.47 45.37 3.49
6422 6477 4.284550 GTGCAAGAGGTGGCCCCA 62.285 66.667 12.24 0.00 34.66 4.96
6750 6807 1.301716 GCTCGAAGGGTCACAGCAA 60.302 57.895 0.00 0.00 32.01 3.91
6898 6956 4.025040 TGATGTGCAAGATTCCAGTCTT 57.975 40.909 0.00 0.00 38.95 3.01
7059 7117 4.590850 AAACATGGCTCAAAACTCCTTC 57.409 40.909 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.