Multiple sequence alignment - TraesCS1A01G222400

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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 TraesCS1A01G222400 chr1A 100.000 5225 0 0 1 5225 392057042 392062266 0.000000e+00 9649
1 TraesCS1A01G222400 chr1A 96.868 5236 149 8 1 5225 453554499 453559730 0.000000e+00 8746
2 TraesCS1A01G222400 chr1A 96.601 5237 163 8 1 5225 552093515 552098748 0.000000e+00 8671
3 TraesCS1A01G222400 chr1A 100.000 61 0 0 5506 5566 392062547 392062607 4.560000e-21 113
4 TraesCS1A01G222400 chr1A 100.000 61 0 0 5506 5566 479849868 479849928 4.560000e-21 113
5 TraesCS1A01G222400 chr6A 97.248 5233 136 3 1 5225 561685591 561690823 0.000000e+00 8859
6 TraesCS1A01G222400 chr6A 97.212 5237 134 5 1 5225 212845802 212840566 0.000000e+00 8852
7 TraesCS1A01G222400 chr3A 97.095 5233 142 5 1 5225 673191361 673186131 0.000000e+00 8813
8 TraesCS1A01G222400 chr3A 100.000 61 0 0 5506 5566 673185670 673185610 4.560000e-21 113
9 TraesCS1A01G222400 chr3A 98.361 61 1 0 5506 5566 661458877 661458937 2.120000e-19 108
10 TraesCS1A01G222400 chr2A 97.345 5160 124 8 1 5151 409606935 409601780 0.000000e+00 8757
11 TraesCS1A01G222400 chr2A 96.487 5237 163 12 1 5225 591700620 591705847 0.000000e+00 8632
12 TraesCS1A01G222400 chr2A 98.361 61 1 0 5506 5566 72498660 72498720 2.120000e-19 108
13 TraesCS1A01G222400 chr2A 98.361 61 1 0 5506 5566 409598611 409598551 2.120000e-19 108
14 TraesCS1A01G222400 chr2A 98.361 61 1 0 5506 5566 409599870 409599810 2.120000e-19 108
15 TraesCS1A01G222400 chr4A 96.829 5235 155 6 1 5225 185150125 185144892 0.000000e+00 8737
16 TraesCS1A01G222400 chr4A 98.387 62 0 1 5506 5566 185144868 185144807 2.120000e-19 108
17 TraesCS1A01G222400 chr4A 98.361 61 1 0 5506 5566 494359709 494359769 2.120000e-19 108
18 TraesCS1A01G222400 chr7A 96.465 5234 172 8 1 5225 447290199 447295428 0.000000e+00 8628
19 TraesCS1A01G222400 chr5A 100.000 61 0 0 5506 5566 222748043 222748103 4.560000e-21 113


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 TraesCS1A01G222400 chr1A 392057042 392062607 5565 False 4881.0 9649 100.000000 1 5566 2 chr1A.!!$F4 5565
1 TraesCS1A01G222400 chr1A 453554499 453559730 5231 False 8746.0 8746 96.868000 1 5225 1 chr1A.!!$F1 5224
2 TraesCS1A01G222400 chr1A 552093515 552098748 5233 False 8671.0 8671 96.601000 1 5225 1 chr1A.!!$F3 5224
3 TraesCS1A01G222400 chr6A 561685591 561690823 5232 False 8859.0 8859 97.248000 1 5225 1 chr6A.!!$F1 5224
4 TraesCS1A01G222400 chr6A 212840566 212845802 5236 True 8852.0 8852 97.212000 1 5225 1 chr6A.!!$R1 5224
5 TraesCS1A01G222400 chr3A 673185610 673191361 5751 True 4463.0 8813 98.547500 1 5566 2 chr3A.!!$R1 5565
6 TraesCS1A01G222400 chr2A 591700620 591705847 5227 False 8632.0 8632 96.487000 1 5225 1 chr2A.!!$F2 5224
7 TraesCS1A01G222400 chr2A 409598551 409606935 8384 True 2991.0 8757 98.022333 1 5566 3 chr2A.!!$R1 5565
8 TraesCS1A01G222400 chr4A 185144807 185150125 5318 True 4422.5 8737 97.608000 1 5566 2 chr4A.!!$R1 5565
9 TraesCS1A01G222400 chr7A 447290199 447295428 5229 False 8628.0 8628 96.465000 1 5225 1 chr7A.!!$F1 5224

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
265 269 3.342627 CCGACCGTTTGCTTGCGA 61.343 61.111 0.00 0.0 0.00 5.10 F
1249 1257 1.021390 CCAACCTCATGACGGTGAGC 61.021 60.000 10.89 0.0 43.36 4.26 F
1701 1710 0.035881 CCTCTCTGAAAGTGCTGCCA 59.964 55.000 0.00 0.0 33.76 4.92 F
2537 2552 1.142748 GATCCACTGAGCCGACTGG 59.857 63.158 0.00 0.0 38.77 4.00 F
3652 3679 0.449388 GCTGGCGAGGTTTCTCATTG 59.551 55.000 0.00 0.0 39.95 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1710 0.108585 TGACTTGCGCCTTTTCCTCT 59.891 50.000 4.18 0.00 0.00 3.69 R
3221 3242 0.035056 GCCAGCAGTCCACCATAGTT 60.035 55.000 0.00 0.00 0.00 2.24 R
3652 3679 2.528041 AAGGGAAGTCACTCGTCAAC 57.472 50.000 0.00 0.00 0.00 3.18 R
4501 4528 1.964223 AGTCGATCCCGTCTGCAATAT 59.036 47.619 0.00 0.00 33.24 1.28 R
4732 4760 1.179174 GGTGAAGGCCAAGTTCCACC 61.179 60.000 5.01 8.89 0.00 4.61 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
119 123 3.962557 CTGCTACTGAGGAGGGGG 58.037 66.667 0.00 0.0 37.49 5.40
240 244 8.200024 AGTGCTATGATGACCATAAAGACTAT 57.800 34.615 0.00 0.0 37.30 2.12
265 269 3.342627 CCGACCGTTTGCTTGCGA 61.343 61.111 0.00 0.0 0.00 5.10
1249 1257 1.021390 CCAACCTCATGACGGTGAGC 61.021 60.000 10.89 0.0 43.36 4.26
1277 1285 1.072173 CCTCGCCACCCATATCAATCA 59.928 52.381 0.00 0.0 0.00 2.57
1701 1710 0.035881 CCTCTCTGAAAGTGCTGCCA 59.964 55.000 0.00 0.0 33.76 4.92
1953 1962 3.003763 GACAACCCCCGAGGAGCT 61.004 66.667 0.00 0.0 39.89 4.09
2350 2365 1.300697 GTTGGGCAGTCGTCGAAGT 60.301 57.895 0.00 0.0 0.00 3.01
2358 2373 2.981909 TCGTCGAAGTGCCCTCGT 60.982 61.111 0.00 0.0 0.00 4.18
2537 2552 1.142748 GATCCACTGAGCCGACTGG 59.857 63.158 0.00 0.0 38.77 4.00
2646 2661 6.327386 ACCCTGGTATGATTACTGATGTTT 57.673 37.500 0.00 0.0 0.00 2.83
2750 2765 2.430244 GACGAAGACGAAGCGCCA 60.430 61.111 2.29 0.0 42.66 5.69
3061 3081 5.700846 CGAGTTTAGCTCTTCAGAGTAACA 58.299 41.667 5.72 0.0 43.85 2.41
3111 3131 4.530553 TCTGTTAGGGTATGCTGTCTGAAA 59.469 41.667 0.00 0.0 0.00 2.69
3147 3167 8.311836 TCCGAAGATCTTTTAAATCTGTACACT 58.688 33.333 9.87 0.0 33.78 3.55
3470 3497 5.639506 CGTCATCATTGTCTCTTGGTTACTT 59.360 40.000 0.00 0.0 0.00 2.24
3493 3520 4.202567 TGGAAGCAACTTATCTTGGACCTT 60.203 41.667 0.00 0.0 0.00 3.50
3652 3679 0.449388 GCTGGCGAGGTTTCTCATTG 59.551 55.000 0.00 0.0 39.95 2.82
3704 3731 5.139435 TCTTGATGTTGAGTTCACTCGAT 57.861 39.130 0.06 0.0 45.72 3.59
4235 4262 2.669569 GCTCGGCTGAAGGTTGCA 60.670 61.111 0.00 0.0 0.00 4.08
4373 4400 2.765699 TGCTAGATGTGGTGCTGATGTA 59.234 45.455 0.00 0.0 0.00 2.29
4428 4455 0.957888 GCGAGAAGAAAAGCTGGCCT 60.958 55.000 3.32 0.0 30.82 5.19
4501 4528 2.477845 TTCATTGCTGCTGCTACTCA 57.522 45.000 17.00 0.0 40.48 3.41
4606 4634 1.265236 AAATTTGCCTCGGAATGCCA 58.735 45.000 0.00 0.0 0.00 4.92
4732 4760 1.070134 TCTTCGGGAATTATCTGCCGG 59.930 52.381 0.00 0.0 32.97 6.13
4751 4779 1.179174 GGTGGAACTTGGCCTTCACC 61.179 60.000 3.32 4.0 36.74 4.02
4816 4845 1.284657 CAGTCGATTCGCATCTTGCT 58.715 50.000 0.00 0.0 42.25 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.321298 GGGCTGTTACTTCTTCCGCA 60.321 55.000 0.00 0.00 0.00 5.69
119 123 3.006537 TGGCGAACTCTATATAAGCCACC 59.993 47.826 1.80 0.00 46.73 4.61
240 244 0.241481 GCAAACGGTCGGCCATTAAA 59.759 50.000 6.96 0.00 34.09 1.52
265 269 5.777732 ACTGACAGGAGATCTAAAGTCACTT 59.222 40.000 15.63 6.86 33.06 3.16
362 366 6.097915 AGAAGTCACCTTTCAATCGACTTA 57.902 37.500 0.00 0.00 44.66 2.24
893 901 3.357079 GCACACTGTTGGGGAGCG 61.357 66.667 0.00 0.00 0.00 5.03
1277 1285 3.709587 TGAGGAGGTAGAGAAAATCCGT 58.290 45.455 0.00 0.00 35.13 4.69
1701 1710 0.108585 TGACTTGCGCCTTTTCCTCT 59.891 50.000 4.18 0.00 0.00 3.69
1924 1933 0.673985 GGGTTGTCTTTGTTCCCTGC 59.326 55.000 0.00 0.00 35.63 4.85
2150 2159 3.939837 CTGCTTTCGCCTCCGCTCA 62.940 63.158 0.00 0.00 34.43 4.26
2350 2365 0.683504 GGAGAAGAGGTACGAGGGCA 60.684 60.000 0.00 0.00 0.00 5.36
2358 2373 2.415608 CGGCGCTGGAGAAGAGGTA 61.416 63.158 8.83 0.00 0.00 3.08
2537 2552 3.060339 CACTGCAAATTTTGAAAGACCGC 60.060 43.478 13.26 0.00 0.00 5.68
2646 2661 1.000394 TCGTCAGTCGATTCAAGGCAA 60.000 47.619 0.00 0.00 44.01 4.52
2750 2765 0.827925 TGTTCCGCCTCACTCTCAGT 60.828 55.000 0.00 0.00 0.00 3.41
3061 3081 2.167281 CAGTGAATCGACTGACCTGGAT 59.833 50.000 0.00 0.00 45.39 3.41
3147 3167 4.497291 ACTTAACAGAAACACCCAGTGA 57.503 40.909 0.96 0.00 36.96 3.41
3215 3236 1.553248 CAGTCCACCATAGTTTCGGGA 59.447 52.381 0.00 0.00 0.00 5.14
3221 3242 0.035056 GCCAGCAGTCCACCATAGTT 60.035 55.000 0.00 0.00 0.00 2.24
3470 3497 3.330701 AGGTCCAAGATAAGTTGCTTCCA 59.669 43.478 0.00 0.00 0.00 3.53
3493 3520 2.899976 TCTGCAAAAGTCAGTCGACAA 58.100 42.857 19.50 1.95 45.23 3.18
3652 3679 2.528041 AAGGGAAGTCACTCGTCAAC 57.472 50.000 0.00 0.00 0.00 3.18
3704 3731 6.574465 GCTTCCTCCAGTTTATCTACAGAACA 60.574 42.308 0.00 0.00 0.00 3.18
4373 4400 2.347322 GCGGACCAGAGACAGAGCT 61.347 63.158 0.00 0.00 0.00 4.09
4428 4455 2.042297 TGGTATTGGCAACTTGGATGGA 59.958 45.455 0.00 0.00 37.61 3.41
4501 4528 1.964223 AGTCGATCCCGTCTGCAATAT 59.036 47.619 0.00 0.00 33.24 1.28
4606 4634 6.293698 AGTTTAACGGTTACAGAATCCACTT 58.706 36.000 0.00 0.00 0.00 3.16
4732 4760 1.179174 GGTGAAGGCCAAGTTCCACC 61.179 60.000 5.01 8.89 0.00 4.61
5012 5042 1.608717 CCCACTCGAGGCTTAGCTGT 61.609 60.000 18.41 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.