Multiple sequence alignment - TraesCS6A01G086500

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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 TraesCS6A01G086500 chr6A 100.000 4190 0 0 1 4190 55278726 55282915 0.000000e+00 7738
1 TraesCS6A01G086500 chr6B 97.187 3164 80 3 809 3966 100954351 100951191 0.000000e+00 5341
2 TraesCS6A01G086500 chr6B 97.378 801 19 2 1 800 100955943 100955144 0.000000e+00 1362
3 TraesCS6A01G086500 chr6B 85.880 517 64 5 2210 2719 100551247 100550733 3.680000e-150 542
4 TraesCS6A01G086500 chr6B 95.556 225 9 1 3965 4188 100927004 100926780 3.980000e-95 359
5 TraesCS6A01G086500 chr6B 83.838 198 17 9 4004 4189 100547726 100547532 1.550000e-39 174
6 TraesCS6A01G086500 chrUn 94.478 2952 122 27 809 3731 69319703 69316764 0.000000e+00 4510
7 TraesCS6A01G086500 chrUn 95.750 800 31 3 1 800 69321265 69320469 0.000000e+00 1286
8 TraesCS6A01G086500 chrUn 86.927 436 31 8 3724 4135 69283891 69283458 2.280000e-127 466
9 TraesCS6A01G086500 chrUn 85.957 235 31 2 2210 2443 70408207 70408440 2.500000e-62 250
10 TraesCS6A01G086500 chrUn 84.568 162 24 1 2471 2632 70408438 70408598 4.340000e-35 159
11 TraesCS6A01G086500 chr6D 81.909 1896 227 65 896 2761 492853 491044 0.000000e+00 1495
12 TraesCS6A01G086500 chr7B 78.421 1900 282 66 854 2716 745403761 745401953 0.000000e+00 1120
13 TraesCS6A01G086500 chr2D 77.002 1961 322 81 811 2716 5688513 5690399 0.000000e+00 1003
14 TraesCS6A01G086500 chr2A 77.963 1443 243 41 1298 2716 4180564 4181955 0.000000e+00 833


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 TraesCS6A01G086500 chr6A 55278726 55282915 4189 False 7738.0 7738 100.0000 1 4190 1 chr6A.!!$F1 4189
1 TraesCS6A01G086500 chr6B 100951191 100955943 4752 True 3351.5 5341 97.2825 1 3966 2 chr6B.!!$R3 3965
2 TraesCS6A01G086500 chr6B 100547532 100551247 3715 True 358.0 542 84.8590 2210 4189 2 chr6B.!!$R2 1979
3 TraesCS6A01G086500 chrUn 69316764 69321265 4501 True 2898.0 4510 95.1140 1 3731 2 chrUn.!!$R2 3730
4 TraesCS6A01G086500 chr6D 491044 492853 1809 True 1495.0 1495 81.9090 896 2761 1 chr6D.!!$R1 1865
5 TraesCS6A01G086500 chr7B 745401953 745403761 1808 True 1120.0 1120 78.4210 854 2716 1 chr7B.!!$R1 1862
6 TraesCS6A01G086500 chr2D 5688513 5690399 1886 False 1003.0 1003 77.0020 811 2716 1 chr2D.!!$F1 1905
7 TraesCS6A01G086500 chr2A 4180564 4181955 1391 False 833.0 833 77.9630 1298 2716 1 chr2A.!!$F1 1418

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
796 798 0.400594 ACTACAGTTGGGTCAAGGGC 59.599 55.000 0.00 0.00 0.00 5.19 F
807 809 0.609662 GTCAAGGGCATGCCATGTTT 59.390 50.000 36.56 21.43 37.98 2.83 F
1909 2753 1.063942 TCTCCTTCGCCTCCATAGTGA 60.064 52.381 0.00 0.00 0.00 3.41 F
2283 3154 1.896465 GACAGAAGGTGGAGTAGCACT 59.104 52.381 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2641 0.755698 TAAGCTCGATCTCCGCCCTT 60.756 55.0 0.00 0.0 38.37 3.95 R
2343 3220 1.047596 TGTGGGCATGCTTGGTGTTT 61.048 50.0 18.92 0.0 0.00 2.83 R
3030 5092 0.597568 CCATCAGCAGCCAAACGAAA 59.402 50.0 0.00 0.0 0.00 3.46 R
4119 6969 0.034756 AACAGCTGGTCGTACATGCA 59.965 50.0 19.93 0.0 0.00 3.96 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
463 465 6.434340 GGATGTTAAACAAGTGGAGAGGAAAT 59.566 38.462 0.00 0.00 0.00 2.17
480 482 6.157123 AGAGGAAATCTGGGTCTAAGGTAAAG 59.843 42.308 0.00 0.00 36.69 1.85
796 798 0.400594 ACTACAGTTGGGTCAAGGGC 59.599 55.000 0.00 0.00 0.00 5.19
800 802 1.607467 AGTTGGGTCAAGGGCATGC 60.607 57.895 9.90 9.90 0.00 4.06
801 803 2.283821 TTGGGTCAAGGGCATGCC 60.284 61.111 29.47 29.47 0.00 4.40
802 804 3.157733 TTGGGTCAAGGGCATGCCA 62.158 57.895 36.56 15.10 37.98 4.92
803 805 2.042639 GGGTCAAGGGCATGCCAT 60.043 61.111 36.56 29.47 37.98 4.40
805 807 1.683365 GGTCAAGGGCATGCCATGT 60.683 57.895 36.56 18.78 37.98 3.21
806 808 1.259840 GGTCAAGGGCATGCCATGTT 61.260 55.000 36.56 23.31 37.98 2.71
807 809 0.609662 GTCAAGGGCATGCCATGTTT 59.390 50.000 36.56 21.43 37.98 2.83
960 1778 4.494350 GCAGTTGCAAATCAAGAGAGAA 57.506 40.909 0.00 0.00 41.59 2.87
968 1790 3.528597 AATCAAGAGAGAACCGGCTAC 57.471 47.619 0.00 0.00 0.00 3.58
1287 2119 1.152830 GCCCAGTGAAACCCCTCAA 59.847 57.895 0.00 0.00 37.80 3.02
1446 2280 2.897271 ATGTGCTGTGGAAATGGGTA 57.103 45.000 0.00 0.00 0.00 3.69
1797 2641 4.502950 GGGGATGCACAACTGAATTTCAAA 60.503 41.667 0.01 0.00 0.00 2.69
1883 2727 2.586792 GTCTGGCGCCATCCTTCT 59.413 61.111 32.87 0.00 0.00 2.85
1909 2753 1.063942 TCTCCTTCGCCTCCATAGTGA 60.064 52.381 0.00 0.00 0.00 3.41
1986 2833 7.885297 AGCAAACAACATCAGTATACAACAAT 58.115 30.769 5.50 0.00 0.00 2.71
2283 3154 1.896465 GACAGAAGGTGGAGTAGCACT 59.104 52.381 0.00 0.00 0.00 4.40
2325 3202 2.500098 AGGCGTATTTGGAGCTAGTGAA 59.500 45.455 0.00 0.00 0.00 3.18
2409 3286 4.250464 TCCACGAAACAATAGGTCATGAC 58.750 43.478 17.91 17.91 0.00 3.06
2582 3474 4.096003 CCCGATTGACCTGGCCGT 62.096 66.667 0.00 0.00 0.00 5.68
2612 3510 2.281970 CCAAGAGGCAGCACAGCA 60.282 61.111 0.00 0.00 35.83 4.41
2762 3877 3.403558 GTCCAGGGGTGCCTCCTC 61.404 72.222 0.00 0.00 36.82 3.71
2763 3878 4.741239 TCCAGGGGTGCCTCCTCC 62.741 72.222 0.00 0.00 37.41 4.30
2764 3879 4.748798 CCAGGGGTGCCTCCTCCT 62.749 72.222 0.00 0.00 37.41 3.69
3030 5092 0.760945 CCGGGGGAGAGCTCATTACT 60.761 60.000 17.77 0.00 0.00 2.24
3123 5642 1.896220 TCAGCGCAGGACATCTTTTT 58.104 45.000 11.47 0.00 0.00 1.94
3153 5672 5.141182 ACTACTGCTAGCATACCATACTGT 58.859 41.667 19.72 11.56 0.00 3.55
3165 5684 6.207417 GCATACCATACTGTAGGCAAATTGAT 59.793 38.462 0.00 0.00 45.25 2.57
3350 5914 4.743151 CCAGCATGTATGATTGATTTGTGC 59.257 41.667 0.00 0.00 0.00 4.57
3351 5915 5.344884 CAGCATGTATGATTGATTTGTGCA 58.655 37.500 0.00 0.00 32.82 4.57
3356 5920 7.306574 GCATGTATGATTGATTTGTGCATTGAG 60.307 37.037 0.00 0.00 0.00 3.02
3461 6025 0.687354 ATTTCAGCACAGACTCCGGT 59.313 50.000 0.00 0.00 0.00 5.28
3572 6136 1.861982 AATGCCCTGTACTACGGTCT 58.138 50.000 0.00 0.00 0.00 3.85
3658 6226 3.319198 GGGGAGGTGGTGCTCGAA 61.319 66.667 0.00 0.00 0.00 3.71
3971 6784 2.866156 TCAGGCTTTAATCTGATTCGCG 59.134 45.455 6.10 0.00 35.37 5.87
3976 6789 3.181510 GCTTTAATCTGATTCGCGGTTGT 60.182 43.478 6.13 0.00 0.00 3.32
3977 6790 4.334443 CTTTAATCTGATTCGCGGTTGTG 58.666 43.478 6.13 0.00 0.00 3.33
3988 6801 2.159366 TCGCGGTTGTGTTTTGAACAAT 60.159 40.909 6.13 0.00 44.16 2.71
3990 6803 3.061429 CGCGGTTGTGTTTTGAACAATTT 59.939 39.130 0.00 0.00 44.16 1.82
3995 6808 7.567952 GCGGTTGTGTTTTGAACAATTTATACC 60.568 37.037 0.00 0.00 44.16 2.73
3997 6810 9.968870 GGTTGTGTTTTGAACAATTTATACCTA 57.031 29.630 0.00 0.00 44.16 3.08
4006 6846 8.746052 TGAACAATTTATACCTAGTCATTGGG 57.254 34.615 0.00 0.00 0.00 4.12
4009 6849 7.122715 ACAATTTATACCTAGTCATTGGGCAA 58.877 34.615 0.00 0.00 0.00 4.52
4024 6864 2.890945 TGGGCAAGCTAGGTTCTTTTTC 59.109 45.455 3.68 0.00 0.00 2.29
4028 6868 3.320826 GCAAGCTAGGTTCTTTTTCCCAA 59.679 43.478 3.68 0.00 0.00 4.12
4040 6880 7.309316 GGTTCTTTTTCCCAACGGATGTAATAA 60.309 37.037 0.00 0.00 38.24 1.40
4041 6881 7.385778 TCTTTTTCCCAACGGATGTAATAAG 57.614 36.000 0.00 0.00 38.24 1.73
4042 6882 7.169591 TCTTTTTCCCAACGGATGTAATAAGA 58.830 34.615 0.00 0.00 38.24 2.10
4043 6883 6.995511 TTTTCCCAACGGATGTAATAAGAG 57.004 37.500 0.00 0.00 38.24 2.85
4046 6888 3.181454 CCCAACGGATGTAATAAGAGCCT 60.181 47.826 0.00 0.00 0.00 4.58
4050 6892 6.258160 CAACGGATGTAATAAGAGCCTTTTG 58.742 40.000 0.00 0.00 0.00 2.44
4051 6893 5.741011 ACGGATGTAATAAGAGCCTTTTGA 58.259 37.500 0.00 0.00 0.00 2.69
4087 6936 5.721960 ACAGGGAGATGTCAGTATTACTGTT 59.278 40.000 20.43 9.28 46.03 3.16
4104 6954 3.323979 ACTGTTGTTGGATAGGAAGACGT 59.676 43.478 0.00 0.00 0.00 4.34
4113 6963 0.888619 TAGGAAGACGTCAGTGCTGG 59.111 55.000 19.50 0.00 0.00 4.85
4122 6972 2.281276 CAGTGCTGGACTGCTGCA 60.281 61.111 16.37 0.88 45.72 4.41
4123 6973 1.674651 CAGTGCTGGACTGCTGCAT 60.675 57.895 16.37 0.00 45.72 3.96
4124 6974 1.674651 AGTGCTGGACTGCTGCATG 60.675 57.895 1.31 0.00 39.00 4.06
4130 6980 0.389817 TGGACTGCTGCATGTACGAC 60.390 55.000 1.31 0.00 0.00 4.34
4133 6983 0.390340 ACTGCTGCATGTACGACCAG 60.390 55.000 1.31 3.03 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.975616 CAGAAAGTTCATTTTTCTCTTTGTCCA 59.024 33.333 0.00 0.00 41.60 4.02
463 465 5.013808 CCTTTTCCTTTACCTTAGACCCAGA 59.986 44.000 0.00 0.00 0.00 3.86
480 482 6.877236 TCATCCTTATTGCAAATCCTTTTCC 58.123 36.000 1.71 0.00 0.00 3.13
796 798 4.685169 AGTACTTTCGAAACATGGCATG 57.315 40.909 25.31 25.31 0.00 4.06
800 802 7.416154 TGACTAAAGTACTTTCGAAACATGG 57.584 36.000 23.76 2.98 34.23 3.66
801 803 8.708742 TCATGACTAAAGTACTTTCGAAACATG 58.291 33.333 27.22 27.22 34.23 3.21
802 804 8.827177 TCATGACTAAAGTACTTTCGAAACAT 57.173 30.769 23.76 19.26 34.23 2.71
803 805 7.924412 ACTCATGACTAAAGTACTTTCGAAACA 59.076 33.333 23.76 18.17 34.23 2.83
805 807 8.139350 TGACTCATGACTAAAGTACTTTCGAAA 58.861 33.333 23.76 10.71 34.23 3.46
806 808 7.654568 TGACTCATGACTAAAGTACTTTCGAA 58.345 34.615 23.76 12.06 34.23 3.71
807 809 7.210718 TGACTCATGACTAAAGTACTTTCGA 57.789 36.000 23.76 7.36 34.23 3.71
960 1778 1.408453 GGCAATCCTAGGTAGCCGGT 61.408 60.000 20.47 0.00 35.42 5.28
968 1790 2.431057 ACGTACTCTTGGCAATCCTAGG 59.569 50.000 0.82 0.82 36.14 3.02
1287 2119 1.683011 GCCCACAATACCATGAGCTGT 60.683 52.381 0.00 0.00 0.00 4.40
1797 2641 0.755698 TAAGCTCGATCTCCGCCCTT 60.756 55.000 0.00 0.00 38.37 3.95
1883 2727 1.666011 GAGGCGAAGGAGACACACA 59.334 57.895 0.00 0.00 0.00 3.72
1909 2753 3.689347 TGACATAGAGCACAAAGGCAAT 58.311 40.909 0.00 0.00 35.83 3.56
1986 2833 5.549347 ACTCTACTTCTTCTGTAGTCGACA 58.451 41.667 19.50 0.48 38.67 4.35
2283 3154 3.688235 TGCCATCTTTGACATGATGACA 58.312 40.909 16.07 10.51 41.69 3.58
2325 3202 5.531287 GGTGTTTCTTATCTTGTTCCACAGT 59.469 40.000 0.00 0.00 0.00 3.55
2343 3220 1.047596 TGTGGGCATGCTTGGTGTTT 61.048 50.000 18.92 0.00 0.00 2.83
2409 3286 2.935481 TCAGGAAGCCACCCCCTG 60.935 66.667 0.00 0.00 46.64 4.45
2575 3467 2.032528 TTGCTCTTGGACGGCCAG 59.967 61.111 11.51 5.06 46.91 4.85
2582 3474 1.349026 CCTCTTGGTCTTGCTCTTGGA 59.651 52.381 0.00 0.00 0.00 3.53
2612 3510 1.686325 ATCCATAAGACGCCGCCACT 61.686 55.000 0.00 0.00 0.00 4.00
2762 3877 1.521450 CTGCACCTTGCTGTTGGAGG 61.521 60.000 0.00 0.00 45.31 4.30
2763 3878 1.521450 CCTGCACCTTGCTGTTGGAG 61.521 60.000 0.00 0.00 45.31 3.86
2764 3879 1.529010 CCTGCACCTTGCTGTTGGA 60.529 57.895 0.00 0.00 45.31 3.53
2885 4648 2.811431 TGTTGATTTTCTAGCACCACCG 59.189 45.455 0.00 0.00 0.00 4.94
3012 5074 1.123928 AAGTAATGAGCTCTCCCCCG 58.876 55.000 16.19 0.00 0.00 5.73
3030 5092 0.597568 CCATCAGCAGCCAAACGAAA 59.402 50.000 0.00 0.00 0.00 3.46
3153 5672 5.369404 TGACTCCTCCATATCAATTTGCCTA 59.631 40.000 0.00 0.00 0.00 3.93
3350 5914 0.659427 AATGCGCCGTGATCTCAATG 59.341 50.000 4.18 0.00 0.00 2.82
3351 5915 0.940126 GAATGCGCCGTGATCTCAAT 59.060 50.000 4.18 0.00 0.00 2.57
3356 5920 1.060937 GTGTGAATGCGCCGTGATC 59.939 57.895 4.18 0.00 0.00 2.92
3401 5965 3.924114 TTGTTCAGACCACTCCTTGAA 57.076 42.857 0.00 0.00 0.00 2.69
3402 5966 5.762179 ATATTGTTCAGACCACTCCTTGA 57.238 39.130 0.00 0.00 0.00 3.02
3461 6025 3.195610 AGCAATGTCTCCATAACTGACGA 59.804 43.478 0.00 0.00 33.81 4.20
3572 6136 7.652524 TCTGGGCATTTATTTATTTACTGCA 57.347 32.000 0.00 0.00 0.00 4.41
3674 6242 5.460416 AGGAAGGGAGAGTAGGAAGATAAC 58.540 45.833 0.00 0.00 0.00 1.89
3677 6245 4.265078 ACAAGGAAGGGAGAGTAGGAAGAT 60.265 45.833 0.00 0.00 0.00 2.40
3678 6246 3.077695 ACAAGGAAGGGAGAGTAGGAAGA 59.922 47.826 0.00 0.00 0.00 2.87
3971 6784 8.880878 AGGTATAAATTGTTCAAAACACAACC 57.119 30.769 0.00 0.00 41.97 3.77
3988 6801 5.104109 AGCTTGCCCAATGACTAGGTATAAA 60.104 40.000 0.00 0.00 0.00 1.40
3990 6803 3.973973 AGCTTGCCCAATGACTAGGTATA 59.026 43.478 0.00 0.00 0.00 1.47
3995 6808 2.171448 ACCTAGCTTGCCCAATGACTAG 59.829 50.000 0.00 0.00 0.00 2.57
3997 6810 0.995024 ACCTAGCTTGCCCAATGACT 59.005 50.000 0.00 0.00 0.00 3.41
4000 6813 2.134789 AGAACCTAGCTTGCCCAATG 57.865 50.000 0.00 0.00 0.00 2.82
4006 6846 2.890945 TGGGAAAAAGAACCTAGCTTGC 59.109 45.455 0.00 0.00 0.00 4.01
4009 6849 3.146847 CGTTGGGAAAAAGAACCTAGCT 58.853 45.455 0.00 0.00 0.00 3.32
4024 6864 3.139077 GGCTCTTATTACATCCGTTGGG 58.861 50.000 0.00 0.00 0.00 4.12
4028 6868 5.741011 TCAAAAGGCTCTTATTACATCCGT 58.259 37.500 0.00 0.00 0.00 4.69
4040 6880 5.649831 GTCCAAGAATACATCAAAAGGCTCT 59.350 40.000 0.00 0.00 0.00 4.09
4041 6881 5.415701 TGTCCAAGAATACATCAAAAGGCTC 59.584 40.000 0.00 0.00 0.00 4.70
4042 6882 5.324409 TGTCCAAGAATACATCAAAAGGCT 58.676 37.500 0.00 0.00 0.00 4.58
4043 6883 5.393461 CCTGTCCAAGAATACATCAAAAGGC 60.393 44.000 0.00 0.00 0.00 4.35
4046 6888 5.886609 TCCCTGTCCAAGAATACATCAAAA 58.113 37.500 0.00 0.00 0.00 2.44
4050 6892 5.163258 ACATCTCCCTGTCCAAGAATACATC 60.163 44.000 0.00 0.00 0.00 3.06
4051 6893 4.723789 ACATCTCCCTGTCCAAGAATACAT 59.276 41.667 0.00 0.00 0.00 2.29
4058 6900 1.905215 ACTGACATCTCCCTGTCCAAG 59.095 52.381 2.08 0.00 43.99 3.61
4060 6902 2.919772 TACTGACATCTCCCTGTCCA 57.080 50.000 2.08 0.00 43.99 4.02
4080 6922 5.011329 ACGTCTTCCTATCCAACAACAGTAA 59.989 40.000 0.00 0.00 0.00 2.24
4087 6936 3.056821 CACTGACGTCTTCCTATCCAACA 60.057 47.826 17.92 0.00 0.00 3.33
4113 6963 0.389817 TGGTCGTACATGCAGCAGTC 60.390 55.000 0.00 0.00 0.00 3.51
4119 6969 0.034756 AACAGCTGGTCGTACATGCA 59.965 50.000 19.93 0.00 0.00 3.96
4122 6972 0.973632 TCCAACAGCTGGTCGTACAT 59.026 50.000 19.93 0.00 46.51 2.29
4123 6973 0.753867 TTCCAACAGCTGGTCGTACA 59.246 50.000 19.93 0.00 46.51 2.90
4124 6974 1.145803 GTTCCAACAGCTGGTCGTAC 58.854 55.000 19.93 4.27 46.51 3.67
4133 6983 3.731867 CGCTCCATATTTGTTCCAACAGC 60.732 47.826 0.00 0.00 40.50 4.40


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

AutoCloner maintained by Alex Coulton.