Multiple sequence alignment - TraesCS2D01G218200

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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 TraesCS2D01G218200 chr2D 100.000 3902 0 0 1 3902 181434198 181438099 0.000000e+00 7206
1 TraesCS2D01G218200 chr2D 91.451 889 63 10 1 879 176585314 176586199 0.000000e+00 1208
2 TraesCS2D01G218200 chr2B 98.711 2561 27 4 932 3488 238254085 238256643 0.000000e+00 4542
3 TraesCS2D01G218200 chr2B 88.773 383 22 8 3524 3902 238256638 238257003 2.140000e-122 449
4 TraesCS2D01G218200 chr2A 90.713 2132 125 34 1801 3902 197216728 197218816 0.000000e+00 2772
5 TraesCS2D01G218200 chr2A 89.034 921 48 17 899 1794 197215669 197216561 0.000000e+00 1092
6 TraesCS2D01G218200 chr2A 85.714 245 24 1 3569 3813 197222467 197222700 8.370000e-62 248
7 TraesCS2D01G218200 chrUn 92.601 892 55 5 1 883 68157664 68156775 0.000000e+00 1271
8 TraesCS2D01G218200 chrUn 92.135 890 58 6 1 880 102557054 102556167 0.000000e+00 1245
9 TraesCS2D01G218200 chr6D 92.120 901 58 7 1 890 463451787 463450889 0.000000e+00 1258
10 TraesCS2D01G218200 chr6D 89.858 917 75 16 1 905 121800410 121799500 0.000000e+00 1162
11 TraesCS2D01G218200 chr3D 92.247 890 57 7 1 880 605996932 605997819 0.000000e+00 1251
12 TraesCS2D01G218200 chr3D 91.011 890 67 11 1 880 253573783 253572897 0.000000e+00 1188
13 TraesCS2D01G218200 chr7D 90.858 897 68 11 1 886 68432606 68433499 0.000000e+00 1190
14 TraesCS2D01G218200 chr5B 90.929 893 69 6 1 883 612294314 612295204 0.000000e+00 1190


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 TraesCS2D01G218200 chr2D 181434198 181438099 3901 False 7206.000000 7206 100.000 1 3902 1 chr2D.!!$F2 3901
1 TraesCS2D01G218200 chr2D 176585314 176586199 885 False 1208.000000 1208 91.451 1 879 1 chr2D.!!$F1 878
2 TraesCS2D01G218200 chr2B 238254085 238257003 2918 False 2495.500000 4542 93.742 932 3902 2 chr2B.!!$F1 2970
3 TraesCS2D01G218200 chr2A 197215669 197222700 7031 False 1370.666667 2772 88.487 899 3902 3 chr2A.!!$F1 3003
4 TraesCS2D01G218200 chrUn 68156775 68157664 889 True 1271.000000 1271 92.601 1 883 1 chrUn.!!$R1 882
5 TraesCS2D01G218200 chrUn 102556167 102557054 887 True 1245.000000 1245 92.135 1 880 1 chrUn.!!$R2 879
6 TraesCS2D01G218200 chr6D 463450889 463451787 898 True 1258.000000 1258 92.120 1 890 1 chr6D.!!$R2 889
7 TraesCS2D01G218200 chr6D 121799500 121800410 910 True 1162.000000 1162 89.858 1 905 1 chr6D.!!$R1 904
8 TraesCS2D01G218200 chr3D 605996932 605997819 887 False 1251.000000 1251 92.247 1 880 1 chr3D.!!$F1 879
9 TraesCS2D01G218200 chr3D 253572897 253573783 886 True 1188.000000 1188 91.011 1 880 1 chr3D.!!$R1 879
10 TraesCS2D01G218200 chr7D 68432606 68433499 893 False 1190.000000 1190 90.858 1 886 1 chr7D.!!$F1 885
11 TraesCS2D01G218200 chr5B 612294314 612295204 890 False 1190.000000 1190 90.929 1 883 1 chr5B.!!$F1 882


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
674 679 0.035915 TCAATCGGTTTGGATGGCGA 60.036 50.000 0.00 0.0 35.92 5.54 F
843 857 0.650512 GGTCGTATGCATCGTTGTGG 59.349 55.000 0.19 0.0 0.00 4.17 F
917 931 2.479837 TGAGAGTGTTTTGGTAGCGTG 58.520 47.619 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 2861 0.395312 GTCGGGAAACAGGTTCTCCA 59.605 55.000 0.0 0.0 32.45 3.86 R
2673 2895 5.073311 TCAAGAACCCTCTTATGACTTCG 57.927 43.478 0.0 0.0 40.05 3.79 R
3343 3565 4.558226 TCAGTGCTTCACTTGACCATAT 57.442 40.909 0.0 0.0 42.59 1.78 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
70 73 0.108804 TTCTCAACGACCCGATCAGC 60.109 55.000 0.00 0.00 0.00 4.26
156 159 7.347252 TCAACTCTAGCTCTATTCCTAGTTCA 58.653 38.462 0.00 0.00 34.18 3.18
249 253 3.701532 TTAACAAAGGACAACTTGGCG 57.298 42.857 0.00 0.00 39.96 5.69
279 283 3.708631 ACTGGACAGGATCTACAAGATGG 59.291 47.826 4.14 0.00 34.53 3.51
382 386 5.292589 CACGTTGCCTTTAATATTACTCCGT 59.707 40.000 0.00 0.00 0.00 4.69
426 430 1.375523 GACGTGGCTTGACGGGATT 60.376 57.895 0.00 0.00 43.84 3.01
444 448 0.796312 TTGATTCCGAAACAGCGAGC 59.204 50.000 0.00 0.00 0.00 5.03
503 507 6.251655 AGTCTGAAACTGCAGAAATGATTC 57.748 37.500 23.35 13.85 45.69 2.52
579 584 1.468565 CGTTGATCCGTATGTGGTCGT 60.469 52.381 0.00 0.00 0.00 4.34
612 617 2.365635 AGGCCAGGGAGCGTATGT 60.366 61.111 5.01 0.00 0.00 2.29
674 679 0.035915 TCAATCGGTTTGGATGGCGA 60.036 50.000 0.00 0.00 35.92 5.54
685 690 6.093495 CGGTTTGGATGGCGATTATGTAATAT 59.907 38.462 0.00 0.00 0.00 1.28
728 733 2.237643 TCTTTCTTATGCCAGCCGGTTA 59.762 45.455 1.90 0.00 33.28 2.85
761 774 6.148264 CCTTTCTTCTCTTTGTGAGCATTTC 58.852 40.000 0.00 0.00 42.38 2.17
840 854 3.381045 AGTATGGTCGTATGCATCGTTG 58.619 45.455 0.19 0.00 0.00 4.10
843 857 0.650512 GGTCGTATGCATCGTTGTGG 59.349 55.000 0.19 0.00 0.00 4.17
914 928 5.243426 TGTTTTGAGAGTGTTTTGGTAGC 57.757 39.130 0.00 0.00 0.00 3.58
917 931 2.479837 TGAGAGTGTTTTGGTAGCGTG 58.520 47.619 0.00 0.00 0.00 5.34
1498 1536 7.453126 ACATTTAAATTGGACCTATGGTGTTGA 59.547 33.333 0.00 0.00 35.25 3.18
1736 1775 8.537728 TGATAAGGGTGAATTTATGCTTTGAT 57.462 30.769 0.00 0.00 0.00 2.57
2415 2622 2.575735 TGGATGGAGAACTGCAATACCA 59.424 45.455 12.58 12.58 33.77 3.25
2427 2635 9.573166 AGAACTGCAATACCAAATATAGCAATA 57.427 29.630 0.00 0.00 0.00 1.90
2639 2861 4.141158 GGATATCTGGGGGAACATGAAAGT 60.141 45.833 0.00 0.00 0.00 2.66
2673 2895 1.471676 CCCGACTCACAGACTTATGCC 60.472 57.143 0.00 0.00 0.00 4.40
3343 3565 7.994425 TTGCTGGTTATTATGAACTTCTGAA 57.006 32.000 0.00 0.00 0.00 3.02
3368 3590 2.880890 GGTCAAGTGAAGCACTGAATGT 59.119 45.455 0.22 0.00 44.62 2.71
3369 3591 4.065088 GGTCAAGTGAAGCACTGAATGTA 58.935 43.478 0.22 0.00 44.62 2.29
3370 3592 4.515191 GGTCAAGTGAAGCACTGAATGTAA 59.485 41.667 0.22 0.00 44.62 2.41
3371 3593 5.444122 GTCAAGTGAAGCACTGAATGTAAC 58.556 41.667 0.22 0.00 44.62 2.50
3372 3594 5.237344 GTCAAGTGAAGCACTGAATGTAACT 59.763 40.000 0.22 0.00 44.62 2.24
3401 3624 5.947443 ACAGAATAAAAGTGAAGCAGATGC 58.053 37.500 0.00 0.00 42.49 3.91
3405 3628 7.220300 CAGAATAAAAGTGAAGCAGATGCATTC 59.780 37.037 0.00 8.45 45.16 2.67
3406 3629 6.770746 ATAAAAGTGAAGCAGATGCATTCT 57.229 33.333 0.00 0.00 45.16 2.40
3409 3632 5.557891 AAGTGAAGCAGATGCATTCTAAC 57.442 39.130 0.00 2.16 45.16 2.34
3424 3647 4.524316 TTCTAACGGCTAGCACAAAGTA 57.476 40.909 18.24 0.00 0.00 2.24
3437 3660 8.381387 GCTAGCACAAAGTACTCATACTAAAAC 58.619 37.037 10.63 0.00 41.00 2.43
3539 3762 9.744468 AACTAAAAAGATTTGTTCATTTACGCT 57.256 25.926 0.00 0.00 0.00 5.07
3552 3775 6.057627 TCATTTACGCTTTTTGGACGTTTA 57.942 33.333 0.00 0.00 40.99 2.01
3553 3776 6.493116 TCATTTACGCTTTTTGGACGTTTAA 58.507 32.000 0.00 0.00 40.99 1.52
3591 3814 7.147707 ACCTACATGTTCCTCTTATCAAGTACC 60.148 40.741 2.30 0.00 0.00 3.34
3618 3841 4.832266 TCAAACAAATATGGTTCTGTGGCT 59.168 37.500 0.00 0.00 32.99 4.75
3663 3886 6.564709 TCTGATTGATGTGCTAATTATGCC 57.435 37.500 4.99 0.00 0.00 4.40
3674 3897 1.392589 AATTATGCCGCAGAACCCTG 58.607 50.000 1.80 0.00 43.22 4.45
3677 3900 2.572095 TATGCCGCAGAACCCTGACG 62.572 60.000 0.00 0.00 43.02 4.35
3706 3933 3.573967 CCCAACCATACTGATTATTGCCC 59.426 47.826 0.00 0.00 0.00 5.36
3710 3937 3.139025 ACCATACTGATTATTGCCCAGCT 59.861 43.478 0.00 0.00 0.00 4.24
3714 3941 2.173356 ACTGATTATTGCCCAGCTAGCA 59.827 45.455 18.83 6.51 38.81 3.49
3716 3943 2.173356 TGATTATTGCCCAGCTAGCAGT 59.827 45.455 18.83 10.22 42.17 4.40
3718 3945 0.181114 TATTGCCCAGCTAGCAGTGG 59.819 55.000 18.83 16.45 42.17 4.00
3719 3946 3.799006 TATTGCCCAGCTAGCAGTGGC 62.799 57.143 26.33 26.33 42.17 5.01
3733 3960 4.439305 GCAGTGGCTTGTTATCATTTGA 57.561 40.909 0.00 0.00 36.96 2.69
3734 3961 4.418392 GCAGTGGCTTGTTATCATTTGAG 58.582 43.478 0.00 0.00 36.96 3.02
3735 3962 4.156556 GCAGTGGCTTGTTATCATTTGAGA 59.843 41.667 0.00 0.00 36.96 3.27
3736 3963 5.335897 GCAGTGGCTTGTTATCATTTGAGAA 60.336 40.000 0.00 0.00 36.96 2.87
3737 3964 6.626623 GCAGTGGCTTGTTATCATTTGAGAAT 60.627 38.462 0.00 0.00 36.96 2.40
3738 3965 6.971184 CAGTGGCTTGTTATCATTTGAGAATC 59.029 38.462 0.00 0.00 0.00 2.52
3841 4070 6.491745 TGGATTTTGAGTTTGCTAACCACATA 59.508 34.615 7.43 2.03 34.71 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 73 2.497675 TCCTAGTTAGCTTCCAGCACAG 59.502 50.000 0.00 0.00 45.56 3.66
156 159 7.547722 GGTACTTTGACTTTCCAAACATGTTTT 59.452 33.333 21.10 5.86 33.07 2.43
203 207 6.050454 TGACTTGTTTATGTACAAACCACG 57.950 37.500 0.00 0.00 37.55 4.94
249 253 1.464997 GATCCTGTCCAGTTGCGTTTC 59.535 52.381 0.00 0.00 0.00 2.78
279 283 5.449177 GGATTCATCCCGATCACAAAAACTC 60.449 44.000 0.00 0.00 41.20 3.01
382 386 9.537192 CCCAAATAACGTACTGATAGTATTCAA 57.463 33.333 0.00 0.00 32.65 2.69
426 430 0.037326 AGCTCGCTGTTTCGGAATCA 60.037 50.000 1.87 1.87 0.00 2.57
503 507 5.632959 TGTTTGTTGTTCTGTTAAAGACCG 58.367 37.500 0.00 0.00 33.46 4.79
536 541 3.502211 CAGTGGCTCGAAAAATAACCTGT 59.498 43.478 0.00 0.00 0.00 4.00
685 690 6.721318 AGACAGGAAAACTAATTGCCTATCA 58.279 36.000 0.00 0.00 46.36 2.15
728 733 6.015940 CACAAAGAGAAGAAAGGTAAAGCCAT 60.016 38.462 0.00 0.00 40.61 4.40
761 774 6.966632 TCATGTCTCAAAACAAAAGAACGAAG 59.033 34.615 0.00 0.00 31.81 3.79
817 831 3.381045 ACGATGCATACGACCATACTTG 58.619 45.455 20.36 0.00 34.70 3.16
886 900 6.368516 ACCAAAACACTCTCAAAACATGTTTG 59.631 34.615 23.93 16.99 41.39 2.93
890 904 5.687285 GCTACCAAAACACTCTCAAAACATG 59.313 40.000 0.00 0.00 0.00 3.21
892 906 4.201871 CGCTACCAAAACACTCTCAAAACA 60.202 41.667 0.00 0.00 0.00 2.83
893 907 4.201881 ACGCTACCAAAACACTCTCAAAAC 60.202 41.667 0.00 0.00 0.00 2.43
894 908 3.942748 ACGCTACCAAAACACTCTCAAAA 59.057 39.130 0.00 0.00 0.00 2.44
895 909 3.311322 CACGCTACCAAAACACTCTCAAA 59.689 43.478 0.00 0.00 0.00 2.69
896 910 2.869801 CACGCTACCAAAACACTCTCAA 59.130 45.455 0.00 0.00 0.00 3.02
897 911 2.479837 CACGCTACCAAAACACTCTCA 58.520 47.619 0.00 0.00 0.00 3.27
928 942 1.647334 TTGGGTTTGGGTTCGGAGGT 61.647 55.000 0.00 0.00 0.00 3.85
929 943 1.151908 TTGGGTTTGGGTTCGGAGG 59.848 57.895 0.00 0.00 0.00 4.30
930 944 1.176619 GGTTGGGTTTGGGTTCGGAG 61.177 60.000 0.00 0.00 0.00 4.63
1299 1314 1.898154 GGAGAGCTTGTCCGCCTTA 59.102 57.895 0.53 0.00 0.00 2.69
1736 1775 8.561769 TCTAATTTAGGGGTACAAATCCATTCA 58.438 33.333 3.66 0.00 0.00 2.57
1952 2154 7.308435 CAAAGTGTGATTGATAGGGAAGAAAC 58.692 38.462 0.00 0.00 0.00 2.78
2427 2635 9.553064 GACATGAAGGAATGAGACTTATTGTAT 57.447 33.333 0.00 0.00 0.00 2.29
2639 2861 0.395312 GTCGGGAAACAGGTTCTCCA 59.605 55.000 0.00 0.00 32.45 3.86
2673 2895 5.073311 TCAAGAACCCTCTTATGACTTCG 57.927 43.478 0.00 0.00 40.05 3.79
3343 3565 4.558226 TCAGTGCTTCACTTGACCATAT 57.442 40.909 0.00 0.00 42.59 1.78
3368 3590 8.911918 TTCACTTTTATTCTGTTAGCCAGTTA 57.088 30.769 0.00 0.00 42.19 2.24
3369 3591 7.522236 GCTTCACTTTTATTCTGTTAGCCAGTT 60.522 37.037 0.00 0.00 42.19 3.16
3370 3592 6.072452 GCTTCACTTTTATTCTGTTAGCCAGT 60.072 38.462 0.00 0.00 42.19 4.00
3371 3593 6.072508 TGCTTCACTTTTATTCTGTTAGCCAG 60.073 38.462 0.00 0.00 42.97 4.85
3372 3594 5.767665 TGCTTCACTTTTATTCTGTTAGCCA 59.232 36.000 0.00 0.00 0.00 4.75
3401 3624 3.684788 ACTTTGTGCTAGCCGTTAGAATG 59.315 43.478 13.29 3.41 0.00 2.67
3405 3628 3.846360 AGTACTTTGTGCTAGCCGTTAG 58.154 45.455 13.29 7.32 0.00 2.34
3406 3629 3.256383 TGAGTACTTTGTGCTAGCCGTTA 59.744 43.478 13.29 0.00 0.00 3.18
3409 3632 2.363788 TGAGTACTTTGTGCTAGCCG 57.636 50.000 13.29 0.00 0.00 5.52
3424 3647 7.041721 TGCTTCATCATCGTTTTAGTATGAGT 58.958 34.615 0.00 0.00 33.40 3.41
3437 3660 4.319333 GCTACTCCATTTGCTTCATCATCG 60.319 45.833 0.00 0.00 0.00 3.84
3489 3712 5.875910 TCTGAAGAACCGAACAAAGTTTACA 59.124 36.000 0.00 0.00 0.00 2.41
3492 3715 5.637809 GTTCTGAAGAACCGAACAAAGTTT 58.362 37.500 11.41 0.00 46.42 2.66
3539 3762 7.581476 TGCAAAACAAATTAAACGTCCAAAAA 58.419 26.923 0.00 0.00 0.00 1.94
3552 3775 6.259829 GGAACATGTAGGTTGCAAAACAAATT 59.740 34.615 0.00 5.36 40.82 1.82
3553 3776 5.757808 GGAACATGTAGGTTGCAAAACAAAT 59.242 36.000 0.00 0.00 40.82 2.32
3591 3814 5.624900 CACAGAACCATATTTGTTTGACACG 59.375 40.000 0.00 0.00 0.00 4.49
3618 3841 3.887352 TGGTACAACAGCACAAAACCTA 58.113 40.909 0.00 0.00 31.92 3.08
3663 3886 0.179100 ATGATCGTCAGGGTTCTGCG 60.179 55.000 0.00 0.00 40.69 5.18
3674 3897 3.809832 CAGTATGGTTGGGAATGATCGTC 59.190 47.826 0.00 0.00 0.00 4.20
3677 3900 8.517878 CAATAATCAGTATGGTTGGGAATGATC 58.482 37.037 0.00 0.00 41.38 2.92
3714 3941 6.888632 AGATTCTCAAATGATAACAAGCCACT 59.111 34.615 0.00 0.00 0.00 4.00
3716 3943 7.114754 AGAGATTCTCAAATGATAACAAGCCA 58.885 34.615 15.83 0.00 32.06 4.75
3718 3945 7.431668 GCAAGAGATTCTCAAATGATAACAAGC 59.568 37.037 15.83 0.00 32.06 4.01
3719 3946 8.675504 AGCAAGAGATTCTCAAATGATAACAAG 58.324 33.333 15.83 0.00 32.06 3.16
3721 3948 9.671279 TTAGCAAGAGATTCTCAAATGATAACA 57.329 29.630 15.83 0.00 32.06 2.41
3725 3952 8.975663 TGATTAGCAAGAGATTCTCAAATGAT 57.024 30.769 15.83 11.89 32.06 2.45
3726 3953 7.498239 CCTGATTAGCAAGAGATTCTCAAATGA 59.502 37.037 15.83 1.93 32.06 2.57
3727 3954 7.498239 TCCTGATTAGCAAGAGATTCTCAAATG 59.502 37.037 15.83 11.80 32.06 2.32
3728 3955 7.571919 TCCTGATTAGCAAGAGATTCTCAAAT 58.428 34.615 15.83 7.07 32.06 2.32
3729 3956 6.950842 TCCTGATTAGCAAGAGATTCTCAAA 58.049 36.000 15.83 2.93 32.06 2.69
3730 3957 6.550938 TCCTGATTAGCAAGAGATTCTCAA 57.449 37.500 15.83 1.52 32.06 3.02
3731 3958 6.325804 TGATCCTGATTAGCAAGAGATTCTCA 59.674 38.462 15.83 0.00 32.06 3.27
3732 3959 6.757237 TGATCCTGATTAGCAAGAGATTCTC 58.243 40.000 5.49 5.49 0.00 2.87
3733 3960 6.744175 TGATCCTGATTAGCAAGAGATTCT 57.256 37.500 0.00 0.00 0.00 2.40
3734 3961 6.935771 ACATGATCCTGATTAGCAAGAGATTC 59.064 38.462 0.00 0.00 0.00 2.52
3735 3962 6.839454 ACATGATCCTGATTAGCAAGAGATT 58.161 36.000 0.00 0.00 0.00 2.40
3736 3963 6.436738 ACATGATCCTGATTAGCAAGAGAT 57.563 37.500 0.00 0.00 0.00 2.75
3737 3964 5.883685 ACATGATCCTGATTAGCAAGAGA 57.116 39.130 0.00 0.00 0.00 3.10
3738 3965 6.147492 GCTAACATGATCCTGATTAGCAAGAG 59.853 42.308 23.74 4.93 44.58 2.85
3818 4047 8.986477 AATATGTGGTTAGCAAACTCAAAATC 57.014 30.769 0.00 0.00 35.81 2.17
3841 4070 2.046314 CTCCCAACCGCGTGGAAT 60.046 61.111 24.59 7.18 41.65 3.01



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

AutoCloner maintained by Alex Coulton.