Multiple sequence alignment - TraesCS2A01G287500

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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 TraesCS2A01G287500 chr2A 100.000 4291 0 0 1 4291 490658591 490662881 0 7925
1 TraesCS2A01G287500 chr2D 97.208 3582 78 15 721 4291 364163688 364167258 0 6041
2 TraesCS2A01G287500 chr2D 88.658 723 71 11 5 720 78341511 78342229 0 870
3 TraesCS2A01G287500 chr2D 88.299 735 72 8 3 734 38130135 38129412 0 869
4 TraesCS2A01G287500 chr2B 95.789 3562 96 20 744 4291 432553514 432557035 0 5698
5 TraesCS2A01G287500 chr4D 91.563 723 51 6 3 723 170246699 170247413 0 989
6 TraesCS2A01G287500 chr4D 89.736 721 61 6 3 720 370630579 370629869 0 909
7 TraesCS2A01G287500 chr7D 88.781 722 75 4 3 721 129779132 129779850 0 880
8 TraesCS2A01G287500 chr5D 88.736 728 68 13 3 724 188384899 188385618 0 878
9 TraesCS2A01G287500 chr5D 88.999 709 66 9 4 708 551048266 551048966 0 867
10 TraesCS2A01G287500 chr5D 88.056 720 77 7 4 719 45264999 45264285 0 845
11 TraesCS2A01G287500 chr3D 87.933 721 75 8 3 720 554203538 554202827 0 839


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 TraesCS2A01G287500 chr2A 490658591 490662881 4290 False 7925 7925 100.000 1 4291 1 chr2A.!!$F1 4290
1 TraesCS2A01G287500 chr2D 364163688 364167258 3570 False 6041 6041 97.208 721 4291 1 chr2D.!!$F2 3570
2 TraesCS2A01G287500 chr2D 78341511 78342229 718 False 870 870 88.658 5 720 1 chr2D.!!$F1 715
3 TraesCS2A01G287500 chr2D 38129412 38130135 723 True 869 869 88.299 3 734 1 chr2D.!!$R1 731
4 TraesCS2A01G287500 chr2B 432553514 432557035 3521 False 5698 5698 95.789 744 4291 1 chr2B.!!$F1 3547
5 TraesCS2A01G287500 chr4D 170246699 170247413 714 False 989 989 91.563 3 723 1 chr4D.!!$F1 720
6 TraesCS2A01G287500 chr4D 370629869 370630579 710 True 909 909 89.736 3 720 1 chr4D.!!$R1 717
7 TraesCS2A01G287500 chr7D 129779132 129779850 718 False 880 880 88.781 3 721 1 chr7D.!!$F1 718
8 TraesCS2A01G287500 chr5D 188384899 188385618 719 False 878 878 88.736 3 724 1 chr5D.!!$F1 721
9 TraesCS2A01G287500 chr5D 551048266 551048966 700 False 867 867 88.999 4 708 1 chr5D.!!$F2 704
10 TraesCS2A01G287500 chr5D 45264285 45264999 714 True 845 845 88.056 4 719 1 chr5D.!!$R1 715
11 TraesCS2A01G287500 chr3D 554202827 554203538 711 True 839 839 87.933 3 720 1 chr3D.!!$R1 717

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
696 719 0.107214 ACAACCACCCGATATGCCAG 60.107 55.000 0.0 0.0 0.00 4.85 F
1362 1386 1.152525 GAGGGGCGAGGACCATAGA 60.153 63.158 0.0 0.0 27.52 1.98 F
2279 2312 2.358898 CCAACTCAAACCAAGGAGTGTG 59.641 50.000 0.0 0.0 43.26 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2312 1.012486 GCTTGCATTCCAGCAGTTGC 61.012 55.000 3.21 0.00 46.54 4.17 R
2301 2334 1.198867 CACCGATATCCTGAGCTCTCG 59.801 57.143 16.19 14.01 0.00 4.04 R
3554 3593 1.537202 CTGACAAGCTGTAGTTTGCCC 59.463 52.381 8.16 2.53 39.43 5.36 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
78 81 2.444766 CCTCCCTATGCCAAATTCCTCT 59.555 50.000 0.00 0.00 0.00 3.69
86 91 6.379417 CCTATGCCAAATTCCTCTTTTCTCTT 59.621 38.462 0.00 0.00 0.00 2.85
125 131 0.808755 CGCACCCTTCATTACCAACC 59.191 55.000 0.00 0.00 0.00 3.77
196 202 1.473257 GGCAGATCTGGCGTATGTTGA 60.473 52.381 30.74 0.00 46.08 3.18
220 226 2.661195 GGCAAATGCGAATACACACAAC 59.339 45.455 0.00 0.00 43.26 3.32
224 230 2.535012 TGCGAATACACACAACTCCA 57.465 45.000 0.00 0.00 0.00 3.86
244 251 4.268720 GGGTGTTTGCCCTGACAA 57.731 55.556 0.00 0.00 45.22 3.18
259 266 2.418976 CTGACAACGTGGATCTAGTCGA 59.581 50.000 0.00 0.00 0.00 4.20
317 325 5.422331 TGGACAGAAGAAGGACGAGAAATAT 59.578 40.000 0.00 0.00 0.00 1.28
321 329 8.294954 ACAGAAGAAGGACGAGAAATATAAGA 57.705 34.615 0.00 0.00 0.00 2.10
372 393 1.462627 TCTTGGGAGGACGGGGTTT 60.463 57.895 0.00 0.00 0.00 3.27
378 399 4.932605 AGGACGGGGTTTGGGGGT 62.933 66.667 0.00 0.00 0.00 4.95
385 406 4.631740 GGTTTGGGGGTGGGGGTG 62.632 72.222 0.00 0.00 0.00 4.61
401 422 4.338710 TGGGTGGGTGTTAGCGGC 62.339 66.667 0.00 0.00 0.00 6.53
431 452 2.114616 CTAGGGATCTGCTCTGGTTGT 58.885 52.381 0.00 0.00 0.00 3.32
438 459 0.322277 CTGCTCTGGTTGTCATGGCT 60.322 55.000 0.00 0.00 0.00 4.75
453 474 2.623418 TGGCTACCAGAGAAGGAAGA 57.377 50.000 0.00 0.00 0.00 2.87
459 480 2.808919 ACCAGAGAAGGAAGACGATGA 58.191 47.619 0.00 0.00 0.00 2.92
477 498 0.963225 GAAGGTAGGGGATCGAGAGC 59.037 60.000 0.00 0.00 0.00 4.09
566 588 1.522355 CGGGCAGCACGATCATTCT 60.522 57.895 13.22 0.00 0.00 2.40
580 602 1.911766 ATTCTCCCGGACGTGTGGT 60.912 57.895 0.73 0.00 0.00 4.16
668 691 2.842462 TCTCCGTGCCACACAGGT 60.842 61.111 0.00 0.00 40.61 4.00
696 719 0.107214 ACAACCACCCGATATGCCAG 60.107 55.000 0.00 0.00 0.00 4.85
702 725 1.956170 CCCGATATGCCAGACGTGC 60.956 63.158 0.00 0.00 0.00 5.34
978 1002 3.308323 CGAGAAGCTTCTGTAAGATTGGC 59.692 47.826 33.07 13.29 46.36 4.52
1119 1143 2.584873 TACCGAGCTCCTCCTTCCCC 62.585 65.000 8.47 0.00 0.00 4.81
1362 1386 1.152525 GAGGGGCGAGGACCATAGA 60.153 63.158 0.00 0.00 27.52 1.98
1483 1507 5.895636 TGATTTGACCATTTGCTATTCGT 57.104 34.783 0.00 0.00 0.00 3.85
1514 1538 3.582208 TGCTTGTGGAAATTAGGGCATTT 59.418 39.130 0.00 0.00 0.00 2.32
1566 1594 5.196341 TCATTTGCTACTCATACCCTACG 57.804 43.478 0.00 0.00 0.00 3.51
1678 1707 5.571784 ATCGTTGTCATCAATTTGCTCAT 57.428 34.783 0.00 0.00 35.92 2.90
1706 1735 6.551385 TGTTGTTTGCTTGTTGTGATTTTT 57.449 29.167 0.00 0.00 0.00 1.94
1737 1766 3.483808 TTTGCAATGGGGTCTTTTTCC 57.516 42.857 0.00 0.00 0.00 3.13
1817 1849 4.405358 ACTGTTCATTTCTTTTGAAGGCCA 59.595 37.500 5.01 0.00 39.88 5.36
2154 2187 3.181461 CCTGACCTCCTTGATGATACCAC 60.181 52.174 0.00 0.00 0.00 4.16
2253 2286 4.234574 GGTTCAGTTAAAATTGGCCTTCG 58.765 43.478 3.32 0.00 0.00 3.79
2279 2312 2.358898 CCAACTCAAACCAAGGAGTGTG 59.641 50.000 0.00 0.00 43.26 3.82
2487 2520 1.067060 GGTCACAACAAAGGGCAACTC 59.933 52.381 0.00 0.00 0.00 3.01
2578 2611 2.217510 TGGAGACACCAGAGAGTACC 57.782 55.000 0.00 0.00 44.64 3.34
2856 2889 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
2857 2890 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
2858 2891 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
3008 3042 4.507756 TCGATGATGCTACATGTGTTTAGC 59.492 41.667 9.11 10.09 36.20 3.09
3155 3189 4.378874 GCAGTTGCACTCCTAGAATTCAAC 60.379 45.833 8.44 0.70 41.59 3.18
3274 3313 4.103153 ACTTGGAGAGAAACAGAACATCCA 59.897 41.667 0.00 0.00 33.68 3.41
3399 3438 3.091545 GCATCTCCCATGAGGAAAACAA 58.908 45.455 0.00 0.00 46.94 2.83
3473 3512 3.741249 TCGAATGCCGAGATACTCTACT 58.259 45.455 0.00 0.00 43.23 2.57
3554 3593 1.136690 TGCTCAAGACGTTTACAGCG 58.863 50.000 0.00 0.00 0.00 5.18
3900 3939 3.118408 AGGTAGTGCTGTTGTTTGTCTCA 60.118 43.478 0.00 0.00 0.00 3.27
3975 4014 7.094205 GGGAGAACTTCATCTTGCTGAAATAAA 60.094 37.037 0.00 0.00 34.86 1.40
4017 4056 6.524734 TGTTTCTTCTCAACTCTCATAAGCA 58.475 36.000 0.00 0.00 0.00 3.91
4110 4153 5.935206 TCACTAATGTAAGACGATTTGGCAA 59.065 36.000 0.00 0.00 0.00 4.52
4159 4202 3.191791 GCCAAACGGCTTAAATTAGTGGA 59.808 43.478 0.00 0.00 46.85 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.474879 TGCCATCTATCGTTGTCGTCA 59.525 47.619 0.00 0.00 38.33 4.35
1 2 2.203800 TGCCATCTATCGTTGTCGTC 57.796 50.000 0.00 0.00 38.33 4.20
21 22 5.585820 TGCCACTTGTATATAACGTCAGA 57.414 39.130 0.00 0.00 0.00 3.27
110 116 2.356135 CGAGTGGTTGGTAATGAAGGG 58.644 52.381 0.00 0.00 0.00 3.95
125 131 2.639286 GTTGGCTTGGTGCGAGTG 59.361 61.111 0.00 0.00 44.05 3.51
196 202 2.098614 TGTGTATTCGCATTTGCCCAT 58.901 42.857 0.00 0.00 37.91 4.00
220 226 1.984026 GGGCAAACACCCCATGGAG 60.984 63.158 15.22 0.97 45.00 3.86
244 251 2.920524 AGATGTCGACTAGATCCACGT 58.079 47.619 17.92 0.00 0.00 4.49
259 266 1.742761 CAGATTGCCCACGAAGATGT 58.257 50.000 0.00 0.00 0.00 3.06
317 325 3.891977 CAGGTGGATCTCCGATCTTCTTA 59.108 47.826 4.10 0.00 39.43 2.10
321 329 2.166907 ACAGGTGGATCTCCGATCTT 57.833 50.000 4.10 0.00 39.43 2.40
378 399 3.751767 TAACACCCACCCACCCCCA 62.752 63.158 0.00 0.00 0.00 4.96
384 405 4.338710 GCCGCTAACACCCACCCA 62.339 66.667 0.00 0.00 0.00 4.51
390 411 4.832608 CTCCCCGCCGCTAACACC 62.833 72.222 0.00 0.00 0.00 4.16
391 412 4.832608 CCTCCCCGCCGCTAACAC 62.833 72.222 0.00 0.00 0.00 3.32
431 452 2.550277 TCCTTCTCTGGTAGCCATGA 57.450 50.000 0.00 0.00 30.82 3.07
438 459 3.964411 TCATCGTCTTCCTTCTCTGGTA 58.036 45.455 0.00 0.00 0.00 3.25
453 474 1.133575 TCGATCCCCTACCTTCATCGT 60.134 52.381 0.00 0.00 38.02 3.73
459 480 0.558712 AGCTCTCGATCCCCTACCTT 59.441 55.000 0.00 0.00 0.00 3.50
477 498 4.253257 GCCGCCGTCGTCTCCTAG 62.253 72.222 0.00 0.00 0.00 3.02
566 588 4.953010 TCGACCACACGTCCGGGA 62.953 66.667 0.00 0.00 38.36 5.14
580 602 0.393448 TCCGGTGTGTGGAAAATCGA 59.607 50.000 0.00 0.00 30.98 3.59
696 719 1.515519 TCGATAACTGCCGCACGTC 60.516 57.895 0.00 0.00 0.00 4.34
702 725 0.457166 TTGGACGTCGATAACTGCCG 60.457 55.000 9.92 0.00 0.00 5.69
765 789 6.497437 ACGTCACATGCATAGTTAATACGTA 58.503 36.000 0.00 0.00 37.99 3.57
767 791 5.883328 ACGTCACATGCATAGTTAATACG 57.117 39.130 0.00 5.69 0.00 3.06
777 801 1.656652 GGCTAGAACGTCACATGCAT 58.343 50.000 0.00 0.00 0.00 3.96
830 854 0.325602 TAATCGTTTCCGGCTTGGGT 59.674 50.000 0.00 0.00 38.76 4.51
994 1018 4.996434 CTCGGCCGCCATGGATCC 62.996 72.222 23.51 11.52 42.00 3.36
1101 1125 2.364448 GGGAAGGAGGAGCTCGGT 60.364 66.667 7.83 0.00 0.00 4.69
1119 1143 4.379243 ACGGACCAGGAAGCTGCG 62.379 66.667 0.00 0.00 0.00 5.18
1362 1386 1.261238 CCTCGTCCTGCTCCTCCTTT 61.261 60.000 0.00 0.00 0.00 3.11
1483 1507 4.870123 ATTTCCACAAGCAATACAGCAA 57.130 36.364 0.00 0.00 36.85 3.91
1566 1594 2.223479 TGAAACGTTTCTTCAGCAAGCC 60.223 45.455 33.94 10.96 38.02 4.35
1678 1707 5.233225 TCACAACAAGCAAACAACATGAAA 58.767 33.333 0.00 0.00 0.00 2.69
1706 1735 3.568853 CCCCATTGCAAAAATCAAAAGCA 59.431 39.130 1.71 0.00 0.00 3.91
1737 1766 3.142838 CCCTGCGGCATTTCCCTG 61.143 66.667 1.75 0.00 0.00 4.45
1922 1954 9.125026 CCTTACCTGCATTTAGTATCAGATTTT 57.875 33.333 0.00 0.00 0.00 1.82
2154 2187 4.880759 AGATAAACCGCAGATCTCATCAG 58.119 43.478 0.00 0.00 0.00 2.90
2253 2286 3.551846 TCCTTGGTTTGAGTTGGAGAAC 58.448 45.455 0.00 0.00 0.00 3.01
2279 2312 1.012486 GCTTGCATTCCAGCAGTTGC 61.012 55.000 3.21 0.00 46.54 4.17
2301 2334 1.198867 CACCGATATCCTGAGCTCTCG 59.801 57.143 16.19 14.01 0.00 4.04
2578 2611 2.356382 AGCTCTCCTGTTAGATTCGTCG 59.644 50.000 0.00 0.00 0.00 5.12
2856 2889 2.469274 AGAGTTGGTCTGCATCAGTG 57.531 50.000 0.00 0.00 32.57 3.66
2857 2890 3.834813 TCTTAGAGTTGGTCTGCATCAGT 59.165 43.478 0.00 0.00 36.64 3.41
2858 2891 4.462508 TCTTAGAGTTGGTCTGCATCAG 57.537 45.455 0.00 0.00 36.64 2.90
3008 3042 4.510340 GGCATAGGTACAACAAAGTATCCG 59.490 45.833 0.00 0.00 0.00 4.18
3155 3189 4.060900 ACACTGCTCATCACTGTAACTTG 58.939 43.478 0.00 0.00 0.00 3.16
3195 3229 4.124970 GTCACGAAACTACAAAGGGAAGT 58.875 43.478 0.00 0.00 0.00 3.01
3274 3313 2.493278 GGTGCTTAATTGTGGACTGCAT 59.507 45.455 0.00 0.00 0.00 3.96
3348 3387 8.239314 AGCTTGATAACATTTGTTGTACATCAG 58.761 33.333 6.71 0.00 39.33 2.90
3399 3438 2.026449 CAGAAACCTGAAGGAGATGGCT 60.026 50.000 2.62 0.00 38.94 4.75
3554 3593 1.537202 CTGACAAGCTGTAGTTTGCCC 59.463 52.381 8.16 2.53 39.43 5.36
3848 3887 4.990426 CCAAATTTTTAACAGCAGGGACAG 59.010 41.667 0.00 0.00 0.00 3.51
3884 3923 2.419673 CAGTGTGAGACAAACAACAGCA 59.580 45.455 0.00 0.00 0.00 4.41
4017 4056 6.731292 ACAGAGCCCAAAACTTTTAGATTT 57.269 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.