Multiple sequence alignment - TraesCS2A01G476200

Loading Multiple Alignment...

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 TraesCS2A01G476200 chr2A 100.000 4078 0 0 1 4078 716227008 716231085 0 7531
1 TraesCS2A01G476200 chr2D 90.614 4070 255 63 2 4038 578696103 578700078 0 5282
2 TraesCS2A01G476200 chr2B 94.040 3406 169 24 700 4077 695587622 695591021 0 5134


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 TraesCS2A01G476200 chr2A 716227008 716231085 4077 False 7531 7531 100.000 1 4078 1 chr2A.!!$F1 4077
1 TraesCS2A01G476200 chr2D 578696103 578700078 3975 False 5282 5282 90.614 2 4038 1 chr2D.!!$F1 4036
2 TraesCS2A01G476200 chr2B 695587622 695591021 3399 False 5134 5134 94.040 700 4077 1 chr2B.!!$F1 3377

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
747 761 0.178970 GCCCAGGAGACCGGTATCTA 60.179 60.000 27.17 0.0 0.00 1.98 F
882 902 0.948623 CGCCATCGTCACTGACCAAA 60.949 55.000 3.50 0.0 0.00 3.28 F
1637 1665 1.228337 TGCCACTCATTGCACTGCT 60.228 52.632 1.98 0.0 31.31 4.24 F
2799 2843 0.617820 GGGGTCAGTTAGAGGAGGCA 60.618 60.000 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1665 0.313672 GCGGGACTGCACATTTCAAA 59.686 50.0 0.00 0.0 34.15 2.69 R
2796 2840 0.833287 TCTCCACTAGCTTCCATGCC 59.167 55.0 0.00 0.0 0.00 4.40 R
2892 2936 0.603707 TCTTGGCTGCAGTTTCTCCG 60.604 55.0 16.64 0.0 0.00 4.63 R
3632 3681 5.248020 AGAAATGGATAGCATAGAGTGGGAG 59.752 44.0 0.00 0.0 0.00 4.30 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
45 46 9.678941 GTTTCTAAACAAGGGATTTTCTGTTAG 57.321 33.333 0.74 0.00 38.74 2.34
50 51 7.511959 AACAAGGGATTTTCTGTTAGTTCTC 57.488 36.000 0.00 0.00 0.00 2.87
75 76 8.916062 TCTATTAGGTTTTTCGGTTTCCTTTTT 58.084 29.630 0.00 0.00 0.00 1.94
76 77 7.780008 ATTAGGTTTTTCGGTTTCCTTTTTG 57.220 32.000 0.00 0.00 0.00 2.44
77 78 4.509616 AGGTTTTTCGGTTTCCTTTTTGG 58.490 39.130 0.00 0.00 37.10 3.28
80 81 5.181622 GGTTTTTCGGTTTCCTTTTTGGTTT 59.818 36.000 0.00 0.00 37.07 3.27
82 83 6.879276 TTTTCGGTTTCCTTTTTGGTTTTT 57.121 29.167 0.00 0.00 37.07 1.94
83 84 7.974482 TTTTCGGTTTCCTTTTTGGTTTTTA 57.026 28.000 0.00 0.00 37.07 1.52
85 86 8.563123 TTTCGGTTTCCTTTTTGGTTTTTATT 57.437 26.923 0.00 0.00 37.07 1.40
86 87 7.773864 TCGGTTTCCTTTTTGGTTTTTATTC 57.226 32.000 0.00 0.00 37.07 1.75
87 88 7.557724 TCGGTTTCCTTTTTGGTTTTTATTCT 58.442 30.769 0.00 0.00 37.07 2.40
89 90 8.332464 CGGTTTCCTTTTTGGTTTTTATTCTTC 58.668 33.333 0.00 0.00 37.07 2.87
256 260 7.593875 TGTTCACCTTTTGTTTTCTGAATTG 57.406 32.000 0.00 0.00 0.00 2.32
475 479 7.336931 ACTTGAAAAATACTCCTATGTTGCGAT 59.663 33.333 0.00 0.00 0.00 4.58
500 504 7.262772 TGCTACAGTAATCATACAGTAACACC 58.737 38.462 0.00 0.00 34.72 4.16
509 513 0.831966 ACAGTAACACCGGGACAACA 59.168 50.000 6.32 0.00 0.00 3.33
516 520 5.771165 AGTAACACCGGGACAACAAATAATT 59.229 36.000 6.32 0.00 0.00 1.40
528 532 6.381801 ACAACAAATAATTGCTACAGTGCTC 58.618 36.000 0.00 0.00 40.34 4.26
542 546 1.665916 TGCTCTCGCTGCACTGAAC 60.666 57.895 0.00 0.00 35.31 3.18
574 578 4.389992 AGTCAGTGATTGTTTGATACAGCG 59.610 41.667 0.00 0.00 38.19 5.18
696 707 1.304547 CCCTCACTCCTCGTCCTGT 60.305 63.158 0.00 0.00 0.00 4.00
747 761 0.178970 GCCCAGGAGACCGGTATCTA 60.179 60.000 27.17 0.00 0.00 1.98
755 769 3.374678 GGAGACCGGTATCTAGATTAGCG 59.625 52.174 27.17 16.14 34.90 4.26
788 802 1.000506 GCCTTAATGCCAGCCATCATG 59.999 52.381 0.00 0.00 31.43 3.07
793 813 1.855295 ATGCCAGCCATCATGAACAA 58.145 45.000 0.00 0.00 0.00 2.83
874 894 4.451150 TCCCTGCGCCATCGTCAC 62.451 66.667 4.18 0.00 38.14 3.67
882 902 0.948623 CGCCATCGTCACTGACCAAA 60.949 55.000 3.50 0.00 0.00 3.28
916 936 1.304713 TCCCACGAGGAGGTACACC 60.305 63.158 0.00 0.00 40.93 4.16
977 997 4.211125 AGCTTCTCTATTCCACATCTCGA 58.789 43.478 0.00 0.00 0.00 4.04
1293 1314 2.434884 CTCATGCGCACTTCCGGT 60.435 61.111 14.90 0.00 0.00 5.28
1406 1427 3.647771 GGCCAAGGGGAGGTTCGT 61.648 66.667 0.00 0.00 35.59 3.85
1431 1452 3.121030 ATGTTCGTGCAGAGCGCC 61.121 61.111 2.29 0.00 41.33 6.53
1470 1491 4.314440 TGCGGGTCTGTGGCTGAC 62.314 66.667 0.00 0.00 0.00 3.51
1490 1511 1.375396 CGAGGCGGATGTTTGTGGA 60.375 57.895 0.00 0.00 0.00 4.02
1515 1536 2.573915 GGAGAGGAAGGATGTGGTTTCT 59.426 50.000 0.00 0.00 0.00 2.52
1637 1665 1.228337 TGCCACTCATTGCACTGCT 60.228 52.632 1.98 0.00 31.31 4.24
1671 1699 2.557056 GTCCCGCTCACATACTGCTATA 59.443 50.000 0.00 0.00 0.00 1.31
1686 1714 4.876107 ACTGCTATAAACACCTCAAATCCG 59.124 41.667 0.00 0.00 0.00 4.18
1712 1748 5.393027 GCCCTTCATTGTAATTGTAGTGTGG 60.393 44.000 0.00 0.00 0.00 4.17
1739 1775 8.492748 CATGCATGCCATATTTGATTTTAGTTC 58.507 33.333 14.93 0.00 31.47 3.01
1866 1903 7.604927 TGAGGTAACGTTGACATAAAATTAGCT 59.395 33.333 11.99 0.51 46.39 3.32
1874 1911 9.393249 CGTTGACATAAAATTAGCTCTTTCAAA 57.607 29.630 0.00 0.00 0.00 2.69
1907 1949 4.331968 TCCACTGTTCAACTTCTGTTTGT 58.668 39.130 0.00 0.00 33.52 2.83
1953 1996 9.825972 AAATTTCTGTTATACTGTCGTTGAATG 57.174 29.630 0.00 0.00 0.00 2.67
2040 2084 4.240096 CTGACCATTTCACATTTGGAAGC 58.760 43.478 0.00 0.00 34.52 3.86
2122 2166 5.130350 GCATAATAAAGTTGGGCTACTGGA 58.870 41.667 0.00 0.00 0.00 3.86
2271 2315 4.643334 GGGTACTCCATGGATAAAAACCAC 59.357 45.833 16.63 8.75 40.36 4.16
2292 2336 2.753452 CACTGAAGATGCAATGGAGCTT 59.247 45.455 4.65 4.65 34.99 3.74
2370 2414 2.289010 GCTTGGCCTTTGTGCTAATGTT 60.289 45.455 3.32 0.00 30.97 2.71
2593 2637 2.373707 GGGGGAGATGCTGTGAGCT 61.374 63.158 0.00 0.00 42.97 4.09
2796 2840 1.196012 GTGGGGGTCAGTTAGAGGAG 58.804 60.000 0.00 0.00 0.00 3.69
2799 2843 0.617820 GGGGTCAGTTAGAGGAGGCA 60.618 60.000 0.00 0.00 0.00 4.75
2827 2871 4.586841 AGCTAGTGGAGAATGTGGATACTC 59.413 45.833 0.00 0.00 37.61 2.59
2964 3008 3.343617 ACACTATACCGTGCTTGCAAAT 58.656 40.909 0.00 0.00 38.45 2.32
2965 3009 3.756434 ACACTATACCGTGCTTGCAAATT 59.244 39.130 0.00 0.00 38.45 1.82
2973 3017 2.222332 CGTGCTTGCAAATTTGTATGCG 60.222 45.455 28.79 18.46 45.47 4.73
3033 3077 6.127366 GGAAATTAATGGCTGAAACATCTGGA 60.127 38.462 0.00 0.00 0.00 3.86
3054 3098 2.760387 GCAAGGAAGCTGGTTGCAGC 62.760 60.000 18.35 12.23 44.87 5.25
3122 3166 5.303589 CAGATAATGGTCATTTGCCCTGATT 59.696 40.000 1.28 0.00 32.50 2.57
3148 3192 4.987408 CACCAAATGCATCTGGATTACA 57.013 40.909 25.94 0.00 34.94 2.41
3199 3243 2.158900 CCGATCCAACATGTAGAGCCTT 60.159 50.000 0.00 0.00 0.00 4.35
3378 3423 6.969043 TGGATAATCTGTTGGGTTACATTCT 58.031 36.000 0.00 0.00 0.00 2.40
3431 3476 3.119495 ACTGTAAAAGATTTGCGGATGCC 60.119 43.478 6.73 0.00 41.78 4.40
3475 3520 5.753438 TGTCAGTATTCTCAATTATGTCCGC 59.247 40.000 0.00 0.00 0.00 5.54
3487 3532 6.542005 TCAATTATGTCCGCTGTATTGATTGT 59.458 34.615 0.00 0.00 29.76 2.71
3520 3565 8.585018 ACAGGTTTATGGTCTTAATCCTTTTTG 58.415 33.333 4.47 0.00 31.71 2.44
3528 3574 8.754991 TGGTCTTAATCCTTTTTGTTACTTCA 57.245 30.769 0.00 0.00 0.00 3.02
3632 3681 4.219944 TGACTATATGGCGATACCCTGTTC 59.780 45.833 0.00 0.00 37.83 3.18
3634 3683 3.963428 ATATGGCGATACCCTGTTCTC 57.037 47.619 0.00 0.00 37.83 2.87
3643 3692 2.950990 ACCCTGTTCTCCCACTCTAT 57.049 50.000 0.00 0.00 0.00 1.98
3815 3865 1.670087 CGGTGTCGAGTGAAGCAGATT 60.670 52.381 0.00 0.00 39.00 2.40
3861 3911 1.034838 AAAGCCACCACGTTTCAGCA 61.035 50.000 0.00 0.00 0.00 4.41
3864 3914 1.358759 CCACCACGTTTCAGCAACC 59.641 57.895 0.00 0.00 30.65 3.77
3902 3953 2.627945 TGTTATCGAACCCATGTGCTC 58.372 47.619 0.00 0.00 34.38 4.26
3980 4031 7.816031 CACTACTTTTGATCTGAATGGCAAAAT 59.184 33.333 0.00 0.00 38.89 1.82
3981 4032 9.023962 ACTACTTTTGATCTGAATGGCAAAATA 57.976 29.630 0.00 0.00 38.89 1.40
4077 4130 6.014771 AGTATAGTCCTGACTGATACACCA 57.985 41.667 10.02 0.00 42.52 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.746535 AACAAAGGTTTCCAAAACCGAT 57.253 36.364 14.21 6.55 44.82 4.18
19 20 9.678941 CTAACAGAAAATCCCTTGTTTAGAAAC 57.321 33.333 0.00 0.00 39.33 2.78
22 23 8.990163 AACTAACAGAAAATCCCTTGTTTAGA 57.010 30.769 0.00 0.00 0.00 2.10
28 29 9.454859 AATAGAGAACTAACAGAAAATCCCTTG 57.545 33.333 0.00 0.00 32.04 3.61
45 46 7.389884 AGGAAACCGAAAAACCTAATAGAGAAC 59.610 37.037 0.00 0.00 0.00 3.01
50 51 8.974408 CAAAAAGGAAACCGAAAAACCTAATAG 58.026 33.333 0.00 0.00 0.00 1.73
56 57 4.255301 ACCAAAAAGGAAACCGAAAAACC 58.745 39.130 0.00 0.00 41.22 3.27
126 127 9.703892 TTTGAATTTCAAAAGAGTTCTGAAACA 57.296 25.926 19.57 0.00 42.72 2.83
232 234 7.382110 TCAATTCAGAAAACAAAAGGTGAACA 58.618 30.769 0.00 0.00 0.00 3.18
461 465 3.055591 CTGTAGCATCGCAACATAGGAG 58.944 50.000 0.00 0.00 0.00 3.69
463 467 2.826428 ACTGTAGCATCGCAACATAGG 58.174 47.619 0.00 0.00 0.00 2.57
464 468 5.691754 TGATTACTGTAGCATCGCAACATAG 59.308 40.000 0.00 0.00 0.00 2.23
465 469 5.596845 TGATTACTGTAGCATCGCAACATA 58.403 37.500 0.00 0.00 0.00 2.29
466 470 4.441792 TGATTACTGTAGCATCGCAACAT 58.558 39.130 0.00 0.00 0.00 2.71
467 471 3.855858 TGATTACTGTAGCATCGCAACA 58.144 40.909 0.00 0.00 0.00 3.33
468 472 5.462068 TGTATGATTACTGTAGCATCGCAAC 59.538 40.000 8.06 3.82 0.00 4.17
472 476 7.860872 TGTTACTGTATGATTACTGTAGCATCG 59.139 37.037 12.32 3.48 42.91 3.84
475 479 7.262772 GGTGTTACTGTATGATTACTGTAGCA 58.737 38.462 12.32 12.32 44.16 3.49
500 504 5.106317 ACTGTAGCAATTATTTGTTGTCCCG 60.106 40.000 0.00 0.00 35.17 5.14
509 513 5.725110 CGAGAGCACTGTAGCAATTATTT 57.275 39.130 0.00 0.00 36.85 1.40
528 532 1.010935 ACGATGTTCAGTGCAGCGAG 61.011 55.000 14.01 0.00 46.90 5.03
542 546 5.845985 AACAATCACTGACTGTAACGATG 57.154 39.130 0.00 0.00 0.00 3.84
603 607 3.827634 GCTTATTGCGTCCAGGGG 58.172 61.111 0.00 0.00 0.00 4.79
624 628 4.301072 AGAGCGAGAGGAGCTTCTATAT 57.699 45.455 0.00 0.00 46.13 0.86
630 634 2.428544 TAGAAGAGCGAGAGGAGCTT 57.571 50.000 0.00 0.00 46.13 3.74
731 742 4.396790 GCTAATCTAGATACCGGTCTCCTG 59.603 50.000 12.40 6.93 0.00 3.86
742 756 1.472878 CCGGCAGCGCTAATCTAGATA 59.527 52.381 10.99 0.00 0.00 1.98
747 761 4.918201 GGCCGGCAGCGCTAATCT 62.918 66.667 30.85 0.00 45.17 2.40
778 792 0.522626 TGCGTTGTTCATGATGGCTG 59.477 50.000 0.00 0.00 0.00 4.85
788 802 0.235926 GCTCTCAGGTTGCGTTGTTC 59.764 55.000 0.00 0.00 0.00 3.18
793 813 4.368391 CAAGCTCTCAGGTTGCGT 57.632 55.556 2.70 0.00 45.12 5.24
871 891 1.227823 CGCCTGGTTTGGTCAGTGA 60.228 57.895 0.00 0.00 0.00 3.41
874 894 3.365265 GCCGCCTGGTTTGGTCAG 61.365 66.667 0.00 0.00 37.67 3.51
910 930 2.164624 CAGTCTACCAGAGCAGGTGTAC 59.835 54.545 5.84 4.28 43.14 2.90
1020 1041 1.011595 AGCTCTGGAGGAGGGAGTAA 58.988 55.000 0.00 0.00 42.08 2.24
1069 1090 4.803426 GACGAGCCTGCGGTGGAG 62.803 72.222 0.00 0.00 35.12 3.86
1283 1304 4.980805 TGGCGTCACCGGAAGTGC 62.981 66.667 9.46 6.72 46.81 4.40
1406 1427 2.033448 GCACGAACATGTCCCCCA 59.967 61.111 0.00 0.00 0.00 4.96
1431 1452 2.103771 CCTCAGGTACATGTCCATGAGG 59.896 54.545 29.84 29.84 41.20 3.86
1487 1508 2.022625 ACATCCTTCCTCTCCATCTCCA 60.023 50.000 0.00 0.00 0.00 3.86
1490 1511 2.293452 ACCACATCCTTCCTCTCCATCT 60.293 50.000 0.00 0.00 0.00 2.90
1515 1536 0.612732 CCCTGAGCAAGGCATTCCAA 60.613 55.000 0.00 0.00 45.89 3.53
1601 1622 1.411394 CAGATTTTGTTGCCAGCACG 58.589 50.000 0.00 0.00 0.00 5.34
1622 1643 3.358707 TTCAAAGCAGTGCAATGAGTG 57.641 42.857 20.00 11.71 29.95 3.51
1637 1665 0.313672 GCGGGACTGCACATTTCAAA 59.686 50.000 0.00 0.00 34.15 2.69
1649 1677 0.972983 AGCAGTATGTGAGCGGGACT 60.973 55.000 0.00 0.00 39.31 3.85
1671 1699 0.958822 GGCACGGATTTGAGGTGTTT 59.041 50.000 0.00 0.00 34.25 2.83
1686 1714 5.183140 ACACTACAATTACAATGAAGGGCAC 59.817 40.000 0.00 0.00 0.00 5.01
1795 1831 7.070322 GGTTACCCTGTCTGGTACATTTCTATA 59.930 40.741 0.00 0.00 40.55 1.31
1874 1911 9.750125 GAAGTTGAACAGTGGATTTATTTTTCT 57.250 29.630 0.00 0.00 0.00 2.52
1875 1912 9.750125 AGAAGTTGAACAGTGGATTTATTTTTC 57.250 29.630 0.00 0.00 0.00 2.29
1897 1939 6.136541 ACAAGCCTAAAAGACAAACAGAAG 57.863 37.500 0.00 0.00 0.00 2.85
1945 1987 6.932901 AATATGCACTTTGAACATTCAACG 57.067 33.333 6.55 7.78 45.99 4.10
1953 1996 8.437742 CAATCAAGGAAAATATGCACTTTGAAC 58.562 33.333 0.00 0.00 33.56 3.18
1966 2009 8.428063 TGTGAATGGTTAACAATCAAGGAAAAT 58.572 29.630 8.10 0.00 40.50 1.82
2122 2166 6.777580 AGTGATCCAATAACAACCTTTTCACT 59.222 34.615 0.00 0.00 36.26 3.41
2271 2315 2.366533 AGCTCCATTGCATCTTCAGTG 58.633 47.619 0.00 0.00 34.99 3.66
2292 2336 5.123227 CCCCTACGATAAATCTTGCAGAAA 58.877 41.667 0.00 0.00 0.00 2.52
2370 2414 4.202451 TGTGTCCCAAATCTGAGACATGAA 60.202 41.667 0.00 0.00 41.01 2.57
2796 2840 0.833287 TCTCCACTAGCTTCCATGCC 59.167 55.000 0.00 0.00 0.00 4.40
2799 2843 3.118112 CCACATTCTCCACTAGCTTCCAT 60.118 47.826 0.00 0.00 0.00 3.41
2827 2871 4.355543 CCAATATTGACGAGTTGGGTTG 57.644 45.455 17.23 0.00 37.92 3.77
2892 2936 0.603707 TCTTGGCTGCAGTTTCTCCG 60.604 55.000 16.64 0.00 0.00 4.63
2964 3008 7.721842 TCCCATAAATTAGATTCCGCATACAAA 59.278 33.333 0.00 0.00 0.00 2.83
2965 3009 7.227873 TCCCATAAATTAGATTCCGCATACAA 58.772 34.615 0.00 0.00 0.00 2.41
2973 3017 6.488715 AGCATCCTCCCATAAATTAGATTCC 58.511 40.000 0.00 0.00 0.00 3.01
3033 3077 1.905354 GCAACCAGCTTCCTTGCCT 60.905 57.895 8.09 0.00 41.15 4.75
3081 3125 9.021807 CCATTATCTGAATATCTTGGAAAGCAT 57.978 33.333 0.00 0.00 45.70 3.79
3148 3192 1.507140 TGTGGACAAAGGTCTGAGGT 58.493 50.000 0.00 0.00 43.77 3.85
3199 3243 7.039923 AGTCGGTTAGAGTTTACAAAGATCTGA 60.040 37.037 0.00 0.00 0.00 3.27
3341 3385 8.918658 CAACAGATTATCCAAATGAACAAACTG 58.081 33.333 0.00 0.00 0.00 3.16
3487 3532 5.818678 AAGACCATAAACCTGTGACTGTA 57.181 39.130 0.00 0.00 0.00 2.74
3520 3565 9.646427 ATCAGATAGAGACAACTTTGAAGTAAC 57.354 33.333 0.00 0.00 38.57 2.50
3632 3681 5.248020 AGAAATGGATAGCATAGAGTGGGAG 59.752 44.000 0.00 0.00 0.00 4.30
3634 3683 5.248020 AGAGAAATGGATAGCATAGAGTGGG 59.752 44.000 0.00 0.00 0.00 4.61
3643 3692 7.449395 CCCATATCAAAAGAGAAATGGATAGCA 59.551 37.037 0.00 0.00 36.76 3.49
3815 3865 9.165035 TGGTTTCTCGAGACTTAAAAGTTTAAA 57.835 29.630 16.36 0.00 39.88 1.52
3902 3953 8.742554 ACTCAACAAACAAAACTTAAGTCAAG 57.257 30.769 8.95 4.22 40.38 3.02


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

AutoCloner maintained by Alex Coulton.