Multiple sequence alignment - TraesCS2A01G282700

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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 TraesCS2A01G282700 chr2A 100.000 2543 0 0 1 2543 473644979 473642437 0 4697
1 TraesCS2A01G282700 chr2D 91.564 2608 64 39 1 2543 354391795 354389279 0 3454
2 TraesCS2A01G282700 chr2B 89.866 2605 86 63 42 2543 421259879 421257350 0 3184


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 TraesCS2A01G282700 chr2A 473642437 473644979 2542 True 4697 4697 100.000 1 2543 1 chr2A.!!$R1 2542
1 TraesCS2A01G282700 chr2D 354389279 354391795 2516 True 3454 3454 91.564 1 2543 1 chr2D.!!$R1 2542
2 TraesCS2A01G282700 chr2B 421257350 421259879 2529 True 3184 3184 89.866 42 2543 1 chr2B.!!$R1 2501

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
760 809 0.107017 AGAGTGCACAAAGCCACACT 60.107 50.0 21.04 0.0 45.66 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2062 0.038251 TCACCGCACTAGCTCAACAG 60.038 55.0 0.0 0.0 39.1 3.16 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
25 26 8.870075 AGCTAGTTGATCTTTTTAAAGGTGAT 57.130 30.769 2.63 0.00 36.67 3.06
432 443 1.072159 GGCATCGATCCCTTCCCTG 59.928 63.158 0.00 0.00 0.00 4.45
517 549 1.082300 CTCGTATCGCCGTACGCAT 60.082 57.895 10.49 3.82 45.20 4.73
527 573 2.384309 CGTACGCATGGCAAACCGA 61.384 57.895 0.52 0.00 39.70 4.69
538 584 4.664150 TGGCAAACCGAAAGAAGAAAAT 57.336 36.364 0.00 0.00 39.70 1.82
554 600 5.051891 AGAAAATTCTGAATTGCGTCCAG 57.948 39.130 15.80 0.00 35.89 3.86
670 719 2.269241 GGCTGAAACCGAGGAGGG 59.731 66.667 0.00 0.00 46.96 4.30
686 735 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
687 736 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
688 737 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
689 738 4.179599 GAGGGAGGGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
691 740 3.040814 GGGAGGGAGGGAGGGGTA 61.041 72.222 0.00 0.00 0.00 3.69
692 741 2.286213 GGAGGGAGGGAGGGGTAC 59.714 72.222 0.00 0.00 0.00 3.34
760 809 0.107017 AGAGTGCACAAAGCCACACT 60.107 50.000 21.04 0.00 45.66 3.55
764 813 2.332514 CACAAAGCCACACTGCCG 59.667 61.111 0.00 0.00 0.00 5.69
765 814 2.124320 ACAAAGCCACACTGCCGT 60.124 55.556 0.00 0.00 0.00 5.68
930 980 5.811100 CACCTAACTAAGCTAGGCTAACAAC 59.189 44.000 0.00 0.00 38.25 3.32
943 993 2.726633 CTAACAACCCAAAGCACAACG 58.273 47.619 0.00 0.00 0.00 4.10
944 994 0.459411 AACAACCCAAAGCACAACGC 60.459 50.000 0.00 0.00 42.91 4.84
954 1004 3.726517 CACAACGCGGGGAAGCAG 61.727 66.667 12.47 0.00 36.85 4.24
970 1020 4.150454 AGGCGGGAGAGAGGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1416 1487 2.131405 CAGGATGATCTGGGAGCGT 58.869 57.895 0.00 0.00 39.69 5.07
1606 1697 3.431486 GCCATTGCTAGCTGTAACTCTCT 60.431 47.826 17.23 0.00 33.53 3.10
1607 1698 4.367450 CCATTGCTAGCTGTAACTCTCTC 58.633 47.826 17.23 0.00 0.00 3.20
1608 1699 4.099266 CCATTGCTAGCTGTAACTCTCTCT 59.901 45.833 17.23 0.00 0.00 3.10
1609 1700 4.974368 TTGCTAGCTGTAACTCTCTCTC 57.026 45.455 17.23 0.00 0.00 3.20
1610 1701 4.229304 TGCTAGCTGTAACTCTCTCTCT 57.771 45.455 17.23 0.00 0.00 3.10
1611 1702 4.196193 TGCTAGCTGTAACTCTCTCTCTC 58.804 47.826 17.23 0.00 0.00 3.20
1612 1703 4.080582 TGCTAGCTGTAACTCTCTCTCTCT 60.081 45.833 17.23 0.00 0.00 3.10
1613 1704 4.511826 GCTAGCTGTAACTCTCTCTCTCTC 59.488 50.000 7.70 0.00 0.00 3.20
1614 1705 4.844349 AGCTGTAACTCTCTCTCTCTCT 57.156 45.455 0.00 0.00 0.00 3.10
1615 1706 4.770795 AGCTGTAACTCTCTCTCTCTCTC 58.229 47.826 0.00 0.00 0.00 3.20
1616 1707 4.225042 AGCTGTAACTCTCTCTCTCTCTCA 59.775 45.833 0.00 0.00 0.00 3.27
1617 1708 4.332819 GCTGTAACTCTCTCTCTCTCTCAC 59.667 50.000 0.00 0.00 0.00 3.51
1618 1709 5.734720 CTGTAACTCTCTCTCTCTCTCACT 58.265 45.833 0.00 0.00 0.00 3.41
1619 1710 5.730550 TGTAACTCTCTCTCTCTCTCACTC 58.269 45.833 0.00 0.00 0.00 3.51
1620 1711 5.483937 TGTAACTCTCTCTCTCTCTCACTCT 59.516 44.000 0.00 0.00 0.00 3.24
1621 1712 6.666113 TGTAACTCTCTCTCTCTCTCACTCTA 59.334 42.308 0.00 0.00 0.00 2.43
1622 1713 6.814954 AACTCTCTCTCTCTCTCACTCTAT 57.185 41.667 0.00 0.00 0.00 1.98
1623 1714 6.412362 ACTCTCTCTCTCTCTCACTCTATC 57.588 45.833 0.00 0.00 0.00 2.08
1624 1715 6.139671 ACTCTCTCTCTCTCTCACTCTATCT 58.860 44.000 0.00 0.00 0.00 1.98
1625 1716 7.298374 ACTCTCTCTCTCTCTCACTCTATCTA 58.702 42.308 0.00 0.00 0.00 1.98
1626 1717 7.952930 ACTCTCTCTCTCTCTCACTCTATCTAT 59.047 40.741 0.00 0.00 0.00 1.98
1627 1718 8.354711 TCTCTCTCTCTCTCACTCTATCTATC 57.645 42.308 0.00 0.00 0.00 2.08
1628 1719 8.173412 TCTCTCTCTCTCTCACTCTATCTATCT 58.827 40.741 0.00 0.00 0.00 1.98
1629 1720 8.727100 TCTCTCTCTCTCACTCTATCTATCTT 57.273 38.462 0.00 0.00 0.00 2.40
1708 1809 2.492019 CATCTGGTTGATGCATGCAG 57.508 50.000 26.69 10.51 44.96 4.41
1845 1946 6.263168 AGAAACAAGGGAGTAAACAACTGATG 59.737 38.462 0.00 0.00 39.07 3.07
1959 2061 2.422519 GGACGGATCCCTCTGTACTGTA 60.423 54.545 6.06 0.00 41.19 2.74
1960 2062 2.617774 GACGGATCCCTCTGTACTGTAC 59.382 54.545 10.98 10.98 41.19 2.90
1961 2063 2.241685 ACGGATCCCTCTGTACTGTACT 59.758 50.000 17.98 0.00 39.28 2.73
1962 2064 2.619177 CGGATCCCTCTGTACTGTACTG 59.381 54.545 17.98 16.98 0.00 2.74
1963 2065 3.633418 GGATCCCTCTGTACTGTACTGT 58.367 50.000 17.98 10.46 0.00 3.55
2066 2171 1.222936 GCATGCTAGTGGACTGCCT 59.777 57.895 11.37 0.00 34.31 4.75
2067 2172 0.813210 GCATGCTAGTGGACTGCCTC 60.813 60.000 11.37 0.00 34.31 4.70
2068 2173 0.829333 CATGCTAGTGGACTGCCTCT 59.171 55.000 0.00 0.00 40.85 3.69
2069 2174 1.118838 ATGCTAGTGGACTGCCTCTC 58.881 55.000 0.00 0.00 38.81 3.20
2070 2175 0.972983 TGCTAGTGGACTGCCTCTCC 60.973 60.000 0.00 0.00 38.81 3.71
2071 2176 0.686112 GCTAGTGGACTGCCTCTCCT 60.686 60.000 0.00 0.00 38.81 3.69
2072 2177 1.859302 CTAGTGGACTGCCTCTCCTT 58.141 55.000 0.00 0.00 38.81 3.36
2172 2285 2.448153 ATTGTTCACTGCGCTGCGTG 62.448 55.000 24.04 18.16 35.60 5.34
2436 2577 1.302949 GGATTGTACCCTGCCTGCA 59.697 57.895 0.00 0.00 0.00 4.41
2440 2581 2.747855 GTACCCTGCCTGCACAGC 60.748 66.667 0.00 0.00 36.29 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.566079 ATTGTCTTATTGACTCCATCCTCA 57.434 37.500 0.00 0.00 45.54 3.86
51 52 4.898829 TCGTTAATCAATGCCTGGATTG 57.101 40.909 0.00 5.14 35.49 2.67
52 53 4.520492 GGATCGTTAATCAATGCCTGGATT 59.480 41.667 0.00 0.00 35.96 3.01
154 156 4.156182 GTGCAAAAACTATTCGCCTACAC 58.844 43.478 0.00 0.00 0.00 2.90
432 443 1.379176 GGCCTCAAGGAAGGAAGGC 60.379 63.158 0.00 3.64 38.87 4.35
517 549 4.664150 ATTTTCTTCTTTCGGTTTGCCA 57.336 36.364 0.00 0.00 34.09 4.92
527 573 6.642540 GGACGCAATTCAGAATTTTCTTCTTT 59.357 34.615 5.58 0.00 34.74 2.52
538 584 1.623311 TCTCCTGGACGCAATTCAGAA 59.377 47.619 0.00 0.00 0.00 3.02
554 600 3.055094 TCTGCAAACCCTCTTGTATCTCC 60.055 47.826 0.00 0.00 0.00 3.71
595 641 2.218075 CACATCTCTCGTCGATGCAATG 59.782 50.000 0.00 3.70 41.45 2.82
596 642 2.467838 CACATCTCTCGTCGATGCAAT 58.532 47.619 0.00 0.00 41.45 3.56
597 643 1.469767 CCACATCTCTCGTCGATGCAA 60.470 52.381 0.00 0.00 41.45 4.08
598 644 0.101219 CCACATCTCTCGTCGATGCA 59.899 55.000 0.00 0.00 41.45 3.96
599 645 0.101399 ACCACATCTCTCGTCGATGC 59.899 55.000 0.00 0.00 41.45 3.91
663 712 4.179599 CCCTCCCTCCCCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
664 713 4.761304 TCCCTCCCTCCCCCTCCT 62.761 72.222 0.00 0.00 0.00 3.69
665 714 4.179599 CTCCCTCCCTCCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
666 715 4.179599 CCTCCCTCCCTCCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
670 719 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
689 738 3.313392 CCACGAGGAGAGGACGTAGTAC 61.313 59.091 0.00 0.00 38.05 2.73
690 739 1.134580 CCACGAGGAGAGGACGTAGTA 60.135 57.143 0.00 0.00 38.05 1.82
691 740 0.392729 CCACGAGGAGAGGACGTAGT 60.393 60.000 0.00 0.00 40.79 2.73
692 741 1.716826 GCCACGAGGAGAGGACGTAG 61.717 65.000 1.86 0.00 38.47 3.51
930 980 4.341502 CCCGCGTTGTGCTTTGGG 62.342 66.667 4.92 0.00 43.27 4.12
948 998 2.498726 CTCTCTCCCGCCTGCTTC 59.501 66.667 0.00 0.00 0.00 3.86
949 999 3.080121 CCTCTCTCCCGCCTGCTT 61.080 66.667 0.00 0.00 0.00 3.91
952 1002 2.837291 CTCCCTCTCTCCCGCCTG 60.837 72.222 0.00 0.00 0.00 4.85
953 1003 4.150454 CCTCCCTCTCTCCCGCCT 62.150 72.222 0.00 0.00 0.00 5.52
954 1004 2.374781 ATACCTCCCTCTCTCCCGCC 62.375 65.000 0.00 0.00 0.00 6.13
955 1005 0.404812 TATACCTCCCTCTCTCCCGC 59.595 60.000 0.00 0.00 0.00 6.13
956 1006 1.272037 GGTATACCTCCCTCTCTCCCG 60.272 61.905 15.09 0.00 0.00 5.14
957 1007 2.075383 AGGTATACCTCCCTCTCTCCC 58.925 57.143 19.27 0.00 44.77 4.30
970 1020 0.880718 GGCCAAGCAGCGAGGTATAC 60.881 60.000 0.00 0.00 0.00 1.47
1110 1160 1.012086 CAATGCTCATGGACAGGTCG 58.988 55.000 0.00 0.00 0.00 4.79
1606 1697 9.159254 AGAAAGATAGATAGAGTGAGAGAGAGA 57.841 37.037 0.00 0.00 0.00 3.10
1614 1705 9.869757 CGAGAGATAGAAAGATAGATAGAGTGA 57.130 37.037 0.00 0.00 0.00 3.41
1615 1706 9.653287 ACGAGAGATAGAAAGATAGATAGAGTG 57.347 37.037 0.00 0.00 0.00 3.51
1621 1712 9.832445 GGAGATACGAGAGATAGAAAGATAGAT 57.168 37.037 0.00 0.00 0.00 1.98
1622 1713 9.042450 AGGAGATACGAGAGATAGAAAGATAGA 57.958 37.037 0.00 0.00 0.00 1.98
1623 1714 9.098355 CAGGAGATACGAGAGATAGAAAGATAG 57.902 40.741 0.00 0.00 0.00 2.08
1624 1715 8.598916 ACAGGAGATACGAGAGATAGAAAGATA 58.401 37.037 0.00 0.00 0.00 1.98
1625 1716 7.458397 ACAGGAGATACGAGAGATAGAAAGAT 58.542 38.462 0.00 0.00 0.00 2.40
1626 1717 6.833041 ACAGGAGATACGAGAGATAGAAAGA 58.167 40.000 0.00 0.00 0.00 2.52
1627 1718 6.934645 AGACAGGAGATACGAGAGATAGAAAG 59.065 42.308 0.00 0.00 0.00 2.62
1628 1719 6.833041 AGACAGGAGATACGAGAGATAGAAA 58.167 40.000 0.00 0.00 0.00 2.52
1629 1720 6.428083 AGACAGGAGATACGAGAGATAGAA 57.572 41.667 0.00 0.00 0.00 2.10
1643 1734 0.681733 GGCACTCACAAGACAGGAGA 59.318 55.000 0.00 0.00 33.00 3.71
1729 1830 6.872628 TGTACACCCGATGTATAGAGTAAG 57.127 41.667 0.00 0.00 45.59 2.34
1815 1916 9.197306 AGTTGTTTACTCCCTTGTTTCTTTATT 57.803 29.630 0.00 0.00 28.23 1.40
1959 2061 0.319900 CACCGCACTAGCTCAACAGT 60.320 55.000 0.00 0.00 39.10 3.55
1960 2062 0.038251 TCACCGCACTAGCTCAACAG 60.038 55.000 0.00 0.00 39.10 3.16
1961 2063 0.319555 GTCACCGCACTAGCTCAACA 60.320 55.000 0.00 0.00 39.10 3.33
1962 2064 0.319555 TGTCACCGCACTAGCTCAAC 60.320 55.000 0.00 0.00 39.10 3.18
1963 2065 0.038251 CTGTCACCGCACTAGCTCAA 60.038 55.000 0.00 0.00 39.10 3.02
2066 2171 4.959210 CCTTGTTCATCTAGGAGAAGGAGA 59.041 45.833 0.00 0.00 40.60 3.71
2067 2172 4.959210 TCCTTGTTCATCTAGGAGAAGGAG 59.041 45.833 0.00 6.08 41.66 3.69
2068 2173 4.947883 TCCTTGTTCATCTAGGAGAAGGA 58.052 43.478 0.00 0.00 41.66 3.36
2069 2174 5.423610 TCTTCCTTGTTCATCTAGGAGAAGG 59.576 44.000 0.00 0.00 45.61 3.46
2070 2175 6.537453 TCTTCCTTGTTCATCTAGGAGAAG 57.463 41.667 0.00 0.00 45.61 2.85
2071 2176 6.669591 TGATCTTCCTTGTTCATCTAGGAGAA 59.330 38.462 0.00 0.00 45.61 2.87
2072 2177 6.197903 TGATCTTCCTTGTTCATCTAGGAGA 58.802 40.000 0.00 0.00 45.61 3.71
2172 2285 5.152623 TGAGCCATTATGAGTAGCCATAC 57.847 43.478 0.00 0.00 0.00 2.39
2229 2342 3.201290 CAAACACAACTGCAGTCTCTCT 58.799 45.455 21.95 0.00 0.00 3.10
2297 2410 9.231297 ACATGTATATATATTGGTGTCAAAGCC 57.769 33.333 0.00 0.00 36.36 4.35
2336 2477 2.026822 CCTCCTGCAAACCTGTATCTGT 60.027 50.000 0.00 0.00 0.00 3.41
2440 2581 2.126071 ATGACTGAACGGCGTCGG 60.126 61.111 15.17 14.44 41.39 4.79


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

AutoCloner maintained by Alex Coulton.