Multiple sequence alignment - TraesCS2D01G034300

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 TraesCS2D01G034300 chr2D 100.000 3856 0 0 1 3856 13217828 13221683 0.000000e+00 7121.0
1 TraesCS2D01G034300 chr2D 89.921 764 61 12 10 767 13440727 13439974 0.000000e+00 970.0
2 TraesCS2D01G034300 chr2D 89.273 289 24 4 2930 3214 13428294 13428009 4.740000e-94 355.0
3 TraesCS2D01G034300 chr2B 91.344 2969 189 28 936 3856 23808615 23811563 0.000000e+00 3997.0
4 TraesCS2D01G034300 chr2B 93.200 897 53 5 3 891 24100154 24099258 0.000000e+00 1312.0
5 TraesCS2D01G034300 chr2A 94.789 1516 68 6 936 2443 15235771 15237283 0.000000e+00 2351.0
6 TraesCS2D01G034300 chr2A 96.493 1169 26 5 2445 3600 15237333 15238499 0.000000e+00 1917.0
7 TraesCS2D01G034300 chr2A 91.595 928 70 6 12 935 15451488 15450565 0.000000e+00 1275.0
8 TraesCS2D01G034300 chr2A 94.064 219 5 1 3598 3816 15238774 15238984 3.720000e-85 326.0
9 TraesCS2D01G034300 chr2A 86.873 259 23 9 2963 3214 15403722 15403468 2.930000e-71 279.0
10 TraesCS2D01G034300 chr2A 97.917 48 0 1 3810 3856 15239177 15239224 8.880000e-12 82.4


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 TraesCS2D01G034300 chr2D 13217828 13221683 3855 False 7121.0 7121 100.00000 1 3856 1 chr2D.!!$F1 3855
1 TraesCS2D01G034300 chr2D 13439974 13440727 753 True 970.0 970 89.92100 10 767 1 chr2D.!!$R2 757
2 TraesCS2D01G034300 chr2B 23808615 23811563 2948 False 3997.0 3997 91.34400 936 3856 1 chr2B.!!$F1 2920
3 TraesCS2D01G034300 chr2B 24099258 24100154 896 True 1312.0 1312 93.20000 3 891 1 chr2B.!!$R1 888
4 TraesCS2D01G034300 chr2A 15450565 15451488 923 True 1275.0 1275 91.59500 12 935 1 chr2A.!!$R2 923
5 TraesCS2D01G034300 chr2A 15235771 15239224 3453 False 1169.1 2351 95.81575 936 3856 4 chr2A.!!$F1 2920

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
922 935 0.104144 TTTCCTTCAGTGGAGGGGGA 60.104 55.0 18.01 1.38 40.57 4.81 F
2031 2052 0.248094 CGTCGCGTGCTCTCTCAATA 60.248 55.0 5.77 0.00 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2156 0.392193 CTCCCTTGAGTGCGCAGATT 60.392 55.000 12.22 0.0 33.70 2.40 R
3717 4117 1.978580 CCACCCTGGTTCTACACTTCT 59.021 52.381 0.00 0.0 31.35 2.85 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
59 63 3.518303 ACCTACCTCTGGTGGTATTCAAC 59.482 47.826 8.40 0.00 41.24 3.18
123 131 4.364415 TGTGCAGTAACCTTGTGTTTTC 57.636 40.909 0.00 0.00 38.42 2.29
241 249 0.611200 TGTGAAGGGGGTGTATGTCG 59.389 55.000 0.00 0.00 0.00 4.35
242 250 0.899720 GTGAAGGGGGTGTATGTCGA 59.100 55.000 0.00 0.00 0.00 4.20
336 344 1.291877 GCGACGTGCTCAACATCCTT 61.292 55.000 0.00 0.00 41.73 3.36
476 484 3.806380 AGATCTCAAAATGAGCAGCGAT 58.194 40.909 2.48 0.00 43.95 4.58
513 525 2.669391 GCAAAGAGGATTTTCAGGCACG 60.669 50.000 0.00 0.00 0.00 5.34
605 617 7.748691 AAATAACAAAATCAGGCTGCAAAAT 57.251 28.000 10.34 0.00 0.00 1.82
609 621 3.323751 AAATCAGGCTGCAAAATGTCC 57.676 42.857 10.34 0.00 0.00 4.02
611 623 1.999648 TCAGGCTGCAAAATGTCCTT 58.000 45.000 10.34 0.00 0.00 3.36
624 636 6.402442 GCAAAATGTCCTTGAATTTGGTATGC 60.402 38.462 0.00 0.00 32.91 3.14
626 638 3.680490 TGTCCTTGAATTTGGTATGCGA 58.320 40.909 0.00 0.00 0.00 5.10
685 697 3.454371 TCCAAGATTAAGCTCGTAGGC 57.546 47.619 0.00 0.00 0.00 3.93
708 720 3.622828 CCTCGTAGTCGATGAGAACATG 58.377 50.000 3.90 0.00 43.06 3.21
711 723 3.108881 CGTAGTCGATGAGAACATGGTG 58.891 50.000 0.00 0.00 39.71 4.17
824 836 5.016831 TGCAGGACTTGAGATAGTTGTAGA 58.983 41.667 0.00 0.00 0.00 2.59
827 839 7.142680 GCAGGACTTGAGATAGTTGTAGATAC 58.857 42.308 0.00 0.00 0.00 2.24
859 871 8.851541 AATGTAACGGAAAGTAATGGAACTAA 57.148 30.769 0.00 0.00 0.00 2.24
867 879 7.120726 CGGAAAGTAATGGAACTAAGGAACAAT 59.879 37.037 0.00 0.00 0.00 2.71
884 896 7.354312 AGGAACAATAGGCCACAAGTAAATAT 58.646 34.615 5.01 0.00 0.00 1.28
885 897 8.499406 AGGAACAATAGGCCACAAGTAAATATA 58.501 33.333 5.01 0.00 0.00 0.86
886 898 8.784043 GGAACAATAGGCCACAAGTAAATATAG 58.216 37.037 5.01 0.00 0.00 1.31
887 899 7.745620 ACAATAGGCCACAAGTAAATATAGC 57.254 36.000 5.01 0.00 0.00 2.97
888 900 7.518188 ACAATAGGCCACAAGTAAATATAGCT 58.482 34.615 5.01 0.00 0.00 3.32
889 901 7.445402 ACAATAGGCCACAAGTAAATATAGCTG 59.555 37.037 5.01 0.00 0.00 4.24
890 902 5.630415 AGGCCACAAGTAAATATAGCTGA 57.370 39.130 5.01 0.00 0.00 4.26
897 910 8.137437 CCACAAGTAAATATAGCTGAAAATGGG 58.863 37.037 0.00 0.00 0.00 4.00
918 931 1.878102 CGGTGTTTCCTTCAGTGGAGG 60.878 57.143 11.80 11.80 37.43 4.30
922 935 0.104144 TTTCCTTCAGTGGAGGGGGA 60.104 55.000 18.01 1.38 40.57 4.81
932 945 2.792951 GAGGGGGAAGGGGTAGGT 59.207 66.667 0.00 0.00 0.00 3.08
1080 1093 4.460683 TACCTTCGCCGCGCCAAT 62.461 61.111 8.21 0.00 0.00 3.16
1543 1561 6.857777 ATAGCAGCAGACACATTATTTCTC 57.142 37.500 0.00 0.00 0.00 2.87
1704 1722 2.949714 ATTGCTCAACGAGAACAACG 57.050 45.000 0.00 0.00 35.33 4.10
1751 1769 5.435041 ACCTCATATTGATTCCCCCAAGTTA 59.565 40.000 0.00 0.00 0.00 2.24
1762 1780 2.094752 CCCCCAAGTTATGTTCTTTGCG 60.095 50.000 0.00 0.00 0.00 4.85
1778 1799 9.976255 TGTTCTTTGCGTACATATGTTTTATAC 57.024 29.630 14.77 4.64 0.00 1.47
1823 1844 9.537192 CTGATGTCAATATTTATTGCAATGGTT 57.463 29.630 22.27 8.42 42.06 3.67
1904 1925 4.101448 AGGCGGCTCGAGGCATTT 62.101 61.111 34.57 18.17 44.01 2.32
1986 2007 3.814504 ATTTCCCCAGTGTCATCAACT 57.185 42.857 0.00 0.00 0.00 3.16
1988 2009 2.566833 TCCCCAGTGTCATCAACTTG 57.433 50.000 0.00 0.00 0.00 3.16
1997 2018 2.266554 GTCATCAACTTGGCTCTCGAG 58.733 52.381 5.93 5.93 0.00 4.04
2003 2024 0.681564 ACTTGGCTCTCGAGTCCGAT 60.682 55.000 13.13 2.35 44.62 4.18
2022 2043 4.419939 TGCTCATCGTCGCGTGCT 62.420 61.111 5.77 0.00 0.00 4.40
2031 2052 0.248094 CGTCGCGTGCTCTCTCAATA 60.248 55.000 5.77 0.00 0.00 1.90
2093 2114 0.899720 TAGGGAAAGACGGCGTCATT 59.100 50.000 37.71 32.85 34.60 2.57
2135 2156 3.224324 GTCGATGAGGCGGCCCTA 61.224 66.667 17.02 5.19 43.12 3.53
2139 2160 1.821061 CGATGAGGCGGCCCTAATCT 61.821 60.000 17.02 0.00 44.27 2.40
2384 2405 7.686438 AATGCTGTAGATGATACAACAACAA 57.314 32.000 0.00 0.00 28.98 2.83
2385 2406 6.726258 TGCTGTAGATGATACAACAACAAG 57.274 37.500 0.00 0.00 0.00 3.16
2713 2790 3.473147 CTCCAGTAGCTGCTGCATT 57.527 52.632 24.83 0.14 42.74 3.56
2747 2824 3.256383 AGGTGTGTACATGTACGTAGCAA 59.744 43.478 28.07 13.23 38.85 3.91
2928 3005 1.303309 ATGCAGTAAATGAGCTCGCC 58.697 50.000 9.64 0.00 0.00 5.54
3008 3086 1.205655 CCATGACTCTCTGAAGGCGAA 59.794 52.381 0.00 0.00 0.00 4.70
3085 3169 1.300481 GCGAAGGATGAAGGTTAGGC 58.700 55.000 0.00 0.00 0.00 3.93
3086 3170 1.571919 CGAAGGATGAAGGTTAGGCG 58.428 55.000 0.00 0.00 0.00 5.52
3087 3171 1.300481 GAAGGATGAAGGTTAGGCGC 58.700 55.000 0.00 0.00 0.00 6.53
3490 3605 4.699522 GAGACGGGCGGGCAAAGT 62.700 66.667 3.27 0.00 0.00 2.66
3530 3646 0.171455 GGAACAGACGAGCGTGAGAT 59.829 55.000 0.00 0.00 0.00 2.75
3590 3706 2.041081 TGAAACATGGTAGGGTTGAGGG 59.959 50.000 0.00 0.00 0.00 4.30
3627 4020 3.320541 CAGAGGATTCGATGCTAGAGGTT 59.679 47.826 0.00 0.00 0.00 3.50
3718 4118 3.403936 GCATACCTGCCCCAAGTAG 57.596 57.895 0.00 0.00 42.88 2.57
3719 4119 0.837272 GCATACCTGCCCCAAGTAGA 59.163 55.000 0.00 0.00 42.88 2.59
3720 4120 1.211949 GCATACCTGCCCCAAGTAGAA 59.788 52.381 0.00 0.00 42.88 2.10
3721 4121 2.746472 GCATACCTGCCCCAAGTAGAAG 60.746 54.545 0.00 0.00 42.88 2.85
3722 4122 2.337359 TACCTGCCCCAAGTAGAAGT 57.663 50.000 0.00 0.00 0.00 3.01
3723 4123 0.693049 ACCTGCCCCAAGTAGAAGTG 59.307 55.000 0.00 0.00 0.00 3.16
3724 4124 0.693049 CCTGCCCCAAGTAGAAGTGT 59.307 55.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.934023 AAATTAATAGGAAGAACTGAACCACA 57.066 30.769 0.00 0.00 0.00 4.17
1 2 9.010029 TGAAATTAATAGGAAGAACTGAACCAC 57.990 33.333 0.00 0.00 0.00 4.16
38 42 3.517901 TGTTGAATACCACCAGAGGTAGG 59.482 47.826 0.59 0.00 46.63 3.18
59 63 7.741027 AGCACAGAATGGTCTATTATGAATG 57.259 36.000 10.17 1.20 43.62 2.67
336 344 1.065926 ACATCGCCTTGCAGATTCTGA 60.066 47.619 17.87 0.08 32.44 3.27
476 484 1.055849 TTGCTGCTTGGTCCTGACTA 58.944 50.000 0.00 0.00 0.00 2.59
513 525 2.338500 GAACTGAGATCAACGACCACC 58.662 52.381 0.00 0.00 0.00 4.61
587 599 3.434299 GGACATTTTGCAGCCTGATTTTG 59.566 43.478 0.00 0.00 0.00 2.44
605 617 3.680490 TCGCATACCAAATTCAAGGACA 58.320 40.909 0.00 0.00 0.00 4.02
609 621 6.144854 CCACATATCGCATACCAAATTCAAG 58.855 40.000 0.00 0.00 0.00 3.02
611 623 5.129634 ACCACATATCGCATACCAAATTCA 58.870 37.500 0.00 0.00 0.00 2.57
624 636 6.238374 GGAGAACCAACAAATACCACATATCG 60.238 42.308 0.00 0.00 35.97 2.92
626 638 6.731467 AGGAGAACCAACAAATACCACATAT 58.269 36.000 0.00 0.00 38.94 1.78
708 720 3.684788 ACATATTCTTTGCGTGAGACACC 59.315 43.478 0.00 0.00 0.00 4.16
711 723 5.530519 TCAACATATTCTTTGCGTGAGAC 57.469 39.130 0.00 0.00 0.00 3.36
758 770 3.322254 ACTCAAGACTAGTGACACCTTGG 59.678 47.826 16.83 11.83 36.01 3.61
824 836 6.698380 ACTTTCCGTTACATTCACTCTGTAT 58.302 36.000 0.00 0.00 0.00 2.29
827 839 7.413000 CCATTACTTTCCGTTACATTCACTCTG 60.413 40.741 0.00 0.00 0.00 3.35
859 871 4.650972 TTACTTGTGGCCTATTGTTCCT 57.349 40.909 3.32 0.00 0.00 3.36
867 879 6.740944 TCAGCTATATTTACTTGTGGCCTA 57.259 37.500 3.32 0.00 0.00 3.93
884 896 0.037590 ACACCGCCCATTTTCAGCTA 59.962 50.000 0.00 0.00 0.00 3.32
885 897 0.827507 AACACCGCCCATTTTCAGCT 60.828 50.000 0.00 0.00 0.00 4.24
886 898 0.033366 AAACACCGCCCATTTTCAGC 59.967 50.000 0.00 0.00 0.00 4.26
887 899 1.336795 GGAAACACCGCCCATTTTCAG 60.337 52.381 0.00 0.00 30.88 3.02
888 900 0.676736 GGAAACACCGCCCATTTTCA 59.323 50.000 0.00 0.00 30.88 2.69
889 901 0.966179 AGGAAACACCGCCCATTTTC 59.034 50.000 0.00 0.00 44.74 2.29
890 902 1.343142 GAAGGAAACACCGCCCATTTT 59.657 47.619 0.00 0.00 44.74 1.82
897 910 0.534203 TCCACTGAAGGAAACACCGC 60.534 55.000 0.00 0.00 44.74 5.68
918 931 2.240667 GACTTAAACCTACCCCTTCCCC 59.759 54.545 0.00 0.00 0.00 4.81
922 935 2.027469 CAGCGACTTAAACCTACCCCTT 60.027 50.000 0.00 0.00 0.00 3.95
932 945 1.202710 TCTTGTGGCCAGCGACTTAAA 60.203 47.619 5.11 0.00 0.00 1.52
1372 1385 3.188786 GTGATCCGCCACGTCAGC 61.189 66.667 0.00 0.00 0.00 4.26
1543 1561 6.426937 TCCGGATCAAGAAAAGTAAAGACTTG 59.573 38.462 0.00 0.00 45.50 3.16
1592 1610 7.279758 GGACCAAAATTTGTTGTGATTTTCAGA 59.720 33.333 4.92 0.00 34.25 3.27
1704 1722 5.845391 ACTCTGAATTCTAGCACTCTACC 57.155 43.478 7.05 0.00 0.00 3.18
1815 1836 0.524862 CTGAGCTGGTGAACCATTGC 59.475 55.000 1.88 4.13 46.46 3.56
1817 1838 1.546323 CCACTGAGCTGGTGAACCATT 60.546 52.381 15.48 0.00 46.46 3.16
1823 1844 1.071987 CTTGCCACTGAGCTGGTGA 59.928 57.895 15.48 0.00 36.89 4.02
1896 1917 2.277591 TGGTGCAGCCAAATGCCTC 61.278 57.895 14.36 0.00 45.94 4.70
2003 2024 2.804931 CACGCGACGATGAGCACA 60.805 61.111 15.93 0.00 0.00 4.57
2022 2043 7.509141 TGTGCTTTGTTTGATTATTGAGAGA 57.491 32.000 0.00 0.00 0.00 3.10
2031 2052 5.873712 TGTTGACAATGTGCTTTGTTTGATT 59.126 32.000 0.00 0.00 39.85 2.57
2093 2114 3.361158 CCGCGGGCAATGTTCACA 61.361 61.111 20.10 0.00 0.00 3.58
2132 2153 1.293924 CCTTGAGTGCGCAGATTAGG 58.706 55.000 12.22 12.37 0.00 2.69
2135 2156 0.392193 CTCCCTTGAGTGCGCAGATT 60.392 55.000 12.22 0.00 33.70 2.40
2139 2160 4.020617 CCCTCCCTTGAGTGCGCA 62.021 66.667 5.66 5.66 36.86 6.09
2384 2405 1.068741 GAAACCTGACGTGGTCTGACT 59.931 52.381 7.85 0.00 39.83 3.41
2385 2406 1.202486 TGAAACCTGACGTGGTCTGAC 60.202 52.381 0.00 0.00 39.83 3.51
2607 2684 6.691754 TCAGTAAAACATTGAGCAGTCAAA 57.308 33.333 0.00 0.00 45.88 2.69
2713 2790 3.452990 TGTACACACCTGGTTCTTCAGAA 59.547 43.478 0.00 0.00 36.93 3.02
2747 2824 4.789012 CACAATCAAAATAGCTGTGGGT 57.211 40.909 0.00 0.00 34.97 4.51
3530 3646 2.238521 GGCACCATTTGAAGTCCTTCA 58.761 47.619 5.64 5.64 46.72 3.02
3590 3706 2.124695 CTGCCCCTTAAGACGGCC 60.125 66.667 23.20 0.00 42.29 6.13
3627 4020 3.457749 TGCATCATCATAACCCCACTACA 59.542 43.478 0.00 0.00 0.00 2.74
3716 4116 3.170717 CCACCCTGGTTCTACACTTCTA 58.829 50.000 0.00 0.00 31.35 2.10
3717 4117 1.978580 CCACCCTGGTTCTACACTTCT 59.021 52.381 0.00 0.00 31.35 2.85
3718 4118 2.474410 CCACCCTGGTTCTACACTTC 57.526 55.000 0.00 0.00 31.35 3.01
3757 4157 4.273235 GCTGCTTTTTGTGCCATTAAGTTT 59.727 37.500 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.