Multiple sequence alignment - TraesCS7A01G275100

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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 TraesCS7A01G275100 chr7A 100.000 5692 0 0 1 5692 287818846 287824537 0.000000e+00 10512
1 TraesCS7A01G275100 chr7A 96.311 1247 39 6 4448 5689 685695181 685696425 0.000000e+00 2041
2 TraesCS7A01G275100 chr7A 96.074 1248 36 6 4448 5692 116521723 116520486 0.000000e+00 2021
3 TraesCS7A01G275100 chr1A 94.696 2319 111 6 2142 4449 257564735 257562418 0.000000e+00 3591
4 TraesCS7A01G275100 chr3B 94.041 2316 127 9 2142 4449 473697384 473699696 0.000000e+00 3502
5 TraesCS7A01G275100 chr3B 93.970 2305 133 5 2150 4449 223525687 223523384 0.000000e+00 3482
6 TraesCS7A01G275100 chr3B 85.751 386 55 0 772 1157 780340658 780340273 5.310000e-110 409
7 TraesCS7A01G275100 chr7B 93.359 2319 141 8 2142 4449 145700622 145702938 0.000000e+00 3417
8 TraesCS7A01G275100 chr7B 94.094 982 35 2 772 1732 244631675 244632654 0.000000e+00 1471
9 TraesCS7A01G275100 chr7B 81.745 871 123 18 773 1618 244635920 244636779 0.000000e+00 695
10 TraesCS7A01G275100 chr7B 79.303 947 133 21 772 1685 244601010 244601926 6.310000e-169 604
11 TraesCS7A01G275100 chr7B 95.687 371 16 0 1772 2142 244632858 244633228 1.060000e-166 597
12 TraesCS7A01G275100 chr6A 92.623 2318 158 8 2141 4449 495119161 495121474 0.000000e+00 3321
13 TraesCS7A01G275100 chr6A 95.853 1254 38 10 4448 5689 102929251 102930502 0.000000e+00 2015
14 TraesCS7A01G275100 chr6A 91.847 785 46 7 1 772 457311759 457310980 0.000000e+00 1079
15 TraesCS7A01G275100 chr6A 82.278 869 123 21 772 1621 34277909 34277053 0.000000e+00 723
16 TraesCS7A01G275100 chr6A 83.671 790 95 26 1 772 615453897 615454670 0.000000e+00 713
17 TraesCS7A01G275100 chr6A 82.078 876 118 19 772 1617 34279993 34279127 0.000000e+00 712
18 TraesCS7A01G275100 chr6A 81.849 876 120 19 772 1617 34392560 34391694 0.000000e+00 701
19 TraesCS7A01G275100 chr6A 81.818 858 122 23 779 1617 34390472 34389630 0.000000e+00 689
20 TraesCS7A01G275100 chr6A 80.800 875 131 17 772 1617 34275166 34274300 0.000000e+00 651
21 TraesCS7A01G275100 chr6A 80.783 869 129 20 772 1614 34283990 34283134 0.000000e+00 645
22 TraesCS7A01G275100 chr4A 92.578 2304 165 5 2150 4449 479615163 479617464 0.000000e+00 3302
23 TraesCS7A01G275100 chr4A 96.320 1250 41 4 4448 5692 183957914 183956665 0.000000e+00 2049
24 TraesCS7A01G275100 chr4A 96.163 1251 39 7 4448 5692 533009740 533008493 0.000000e+00 2036
25 TraesCS7A01G275100 chr4A 96.148 1246 41 7 4448 5689 683391894 683393136 0.000000e+00 2028
26 TraesCS7A01G275100 chr5D 92.526 2288 164 6 2168 4449 250594752 250592466 0.000000e+00 3271
27 TraesCS7A01G275100 chr5D 91.248 777 58 10 1 771 387992055 387991283 0.000000e+00 1050
28 TraesCS7A01G275100 chr5D 89.602 779 63 13 1 771 27625643 27626411 0.000000e+00 974
29 TraesCS7A01G275100 chr5D 89.474 779 70 9 1 772 458782143 458781370 0.000000e+00 974
30 TraesCS7A01G275100 chr5D 87.371 776 83 12 1 771 545627013 545627778 0.000000e+00 876
31 TraesCS7A01G275100 chr5D 88.824 340 34 4 73 409 522696181 522696519 1.140000e-111 414
32 TraesCS7A01G275100 chr3D 92.486 2289 163 6 2168 4449 443418767 443416481 0.000000e+00 3265
33 TraesCS7A01G275100 chr3D 91.592 785 47 12 1 771 472691887 472692666 0.000000e+00 1066
34 TraesCS7A01G275100 chr3D 89.017 783 70 9 2 771 557635742 557636521 0.000000e+00 955
35 TraesCS7A01G275100 chr3D 82.225 872 123 13 772 1619 583181320 583180457 0.000000e+00 723
36 TraesCS7A01G275100 chr3D 81.808 874 122 17 772 1619 583277924 583277062 0.000000e+00 699
37 TraesCS7A01G275100 chr3D 81.379 870 124 25 772 1621 583026815 583025964 0.000000e+00 675
38 TraesCS7A01G275100 chr3D 81.393 876 119 21 772 1621 583282152 583281295 0.000000e+00 675
39 TraesCS7A01G275100 chr3D 81.013 869 135 19 772 1621 583185272 583184415 0.000000e+00 664
40 TraesCS7A01G275100 chr3D 80.778 874 134 18 772 1619 583187310 583186445 0.000000e+00 652
41 TraesCS7A01G275100 chr3D 80.903 864 129 20 776 1620 583222719 583221873 0.000000e+00 649
42 TraesCS7A01G275100 chr3D 80.343 875 135 13 772 1621 583289680 583288818 3.740000e-176 628
43 TraesCS7A01G275100 chr3D 80.797 828 120 25 772 1574 583274887 583274074 3.770000e-171 612
44 TraesCS7A01G275100 chr6B 92.131 2313 176 4 2143 4449 29989065 29986753 0.000000e+00 3258
45 TraesCS7A01G275100 chr6B 82.274 818 115 14 772 1572 62633909 62633105 0.000000e+00 680
46 TraesCS7A01G275100 chr2A 96.554 1248 37 5 4448 5692 623750835 623749591 0.000000e+00 2061
47 TraesCS7A01G275100 chr3A 96.549 1246 33 6 4448 5689 732440190 732441429 0.000000e+00 2054
48 TraesCS7A01G275100 chr3A 96.077 1249 42 4 4448 5692 119767941 119766696 0.000000e+00 2028
49 TraesCS7A01G275100 chr3A 91.892 777 55 8 1 772 257086002 257086775 0.000000e+00 1079
50 TraesCS7A01G275100 chr7D 93.738 1006 39 3 772 1756 264315388 264316390 0.000000e+00 1487
51 TraesCS7A01G275100 chr7D 84.930 783 94 20 1 772 37147300 37146531 0.000000e+00 771
52 TraesCS7A01G275100 chr7D 80.328 915 119 20 772 1653 264311962 264312848 2.240000e-178 636
53 TraesCS7A01G275100 chr7D 93.841 276 17 0 1867 2142 264316880 264317155 3.170000e-112 416
54 TraesCS7A01G275100 chr5B 91.923 780 52 9 1 771 566047491 566046714 0.000000e+00 1081
55 TraesCS7A01G275100 chr5B 91.060 783 57 11 1 773 692301649 692300870 0.000000e+00 1046
56 TraesCS7A01G275100 chr1D 91.730 786 48 11 1 772 56516924 56516142 0.000000e+00 1075
57 TraesCS7A01G275100 chr1D 90.956 774 66 4 1 771 201774197 201774969 0.000000e+00 1038
58 TraesCS7A01G275100 chr1D 90.689 784 58 8 1 771 440060294 440061075 0.000000e+00 1029
59 TraesCS7A01G275100 chr1D 90.482 788 58 12 1 775 461561589 461560806 0.000000e+00 1024
60 TraesCS7A01G275100 chr1D 90.355 788 59 12 1 775 461499250 461500033 0.000000e+00 1018
61 TraesCS7A01G275100 chr1D 89.949 786 61 10 1 771 475123840 475123058 0.000000e+00 998
62 TraesCS7A01G275100 chr4D 91.083 785 53 9 1 772 78582888 78582108 0.000000e+00 1046
63 TraesCS7A01G275100 chr4D 90.179 784 59 8 1 771 489745745 489746523 0.000000e+00 1005
64 TraesCS7A01G275100 chr4D 88.959 788 64 14 1 771 248943859 248943078 0.000000e+00 952
65 TraesCS7A01G275100 chr4D 88.437 787 72 11 1 771 203801195 203800412 0.000000e+00 931
66 TraesCS7A01G275100 chr4D 87.867 783 55 20 1 771 64630722 64631476 0.000000e+00 883
67 TraesCS7A01G275100 chrUn 90.828 785 58 9 1 772 398717825 398717042 0.000000e+00 1038
68 TraesCS7A01G275100 chrUn 90.701 785 56 11 1 771 47641488 47640707 0.000000e+00 1029
69 TraesCS7A01G275100 chrUn 90.839 775 62 9 1 771 310746003 310745234 0.000000e+00 1029
70 TraesCS7A01G275100 chrUn 90.434 784 61 8 1 771 281036701 281037483 0.000000e+00 1020
71 TraesCS7A01G275100 chrUn 90.434 784 57 10 2 771 9721232 9720453 0.000000e+00 1016
72 TraesCS7A01G275100 chrUn 91.859 737 44 10 1 723 194991728 194990994 0.000000e+00 1014
73 TraesCS7A01G275100 chrUn 90.216 787 58 11 1 772 91230110 91230892 0.000000e+00 1009
74 TraesCS7A01G275100 chrUn 90.051 784 64 6 1 772 150856345 150857126 0.000000e+00 1003
75 TraesCS7A01G275100 chrUn 90.051 784 63 7 1 772 150872679 150873459 0.000000e+00 1002
76 TraesCS7A01G275100 chrUn 89.796 784 66 6 1 772 150866775 150867556 0.000000e+00 992
77 TraesCS7A01G275100 chrUn 89.796 784 65 7 1 772 150869004 150869784 0.000000e+00 990
78 TraesCS7A01G275100 chrUn 91.022 724 50 7 52 763 418725403 418726123 0.000000e+00 963
79 TraesCS7A01G275100 chrUn 91.133 609 42 4 173 771 150889652 150890258 0.000000e+00 815
80 TraesCS7A01G275100 chrUn 91.133 609 42 4 173 771 150928695 150929301 0.000000e+00 815
81 TraesCS7A01G275100 chrUn 88.263 639 60 7 1 626 470492680 470492044 0.000000e+00 750
82 TraesCS7A01G275100 chrUn 82.893 871 110 17 772 1621 101987341 101986489 0.000000e+00 747
83 TraesCS7A01G275100 chrUn 88.361 610 57 9 1 597 288981950 288981342 0.000000e+00 721
84 TraesCS7A01G275100 chrUn 88.361 610 57 9 1 597 288990675 288991283 0.000000e+00 721
85 TraesCS7A01G275100 chrUn 81.943 875 121 17 772 1617 101989438 101988572 0.000000e+00 706
86 TraesCS7A01G275100 chrUn 81.744 860 128 17 772 1614 101983999 101983152 0.000000e+00 691
87 TraesCS7A01G275100 chrUn 81.787 862 120 22 772 1612 41699237 41700082 0.000000e+00 688
88 TraesCS7A01G275100 chrUn 81.250 864 122 24 772 1614 352585994 352586838 0.000000e+00 662
89 TraesCS7A01G275100 chrUn 82.330 781 102 17 772 1528 101991684 101990916 0.000000e+00 645
90 TraesCS7A01G275100 chrUn 79.157 878 136 23 772 1619 41697355 41698215 1.070000e-156 564
91 TraesCS7A01G275100 chr6D 90.665 782 60 5 1 771 351974933 351974154 0.000000e+00 1027
92 TraesCS7A01G275100 chr6D 89.359 780 68 13 1 772 122736121 122736893 0.000000e+00 966
93 TraesCS7A01G275100 chr6D 91.629 669 43 6 114 771 194181925 194181259 0.000000e+00 913
94 TraesCS7A01G275100 chr6D 88.123 783 64 13 1 771 235782661 235783426 0.000000e+00 904
95 TraesCS7A01G275100 chr6D 87.589 564 53 8 1 551 166169944 166170503 6.220000e-179 638
96 TraesCS7A01G275100 chr5A 89.806 775 73 6 1 771 544249234 544248462 0.000000e+00 989
97 TraesCS7A01G275100 chr2D 89.820 776 66 11 1 771 596032419 596031652 0.000000e+00 983
98 TraesCS7A01G275100 chr2D 90.227 706 60 9 1 700 635178420 635179122 0.000000e+00 913
99 TraesCS7A01G275100 chr1B 88.689 778 69 14 1 771 629293282 629294047 0.000000e+00 931


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 TraesCS7A01G275100 chr7A 287818846 287824537 5691 False 10512.000000 10512 100.000000 1 5692 1 chr7A.!!$F1 5691
1 TraesCS7A01G275100 chr7A 685695181 685696425 1244 False 2041.000000 2041 96.311000 4448 5689 1 chr7A.!!$F2 1241
2 TraesCS7A01G275100 chr7A 116520486 116521723 1237 True 2021.000000 2021 96.074000 4448 5692 1 chr7A.!!$R1 1244
3 TraesCS7A01G275100 chr1A 257562418 257564735 2317 True 3591.000000 3591 94.696000 2142 4449 1 chr1A.!!$R1 2307
4 TraesCS7A01G275100 chr3B 473697384 473699696 2312 False 3502.000000 3502 94.041000 2142 4449 1 chr3B.!!$F1 2307
5 TraesCS7A01G275100 chr3B 223523384 223525687 2303 True 3482.000000 3482 93.970000 2150 4449 1 chr3B.!!$R1 2299
6 TraesCS7A01G275100 chr7B 145700622 145702938 2316 False 3417.000000 3417 93.359000 2142 4449 1 chr7B.!!$F1 2307
7 TraesCS7A01G275100 chr7B 244631675 244636779 5104 False 921.000000 1471 90.508667 772 2142 3 chr7B.!!$F3 1370
8 TraesCS7A01G275100 chr7B 244601010 244601926 916 False 604.000000 604 79.303000 772 1685 1 chr7B.!!$F2 913
9 TraesCS7A01G275100 chr6A 495119161 495121474 2313 False 3321.000000 3321 92.623000 2141 4449 1 chr6A.!!$F2 2308
10 TraesCS7A01G275100 chr6A 102929251 102930502 1251 False 2015.000000 2015 95.853000 4448 5689 1 chr6A.!!$F1 1241
11 TraesCS7A01G275100 chr6A 457310980 457311759 779 True 1079.000000 1079 91.847000 1 772 1 chr6A.!!$R1 771
12 TraesCS7A01G275100 chr6A 615453897 615454670 773 False 713.000000 713 83.671000 1 772 1 chr6A.!!$F3 771
13 TraesCS7A01G275100 chr6A 34389630 34392560 2930 True 695.000000 701 81.833500 772 1617 2 chr6A.!!$R3 845
14 TraesCS7A01G275100 chr6A 34274300 34283990 9690 True 682.750000 723 81.484750 772 1621 4 chr6A.!!$R2 849
15 TraesCS7A01G275100 chr4A 479615163 479617464 2301 False 3302.000000 3302 92.578000 2150 4449 1 chr4A.!!$F1 2299
16 TraesCS7A01G275100 chr4A 183956665 183957914 1249 True 2049.000000 2049 96.320000 4448 5692 1 chr4A.!!$R1 1244
17 TraesCS7A01G275100 chr4A 533008493 533009740 1247 True 2036.000000 2036 96.163000 4448 5692 1 chr4A.!!$R2 1244
18 TraesCS7A01G275100 chr4A 683391894 683393136 1242 False 2028.000000 2028 96.148000 4448 5689 1 chr4A.!!$F2 1241
19 TraesCS7A01G275100 chr5D 250592466 250594752 2286 True 3271.000000 3271 92.526000 2168 4449 1 chr5D.!!$R1 2281
20 TraesCS7A01G275100 chr5D 387991283 387992055 772 True 1050.000000 1050 91.248000 1 771 1 chr5D.!!$R2 770
21 TraesCS7A01G275100 chr5D 27625643 27626411 768 False 974.000000 974 89.602000 1 771 1 chr5D.!!$F1 770
22 TraesCS7A01G275100 chr5D 458781370 458782143 773 True 974.000000 974 89.474000 1 772 1 chr5D.!!$R3 771
23 TraesCS7A01G275100 chr5D 545627013 545627778 765 False 876.000000 876 87.371000 1 771 1 chr5D.!!$F3 770
24 TraesCS7A01G275100 chr3D 443416481 443418767 2286 True 3265.000000 3265 92.486000 2168 4449 1 chr3D.!!$R1 2281
25 TraesCS7A01G275100 chr3D 472691887 472692666 779 False 1066.000000 1066 91.592000 1 771 1 chr3D.!!$F1 770
26 TraesCS7A01G275100 chr3D 557635742 557636521 779 False 955.000000 955 89.017000 2 771 1 chr3D.!!$F2 769
27 TraesCS7A01G275100 chr3D 583180457 583187310 6853 True 679.666667 723 81.338667 772 1621 3 chr3D.!!$R5 849
28 TraesCS7A01G275100 chr3D 583025964 583026815 851 True 675.000000 675 81.379000 772 1621 1 chr3D.!!$R2 849
29 TraesCS7A01G275100 chr3D 583274074 583282152 8078 True 662.000000 699 81.332667 772 1621 3 chr3D.!!$R6 849
30 TraesCS7A01G275100 chr3D 583221873 583222719 846 True 649.000000 649 80.903000 776 1620 1 chr3D.!!$R3 844
31 TraesCS7A01G275100 chr3D 583288818 583289680 862 True 628.000000 628 80.343000 772 1621 1 chr3D.!!$R4 849
32 TraesCS7A01G275100 chr6B 29986753 29989065 2312 True 3258.000000 3258 92.131000 2143 4449 1 chr6B.!!$R1 2306
33 TraesCS7A01G275100 chr6B 62633105 62633909 804 True 680.000000 680 82.274000 772 1572 1 chr6B.!!$R2 800
34 TraesCS7A01G275100 chr2A 623749591 623750835 1244 True 2061.000000 2061 96.554000 4448 5692 1 chr2A.!!$R1 1244
35 TraesCS7A01G275100 chr3A 732440190 732441429 1239 False 2054.000000 2054 96.549000 4448 5689 1 chr3A.!!$F2 1241
36 TraesCS7A01G275100 chr3A 119766696 119767941 1245 True 2028.000000 2028 96.077000 4448 5692 1 chr3A.!!$R1 1244
37 TraesCS7A01G275100 chr3A 257086002 257086775 773 False 1079.000000 1079 91.892000 1 772 1 chr3A.!!$F1 771
38 TraesCS7A01G275100 chr7D 264311962 264317155 5193 False 846.333333 1487 89.302333 772 2142 3 chr7D.!!$F1 1370
39 TraesCS7A01G275100 chr7D 37146531 37147300 769 True 771.000000 771 84.930000 1 772 1 chr7D.!!$R1 771
40 TraesCS7A01G275100 chr5B 566046714 566047491 777 True 1081.000000 1081 91.923000 1 771 1 chr5B.!!$R1 770
41 TraesCS7A01G275100 chr5B 692300870 692301649 779 True 1046.000000 1046 91.060000 1 773 1 chr5B.!!$R2 772
42 TraesCS7A01G275100 chr1D 56516142 56516924 782 True 1075.000000 1075 91.730000 1 772 1 chr1D.!!$R1 771
43 TraesCS7A01G275100 chr1D 201774197 201774969 772 False 1038.000000 1038 90.956000 1 771 1 chr1D.!!$F1 770
44 TraesCS7A01G275100 chr1D 440060294 440061075 781 False 1029.000000 1029 90.689000 1 771 1 chr1D.!!$F2 770
45 TraesCS7A01G275100 chr1D 461560806 461561589 783 True 1024.000000 1024 90.482000 1 775 1 chr1D.!!$R2 774
46 TraesCS7A01G275100 chr1D 461499250 461500033 783 False 1018.000000 1018 90.355000 1 775 1 chr1D.!!$F3 774
47 TraesCS7A01G275100 chr1D 475123058 475123840 782 True 998.000000 998 89.949000 1 771 1 chr1D.!!$R3 770
48 TraesCS7A01G275100 chr4D 78582108 78582888 780 True 1046.000000 1046 91.083000 1 772 1 chr4D.!!$R1 771
49 TraesCS7A01G275100 chr4D 489745745 489746523 778 False 1005.000000 1005 90.179000 1 771 1 chr4D.!!$F2 770
50 TraesCS7A01G275100 chr4D 248943078 248943859 781 True 952.000000 952 88.959000 1 771 1 chr4D.!!$R3 770
51 TraesCS7A01G275100 chr4D 203800412 203801195 783 True 931.000000 931 88.437000 1 771 1 chr4D.!!$R2 770
52 TraesCS7A01G275100 chr4D 64630722 64631476 754 False 883.000000 883 87.867000 1 771 1 chr4D.!!$F1 770
53 TraesCS7A01G275100 chrUn 398717042 398717825 783 True 1038.000000 1038 90.828000 1 772 1 chrUn.!!$R6 771
54 TraesCS7A01G275100 chrUn 47640707 47641488 781 True 1029.000000 1029 90.701000 1 771 1 chrUn.!!$R2 770
55 TraesCS7A01G275100 chrUn 310745234 310746003 769 True 1029.000000 1029 90.839000 1 771 1 chrUn.!!$R5 770
56 TraesCS7A01G275100 chrUn 281036701 281037483 782 False 1020.000000 1020 90.434000 1 771 1 chrUn.!!$F5 770
57 TraesCS7A01G275100 chrUn 9720453 9721232 779 True 1016.000000 1016 90.434000 2 771 1 chrUn.!!$R1 769
58 TraesCS7A01G275100 chrUn 194990994 194991728 734 True 1014.000000 1014 91.859000 1 723 1 chrUn.!!$R3 722
59 TraesCS7A01G275100 chrUn 91230110 91230892 782 False 1009.000000 1009 90.216000 1 772 1 chrUn.!!$F1 771
60 TraesCS7A01G275100 chrUn 150856345 150857126 781 False 1003.000000 1003 90.051000 1 772 1 chrUn.!!$F2 771
61 TraesCS7A01G275100 chrUn 150866775 150873459 6684 False 994.666667 1002 89.881000 1 772 3 chrUn.!!$F10 771
62 TraesCS7A01G275100 chrUn 418725403 418726123 720 False 963.000000 963 91.022000 52 763 1 chrUn.!!$F8 711
63 TraesCS7A01G275100 chrUn 150889652 150890258 606 False 815.000000 815 91.133000 173 771 1 chrUn.!!$F3 598
64 TraesCS7A01G275100 chrUn 150928695 150929301 606 False 815.000000 815 91.133000 173 771 1 chrUn.!!$F4 598
65 TraesCS7A01G275100 chrUn 470492044 470492680 636 True 750.000000 750 88.263000 1 626 1 chrUn.!!$R7 625
66 TraesCS7A01G275100 chrUn 288981342 288981950 608 True 721.000000 721 88.361000 1 597 1 chrUn.!!$R4 596
67 TraesCS7A01G275100 chrUn 288990675 288991283 608 False 721.000000 721 88.361000 1 597 1 chrUn.!!$F6 596
68 TraesCS7A01G275100 chrUn 101983152 101991684 8532 True 697.250000 747 82.227500 772 1621 4 chrUn.!!$R8 849
69 TraesCS7A01G275100 chrUn 352585994 352586838 844 False 662.000000 662 81.250000 772 1614 1 chrUn.!!$F7 842
70 TraesCS7A01G275100 chrUn 41697355 41700082 2727 False 626.000000 688 80.472000 772 1619 2 chrUn.!!$F9 847
71 TraesCS7A01G275100 chr6D 351974154 351974933 779 True 1027.000000 1027 90.665000 1 771 1 chr6D.!!$R2 770
72 TraesCS7A01G275100 chr6D 122736121 122736893 772 False 966.000000 966 89.359000 1 772 1 chr6D.!!$F1 771
73 TraesCS7A01G275100 chr6D 194181259 194181925 666 True 913.000000 913 91.629000 114 771 1 chr6D.!!$R1 657
74 TraesCS7A01G275100 chr6D 235782661 235783426 765 False 904.000000 904 88.123000 1 771 1 chr6D.!!$F3 770
75 TraesCS7A01G275100 chr6D 166169944 166170503 559 False 638.000000 638 87.589000 1 551 1 chr6D.!!$F2 550
76 TraesCS7A01G275100 chr5A 544248462 544249234 772 True 989.000000 989 89.806000 1 771 1 chr5A.!!$R1 770
77 TraesCS7A01G275100 chr2D 596031652 596032419 767 True 983.000000 983 89.820000 1 771 1 chr2D.!!$R1 770
78 TraesCS7A01G275100 chr2D 635178420 635179122 702 False 913.000000 913 90.227000 1 700 1 chr2D.!!$F1 699
79 TraesCS7A01G275100 chr1B 629293282 629294047 765 False 931.000000 931 88.689000 1 771 1 chr1B.!!$F1 770

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
884 7971 1.064832 GGAGGCAAGCATCTCTTCCTT 60.065 52.381 6.67 0.00 34.58 3.36 F
1803 11188 1.466167 GTTGTGCAGTCTGGCAGTATG 59.534 52.381 15.27 14.86 45.96 2.39 F
3593 26674 0.324285 CTCTGCTCCTGCTGGAAACT 59.676 55.000 13.89 0.00 42.66 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 18992 0.750249 TTCACGAAGGCACAGACTCA 59.250 50.000 0.00 0.00 0.00 3.41 R
3669 26750 0.253044 CCGGTGTTCATCCCATCACT 59.747 55.000 0.00 0.00 0.00 3.41 R
5086 28327 1.359117 GCCCGAGATTCGATCGTCA 59.641 57.895 15.94 3.44 43.74 4.35 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
50 57 6.889177 TGACTATAAGCAATGGTGAAATTCCA 59.111 34.615 0.00 0.00 39.41 3.53
83 91 3.751518 ACATGCGGTTAAGAAAGGAGTT 58.248 40.909 0.00 0.00 0.00 3.01
105 123 3.181464 TGTGATGTTGAGTTCGGGTAACA 60.181 43.478 0.00 0.00 40.83 2.41
520 583 9.702253 CTTGTATCCTAGGCCTCTCTTATATAA 57.298 37.037 9.68 5.64 0.00 0.98
750 6723 2.963101 TCCTCGGATGATTGACGGTATT 59.037 45.455 0.00 0.00 0.00 1.89
795 7882 3.565764 TCAGATATGGCTTTCCACCTG 57.434 47.619 0.00 0.00 46.92 4.00
884 7971 1.064832 GGAGGCAAGCATCTCTTCCTT 60.065 52.381 6.67 0.00 34.58 3.36
896 7983 5.740224 GCATCTCTTCCTTCATTACCATCGA 60.740 44.000 0.00 0.00 0.00 3.59
988 8075 1.952367 GCAACCAAGTATGCTCTGCCT 60.952 52.381 0.00 0.00 39.46 4.75
1047 8134 6.247229 TCTCTTGAGCTACTAGATCTCTGT 57.753 41.667 0.00 2.25 30.68 3.41
1163 8271 6.234177 CCAAGATCCAGTCTTACAAGAAACT 58.766 40.000 0.00 0.00 45.35 2.66
1176 8284 8.388103 TCTTACAAGAAACTTTTCAAGAAGACG 58.612 33.333 4.58 0.00 39.61 4.18
1254 8362 4.357918 AGAGGTCTCTATCTCTCTGCTC 57.642 50.000 0.00 0.00 39.03 4.26
1324 8432 5.884792 CAGTCTCTTATCTCCAAGGCATTTT 59.115 40.000 0.00 0.00 0.00 1.82
1331 8439 8.055181 TCTTATCTCCAAGGCATTTTACAAGAT 58.945 33.333 0.00 0.00 0.00 2.40
1430 10635 5.065731 CAGGACATCTGTTCAGGAAATTAGC 59.934 44.000 0.00 0.00 38.64 3.09
1470 10675 6.931840 CCCTCCTAAACATTCTTAGCTCATAC 59.068 42.308 0.00 0.00 0.00 2.39
1547 10753 8.814038 ATTAGCCAATCTTGATACAGTTTTCT 57.186 30.769 0.00 0.00 0.00 2.52
1711 10932 8.355169 ACATTATGTATGCCAAATCAAAGCTAG 58.645 33.333 0.00 0.00 37.81 3.42
1769 10990 6.235664 TCAATTAATTAGTAAGATCGCCCCC 58.764 40.000 0.00 0.00 0.00 5.40
1803 11188 1.466167 GTTGTGCAGTCTGGCAGTATG 59.534 52.381 15.27 14.86 45.96 2.39
1906 11708 8.732746 TCTACCTGCTCTTGGAATAATTAAAC 57.267 34.615 0.00 0.00 0.00 2.01
1908 11710 6.494059 ACCTGCTCTTGGAATAATTAAACCT 58.506 36.000 10.99 0.00 0.00 3.50
1955 11757 3.801114 AACTGTTTTGCTCCTTTCCAC 57.199 42.857 0.00 0.00 0.00 4.02
1961 11763 6.719370 ACTGTTTTGCTCCTTTCCACATAATA 59.281 34.615 0.00 0.00 0.00 0.98
2082 11884 3.185246 GGTGACGATCTGATGGAATGT 57.815 47.619 6.67 0.00 0.00 2.71
2121 11923 4.521146 ACAGAGCCAAGAATTATGTGGAG 58.479 43.478 5.85 0.00 34.05 3.86
2161 18792 6.803154 AAACTGTTAGGAATGAGCAACTAC 57.197 37.500 0.00 0.00 0.00 2.73
2291 18954 4.275810 CCTCAAACTCATGGTGGATCAAT 58.724 43.478 0.00 0.00 0.00 2.57
2329 18992 1.070601 GGAAAAACCCATGCTGTGCTT 59.929 47.619 0.00 0.00 0.00 3.91
2370 19033 3.643792 AGAAGTCAGCCAACTGTAACTCT 59.356 43.478 0.00 0.00 44.77 3.24
2477 20644 4.619227 CTTCACCGGGGCACGTGT 62.619 66.667 18.38 2.36 42.24 4.49
2532 20699 3.626930 AGGAGTTGAGGTAGTAGCAGAG 58.373 50.000 1.58 0.00 0.00 3.35
2556 20723 5.393866 ACACCAAAATCCTCAAGTAACCAT 58.606 37.500 0.00 0.00 0.00 3.55
2633 21877 1.681945 CTCGAGCGAGAAACTGCAGC 61.682 60.000 15.27 0.00 44.53 5.25
2652 21896 1.956477 GCCTGCTTCTTTGTCTTCCAA 59.044 47.619 0.00 0.00 0.00 3.53
2778 25150 0.768622 TGGAGCGGGGAAAGAAAAGA 59.231 50.000 0.00 0.00 0.00 2.52
2798 25170 1.216444 GCTGAGAGATCGTGCCACA 59.784 57.895 0.00 0.00 0.00 4.17
2836 25208 1.964933 GGAGGAGGTGACTATAGTGGC 59.035 57.143 10.90 2.44 44.43 5.01
2883 25255 3.900601 GACTCAGGATGTGGACAGGATAT 59.099 47.826 0.00 0.00 37.40 1.63
3096 26177 0.820871 AGAAGCCATCAGAGGTCGAC 59.179 55.000 7.13 7.13 0.00 4.20
3202 26283 2.025898 TGTACACAGAGTCGTCACCAA 58.974 47.619 0.00 0.00 0.00 3.67
3218 26299 7.384932 GTCGTCACCAATAATGATCATGTCATA 59.615 37.037 9.46 0.00 46.80 2.15
3502 26583 4.274147 AGAGATAGACCACTGACGAACAT 58.726 43.478 0.00 0.00 0.00 2.71
3523 26604 5.012148 ACATAAGCCACTACAAGAAGAGTGT 59.988 40.000 1.72 0.00 41.28 3.55
3529 26610 4.442893 CCACTACAAGAAGAGTGTGGACAA 60.443 45.833 4.14 0.00 45.37 3.18
3575 26656 3.990318 TGTCTCATCATAATCGCGTCT 57.010 42.857 5.77 0.00 0.00 4.18
3593 26674 0.324285 CTCTGCTCCTGCTGGAAACT 59.676 55.000 13.89 0.00 42.66 2.66
3641 26722 1.205655 CTCAAGAGAACCATCGGAGCA 59.794 52.381 0.00 0.00 0.00 4.26
3669 26750 1.493022 ACCTTGTAGACCCACTTGCAA 59.507 47.619 0.00 0.00 0.00 4.08
3783 26865 0.982704 AGGCTGAGTCATTGCAGTCT 59.017 50.000 6.69 0.00 41.89 3.24
3825 26907 1.716826 GGCAGAGAGACCGTACCGAG 61.717 65.000 0.00 0.00 0.00 4.63
3828 26910 0.107116 AGAGAGACCGTACCGAGCAT 60.107 55.000 0.00 0.00 0.00 3.79
3878 26961 0.396435 AGCACGGAGATTGTGAACCA 59.604 50.000 0.00 0.00 39.73 3.67
3896 26979 0.978146 CAGGGGAGACGTGAAGGGAT 60.978 60.000 0.00 0.00 37.13 3.85
4021 27258 1.075600 GAGAGGTGGAGGAGGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
4176 27413 4.351127 AGAAGGACGTGGGTAGTAAGAAT 58.649 43.478 0.00 0.00 0.00 2.40
4208 27445 3.503827 AAAGTCACATCACGCGAGATA 57.496 42.857 18.63 0.88 0.00 1.98
4314 27551 2.035066 GCAGTCAGTTTGGTGCATTCTT 59.965 45.455 0.00 0.00 35.91 2.52
4346 27583 0.713883 GAACGTAGCACACACATCCG 59.286 55.000 0.00 0.00 0.00 4.18
4421 27658 2.320681 TACCACCCTGTAGAGCAGTT 57.679 50.000 0.00 0.00 43.55 3.16
4802 28043 8.530311 CCTATGACTATGAGATTATGCAACTCT 58.470 37.037 0.00 0.00 0.00 3.24
4884 28125 1.076350 AGGTGCTCTACAGGTGTCTCT 59.924 52.381 0.00 0.00 0.00 3.10
5055 28296 3.306156 GGAACGAGTAAAGAGACTTGCCT 60.306 47.826 0.00 0.00 34.59 4.75
5086 28327 8.788806 CGAGATTGAACTAGGTATTGAGATACT 58.211 37.037 0.00 0.00 38.53 2.12
5181 28422 7.755822 ACCGATAAAGATCTTCGTAGAATATGC 59.244 37.037 8.78 0.00 45.90 3.14
5225 28466 4.080526 AGGTTCCGCTATTGGTTATTGACT 60.081 41.667 0.00 0.00 0.00 3.41
5360 28601 1.051812 GGAGTCCCGGATGTGATCAT 58.948 55.000 0.73 0.00 36.95 2.45
5471 28712 3.631145 TCGGGATTTTATCGGAGTACG 57.369 47.619 0.00 0.00 46.11 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 57 2.783135 ACCGCATGTCTGAAACTTGAT 58.217 42.857 0.00 0.00 35.55 2.57
83 91 3.181464 TGTTACCCGAACTCAACATCACA 60.181 43.478 0.00 0.00 38.98 3.58
105 123 5.647658 CACATATTGGGTGTCACACATAAGT 59.352 40.000 9.16 3.19 35.86 2.24
520 583 1.304713 ATCGTGTGTCTACCCCCGT 60.305 57.895 0.00 0.00 0.00 5.28
750 6723 6.411376 TCTTTGTTAGAATAAATCCGAGGCA 58.589 36.000 0.00 0.00 0.00 4.75
795 7882 5.923684 CCTAGAAGGCAAACTTATCGATCTC 59.076 44.000 0.00 0.00 40.21 2.75
862 7949 1.340405 GGAAGAGATGCTTGCCTCCAA 60.340 52.381 0.00 0.00 38.86 3.53
864 7951 0.545646 AGGAAGAGATGCTTGCCTCC 59.454 55.000 0.00 0.00 45.16 4.30
884 7971 3.373748 GCACATTGTGTCGATGGTAATGA 59.626 43.478 17.64 0.00 35.75 2.57
896 7983 0.108585 AAGACCCTCGCACATTGTGT 59.891 50.000 17.64 0.00 35.75 3.72
984 8071 2.768527 CAACATCTTCCTCTCCTAGGCA 59.231 50.000 2.96 0.00 46.10 4.75
988 8075 3.969976 CCATCCAACATCTTCCTCTCCTA 59.030 47.826 0.00 0.00 0.00 2.94
1047 8134 4.202192 ACGAAGATCTCTTGCATGATGCTA 60.202 41.667 19.19 10.32 45.31 3.49
1163 8271 4.202010 CCTTCTTTGCCGTCTTCTTGAAAA 60.202 41.667 0.00 0.00 0.00 2.29
1254 8362 1.479709 AGAGGAGGACTGTGGATTCG 58.520 55.000 0.00 0.00 0.00 3.34
1324 8432 4.973168 ACAACTGGCTTCTTCATCTTGTA 58.027 39.130 0.00 0.00 0.00 2.41
1331 8439 3.351740 TCACAAACAACTGGCTTCTTCA 58.648 40.909 0.00 0.00 0.00 3.02
1430 10635 0.251634 GAGGGAAACTCTGCTCTGGG 59.748 60.000 0.00 0.00 43.14 4.45
1711 10932 2.355010 ATCACATCCTTAGCCCTTGC 57.645 50.000 0.00 0.00 37.95 4.01
1803 11188 1.885887 TGTTTGCTATGGAGGTTGTGC 59.114 47.619 0.00 0.00 0.00 4.57
1817 11202 3.825308 CTGTACACCATGACATGTTTGC 58.175 45.455 14.26 2.66 0.00 3.68
1906 11708 2.289010 GGGGCAAGTTTTGATGTTCAGG 60.289 50.000 0.00 0.00 0.00 3.86
1908 11710 1.339610 CGGGGCAAGTTTTGATGTTCA 59.660 47.619 0.00 0.00 0.00 3.18
1971 11773 8.523915 TCGTATAGGAAATCTACTGGTGTTAA 57.476 34.615 0.00 0.00 0.00 2.01
2082 11884 0.833949 TGTAACCAGCATATGCCCGA 59.166 50.000 23.96 2.78 43.38 5.14
2121 11923 6.382869 ACAGTTTTGATATTAGCTGATGGC 57.617 37.500 0.32 0.00 42.19 4.40
2161 18792 2.648059 CCATTGGCCCTCAGTAAAGAG 58.352 52.381 0.00 0.00 35.39 2.85
2291 18954 5.623956 TTTCCTCTCCAAACTCAGTGTTA 57.376 39.130 0.00 0.00 38.03 2.41
2329 18992 0.750249 TTCACGAAGGCACAGACTCA 59.250 50.000 0.00 0.00 0.00 3.41
2370 19033 2.234661 CACTCTTCACTATGTGCCCTCA 59.765 50.000 0.00 0.00 32.98 3.86
2477 20644 4.772624 ACAGCACAGGTTCTCTCAGTATTA 59.227 41.667 0.00 0.00 0.00 0.98
2532 20699 4.825085 TGGTTACTTGAGGATTTTGGTGTC 59.175 41.667 0.00 0.00 0.00 3.67
2556 20723 1.476891 GCTGAGGTGATCTGGTTACGA 59.523 52.381 0.00 0.00 0.00 3.43
2633 21877 2.030451 GCTTGGAAGACAAAGAAGCAGG 60.030 50.000 0.00 0.00 38.91 4.85
2652 21896 1.547372 CTTGGTGGCTTGCTTATTGCT 59.453 47.619 0.00 0.00 43.37 3.91
2778 25150 2.343426 TGGCACGATCTCTCAGCGT 61.343 57.895 0.00 0.00 39.04 5.07
2836 25208 2.538141 TTTCAGCCCCCACCTCTGG 61.538 63.158 0.00 0.00 37.29 3.86
2883 25255 2.571202 TGTTACATGCCCTCACATCTCA 59.429 45.455 0.00 0.00 0.00 3.27
3096 26177 6.073331 GCTATTTTCTTGGGATTGAGATCTCG 60.073 42.308 17.76 1.18 35.39 4.04
3187 26268 4.801330 TCATTATTGGTGACGACTCTGT 57.199 40.909 0.00 0.00 0.00 3.41
3218 26299 5.126384 CGGACTCTTCTCCTTCTCTATGTTT 59.874 44.000 0.00 0.00 0.00 2.83
3502 26583 4.262463 CCACACTCTTCTTGTAGTGGCTTA 60.262 45.833 7.33 0.00 45.94 3.09
3523 26604 0.611618 GCCCACATGACCATTGTCCA 60.612 55.000 0.00 0.00 41.01 4.02
3529 26610 3.179284 TGTGGCCCACATGACCAT 58.821 55.556 13.83 0.00 39.62 3.55
3547 26628 4.919754 CGATTATGATGAGACATTCGCTCA 59.080 41.667 0.00 0.00 45.52 4.26
3575 26656 1.276421 GTAGTTTCCAGCAGGAGCAGA 59.724 52.381 0.00 0.00 46.74 4.26
3593 26674 2.967397 CTCGTCTTGTGGCCCGTA 59.033 61.111 0.00 0.00 0.00 4.02
3641 26722 4.906060 AGTGGGTCTACAAGGTTAAGACTT 59.094 41.667 0.00 0.00 39.65 3.01
3669 26750 0.253044 CCGGTGTTCATCCCATCACT 59.747 55.000 0.00 0.00 0.00 3.41
3783 26865 0.833287 GCTGAGCCCACTTCCTATCA 59.167 55.000 0.00 0.00 0.00 2.15
3825 26907 0.320247 CCTGATCGCTACTCCCATGC 60.320 60.000 0.00 0.00 0.00 4.06
3828 26910 1.381191 TGCCTGATCGCTACTCCCA 60.381 57.895 0.00 0.00 0.00 4.37
3878 26961 0.978146 CATCCCTTCACGTCTCCCCT 60.978 60.000 0.00 0.00 0.00 4.79
3911 26994 1.008327 TGTCTCCCCTGATGAGCCTTA 59.992 52.381 0.00 0.00 0.00 2.69
3935 27018 0.314302 ATACTCGTCGCCCATACTGC 59.686 55.000 0.00 0.00 0.00 4.40
4021 27258 1.265454 ACCGACCCCATCTTCTCCAC 61.265 60.000 0.00 0.00 0.00 4.02
4100 27337 3.117093 TCCTTCTCCTTCCCGATACATCT 60.117 47.826 0.00 0.00 0.00 2.90
4102 27339 3.330126 TCCTTCTCCTTCCCGATACAT 57.670 47.619 0.00 0.00 0.00 2.29
4176 27413 5.698089 GTGATGTGACTTTTGATGAGTCTCA 59.302 40.000 4.68 4.68 45.81 3.27
4331 27568 1.790755 TGTTCGGATGTGTGTGCTAC 58.209 50.000 0.00 0.00 0.00 3.58
4346 27583 2.656560 ACTCAGCTGTCCGTATGTTC 57.343 50.000 14.67 0.00 0.00 3.18
4357 27594 1.405105 GCTCTCCTGACTACTCAGCTG 59.595 57.143 7.63 7.63 42.55 4.24
4421 27658 4.224991 TCTCATCAACATTCAGCCATCA 57.775 40.909 0.00 0.00 0.00 3.07
4541 27778 9.454859 TGTATTCACACATGTATTATGTTTCCA 57.545 29.630 0.00 0.00 0.00 3.53
4884 28125 2.938838 CCAACCCAACAAGTACCTTCA 58.061 47.619 0.00 0.00 0.00 3.02
5055 28296 8.058667 TCAATACCTAGTTCAATCTCGTTACA 57.941 34.615 0.00 0.00 0.00 2.41
5086 28327 1.359117 GCCCGAGATTCGATCGTCA 59.641 57.895 15.94 3.44 43.74 4.35
5181 28422 2.224695 TGGATGCTCATATTGGCTCCTG 60.225 50.000 12.11 0.00 31.74 3.86
5360 28601 3.395054 AGAGACTCCTCATCATGTCCA 57.605 47.619 0.00 0.00 41.87 4.02
5369 28610 3.948473 CTCGACCATTTAGAGACTCCTCA 59.052 47.826 0.00 0.00 41.87 3.86


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

AutoCloner maintained by Alex Coulton.