Multiple sequence alignment - TraesCS4B01G278200

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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 TraesCS4B01G278200 chr4B 100.000 4459 0 0 1 4459 560025496 560021038 0.000000e+00 8235.0
1 TraesCS4B01G278200 chr4B 88.217 2529 210 42 940 3433 222962987 222965462 0.000000e+00 2939.0
2 TraesCS4B01G278200 chr4B 100.000 1419 0 0 4806 6224 560020691 560019273 0.000000e+00 2621.0
3 TraesCS4B01G278200 chr4B 90.657 1659 116 13 969 2596 108079573 108081223 0.000000e+00 2169.0
4 TraesCS4B01G278200 chr4B 92.398 763 50 6 5070 5829 666837874 666837117 0.000000e+00 1081.0
5 TraesCS4B01G278200 chr4B 88.692 902 78 13 2195 3093 102826821 102827701 0.000000e+00 1079.0
6 TraesCS4B01G278200 chr4B 87.946 896 81 16 2201 3093 440772668 440773539 0.000000e+00 1031.0
7 TraesCS4B01G278200 chr4B 92.636 258 19 0 4812 5069 531454422 531454679 7.620000e-99 372.0
8 TraesCS4B01G278200 chr4B 92.268 194 14 1 1355 1548 389774492 389774684 2.210000e-69 274.0
9 TraesCS4B01G278200 chr4B 83.984 256 32 5 1104 1358 389772404 389772651 2.900000e-58 237.0
10 TraesCS4B01G278200 chr4B 92.742 124 9 0 2198 2321 1125197 1125320 4.960000e-41 180.0
11 TraesCS4B01G278200 chr4B 95.699 93 4 0 1456 1548 102811732 102811824 3.890000e-32 150.0
12 TraesCS4B01G278200 chr4B 94.624 93 5 0 1456 1548 102792200 102792292 1.810000e-30 145.0
13 TraesCS4B01G278200 chr2B 93.921 3537 168 15 940 4457 311834371 311837879 0.000000e+00 5297.0
14 TraesCS4B01G278200 chr2B 92.042 2375 129 29 937 3292 22380696 22383029 0.000000e+00 3284.0
15 TraesCS4B01G278200 chr2B 89.728 1139 87 16 5070 6191 735708698 735707573 0.000000e+00 1428.0
16 TraesCS4B01G278200 chr2B 88.532 1151 88 26 5070 6191 677848939 677850074 0.000000e+00 1354.0
17 TraesCS4B01G278200 chr2B 87.336 1145 104 34 5070 6193 560371840 560372964 0.000000e+00 1273.0
18 TraesCS4B01G278200 chr2B 90.670 911 55 16 5070 5962 771073807 771074705 0.000000e+00 1184.0
19 TraesCS4B01G278200 chr2B 91.268 836 64 4 3631 4459 22383281 22384114 0.000000e+00 1131.0
20 TraesCS4B01G278200 chr2B 84.410 1084 112 29 5146 6191 135863295 135862231 0.000000e+00 1013.0
21 TraesCS4B01G278200 chr2B 90.582 361 18 4 5831 6191 36284941 36284597 1.220000e-126 464.0
22 TraesCS4B01G278200 chr2B 93.798 258 16 0 4812 5069 311837916 311838173 7.570000e-104 388.0
23 TraesCS4B01G278200 chr2B 92.248 258 20 0 4812 5069 22384154 22384411 3.550000e-97 366.0
24 TraesCS4B01G278200 chr5B 92.833 2372 123 29 940 3292 10496312 10498655 0.000000e+00 3395.0
25 TraesCS4B01G278200 chr5B 90.525 1752 124 22 940 2657 49392385 49394128 0.000000e+00 2278.0
26 TraesCS4B01G278200 chr5B 90.323 1147 71 19 5070 6191 545947659 545946528 0.000000e+00 1467.0
27 TraesCS4B01G278200 chr5B 91.756 837 60 4 3631 4459 49451104 49451939 0.000000e+00 1155.0
28 TraesCS4B01G278200 chr5B 92.095 759 53 4 5070 5824 667405157 667405912 0.000000e+00 1062.0
29 TraesCS4B01G278200 chr5B 88.472 373 17 10 5829 6191 437439256 437439612 1.600000e-115 427.0
30 TraesCS4B01G278200 chr5B 93.243 222 13 2 3412 3631 49450375 49450596 6.020000e-85 326.0
31 TraesCS4B01G278200 chr5B 93.478 46 0 2 897 940 217709298 217709342 1.450000e-06 65.8
32 TraesCS4B01G278200 chr1D 91.254 2527 129 41 940 3433 417757780 417760247 0.000000e+00 3358.0
33 TraesCS4B01G278200 chr1D 89.066 439 35 9 1105 1541 171321370 171321797 3.300000e-147 532.0
34 TraesCS4B01G278200 chr1D 88.679 53 4 2 2415 2465 4996560 4996612 5.210000e-06 63.9
35 TraesCS4B01G278200 chr3B 92.666 2318 117 25 940 3239 436378395 436376113 0.000000e+00 3290.0
36 TraesCS4B01G278200 chr3B 91.742 1659 98 18 969 2596 21575545 21573895 0.000000e+00 2268.0
37 TraesCS4B01G278200 chr3B 88.889 1152 72 22 5070 6193 493157585 493158708 0.000000e+00 1367.0
38 TraesCS4B01G278200 chr3B 90.552 942 74 13 2 940 739021944 739022873 0.000000e+00 1232.0
39 TraesCS4B01G278200 chr3B 89.157 913 59 17 5070 5965 685377228 685378117 0.000000e+00 1101.0
40 TraesCS4B01G278200 chr3B 84.893 1079 111 21 5146 6193 14517874 14518931 0.000000e+00 1042.0
41 TraesCS4B01G278200 chr3B 92.248 258 20 0 4812 5069 803878054 803877797 3.550000e-97 366.0
42 TraesCS4B01G278200 chr3B 90.950 221 18 2 3413 3631 787974649 787974869 4.720000e-76 296.0
43 TraesCS4B01G278200 chr7B 91.494 2316 157 21 940 3235 101714891 101717186 0.000000e+00 3149.0
44 TraesCS4B01G278200 chr7B 99.045 942 5 3 1 940 742144075 742145014 0.000000e+00 1687.0
45 TraesCS4B01G278200 chr7B 98.937 941 8 2 1 941 720140429 720141367 0.000000e+00 1681.0
46 TraesCS4B01G278200 chr7B 90.718 1142 76 16 5070 6191 698907920 698906789 0.000000e+00 1495.0
47 TraesCS4B01G278200 chr7B 92.077 833 58 3 3634 4459 60578220 60577389 0.000000e+00 1166.0
48 TraesCS4B01G278200 chr7B 91.388 836 64 3 3631 4459 549271499 549270665 0.000000e+00 1138.0
49 TraesCS4B01G278200 chr7B 94.587 702 36 2 5070 5771 40423821 40423122 0.000000e+00 1085.0
50 TraesCS4B01G278200 chr7B 95.950 321 12 1 2451 2770 60579140 60578820 2.570000e-143 520.0
51 TraesCS4B01G278200 chr7B 87.738 367 29 5 5829 6191 703820914 703820560 1.250000e-111 414.0
52 TraesCS4B01G278200 chr5A 92.465 2057 95 15 1407 3433 693881418 693879392 0.000000e+00 2885.0
53 TraesCS4B01G278200 chr5A 99.150 941 7 1 1 941 562855610 562854671 0.000000e+00 1692.0
54 TraesCS4B01G278200 chr5A 88.532 436 44 2 940 1374 693881841 693881411 1.990000e-144 523.0
55 TraesCS4B01G278200 chr6D 94.326 1551 69 9 1894 3433 56532 54990 0.000000e+00 2359.0
56 TraesCS4B01G278200 chr6D 91.139 474 32 6 2234 2706 280313824 280314288 8.800000e-178 634.0
57 TraesCS4B01G278200 chr6D 89.091 440 33 7 1104 1541 17947836 17947410 3.300000e-147 532.0
58 TraesCS4B01G278200 chr6D 88.636 440 38 7 1104 1541 281545727 281545298 5.530000e-145 525.0
59 TraesCS4B01G278200 chr6D 90.637 267 22 2 4806 5069 160226839 160227105 9.930000e-93 351.0
60 TraesCS4B01G278200 chr6D 90.576 191 18 0 1184 1374 57003 56813 2.880000e-63 254.0
61 TraesCS4B01G278200 chr6D 85.859 99 9 1 1444 1537 56140286 56140188 3.970000e-17 100.0
62 TraesCS4B01G278200 chr6D 92.424 66 4 1 1703 1767 56659 56594 6.640000e-15 93.5
63 TraesCS4B01G278200 chr6D 88.136 59 5 1 884 940 73712818 73712876 1.120000e-07 69.4
64 TraesCS4B01G278200 chr6B 91.863 1659 95 12 969 2596 648885883 648887532 0.000000e+00 2279.0
65 TraesCS4B01G278200 chr6B 91.802 1659 95 19 969 2596 648849835 648851483 0.000000e+00 2272.0
66 TraesCS4B01G278200 chr6B 99.894 942 0 1 1 941 508615658 508614717 0.000000e+00 1733.0
67 TraesCS4B01G278200 chr6B 88.358 1151 77 19 5070 6196 658304409 658303292 0.000000e+00 1330.0
68 TraesCS4B01G278200 chr6B 91.274 871 59 10 1 861 55672050 55671187 0.000000e+00 1171.0
69 TraesCS4B01G278200 chr6B 91.627 836 60 7 3631 4459 14256595 14255763 0.000000e+00 1147.0
70 TraesCS4B01G278200 chr6B 93.716 732 41 3 5070 5798 668145001 668144272 0.000000e+00 1092.0
71 TraesCS4B01G278200 chr6B 83.113 379 41 9 5829 6192 128175604 128175234 2.160000e-84 324.0
72 TraesCS4B01G278200 chr6B 82.732 388 34 17 5829 6191 547315315 547314936 1.300000e-81 315.0
73 TraesCS4B01G278200 chr2D 95.861 1184 44 5 2451 3631 573297949 573299130 0.000000e+00 1910.0
74 TraesCS4B01G278200 chr2D 95.567 812 34 2 2623 3433 613465702 613466512 0.000000e+00 1299.0
75 TraesCS4B01G278200 chr2D 86.897 1160 92 30 5065 6191 44710962 44709830 0.000000e+00 1245.0
76 TraesCS4B01G278200 chr2D 92.649 721 44 8 1 717 620007766 620008481 0.000000e+00 1029.0
77 TraesCS4B01G278200 chr2D 92.544 228 16 1 713 940 620017183 620017409 6.020000e-85 326.0
78 TraesCS4B01G278200 chr1B 95.599 977 39 4 2665 3638 92852646 92851671 0.000000e+00 1563.0
79 TraesCS4B01G278200 chr1B 95.329 835 29 7 2459 3292 678500221 678501046 0.000000e+00 1317.0
80 TraesCS4B01G278200 chr1B 91.038 915 63 8 940 1840 92853557 92852648 0.000000e+00 1218.0
81 TraesCS4B01G278200 chr1B 88.596 1026 78 20 940 1947 678499218 678500222 0.000000e+00 1210.0
82 TraesCS4B01G278200 chr1B 92.105 836 57 4 3631 4459 678501296 678502129 0.000000e+00 1170.0
83 TraesCS4B01G278200 chr1B 88.595 982 65 18 1 942 456188992 456189966 0.000000e+00 1149.0
84 TraesCS4B01G278200 chr1B 92.447 331 20 3 5862 6191 28351681 28352007 9.450000e-128 468.0
85 TraesCS4B01G278200 chr1B 91.892 259 21 0 4812 5070 678502170 678502428 4.590000e-96 363.0
86 TraesCS4B01G278200 chr1B 82.768 383 35 9 5829 6191 677675779 677676150 4.680000e-81 313.0
87 TraesCS4B01G278200 chr7D 92.593 945 56 12 1 940 362363104 362364039 0.000000e+00 1345.0
88 TraesCS4B01G278200 chr7D 92.720 261 19 0 4809 5069 618626842 618626582 1.640000e-100 377.0
89 TraesCS4B01G278200 chr7D 86.154 195 7 4 1366 1543 3390747 3390556 6.370000e-45 193.0
90 TraesCS4B01G278200 chr5D 86.788 1158 95 28 5065 6191 291519074 291520204 0.000000e+00 1238.0
91 TraesCS4B01G278200 chr5D 86.723 949 73 25 5269 6191 511030448 511029527 0.000000e+00 1005.0
92 TraesCS4B01G278200 chr5D 88.558 437 36 8 1109 1541 486413546 486413972 9.250000e-143 518.0
93 TraesCS4B01G278200 chr5D 91.469 211 14 4 3431 3638 235441994 235441785 2.840000e-73 287.0
94 TraesCS4B01G278200 chr4D 92.943 836 50 4 3631 4459 437398560 437397727 0.000000e+00 1208.0
95 TraesCS4B01G278200 chr4D 90.234 942 64 13 1 940 3914161 3915076 0.000000e+00 1205.0
96 TraesCS4B01G278200 chr4D 91.729 266 20 1 4806 5069 437397690 437397425 9.860000e-98 368.0
97 TraesCS4B01G278200 chr4D 95.023 221 9 2 3413 3631 115696528 115696748 4.620000e-91 346.0
98 TraesCS4B01G278200 chr4D 95.755 212 7 2 3422 3631 437399281 437399070 2.150000e-89 340.0
99 TraesCS4B01G278200 chr1A 89.811 952 65 20 1 948 567626861 567625938 0.000000e+00 1192.0
100 TraesCS4B01G278200 chr7A 91.627 836 62 3 3631 4459 114451247 114450413 0.000000e+00 1149.0
101 TraesCS4B01G278200 chr7A 94.860 214 9 2 3420 3631 114452549 114452336 3.600000e-87 333.0
102 TraesCS4B01G278200 chr6A 89.321 899 71 14 2201 3096 58467075 58466199 0.000000e+00 1105.0
103 TraesCS4B01G278200 chr6A 88.914 902 75 14 2195 3093 281226224 281227103 0.000000e+00 1088.0
104 TraesCS4B01G278200 chr6A 88.679 53 4 2 2415 2465 183199858 183199910 5.210000e-06 63.9
105 TraesCS4B01G278200 chr6A 91.111 45 3 1 2422 2465 233324597 233324553 6.740000e-05 60.2
106 TraesCS4B01G278200 chr3A 84.952 937 78 28 2198 3087 530225534 530224614 0.000000e+00 891.0
107 TraesCS4B01G278200 chr3A 91.353 266 21 1 4806 5069 160893530 160893265 4.590000e-96 363.0
108 TraesCS4B01G278200 chr2A 92.814 167 12 0 2475 2641 71088812 71088646 6.230000e-60 243.0
109 TraesCS4B01G278200 chr3D 84.746 59 7 2 2415 2471 609319427 609319369 2.420000e-04 58.4


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 TraesCS4B01G278200 chr4B 560019273 560025496 6223 True 5428.000000 8235 100.000000 1 6224 2 chr4B.!!$R2 6223
1 TraesCS4B01G278200 chr4B 222962987 222965462 2475 False 2939.000000 2939 88.217000 940 3433 1 chr4B.!!$F6 2493
2 TraesCS4B01G278200 chr4B 108079573 108081223 1650 False 2169.000000 2169 90.657000 969 2596 1 chr4B.!!$F5 1627
3 TraesCS4B01G278200 chr4B 666837117 666837874 757 True 1081.000000 1081 92.398000 5070 5829 1 chr4B.!!$R1 759
4 TraesCS4B01G278200 chr4B 102826821 102827701 880 False 1079.000000 1079 88.692000 2195 3093 1 chr4B.!!$F4 898
5 TraesCS4B01G278200 chr4B 440772668 440773539 871 False 1031.000000 1031 87.946000 2201 3093 1 chr4B.!!$F7 892
6 TraesCS4B01G278200 chr4B 389772404 389774684 2280 False 255.500000 274 88.126000 1104 1548 2 chr4B.!!$F9 444
7 TraesCS4B01G278200 chr2B 311834371 311838173 3802 False 2842.500000 5297 93.859500 940 5069 2 chr2B.!!$F5 4129
8 TraesCS4B01G278200 chr2B 22380696 22384411 3715 False 1593.666667 3284 91.852667 937 5069 3 chr2B.!!$F4 4132
9 TraesCS4B01G278200 chr2B 735707573 735708698 1125 True 1428.000000 1428 89.728000 5070 6191 1 chr2B.!!$R3 1121
10 TraesCS4B01G278200 chr2B 677848939 677850074 1135 False 1354.000000 1354 88.532000 5070 6191 1 chr2B.!!$F2 1121
11 TraesCS4B01G278200 chr2B 560371840 560372964 1124 False 1273.000000 1273 87.336000 5070 6193 1 chr2B.!!$F1 1123
12 TraesCS4B01G278200 chr2B 771073807 771074705 898 False 1184.000000 1184 90.670000 5070 5962 1 chr2B.!!$F3 892
13 TraesCS4B01G278200 chr2B 135862231 135863295 1064 True 1013.000000 1013 84.410000 5146 6191 1 chr2B.!!$R2 1045
14 TraesCS4B01G278200 chr5B 10496312 10498655 2343 False 3395.000000 3395 92.833000 940 3292 1 chr5B.!!$F1 2352
15 TraesCS4B01G278200 chr5B 49392385 49394128 1743 False 2278.000000 2278 90.525000 940 2657 1 chr5B.!!$F2 1717
16 TraesCS4B01G278200 chr5B 545946528 545947659 1131 True 1467.000000 1467 90.323000 5070 6191 1 chr5B.!!$R1 1121
17 TraesCS4B01G278200 chr5B 667405157 667405912 755 False 1062.000000 1062 92.095000 5070 5824 1 chr5B.!!$F5 754
18 TraesCS4B01G278200 chr5B 49450375 49451939 1564 False 740.500000 1155 92.499500 3412 4459 2 chr5B.!!$F6 1047
19 TraesCS4B01G278200 chr1D 417757780 417760247 2467 False 3358.000000 3358 91.254000 940 3433 1 chr1D.!!$F3 2493
20 TraesCS4B01G278200 chr3B 436376113 436378395 2282 True 3290.000000 3290 92.666000 940 3239 1 chr3B.!!$R2 2299
21 TraesCS4B01G278200 chr3B 21573895 21575545 1650 True 2268.000000 2268 91.742000 969 2596 1 chr3B.!!$R1 1627
22 TraesCS4B01G278200 chr3B 493157585 493158708 1123 False 1367.000000 1367 88.889000 5070 6193 1 chr3B.!!$F2 1123
23 TraesCS4B01G278200 chr3B 739021944 739022873 929 False 1232.000000 1232 90.552000 2 940 1 chr3B.!!$F4 938
24 TraesCS4B01G278200 chr3B 685377228 685378117 889 False 1101.000000 1101 89.157000 5070 5965 1 chr3B.!!$F3 895
25 TraesCS4B01G278200 chr3B 14517874 14518931 1057 False 1042.000000 1042 84.893000 5146 6193 1 chr3B.!!$F1 1047
26 TraesCS4B01G278200 chr7B 101714891 101717186 2295 False 3149.000000 3149 91.494000 940 3235 1 chr7B.!!$F1 2295
27 TraesCS4B01G278200 chr7B 742144075 742145014 939 False 1687.000000 1687 99.045000 1 940 1 chr7B.!!$F3 939
28 TraesCS4B01G278200 chr7B 720140429 720141367 938 False 1681.000000 1681 98.937000 1 941 1 chr7B.!!$F2 940
29 TraesCS4B01G278200 chr7B 698906789 698907920 1131 True 1495.000000 1495 90.718000 5070 6191 1 chr7B.!!$R3 1121
30 TraesCS4B01G278200 chr7B 549270665 549271499 834 True 1138.000000 1138 91.388000 3631 4459 1 chr7B.!!$R2 828
31 TraesCS4B01G278200 chr7B 40423122 40423821 699 True 1085.000000 1085 94.587000 5070 5771 1 chr7B.!!$R1 701
32 TraesCS4B01G278200 chr7B 60577389 60579140 1751 True 843.000000 1166 94.013500 2451 4459 2 chr7B.!!$R5 2008
33 TraesCS4B01G278200 chr5A 693879392 693881841 2449 True 1704.000000 2885 90.498500 940 3433 2 chr5A.!!$R2 2493
34 TraesCS4B01G278200 chr5A 562854671 562855610 939 True 1692.000000 1692 99.150000 1 941 1 chr5A.!!$R1 940
35 TraesCS4B01G278200 chr6D 54990 57003 2013 True 902.166667 2359 92.442000 1184 3433 3 chr6D.!!$R4 2249
36 TraesCS4B01G278200 chr6B 648885883 648887532 1649 False 2279.000000 2279 91.863000 969 2596 1 chr6B.!!$F2 1627
37 TraesCS4B01G278200 chr6B 648849835 648851483 1648 False 2272.000000 2272 91.802000 969 2596 1 chr6B.!!$F1 1627
38 TraesCS4B01G278200 chr6B 508614717 508615658 941 True 1733.000000 1733 99.894000 1 941 1 chr6B.!!$R4 940
39 TraesCS4B01G278200 chr6B 658303292 658304409 1117 True 1330.000000 1330 88.358000 5070 6196 1 chr6B.!!$R6 1126
40 TraesCS4B01G278200 chr6B 55671187 55672050 863 True 1171.000000 1171 91.274000 1 861 1 chr6B.!!$R2 860
41 TraesCS4B01G278200 chr6B 14255763 14256595 832 True 1147.000000 1147 91.627000 3631 4459 1 chr6B.!!$R1 828
42 TraesCS4B01G278200 chr6B 668144272 668145001 729 True 1092.000000 1092 93.716000 5070 5798 1 chr6B.!!$R7 728
43 TraesCS4B01G278200 chr2D 573297949 573299130 1181 False 1910.000000 1910 95.861000 2451 3631 1 chr2D.!!$F1 1180
44 TraesCS4B01G278200 chr2D 613465702 613466512 810 False 1299.000000 1299 95.567000 2623 3433 1 chr2D.!!$F2 810
45 TraesCS4B01G278200 chr2D 44709830 44710962 1132 True 1245.000000 1245 86.897000 5065 6191 1 chr2D.!!$R1 1126
46 TraesCS4B01G278200 chr2D 620007766 620008481 715 False 1029.000000 1029 92.649000 1 717 1 chr2D.!!$F3 716
47 TraesCS4B01G278200 chr1B 92851671 92853557 1886 True 1390.500000 1563 93.318500 940 3638 2 chr1B.!!$R1 2698
48 TraesCS4B01G278200 chr1B 456188992 456189966 974 False 1149.000000 1149 88.595000 1 942 1 chr1B.!!$F2 941
49 TraesCS4B01G278200 chr1B 678499218 678502428 3210 False 1015.000000 1317 91.980500 940 5070 4 chr1B.!!$F4 4130
50 TraesCS4B01G278200 chr7D 362363104 362364039 935 False 1345.000000 1345 92.593000 1 940 1 chr7D.!!$F1 939
51 TraesCS4B01G278200 chr5D 291519074 291520204 1130 False 1238.000000 1238 86.788000 5065 6191 1 chr5D.!!$F1 1126
52 TraesCS4B01G278200 chr5D 511029527 511030448 921 True 1005.000000 1005 86.723000 5269 6191 1 chr5D.!!$R2 922
53 TraesCS4B01G278200 chr4D 3914161 3915076 915 False 1205.000000 1205 90.234000 1 940 1 chr4D.!!$F1 939
54 TraesCS4B01G278200 chr4D 437397425 437399281 1856 True 638.666667 1208 93.475667 3422 5069 3 chr4D.!!$R1 1647
55 TraesCS4B01G278200 chr1A 567625938 567626861 923 True 1192.000000 1192 89.811000 1 948 1 chr1A.!!$R1 947
56 TraesCS4B01G278200 chr7A 114450413 114452549 2136 True 741.000000 1149 93.243500 3420 4459 2 chr7A.!!$R1 1039
57 TraesCS4B01G278200 chr6A 58466199 58467075 876 True 1105.000000 1105 89.321000 2201 3096 1 chr6A.!!$R1 895
58 TraesCS4B01G278200 chr6A 281226224 281227103 879 False 1088.000000 1088 88.914000 2195 3093 1 chr6A.!!$F2 898
59 TraesCS4B01G278200 chr3A 530224614 530225534 920 True 891.000000 891 84.952000 2198 3087 1 chr3A.!!$R2 889

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
974 1042 2.485966 AGATCAGCTGATGTACCCCT 57.514 50.0 33.33 19.29 34.37 4.79 F
1143 1239 0.249322 CAAACGACGGCGATAGGGAT 60.249 55.0 22.49 0.00 41.64 3.85 F
2012 3984 0.251564 TTTGCCGGGTCATTGGATGT 60.252 50.0 2.18 0.00 0.00 3.06 F
3878 7018 0.035056 CCCGCCCTTCTTCATGTCTT 60.035 55.0 0.00 0.00 0.00 3.01 F
4936 8077 0.179129 GCACCCGCGCTACTACTAAA 60.179 55.0 5.56 0.00 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2742 4771 0.465097 AAGAGCATGCATCCCTTCGG 60.465 55.0 21.98 0.0 0.00 4.30 R
2743 4772 0.942962 GAAGAGCATGCATCCCTTCG 59.057 55.0 21.98 0.0 0.00 3.79 R
3957 7097 0.034198 TCGTCAGCGTCCAAATCCAA 59.966 50.0 0.00 0.0 39.49 3.53 R
5196 8339 0.113190 AACTTTGCCTAAGCCCTGCT 59.887 50.0 0.00 0.0 42.56 4.24 R
6167 9446 0.109723 AGTGCAGAACCGGGCTTTAA 59.890 50.0 6.32 0.0 0.00 1.52 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
955 1023 4.901868 AGTCGCCTACTTTAAATTGACCA 58.098 39.130 0.00 0.00 33.35 4.02
974 1042 2.485966 AGATCAGCTGATGTACCCCT 57.514 50.000 33.33 19.29 34.37 4.79
1046 1129 1.073284 ACCGCACCACAACCTTATCTT 59.927 47.619 0.00 0.00 0.00 2.40
1054 1137 3.262420 CACAACCTTATCTTCCCTGTCG 58.738 50.000 0.00 0.00 0.00 4.35
1143 1239 0.249322 CAAACGACGGCGATAGGGAT 60.249 55.000 22.49 0.00 41.64 3.85
1338 1439 1.940957 ACTCCTCCTTCCATCCCTAGT 59.059 52.381 0.00 0.00 0.00 2.57
1345 1446 4.301027 CCATCCCTAGTCGCGGCC 62.301 72.222 7.31 0.00 0.00 6.13
1439 3393 7.038302 TCCAAAAGTAGCATCTTCTTCTTCCTA 60.038 37.037 0.00 0.00 0.00 2.94
1653 3625 1.955080 GTCGTCATATCCCTTCTCCGT 59.045 52.381 0.00 0.00 0.00 4.69
1751 3723 4.278170 GCTGCTTGTGTTTATGCCCATATA 59.722 41.667 0.00 0.00 0.00 0.86
1760 3732 9.688091 TGTGTTTATGCCCATATAGTTTTTCTA 57.312 29.630 0.00 0.00 0.00 2.10
1843 3815 5.748670 TTAGTGCTCACTAACCCACATTA 57.251 39.130 16.09 0.00 45.82 1.90
2012 3984 0.251564 TTTGCCGGGTCATTGGATGT 60.252 50.000 2.18 0.00 0.00 3.06
2530 4547 3.222603 TCCTTCTCTTTTTGGTTGCCTC 58.777 45.455 0.00 0.00 0.00 4.70
2742 4771 5.863935 CACAAGAAGCTATTTTTGGCTTACC 59.136 40.000 0.00 0.00 46.91 2.85
2743 4772 5.047306 ACAAGAAGCTATTTTTGGCTTACCC 60.047 40.000 0.00 0.00 46.91 3.69
2820 4851 2.552315 CGCCTTTGTTTCCTTCAGCTTA 59.448 45.455 0.00 0.00 0.00 3.09
3163 5200 6.655078 ATTTACTTGAAGGACTGCATGTTT 57.345 33.333 4.39 0.00 0.00 2.83
3373 5410 2.072487 GCCTGTCTCATAGGGCCCA 61.072 63.158 27.56 10.89 38.77 5.36
3440 5478 8.108782 CGATTGTCGTAGGATTTTAGAGAAAAC 58.891 37.037 0.00 0.00 34.79 2.43
3482 5522 7.193595 AGTGTTTATGAAACTACTGTTGTTGC 58.806 34.615 8.32 7.22 41.90 4.17
3666 6799 1.137513 CGTCTCGAAACTGTCAACCC 58.862 55.000 0.00 0.00 0.00 4.11
3771 6911 2.361789 TCCTTACAACTTTATGCGCCC 58.638 47.619 4.18 0.00 0.00 6.13
3794 6934 3.049344 AGCTATTTACAGAAGGAGGGGG 58.951 50.000 0.00 0.00 0.00 5.40
3828 6968 4.427661 GCTCGCGGCAGTGTCTCT 62.428 66.667 6.13 0.00 41.35 3.10
3878 7018 0.035056 CCCGCCCTTCTTCATGTCTT 60.035 55.000 0.00 0.00 0.00 3.01
3886 7026 3.567164 CCTTCTTCATGTCTTGTGCAACT 59.433 43.478 0.00 0.00 38.04 3.16
3981 7121 2.636778 TTTGGACGCTGACGAGCACA 62.637 55.000 0.00 0.00 46.62 4.57
4091 7231 0.818040 GGTGGACTTTGCCGTGAAGT 60.818 55.000 0.00 0.00 39.90 3.01
4284 7425 3.865571 TGGAACACTAGGAAAGGTACCT 58.134 45.455 9.21 9.21 41.05 3.08
4308 7449 5.254901 ACCTTTGGTTGTGTGTGTTTACTA 58.745 37.500 0.00 0.00 27.29 1.82
4920 8061 1.447314 GTAGTAGCGTGGGTGGCAC 60.447 63.158 9.70 9.70 0.00 5.01
4936 8077 0.179129 GCACCCGCGCTACTACTAAA 60.179 55.000 5.56 0.00 0.00 1.85
4937 8078 1.736696 GCACCCGCGCTACTACTAAAA 60.737 52.381 5.56 0.00 0.00 1.52
4938 8079 2.609350 CACCCGCGCTACTACTAAAAA 58.391 47.619 5.56 0.00 0.00 1.94
4939 8080 2.601763 CACCCGCGCTACTACTAAAAAG 59.398 50.000 5.56 0.00 0.00 2.27
4955 8096 7.219484 ACTAAAAAGTTAGTAGTAGCGTGGA 57.781 36.000 0.00 0.00 46.59 4.02
5060 8201 1.134670 CGCTGCTAGTAGCCTTTTCCT 60.135 52.381 24.74 0.00 41.51 3.36
5108 8249 7.342026 GGGGATAGTCAACAGGTAATTTCAATT 59.658 37.037 0.00 0.00 0.00 2.32
5196 8339 3.859411 ATTAATTTTCTTTGCCGGCGA 57.141 38.095 23.90 19.26 0.00 5.54
5448 8597 2.412089 GCATTCTACGTTTGCGAGAACT 59.588 45.455 0.00 0.00 42.00 3.01
5453 8602 1.563111 ACGTTTGCGAGAACTTTCGA 58.437 45.000 0.00 0.00 43.03 3.71
5487 8636 4.948621 CCAAAAGGAGCAGATCTCAAAGAT 59.051 41.667 0.00 0.00 43.70 2.40
5491 8640 4.555689 AGGAGCAGATCTCAAAGATAGGT 58.444 43.478 0.00 0.00 43.70 3.08
5630 8806 1.802880 CGGAGCGCATACTAGCACTTT 60.803 52.381 11.47 0.00 35.48 2.66
5702 8878 1.767759 ATACTGTTACCCGCTACCGT 58.232 50.000 0.00 0.00 0.00 4.83
5703 8879 1.544724 TACTGTTACCCGCTACCGTT 58.455 50.000 0.00 0.00 0.00 4.44
5732 8908 1.271325 ACCATTTGTCATCGTGCTCCA 60.271 47.619 0.00 0.00 0.00 3.86
5777 8953 4.342772 GAGAAATTGTGTGTGTGTGTGTC 58.657 43.478 0.00 0.00 0.00 3.67
5807 9017 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
5825 9035 2.675348 TGTATGTGTGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
5826 9036 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
5827 9037 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6037 9314 0.554305 TCTACCAGCATCCGGACCTA 59.446 55.000 6.12 0.00 0.00 3.08
6147 9426 2.685850 GGTTGTAGAACCGGCACTAT 57.314 50.000 5.96 0.00 42.47 2.12
6202 9481 2.553079 CACTAGTGCTCCTCGACTTC 57.447 55.000 10.54 0.00 0.00 3.01
6203 9482 2.088423 CACTAGTGCTCCTCGACTTCT 58.912 52.381 10.54 0.00 0.00 2.85
6204 9483 2.490115 CACTAGTGCTCCTCGACTTCTT 59.510 50.000 10.54 0.00 0.00 2.52
6205 9484 2.490115 ACTAGTGCTCCTCGACTTCTTG 59.510 50.000 0.00 0.00 0.00 3.02
6206 9485 1.621992 AGTGCTCCTCGACTTCTTGA 58.378 50.000 0.00 0.00 0.00 3.02
6207 9486 1.271102 AGTGCTCCTCGACTTCTTGAC 59.729 52.381 0.00 0.00 0.00 3.18
6208 9487 0.603569 TGCTCCTCGACTTCTTGACC 59.396 55.000 0.00 0.00 0.00 4.02
6209 9488 0.603569 GCTCCTCGACTTCTTGACCA 59.396 55.000 0.00 0.00 0.00 4.02
6210 9489 1.205893 GCTCCTCGACTTCTTGACCAT 59.794 52.381 0.00 0.00 0.00 3.55
6211 9490 2.354203 GCTCCTCGACTTCTTGACCATT 60.354 50.000 0.00 0.00 0.00 3.16
6212 9491 3.257393 CTCCTCGACTTCTTGACCATTG 58.743 50.000 0.00 0.00 0.00 2.82
6213 9492 2.897326 TCCTCGACTTCTTGACCATTGA 59.103 45.455 0.00 0.00 0.00 2.57
6214 9493 3.515502 TCCTCGACTTCTTGACCATTGAT 59.484 43.478 0.00 0.00 0.00 2.57
6215 9494 4.020218 TCCTCGACTTCTTGACCATTGATT 60.020 41.667 0.00 0.00 0.00 2.57
6216 9495 5.186992 TCCTCGACTTCTTGACCATTGATTA 59.813 40.000 0.00 0.00 0.00 1.75
6217 9496 6.051717 CCTCGACTTCTTGACCATTGATTAT 58.948 40.000 0.00 0.00 0.00 1.28
6218 9497 6.018425 CCTCGACTTCTTGACCATTGATTATG 60.018 42.308 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
955 1023 2.090831 AGAGGGGTACATCAGCTGATCT 60.091 50.000 26.44 18.41 31.21 2.75
974 1042 0.320683 TGCTTCGCTGCTGCTAAAGA 60.321 50.000 22.85 8.71 33.97 2.52
1001 1069 1.153429 CCACTAGTTGTAGGGCGGC 60.153 63.158 0.00 0.00 0.00 6.53
1006 1074 0.739813 GCGGTGCCACTAGTTGTAGG 60.740 60.000 0.00 0.00 0.00 3.18
1338 1439 3.949885 TAGAGGTTGGAGGCCGCGA 62.950 63.158 8.23 0.00 0.00 5.87
1345 1446 1.810030 GCGGCGTTAGAGGTTGGAG 60.810 63.158 9.37 0.00 0.00 3.86
1439 3393 3.307762 CGGGGAAGAAGAAGAAGAACCAT 60.308 47.826 0.00 0.00 0.00 3.55
1529 3488 2.993264 CCCCCACCTTGCAGCTTG 60.993 66.667 0.00 0.00 0.00 4.01
1653 3625 2.771089 CTTGCTTCCAGTAACAGCAGA 58.229 47.619 0.00 0.00 44.21 4.26
1751 3723 4.070009 GGGTGTCGGTGAATAGAAAAACT 58.930 43.478 0.00 0.00 0.00 2.66
1760 3732 2.754375 GTGGGGGTGTCGGTGAAT 59.246 61.111 0.00 0.00 0.00 2.57
1843 3815 7.497595 CATTCATTCATTGACTGGGATCATTT 58.502 34.615 4.40 0.00 32.77 2.32
1923 3895 5.211201 AGCAGGCAAAAGTATATGGGAAAT 58.789 37.500 0.00 0.00 0.00 2.17
2012 3984 9.238368 CCCACCAAAGTCTTAAACTATGATTAA 57.762 33.333 0.00 0.00 37.17 1.40
2196 4180 5.996513 AGCAAGAAATATAGTGCAGGATGAG 59.003 40.000 0.00 0.00 39.69 2.90
2473 4490 7.750229 TGGGCAAAAATGCACATTAAATTAA 57.250 28.000 0.85 0.00 44.12 1.40
2742 4771 0.465097 AAGAGCATGCATCCCTTCGG 60.465 55.000 21.98 0.00 0.00 4.30
2743 4772 0.942962 GAAGAGCATGCATCCCTTCG 59.057 55.000 21.98 0.00 0.00 3.79
2858 4889 8.430801 AGTAGCTTTGCTTAAGAACATGATAG 57.569 34.615 6.67 0.00 40.44 2.08
3087 5124 4.689612 TCTATTTGACCCCAGTATCTGC 57.310 45.455 0.00 0.00 0.00 4.26
3163 5200 4.352009 ACATGGGGCATACAAAGATGAAA 58.648 39.130 0.00 0.00 0.00 2.69
3373 5410 1.867363 AACTTAGGTCTCGCTGGGAT 58.133 50.000 0.00 0.00 0.00 3.85
3482 5522 3.214328 ACTGTGAGGTGTTTGGCTAAAG 58.786 45.455 0.00 0.00 0.00 1.85
3624 5664 5.752472 CGGCATAAGCATCCTAGATATTCAG 59.248 44.000 0.00 0.00 44.61 3.02
3765 6905 0.529773 CTGTAAATAGCTCGGGCGCA 60.530 55.000 10.83 0.00 44.37 6.09
3771 6911 3.243907 CCCCTCCTTCTGTAAATAGCTCG 60.244 52.174 0.00 0.00 0.00 5.03
3794 6934 2.815647 CCGTGAAGAAGGCCGAGC 60.816 66.667 0.00 0.00 0.00 5.03
3828 6968 1.071107 GTTGCACGAACGAATCAACGA 60.071 47.619 0.14 0.00 37.03 3.85
3878 7018 2.289444 GCTGGTCCTTACTAGTTGCACA 60.289 50.000 0.00 0.00 36.62 4.57
3886 7026 2.160721 CAGAGGGCTGGTCCTTACTA 57.839 55.000 0.00 0.00 38.51 1.82
3957 7097 0.034198 TCGTCAGCGTCCAAATCCAA 59.966 50.000 0.00 0.00 39.49 3.53
3981 7121 4.673320 CGTCGGGAAAGTGAAAACTTGTTT 60.673 41.667 0.00 0.00 0.00 2.83
4284 7425 5.254901 AGTAAACACACACAACCAAAGGTA 58.745 37.500 0.00 0.00 33.12 3.08
4308 7449 9.417561 ACAAGAGATCATGTGATTCCATTTAAT 57.582 29.630 0.00 0.00 34.37 1.40
4806 7947 1.497161 ACTAGTAGCACACATCCCCC 58.503 55.000 0.00 0.00 0.00 5.40
4807 7948 4.957684 AATACTAGTAGCACACATCCCC 57.042 45.455 8.85 0.00 0.00 4.81
4808 7949 7.723324 TCTTAAATACTAGTAGCACACATCCC 58.277 38.462 8.85 0.00 0.00 3.85
4853 7994 5.763698 ACAGAATAGTAGTAGCGCATCTGTA 59.236 40.000 11.47 4.41 43.07 2.74
4920 8061 2.884827 ACTTTTTAGTAGTAGCGCGGG 58.115 47.619 8.83 0.00 0.00 6.13
4936 8077 4.430908 GCATCCACGCTACTACTAACTTT 58.569 43.478 0.00 0.00 0.00 2.66
4937 8078 3.181478 GGCATCCACGCTACTACTAACTT 60.181 47.826 0.00 0.00 0.00 2.66
4938 8079 2.361438 GGCATCCACGCTACTACTAACT 59.639 50.000 0.00 0.00 0.00 2.24
4939 8080 2.100252 TGGCATCCACGCTACTACTAAC 59.900 50.000 0.00 0.00 0.00 2.34
4952 8093 3.006133 TAGCGTGGGTGGCATCCA 61.006 61.111 17.39 17.39 0.00 3.41
4955 8096 0.976073 AGTAGTAGCGTGGGTGGCAT 60.976 55.000 0.00 0.00 0.00 4.40
5018 8159 4.560108 CGCGGGTAAATTGGCTACTAGTAT 60.560 45.833 2.33 0.00 0.00 2.12
5060 8201 4.082408 CCTTCACGATGGTGTCACTACTAA 60.082 45.833 7.79 0.00 44.68 2.24
5168 8311 5.815222 CGGCAAAGAAAATTAATAAAGGGGG 59.185 40.000 0.00 0.00 0.00 5.40
5196 8339 0.113190 AACTTTGCCTAAGCCCTGCT 59.887 50.000 0.00 0.00 42.56 4.24
5206 8349 2.887152 GTCACCTTGATGAACTTTGCCT 59.113 45.455 0.00 0.00 0.00 4.75
5448 8597 1.814793 TTGGACGCCATCATTCGAAA 58.185 45.000 0.00 0.00 31.53 3.46
5453 8602 2.094675 CTCCTTTTGGACGCCATCATT 58.905 47.619 0.00 0.00 45.19 2.57
5487 8636 3.387374 TCTGACAAACGTACCCAAACCTA 59.613 43.478 0.00 0.00 0.00 3.08
5491 8640 8.795842 ATATTATTCTGACAAACGTACCCAAA 57.204 30.769 0.00 0.00 0.00 3.28
5630 8806 5.067283 GCAAAAATCCCGCTATTTCCTCTTA 59.933 40.000 0.00 0.00 0.00 2.10
5702 8878 3.251016 TGACAAATGGTTCATGGGGAA 57.749 42.857 0.00 0.00 0.00 3.97
5703 8879 2.988636 TGACAAATGGTTCATGGGGA 57.011 45.000 0.00 0.00 0.00 4.81
5716 8892 1.879380 CCTTTGGAGCACGATGACAAA 59.121 47.619 0.00 0.00 0.00 2.83
5732 8908 0.393820 CATGTTGCCTTGGTGCCTTT 59.606 50.000 0.00 0.00 0.00 3.11
5777 8953 6.589907 ACACACACACACACACACATATATAG 59.410 38.462 0.00 0.00 0.00 1.31
5807 9017 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
5825 9035 2.104144 CGTACGTAGAACCGCATACAC 58.896 52.381 7.22 0.00 0.00 2.90
5826 9036 2.006169 TCGTACGTAGAACCGCATACA 58.994 47.619 16.05 0.00 0.00 2.29
5827 9037 2.285220 TCTCGTACGTAGAACCGCATAC 59.715 50.000 16.05 0.00 0.00 2.39
5970 9236 2.026075 CCGGTACTAAATGTTTGGGGGA 60.026 50.000 0.00 0.00 0.00 4.81
6001 9278 3.701040 GGTAGACCATTAGTACCGGTTGA 59.299 47.826 15.04 0.00 35.64 3.18
6028 9305 3.138798 GCACGAGCTAGGTCCGGA 61.139 66.667 16.06 0.00 37.91 5.14
6037 9314 4.969196 CACCACGTGGCACGAGCT 62.969 66.667 42.65 22.47 46.05 4.09
6114 9393 4.081406 TCTACAACCGGCACTAAAGAGTA 58.919 43.478 0.00 0.00 33.32 2.59
6147 9426 4.090588 CCGGTTCGCAAGGGCCTA 62.091 66.667 6.41 0.00 36.38 3.93
6156 9435 2.202260 GCTTTAACGCCGGTTCGC 60.202 61.111 1.90 0.00 37.58 4.70
6167 9446 0.109723 AGTGCAGAACCGGGCTTTAA 59.890 50.000 6.32 0.00 0.00 1.52
6193 9472 3.319137 TCAATGGTCAAGAAGTCGAGG 57.681 47.619 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.