Multiple sequence alignment - TraesCS2D01G222500

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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 TraesCS2D01G222500 chr2D 100.000 6160 0 0 1 6160 189533895 189527736 0.000000e+00 11376.0
1 TraesCS2D01G222500 chr2D 93.667 1279 54 13 2621 3887 86068232 86069495 0.000000e+00 1888.0
2 TraesCS2D01G222500 chr2D 92.667 1241 71 10 2657 3892 565161315 565160090 0.000000e+00 1770.0
3 TraesCS2D01G222500 chr2D 94.161 805 39 8 1824 2623 25066953 25066152 0.000000e+00 1219.0
4 TraesCS2D01G222500 chr2D 93.665 805 45 6 1824 2623 79276847 79277650 0.000000e+00 1199.0
5 TraesCS2D01G222500 chr2D 93.540 805 45 6 1824 2623 14886231 14885429 0.000000e+00 1192.0
6 TraesCS2D01G222500 chr2D 91.986 574 30 10 3317 3887 25065929 25065369 0.000000e+00 791.0
7 TraesCS2D01G222500 chr2D 80.186 646 114 13 1168 1810 189389542 189388908 7.230000e-129 472.0
8 TraesCS2D01G222500 chr2D 77.143 560 106 20 1170 1718 188836382 188836930 7.760000e-79 305.0
9 TraesCS2D01G222500 chr2A 95.539 1883 60 12 3962 5828 203328148 203326274 0.000000e+00 2990.0
10 TraesCS2D01G222500 chr2A 95.170 1822 83 5 1 1817 203330012 203328191 0.000000e+00 2872.0
11 TraesCS2D01G222500 chr2A 88.950 1276 105 19 2621 3887 773271953 773273201 0.000000e+00 1543.0
12 TraesCS2D01G222500 chr2A 93.532 804 47 5 1824 2623 25355983 25356785 0.000000e+00 1192.0
13 TraesCS2D01G222500 chr2A 80.526 647 110 13 1168 1810 203321774 203321140 3.340000e-132 483.0
14 TraesCS2D01G222500 chr2A 96.923 130 3 1 5970 6098 203326265 203326136 3.740000e-52 217.0
15 TraesCS2D01G222500 chr2A 100.000 48 0 0 3885 3932 203328201 203328154 8.500000e-14 89.8
16 TraesCS2D01G222500 chr2B 97.200 1643 32 7 4192 5826 245822306 245820670 0.000000e+00 2767.0
17 TraesCS2D01G222500 chr2B 97.404 963 21 2 856 1817 245823646 245822687 0.000000e+00 1637.0
18 TraesCS2D01G222500 chr2B 98.387 310 4 1 3885 4193 245822697 245822388 1.510000e-150 544.0
19 TraesCS2D01G222500 chr2B 79.102 646 109 13 1168 1810 245794066 245793444 7.380000e-114 422.0
20 TraesCS2D01G222500 chr2B 75.313 559 118 18 1170 1718 244934583 244935131 3.690000e-62 250.0
21 TraesCS2D01G222500 chr2B 95.385 130 5 1 5970 6098 245820659 245820530 8.090000e-49 206.0
22 TraesCS2D01G222500 chr2B 94.949 99 1 1 5824 5922 715814806 715814712 1.070000e-32 152.0
23 TraesCS2D01G222500 chr2B 94.845 97 4 1 5826 5921 101490640 101490544 3.850000e-32 150.0
24 TraesCS2D01G222500 chr3D 94.214 1279 50 10 2621 3887 110279210 110280476 0.000000e+00 1930.0
25 TraesCS2D01G222500 chr3D 92.368 1271 79 11 2621 3887 339302312 339301056 0.000000e+00 1794.0
26 TraesCS2D01G222500 chr3D 91.654 1282 78 17 2621 3887 2740778 2742045 0.000000e+00 1748.0
27 TraesCS2D01G222500 chr1D 93.427 1278 60 8 2621 3887 297520379 297519115 0.000000e+00 1873.0
28 TraesCS2D01G222500 chr1D 92.009 876 48 12 3017 3890 240585205 240584350 0.000000e+00 1210.0
29 TraesCS2D01G222500 chr1D 93.649 803 45 6 1824 2623 469045378 469046177 0.000000e+00 1195.0
30 TraesCS2D01G222500 chr1D 91.275 149 6 3 5823 5969 494045183 494045040 4.870000e-46 196.0
31 TraesCS2D01G222500 chr1D 94.792 96 2 1 5879 5971 75879652 75879747 4.980000e-31 147.0
32 TraesCS2D01G222500 chr1D 93.684 95 3 1 5880 5971 75879739 75879645 8.330000e-29 139.0
33 TraesCS2D01G222500 chr1D 77.251 211 42 5 5393 5601 481557584 481557378 1.080000e-22 119.0
34 TraesCS2D01G222500 chr1D 100.000 57 0 0 5824 5880 471188920 471188864 8.440000e-19 106.0
35 TraesCS2D01G222500 chrUn 93.432 1279 47 17 2621 3887 94193599 94194852 0.000000e+00 1862.0
36 TraesCS2D01G222500 chrUn 92.885 1279 67 12 2621 3887 96048458 96049724 0.000000e+00 1836.0
37 TraesCS2D01G222500 chrUn 92.607 1285 56 19 2621 3891 320127113 320128372 0.000000e+00 1810.0
38 TraesCS2D01G222500 chrUn 90.867 1281 88 15 2621 3885 27712043 27713310 0.000000e+00 1690.0
39 TraesCS2D01G222500 chrUn 89.556 1283 109 12 2621 3891 305006623 305007892 0.000000e+00 1604.0
40 TraesCS2D01G222500 chrUn 94.030 804 43 5 1824 2623 94192770 94193572 0.000000e+00 1214.0
41 TraesCS2D01G222500 chrUn 91.201 841 57 9 3048 3887 382211796 382212620 0.000000e+00 1127.0
42 TraesCS2D01G222500 chrUn 93.269 104 4 1 5879 5979 389647839 389647942 3.850000e-32 150.0
43 TraesCS2D01G222500 chrUn 92.632 95 4 1 5880 5971 389647926 389647832 3.870000e-27 134.0
44 TraesCS2D01G222500 chrUn 83.221 149 5 11 5823 5971 128516274 128516402 1.080000e-22 119.0
45 TraesCS2D01G222500 chrUn 83.108 148 5 10 5824 5971 19647286 19647159 3.900000e-22 117.0
46 TraesCS2D01G222500 chrUn 83.108 148 5 10 5824 5971 104559179 104559306 3.900000e-22 117.0
47 TraesCS2D01G222500 chrUn 83.108 148 5 13 5824 5971 154681608 154681481 3.900000e-22 117.0
48 TraesCS2D01G222500 chrUn 82.432 148 6 10 5824 5971 73486536 73486409 1.820000e-20 111.0
49 TraesCS2D01G222500 chrUn 82.432 148 6 10 5824 5971 102887927 102887800 1.820000e-20 111.0
50 TraesCS2D01G222500 chrUn 82.432 148 6 10 5824 5971 254470448 254470575 1.820000e-20 111.0
51 TraesCS2D01G222500 chrUn 81.410 156 9 11 5824 5979 19647154 19647289 6.530000e-20 110.0
52 TraesCS2D01G222500 chrUn 81.699 153 8 11 5827 5979 104559308 104559176 6.530000e-20 110.0
53 TraesCS2D01G222500 chrUn 81.410 156 9 10 5824 5979 154681476 154681611 6.530000e-20 110.0
54 TraesCS2D01G222500 chrUn 81.757 148 7 10 5824 5971 262619269 262619396 8.440000e-19 106.0
55 TraesCS2D01G222500 chrUn 80.769 156 10 11 5824 5979 73486404 73486539 3.040000e-18 104.0
56 TraesCS2D01G222500 chrUn 80.769 156 10 11 5824 5979 102887795 102887930 3.040000e-18 104.0
57 TraesCS2D01G222500 chrUn 98.305 59 1 0 5921 5979 254470503 254470445 3.040000e-18 104.0
58 TraesCS2D01G222500 chrUn 98.305 59 1 0 5921 5979 262619324 262619266 3.040000e-18 104.0
59 TraesCS2D01G222500 chrUn 98.246 57 1 0 5823 5879 87983127 87983183 3.930000e-17 100.0
60 TraesCS2D01G222500 chrUn 87.097 93 6 5 5881 5971 362729149 362729061 3.930000e-17 100.0
61 TraesCS2D01G222500 chrUn 86.170 94 7 5 5880 5971 362729069 362729158 5.080000e-16 97.1
62 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 19647273 19647231 5.120000e-11 80.5
63 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 36371391 36371349 5.120000e-11 80.5
64 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 64149818 64149776 5.120000e-11 80.5
65 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 66416419 66416461 5.120000e-11 80.5
66 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 73486523 73486481 5.120000e-11 80.5
67 TraesCS2D01G222500 chr5D 92.763 1285 63 13 2621 3887 374396826 374398098 0.000000e+00 1831.0
68 TraesCS2D01G222500 chr5D 92.796 930 50 11 2965 3892 238113633 238112719 0.000000e+00 1330.0
69 TraesCS2D01G222500 chr5D 93.524 803 43 7 1824 2623 425842803 425843599 0.000000e+00 1186.0
70 TraesCS2D01G222500 chr5D 96.703 91 1 2 5880 5970 462044298 462044386 3.850000e-32 150.0
71 TraesCS2D01G222500 chr5D 97.222 72 2 0 6089 6160 64653844 64653915 8.390000e-24 122.0
72 TraesCS2D01G222500 chr4D 92.547 1288 69 13 2621 3892 8007023 8005747 0.000000e+00 1821.0
73 TraesCS2D01G222500 chr4D 92.416 1279 69 13 2624 3889 505822526 505821263 0.000000e+00 1799.0
74 TraesCS2D01G222500 chr4D 92.410 1278 58 12 2624 3890 502597436 502596187 0.000000e+00 1786.0
75 TraesCS2D01G222500 chr4D 94.059 101 2 1 5879 5979 312648929 312649025 3.850000e-32 150.0
76 TraesCS2D01G222500 chr4D 94.565 92 4 1 5881 5971 333016938 333017029 2.310000e-29 141.0
77 TraesCS2D01G222500 chr4D 93.478 92 2 1 5880 5971 312649009 312648922 3.870000e-27 134.0
78 TraesCS2D01G222500 chr4D 92.473 93 6 1 5880 5971 333017021 333016929 1.390000e-26 132.0
79 TraesCS2D01G222500 chr4D 90.722 97 5 1 5826 5922 10405778 10405870 6.480000e-25 126.0
80 TraesCS2D01G222500 chr4D 92.391 92 2 1 5880 5971 496945858 496945772 6.480000e-25 126.0
81 TraesCS2D01G222500 chr4D 90.625 96 4 1 5880 5975 496945780 496945870 8.390000e-24 122.0
82 TraesCS2D01G222500 chr4D 82.000 150 7 6 5824 5973 407364125 407364254 6.530000e-20 110.0
83 TraesCS2D01G222500 chr4D 87.500 96 6 5 5880 5975 397678215 397678304 8.440000e-19 106.0
84 TraesCS2D01G222500 chr7D 92.344 1280 75 10 2621 3887 570329336 570330605 0.000000e+00 1799.0
85 TraesCS2D01G222500 chr7D 93.905 804 44 5 1824 2623 9964523 9965325 0.000000e+00 1208.0
86 TraesCS2D01G222500 chr7D 98.387 62 1 0 6098 6159 616752976 616752915 6.530000e-20 110.0
87 TraesCS2D01G222500 chr7D 96.825 63 2 0 6097 6159 169033563 169033501 8.440000e-19 106.0
88 TraesCS2D01G222500 chr7D 97.959 49 1 0 6112 6160 169033379 169033331 1.100000e-12 86.1
89 TraesCS2D01G222500 chr6D 92.344 1280 65 15 2621 3887 276127004 276128263 0.000000e+00 1790.0
90 TraesCS2D01G222500 chr6D 87.857 1227 120 18 2621 3841 368142023 368143226 0.000000e+00 1413.0
91 TraesCS2D01G222500 chr6D 92.797 944 54 8 2947 3887 450665480 450666412 0.000000e+00 1354.0
92 TraesCS2D01G222500 chr6D 92.780 928 54 7 2961 3887 23776019 23775104 0.000000e+00 1330.0
93 TraesCS2D01G222500 chr6D 94.140 802 40 6 1825 2623 276126180 276126977 0.000000e+00 1214.0
94 TraesCS2D01G222500 chr6D 97.917 96 1 1 5880 5974 129156600 129156505 1.370000e-36 165.0
95 TraesCS2D01G222500 chr6D 98.925 93 0 1 5880 5971 129156516 129156608 1.370000e-36 165.0
96 TraesCS2D01G222500 chr6D 94.898 98 3 1 5825 5922 312136255 312136350 1.070000e-32 152.0
97 TraesCS2D01G222500 chr6D 83.108 148 5 9 5824 5971 421855390 421855263 3.900000e-22 117.0
98 TraesCS2D01G222500 chr6D 89.888 89 4 2 5833 5921 456337272 456337189 6.530000e-20 110.0
99 TraesCS2D01G222500 chr6D 100.000 57 0 0 5823 5879 445850827 445850883 8.440000e-19 106.0
100 TraesCS2D01G222500 chr6D 98.305 59 1 0 5821 5879 403312402 403312344 3.040000e-18 104.0
101 TraesCS2D01G222500 chr5B 90.966 1273 100 12 2621 3891 10451525 10452784 0.000000e+00 1700.0
102 TraesCS2D01G222500 chr5B 94.231 104 3 1 5879 5979 460590056 460589953 8.270000e-34 156.0
103 TraesCS2D01G222500 chr5B 94.175 103 4 1 5879 5979 663324510 663324408 8.270000e-34 156.0
104 TraesCS2D01G222500 chr5B 90.110 91 9 0 5832 5922 618275056 618275146 1.080000e-22 119.0
105 TraesCS2D01G222500 chr5B 100.000 62 0 0 6097 6158 292194423 292194362 1.400000e-21 115.0
106 TraesCS2D01G222500 chr4A 89.889 1266 110 12 2622 3884 166334039 166335289 0.000000e+00 1613.0
107 TraesCS2D01G222500 chr4A 90.260 154 3 2 5827 5971 278325735 278325885 2.270000e-44 191.0
108 TraesCS2D01G222500 chr4A 83.041 171 29 0 1229 1399 725907051 725906881 8.270000e-34 156.0
109 TraesCS2D01G222500 chr4A 100.000 62 0 0 6097 6158 488011234 488011173 1.400000e-21 115.0
110 TraesCS2D01G222500 chr6A 89.548 1282 112 11 2622 3890 78569527 78568255 0.000000e+00 1605.0
111 TraesCS2D01G222500 chr6A 91.241 137 5 2 5841 5974 200245953 200245821 4.910000e-41 180.0
112 TraesCS2D01G222500 chr6A 98.020 101 1 1 5879 5979 61597805 61597904 2.280000e-39 174.0
113 TraesCS2D01G222500 chr6A 97.826 92 1 1 5880 5971 61597888 61597798 2.300000e-34 158.0
114 TraesCS2D01G222500 chr6A 100.000 62 0 0 6097 6158 561439474 561439535 1.400000e-21 115.0
115 TraesCS2D01G222500 chr6A 100.000 62 0 0 6097 6158 561614408 561614347 1.400000e-21 115.0
116 TraesCS2D01G222500 chr6A 88.172 93 6 1 5827 5919 556981064 556980977 8.440000e-19 106.0
117 TraesCS2D01G222500 chr5A 89.056 1197 110 11 2621 3805 653567284 653568471 0.000000e+00 1465.0
118 TraesCS2D01G222500 chr5A 92.553 94 5 1 5829 5922 25705146 25705055 3.870000e-27 134.0
119 TraesCS2D01G222500 chr3B 75.456 493 93 19 349 820 571999437 571999922 1.340000e-51 215.0
120 TraesCS2D01G222500 chr3B 91.391 151 7 2 5825 5971 732905447 732905299 1.050000e-47 202.0
121 TraesCS2D01G222500 chr3B 95.146 103 3 1 5879 5979 283473991 283474093 1.780000e-35 161.0
122 TraesCS2D01G222500 chr3B 100.000 63 0 0 6096 6158 71553670 71553608 3.900000e-22 117.0
123 TraesCS2D01G222500 chr7B 86.335 161 15 7 5834 5990 593418009 593418166 1.060000e-37 169.0
124 TraesCS2D01G222500 chr7B 94.340 106 1 1 5879 5979 624570254 624570149 2.300000e-34 158.0
125 TraesCS2D01G222500 chr7B 93.617 94 6 0 5827 5920 593417959 593418052 2.310000e-29 141.0
126 TraesCS2D01G222500 chr7B 90.000 100 7 1 5826 5922 392820020 392819921 6.480000e-25 126.0
127 TraesCS2D01G222500 chr7B 100.000 62 0 0 6097 6158 350693656 350693595 1.400000e-21 115.0
128 TraesCS2D01G222500 chr7A 87.097 155 10 7 5823 5971 493700368 493700518 3.820000e-37 167.0
129 TraesCS2D01G222500 chr1A 96.842 95 1 1 5879 5971 202090603 202090509 2.300000e-34 158.0
130 TraesCS2D01G222500 chr1A 96.842 95 1 1 5879 5971 202090516 202090610 2.300000e-34 158.0
131 TraesCS2D01G222500 chr1A 95.918 98 2 1 5827 5922 276575262 276575165 2.300000e-34 158.0
132 TraesCS2D01G222500 chr1A 88.660 97 11 0 5826 5922 95827388 95827484 1.080000e-22 119.0
133 TraesCS2D01G222500 chr1A 79.856 139 25 3 293 429 21835187 21835324 1.410000e-16 99.0
134 TraesCS2D01G222500 chr6B 93.333 105 3 1 5879 5979 174298378 174298274 1.070000e-32 152.0
135 TraesCS2D01G222500 chr1B 91.262 103 4 2 5825 5922 677272745 677272847 1.080000e-27 135.0
136 TraesCS2D01G222500 chr1B 89.000 100 5 3 5827 5920 675092970 675093069 1.080000e-22 119.0
137 TraesCS2D01G222500 chr3A 74.098 305 67 9 1153 1448 719835844 719836145 1.400000e-21 115.0
138 TraesCS2D01G222500 chr4B 96.825 63 1 1 5817 5879 450453463 450453524 3.040000e-18 104.0


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 TraesCS2D01G222500 chr2D 189527736 189533895 6159 True 11376.0 11376 100.0000 1 6160 1 chr2D.!!$R3 6159
1 TraesCS2D01G222500 chr2D 86068232 86069495 1263 False 1888.0 1888 93.6670 2621 3887 1 chr2D.!!$F2 1266
2 TraesCS2D01G222500 chr2D 565160090 565161315 1225 True 1770.0 1770 92.6670 2657 3892 1 chr2D.!!$R4 1235
3 TraesCS2D01G222500 chr2D 79276847 79277650 803 False 1199.0 1199 93.6650 1824 2623 1 chr2D.!!$F1 799
4 TraesCS2D01G222500 chr2D 14885429 14886231 802 True 1192.0 1192 93.5400 1824 2623 1 chr2D.!!$R1 799
5 TraesCS2D01G222500 chr2D 25065369 25066953 1584 True 1005.0 1219 93.0735 1824 3887 2 chr2D.!!$R5 2063
6 TraesCS2D01G222500 chr2D 189388908 189389542 634 True 472.0 472 80.1860 1168 1810 1 chr2D.!!$R2 642
7 TraesCS2D01G222500 chr2D 188836382 188836930 548 False 305.0 305 77.1430 1170 1718 1 chr2D.!!$F3 548
8 TraesCS2D01G222500 chr2A 773271953 773273201 1248 False 1543.0 1543 88.9500 2621 3887 1 chr2A.!!$F2 1266
9 TraesCS2D01G222500 chr2A 203326136 203330012 3876 True 1542.2 2990 96.9080 1 6098 4 chr2A.!!$R2 6097
10 TraesCS2D01G222500 chr2A 25355983 25356785 802 False 1192.0 1192 93.5320 1824 2623 1 chr2A.!!$F1 799
11 TraesCS2D01G222500 chr2A 203321140 203321774 634 True 483.0 483 80.5260 1168 1810 1 chr2A.!!$R1 642
12 TraesCS2D01G222500 chr2B 245820530 245823646 3116 True 1288.5 2767 97.0940 856 6098 4 chr2B.!!$R4 5242
13 TraesCS2D01G222500 chr2B 245793444 245794066 622 True 422.0 422 79.1020 1168 1810 1 chr2B.!!$R2 642
14 TraesCS2D01G222500 chr2B 244934583 244935131 548 False 250.0 250 75.3130 1170 1718 1 chr2B.!!$F1 548
15 TraesCS2D01G222500 chr3D 110279210 110280476 1266 False 1930.0 1930 94.2140 2621 3887 1 chr3D.!!$F2 1266
16 TraesCS2D01G222500 chr3D 339301056 339302312 1256 True 1794.0 1794 92.3680 2621 3887 1 chr3D.!!$R1 1266
17 TraesCS2D01G222500 chr3D 2740778 2742045 1267 False 1748.0 1748 91.6540 2621 3887 1 chr3D.!!$F1 1266
18 TraesCS2D01G222500 chr1D 297519115 297520379 1264 True 1873.0 1873 93.4270 2621 3887 1 chr1D.!!$R3 1266
19 TraesCS2D01G222500 chr1D 240584350 240585205 855 True 1210.0 1210 92.0090 3017 3890 1 chr1D.!!$R2 873
20 TraesCS2D01G222500 chr1D 469045378 469046177 799 False 1195.0 1195 93.6490 1824 2623 1 chr1D.!!$F2 799
21 TraesCS2D01G222500 chrUn 96048458 96049724 1266 False 1836.0 1836 92.8850 2621 3887 1 chrUn.!!$F6 1266
22 TraesCS2D01G222500 chrUn 320127113 320128372 1259 False 1810.0 1810 92.6070 2621 3891 1 chrUn.!!$F14 1270
23 TraesCS2D01G222500 chrUn 27712043 27713310 1267 False 1690.0 1690 90.8670 2621 3885 1 chrUn.!!$F2 1264
24 TraesCS2D01G222500 chrUn 305006623 305007892 1269 False 1604.0 1604 89.5560 2621 3891 1 chrUn.!!$F13 1270
25 TraesCS2D01G222500 chrUn 94192770 94194852 2082 False 1538.0 1862 93.7310 1824 3887 2 chrUn.!!$F18 2063
26 TraesCS2D01G222500 chrUn 382211796 382212620 824 False 1127.0 1127 91.2010 3048 3887 1 chrUn.!!$F16 839
27 TraesCS2D01G222500 chr5D 374396826 374398098 1272 False 1831.0 1831 92.7630 2621 3887 1 chr5D.!!$F2 1266
28 TraesCS2D01G222500 chr5D 238112719 238113633 914 True 1330.0 1330 92.7960 2965 3892 1 chr5D.!!$R1 927
29 TraesCS2D01G222500 chr5D 425842803 425843599 796 False 1186.0 1186 93.5240 1824 2623 1 chr5D.!!$F3 799
30 TraesCS2D01G222500 chr4D 8005747 8007023 1276 True 1821.0 1821 92.5470 2621 3892 1 chr4D.!!$R1 1271
31 TraesCS2D01G222500 chr4D 505821263 505822526 1263 True 1799.0 1799 92.4160 2624 3889 1 chr4D.!!$R6 1265
32 TraesCS2D01G222500 chr4D 502596187 502597436 1249 True 1786.0 1786 92.4100 2624 3890 1 chr4D.!!$R5 1266
33 TraesCS2D01G222500 chr7D 570329336 570330605 1269 False 1799.0 1799 92.3440 2621 3887 1 chr7D.!!$F2 1266
34 TraesCS2D01G222500 chr7D 9964523 9965325 802 False 1208.0 1208 93.9050 1824 2623 1 chr7D.!!$F1 799
35 TraesCS2D01G222500 chr6D 276126180 276128263 2083 False 1502.0 1790 93.2420 1825 3887 2 chr6D.!!$F6 2062
36 TraesCS2D01G222500 chr6D 368142023 368143226 1203 False 1413.0 1413 87.8570 2621 3841 1 chr6D.!!$F3 1220
37 TraesCS2D01G222500 chr6D 450665480 450666412 932 False 1354.0 1354 92.7970 2947 3887 1 chr6D.!!$F5 940
38 TraesCS2D01G222500 chr6D 23775104 23776019 915 True 1330.0 1330 92.7800 2961 3887 1 chr6D.!!$R1 926
39 TraesCS2D01G222500 chr5B 10451525 10452784 1259 False 1700.0 1700 90.9660 2621 3891 1 chr5B.!!$F1 1270
40 TraesCS2D01G222500 chr4A 166334039 166335289 1250 False 1613.0 1613 89.8890 2622 3884 1 chr4A.!!$F1 1262
41 TraesCS2D01G222500 chr6A 78568255 78569527 1272 True 1605.0 1605 89.5480 2622 3890 1 chr6A.!!$R2 1268
42 TraesCS2D01G222500 chr5A 653567284 653568471 1187 False 1465.0 1465 89.0560 2621 3805 1 chr5A.!!$F1 1184

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
91 92 0.389817 TGTTTCGTGGATGAGCCGAG 60.390 55.0 0.00 0.00 40.66 4.63 F
721 725 0.392998 GGTCATGTGCCCTGGTGTAG 60.393 60.0 0.00 0.00 0.00 2.74 F
1821 1830 0.322975 TTCTTCTCAGACAGCTGGCC 59.677 55.0 18.28 8.21 42.53 5.36 F
2683 2730 0.249120 TGTGAGTTCCTGGCATACCG 59.751 55.0 0.00 0.00 39.70 4.02 F
3960 4067 0.888736 CACCAGTGGACATTTCGCCA 60.889 55.0 18.40 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1825 0.030638 CGATTTTTATGCGGGGCCAG 59.969 55.000 4.39 1.12 0.00 4.85 R
2257 2275 0.249398 GTTGATCACCAGCTACCGGT 59.751 55.000 13.98 13.98 37.16 5.28 R
3330 3398 0.818296 CCGACGTCCAGGAAGAAGAT 59.182 55.000 10.58 0.00 0.00 2.40 R
4247 4445 1.660052 CGGTCAAGTGTGCATTGTTCG 60.660 52.381 0.00 0.00 0.00 3.95 R
5952 6165 0.323451 GCTCCCTCCGTCCCAAAATT 60.323 55.000 0.00 0.00 0.00 1.82 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)


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

AutoCloner maintained by Alex Coulton.