Multiple sequence alignment - TraesCS2A01G211600

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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 TraesCS2A01G211600 chr2A 100.000 7548 0 0 1 7548 195818309 195825856 0.000000e+00 13939.0
1 TraesCS2A01G211600 chr2A 87.406 1334 109 23 3 1304 196118754 196120060 0.000000e+00 1478.0
2 TraesCS2A01G211600 chr2A 87.512 1081 86 19 3171 4216 196121699 196122765 0.000000e+00 1203.0
3 TraesCS2A01G211600 chr2A 89.453 768 77 4 1409 2174 196120230 196120995 0.000000e+00 966.0
4 TraesCS2A01G211600 chr2A 89.402 736 53 9 1 715 196327814 196327083 0.000000e+00 904.0
5 TraesCS2A01G211600 chr2A 88.980 735 57 11 1 715 196317216 196316486 0.000000e+00 887.0
6 TraesCS2A01G211600 chr2A 88.995 736 56 9 1 715 196346106 196345375 0.000000e+00 887.0
7 TraesCS2A01G211600 chr2A 88.163 735 61 9 3 715 196324009 196323279 0.000000e+00 852.0
8 TraesCS2A01G211600 chr2A 88.163 735 61 9 3 715 196356392 196355662 0.000000e+00 852.0
9 TraesCS2A01G211600 chr2A 89.633 463 31 9 5760 6218 196125250 196125699 2.360000e-159 573.0
10 TraesCS2A01G211600 chr2A 88.760 258 13 7 5309 5560 196124250 196124497 1.230000e-77 302.0
11 TraesCS2A01G211600 chr2A 91.705 217 16 2 2663 2877 196121115 196121331 4.430000e-77 300.0
12 TraesCS2A01G211600 chr2A 91.875 160 12 1 2980 3139 196121467 196121625 9.860000e-54 222.0
13 TraesCS2A01G211600 chr2A 86.339 183 25 0 6428 6610 196315070 196314888 4.620000e-47 200.0
14 TraesCS2A01G211600 chr2A 82.500 120 5 5 4203 4322 196122969 196123072 2.900000e-14 91.6
15 TraesCS2A01G211600 chr4A 99.076 5087 43 4 2463 7548 585689660 585694743 0.000000e+00 9130.0
16 TraesCS2A01G211600 chr4A 99.310 1305 9 0 1 1305 585686978 585688282 0.000000e+00 2361.0
17 TraesCS2A01G211600 chr4A 99.150 1059 9 0 1314 2372 585688327 585689385 0.000000e+00 1906.0
18 TraesCS2A01G211600 chr4A 87.779 1342 111 21 1 1305 586678549 586677224 0.000000e+00 1520.0
19 TraesCS2A01G211600 chr4A 87.416 1335 107 23 3 1304 538493023 538491717 0.000000e+00 1478.0
20 TraesCS2A01G211600 chr4A 86.632 1354 113 27 3 1305 456415356 456414020 0.000000e+00 1435.0
21 TraesCS2A01G211600 chr4A 93.882 850 49 3 6701 7548 5352012 5351164 0.000000e+00 1279.0
22 TraesCS2A01G211600 chr4A 92.453 848 59 4 6701 7548 320723194 320722352 0.000000e+00 1206.0
23 TraesCS2A01G211600 chr4A 85.289 1210 128 25 2982 4157 456402327 456401134 0.000000e+00 1203.0
24 TraesCS2A01G211600 chr4A 87.512 1081 86 19 3171 4216 538490076 538489010 0.000000e+00 1203.0
25 TraesCS2A01G211600 chr4A 85.041 1210 137 24 2982 4157 586676029 586674830 0.000000e+00 1192.0
26 TraesCS2A01G211600 chr4A 88.627 765 82 5 1412 2174 538491545 538490784 0.000000e+00 926.0
27 TraesCS2A01G211600 chr4A 93.039 589 36 4 6961 7548 283599402 283598818 0.000000e+00 856.0
28 TraesCS2A01G211600 chr4A 92.150 586 44 2 1642 2227 586676896 586676313 0.000000e+00 826.0
29 TraesCS2A01G211600 chr4A 90.879 614 45 6 4360 4968 586089515 586090122 0.000000e+00 813.0
30 TraesCS2A01G211600 chr4A 89.319 646 52 8 4328 4968 456400803 456400170 0.000000e+00 795.0
31 TraesCS2A01G211600 chr4A 89.009 646 54 8 4328 4968 586674499 586673866 0.000000e+00 784.0
32 TraesCS2A01G211600 chr4A 87.207 555 48 6 3721 4257 586082062 586082611 1.800000e-170 610.0
33 TraesCS2A01G211600 chr4A 90.437 366 23 9 6061 6423 586091068 586091424 8.870000e-129 472.0
34 TraesCS2A01G211600 chr4A 92.473 279 20 1 5127 5404 586090121 586090399 1.530000e-106 398.0
35 TraesCS2A01G211600 chr4A 82.301 452 51 14 5130 5560 576593650 576593207 1.550000e-96 364.0
36 TraesCS2A01G211600 chr4A 92.237 219 11 4 2663 2877 538490664 538490448 9.520000e-79 305.0
37 TraesCS2A01G211600 chr4A 94.318 176 9 1 4965 5140 669198141 669197967 1.250000e-67 268.0
38 TraesCS2A01G211600 chr4A 89.617 183 18 1 6428 6610 538487493 538487312 1.640000e-56 231.0
39 TraesCS2A01G211600 chr4A 90.798 163 14 1 2980 3142 538490312 538490151 4.590000e-52 217.0
40 TraesCS2A01G211600 chr4A 86.842 190 20 3 6422 6610 586091489 586091674 2.760000e-49 207.0
41 TraesCS2A01G211600 chr4A 85.792 183 26 0 6428 6610 456398841 456398659 2.150000e-45 195.0
42 TraesCS2A01G211600 chr4A 91.429 70 6 0 4254 4323 586088079 586088148 6.230000e-16 97.1
43 TraesCS2A01G211600 chr4A 82.500 120 5 5 4203 4322 538488846 538488743 2.900000e-14 91.6
44 TraesCS2A01G211600 chr4B 93.957 2019 70 13 2980 4968 25388354 25386358 0.000000e+00 3005.0
45 TraesCS2A01G211600 chr4B 94.724 1611 57 15 726 2312 25393535 25391929 0.000000e+00 2479.0
46 TraesCS2A01G211600 chr4B 80.051 2361 298 84 3 2283 39241575 39243842 0.000000e+00 1591.0
47 TraesCS2A01G211600 chr4B 87.913 1332 116 17 4 1305 24764160 24765476 0.000000e+00 1526.0
48 TraesCS2A01G211600 chr4B 91.585 915 61 12 1314 2227 24765521 24766420 0.000000e+00 1249.0
49 TraesCS2A01G211600 chr4B 85.504 1221 109 27 3135 4323 24766827 24768011 0.000000e+00 1212.0
50 TraesCS2A01G211600 chr4B 89.072 970 60 20 5760 6701 24769331 24770282 0.000000e+00 1162.0
51 TraesCS2A01G211600 chr4B 91.063 649 46 6 4325 4968 24768049 24768690 0.000000e+00 867.0
52 TraesCS2A01G211600 chr4B 88.856 673 50 15 5759 6422 24832665 24833321 0.000000e+00 804.0
53 TraesCS2A01G211600 chr4B 93.091 550 31 1 6157 6699 25385360 25384811 0.000000e+00 798.0
54 TraesCS2A01G211600 chr4B 90.778 553 41 7 3 552 25394242 25393697 0.000000e+00 730.0
55 TraesCS2A01G211600 chr4B 85.577 520 44 12 5653 6155 25385933 25385428 4.040000e-142 516.0
56 TraesCS2A01G211600 chr4B 96.013 301 10 1 2576 2874 25388944 25388644 8.800000e-134 488.0
57 TraesCS2A01G211600 chr4B 88.235 408 35 7 6020 6423 25351967 25351569 6.850000e-130 475.0
58 TraesCS2A01G211600 chr4B 85.160 438 41 13 5127 5560 24768689 24769106 1.950000e-115 427.0
59 TraesCS2A01G211600 chr4B 87.500 296 14 3 2315 2589 25390830 25390537 3.400000e-83 320.0
60 TraesCS2A01G211600 chr4B 85.240 271 36 4 197 464 24756069 24756338 7.460000e-70 276.0
61 TraesCS2A01G211600 chr4B 95.758 165 7 0 4969 5133 483266540 483266376 4.490000e-67 267.0
62 TraesCS2A01G211600 chr4B 92.523 107 8 0 611 717 25393685 25393579 3.650000e-33 154.0
63 TraesCS2A01G211600 chr4B 98.571 70 0 1 2980 3049 25388432 25388364 1.030000e-23 122.0
64 TraesCS2A01G211600 chr4D 88.869 1716 118 23 611 2274 15157401 15155707 0.000000e+00 2043.0
65 TraesCS2A01G211600 chr4D 86.224 1401 125 16 2980 4323 15153820 15152431 0.000000e+00 1456.0
66 TraesCS2A01G211600 chr4D 87.388 1229 88 14 129 1305 14924629 14925842 0.000000e+00 1349.0
67 TraesCS2A01G211600 chr4D 91.937 955 69 6 1334 2283 14403828 14402877 0.000000e+00 1330.0
68 TraesCS2A01G211600 chr4D 85.726 1240 95 25 129 1305 14424392 14423172 0.000000e+00 1234.0
69 TraesCS2A01G211600 chr4D 80.976 1640 200 46 644 2236 26896032 26897606 0.000000e+00 1197.0
70 TraesCS2A01G211600 chr4D 87.312 796 73 18 5639 6423 14399697 14398919 0.000000e+00 885.0
71 TraesCS2A01G211600 chr4D 91.345 647 47 8 1639 2283 14926167 14926806 0.000000e+00 876.0
72 TraesCS2A01G211600 chr4D 90.726 647 48 6 4328 4967 14400757 14400116 0.000000e+00 852.0
73 TraesCS2A01G211600 chr4D 90.755 649 45 7 4325 4968 14927054 14927692 0.000000e+00 852.0
74 TraesCS2A01G211600 chr4D 89.644 618 48 8 4361 4968 15151055 15150444 0.000000e+00 773.0
75 TraesCS2A01G211600 chr4D 86.834 638 49 13 3713 4323 14401427 14400798 0.000000e+00 680.0
76 TraesCS2A01G211600 chr4D 87.884 553 60 5 1 552 15157959 15157413 1.780000e-180 643.0
77 TraesCS2A01G211600 chr4D 86.757 589 52 18 5639 6218 14928102 14928673 3.840000e-177 632.0
78 TraesCS2A01G211600 chr4D 88.018 434 38 11 5130 5560 14400113 14399691 1.130000e-137 501.0
79 TraesCS2A01G211600 chr4D 90.000 390 18 5 2489 2874 15154416 15154044 1.140000e-132 484.0
80 TraesCS2A01G211600 chr4D 90.515 369 27 8 6061 6426 15149566 15149203 1.470000e-131 481.0
81 TraesCS2A01G211600 chr4D 92.029 276 21 1 5130 5404 15150442 15150167 3.300000e-103 387.0
82 TraesCS2A01G211600 chr4D 82.418 455 54 10 5130 5560 26898916 26899368 2.570000e-99 374.0
83 TraesCS2A01G211600 chr4D 86.943 314 28 2 2988 3288 14401971 14401658 2.610000e-89 340.0
84 TraesCS2A01G211600 chr4D 87.368 190 19 3 6422 6610 15149141 15148956 5.930000e-51 213.0
85 TraesCS2A01G211600 chr4D 86.957 138 17 1 2294 2430 14926790 14926927 3.650000e-33 154.0
86 TraesCS2A01G211600 chr4D 87.218 133 13 1 2297 2429 14402890 14402762 1.700000e-31 148.0
87 TraesCS2A01G211600 chr4D 88.732 71 7 1 2211 2281 14926793 14926862 1.350000e-12 86.1
88 TraesCS2A01G211600 chr4D 87.324 71 8 1 2211 2281 14402890 14402821 6.280000e-11 80.5
89 TraesCS2A01G211600 chr4D 89.474 57 6 0 2898 2954 9745500 9745444 1.050000e-08 73.1
90 TraesCS2A01G211600 chr3B 87.212 1345 109 22 3 1305 452703254 452701931 0.000000e+00 1472.0
91 TraesCS2A01G211600 chr3B 84.919 1366 131 31 2982 4323 452699703 452698389 0.000000e+00 1312.0
92 TraesCS2A01G211600 chr3B 88.018 1110 70 22 5639 6701 452697322 452696229 0.000000e+00 1254.0
93 TraesCS2A01G211600 chr3B 88.852 915 67 12 1314 2227 452701886 452701006 0.000000e+00 1092.0
94 TraesCS2A01G211600 chr3B 89.474 532 38 13 5759 6285 452564204 452563686 0.000000e+00 656.0
95 TraesCS2A01G211600 chr3B 89.247 93 10 0 2888 2980 670397494 670397586 4.790000e-22 117.0
96 TraesCS2A01G211600 chr5A 85.246 1403 120 28 2980 4323 40874652 40876026 0.000000e+00 1363.0
97 TraesCS2A01G211600 chr5A 92.290 856 58 6 6694 7548 349874970 349875818 0.000000e+00 1208.0
98 TraesCS2A01G211600 chr5A 89.306 533 39 11 5760 6285 40877374 40877895 0.000000e+00 652.0
99 TraesCS2A01G211600 chr5A 91.071 392 26 7 2489 2874 40874041 40874429 8.680000e-144 521.0
100 TraesCS2A01G211600 chr5A 86.468 436 49 8 5127 5558 40876698 40877127 3.190000e-128 470.0
101 TraesCS2A01G211600 chr5A 93.069 101 6 1 2883 2983 34326517 34326616 6.100000e-31 147.0
102 TraesCS2A01G211600 chr5A 88.660 97 11 0 2883 2979 350525103 350525199 1.330000e-22 119.0
103 TraesCS2A01G211600 chr5D 85.252 1390 127 35 2980 4323 51842513 51843870 0.000000e+00 1360.0
104 TraesCS2A01G211600 chr5D 89.796 392 33 5 2489 2874 51841902 51842292 5.260000e-136 496.0
105 TraesCS2A01G211600 chr5D 92.727 165 11 1 5129 5293 51844699 51844862 3.520000e-58 237.0
106 TraesCS2A01G211600 chr5D 91.667 48 3 1 6695 6741 354870 354823 1.760000e-06 65.8
107 TraesCS2A01G211600 chr3A 92.732 853 54 6 6698 7548 324869054 324869900 0.000000e+00 1225.0
108 TraesCS2A01G211600 chr3A 88.372 86 10 0 5558 5643 47074676 47074591 3.730000e-18 104.0
109 TraesCS2A01G211600 chr1B 83.394 1367 142 37 1 1305 433420520 433421863 0.000000e+00 1188.0
110 TraesCS2A01G211600 chr1B 88.048 912 87 13 1314 2211 433421908 433422811 0.000000e+00 1061.0
111 TraesCS2A01G211600 chr1B 84.300 1121 115 16 2981 4055 433424445 433425550 0.000000e+00 1038.0
112 TraesCS2A01G211600 chr1B 86.434 258 31 4 5137 5393 433426240 433426494 5.770000e-71 279.0
113 TraesCS2A01G211600 chr1B 95.266 169 8 0 4965 5133 183877365 183877197 1.250000e-67 268.0
114 TraesCS2A01G211600 chr1B 88.889 99 9 2 5547 5645 296488088 296487992 3.700000e-23 121.0
115 TraesCS2A01G211600 chr1D 83.113 1362 143 34 1 1305 320382124 320383455 0.000000e+00 1160.0
116 TraesCS2A01G211600 chr1D 88.865 916 82 11 1314 2211 320383500 320384413 0.000000e+00 1109.0
117 TraesCS2A01G211600 chr1D 82.756 1125 121 18 2981 4055 320387409 320388510 0.000000e+00 935.0
118 TraesCS2A01G211600 chr1D 87.240 674 66 12 5760 6427 320390444 320391103 0.000000e+00 750.0
119 TraesCS2A01G211600 chr1D 94.643 112 6 0 2555 2666 320386989 320387100 2.800000e-39 174.0
120 TraesCS2A01G211600 chr5B 86.217 711 67 10 2988 3670 54825699 54826406 0.000000e+00 741.0
121 TraesCS2A01G211600 chr5B 89.498 438 42 3 5127 5560 54827865 54828302 1.110000e-152 551.0
122 TraesCS2A01G211600 chr5B 94.536 183 8 2 2542 2724 54825175 54825355 1.600000e-71 281.0
123 TraesCS2A01G211600 chr5B 90.426 94 9 0 2886 2979 600136411 600136318 2.860000e-24 124.0
124 TraesCS2A01G211600 chr5B 87.912 91 11 0 2886 2976 548312228 548312318 2.880000e-19 108.0
125 TraesCS2A01G211600 chr5B 85.859 99 12 2 5550 5647 211588018 211587921 3.730000e-18 104.0
126 TraesCS2A01G211600 chr2D 91.611 298 23 1 6700 6995 188883210 188882913 1.960000e-110 411.0
127 TraesCS2A01G211600 chr2D 94.898 98 5 0 2886 2983 330456093 330456190 3.650000e-33 154.0
128 TraesCS2A01G211600 chr2D 89.773 88 7 2 5557 5643 500366523 500366609 2.230000e-20 111.0
129 TraesCS2A01G211600 chr2D 87.500 88 11 0 5558 5645 311551653 311551740 1.340000e-17 102.0
130 TraesCS2A01G211600 chr2B 96.364 165 6 0 4966 5130 454080652 454080488 9.650000e-69 272.0
131 TraesCS2A01G211600 chr3D 94.798 173 9 0 4965 5137 571465363 571465535 3.470000e-68 270.0
132 TraesCS2A01G211600 chr3D 94.798 173 9 0 4965 5137 579494957 579494785 3.470000e-68 270.0
133 TraesCS2A01G211600 chr6D 94.737 171 8 1 4966 5136 311580531 311580700 1.610000e-66 265.0
134 TraesCS2A01G211600 chr6D 90.110 91 7 2 5558 5647 438896968 438897057 4.790000e-22 117.0
135 TraesCS2A01G211600 chr7D 91.489 188 15 1 4945 5131 414094747 414094934 2.700000e-64 257.0
136 TraesCS2A01G211600 chr7A 93.548 93 6 0 2886 2978 3589558 3589650 1.020000e-28 139.0
137 TraesCS2A01G211600 chr7A 95.122 41 1 1 6700 6740 379964114 379964075 6.320000e-06 63.9
138 TraesCS2A01G211600 chr7B 90.426 94 9 0 2886 2979 61611957 61611864 2.860000e-24 124.0
139 TraesCS2A01G211600 chr7B 88.764 89 10 0 5557 5645 54323350 54323438 8.010000e-20 110.0
140 TraesCS2A01G211600 chrUn 88.000 100 9 2 5547 5643 352394923 352394824 1.720000e-21 115.0
141 TraesCS2A01G211600 chrUn 92.857 42 3 0 6701 6742 181247565 181247524 2.270000e-05 62.1


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 TraesCS2A01G211600 chr2A 195818309 195825856 7547 False 13939.000000 13939 100.000000 1 7548 1 chr2A.!!$F1 7547
1 TraesCS2A01G211600 chr2A 196345375 196346106 731 True 887.000000 887 88.995000 1 715 1 chr2A.!!$R1 714
2 TraesCS2A01G211600 chr2A 196323279 196327814 4535 True 878.000000 904 88.782500 1 715 2 chr2A.!!$R4 714
3 TraesCS2A01G211600 chr2A 196355662 196356392 730 True 852.000000 852 88.163000 3 715 1 chr2A.!!$R2 712
4 TraesCS2A01G211600 chr2A 196118754 196125699 6945 False 641.950000 1478 88.605500 3 6218 8 chr2A.!!$F2 6215
5 TraesCS2A01G211600 chr2A 196314888 196317216 2328 True 543.500000 887 87.659500 1 6610 2 chr2A.!!$R3 6609
6 TraesCS2A01G211600 chr4A 585686978 585694743 7765 False 4465.666667 9130 99.178667 1 7548 3 chr4A.!!$F2 7547
7 TraesCS2A01G211600 chr4A 456414020 456415356 1336 True 1435.000000 1435 86.632000 3 1305 1 chr4A.!!$R4 1302
8 TraesCS2A01G211600 chr4A 5351164 5352012 848 True 1279.000000 1279 93.882000 6701 7548 1 chr4A.!!$R1 847
9 TraesCS2A01G211600 chr4A 320722352 320723194 842 True 1206.000000 1206 92.453000 6701 7548 1 chr4A.!!$R3 847
10 TraesCS2A01G211600 chr4A 586673866 586678549 4683 True 1080.500000 1520 88.494750 1 4968 4 chr4A.!!$R9 4967
11 TraesCS2A01G211600 chr4A 283598818 283599402 584 True 856.000000 856 93.039000 6961 7548 1 chr4A.!!$R2 587
12 TraesCS2A01G211600 chr4A 456398659 456402327 3668 True 731.000000 1203 86.800000 2982 6610 3 chr4A.!!$R7 3628
13 TraesCS2A01G211600 chr4A 538487312 538493023 5711 True 635.942857 1478 88.386714 3 6610 7 chr4A.!!$R8 6607
14 TraesCS2A01G211600 chr4A 586082062 586082611 549 False 610.000000 610 87.207000 3721 4257 1 chr4A.!!$F1 536
15 TraesCS2A01G211600 chr4A 586088079 586091674 3595 False 397.420000 813 90.412000 4254 6610 5 chr4A.!!$F3 2356
16 TraesCS2A01G211600 chr4B 39241575 39243842 2267 False 1591.000000 1591 80.051000 3 2283 1 chr4B.!!$F3 2280
17 TraesCS2A01G211600 chr4B 24764160 24770282 6122 False 1073.833333 1526 88.382833 4 6701 6 chr4B.!!$F4 6697
18 TraesCS2A01G211600 chr4B 25384811 25394242 9431 True 956.888889 3005 92.526000 3 6699 9 chr4B.!!$R3 6696
19 TraesCS2A01G211600 chr4B 24832665 24833321 656 False 804.000000 804 88.856000 5759 6422 1 chr4B.!!$F2 663
20 TraesCS2A01G211600 chr4D 14423172 14424392 1220 True 1234.000000 1234 85.726000 129 1305 1 chr4D.!!$R2 1176
21 TraesCS2A01G211600 chr4D 15148956 15157959 9003 True 810.000000 2043 89.066625 1 6610 8 chr4D.!!$R4 6609
22 TraesCS2A01G211600 chr4D 26896032 26899368 3336 False 785.500000 1197 81.697000 644 5560 2 chr4D.!!$F2 4916
23 TraesCS2A01G211600 chr4D 14924629 14928673 4044 False 658.183333 1349 88.655667 129 6218 6 chr4D.!!$F1 6089
24 TraesCS2A01G211600 chr4D 14398919 14403828 4909 True 602.062500 1330 88.289000 1334 6423 8 chr4D.!!$R3 5089
25 TraesCS2A01G211600 chr3B 452696229 452703254 7025 True 1282.500000 1472 87.250250 3 6701 4 chr3B.!!$R2 6698
26 TraesCS2A01G211600 chr3B 452563686 452564204 518 True 656.000000 656 89.474000 5759 6285 1 chr3B.!!$R1 526
27 TraesCS2A01G211600 chr5A 349874970 349875818 848 False 1208.000000 1208 92.290000 6694 7548 1 chr5A.!!$F2 854
28 TraesCS2A01G211600 chr5A 40874041 40877895 3854 False 751.500000 1363 88.022750 2489 6285 4 chr5A.!!$F4 3796
29 TraesCS2A01G211600 chr5D 51841902 51844862 2960 False 697.666667 1360 89.258333 2489 5293 3 chr5D.!!$F1 2804
30 TraesCS2A01G211600 chr3A 324869054 324869900 846 False 1225.000000 1225 92.732000 6698 7548 1 chr3A.!!$F1 850
31 TraesCS2A01G211600 chr1B 433420520 433426494 5974 False 891.500000 1188 85.544000 1 5393 4 chr1B.!!$F1 5392
32 TraesCS2A01G211600 chr1D 320382124 320391103 8979 False 825.600000 1160 87.323400 1 6427 5 chr1D.!!$F1 6426
33 TraesCS2A01G211600 chr5B 54825175 54828302 3127 False 524.333333 741 90.083667 2542 5560 3 chr5B.!!$F2 3018

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
965 1105 2.772191 AGGCCGGGGCATGTCATA 60.772 61.111 23.67 0.0 44.11 2.15 F
1249 1401 0.033503 TCTACTCCCGCTCCATGTCA 60.034 55.000 0.00 0.0 0.00 3.58 F
1309 1461 1.871418 TCTGGAGGACAATCTGGAGG 58.129 55.000 0.00 0.0 0.00 4.30 F
1673 1911 2.420129 GGAGGAAACATGGCGATACACT 60.420 50.000 0.00 0.0 0.00 3.55 F
2946 10231 3.969117 TTGCTATATTTGCCTTCTGCG 57.031 42.857 0.00 0.0 45.60 5.18 F
3731 11507 1.275856 GCTGTTTGGCATGATTCCCAA 59.724 47.619 0.00 0.0 39.23 4.12 F
5219 16259 3.748568 GGCTCGTTTTCTTGACTTCTGAT 59.251 43.478 0.00 0.0 0.00 2.90 F
5436 17545 3.055530 TGATGGTTTTGGTGTTGCAAAGT 60.056 39.130 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 4022 1.281867 CCATTGTGCCTTGGTCCTAGA 59.718 52.381 1.39 0.0 0.00 2.43 R
2458 4105 2.185004 ACTCTTGCATTAACCGCTGT 57.815 45.000 0.00 0.0 0.00 4.40 R
2946 10231 2.416680 AGAGAAGAAATGCTGGAGGC 57.583 50.000 0.00 0.0 42.22 4.70 R
3308 10906 6.942532 AGTTGTAGTGTGTGAATTCAATGT 57.057 33.333 10.35 0.0 0.00 2.71 R
4662 15674 3.463048 AAAGAATCACTTGAGCCCCAT 57.537 42.857 0.00 0.0 38.98 4.00 R
5436 17545 1.616159 GGTACTGCAAAGCTTCCCAA 58.384 50.000 0.00 0.0 0.00 4.12 R
6488 20596 0.877743 GCAGTGACAAAGCTCCTTCC 59.122 55.000 0.00 0.0 0.00 3.46 R
6789 20903 1.067142 GGATGTCGTCTTGCTGGTACA 60.067 52.381 0.00 0.0 0.00 2.90 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
378 420 5.946377 GTGTGATGTTTCTCTCCCCTTATTT 59.054 40.000 0.00 0.00 0.00 1.40
379 421 7.110155 GTGTGATGTTTCTCTCCCCTTATTTA 58.890 38.462 0.00 0.00 0.00 1.40
965 1105 2.772191 AGGCCGGGGCATGTCATA 60.772 61.111 23.67 0.00 44.11 2.15
1249 1401 0.033503 TCTACTCCCGCTCCATGTCA 60.034 55.000 0.00 0.00 0.00 3.58
1305 1457 3.199508 AGGACAATCTGGAGGACAATCTG 59.800 47.826 0.00 0.00 0.00 2.90
1306 1458 3.539604 GACAATCTGGAGGACAATCTGG 58.460 50.000 0.00 0.00 0.00 3.86
1307 1459 3.184628 ACAATCTGGAGGACAATCTGGA 58.815 45.455 0.00 0.00 0.00 3.86
1308 1460 3.199508 ACAATCTGGAGGACAATCTGGAG 59.800 47.826 0.00 0.00 0.00 3.86
1309 1461 1.871418 TCTGGAGGACAATCTGGAGG 58.129 55.000 0.00 0.00 0.00 4.30
1318 1506 3.054802 GGACAATCTGGAGGACAATCTGT 60.055 47.826 0.00 0.00 0.00 3.41
1355 1543 2.445145 TGGTCTGTTTCATTTCCCTCCA 59.555 45.455 0.00 0.00 0.00 3.86
1396 1587 3.882288 TGCAGCATGACACAAAGAGTAAA 59.118 39.130 0.00 0.00 39.69 2.01
1673 1911 2.420129 GGAGGAAACATGGCGATACACT 60.420 50.000 0.00 0.00 0.00 3.55
2458 4105 3.985019 TCTTGCCCCTGTAATTAACGA 57.015 42.857 0.00 0.00 0.00 3.85
2946 10231 3.969117 TTGCTATATTTGCCTTCTGCG 57.031 42.857 0.00 0.00 45.60 5.18
3152 10668 5.093236 AGTTATCCACATCAGATCCCCTA 57.907 43.478 0.00 0.00 0.00 3.53
3537 11162 2.730183 TTTCTCGTTTTGTCACTGCG 57.270 45.000 0.00 0.00 0.00 5.18
3731 11507 1.275856 GCTGTTTGGCATGATTCCCAA 59.724 47.619 0.00 0.00 39.23 4.12
4333 12585 9.712305 CCTTCCAACTCATATTAATTATCTCGT 57.288 33.333 0.00 0.00 0.00 4.18
4662 15674 3.926214 ATGCAAAGGTGGGGGCCA 61.926 61.111 4.39 0.00 0.00 5.36
4845 15872 7.683704 GCGGTTGATCTAGTTTTGGATAGACTA 60.684 40.741 0.00 0.00 31.09 2.59
5219 16259 3.748568 GGCTCGTTTTCTTGACTTCTGAT 59.251 43.478 0.00 0.00 0.00 2.90
5436 17545 3.055530 TGATGGTTTTGGTGTTGCAAAGT 60.056 39.130 0.00 0.00 0.00 2.66
5681 17801 6.297582 TCTAGCCTAGAATACCTAGTGTGTC 58.702 44.000 0.00 0.00 42.63 3.67
6488 20596 3.634568 TTACAAGCAACAATCAACCCG 57.365 42.857 0.00 0.00 0.00 5.28
6875 20990 2.093128 TCTCCGAACAATTTAGGCCTCC 60.093 50.000 9.68 0.00 0.00 4.30
6982 21097 7.686438 AAAATACTCATAGTGTCATGCAACA 57.314 32.000 0.00 0.00 0.00 3.33
7099 21216 6.021596 CGTCCTAAATCCATCGTTTCTTTTG 58.978 40.000 0.00 0.00 0.00 2.44
7208 21325 1.269012 AACGGGTGGGAATCGTCTTA 58.731 50.000 0.00 0.00 36.01 2.10
7352 21469 2.500910 TCAAATAGGCCCAGCAATTTGG 59.499 45.455 18.54 0.75 40.50 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
378 420 6.763355 AGAGTCAGCAGTGAGAAAGAAAATA 58.237 36.000 0.00 0.00 31.53 1.40
379 421 5.619220 AGAGTCAGCAGTGAGAAAGAAAAT 58.381 37.500 0.00 0.00 31.53 1.82
389 435 3.323115 AGAATGTCAAGAGTCAGCAGTGA 59.677 43.478 0.00 0.00 0.00 3.41
965 1105 1.139058 GTGCGGTGATGGTAAGATCCT 59.861 52.381 0.00 0.00 0.00 3.24
1249 1401 5.808366 TGGAGACAAGTATTCTCAACTGT 57.192 39.130 2.02 0.00 41.26 3.55
1305 1457 3.409026 AGACACAACAGATTGTCCTCC 57.591 47.619 0.00 0.00 46.46 4.30
1306 1458 4.021016 AGGTAGACACAACAGATTGTCCTC 60.021 45.833 0.00 0.00 46.46 3.71
1307 1459 3.904339 AGGTAGACACAACAGATTGTCCT 59.096 43.478 0.00 0.00 46.46 3.85
1308 1460 3.997021 CAGGTAGACACAACAGATTGTCC 59.003 47.826 0.00 0.00 46.46 4.02
1309 1461 4.883083 TCAGGTAGACACAACAGATTGTC 58.117 43.478 0.00 0.00 46.46 3.18
1318 1506 3.511540 CAGACCATCTCAGGTAGACACAA 59.488 47.826 0.00 0.00 43.38 3.33
1850 2088 2.897326 TGAGCAGCCAGTAGTAGAACAA 59.103 45.455 0.00 0.00 0.00 2.83
2390 4013 2.159379 GCCTTGGTCCTAGAATTTTGCG 60.159 50.000 1.39 0.00 0.00 4.85
2398 4022 1.281867 CCATTGTGCCTTGGTCCTAGA 59.718 52.381 1.39 0.00 0.00 2.43
2458 4105 2.185004 ACTCTTGCATTAACCGCTGT 57.815 45.000 0.00 0.00 0.00 4.40
2946 10231 2.416680 AGAGAAGAAATGCTGGAGGC 57.583 50.000 0.00 0.00 42.22 4.70
3308 10906 6.942532 AGTTGTAGTGTGTGAATTCAATGT 57.057 33.333 10.35 0.00 0.00 2.71
3537 11162 8.360132 CAATTTTACGGCTAAAAACGATACAAC 58.640 33.333 0.00 0.00 35.83 3.32
3731 11507 4.721776 TCCAGCACCTAGAATATTTGGAGT 59.278 41.667 9.21 0.00 0.00 3.85
4333 12585 8.310382 AGCAATTACATAACCAATTGTAAGCAA 58.690 29.630 4.43 0.00 41.87 3.91
4662 15674 3.463048 AAAGAATCACTTGAGCCCCAT 57.537 42.857 0.00 0.00 38.98 4.00
4845 15872 3.505480 TTACCCGTTACCAACACCATT 57.495 42.857 0.00 0.00 0.00 3.16
4973 16012 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
5071 16110 5.362717 AGATTTCACTATGGACCACATACGA 59.637 40.000 0.00 0.00 41.03 3.43
5219 16259 5.451937 CGAGATTAGGGCAAGATGAGTACAA 60.452 44.000 0.00 0.00 0.00 2.41
5436 17545 1.616159 GGTACTGCAAAGCTTCCCAA 58.384 50.000 0.00 0.00 0.00 4.12
5681 17801 8.757164 TGTAGTTTCTATACATGTGTGTGAAG 57.243 34.615 9.11 0.00 39.39 3.02
6488 20596 0.877743 GCAGTGACAAAGCTCCTTCC 59.122 55.000 0.00 0.00 0.00 3.46
6789 20903 1.067142 GGATGTCGTCTTGCTGGTACA 60.067 52.381 0.00 0.00 0.00 2.90
6982 21097 4.459337 GTCGGAACATTCAAGGAAGGAAAT 59.541 41.667 0.00 0.00 0.00 2.17
7099 21216 2.166664 AGAGGGCGACTAAAGTCATGAC 59.833 50.000 18.47 18.47 44.99 3.06
7208 21325 5.780958 AATACTCCTACCTTGCTCCTTTT 57.219 39.130 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.