Multiple sequence alignment - TraesCS2A01G208600

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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 TraesCS2A01G208600 chr2A 100.000 4996 0 0 1 4996 191624433 191619438 0.000000e+00 9226.0
1 TraesCS2A01G208600 chr2A 89.476 2423 193 46 1880 4267 316872177 316869782 0.000000e+00 3005.0
2 TraesCS2A01G208600 chr2A 87.171 2354 230 59 1950 4267 324314204 324316521 0.000000e+00 2608.0
3 TraesCS2A01G208600 chr2A 91.058 1342 84 19 1880 3198 317030980 317029652 0.000000e+00 1781.0
4 TraesCS2A01G208600 chr2A 86.981 699 79 6 1 698 427936674 427937361 0.000000e+00 776.0
5 TraesCS2A01G208600 chr2A 86.099 705 84 13 1 698 98444156 98444853 0.000000e+00 747.0
6 TraesCS2A01G208600 chr2A 82.065 736 112 12 4268 4991 287489873 287490600 1.190000e-170 610.0
7 TraesCS2A01G208600 chr2A 88.208 212 24 1 1296 1506 279647523 279647734 8.300000e-63 252.0
8 TraesCS2A01G208600 chr2A 89.157 83 8 1 1466 1548 435491748 435491829 8.850000e-18 102.0
9 TraesCS2A01G208600 chr2A 91.892 74 5 1 1475 1548 435499598 435499670 8.850000e-18 102.0
10 TraesCS2A01G208600 chr2A 92.453 53 3 1 1302 1353 366239685 366239633 1.930000e-09 75.0
11 TraesCS2A01G208600 chr5A 90.807 2393 167 33 1903 4267 151320356 151317989 0.000000e+00 3151.0
12 TraesCS2A01G208600 chr5A 87.396 2277 202 59 2015 4264 508035367 508037585 0.000000e+00 2536.0
13 TraesCS2A01G208600 chr5A 86.857 700 84 8 1 698 453047434 453048127 0.000000e+00 776.0
14 TraesCS2A01G208600 chr5A 86.286 700 88 8 1 698 453039644 453040337 0.000000e+00 754.0
15 TraesCS2A01G208600 chr5A 85.277 686 89 9 4 683 166670647 166669968 0.000000e+00 697.0
16 TraesCS2A01G208600 chr5A 90.643 171 16 0 1296 1466 139383187 139383017 1.400000e-55 228.0
17 TraesCS2A01G208600 chr5A 90.230 174 15 2 1296 1468 139407763 139407591 5.030000e-55 226.0
18 TraesCS2A01G208600 chr5A 84.971 173 24 2 1525 1696 301732891 301733062 1.850000e-39 174.0
19 TraesCS2A01G208600 chr5A 96.875 32 0 1 729 760 526464480 526464510 9.000000e-03 52.8
20 TraesCS2A01G208600 chr7A 90.492 2398 169 43 1901 4267 424696130 424698499 0.000000e+00 3110.0
21 TraesCS2A01G208600 chr7A 88.281 2210 195 52 2087 4267 381605777 381607951 0.000000e+00 2588.0
22 TraesCS2A01G208600 chr7A 85.887 2062 218 60 2244 4269 450454388 450452364 0.000000e+00 2128.0
23 TraesCS2A01G208600 chr7A 85.791 2048 211 65 2244 4255 450456070 450458073 0.000000e+00 2097.0
24 TraesCS2A01G208600 chr7A 86.838 699 81 5 1 698 615702388 615703076 0.000000e+00 771.0
25 TraesCS2A01G208600 chr7A 86.305 701 81 12 1 698 615710154 615710842 0.000000e+00 749.0
26 TraesCS2A01G208600 chr7A 87.879 198 14 6 1089 1284 180593206 180593395 1.810000e-54 224.0
27 TraesCS2A01G208600 chr7A 84.388 237 16 15 1056 1284 422809719 422809942 3.920000e-51 213.0
28 TraesCS2A01G208600 chr7A 94.231 52 3 0 1417 1468 432453405 432453354 4.150000e-11 80.5
29 TraesCS2A01G208600 chr7A 92.857 56 3 1 1671 1725 583320580 583320525 4.150000e-11 80.5
30 TraesCS2A01G208600 chr7A 90.909 55 5 0 1414 1468 572601238 572601292 1.930000e-09 75.0
31 TraesCS2A01G208600 chr6A 89.740 2388 183 40 1903 4267 425477417 425479765 0.000000e+00 2996.0
32 TraesCS2A01G208600 chr6A 83.534 2909 324 101 1475 4267 340060812 340057943 0.000000e+00 2575.0
33 TraesCS2A01G208600 chr6A 87.732 701 76 9 1 698 107852257 107852950 0.000000e+00 809.0
34 TraesCS2A01G208600 chr6A 87.055 703 81 8 1 698 425483823 425484520 0.000000e+00 785.0
35 TraesCS2A01G208600 chr6A 88.908 568 56 6 1 566 405546364 405545802 0.000000e+00 693.0
36 TraesCS2A01G208600 chr6A 88.556 568 58 6 1 566 405579521 405578959 0.000000e+00 682.0
37 TraesCS2A01G208600 chr6A 86.622 598 72 6 1 595 257963923 257963331 0.000000e+00 654.0
38 TraesCS2A01G208600 chr6A 86.039 616 74 11 1 612 417452696 417453303 0.000000e+00 651.0
39 TraesCS2A01G208600 chr6A 87.009 585 67 8 1 582 417477909 417478487 0.000000e+00 651.0
40 TraesCS2A01G208600 chr6A 84.029 695 85 22 1 684 85856651 85855972 0.000000e+00 645.0
41 TraesCS2A01G208600 chr6A 87.234 329 33 7 1475 1800 340068748 340068426 2.840000e-97 366.0
42 TraesCS2A01G208600 chr6A 90.213 235 15 4 827 1058 322039411 322039182 2.920000e-77 300.0
43 TraesCS2A01G208600 chr6A 90.751 173 16 0 1296 1468 250345141 250344969 1.080000e-56 231.0
44 TraesCS2A01G208600 chr6A 90.751 173 16 0 1296 1468 250366716 250366544 1.080000e-56 231.0
45 TraesCS2A01G208600 chr6A 78.507 335 67 5 365 698 336256084 336256414 1.090000e-51 215.0
46 TraesCS2A01G208600 chr6A 96.842 95 3 0 604 698 425476160 425476254 5.180000e-35 159.0
47 TraesCS2A01G208600 chr6A 89.431 123 11 2 827 948 322031104 322030983 2.410000e-33 154.0
48 TraesCS2A01G208600 chr6A 82.051 156 26 2 405 559 373871380 373871226 1.130000e-26 132.0
49 TraesCS2A01G208600 chr6A 97.826 46 1 0 1423 1468 457723855 457723900 4.150000e-11 80.5
50 TraesCS2A01G208600 chr6A 97.500 40 1 0 1427 1466 457715743 457715782 8.970000e-08 69.4
51 TraesCS2A01G208600 chr1A 84.593 2778 325 82 1557 4267 405936996 405934255 0.000000e+00 2663.0
52 TraesCS2A01G208600 chr1A 91.622 931 46 11 401 1300 291309495 291310424 0.000000e+00 1258.0
53 TraesCS2A01G208600 chr1A 88.214 560 61 5 2 559 482970755 482971311 0.000000e+00 664.0
54 TraesCS2A01G208600 chr1A 86.312 621 69 11 1 614 320916197 320916808 0.000000e+00 662.0
55 TraesCS2A01G208600 chr1A 88.036 560 63 4 1 559 70740651 70741207 0.000000e+00 660.0
56 TraesCS2A01G208600 chr1A 88.014 559 60 6 1 557 322089111 322088558 0.000000e+00 654.0
57 TraesCS2A01G208600 chr1A 86.500 600 71 8 1 596 144483035 144482442 0.000000e+00 651.0
58 TraesCS2A01G208600 chr1A 85.877 616 74 10 1 612 267378340 267378946 1.170000e-180 643.0
59 TraesCS2A01G208600 chr1A 87.411 564 61 8 1 559 536248408 536248966 1.520000e-179 640.0
60 TraesCS2A01G208600 chr1A 87.321 560 67 4 1 559 70733086 70733642 5.450000e-179 638.0
61 TraesCS2A01G208600 chr1A 86.957 575 64 8 1 573 229647997 229647432 1.960000e-178 636.0
62 TraesCS2A01G208600 chr1A 85.833 600 76 7 1 596 144475127 144474533 3.280000e-176 628.0
63 TraesCS2A01G208600 chr1A 85.366 615 81 7 2 612 181084169 181083560 3.280000e-176 628.0
64 TraesCS2A01G208600 chr1A 83.550 693 93 18 1 684 411279827 411279147 3.280000e-176 628.0
65 TraesCS2A01G208600 chr1A 89.062 192 17 4 1089 1277 158725034 158725224 8.360000e-58 235.0
66 TraesCS2A01G208600 chr1A 82.692 156 25 2 405 559 332029681 332029835 2.430000e-28 137.0
67 TraesCS2A01G208600 chr1A 97.778 45 1 0 691 735 193421924 193421968 1.490000e-10 78.7
68 TraesCS2A01G208600 chr1A 95.556 45 2 0 691 735 193414121 193414165 6.940000e-09 73.1
69 TraesCS2A01G208600 chr1A 85.965 57 3 5 1475 1527 405937036 405936981 6.990000e-04 56.5
70 TraesCS2A01G208600 chr3A 87.176 2394 229 62 1902 4267 239575392 239573049 0.000000e+00 2649.0
71 TraesCS2A01G208600 chr3A 86.984 2397 230 66 1902 4267 239583219 239580874 0.000000e+00 2623.0
72 TraesCS2A01G208600 chr3A 91.006 934 49 10 401 1300 255353820 255354752 0.000000e+00 1227.0
73 TraesCS2A01G208600 chr3A 89.696 922 54 15 401 1300 255376159 255377061 0.000000e+00 1138.0
74 TraesCS2A01G208600 chr3A 87.966 698 79 3 1 698 438872661 438871969 0.000000e+00 819.0
75 TraesCS2A01G208600 chr3A 89.408 321 30 4 1475 1795 373250283 373249967 7.790000e-108 401.0
76 TraesCS2A01G208600 chr3A 85.153 229 17 13 1063 1284 583141954 583141736 8.420000e-53 219.0
77 TraesCS2A01G208600 chr3A 87.629 194 15 5 1089 1280 583149867 583149681 3.030000e-52 217.0
78 TraesCS2A01G208600 chr3A 90.123 81 7 1 1475 1555 118515886 118515807 2.460000e-18 104.0
79 TraesCS2A01G208600 chr3A 94.231 52 3 0 1417 1468 500862217 500862166 4.150000e-11 80.5
80 TraesCS2A01G208600 chr3A 94.231 52 3 0 1417 1468 500870268 500870217 4.150000e-11 80.5
81 TraesCS2A01G208600 chr3A 100.000 35 0 0 1266 1300 140079194 140079228 1.160000e-06 65.8
82 TraesCS2A01G208600 chr3A 93.023 43 1 2 1257 1297 140087379 140087421 1.500000e-05 62.1
83 TraesCS2A01G208600 chr3D 84.755 2532 291 79 1776 4267 327290115 327292591 0.000000e+00 2449.0
84 TraesCS2A01G208600 chr3D 89.346 413 44 0 4268 4680 523439701 523439289 2.060000e-143 520.0
85 TraesCS2A01G208600 chr3D 88.889 414 45 1 4268 4680 287716034 287715621 4.460000e-140 508.0
86 TraesCS2A01G208600 chr7B 85.687 2082 217 61 2219 4265 386489995 386487960 0.000000e+00 2119.0
87 TraesCS2A01G208600 chr7B 82.416 745 93 21 4268 4996 368571939 368572661 2.560000e-172 616.0
88 TraesCS2A01G208600 chr4B 83.355 2289 265 93 1690 3900 127552076 127554326 0.000000e+00 2010.0
89 TraesCS2A01G208600 chr4B 83.246 2286 267 94 1690 3900 127560120 127562364 0.000000e+00 1993.0
90 TraesCS2A01G208600 chr4B 81.295 278 38 13 413 683 306390918 306391188 3.920000e-51 213.0
91 TraesCS2A01G208600 chr4B 79.655 290 42 15 401 682 173656889 173657169 5.100000e-45 193.0
92 TraesCS2A01G208600 chr4B 78.457 311 46 15 410 704 479933241 479932936 3.070000e-42 183.0
93 TraesCS2A01G208600 chr4B 74.419 344 63 22 411 738 195574606 195574940 1.890000e-24 124.0
94 TraesCS2A01G208600 chr4B 79.375 160 30 3 401 559 359812760 359812603 5.290000e-20 110.0
95 TraesCS2A01G208600 chr4B 80.851 141 23 4 421 558 195532175 195532314 1.900000e-19 108.0
96 TraesCS2A01G208600 chr4B 91.525 59 4 1 691 748 206435147 206435205 4.150000e-11 80.5
97 TraesCS2A01G208600 chr1B 82.780 2288 271 97 1690 3900 278840615 278838374 0.000000e+00 1929.0
98 TraesCS2A01G208600 chr1B 82.058 719 104 18 4299 4996 157223060 157223774 1.550000e-164 590.0
99 TraesCS2A01G208600 chr1B 96.203 79 2 1 606 683 502176365 502176287 1.460000e-25 128.0
100 TraesCS2A01G208600 chr1B 73.837 344 62 22 411 738 236970315 236970646 1.470000e-20 111.0
101 TraesCS2A01G208600 chr1B 91.525 59 4 1 691 748 185595069 185595127 4.150000e-11 80.5
102 TraesCS2A01G208600 chr1B 89.831 59 5 1 691 748 185588208 185588266 1.930000e-09 75.0
103 TraesCS2A01G208600 chr1B 92.500 40 2 1 1760 1799 259882504 259882542 6.990000e-04 56.5
104 TraesCS2A01G208600 chr1B 96.970 33 1 0 1760 1792 479858735 479858703 6.990000e-04 56.5
105 TraesCS2A01G208600 chr1B 92.500 40 2 1 1760 1799 479881114 479881076 6.990000e-04 56.5
106 TraesCS2A01G208600 chr4A 88.925 921 68 15 405 1300 355574199 355573288 0.000000e+00 1105.0
107 TraesCS2A01G208600 chr4A 89.231 910 58 20 419 1300 355554658 355553761 0.000000e+00 1101.0
108 TraesCS2A01G208600 chr4A 87.500 104 10 3 1365 1468 313685778 313685678 3.160000e-22 117.0
109 TraesCS2A01G208600 chrUn 85.575 617 79 9 1 612 764936 764325 5.450000e-179 638.0
110 TraesCS2A01G208600 chrUn 87.659 551 60 8 1 546 348399441 348399988 7.060000e-178 634.0
111 TraesCS2A01G208600 chrUn 87.818 550 55 8 1 547 448869773 448870313 7.060000e-178 634.0
112 TraesCS2A01G208600 chrUn 87.146 529 62 6 1 526 305486051 305485526 3.330000e-166 595.0
113 TraesCS2A01G208600 chrUn 85.409 562 74 7 1 559 47106215 47105659 1.210000e-160 577.0
114 TraesCS2A01G208600 chrUn 85.336 566 70 11 1 559 52908663 52909222 1.560000e-159 573.0
115 TraesCS2A01G208600 chrUn 85.310 565 71 11 1 559 380607724 380607166 1.560000e-159 573.0
116 TraesCS2A01G208600 chrUn 84.534 569 78 8 1 565 336293363 336293925 5.650000e-154 555.0
117 TraesCS2A01G208600 chrUn 87.247 494 52 8 1 492 429590412 429589928 2.030000e-153 553.0
118 TraesCS2A01G208600 chrUn 84.629 566 74 11 1 559 52916754 52917313 7.310000e-153 551.0
119 TraesCS2A01G208600 chrUn 84.348 575 77 12 1 572 279452078 279451514 7.310000e-153 551.0
120 TraesCS2A01G208600 chrUn 80.435 184 30 6 377 559 404294271 404294093 8.720000e-28 135.0
121 TraesCS2A01G208600 chrUn 96.875 32 0 1 729 760 62292434 62292464 9.000000e-03 52.8
122 TraesCS2A01G208600 chr5D 83.595 701 93 13 4298 4996 171173313 171173993 5.450000e-179 638.0
123 TraesCS2A01G208600 chr5D 96.178 314 12 0 4683 4996 122594267 122594580 9.590000e-142 514.0
124 TraesCS2A01G208600 chr5D 88.889 414 45 1 4268 4680 506069285 506069698 4.460000e-140 508.0
125 TraesCS2A01G208600 chr5D 79.443 287 47 11 401 683 30068616 30068338 5.100000e-45 193.0
126 TraesCS2A01G208600 chr5D 75.896 307 50 17 412 698 399020483 399020785 8.720000e-28 135.0
127 TraesCS2A01G208600 chr5D 75.649 308 52 14 410 698 399028147 399028450 1.130000e-26 132.0
128 TraesCS2A01G208600 chr2D 91.283 413 36 0 4268 4680 325860353 325859941 9.390000e-157 564.0
129 TraesCS2A01G208600 chr2D 90.097 414 39 2 4268 4680 441597616 441598028 2.050000e-148 536.0
130 TraesCS2A01G208600 chr2D 89.209 417 45 0 4268 4684 495636236 495636652 5.730000e-144 521.0
131 TraesCS2A01G208600 chr2D 88.729 417 46 1 4268 4683 325840515 325840099 4.460000e-140 508.0
132 TraesCS2A01G208600 chr2D 88.889 414 44 2 4268 4680 385974335 385974747 4.460000e-140 508.0
133 TraesCS2A01G208600 chr2D 80.139 287 45 11 401 683 438302593 438302871 2.360000e-48 204.0
134 TraesCS2A01G208600 chr2D 79.649 285 49 9 402 683 438295109 438295387 3.950000e-46 196.0
135 TraesCS2A01G208600 chr6D 96.166 313 12 0 4684 4996 93799599 93799911 3.450000e-141 512.0
136 TraesCS2A01G208600 chr6D 96.166 313 12 0 4684 4996 141310131 141309819 3.450000e-141 512.0
137 TraesCS2A01G208600 chr6D 96.166 313 12 0 4684 4996 276685604 276685292 3.450000e-141 512.0
138 TraesCS2A01G208600 chr5B 79.520 708 122 15 4295 4996 443092934 443092244 2.700000e-132 483.0
139 TraesCS2A01G208600 chr5B 91.525 59 4 1 691 748 443886743 443886685 4.150000e-11 80.5
140 TraesCS2A01G208600 chr7D 81.227 277 44 8 410 683 470535247 470535518 3.030000e-52 217.0
141 TraesCS2A01G208600 chr1D 80.866 277 45 8 410 683 144771701 144771430 1.410000e-50 211.0
142 TraesCS2A01G208600 chr1D 80.505 277 46 8 410 683 144779422 144779151 6.560000e-49 206.0
143 TraesCS2A01G208600 chr1D 78.041 296 43 15 419 698 386798769 386799058 3.090000e-37 167.0
144 TraesCS2A01G208600 chr1D 77.023 309 46 18 405 698 386806763 386807061 2.410000e-33 154.0
145 TraesCS2A01G208600 chr1D 80.435 184 30 6 377 559 246493272 246493094 8.720000e-28 135.0
146 TraesCS2A01G208600 chr1D 80.435 184 30 6 377 559 246504277 246504099 8.720000e-28 135.0
147 TraesCS2A01G208600 chr4D 92.308 78 6 0 606 683 154203666 154203743 1.470000e-20 111.0
148 TraesCS2A01G208600 chr4D 86.275 102 11 3 606 704 154221273 154221374 1.900000e-19 108.0
149 TraesCS2A01G208600 chr6B 80.132 151 26 4 411 558 262703386 262703535 5.290000e-20 110.0
150 TraesCS2A01G208600 chr6B 79.605 152 28 3 405 555 522256151 522256002 6.840000e-19 106.0


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 TraesCS2A01G208600 chr2A 191619438 191624433 4995 True 9226.00 9226 100.000 1 4996 1 chr2A.!!$R1 4995
1 TraesCS2A01G208600 chr2A 316869782 316872177 2395 True 3005.00 3005 89.476 1880 4267 1 chr2A.!!$R2 2387
2 TraesCS2A01G208600 chr2A 324314204 324316521 2317 False 2608.00 2608 87.171 1950 4267 1 chr2A.!!$F4 2317
3 TraesCS2A01G208600 chr2A 317029652 317030980 1328 True 1781.00 1781 91.058 1880 3198 1 chr2A.!!$R3 1318
4 TraesCS2A01G208600 chr2A 427936674 427937361 687 False 776.00 776 86.981 1 698 1 chr2A.!!$F5 697
5 TraesCS2A01G208600 chr2A 98444156 98444853 697 False 747.00 747 86.099 1 698 1 chr2A.!!$F1 697
6 TraesCS2A01G208600 chr2A 287489873 287490600 727 False 610.00 610 82.065 4268 4991 1 chr2A.!!$F3 723
7 TraesCS2A01G208600 chr5A 151317989 151320356 2367 True 3151.00 3151 90.807 1903 4267 1 chr5A.!!$R3 2364
8 TraesCS2A01G208600 chr5A 508035367 508037585 2218 False 2536.00 2536 87.396 2015 4264 1 chr5A.!!$F4 2249
9 TraesCS2A01G208600 chr5A 453047434 453048127 693 False 776.00 776 86.857 1 698 1 chr5A.!!$F3 697
10 TraesCS2A01G208600 chr5A 453039644 453040337 693 False 754.00 754 86.286 1 698 1 chr5A.!!$F2 697
11 TraesCS2A01G208600 chr5A 166669968 166670647 679 True 697.00 697 85.277 4 683 1 chr5A.!!$R4 679
12 TraesCS2A01G208600 chr7A 424696130 424698499 2369 False 3110.00 3110 90.492 1901 4267 1 chr7A.!!$F4 2366
13 TraesCS2A01G208600 chr7A 381605777 381607951 2174 False 2588.00 2588 88.281 2087 4267 1 chr7A.!!$F2 2180
14 TraesCS2A01G208600 chr7A 450452364 450454388 2024 True 2128.00 2128 85.887 2244 4269 1 chr7A.!!$R2 2025
15 TraesCS2A01G208600 chr7A 450456070 450458073 2003 False 2097.00 2097 85.791 2244 4255 1 chr7A.!!$F5 2011
16 TraesCS2A01G208600 chr7A 615702388 615703076 688 False 771.00 771 86.838 1 698 1 chr7A.!!$F7 697
17 TraesCS2A01G208600 chr7A 615710154 615710842 688 False 749.00 749 86.305 1 698 1 chr7A.!!$F8 697
18 TraesCS2A01G208600 chr6A 340057943 340060812 2869 True 2575.00 2575 83.534 1475 4267 1 chr6A.!!$R7 2792
19 TraesCS2A01G208600 chr6A 425476160 425479765 3605 False 1577.50 2996 93.291 604 4267 2 chr6A.!!$F8 3663
20 TraesCS2A01G208600 chr6A 107852257 107852950 693 False 809.00 809 87.732 1 698 1 chr6A.!!$F1 697
21 TraesCS2A01G208600 chr6A 425483823 425484520 697 False 785.00 785 87.055 1 698 1 chr6A.!!$F5 697
22 TraesCS2A01G208600 chr6A 405545802 405546364 562 True 693.00 693 88.908 1 566 1 chr6A.!!$R10 565
23 TraesCS2A01G208600 chr6A 405578959 405579521 562 True 682.00 682 88.556 1 566 1 chr6A.!!$R11 565
24 TraesCS2A01G208600 chr6A 257963331 257963923 592 True 654.00 654 86.622 1 595 1 chr6A.!!$R4 594
25 TraesCS2A01G208600 chr6A 417452696 417453303 607 False 651.00 651 86.039 1 612 1 chr6A.!!$F3 611
26 TraesCS2A01G208600 chr6A 417477909 417478487 578 False 651.00 651 87.009 1 582 1 chr6A.!!$F4 581
27 TraesCS2A01G208600 chr6A 85855972 85856651 679 True 645.00 645 84.029 1 684 1 chr6A.!!$R1 683
28 TraesCS2A01G208600 chr1A 405934255 405937036 2781 True 1359.75 2663 85.279 1475 4267 2 chr1A.!!$R7 2792
29 TraesCS2A01G208600 chr1A 291309495 291310424 929 False 1258.00 1258 91.622 401 1300 1 chr1A.!!$F7 899
30 TraesCS2A01G208600 chr1A 482970755 482971311 556 False 664.00 664 88.214 2 559 1 chr1A.!!$F10 557
31 TraesCS2A01G208600 chr1A 320916197 320916808 611 False 662.00 662 86.312 1 614 1 chr1A.!!$F8 613
32 TraesCS2A01G208600 chr1A 70740651 70741207 556 False 660.00 660 88.036 1 559 1 chr1A.!!$F2 558
33 TraesCS2A01G208600 chr1A 322088558 322089111 553 True 654.00 654 88.014 1 557 1 chr1A.!!$R5 556
34 TraesCS2A01G208600 chr1A 144482442 144483035 593 True 651.00 651 86.500 1 596 1 chr1A.!!$R2 595
35 TraesCS2A01G208600 chr1A 267378340 267378946 606 False 643.00 643 85.877 1 612 1 chr1A.!!$F6 611
36 TraesCS2A01G208600 chr1A 536248408 536248966 558 False 640.00 640 87.411 1 559 1 chr1A.!!$F11 558
37 TraesCS2A01G208600 chr1A 70733086 70733642 556 False 638.00 638 87.321 1 559 1 chr1A.!!$F1 558
38 TraesCS2A01G208600 chr1A 229647432 229647997 565 True 636.00 636 86.957 1 573 1 chr1A.!!$R4 572
39 TraesCS2A01G208600 chr1A 144474533 144475127 594 True 628.00 628 85.833 1 596 1 chr1A.!!$R1 595
40 TraesCS2A01G208600 chr1A 181083560 181084169 609 True 628.00 628 85.366 2 612 1 chr1A.!!$R3 610
41 TraesCS2A01G208600 chr1A 411279147 411279827 680 True 628.00 628 83.550 1 684 1 chr1A.!!$R6 683
42 TraesCS2A01G208600 chr3A 239573049 239575392 2343 True 2649.00 2649 87.176 1902 4267 1 chr3A.!!$R2 2365
43 TraesCS2A01G208600 chr3A 239580874 239583219 2345 True 2623.00 2623 86.984 1902 4267 1 chr3A.!!$R3 2365
44 TraesCS2A01G208600 chr3A 255353820 255354752 932 False 1227.00 1227 91.006 401 1300 1 chr3A.!!$F3 899
45 TraesCS2A01G208600 chr3A 255376159 255377061 902 False 1138.00 1138 89.696 401 1300 1 chr3A.!!$F4 899
46 TraesCS2A01G208600 chr3A 438871969 438872661 692 True 819.00 819 87.966 1 698 1 chr3A.!!$R5 697
47 TraesCS2A01G208600 chr3D 327290115 327292591 2476 False 2449.00 2449 84.755 1776 4267 1 chr3D.!!$F1 2491
48 TraesCS2A01G208600 chr7B 386487960 386489995 2035 True 2119.00 2119 85.687 2219 4265 1 chr7B.!!$R1 2046
49 TraesCS2A01G208600 chr7B 368571939 368572661 722 False 616.00 616 82.416 4268 4996 1 chr7B.!!$F1 728
50 TraesCS2A01G208600 chr4B 127552076 127554326 2250 False 2010.00 2010 83.355 1690 3900 1 chr4B.!!$F1 2210
51 TraesCS2A01G208600 chr4B 127560120 127562364 2244 False 1993.00 1993 83.246 1690 3900 1 chr4B.!!$F2 2210
52 TraesCS2A01G208600 chr1B 278838374 278840615 2241 True 1929.00 1929 82.780 1690 3900 1 chr1B.!!$R1 2210
53 TraesCS2A01G208600 chr1B 157223060 157223774 714 False 590.00 590 82.058 4299 4996 1 chr1B.!!$F1 697
54 TraesCS2A01G208600 chr4A 355573288 355574199 911 True 1105.00 1105 88.925 405 1300 1 chr4A.!!$R3 895
55 TraesCS2A01G208600 chr4A 355553761 355554658 897 True 1101.00 1101 89.231 419 1300 1 chr4A.!!$R2 881
56 TraesCS2A01G208600 chrUn 764325 764936 611 True 638.00 638 85.575 1 612 1 chrUn.!!$R1 611
57 TraesCS2A01G208600 chrUn 348399441 348399988 547 False 634.00 634 87.659 1 546 1 chrUn.!!$F5 545
58 TraesCS2A01G208600 chrUn 448869773 448870313 540 False 634.00 634 87.818 1 547 1 chrUn.!!$F6 546
59 TraesCS2A01G208600 chrUn 305485526 305486051 525 True 595.00 595 87.146 1 526 1 chrUn.!!$R4 525
60 TraesCS2A01G208600 chrUn 47105659 47106215 556 True 577.00 577 85.409 1 559 1 chrUn.!!$R2 558
61 TraesCS2A01G208600 chrUn 52908663 52909222 559 False 573.00 573 85.336 1 559 1 chrUn.!!$F1 558
62 TraesCS2A01G208600 chrUn 380607166 380607724 558 True 573.00 573 85.310 1 559 1 chrUn.!!$R5 558
63 TraesCS2A01G208600 chrUn 336293363 336293925 562 False 555.00 555 84.534 1 565 1 chrUn.!!$F4 564
64 TraesCS2A01G208600 chrUn 52916754 52917313 559 False 551.00 551 84.629 1 559 1 chrUn.!!$F2 558
65 TraesCS2A01G208600 chrUn 279451514 279452078 564 True 551.00 551 84.348 1 572 1 chrUn.!!$R3 571
66 TraesCS2A01G208600 chr5D 171173313 171173993 680 False 638.00 638 83.595 4298 4996 1 chr5D.!!$F2 698
67 TraesCS2A01G208600 chr5B 443092244 443092934 690 True 483.00 483 79.520 4295 4996 1 chr5B.!!$R1 701


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
846 1014 1.135333 CTACCTCCTTCAACCTCGCTC 59.865 57.143 0.0 0.0 0.0 5.03 F
1404 1671 0.106149 ACGTCCCCTATTTCGCATCC 59.894 55.000 0.0 0.0 0.0 3.51 F
2554 3083 0.383949 TGCTTCTTTTCGGTGTTGCC 59.616 50.000 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 2227 0.877743 GGGCTGAAACTGAACTGAGC 59.122 55.000 0.00 0.0 0.00 4.26 R
2736 3294 1.063038 TGGCAATATGGGAGGCATTGT 60.063 47.619 0.00 0.0 33.22 2.71 R
4364 5082 0.035056 ATAAAGAGGCAAGCGCAGGT 60.035 50.000 11.47 0.0 41.24 4.00 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
134 147 8.823220 ATAGTGTTTTATAAGTGGCTGGAAAT 57.177 30.769 0.00 0.00 0.00 2.17
162 175 1.970640 GGAATGGGTTGAAAGTTGGCT 59.029 47.619 0.00 0.00 0.00 4.75
496 527 5.476599 TCCCCAAACATCTACAAAACATCTG 59.523 40.000 0.00 0.00 0.00 2.90
768 936 4.735132 AGCAGCCTCGCGCGTAAA 62.735 61.111 30.98 9.98 44.76 2.01
846 1014 1.135333 CTACCTCCTTCAACCTCGCTC 59.865 57.143 0.00 0.00 0.00 5.03
942 1129 1.329292 CTCTCTACCGTTGCTCTCTCG 59.671 57.143 0.00 0.00 0.00 4.04
1080 1324 2.052690 CCGTGACCCTGATCCGACT 61.053 63.158 0.00 0.00 0.00 4.18
1081 1325 1.139734 CGTGACCCTGATCCGACTG 59.860 63.158 0.00 0.00 0.00 3.51
1082 1326 1.517832 GTGACCCTGATCCGACTGG 59.482 63.158 0.00 0.00 0.00 4.00
1084 1328 2.284625 ACCCTGATCCGACTGGCA 60.285 61.111 0.00 0.00 34.14 4.92
1086 1330 2.362369 CCCTGATCCGACTGGCACT 61.362 63.158 0.00 0.00 34.14 4.40
1087 1331 1.142748 CCTGATCCGACTGGCACTC 59.857 63.158 0.00 0.00 34.14 3.51
1315 1582 4.643387 GCGACACCACCCCAAGCT 62.643 66.667 0.00 0.00 0.00 3.74
1316 1583 2.669569 CGACACCACCCCAAGCTG 60.670 66.667 0.00 0.00 0.00 4.24
1317 1584 2.985847 GACACCACCCCAAGCTGC 60.986 66.667 0.00 0.00 0.00 5.25
1318 1585 3.497884 GACACCACCCCAAGCTGCT 62.498 63.158 0.00 0.00 0.00 4.24
1319 1586 2.674380 CACCACCCCAAGCTGCTC 60.674 66.667 1.00 0.00 0.00 4.26
1320 1587 3.971702 ACCACCCCAAGCTGCTCC 61.972 66.667 1.00 0.00 0.00 4.70
1348 1615 4.838152 CATGGACGGCCCCGACAG 62.838 72.222 14.44 0.00 42.83 3.51
1360 1627 4.749310 CGACAGCCGCTTGGAGCT 62.749 66.667 0.00 0.00 39.60 4.09
1361 1628 2.817396 GACAGCCGCTTGGAGCTC 60.817 66.667 4.71 4.71 39.60 4.09
1362 1629 4.749310 ACAGCCGCTTGGAGCTCG 62.749 66.667 7.83 0.00 39.60 5.03
1394 1661 3.449227 CTCGCTGCACGTCCCCTA 61.449 66.667 0.00 0.00 44.19 3.53
1395 1662 2.758327 TCGCTGCACGTCCCCTAT 60.758 61.111 0.00 0.00 44.19 2.57
1396 1663 2.186903 CGCTGCACGTCCCCTATT 59.813 61.111 0.00 0.00 36.87 1.73
1397 1664 1.449601 CGCTGCACGTCCCCTATTT 60.450 57.895 0.00 0.00 36.87 1.40
1398 1665 1.429148 CGCTGCACGTCCCCTATTTC 61.429 60.000 0.00 0.00 36.87 2.17
1399 1666 1.429148 GCTGCACGTCCCCTATTTCG 61.429 60.000 0.00 0.00 0.00 3.46
1400 1667 1.429148 CTGCACGTCCCCTATTTCGC 61.429 60.000 0.00 0.00 0.00 4.70
1401 1668 1.448893 GCACGTCCCCTATTTCGCA 60.449 57.895 0.00 0.00 0.00 5.10
1402 1669 0.814010 GCACGTCCCCTATTTCGCAT 60.814 55.000 0.00 0.00 0.00 4.73
1403 1670 1.217882 CACGTCCCCTATTTCGCATC 58.782 55.000 0.00 0.00 0.00 3.91
1404 1671 0.106149 ACGTCCCCTATTTCGCATCC 59.894 55.000 0.00 0.00 0.00 3.51
1405 1672 0.602905 CGTCCCCTATTTCGCATCCC 60.603 60.000 0.00 0.00 0.00 3.85
1406 1673 0.602905 GTCCCCTATTTCGCATCCCG 60.603 60.000 0.00 0.00 38.61 5.14
1407 1674 1.966451 CCCCTATTTCGCATCCCGC 60.966 63.158 0.00 0.00 36.73 6.13
1423 1690 4.443266 GCGCCGAGCTCCTCAAGT 62.443 66.667 8.47 0.00 44.04 3.16
1424 1691 2.262915 CGCCGAGCTCCTCAAGTT 59.737 61.111 8.47 0.00 0.00 2.66
1425 1692 1.807573 CGCCGAGCTCCTCAAGTTC 60.808 63.158 8.47 0.00 32.22 3.01
1426 1693 1.448717 GCCGAGCTCCTCAAGTTCC 60.449 63.158 8.47 0.00 31.88 3.62
1427 1694 1.153745 CCGAGCTCCTCAAGTTCCG 60.154 63.158 8.47 0.00 31.88 4.30
1428 1695 1.807573 CGAGCTCCTCAAGTTCCGC 60.808 63.158 8.47 0.00 31.88 5.54
1429 1696 1.807573 GAGCTCCTCAAGTTCCGCG 60.808 63.158 0.87 0.00 0.00 6.46
1430 1697 2.048127 GCTCCTCAAGTTCCGCGT 60.048 61.111 4.92 0.00 0.00 6.01
1431 1698 2.095252 GCTCCTCAAGTTCCGCGTC 61.095 63.158 4.92 0.00 0.00 5.19
1432 1699 1.446272 CTCCTCAAGTTCCGCGTCC 60.446 63.158 4.92 0.00 0.00 4.79
1433 1700 2.809601 CCTCAAGTTCCGCGTCCG 60.810 66.667 4.92 0.00 0.00 4.79
1434 1701 3.479269 CTCAAGTTCCGCGTCCGC 61.479 66.667 4.92 0.68 37.85 5.54
1453 1720 3.127533 GTGGCCGTGGAGCACATC 61.128 66.667 0.00 0.00 33.40 3.06
1454 1721 4.758251 TGGCCGTGGAGCACATCG 62.758 66.667 0.00 0.00 33.40 3.84
1459 1726 3.188786 GTGGAGCACATCGGCGTC 61.189 66.667 6.85 0.00 39.27 5.19
1460 1727 4.794439 TGGAGCACATCGGCGTCG 62.794 66.667 1.15 1.15 39.27 5.12
1461 1728 4.796231 GGAGCACATCGGCGTCGT 62.796 66.667 10.18 1.93 39.27 4.34
1462 1729 3.248171 GAGCACATCGGCGTCGTC 61.248 66.667 10.18 0.00 39.27 4.20
1463 1730 4.796231 AGCACATCGGCGTCGTCC 62.796 66.667 10.18 0.00 39.27 4.79
1464 1731 4.796231 GCACATCGGCGTCGTCCT 62.796 66.667 10.18 0.00 37.69 3.85
1465 1732 2.579787 CACATCGGCGTCGTCCTC 60.580 66.667 10.18 0.00 37.69 3.71
1466 1733 4.175489 ACATCGGCGTCGTCCTCG 62.175 66.667 10.18 0.00 37.69 4.63
1473 1740 4.592936 CGTCGTCCTCGCTAGCGG 62.593 72.222 34.76 24.53 40.25 5.52
1474 1741 4.908877 GTCGTCCTCGCTAGCGGC 62.909 72.222 34.76 20.95 40.25 6.53
1506 1773 0.405198 TGCTTCCCTGCTCCAAATCA 59.595 50.000 0.00 0.00 0.00 2.57
1508 1775 1.203287 GCTTCCCTGCTCCAAATCAAC 59.797 52.381 0.00 0.00 0.00 3.18
1514 1781 1.879380 CTGCTCCAAATCAACCGTCAA 59.121 47.619 0.00 0.00 0.00 3.18
1522 1789 2.765250 ATCAACCGTCAAGCGTCGCT 62.765 55.000 15.47 15.47 42.56 4.93
1639 1997 0.671781 TCGCCTCTTCTGCTTCAAGC 60.672 55.000 1.04 1.04 42.82 4.01
1641 1999 0.607489 GCCTCTTCTGCTTCAAGCCA 60.607 55.000 7.01 0.00 41.51 4.75
1667 2025 1.153369 CGCATCGATGGTGGAGGTT 60.153 57.895 26.00 0.00 0.00 3.50
1676 2034 2.886124 GTGGAGGTTAGCGCGCTC 60.886 66.667 40.23 24.65 0.00 5.03
1711 2069 4.162690 GCCCGCTCGATTCCCTGT 62.163 66.667 0.00 0.00 0.00 4.00
1740 2098 3.801997 CTGGAGCCGGCCCATCTT 61.802 66.667 29.49 10.19 32.49 2.40
1811 2231 2.041508 CTCCCCTAGCCCAGCTCA 60.042 66.667 0.00 0.00 40.44 4.26
1813 2233 2.366167 CCCCTAGCCCAGCTCAGT 60.366 66.667 0.00 0.00 40.44 3.41
1814 2234 1.997874 CCCCTAGCCCAGCTCAGTT 60.998 63.158 0.00 0.00 40.44 3.16
1866 2368 5.376537 GCTGCTGCAAATTTGACAAATAAC 58.623 37.500 22.31 7.20 39.41 1.89
1868 2370 5.363101 TGCTGCAAATTTGACAAATAACCA 58.637 33.333 22.31 9.63 0.00 3.67
1869 2371 5.466058 TGCTGCAAATTTGACAAATAACCAG 59.534 36.000 22.31 17.56 0.00 4.00
1934 2438 4.685169 AATAACTCTCAAACCGTGCATG 57.315 40.909 0.00 0.00 0.00 4.06
2214 2725 3.751698 GGCAGAACAGTACCAAACCTAAG 59.248 47.826 0.00 0.00 0.00 2.18
2377 2899 9.256228 AGAGAGAACTAAATAAGTCATGTGGTA 57.744 33.333 0.00 0.00 37.50 3.25
2397 2919 8.243426 TGTGGTATTTTCTTCAATATGCAACTC 58.757 33.333 0.00 0.00 0.00 3.01
2554 3083 0.383949 TGCTTCTTTTCGGTGTTGCC 59.616 50.000 0.00 0.00 0.00 4.52
2735 3293 4.122776 CTGCGATACCTATCACTTGCTTT 58.877 43.478 0.00 0.00 32.98 3.51
2736 3294 5.270893 TGCGATACCTATCACTTGCTTTA 57.729 39.130 0.00 0.00 32.98 1.85
2738 3296 5.047847 GCGATACCTATCACTTGCTTTACA 58.952 41.667 0.00 0.00 32.98 2.41
2992 3592 2.281484 GTTCCACTCTTGCCGCCA 60.281 61.111 0.00 0.00 0.00 5.69
3188 3797 6.761714 TCTCGAGGGTCATCTTTATTTTAAGC 59.238 38.462 13.56 0.00 0.00 3.09
3189 3798 5.820947 TCGAGGGTCATCTTTATTTTAAGCC 59.179 40.000 0.00 0.00 0.00 4.35
3190 3799 5.008712 CGAGGGTCATCTTTATTTTAAGCCC 59.991 44.000 0.00 0.00 0.00 5.19
3224 3839 3.002656 CAGTGCTTGTCTAAGTGTTGGTG 59.997 47.826 0.00 0.00 36.27 4.17
3331 3949 2.428530 AGAACGAGATATGTGCAGCTCA 59.571 45.455 0.00 0.00 0.00 4.26
3351 3973 2.763627 TATCGGGATGTCGGCGCATG 62.764 60.000 18.71 0.00 0.00 4.06
3417 4044 1.187087 ACCAGGATTCCGAGTCTGAC 58.813 55.000 0.00 0.00 0.00 3.51
3729 4368 0.305313 GTTTACGACCGTGCTTTGCA 59.695 50.000 5.20 0.00 35.60 4.08
3731 4370 0.793861 TTACGACCGTGCTTTGCATC 59.206 50.000 5.20 0.00 41.91 3.91
3732 4371 0.037697 TACGACCGTGCTTTGCATCT 60.038 50.000 5.20 0.00 41.91 2.90
3733 4372 1.291877 ACGACCGTGCTTTGCATCTC 61.292 55.000 0.00 0.00 41.91 2.75
3736 4375 0.674895 ACCGTGCTTTGCATCTCCTC 60.675 55.000 0.00 0.00 41.91 3.71
3737 4376 0.392193 CCGTGCTTTGCATCTCCTCT 60.392 55.000 0.00 0.00 41.91 3.69
3738 4377 1.005340 CGTGCTTTGCATCTCCTCTC 58.995 55.000 0.00 0.00 41.91 3.20
3743 4382 2.431782 GCTTTGCATCTCCTCTCTCTCT 59.568 50.000 0.00 0.00 0.00 3.10
3924 4585 1.347062 TGATACCAGTGCAGGTGACA 58.653 50.000 7.87 5.23 43.14 3.58
3927 4588 0.392706 TACCAGTGCAGGTGACACAG 59.607 55.000 8.08 0.21 43.14 3.66
4009 4671 0.965866 CAGTAGTGGAGCCCAGTCGA 60.966 60.000 4.98 0.00 38.30 4.20
4181 4889 7.987458 CAGTACATGGGATGTGTAAAGATTACT 59.013 37.037 0.00 0.00 44.60 2.24
4255 4965 1.550524 GTGGGAGATATAGCCGCATCA 59.449 52.381 0.00 0.00 0.00 3.07
4343 5061 2.752903 GCACCGATATGGAAACCTTTGT 59.247 45.455 0.00 0.00 42.00 2.83
4350 5068 5.586243 CGATATGGAAACCTTTGTCTGATGT 59.414 40.000 0.00 0.00 0.00 3.06
4364 5082 0.331616 TGATGTCTCGGGACTCCTCA 59.668 55.000 17.97 13.59 42.54 3.86
4383 5102 0.035056 ACCTGCGCTTGCCTCTTTAT 60.035 50.000 9.73 0.00 38.03 1.40
4387 5106 1.339055 TGCGCTTGCCTCTTTATCACT 60.339 47.619 9.73 0.00 38.03 3.41
4402 5121 7.974504 TCTTTATCACTAAAGAGGAAACTGGT 58.025 34.615 4.18 0.00 44.97 4.00
4405 5124 5.130292 TCACTAAAGAGGAAACTGGTACG 57.870 43.478 0.00 0.00 44.43 3.67
4442 5172 4.394712 CCTGGCCCTGGTCGTCAC 62.395 72.222 0.00 0.00 0.00 3.67
4462 5192 1.601914 CGACTCATGTCACGTGAACCA 60.602 52.381 21.95 15.69 43.06 3.67
4463 5193 2.688507 GACTCATGTCACGTGAACCAT 58.311 47.619 21.95 17.35 42.48 3.55
4494 5224 1.002888 CCCTGCATTGATATCTCCGCT 59.997 52.381 3.98 0.00 0.00 5.52
4511 5242 1.153989 CTCCTCGGGAGCCATCCTA 59.846 63.158 6.97 0.00 43.29 2.94
4515 5246 0.757188 CTCGGGAGCCATCCTAGTGT 60.757 60.000 0.00 0.00 45.85 3.55
4527 5258 3.329889 TAGTGTGGCTGCCCCAGG 61.330 66.667 17.53 0.00 46.54 4.45
4551 5284 3.263503 CTTCGTGTCGTCCGCCTCA 62.264 63.158 0.00 0.00 0.00 3.86
4583 5316 1.030488 CCTCGCGAGGGTCTTGAGTA 61.030 60.000 41.47 0.61 44.87 2.59
4593 5326 2.037251 GGGTCTTGAGTAGTTGCTGTCA 59.963 50.000 0.00 0.00 0.00 3.58
4654 5387 2.300967 CCCCAGGCAGGCAAGTCTA 61.301 63.158 0.00 0.00 35.39 2.59
4657 5390 1.451028 CAGGCAGGCAAGTCTAGGC 60.451 63.158 0.00 0.00 0.00 3.93
4680 5413 2.202932 CGTTCCCAGGATGCCGAG 60.203 66.667 0.00 0.00 31.97 4.63
4682 5418 1.602237 GTTCCCAGGATGCCGAGAA 59.398 57.895 0.00 0.00 31.97 2.87
4806 5543 3.430098 GGAGACACCTGTAGAGCATCTTG 60.430 52.174 0.00 0.00 40.44 3.02
4808 5545 7.625481 GGAGACACCTGTAGAGCATCTTGAC 62.625 52.000 0.00 0.00 40.44 3.18
4879 5616 4.562082 CGGTATTCGGGAGTTGCATAATA 58.438 43.478 0.00 0.00 34.75 0.98
4887 5624 7.712204 TCGGGAGTTGCATAATATCATAGTA 57.288 36.000 0.00 0.00 0.00 1.82
4929 5666 7.065563 AGTCATGAAGAAAGCAGTAGCAATAAG 59.934 37.037 0.00 0.00 45.49 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 126 8.088365 AGAACAATTTCCAGCCACTTATAAAAC 58.912 33.333 0.00 0.00 31.28 2.43
134 147 2.940994 TCAACCCATTCCGAGAACAA 57.059 45.000 0.00 0.00 0.00 2.83
162 175 6.720112 ACCTACACTATAATAAGACCGCAA 57.280 37.500 0.00 0.00 0.00 4.85
765 933 1.988015 CTTGGGCTCGGGAGGTTTA 59.012 57.895 0.00 0.00 0.00 2.01
942 1129 2.237534 GAGGTGAGGTGCTGGAGAGC 62.238 65.000 0.00 0.00 46.44 4.09
1023 1251 3.770040 CGGTGAGGATCCACGGCA 61.770 66.667 15.82 3.46 37.91 5.69
1065 1293 2.359169 GCCAGTCGGATCAGGGTCA 61.359 63.158 0.00 0.00 0.00 4.02
1071 1315 2.710902 CGGAGTGCCAGTCGGATCA 61.711 63.158 1.04 0.00 0.00 2.92
1124 1388 4.719369 GGGCGACGTGAGCGAAGT 62.719 66.667 0.00 0.00 42.00 3.01
1300 1567 2.985847 GCAGCTTGGGGTGGTGTC 60.986 66.667 0.00 0.00 40.85 3.67
1331 1598 4.838152 CTGTCGGGGCCGTCCATG 62.838 72.222 0.00 0.00 40.74 3.66
1377 1644 2.298158 AATAGGGGACGTGCAGCGAG 62.298 60.000 9.96 0.00 44.77 5.03
1378 1645 1.895020 AAATAGGGGACGTGCAGCGA 61.895 55.000 9.96 0.00 44.77 4.93
1380 1647 1.429148 CGAAATAGGGGACGTGCAGC 61.429 60.000 9.96 0.00 0.00 5.25
1381 1648 1.429148 GCGAAATAGGGGACGTGCAG 61.429 60.000 9.96 0.00 0.00 4.41
1382 1649 1.448893 GCGAAATAGGGGACGTGCA 60.449 57.895 9.96 0.00 0.00 4.57
1383 1650 0.814010 ATGCGAAATAGGGGACGTGC 60.814 55.000 0.00 0.00 0.00 5.34
1384 1651 1.217882 GATGCGAAATAGGGGACGTG 58.782 55.000 0.00 0.00 0.00 4.49
1385 1652 0.106149 GGATGCGAAATAGGGGACGT 59.894 55.000 0.00 0.00 0.00 4.34
1386 1653 0.602905 GGGATGCGAAATAGGGGACG 60.603 60.000 0.00 0.00 0.00 4.79
1387 1654 0.602905 CGGGATGCGAAATAGGGGAC 60.603 60.000 0.00 0.00 0.00 4.46
1388 1655 1.752198 CGGGATGCGAAATAGGGGA 59.248 57.895 0.00 0.00 0.00 4.81
1389 1656 1.966451 GCGGGATGCGAAATAGGGG 60.966 63.158 0.00 0.00 0.00 4.79
1390 1657 3.655481 GCGGGATGCGAAATAGGG 58.345 61.111 0.00 0.00 0.00 3.53
1406 1673 3.941657 AACTTGAGGAGCTCGGCGC 62.942 63.158 7.83 0.00 39.57 6.53
1407 1674 1.807573 GAACTTGAGGAGCTCGGCG 60.808 63.158 7.83 0.00 32.35 6.46
1408 1675 1.448717 GGAACTTGAGGAGCTCGGC 60.449 63.158 7.83 2.35 32.35 5.54
1409 1676 1.153745 CGGAACTTGAGGAGCTCGG 60.154 63.158 7.83 0.00 32.35 4.63
1410 1677 1.807573 GCGGAACTTGAGGAGCTCG 60.808 63.158 7.83 0.00 32.35 5.03
1411 1678 1.807573 CGCGGAACTTGAGGAGCTC 60.808 63.158 4.71 4.71 0.00 4.09
1412 1679 2.262915 CGCGGAACTTGAGGAGCT 59.737 61.111 0.00 0.00 0.00 4.09
1413 1680 2.048127 ACGCGGAACTTGAGGAGC 60.048 61.111 12.47 0.00 0.00 4.70
1414 1681 1.446272 GGACGCGGAACTTGAGGAG 60.446 63.158 12.47 0.00 0.00 3.69
1415 1682 2.654877 GGACGCGGAACTTGAGGA 59.345 61.111 12.47 0.00 0.00 3.71
1416 1683 2.809601 CGGACGCGGAACTTGAGG 60.810 66.667 12.47 0.00 0.00 3.86
1417 1684 3.479269 GCGGACGCGGAACTTGAG 61.479 66.667 12.47 0.00 0.00 3.02
1436 1703 3.127533 GATGTGCTCCACGGCCAC 61.128 66.667 2.24 0.00 37.14 5.01
1437 1704 4.758251 CGATGTGCTCCACGGCCA 62.758 66.667 2.24 0.00 37.14 5.36
1442 1709 3.188786 GACGCCGATGTGCTCCAC 61.189 66.667 0.00 0.00 34.56 4.02
1443 1710 4.794439 CGACGCCGATGTGCTCCA 62.794 66.667 0.00 0.00 38.22 3.86
1444 1711 4.796231 ACGACGCCGATGTGCTCC 62.796 66.667 0.00 0.00 39.50 4.70
1445 1712 3.248171 GACGACGCCGATGTGCTC 61.248 66.667 0.00 0.00 39.50 4.26
1446 1713 4.796231 GGACGACGCCGATGTGCT 62.796 66.667 0.00 0.00 39.50 4.40
1447 1714 4.796231 AGGACGACGCCGATGTGC 62.796 66.667 0.00 0.00 39.50 4.57
1448 1715 2.579787 GAGGACGACGCCGATGTG 60.580 66.667 0.00 0.00 39.50 3.21
1449 1716 4.175489 CGAGGACGACGCCGATGT 62.175 66.667 0.00 0.00 42.66 3.06
1456 1723 4.592936 CCGCTAGCGAGGACGACG 62.593 72.222 37.39 14.79 42.83 5.12
1457 1724 4.908877 GCCGCTAGCGAGGACGAC 62.909 72.222 37.39 13.60 42.83 4.34
1466 1733 3.865830 GGACTTTGCGCCGCTAGC 61.866 66.667 11.67 4.06 38.52 3.42
1467 1734 3.195698 GGGACTTTGCGCCGCTAG 61.196 66.667 11.67 10.45 0.00 3.42
1468 1735 3.659089 GAGGGACTTTGCGCCGCTA 62.659 63.158 11.67 0.00 41.55 4.26
1471 1738 3.121030 CAGAGGGACTTTGCGCCG 61.121 66.667 4.18 0.00 41.55 6.46
1476 1743 0.695347 AGGGAAGCAGAGGGACTTTG 59.305 55.000 0.00 0.00 44.07 2.77
1477 1744 0.695347 CAGGGAAGCAGAGGGACTTT 59.305 55.000 0.00 0.00 41.55 2.66
1478 1745 1.846712 GCAGGGAAGCAGAGGGACTT 61.847 60.000 0.00 0.00 41.55 3.01
1479 1746 2.762274 AGCAGGGAAGCAGAGGGACT 62.762 60.000 0.00 0.00 38.34 3.85
1639 1997 3.138930 ATCGATGCGGACCGAGTGG 62.139 63.158 20.50 6.34 38.25 4.00
1641 1999 2.413351 CATCGATGCGGACCGAGT 59.587 61.111 20.50 4.31 38.25 4.18
1667 2025 4.538283 GCAGACTCGAGCGCGCTA 62.538 66.667 36.69 19.58 37.46 4.26
1676 2034 1.797933 CGAGGTCAACGCAGACTCG 60.798 63.158 7.63 10.11 38.57 4.18
1711 2069 2.701780 GCTCCAGAACGAGGCGAGA 61.702 63.158 0.00 0.00 0.00 4.04
1754 2112 1.338136 CCCAGGTCGGTAGAGGCAAT 61.338 60.000 0.00 0.00 0.00 3.56
1762 2120 3.006728 CCTTGGCCCAGGTCGGTA 61.007 66.667 15.01 0.00 0.00 4.02
1806 2226 1.544314 GGGCTGAAACTGAACTGAGCT 60.544 52.381 0.00 0.00 0.00 4.09
1807 2227 0.877743 GGGCTGAAACTGAACTGAGC 59.122 55.000 0.00 0.00 0.00 4.26
1808 2228 1.151668 CGGGCTGAAACTGAACTGAG 58.848 55.000 0.00 0.00 0.00 3.35
1811 2231 1.692519 ACTACGGGCTGAAACTGAACT 59.307 47.619 0.00 0.00 0.00 3.01
1813 2233 1.414919 ACACTACGGGCTGAAACTGAA 59.585 47.619 0.00 0.00 0.00 3.02
1814 2234 1.045407 ACACTACGGGCTGAAACTGA 58.955 50.000 0.00 0.00 0.00 3.41
1840 2342 6.809171 TATTTGTCAAATTTGCAGCAGCAGC 61.809 40.000 15.77 2.09 41.04 5.25
2188 2697 3.751698 GGTTTGGTACTGTTCTGCCTAAG 59.248 47.826 0.00 0.00 0.00 2.18
2214 2725 4.883585 TGGAAACTCCTCATGTGCATAATC 59.116 41.667 0.00 0.00 37.46 1.75
2377 2899 6.515272 ACGGAGTTGCATATTGAAGAAAAT 57.485 33.333 0.00 0.00 37.78 1.82
2378 2900 5.957842 ACGGAGTTGCATATTGAAGAAAA 57.042 34.783 0.00 0.00 37.78 2.29
2397 2919 1.331756 GTGGAGCTCAATATGCAACGG 59.668 52.381 17.19 0.00 0.00 4.44
2735 3293 2.176581 TGGCAATATGGGAGGCATTGTA 59.823 45.455 0.00 0.00 33.22 2.41
2736 3294 1.063038 TGGCAATATGGGAGGCATTGT 60.063 47.619 0.00 0.00 33.22 2.71
2738 3296 2.253610 CATGGCAATATGGGAGGCATT 58.746 47.619 0.00 0.00 44.83 3.56
2842 3409 4.263462 ACAAACTCCATCTTCACCTGCATA 60.263 41.667 0.00 0.00 0.00 3.14
2843 3410 3.087031 CAAACTCCATCTTCACCTGCAT 58.913 45.455 0.00 0.00 0.00 3.96
2926 3526 7.638638 GCCTTCCACCCTTTACCAAGTATATAA 60.639 40.741 0.00 0.00 0.00 0.98
2992 3592 4.460948 ACACCGGTATGACGAAAACTAT 57.539 40.909 6.87 0.00 35.47 2.12
3114 3716 3.070302 GGTGGTGAGGCAAATGGTAAAAA 59.930 43.478 0.00 0.00 0.00 1.94
3224 3839 1.996191 CTGCAAAGGACTCTAGTTCGC 59.004 52.381 0.00 0.00 0.00 4.70
3331 3949 1.888436 ATGCGCCGACATCCCGATAT 61.888 55.000 4.18 0.00 0.00 1.63
3417 4044 1.404843 CTTCTCCTAGGAAGACCCGG 58.595 60.000 13.77 0.00 43.70 5.73
3729 4368 5.919348 AATGAGAGAGAGAGAGAGGAGAT 57.081 43.478 0.00 0.00 0.00 2.75
3731 4370 4.037208 GCAAATGAGAGAGAGAGAGAGGAG 59.963 50.000 0.00 0.00 0.00 3.69
3732 4371 3.953612 GCAAATGAGAGAGAGAGAGAGGA 59.046 47.826 0.00 0.00 0.00 3.71
3733 4372 3.243168 CGCAAATGAGAGAGAGAGAGAGG 60.243 52.174 0.00 0.00 0.00 3.69
3736 4375 3.781079 ACGCAAATGAGAGAGAGAGAG 57.219 47.619 0.00 0.00 0.00 3.20
3737 4376 4.642437 ACATACGCAAATGAGAGAGAGAGA 59.358 41.667 2.46 0.00 0.00 3.10
3738 4377 4.930963 ACATACGCAAATGAGAGAGAGAG 58.069 43.478 2.46 0.00 0.00 3.20
3743 4382 4.119862 GGCTAACATACGCAAATGAGAGA 58.880 43.478 2.46 0.00 0.00 3.10
3924 4585 1.123861 TCCCACTTGAGCTCAGCTGT 61.124 55.000 17.43 13.98 39.88 4.40
3927 4588 4.613929 CTCCCACTTGAGCTCAGC 57.386 61.111 17.43 0.00 0.00 4.26
4009 4671 1.979693 GCTAGATCCCCGATCGCCT 60.980 63.158 10.32 3.74 43.17 5.52
4197 4907 5.480772 ACTTAGAGGCATAACCGCATAGTAT 59.519 40.000 0.00 0.00 46.52 2.12
4255 4965 0.685097 AGCGTCACTGTAACACCCAT 59.315 50.000 0.00 0.00 0.00 4.00
4277 4987 0.760567 AGGTCATCGCAGAGCCCATA 60.761 55.000 3.09 0.00 43.63 2.74
4278 4988 2.037620 GAGGTCATCGCAGAGCCCAT 62.038 60.000 3.09 0.00 43.63 4.00
4343 5061 0.626382 AGGAGTCCCGAGACATCAGA 59.374 55.000 5.25 0.00 46.15 3.27
4350 5068 1.000771 CAGGTGAGGAGTCCCGAGA 60.001 63.158 5.25 0.00 37.58 4.04
4364 5082 0.035056 ATAAAGAGGCAAGCGCAGGT 60.035 50.000 11.47 0.00 41.24 4.00
4383 5102 4.560108 GCGTACCAGTTTCCTCTTTAGTGA 60.560 45.833 0.00 0.00 0.00 3.41
4387 5106 3.863400 GCAGCGTACCAGTTTCCTCTTTA 60.863 47.826 0.00 0.00 0.00 1.85
4444 5174 2.416747 CATGGTTCACGTGACATGAGT 58.583 47.619 30.81 11.09 42.39 3.41
4449 5179 0.943835 CTCGCATGGTTCACGTGACA 60.944 55.000 19.90 14.73 38.41 3.58
4476 5206 2.028294 AGGAGCGGAGATATCAATGCAG 60.028 50.000 5.32 0.00 0.00 4.41
4494 5224 1.153989 CTAGGATGGCTCCCGAGGA 59.846 63.158 0.00 0.00 43.21 3.71
4507 5238 3.009115 GGGGCAGCCACACTAGGA 61.009 66.667 15.19 0.00 0.00 2.94
4527 5258 1.212229 GGACGACACGAAGACCTCC 59.788 63.158 0.00 0.00 0.00 4.30
4638 5371 1.222936 CCTAGACTTGCCTGCCTGG 59.777 63.158 0.00 0.00 39.35 4.45
4672 5405 5.403766 CACATCACTATAAGTTCTCGGCATC 59.596 44.000 0.00 0.00 0.00 3.91
4680 5413 6.700081 TCGGTAATGCACATCACTATAAGTTC 59.300 38.462 0.00 0.00 0.00 3.01
4682 5418 6.040504 TCTCGGTAATGCACATCACTATAAGT 59.959 38.462 0.00 0.00 0.00 2.24
4806 5543 4.759693 TCACAACATAACTGGGTGATTGTC 59.240 41.667 0.00 0.00 36.49 3.18
4808 5545 4.378356 CGTCACAACATAACTGGGTGATTG 60.378 45.833 0.00 0.00 40.54 2.67
4929 5666 5.292101 AGCTTAGCACAATGATCGTTTAGTC 59.708 40.000 7.07 0.00 0.00 2.59



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

AutoCloner maintained by Alex Coulton.