Multiple sequence alignment - TraesCS7D01G286200

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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 TraesCS7D01G286200 chr7D 100.000 4423 0 0 1 4423 307131397 307135819 0.000000e+00 8168.0
1 TraesCS7D01G286200 chr7D 100.000 2205 0 0 4674 6878 307136070 307138274 0.000000e+00 4072.0
2 TraesCS7D01G286200 chr7D 92.709 1838 106 22 2597 4422 48702993 48701172 0.000000e+00 2627.0
3 TraesCS7D01G286200 chr7D 92.417 1833 110 25 2594 4414 48655352 48653537 0.000000e+00 2588.0
4 TraesCS7D01G286200 chr7D 92.308 1833 112 25 2594 4414 48739264 48737449 0.000000e+00 2577.0
5 TraesCS7D01G286200 chr7D 96.147 1064 37 4 4675 5737 118206097 118207157 0.000000e+00 1735.0
6 TraesCS7D01G286200 chr7D 95.673 1063 45 1 4675 5737 384679959 384681020 0.000000e+00 1707.0
7 TraesCS7D01G286200 chr7D 95.677 1064 40 5 4675 5737 118213899 118214957 0.000000e+00 1705.0
8 TraesCS7D01G286200 chr7D 96.879 865 26 1 303 1167 307050406 307049543 0.000000e+00 1447.0
9 TraesCS7D01G286200 chr7D 91.683 1046 49 8 1168 2181 329477511 329476472 0.000000e+00 1415.0
10 TraesCS7D01G286200 chr7D 91.221 1048 53 13 1167 2181 329469180 329468139 0.000000e+00 1389.0
11 TraesCS7D01G286200 chr7D 90.131 993 65 28 3444 4423 139057120 139058092 0.000000e+00 1260.0
12 TraesCS7D01G286200 chr7D 89.648 995 68 26 3444 4422 422315663 422314688 0.000000e+00 1234.0
13 TraesCS7D01G286200 chr7D 89.479 998 68 26 3441 4422 138236703 138235727 0.000000e+00 1227.0
14 TraesCS7D01G286200 chr7D 89.178 998 71 26 3441 4422 138244911 138243935 0.000000e+00 1210.0
15 TraesCS7D01G286200 chr7D 87.484 759 61 24 3688 4420 224276698 224275948 0.000000e+00 845.0
16 TraesCS7D01G286200 chr7D 87.320 765 61 26 3688 4423 363582920 363583677 0.000000e+00 843.0
17 TraesCS7D01G286200 chr7D 93.369 558 29 8 3867 4420 170614209 170613656 0.000000e+00 819.0
18 TraesCS7D01G286200 chr7D 93.537 557 23 9 3867 4420 444200352 444200898 0.000000e+00 817.0
19 TraesCS7D01G286200 chr7D 93.393 560 21 11 3867 4423 378069110 378069656 0.000000e+00 815.0
20 TraesCS7D01G286200 chr7D 93.795 419 26 0 2190 2608 359147697 359147279 1.260000e-176 630.0
21 TraesCS7D01G286200 chr7D 97.449 196 5 0 160 355 469162514 469162319 1.110000e-87 335.0
22 TraesCS7D01G286200 chr7D 96.689 151 5 0 1 151 6942723 6942573 1.150000e-62 252.0
23 TraesCS7D01G286200 chr2D 93.722 3297 138 31 1167 4421 84154543 84157812 0.000000e+00 4878.0
24 TraesCS7D01G286200 chr2D 96.497 1142 39 1 5738 6878 377990003 377988862 0.000000e+00 1886.0
25 TraesCS7D01G286200 chr2D 94.611 1169 60 3 1 1167 377991166 377989999 0.000000e+00 1807.0
26 TraesCS7D01G286200 chr2D 95.783 1067 41 4 4675 5739 37581218 37580154 0.000000e+00 1718.0
27 TraesCS7D01G286200 chr2D 94.401 1018 52 2 1 1014 291698047 291697031 0.000000e+00 1559.0
28 TraesCS7D01G286200 chr2D 91.643 1077 49 24 1158 2199 642426475 642427545 0.000000e+00 1452.0
29 TraesCS7D01G286200 chr2D 91.080 1065 49 24 1168 2199 642422341 642423392 0.000000e+00 1399.0
30 TraesCS7D01G286200 chr2D 94.724 417 21 1 2190 2605 192349184 192349600 0.000000e+00 647.0
31 TraesCS7D01G286200 chr2D 94.005 417 24 1 2190 2605 192341589 192342005 1.260000e-176 630.0
32 TraesCS7D01G286200 chr4D 92.981 3234 160 33 1168 4357 240853648 240856858 0.000000e+00 4652.0
33 TraesCS7D01G286200 chr4D 95.318 1068 42 6 4675 5737 112665316 112664252 0.000000e+00 1688.0
34 TraesCS7D01G286200 chr4D 90.687 1063 61 22 1168 2199 225510399 225511454 0.000000e+00 1380.0
35 TraesCS7D01G286200 chr4D 96.254 694 15 8 1168 1856 255758012 255757325 0.000000e+00 1127.0
36 TraesCS7D01G286200 chr4D 96.110 694 19 6 1167 1856 159547657 159546968 0.000000e+00 1125.0
37 TraesCS7D01G286200 chr4D 95.245 694 25 6 1167 1856 159539653 159538964 0.000000e+00 1092.0
38 TraesCS7D01G286200 chr4D 89.601 702 52 15 1167 1856 269731038 269731730 0.000000e+00 872.0
39 TraesCS7D01G286200 chr4D 95.058 344 16 1 366 709 61597658 61597316 2.180000e-149 540.0
40 TraesCS7D01G286200 chr4D 79.101 756 108 41 1166 1900 196485054 196484328 6.240000e-130 475.0
41 TraesCS7D01G286200 chr4D 95.608 296 12 1 1905 2199 313705443 313705738 2.250000e-129 473.0
42 TraesCS7D01G286200 chr4D 93.750 240 13 1 2190 2427 466321228 466321467 6.560000e-95 359.0
43 TraesCS7D01G286200 chr4D 94.152 171 10 0 2029 2199 439633510 439633340 1.900000e-65 261.0
44 TraesCS7D01G286200 chr4D 88.889 117 12 1 2271 2387 191310145 191310030 7.190000e-30 143.0
45 TraesCS7D01G286200 chr4D 88.034 117 13 1 2271 2387 191317656 191317541 3.350000e-28 137.0
46 TraesCS7D01G286200 chr4D 97.368 76 2 0 741 816 123402052 123402127 5.600000e-26 130.0
47 TraesCS7D01G286200 chr4D 94.737 76 4 0 741 816 134963547 134963622 1.210000e-22 119.0
48 TraesCS7D01G286200 chr4D 93.243 74 3 2 1829 1900 313705336 313705409 2.620000e-19 108.0
49 TraesCS7D01G286200 chr4D 89.024 82 8 1 2029 2109 133898032 133897951 4.390000e-17 100.0
50 TraesCS7D01G286200 chr4D 86.458 96 2 3 58 143 135040402 135040496 2.040000e-15 95.3
51 TraesCS7D01G286200 chr4D 93.220 59 2 2 86 143 123562467 123562524 1.230000e-12 86.1
52 TraesCS7D01G286200 chr4D 93.220 59 2 2 86 143 134980830 134980887 1.230000e-12 86.1
53 TraesCS7D01G286200 chr4D 91.525 59 3 2 86 143 123351529 123351586 5.720000e-11 80.5
54 TraesCS7D01G286200 chrUn 92.764 1838 105 22 2597 4422 229119579 229117758 0.000000e+00 2632.0
55 TraesCS7D01G286200 chrUn 92.705 1837 108 20 2597 4422 212066397 212064576 0.000000e+00 2627.0
56 TraesCS7D01G286200 chrUn 96.967 1154 22 2 5738 6878 403938305 403937152 0.000000e+00 1925.0
57 TraesCS7D01G286200 chrUn 96.949 1147 30 2 22 1167 231559513 231560655 0.000000e+00 1919.0
58 TraesCS7D01G286200 chrUn 96.949 1147 30 2 22 1167 273328614 273327472 0.000000e+00 1919.0
59 TraesCS7D01G286200 chrUn 98.299 882 13 1 5997 6878 216514790 216513911 0.000000e+00 1544.0
60 TraesCS7D01G286200 chrUn 97.703 827 18 1 22 847 182426232 182425406 0.000000e+00 1421.0
61 TraesCS7D01G286200 chrUn 96.278 618 10 2 5738 6342 231560651 231561268 0.000000e+00 1002.0
62 TraesCS7D01G286200 chrUn 89.051 822 59 22 3608 4420 387715444 387714645 0.000000e+00 990.0
63 TraesCS7D01G286200 chrUn 86.559 863 84 27 3577 4422 343090016 343089169 0.000000e+00 922.0
64 TraesCS7D01G286200 chr3D 92.166 1570 97 22 2871 4421 246513762 246512200 0.000000e+00 2194.0
65 TraesCS7D01G286200 chr3D 92.102 1570 98 22 2871 4421 246521937 246520375 0.000000e+00 2189.0
66 TraesCS7D01G286200 chr3D 95.723 1169 47 2 1 1167 48694815 48693648 0.000000e+00 1879.0
67 TraesCS7D01G286200 chr3D 95.583 1064 43 4 4675 5737 128114120 128113060 0.000000e+00 1701.0
68 TraesCS7D01G286200 chr3D 95.211 1065 47 4 4675 5737 274615774 274614712 0.000000e+00 1681.0
69 TraesCS7D01G286200 chr3D 92.344 1045 44 7 1167 2181 246515529 246514491 0.000000e+00 1454.0
70 TraesCS7D01G286200 chr3D 91.309 1047 52 9 1167 2181 246523704 246522665 0.000000e+00 1393.0
71 TraesCS7D01G286200 chr3D 90.458 1069 59 28 1168 2199 190906942 190908004 0.000000e+00 1369.0
72 TraesCS7D01G286200 chr3D 90.056 1076 66 20 1158 2199 190914767 190915835 0.000000e+00 1356.0
73 TraesCS7D01G286200 chr3D 94.231 416 24 0 2190 2605 207318521 207318936 2.710000e-178 636.0
74 TraesCS7D01G286200 chr3D 93.556 419 27 0 2190 2608 493928067 493927649 5.860000e-175 625.0
75 TraesCS7D01G286200 chr3D 96.416 279 10 0 1922 2200 137315120 137314842 1.750000e-125 460.0
76 TraesCS7D01G286200 chr3D 96.403 278 10 0 1922 2199 137439670 137439393 6.290000e-125 459.0
77 TraesCS7D01G286200 chr3D 96.241 133 4 1 260 392 191502513 191502644 4.180000e-52 217.0
78 TraesCS7D01G286200 chr3D 98.684 76 1 0 741 816 501886524 501886599 1.200000e-27 135.0
79 TraesCS7D01G286200 chr3D 94.253 87 3 2 58 143 202633315 202633230 1.560000e-26 132.0
80 TraesCS7D01G286200 chr3D 97.260 73 2 0 744 816 602859644 602859572 2.600000e-24 124.0
81 TraesCS7D01G286200 chr3D 98.214 56 1 0 297 352 83740710 83740765 1.580000e-16 99.0
82 TraesCS7D01G286200 chr3D 85.714 98 3 3 56 143 498435970 498436066 7.350000e-15 93.5
83 TraesCS7D01G286200 chr6D 96.832 1168 33 2 1 1167 458917697 458918861 0.000000e+00 1949.0
84 TraesCS7D01G286200 chr6D 98.299 882 15 0 5997 6878 168261483 168262364 0.000000e+00 1546.0
85 TraesCS7D01G286200 chr6D 90.355 705 46 16 1167 1857 364470045 364469349 0.000000e+00 905.0
86 TraesCS7D01G286200 chr6D 93.729 606 29 6 1254 1857 364477792 364477194 0.000000e+00 900.0
87 TraesCS7D01G286200 chr6D 93.333 585 34 4 1251 1835 196849810 196850389 0.000000e+00 859.0
88 TraesCS7D01G286200 chr6D 90.035 572 42 10 1168 1735 242302973 242302413 0.000000e+00 726.0
89 TraesCS7D01G286200 chr6D 89.895 574 43 11 1167 1735 49066321 49065758 0.000000e+00 725.0
90 TraesCS7D01G286200 chr6D 89.062 576 43 15 1167 1735 49074606 49074044 0.000000e+00 697.0
91 TraesCS7D01G286200 chr6D 88.388 577 43 16 1168 1734 235488854 235489416 0.000000e+00 673.0
92 TraesCS7D01G286200 chr6D 82.345 742 95 27 1167 1900 419811337 419810624 4.560000e-171 612.0
93 TraesCS7D01G286200 chr6D 78.715 747 118 32 1167 1900 102391903 102392621 1.750000e-125 460.0
94 TraesCS7D01G286200 chr6D 94.118 238 12 1 2192 2427 135252175 135252412 1.820000e-95 361.0
95 TraesCS7D01G286200 chr6D 98.701 154 2 0 273 426 163975572 163975419 2.440000e-69 274.0
96 TraesCS7D01G286200 chr6D 97.315 149 2 1 120 266 388026033 388025885 1.150000e-62 252.0
97 TraesCS7D01G286200 chr6D 92.308 117 9 0 2077 2193 45260429 45260313 4.270000e-37 167.0
98 TraesCS7D01G286200 chr6D 94.059 101 5 1 2093 2193 423859168 423859069 1.190000e-32 152.0
99 TraesCS7D01G286200 chr6D 93.069 101 6 1 2093 2193 423830717 423830618 5.560000e-31 147.0
100 TraesCS7D01G286200 chr6D 97.260 73 2 0 744 816 57938512 57938440 2.600000e-24 124.0
101 TraesCS7D01G286200 chr6D 97.015 67 2 0 1840 1906 329662244 329662178 5.640000e-21 113.0
102 TraesCS7D01G286200 chr6D 93.750 64 2 2 81 143 183393247 183393185 2.040000e-15 95.3
103 TraesCS7D01G286200 chr6D 93.750 64 2 2 81 143 430477272 430477210 2.040000e-15 95.3
104 TraesCS7D01G286200 chr4B 97.373 1142 29 1 5738 6878 209116013 209114872 0.000000e+00 1941.0
105 TraesCS7D01G286200 chr4B 96.859 1146 32 1 22 1167 495577610 495578751 0.000000e+00 1914.0
106 TraesCS7D01G286200 chr4B 96.558 1104 34 1 64 1167 209117108 209116009 0.000000e+00 1825.0
107 TraesCS7D01G286200 chr4B 94.444 54 1 2 441 492 73578440 73578387 1.590000e-11 82.4
108 TraesCS7D01G286200 chr3A 97.295 1146 27 1 22 1167 495091903 495093044 0.000000e+00 1941.0
109 TraesCS7D01G286200 chr3A 97.140 1154 20 2 5738 6878 495093040 495094193 0.000000e+00 1936.0
110 TraesCS7D01G286200 chr3A 98.299 882 15 0 5997 6878 66013808 66012927 0.000000e+00 1546.0
111 TraesCS7D01G286200 chr3A 98.299 882 15 0 5997 6878 164860248 164859367 0.000000e+00 1546.0
112 TraesCS7D01G286200 chr3A 95.614 228 9 1 5835 6061 107583828 107583601 1.410000e-96 364.0
113 TraesCS7D01G286200 chr2B 97.297 1147 26 2 22 1167 449208691 449209833 0.000000e+00 1941.0
114 TraesCS7D01G286200 chr2B 97.120 1146 29 1 22 1167 234530523 234531664 0.000000e+00 1930.0
115 TraesCS7D01G286200 chr2B 97.054 1154 21 2 5738 6878 449209829 449210982 0.000000e+00 1930.0
116 TraesCS7D01G286200 chr2B 96.967 1154 22 2 5738 6878 234531660 234532813 0.000000e+00 1925.0
117 TraesCS7D01G286200 chr7A 97.208 1146 28 1 22 1167 60220128 60221269 0.000000e+00 1936.0
118 TraesCS7D01G286200 chr7A 96.794 1154 24 2 5738 6878 60221265 60222418 0.000000e+00 1914.0
119 TraesCS7D01G286200 chr3B 97.140 1154 20 2 5738 6878 6001267 6002420 0.000000e+00 1936.0
120 TraesCS7D01G286200 chr3B 96.949 1147 30 2 22 1167 6000129 6001271 0.000000e+00 1919.0
121 TraesCS7D01G286200 chr3B 96.880 1154 23 2 5738 6878 92287243 92288396 0.000000e+00 1919.0
122 TraesCS7D01G286200 chr3B 98.526 882 13 0 5997 6878 101914993 101915874 0.000000e+00 1557.0
123 TraesCS7D01G286200 chr1B 96.422 1146 37 1 22 1167 619184694 619185835 0.000000e+00 1886.0
124 TraesCS7D01G286200 chr1B 84.895 1483 144 55 2971 4423 258492698 258491266 0.000000e+00 1424.0
125 TraesCS7D01G286200 chr1B 87.102 1194 96 38 3253 4423 572943859 572942701 0.000000e+00 1299.0
126 TraesCS7D01G286200 chr1B 90.411 803 48 21 3627 4420 233883498 233882716 0.000000e+00 1029.0
127 TraesCS7D01G286200 chr1B 90.404 792 46 25 3643 4423 500812422 500811650 0.000000e+00 1014.0
128 TraesCS7D01G286200 chr6B 95.466 1169 46 3 1 1167 625612081 625613244 0.000000e+00 1858.0
129 TraesCS7D01G286200 chr7B 95.381 1169 48 3 1 1167 531985625 531986789 0.000000e+00 1855.0
130 TraesCS7D01G286200 chr1D 95.775 1065 40 5 4675 5738 356639140 356638080 0.000000e+00 1712.0
131 TraesCS7D01G286200 chr1D 96.681 693 16 6 1168 1856 155254740 155255429 0.000000e+00 1146.0
132 TraesCS7D01G286200 chr1D 93.353 692 45 1 2083 2773 356641570 356640879 0.000000e+00 1022.0
133 TraesCS7D01G286200 chr1D 91.068 571 35 12 1167 1732 114997185 114997744 0.000000e+00 758.0
134 TraesCS7D01G286200 chr1D 82.566 608 80 24 1167 1764 327356141 327355550 4.760000e-141 512.0
135 TraesCS7D01G286200 chr1D 81.047 707 76 40 1167 1856 343781104 343780439 1.710000e-140 510.0
136 TraesCS7D01G286200 chr1D 82.401 608 81 24 1167 1764 327348397 327347806 2.210000e-139 507.0
137 TraesCS7D01G286200 chr1D 80.654 703 79 39 1168 1855 343788353 343787693 6.200000e-135 492.0
138 TraesCS7D01G286200 chr1D 82.082 586 78 23 1159 1734 139714164 139714732 6.240000e-130 475.0
139 TraesCS7D01G286200 chr1D 95.578 294 13 0 1905 2198 160627319 160627612 8.070000e-129 472.0
140 TraesCS7D01G286200 chr1D 81.849 584 81 24 1168 1739 224535997 224535427 1.040000e-127 468.0
141 TraesCS7D01G286200 chr1D 81.633 588 85 18 1168 1746 280781452 280780879 3.760000e-127 466.0
142 TraesCS7D01G286200 chr1D 81.897 580 80 22 1165 1729 358253217 358253786 3.760000e-127 466.0
143 TraesCS7D01G286200 chr1D 81.395 602 74 33 1164 1756 374431209 374431781 2.260000e-124 457.0
144 TraesCS7D01G286200 chr1D 95.683 278 12 0 1922 2199 30257878 30257601 1.360000e-121 448.0
145 TraesCS7D01G286200 chr1D 91.667 300 19 3 1906 2199 268077884 268078183 1.790000e-110 411.0
146 TraesCS7D01G286200 chr1D 93.750 240 13 1 2190 2427 256724675 256724914 6.560000e-95 359.0
147 TraesCS7D01G286200 chr1D 94.581 203 8 2 317 517 370893709 370893508 1.860000e-80 311.0
148 TraesCS7D01G286200 chr1D 93.939 99 6 0 2083 2181 312154342 312154440 4.300000e-32 150.0
149 TraesCS7D01G286200 chr1D 98.630 73 1 0 744 816 212444180 212444108 5.600000e-26 130.0
150 TraesCS7D01G286200 chr1D 98.630 73 1 0 744 816 275786052 275785980 5.600000e-26 130.0
151 TraesCS7D01G286200 chr1D 94.595 74 2 2 1829 1900 268077740 268077813 5.640000e-21 113.0
152 TraesCS7D01G286200 chr1D 93.151 73 3 2 1829 1899 160627212 160627284 9.430000e-19 106.0
153 TraesCS7D01G286200 chr1D 94.203 69 4 0 2024 2092 314138106 314138174 9.430000e-19 106.0
154 TraesCS7D01G286200 chr1D 92.754 69 5 0 2024 2092 314145858 314145926 4.390000e-17 100.0
155 TraesCS7D01G286200 chr1D 93.750 64 2 2 81 143 141349352 141349414 2.040000e-15 95.3
156 TraesCS7D01G286200 chr1D 92.188 64 3 2 81 143 350969873 350969935 9.500000e-14 89.8
157 TraesCS7D01G286200 chr1D 100.000 47 0 0 200 246 387760391 387760437 3.420000e-13 87.9
158 TraesCS7D01G286200 chr5D 95.301 1064 47 3 4675 5738 405991926 405992986 0.000000e+00 1685.0
159 TraesCS7D01G286200 chr5D 92.199 705 35 13 1168 1865 152270467 152269776 0.000000e+00 979.0
160 TraesCS7D01G286200 chr5D 95.146 412 20 0 2083 2494 558654028 558654439 0.000000e+00 651.0
161 TraesCS7D01G286200 chr5D 92.654 422 29 2 2083 2503 278597596 278597176 2.120000e-169 606.0
162 TraesCS7D01G286200 chr5D 91.200 250 9 2 1922 2171 92617345 92617109 1.850000e-85 327.0
163 TraesCS7D01G286200 chr5D 93.023 86 6 0 627 712 327746947 327746862 7.240000e-25 126.0
164 TraesCS7D01G286200 chr5D 94.595 74 2 2 1829 1900 17756861 17756934 5.640000e-21 113.0
165 TraesCS7D01G286200 chr5D 98.333 60 1 0 210 269 84838356 84838415 9.430000e-19 106.0
166 TraesCS7D01G286200 chr5D 98.077 52 1 0 689 740 388108386 388108335 2.640000e-14 91.6
167 TraesCS7D01G286200 chr1A 98.299 882 15 0 5997 6878 554516065 554516946 0.000000e+00 1546.0
168 TraesCS7D01G286200 chr1A 96.875 480 12 3 1 479 334068267 334068744 0.000000e+00 800.0
169 TraesCS7D01G286200 chr1A 96.552 406 13 1 762 1167 278533840 278533436 0.000000e+00 671.0
170 TraesCS7D01G286200 chr5B 94.271 384 21 1 576 958 498696193 498695810 2.760000e-163 586.0
171 TraesCS7D01G286200 chr5B 94.340 159 9 0 956 1114 449745640 449745482 1.920000e-60 244.0
172 TraesCS7D01G286200 chr5B 97.368 76 2 0 741 816 567280530 567280605 5.600000e-26 130.0
173 TraesCS7D01G286200 chr5B 97.015 67 2 0 514 580 674504408 674504342 5.640000e-21 113.0
174 TraesCS7D01G286200 chr5B 93.750 64 2 2 81 143 127828066 127828004 2.040000e-15 95.3
175 TraesCS7D01G286200 chr5B 93.750 64 2 2 81 143 202677248 202677310 2.040000e-15 95.3
176 TraesCS7D01G286200 chr6A 94.195 379 20 2 790 1167 348583720 348583343 1.660000e-160 577.0
177 TraesCS7D01G286200 chr6A 91.892 296 17 4 873 1167 609563784 609563495 2.310000e-109 407.0
178 TraesCS7D01G286200 chr6A 93.889 180 9 2 5895 6072 66725766 66725587 3.160000e-68 270.0
179 TraesCS7D01G286200 chr6A 91.011 89 7 1 645 732 401411452 401411540 1.210000e-22 119.0


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 TraesCS7D01G286200 chr7D 307131397 307138274 6877 False 6120.0 8168 100.0000 1 6878 2 chr7D.!!$F8 6877
1 TraesCS7D01G286200 chr7D 48701172 48702993 1821 True 2627.0 2627 92.7090 2597 4422 1 chr7D.!!$R3 1825
2 TraesCS7D01G286200 chr7D 48653537 48655352 1815 True 2588.0 2588 92.4170 2594 4414 1 chr7D.!!$R2 1820
3 TraesCS7D01G286200 chr7D 48737449 48739264 1815 True 2577.0 2577 92.3080 2594 4414 1 chr7D.!!$R4 1820
4 TraesCS7D01G286200 chr7D 118206097 118207157 1060 False 1735.0 1735 96.1470 4675 5737 1 chr7D.!!$F1 1062
5 TraesCS7D01G286200 chr7D 384679959 384681020 1061 False 1707.0 1707 95.6730 4675 5737 1 chr7D.!!$F6 1062
6 TraesCS7D01G286200 chr7D 118213899 118214957 1058 False 1705.0 1705 95.6770 4675 5737 1 chr7D.!!$F2 1062
7 TraesCS7D01G286200 chr7D 307049543 307050406 863 True 1447.0 1447 96.8790 303 1167 1 chr7D.!!$R9 864
8 TraesCS7D01G286200 chr7D 329476472 329477511 1039 True 1415.0 1415 91.6830 1168 2181 1 chr7D.!!$R11 1013
9 TraesCS7D01G286200 chr7D 329468139 329469180 1041 True 1389.0 1389 91.2210 1167 2181 1 chr7D.!!$R10 1014
10 TraesCS7D01G286200 chr7D 139057120 139058092 972 False 1260.0 1260 90.1310 3444 4423 1 chr7D.!!$F3 979
11 TraesCS7D01G286200 chr7D 422314688 422315663 975 True 1234.0 1234 89.6480 3444 4422 1 chr7D.!!$R13 978
12 TraesCS7D01G286200 chr7D 138235727 138236703 976 True 1227.0 1227 89.4790 3441 4422 1 chr7D.!!$R5 981
13 TraesCS7D01G286200 chr7D 138243935 138244911 976 True 1210.0 1210 89.1780 3441 4422 1 chr7D.!!$R6 981
14 TraesCS7D01G286200 chr7D 224275948 224276698 750 True 845.0 845 87.4840 3688 4420 1 chr7D.!!$R8 732
15 TraesCS7D01G286200 chr7D 363582920 363583677 757 False 843.0 843 87.3200 3688 4423 1 chr7D.!!$F4 735
16 TraesCS7D01G286200 chr7D 170613656 170614209 553 True 819.0 819 93.3690 3867 4420 1 chr7D.!!$R7 553
17 TraesCS7D01G286200 chr7D 444200352 444200898 546 False 817.0 817 93.5370 3867 4420 1 chr7D.!!$F7 553
18 TraesCS7D01G286200 chr7D 378069110 378069656 546 False 815.0 815 93.3930 3867 4423 1 chr7D.!!$F5 556
19 TraesCS7D01G286200 chr2D 84154543 84157812 3269 False 4878.0 4878 93.7220 1167 4421 1 chr2D.!!$F1 3254
20 TraesCS7D01G286200 chr2D 377988862 377991166 2304 True 1846.5 1886 95.5540 1 6878 2 chr2D.!!$R3 6877
21 TraesCS7D01G286200 chr2D 37580154 37581218 1064 True 1718.0 1718 95.7830 4675 5739 1 chr2D.!!$R1 1064
22 TraesCS7D01G286200 chr2D 291697031 291698047 1016 True 1559.0 1559 94.4010 1 1014 1 chr2D.!!$R2 1013
23 TraesCS7D01G286200 chr2D 642422341 642427545 5204 False 1425.5 1452 91.3615 1158 2199 2 chr2D.!!$F4 1041
24 TraesCS7D01G286200 chr4D 240853648 240856858 3210 False 4652.0 4652 92.9810 1168 4357 1 chr4D.!!$F8 3189
25 TraesCS7D01G286200 chr4D 112664252 112665316 1064 True 1688.0 1688 95.3180 4675 5737 1 chr4D.!!$R2 1062
26 TraesCS7D01G286200 chr4D 225510399 225511454 1055 False 1380.0 1380 90.6870 1168 2199 1 chr4D.!!$F7 1031
27 TraesCS7D01G286200 chr4D 255757325 255758012 687 True 1127.0 1127 96.2540 1168 1856 1 chr4D.!!$R9 688
28 TraesCS7D01G286200 chr4D 159546968 159547657 689 True 1125.0 1125 96.1100 1167 1856 1 chr4D.!!$R5 689
29 TraesCS7D01G286200 chr4D 159538964 159539653 689 True 1092.0 1092 95.2450 1167 1856 1 chr4D.!!$R4 689
30 TraesCS7D01G286200 chr4D 269731038 269731730 692 False 872.0 872 89.6010 1167 1856 1 chr4D.!!$F9 689
31 TraesCS7D01G286200 chr4D 196484328 196485054 726 True 475.0 475 79.1010 1166 1900 1 chr4D.!!$R8 734
32 TraesCS7D01G286200 chrUn 229117758 229119579 1821 True 2632.0 2632 92.7640 2597 4422 1 chrUn.!!$R4 1825
33 TraesCS7D01G286200 chrUn 212064576 212066397 1821 True 2627.0 2627 92.7050 2597 4422 1 chrUn.!!$R2 1825
34 TraesCS7D01G286200 chrUn 403937152 403938305 1153 True 1925.0 1925 96.9670 5738 6878 1 chrUn.!!$R8 1140
35 TraesCS7D01G286200 chrUn 273327472 273328614 1142 True 1919.0 1919 96.9490 22 1167 1 chrUn.!!$R5 1145
36 TraesCS7D01G286200 chrUn 216513911 216514790 879 True 1544.0 1544 98.2990 5997 6878 1 chrUn.!!$R3 881
37 TraesCS7D01G286200 chrUn 231559513 231561268 1755 False 1460.5 1919 96.6135 22 6342 2 chrUn.!!$F1 6320
38 TraesCS7D01G286200 chrUn 182425406 182426232 826 True 1421.0 1421 97.7030 22 847 1 chrUn.!!$R1 825
39 TraesCS7D01G286200 chrUn 387714645 387715444 799 True 990.0 990 89.0510 3608 4420 1 chrUn.!!$R7 812
40 TraesCS7D01G286200 chrUn 343089169 343090016 847 True 922.0 922 86.5590 3577 4422 1 chrUn.!!$R6 845
41 TraesCS7D01G286200 chr3D 48693648 48694815 1167 True 1879.0 1879 95.7230 1 1167 1 chr3D.!!$R1 1166
42 TraesCS7D01G286200 chr3D 246512200 246515529 3329 True 1824.0 2194 92.2550 1167 4421 2 chr3D.!!$R9 3254
43 TraesCS7D01G286200 chr3D 246520375 246523704 3329 True 1791.0 2189 91.7055 1167 4421 2 chr3D.!!$R10 3254
44 TraesCS7D01G286200 chr3D 128113060 128114120 1060 True 1701.0 1701 95.5830 4675 5737 1 chr3D.!!$R2 1062
45 TraesCS7D01G286200 chr3D 274614712 274615774 1062 True 1681.0 1681 95.2110 4675 5737 1 chr3D.!!$R6 1062
46 TraesCS7D01G286200 chr3D 190906942 190908004 1062 False 1369.0 1369 90.4580 1168 2199 1 chr3D.!!$F2 1031
47 TraesCS7D01G286200 chr3D 190914767 190915835 1068 False 1356.0 1356 90.0560 1158 2199 1 chr3D.!!$F3 1041
48 TraesCS7D01G286200 chr6D 458917697 458918861 1164 False 1949.0 1949 96.8320 1 1167 1 chr6D.!!$F6 1166
49 TraesCS7D01G286200 chr6D 168261483 168262364 881 False 1546.0 1546 98.2990 5997 6878 1 chr6D.!!$F3 881
50 TraesCS7D01G286200 chr6D 364469349 364470045 696 True 905.0 905 90.3550 1167 1857 1 chr6D.!!$R9 690
51 TraesCS7D01G286200 chr6D 364477194 364477792 598 True 900.0 900 93.7290 1254 1857 1 chr6D.!!$R10 603
52 TraesCS7D01G286200 chr6D 196849810 196850389 579 False 859.0 859 93.3330 1251 1835 1 chr6D.!!$F4 584
53 TraesCS7D01G286200 chr6D 242302413 242302973 560 True 726.0 726 90.0350 1168 1735 1 chr6D.!!$R7 567
54 TraesCS7D01G286200 chr6D 49065758 49066321 563 True 725.0 725 89.8950 1167 1735 1 chr6D.!!$R2 568
55 TraesCS7D01G286200 chr6D 49074044 49074606 562 True 697.0 697 89.0620 1167 1735 1 chr6D.!!$R3 568
56 TraesCS7D01G286200 chr6D 235488854 235489416 562 False 673.0 673 88.3880 1168 1734 1 chr6D.!!$F5 566
57 TraesCS7D01G286200 chr6D 419810624 419811337 713 True 612.0 612 82.3450 1167 1900 1 chr6D.!!$R12 733
58 TraesCS7D01G286200 chr6D 102391903 102392621 718 False 460.0 460 78.7150 1167 1900 1 chr6D.!!$F1 733
59 TraesCS7D01G286200 chr4B 495577610 495578751 1141 False 1914.0 1914 96.8590 22 1167 1 chr4B.!!$F1 1145
60 TraesCS7D01G286200 chr4B 209114872 209117108 2236 True 1883.0 1941 96.9655 64 6878 2 chr4B.!!$R2 6814
61 TraesCS7D01G286200 chr3A 495091903 495094193 2290 False 1938.5 1941 97.2175 22 6878 2 chr3A.!!$F1 6856
62 TraesCS7D01G286200 chr3A 66012927 66013808 881 True 1546.0 1546 98.2990 5997 6878 1 chr3A.!!$R1 881
63 TraesCS7D01G286200 chr3A 164859367 164860248 881 True 1546.0 1546 98.2990 5997 6878 1 chr3A.!!$R3 881
64 TraesCS7D01G286200 chr2B 449208691 449210982 2291 False 1935.5 1941 97.1755 22 6878 2 chr2B.!!$F2 6856
65 TraesCS7D01G286200 chr2B 234530523 234532813 2290 False 1927.5 1930 97.0435 22 6878 2 chr2B.!!$F1 6856
66 TraesCS7D01G286200 chr7A 60220128 60222418 2290 False 1925.0 1936 97.0010 22 6878 2 chr7A.!!$F1 6856
67 TraesCS7D01G286200 chr3B 6000129 6002420 2291 False 1927.5 1936 97.0445 22 6878 2 chr3B.!!$F3 6856
68 TraesCS7D01G286200 chr3B 92287243 92288396 1153 False 1919.0 1919 96.8800 5738 6878 1 chr3B.!!$F1 1140
69 TraesCS7D01G286200 chr3B 101914993 101915874 881 False 1557.0 1557 98.5260 5997 6878 1 chr3B.!!$F2 881
70 TraesCS7D01G286200 chr1B 619184694 619185835 1141 False 1886.0 1886 96.4220 22 1167 1 chr1B.!!$F1 1145
71 TraesCS7D01G286200 chr1B 258491266 258492698 1432 True 1424.0 1424 84.8950 2971 4423 1 chr1B.!!$R2 1452
72 TraesCS7D01G286200 chr1B 572942701 572943859 1158 True 1299.0 1299 87.1020 3253 4423 1 chr1B.!!$R4 1170
73 TraesCS7D01G286200 chr1B 233882716 233883498 782 True 1029.0 1029 90.4110 3627 4420 1 chr1B.!!$R1 793
74 TraesCS7D01G286200 chr1B 500811650 500812422 772 True 1014.0 1014 90.4040 3643 4423 1 chr1B.!!$R3 780
75 TraesCS7D01G286200 chr6B 625612081 625613244 1163 False 1858.0 1858 95.4660 1 1167 1 chr6B.!!$F1 1166
76 TraesCS7D01G286200 chr7B 531985625 531986789 1164 False 1855.0 1855 95.3810 1 1167 1 chr7B.!!$F1 1166
77 TraesCS7D01G286200 chr1D 356638080 356641570 3490 True 1367.0 1712 94.5640 2083 5738 2 chr1D.!!$R11 3655
78 TraesCS7D01G286200 chr1D 155254740 155255429 689 False 1146.0 1146 96.6810 1168 1856 1 chr1D.!!$F4 688
79 TraesCS7D01G286200 chr1D 114997185 114997744 559 False 758.0 758 91.0680 1167 1732 1 chr1D.!!$F1 565
80 TraesCS7D01G286200 chr1D 327355550 327356141 591 True 512.0 512 82.5660 1167 1764 1 chr1D.!!$R7 597
81 TraesCS7D01G286200 chr1D 343780439 343781104 665 True 510.0 510 81.0470 1167 1856 1 chr1D.!!$R8 689
82 TraesCS7D01G286200 chr1D 327347806 327348397 591 True 507.0 507 82.4010 1167 1764 1 chr1D.!!$R6 597
83 TraesCS7D01G286200 chr1D 343787693 343788353 660 True 492.0 492 80.6540 1168 1855 1 chr1D.!!$R9 687
84 TraesCS7D01G286200 chr1D 139714164 139714732 568 False 475.0 475 82.0820 1159 1734 1 chr1D.!!$F2 575
85 TraesCS7D01G286200 chr1D 224535427 224535997 570 True 468.0 468 81.8490 1168 1739 1 chr1D.!!$R3 571
86 TraesCS7D01G286200 chr1D 280780879 280781452 573 True 466.0 466 81.6330 1168 1746 1 chr1D.!!$R5 578
87 TraesCS7D01G286200 chr1D 358253217 358253786 569 False 466.0 466 81.8970 1165 1729 1 chr1D.!!$F10 564
88 TraesCS7D01G286200 chr1D 374431209 374431781 572 False 457.0 457 81.3950 1164 1756 1 chr1D.!!$F11 592
89 TraesCS7D01G286200 chr5D 405991926 405992986 1060 False 1685.0 1685 95.3010 4675 5738 1 chr5D.!!$F3 1063
90 TraesCS7D01G286200 chr5D 152269776 152270467 691 True 979.0 979 92.1990 1168 1865 1 chr5D.!!$R2 697
91 TraesCS7D01G286200 chr1A 554516065 554516946 881 False 1546.0 1546 98.2990 5997 6878 1 chr1A.!!$F2 881

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
440 442 1.001641 GGAGTGGCAGTGGAAGCAT 60.002 57.895 0.00 0.0 0.00 3.79 F
1963 5069 0.035439 CATCCCGCACCTACACCTTT 60.035 55.000 0.00 0.0 0.00 3.11 F
2517 5751 1.270971 GTCGTTGCGGCGTTATTCTA 58.729 50.000 9.37 0.0 0.00 2.10 F
2919 6314 0.249741 CCGTGGACGTCAAGTTCCTT 60.250 55.000 18.91 0.0 37.74 3.36 F
2929 6324 0.535102 CAAGTTCCTTGCCGTGACCT 60.535 55.000 0.00 0.0 34.63 3.85 F
3953 7431 1.071071 TGTTGCGCTACCTACCACTTT 59.929 47.619 19.09 0.0 0.00 2.66 F
5120 8621 0.538977 AGTCCGGGAAGAGAACACGA 60.539 55.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 5636 1.056700 CCGGGATCAGGGGACTTGAT 61.057 60.000 0.00 0.0 40.21 2.57 R
2823 6102 0.038892 TCTTGGCGACGGTAGTTGTC 60.039 55.000 0.00 0.0 36.90 3.18 R
4212 7702 1.454201 GGAAACTAGGGCAGCAAGAC 58.546 55.000 0.00 0.0 0.00 3.01 R
4357 7850 2.349445 AGGGAAAAAGGCTAGGTGAGT 58.651 47.619 0.00 0.0 0.00 3.41 R
4673 8173 4.497291 TTGGACCAACACTTAGACAAGT 57.503 40.909 1.69 0.0 46.15 3.16 R
5390 8894 0.601046 CCACTTGAGCTCAGTTGCGA 60.601 55.000 17.43 0.0 38.13 5.10 R
6050 9572 1.063717 ACCATATGCACCTCTTTGGGG 60.064 52.381 0.00 0.0 43.81 4.96 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
56 57 4.642429 AGAGTTTGCTTTTACACGGAGAT 58.358 39.130 0.00 0.00 0.00 2.75
176 177 8.651389 CCCATATAGGTCTTTTCTTCATACTCA 58.349 37.037 0.00 0.00 34.66 3.41
246 247 1.078918 TTCGCTCCGAGTCCGACTA 60.079 57.895 0.00 0.00 37.14 2.59
440 442 1.001641 GGAGTGGCAGTGGAAGCAT 60.002 57.895 0.00 0.00 0.00 3.79
623 626 4.490743 CATGCTTGATTTCATGTTGAGCA 58.509 39.130 6.39 6.39 38.55 4.26
655 658 3.857038 GTCAATCCCCGGGCGCTA 61.857 66.667 17.73 0.00 0.00 4.26
722 725 1.614241 TTCTAGGGCGGCAAGGAGAC 61.614 60.000 12.47 0.00 0.00 3.36
1162 1180 8.845413 TTTGGTATTTTCCATTTCTTTGGATG 57.155 30.769 0.00 0.00 45.08 3.51
1164 1182 8.378115 TGGTATTTTCCATTTCTTTGGATGAT 57.622 30.769 0.00 0.00 45.08 2.45
1177 4156 4.431416 TTGGATGATATTGTAACGCCCT 57.569 40.909 0.00 0.00 0.00 5.19
1539 4566 4.876107 TCATTTATCGAGGCTCTTCCAAAC 59.124 41.667 13.50 0.00 37.29 2.93
1703 4735 1.651987 ATTATCCGCGTGTCCAACTG 58.348 50.000 4.92 0.00 0.00 3.16
1963 5069 0.035439 CATCCCGCACCTACACCTTT 60.035 55.000 0.00 0.00 0.00 3.11
2370 5604 3.692406 GTCGAGGTCCCCTGCGTT 61.692 66.667 0.00 0.00 31.76 4.84
2471 5705 2.256461 GGCCTTTGCGTCTGCTTG 59.744 61.111 0.00 0.00 43.34 4.01
2483 5717 1.744368 CTGCTTGCTCCGCATCACT 60.744 57.895 0.00 0.00 38.76 3.41
2517 5751 1.270971 GTCGTTGCGGCGTTATTCTA 58.729 50.000 9.37 0.00 0.00 2.10
2716 5952 4.504596 GCATGCACCCCCGGATCA 62.505 66.667 14.21 0.00 0.00 2.92
2760 6018 2.979649 GTCAAGACCCGGACTCCC 59.020 66.667 0.73 0.00 0.00 4.30
2823 6102 3.005472 TCAAGTTCCTCTACGACTTGTGG 59.995 47.826 13.25 0.00 46.35 4.17
2919 6314 0.249741 CCGTGGACGTCAAGTTCCTT 60.250 55.000 18.91 0.00 37.74 3.36
2929 6324 0.535102 CAAGTTCCTTGCCGTGACCT 60.535 55.000 0.00 0.00 34.63 3.85
2975 6370 4.620982 ACTACAAAACGTGTACCACTACC 58.379 43.478 0.00 0.00 41.98 3.18
3131 6543 2.250939 CCGAGTTGTTCCTTGCGCA 61.251 57.895 5.66 5.66 0.00 6.09
3272 6693 2.219445 CGATATGTTGTCGTGGCATCAG 59.781 50.000 0.00 0.00 34.56 2.90
3468 6904 8.568676 TGAGGATTTATCGGAATTGTTGTTTA 57.431 30.769 0.00 0.00 0.00 2.01
3611 7062 5.752955 GTGGTGTTTTGTCAATATGCAACTT 59.247 36.000 0.00 0.00 0.00 2.66
3615 7066 7.436673 GGTGTTTTGTCAATATGCAACTTGTTA 59.563 33.333 10.37 0.98 0.00 2.41
3730 7183 3.703286 TCATGTCATGCTTATGCTTGC 57.297 42.857 8.03 7.44 42.07 4.01
3759 7212 3.450457 ACCATGTTGTTTGCTTCTTTCCA 59.550 39.130 0.00 0.00 0.00 3.53
3851 7321 3.594603 TCTTCATGGACTCGTTCTTCC 57.405 47.619 0.00 0.00 0.00 3.46
3953 7431 1.071071 TGTTGCGCTACCTACCACTTT 59.929 47.619 19.09 0.00 0.00 2.66
4056 7541 4.844349 TTTGCTCAGCCCTTCTTATAGT 57.156 40.909 0.00 0.00 0.00 2.12
4212 7702 1.110442 TGCCTGGTGTTTTGTTCCAG 58.890 50.000 0.00 0.00 45.67 3.86
4383 7882 2.225267 CCTAGCCTTTTTCCCTTGGGAA 60.225 50.000 16.54 16.54 0.00 3.97
4776 8276 1.090052 GCTTATCCGGTGTGTCCTGC 61.090 60.000 0.00 0.00 0.00 4.85
4947 8447 6.425417 GTGAGAGCTTATAATGGGCTAAGTTC 59.575 42.308 0.00 0.00 36.19 3.01
4958 8458 1.188863 GCTAAGTTCGGACACCCCTA 58.811 55.000 0.00 0.00 0.00 3.53
5120 8621 0.538977 AGTCCGGGAAGAGAACACGA 60.539 55.000 0.00 0.00 0.00 4.35
5134 8635 4.457466 AGAACACGACTTTTGGGTTATGT 58.543 39.130 0.00 0.00 0.00 2.29
5200 8701 2.654912 GACGACCGTTCCGTTGCTG 61.655 63.158 0.00 0.00 40.67 4.41
5233 8734 5.559035 GCTCTTATTTGCGTATGTTAGCCAG 60.559 44.000 0.00 0.00 0.00 4.85
5310 8813 9.469807 CATAAGCTTAAATAGTCTTGATCTCGT 57.530 33.333 10.85 0.00 0.00 4.18
5330 8833 1.421268 TGGGTGTGAGATTGCTGAGTT 59.579 47.619 0.00 0.00 0.00 3.01
5390 8894 0.905357 GAGGATACCAGTGCAGGTGT 59.095 55.000 7.87 0.82 43.14 4.16
5471 8976 1.977854 TGTTGATCAGTAGTGGTGCCT 59.022 47.619 0.00 0.00 0.00 4.75
5677 9186 0.593773 GCGACAAAACCACAATGCGT 60.594 50.000 0.00 0.00 0.00 5.24
5787 9296 2.907695 TTCCAACAGTGGCAGCTGCA 62.908 55.000 37.63 22.06 45.54 4.41
5825 9334 8.617809 TGGATTAGCCATTTTCGTTATTACTTC 58.382 33.333 0.00 0.00 43.33 3.01
5987 9496 8.158169 TCAAATAGCTTCGATTTGCATTATCT 57.842 30.769 13.39 0.00 41.86 1.98
6042 9564 9.613428 AAGATGTACAATCCAATTTCTCGATTA 57.387 29.630 0.00 0.00 0.00 1.75
6290 9812 8.789762 TCGAGTCGATTCCATGATTATAAGTTA 58.210 33.333 12.09 0.00 0.00 2.24
6416 9938 5.975988 AAAGAGGGTATCCTGAGCAATTA 57.024 39.130 0.00 0.00 45.05 1.40
6534 10056 9.424319 GGATCTTCTATAATTTCGCACATAAGA 57.576 33.333 0.00 0.00 0.00 2.10
6552 10074 8.792633 CACATAAGAGGTTATTTCTTGGTTTCA 58.207 33.333 0.00 0.00 36.38 2.69
6556 10078 6.794534 AGAGGTTATTTCTTGGTTTCATCCT 58.205 36.000 0.00 0.00 0.00 3.24
6637 10159 8.049721 AGGAGTCCTATTGAAACCAAGAAATAG 58.950 37.037 10.94 0.00 34.02 1.73
6740 10262 5.137551 AGAGACATAGGGCTAAAGAGAGAC 58.862 45.833 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.899393 AGCAAACTCTCCAAATTTATGACA 57.101 33.333 0.00 0.00 0.00 3.58
56 57 7.182026 TCCTCTATTTGTTTGATAGGGTCTTCA 59.818 37.037 0.00 0.00 0.00 3.02
246 247 2.691252 GGTCCCCCATTCCGTCCT 60.691 66.667 0.00 0.00 0.00 3.85
323 325 1.367471 CGTCCTCACAGTCAGCCAA 59.633 57.895 0.00 0.00 0.00 4.52
440 442 7.396055 CCAATCAAAATAAGGAGGGTTCTGTTA 59.604 37.037 0.00 0.00 0.00 2.41
623 626 0.536687 TTGACGTCGGACTGGAGTCT 60.537 55.000 11.62 0.00 44.20 3.24
655 658 2.301583 GAGTCTGTTCAGGAGCTCCTTT 59.698 50.000 33.33 11.13 46.09 3.11
929 947 2.748532 AGAAGTACTGCGTAGAGTCCAC 59.251 50.000 7.78 0.00 0.00 4.02
944 962 9.959721 AAATTATGTGAGGCTTAGAAAGAAGTA 57.040 29.630 0.00 0.00 0.00 2.24
1162 1180 4.051922 CAGTCTCAGGGCGTTACAATATC 58.948 47.826 0.00 0.00 0.00 1.63
1164 1182 3.093814 TCAGTCTCAGGGCGTTACAATA 58.906 45.455 0.00 0.00 0.00 1.90
1296 4306 9.906660 CCATGCAATTTACTTAGTTGAGTTTTA 57.093 29.630 0.00 0.00 0.00 1.52
1539 4566 7.452880 TGGTAGATCCAAAAATGTTGAGAAG 57.547 36.000 0.00 0.00 44.12 2.85
1703 4735 2.841266 AGAAAGAGAGGTTAGGGGAAGC 59.159 50.000 0.00 0.00 35.67 3.86
1990 5096 4.268687 CGAAGCTCGAGCAAGGTT 57.731 55.556 36.87 23.28 43.74 3.50
2388 5622 4.884257 TGATACGGCGGCGGCTTC 62.884 66.667 35.05 25.76 39.81 3.86
2401 5635 1.717032 CGGGATCAGGGGACTTGATA 58.283 55.000 0.00 0.00 40.21 2.15
2402 5636 1.056700 CCGGGATCAGGGGACTTGAT 61.057 60.000 0.00 0.00 40.21 2.57
2716 5952 2.438021 TGTACTTGGTGCTTGAGGTTCT 59.562 45.455 0.00 0.00 0.00 3.01
2760 6018 2.396601 TCGTAGTTGTACTTGGCGTTG 58.603 47.619 0.00 0.00 0.00 4.10
2823 6102 0.038892 TCTTGGCGACGGTAGTTGTC 60.039 55.000 0.00 0.00 36.90 3.18
2919 6314 1.080093 GATGTTCGAGGTCACGGCA 60.080 57.895 0.00 0.00 0.00 5.69
2929 6324 3.871006 GCACACATTCCATAGATGTTCGA 59.129 43.478 0.00 0.00 0.00 3.71
2975 6370 4.778415 CTCGCGACGGTGGTGGAG 62.778 72.222 3.71 2.11 0.00 3.86
3131 6543 0.323725 ATGGCAAGGCAACGAGGAAT 60.324 50.000 0.00 0.00 46.39 3.01
3417 6848 9.469807 AGTCAATTCGCAATTTAATACAAACAA 57.530 25.926 0.00 0.00 0.00 2.83
3435 6868 7.736447 ATTCCGATAAATCCTCAGTCAATTC 57.264 36.000 0.00 0.00 0.00 2.17
3468 6904 5.351189 GCAATTTAAATGAGGCCGAAACAAT 59.649 36.000 0.39 0.00 0.00 2.71
3474 6911 2.733956 AGGCAATTTAAATGAGGCCGA 58.266 42.857 22.72 0.00 45.79 5.54
3582 7025 7.034397 TGCATATTGACAAAACACCACATATG 58.966 34.615 0.00 0.00 0.00 1.78
3583 7026 7.167924 TGCATATTGACAAAACACCACATAT 57.832 32.000 0.00 0.00 0.00 1.78
3584 7027 6.581171 TGCATATTGACAAAACACCACATA 57.419 33.333 0.00 0.00 0.00 2.29
3611 7062 9.461312 AAATTAAGTGGAGCTCAATATGTAACA 57.539 29.630 17.19 0.00 0.00 2.41
3615 7066 7.944729 ACAAATTAAGTGGAGCTCAATATGT 57.055 32.000 17.19 4.82 0.00 2.29
3720 7172 3.822594 TGGTAAACACGCAAGCATAAG 57.177 42.857 0.00 0.00 45.62 1.73
3730 7183 3.701241 AGCAAACAACATGGTAAACACG 58.299 40.909 0.00 0.00 0.00 4.49
3759 7212 1.896465 AGCTAACGAGAGAAGCCAACT 59.104 47.619 0.00 0.00 42.02 3.16
3953 7431 5.893255 GGCAATATGGGAGGCATGATATAAA 59.107 40.000 0.00 0.00 0.00 1.40
4212 7702 1.454201 GGAAACTAGGGCAGCAAGAC 58.546 55.000 0.00 0.00 0.00 3.01
4357 7850 2.349445 AGGGAAAAAGGCTAGGTGAGT 58.651 47.619 0.00 0.00 0.00 3.41
4673 8173 4.497291 TTGGACCAACACTTAGACAAGT 57.503 40.909 1.69 0.00 46.15 3.16
4915 8415 5.300752 CCATTATAAGCTCTCACGGTCAAT 58.699 41.667 0.00 0.00 0.00 2.57
4958 8458 5.123936 GGCTTTCGAAAGATAATACCCTGT 58.876 41.667 35.88 0.00 41.60 4.00
5112 8613 4.457466 ACATAACCCAAAAGTCGTGTTCT 58.543 39.130 0.00 0.00 0.00 3.01
5120 8621 5.585820 ACGTCAAAACATAACCCAAAAGT 57.414 34.783 0.00 0.00 0.00 2.66
5134 8635 5.302568 TCCTGAACTCCTACTTACGTCAAAA 59.697 40.000 0.00 0.00 0.00 2.44
5200 8701 3.584095 GCAAATAAGAGCGAGAAGAGC 57.416 47.619 0.00 0.00 0.00 4.09
5233 8734 2.012673 AGCAAGCACTAGCATGTAAGC 58.987 47.619 0.00 0.00 45.49 3.09
5310 8813 1.059098 ACTCAGCAATCTCACACCCA 58.941 50.000 0.00 0.00 0.00 4.51
5330 8833 3.690139 GGAAGTATCTGTGAGTCACGAGA 59.310 47.826 18.17 19.52 37.14 4.04
5390 8894 0.601046 CCACTTGAGCTCAGTTGCGA 60.601 55.000 17.43 0.00 38.13 5.10
5471 8976 2.091278 AGATCCCTGATCGTCCCAACTA 60.091 50.000 0.00 0.00 43.17 2.24
5677 9186 2.500098 AGGCACGACTTAGAGGCATAAA 59.500 45.455 0.00 0.00 0.00 1.40
5864 9373 8.458843 CCTGTAGTTATGTTTAACCTTGAATGG 58.541 37.037 0.00 0.00 38.81 3.16
6042 9564 3.181423 TGCACCTCTTTGGGGTTCTATTT 60.181 43.478 0.00 0.00 42.62 1.40
6050 9572 1.063717 ACCATATGCACCTCTTTGGGG 60.064 52.381 0.00 0.00 43.81 4.96
6290 9812 1.202891 GGAATGGGCGCTAGGGTTATT 60.203 52.381 7.64 6.80 0.00 1.40
6416 9938 6.324770 GGAATATCAATGAACCCCATTCTTGT 59.675 38.462 0.00 0.00 43.27 3.16
6534 10056 6.314917 ACAGGATGAAACCAAGAAATAACCT 58.685 36.000 0.00 0.00 39.69 3.50
6749 10271 5.912892 TGCAGGATTATACACGAAAGATCA 58.087 37.500 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.