Multiple sequence alignment - TraesCS6D01G012600

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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 TraesCS6D01G012600 chr6D 100.000 9000 0 0 1 9000 5057981 5066980 0.000000e+00 16620.0
1 TraesCS6D01G012600 chr6D 97.727 2991 56 10 806 3788 5183658 5180672 0.000000e+00 5136.0
2 TraesCS6D01G012600 chr6D 94.586 2826 143 9 5212 8035 5180107 5177290 0.000000e+00 4362.0
3 TraesCS6D01G012600 chr6D 89.203 2862 227 25 5818 8632 5151616 5148790 0.000000e+00 3498.0
4 TraesCS6D01G012600 chr6D 89.172 2586 196 29 5779 8305 5367623 5365063 0.000000e+00 3147.0
5 TraesCS6D01G012600 chr6D 88.825 2273 221 17 5818 8067 5196873 5194611 0.000000e+00 2760.0
6 TraesCS6D01G012600 chr6D 96.247 906 31 2 2886 3788 449814426 449815331 0.000000e+00 1482.0
7 TraesCS6D01G012600 chr6D 79.856 2085 349 43 5901 7949 5421796 5419747 0.000000e+00 1458.0
8 TraesCS6D01G012600 chr6D 91.556 1054 63 3 5779 6811 5368683 5367635 0.000000e+00 1430.0
9 TraesCS6D01G012600 chr6D 88.046 1121 88 18 888 1969 5729581 5728468 0.000000e+00 1286.0
10 TraesCS6D01G012600 chr6D 100.000 613 0 0 9326 9938 5067306 5067918 0.000000e+00 1133.0
11 TraesCS6D01G012600 chr6D 96.721 610 17 1 9332 9938 5193435 5192826 0.000000e+00 1013.0
12 TraesCS6D01G012600 chr6D 76.208 1946 372 54 5838 7745 5770718 5768826 0.000000e+00 944.0
13 TraesCS6D01G012600 chr6D 96.920 552 13 2 4351 4901 120345209 120344661 0.000000e+00 922.0
14 TraesCS6D01G012600 chr6D 83.978 930 113 14 5901 6807 5369634 5368718 0.000000e+00 859.0
15 TraesCS6D01G012600 chr6D 83.668 747 79 18 1993 2730 5728222 5727510 0.000000e+00 664.0
16 TraesCS6D01G012600 chr6D 86.557 610 66 11 9328 9937 5364220 5363627 0.000000e+00 658.0
17 TraesCS6D01G012600 chr6D 91.206 398 30 2 9326 9723 5137038 5136646 4.090000e-148 536.0
18 TraesCS6D01G012600 chr6D 95.000 340 9 2 8633 8971 5137723 5137391 2.460000e-145 527.0
19 TraesCS6D01G012600 chr6D 79.789 757 100 25 19 749 5437789 5437060 1.490000e-137 501.0
20 TraesCS6D01G012600 chr6D 76.667 930 176 28 820 1736 5436682 5435781 2.510000e-130 477.0
21 TraesCS6D01G012600 chr6D 89.014 355 32 5 8633 8985 5194139 5193790 5.510000e-117 433.0
22 TraesCS6D01G012600 chr6D 94.800 250 11 2 4899 5147 18169217 18169465 1.210000e-103 388.0
23 TraesCS6D01G012600 chr6D 85.634 355 48 1 8633 8987 5364842 5364491 4.380000e-98 370.0
24 TraesCS6D01G012600 chr6D 99.408 169 1 0 8464 8632 446953907 446953739 3.490000e-79 307.0
25 TraesCS6D01G012600 chr6D 98.256 172 3 0 8461 8632 4093022 4093193 1.620000e-77 302.0
26 TraesCS6D01G012600 chr6D 98.256 172 3 0 8461 8632 458493677 458493848 1.620000e-77 302.0
27 TraesCS6D01G012600 chr6D 97.688 173 4 0 8460 8632 19125711 19125883 2.100000e-76 298.0
28 TraesCS6D01G012600 chr6D 97.688 173 4 0 8460 8632 448617433 448617605 2.100000e-76 298.0
29 TraesCS6D01G012600 chr6D 96.610 177 6 0 8456 8632 1937995 1938171 2.710000e-75 294.0
30 TraesCS6D01G012600 chr6D 83.235 340 34 9 9601 9938 13766171 13765853 3.510000e-74 291.0
31 TraesCS6D01G012600 chr6D 87.805 205 11 4 5225 5426 5727262 5727069 2.790000e-55 228.0
32 TraesCS6D01G012600 chr6D 81.455 275 30 15 9326 9582 5176217 5175946 1.310000e-48 206.0
33 TraesCS6D01G012600 chr6D 92.391 92 4 2 2757 2845 5727516 5727425 2.910000e-25 128.0
34 TraesCS6D01G012600 chr6D 100.000 68 0 0 5148 5215 14163697 14163630 1.050000e-24 126.0
35 TraesCS6D01G012600 chr6D 98.529 68 1 0 5148 5215 55883830 55883897 4.880000e-23 121.0
36 TraesCS6D01G012600 chr6D 98.529 68 1 0 5148 5215 377175851 377175784 4.880000e-23 121.0
37 TraesCS6D01G012600 chr6D 98.529 68 1 0 5148 5215 449815329 449815396 4.880000e-23 121.0
38 TraesCS6D01G012600 chr6D 85.841 113 14 2 8347 8459 5194263 5194153 1.750000e-22 119.0
39 TraesCS6D01G012600 chr6D 98.485 66 1 0 5148 5213 49184790 49184725 6.310000e-22 117.0
40 TraesCS6D01G012600 chr6D 87.879 99 10 1 644 742 5436880 5436784 2.270000e-21 115.0
41 TraesCS6D01G012600 chr6D 97.059 68 1 1 5148 5215 5180674 5180608 8.160000e-21 113.0
42 TraesCS6D01G012600 chr6D 97.015 67 2 0 5148 5214 306700257 306700191 8.160000e-21 113.0
43 TraesCS6D01G012600 chr6D 93.939 66 4 0 9537 9602 13766400 13766335 6.350000e-17 100.0
44 TraesCS6D01G012600 chr6A 88.788 2988 279 37 5214 8181 4771543 4768592 0.000000e+00 3611.0
45 TraesCS6D01G012600 chr6A 90.437 2447 197 18 5782 8218 4207055 4209474 0.000000e+00 3188.0
46 TraesCS6D01G012600 chr6A 91.437 2289 189 5 5782 8067 4181375 4183659 0.000000e+00 3134.0
47 TraesCS6D01G012600 chr6A 90.344 2382 196 19 5472 7845 4595154 4592799 0.000000e+00 3094.0
48 TraesCS6D01G012600 chr6A 87.780 1784 155 25 251 1986 4774222 4772454 0.000000e+00 2028.0
49 TraesCS6D01G012600 chr6A 90.386 1425 107 4 591 1986 4597916 4596493 0.000000e+00 1845.0
50 TraesCS6D01G012600 chr6A 85.551 1315 129 20 697 1969 4226960 4228255 0.000000e+00 1319.0
51 TraesCS6D01G012600 chr6A 85.475 1315 130 20 697 1969 4176476 4177771 0.000000e+00 1314.0
52 TraesCS6D01G012600 chr6A 86.884 1197 120 11 697 1866 4151582 4152768 0.000000e+00 1306.0
53 TraesCS6D01G012600 chr6A 85.323 1315 132 20 697 1969 4201716 4203011 0.000000e+00 1303.0
54 TraesCS6D01G012600 chr6A 93.355 617 25 8 9326 9938 4184843 4185447 0.000000e+00 898.0
55 TraesCS6D01G012600 chr6A 96.066 483 15 2 9459 9938 4160138 4160619 0.000000e+00 784.0
56 TraesCS6D01G012600 chr6A 89.134 589 59 4 1983 2567 4772414 4771827 0.000000e+00 728.0
57 TraesCS6D01G012600 chr6A 87.710 594 60 12 1979 2567 4596456 4595871 0.000000e+00 680.0
58 TraesCS6D01G012600 chr6A 88.605 509 50 2 19 527 4598450 4597950 6.600000e-171 612.0
59 TraesCS6D01G012600 chr6A 86.694 481 51 3 52 527 4614930 4614458 1.140000e-143 521.0
60 TraesCS6D01G012600 chr6A 89.080 348 31 5 8633 8978 4768293 4767951 9.230000e-115 425.0
61 TraesCS6D01G012600 chr6A 94.681 94 4 1 8368 8460 4183964 4184057 2.890000e-30 145.0
62 TraesCS6D01G012600 chr6A 94.681 94 4 1 8368 8460 4209662 4209755 2.890000e-30 145.0
63 TraesCS6D01G012600 chr6A 86.408 103 7 2 8122 8218 4183675 4183776 1.370000e-18 106.0
64 TraesCS6D01G012600 chr6A 86.047 86 10 2 8347 8432 4768407 4768324 3.820000e-14 91.6
65 TraesCS6D01G012600 chr6A 100.000 34 0 0 8317 8350 4209572 4209605 8.330000e-06 63.9
66 TraesCS6D01G012600 chrUn 85.287 3079 380 47 5275 8304 87339576 87342630 0.000000e+00 3109.0
67 TraesCS6D01G012600 chrUn 86.448 2258 255 22 5868 8102 305210889 305213118 0.000000e+00 2427.0
68 TraesCS6D01G012600 chrUn 86.448 2258 255 23 5868 8102 320034817 320032588 0.000000e+00 2427.0
69 TraesCS6D01G012600 chrUn 95.991 898 32 3 2894 3788 45207432 45208328 0.000000e+00 1456.0
70 TraesCS6D01G012600 chrUn 87.871 1179 117 14 815 1969 87336287 87337463 0.000000e+00 1362.0
71 TraesCS6D01G012600 chrUn 85.323 1315 132 20 697 1969 345034608 345035903 0.000000e+00 1303.0
72 TraesCS6D01G012600 chrUn 88.245 638 58 9 133 757 364737468 364738101 0.000000e+00 747.0
73 TraesCS6D01G012600 chrUn 89.066 503 32 8 9397 9898 87343678 87344158 3.970000e-168 603.0
74 TraesCS6D01G012600 chrUn 88.268 358 29 7 8633 8987 87342801 87343148 5.550000e-112 416.0
75 TraesCS6D01G012600 chrUn 81.748 515 73 10 771 1284 364738193 364738687 2.580000e-110 411.0
76 TraesCS6D01G012600 chrUn 90.584 308 13 6 697 996 378039050 378039349 2.600000e-105 394.0
77 TraesCS6D01G012600 chrUn 88.889 306 28 4 8689 8993 305213718 305214018 1.220000e-98 372.0
78 TraesCS6D01G012600 chrUn 97.727 176 4 0 8457 8632 111382536 111382711 4.510000e-78 303.0
79 TraesCS6D01G012600 chrUn 98.266 173 3 0 8460 8632 156705642 156705470 4.510000e-78 303.0
80 TraesCS6D01G012600 chrUn 98.256 172 3 0 8461 8632 30215085 30215256 1.620000e-77 302.0
81 TraesCS6D01G012600 chrUn 98.817 169 2 0 8464 8632 93755247 93755079 1.620000e-77 302.0
82 TraesCS6D01G012600 chrUn 82.825 361 37 13 1973 2330 87338553 87338891 5.830000e-77 300.0
83 TraesCS6D01G012600 chrUn 82.991 341 35 10 9601 9938 62589054 62588734 4.540000e-73 287.0
84 TraesCS6D01G012600 chrUn 82.698 341 36 10 9601 9938 62343589 62343269 2.110000e-71 281.0
85 TraesCS6D01G012600 chrUn 82.698 341 36 10 9601 9938 247223415 247223095 2.110000e-71 281.0
86 TraesCS6D01G012600 chrUn 82.405 341 37 10 9601 9938 62404930 62404610 9.830000e-70 276.0
87 TraesCS6D01G012600 chrUn 82.405 341 37 10 9601 9938 377413896 377413576 9.830000e-70 276.0
88 TraesCS6D01G012600 chrUn 90.323 93 9 0 8368 8460 305213521 305213613 1.360000e-23 122.0
89 TraesCS6D01G012600 chrUn 98.529 68 1 0 5148 5215 45208326 45208393 4.880000e-23 121.0
90 TraesCS6D01G012600 chrUn 97.059 68 2 0 5148 5215 92140686 92140753 2.270000e-21 115.0
91 TraesCS6D01G012600 chrUn 93.939 66 4 0 9537 9602 62343819 62343754 6.350000e-17 100.0
92 TraesCS6D01G012600 chrUn 93.939 66 4 0 9537 9602 62405160 62405095 6.350000e-17 100.0
93 TraesCS6D01G012600 chrUn 93.939 66 4 0 9537 9602 62460865 62460800 6.350000e-17 100.0
94 TraesCS6D01G012600 chr6B 87.703 2586 271 19 5470 8040 10727376 10724823 0.000000e+00 2970.0
95 TraesCS6D01G012600 chr6B 86.906 2482 245 33 5873 8305 9788351 9785901 0.000000e+00 2710.0
96 TraesCS6D01G012600 chr6B 81.682 1867 261 53 1 1824 9792334 9790506 0.000000e+00 1478.0
97 TraesCS6D01G012600 chr6B 88.615 1054 113 5 815 1866 10730958 10729910 0.000000e+00 1275.0
98 TraesCS6D01G012600 chr6B 86.757 589 69 7 9326 9912 10057316 10057897 0.000000e+00 647.0
99 TraesCS6D01G012600 chr6B 91.810 464 30 4 9455 9918 10723550 10723095 3.030000e-179 640.0
100 TraesCS6D01G012600 chr6B 87.526 473 38 13 82 547 9348306 9347848 2.460000e-145 527.0
101 TraesCS6D01G012600 chr6B 84.530 543 59 14 9379 9919 9784902 9784383 1.910000e-141 514.0
102 TraesCS6D01G012600 chr6B 88.338 343 35 5 8635 8976 10724276 10723938 3.340000e-109 407.0
103 TraesCS6D01G012600 chr6B 85.635 362 43 6 8633 8993 9785750 9785397 1.220000e-98 372.0
104 TraesCS6D01G012600 chr6B 84.463 354 48 5 8633 8986 10056903 10057249 9.560000e-90 342.0
105 TraesCS6D01G012600 chr6B 95.122 123 6 0 627 749 9338115 9337993 2.830000e-45 195.0
106 TraesCS6D01G012600 chr2D 95.698 1139 19 9 3789 4901 590973079 590974213 0.000000e+00 1805.0
107 TraesCS6D01G012600 chr2D 93.833 1135 27 23 3785 4901 24909026 24907917 0.000000e+00 1668.0
108 TraesCS6D01G012600 chr2D 95.590 907 28 7 2888 3786 493077368 493076466 0.000000e+00 1443.0
109 TraesCS6D01G012600 chr2D 98.276 174 3 0 8459 8632 616477935 616477762 1.250000e-78 305.0
110 TraesCS6D01G012600 chr2D 96.667 180 6 0 8453 8632 497118252 497118073 5.830000e-77 300.0
111 TraesCS6D01G012600 chr2D 97.561 41 1 0 9474 9514 644667897 644667937 4.980000e-08 71.3
112 TraesCS6D01G012600 chr3D 94.996 1139 30 7 3789 4901 397749499 397750636 0.000000e+00 1762.0
113 TraesCS6D01G012600 chr3D 95.079 1138 25 8 3788 4901 606822436 606823566 0.000000e+00 1762.0
114 TraesCS6D01G012600 chr3D 95.062 1134 27 10 3789 4901 25941281 25940156 0.000000e+00 1757.0
115 TraesCS6D01G012600 chr3D 93.565 948 31 9 3981 4901 27873561 27872617 0.000000e+00 1386.0
116 TraesCS6D01G012600 chr3D 91.438 911 38 13 4022 4901 579607985 579607084 0.000000e+00 1214.0
117 TraesCS6D01G012600 chr3D 95.618 251 5 5 4899 5147 555300551 555300305 2.010000e-106 398.0
118 TraesCS6D01G012600 chr3D 97.740 177 4 0 8456 8632 563801651 563801827 1.250000e-78 305.0
119 TraesCS6D01G012600 chr3D 96.703 182 6 0 8451 8632 505957325 505957506 4.510000e-78 303.0
120 TraesCS6D01G012600 chr3D 96.175 183 4 2 8450 8632 15870088 15869909 7.550000e-76 296.0
121 TraesCS6D01G012600 chr3D 100.000 67 0 0 5148 5214 597182294 597182228 3.770000e-24 124.0
122 TraesCS6D01G012600 chr3D 100.000 66 0 0 5148 5213 12055640 12055575 1.360000e-23 122.0
123 TraesCS6D01G012600 chr7D 94.580 1144 28 15 3789 4901 616434328 616433188 0.000000e+00 1738.0
124 TraesCS6D01G012600 chr7D 93.863 1157 25 14 3789 4901 75297072 75295918 0.000000e+00 1701.0
125 TraesCS6D01G012600 chr7D 92.857 1162 31 17 3788 4901 41385176 41386333 0.000000e+00 1639.0
126 TraesCS6D01G012600 chr7D 92.397 1118 25 15 3788 4859 19662132 19661029 0.000000e+00 1539.0
127 TraesCS6D01G012600 chr7D 90.468 1175 26 30 3788 4901 59887688 59888837 0.000000e+00 1471.0
128 TraesCS6D01G012600 chr7D 95.884 899 31 5 2895 3789 43790358 43789462 0.000000e+00 1450.0
129 TraesCS6D01G012600 chr7D 95.364 906 32 9 2887 3788 481609937 481609038 0.000000e+00 1432.0
130 TraesCS6D01G012600 chr7D 92.604 960 32 10 3978 4901 51233272 51234228 0.000000e+00 1343.0
131 TraesCS6D01G012600 chr7D 95.600 250 4 5 4899 5147 38895754 38895511 2.600000e-105 394.0
132 TraesCS6D01G012600 chr7D 98.295 176 3 0 8457 8632 575185751 575185576 9.690000e-80 309.0
133 TraesCS6D01G012600 chr7D 98.837 172 2 0 8461 8632 569385313 569385484 3.490000e-79 307.0
134 TraesCS6D01G012600 chr7D 98.276 174 3 0 8459 8632 26470243 26470070 1.250000e-78 305.0
135 TraesCS6D01G012600 chr7D 96.703 182 6 0 8451 8632 620735739 620735558 4.510000e-78 303.0
136 TraesCS6D01G012600 chr7D 100.000 66 0 0 5148 5213 510701987 510701922 1.360000e-23 122.0
137 TraesCS6D01G012600 chr1D 93.275 1145 29 10 3789 4901 364612778 364611650 0.000000e+00 1644.0
138 TraesCS6D01G012600 chr1D 96.796 905 24 4 2888 3788 463249896 463250799 0.000000e+00 1506.0
139 TraesCS6D01G012600 chr1D 94.450 973 28 10 3789 4742 398983969 398984934 0.000000e+00 1474.0
140 TraesCS6D01G012600 chr1D 94.902 765 23 10 4153 4901 419978501 419979265 0.000000e+00 1182.0
141 TraesCS6D01G012600 chr1D 96.429 252 6 3 4899 5149 485484381 485484132 7.180000e-111 412.0
142 TraesCS6D01G012600 chr1D 98.266 173 3 0 8460 8632 447843543 447843371 4.510000e-78 303.0
143 TraesCS6D01G012600 chr1D 98.266 173 3 0 8460 8632 453354803 453354975 4.510000e-78 303.0
144 TraesCS6D01G012600 chr1D 97.714 175 4 0 8458 8632 433969084 433969258 1.620000e-77 302.0
145 TraesCS6D01G012600 chr1D 100.000 66 0 0 5150 5215 490368849 490368914 1.360000e-23 122.0
146 TraesCS6D01G012600 chr1D 98.529 68 1 0 5148 5215 315012978 315012911 4.880000e-23 121.0
147 TraesCS6D01G012600 chr4D 96.878 897 23 4 2896 3788 35124711 35123816 0.000000e+00 1496.0
148 TraesCS6D01G012600 chr4D 96.536 895 25 5 2897 3788 364026895 364026004 0.000000e+00 1476.0
149 TraesCS6D01G012600 chr4D 96.685 181 3 2 8452 8632 480130369 480130546 2.100000e-76 298.0
150 TraesCS6D01G012600 chr4D 97.688 173 4 0 8460 8632 497068242 497068414 2.100000e-76 298.0
151 TraesCS6D01G012600 chr4D 98.225 169 3 0 8464 8632 1166023 1165855 7.550000e-76 296.0
152 TraesCS6D01G012600 chr4D 98.204 167 3 0 8466 8632 105973256 105973090 9.760000e-75 292.0
153 TraesCS6D01G012600 chr4D 96.610 177 4 1 8456 8632 436872618 436872444 9.760000e-75 292.0
154 TraesCS6D01G012600 chr4D 98.204 167 3 0 8466 8632 493799398 493799564 9.760000e-75 292.0
155 TraesCS6D01G012600 chr4D 97.093 172 5 0 8461 8632 401646262 401646433 3.510000e-74 291.0
156 TraesCS6D01G012600 chr4D 97.093 172 5 0 8461 8632 497519151 497519322 3.510000e-74 291.0
157 TraesCS6D01G012600 chr4D 97.633 169 4 0 8464 8632 499477221 499477053 3.510000e-74 291.0
158 TraesCS6D01G012600 chr4D 96.045 177 5 1 8456 8632 489957708 489957882 4.540000e-73 287.0
159 TraesCS6D01G012600 chr4D 100.000 68 0 0 5148 5215 35123818 35123751 1.050000e-24 126.0
160 TraesCS6D01G012600 chr4D 97.059 68 2 0 5148 5215 364026006 364025939 2.270000e-21 115.0
161 TraesCS6D01G012600 chr4D 95.455 66 3 0 5148 5213 483156908 483156973 1.370000e-18 106.0
162 TraesCS6D01G012600 chr4D 95.455 66 3 0 5148 5213 483164704 483164769 1.370000e-18 106.0
163 TraesCS6D01G012600 chr4D 92.958 71 4 1 5148 5217 73989811 73989741 1.770000e-17 102.0
164 TraesCS6D01G012600 chr4D 92.857 70 5 0 5145 5214 479406592 479406661 1.770000e-17 102.0
165 TraesCS6D01G012600 chr4A 91.240 742 42 11 4170 4901 623989628 623990356 0.000000e+00 989.0
166 TraesCS6D01G012600 chr4A 90.433 554 41 9 4590 5135 50576314 50576863 0.000000e+00 719.0
167 TraesCS6D01G012600 chr1B 89.488 371 28 6 9342 9712 21477389 21477748 9.100000e-125 459.0
168 TraesCS6D01G012600 chr3B 96.032 252 6 4 4899 5148 757274853 757275102 3.340000e-109 407.0
169 TraesCS6D01G012600 chr5D 95.219 251 11 1 4899 5148 482326844 482326594 7.230000e-106 396.0
170 TraesCS6D01G012600 chr5D 95.600 250 5 4 4899 5147 496312775 496312531 7.230000e-106 396.0
171 TraesCS6D01G012600 chr5D 98.266 173 3 0 8460 8632 407340633 407340461 4.510000e-78 303.0
172 TraesCS6D01G012600 chr5D 98.266 173 3 0 8460 8632 525266147 525265975 4.510000e-78 303.0
173 TraesCS6D01G012600 chr5D 98.529 68 1 0 5148 5215 510946145 510946212 4.880000e-23 121.0
174 TraesCS6D01G012600 chr5B 94.862 253 10 2 4900 5150 705728587 705728336 9.360000e-105 392.0


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 TraesCS6D01G012600 chr6D 5057981 5067918 9937 False 8876.500000 16620 100.000000 1 9938 2 chr6D.!!$F8 9937
1 TraesCS6D01G012600 chr6D 5148790 5151616 2826 True 3498.000000 3498 89.203000 5818 8632 1 chr6D.!!$R1 2814
2 TraesCS6D01G012600 chr6D 5175946 5183658 7712 True 2454.250000 5136 92.706750 806 9582 4 chr6D.!!$R11 8776
3 TraesCS6D01G012600 chr6D 5419747 5421796 2049 True 1458.000000 1458 79.856000 5901 7949 1 chr6D.!!$R2 2048
4 TraesCS6D01G012600 chr6D 5363627 5369634 6007 True 1292.800000 3147 87.379400 5779 9937 5 chr6D.!!$R13 4158
5 TraesCS6D01G012600 chr6D 5192826 5196873 4047 True 1081.250000 2760 90.100250 5818 9938 4 chr6D.!!$R12 4120
6 TraesCS6D01G012600 chr6D 5768826 5770718 1892 True 944.000000 944 76.208000 5838 7745 1 chr6D.!!$R3 1907
7 TraesCS6D01G012600 chr6D 120344661 120345209 548 True 922.000000 922 96.920000 4351 4901 1 chr6D.!!$R6 550
8 TraesCS6D01G012600 chr6D 449814426 449815396 970 False 801.500000 1482 97.388000 2886 5215 2 chr6D.!!$F9 2329
9 TraesCS6D01G012600 chr6D 5727069 5729581 2512 True 576.500000 1286 87.977500 888 5426 4 chr6D.!!$R15 4538
10 TraesCS6D01G012600 chr6D 5136646 5137723 1077 True 531.500000 536 93.103000 8633 9723 2 chr6D.!!$R10 1090
11 TraesCS6D01G012600 chr6D 5435781 5437789 2008 True 364.333333 501 81.445000 19 1736 3 chr6D.!!$R14 1717
12 TraesCS6D01G012600 chr6A 4592799 4598450 5651 True 1557.750000 3094 89.261250 19 7845 4 chr6A.!!$R2 7826
13 TraesCS6D01G012600 chr6A 4767951 4774222 6271 True 1376.720000 3611 88.165800 251 8978 5 chr6A.!!$R3 8727
14 TraesCS6D01G012600 chr6A 4226960 4228255 1295 False 1319.000000 1319 85.551000 697 1969 1 chr6A.!!$F4 1272
15 TraesCS6D01G012600 chr6A 4151582 4152768 1186 False 1306.000000 1306 86.884000 697 1866 1 chr6A.!!$F1 1169
16 TraesCS6D01G012600 chr6A 4201716 4203011 1295 False 1303.000000 1303 85.323000 697 1969 1 chr6A.!!$F3 1272
17 TraesCS6D01G012600 chr6A 4207055 4209755 2700 False 1132.300000 3188 95.039333 5782 8460 3 chr6A.!!$F6 2678
18 TraesCS6D01G012600 chr6A 4176476 4185447 8971 False 1119.400000 3134 90.271200 697 9938 5 chr6A.!!$F5 9241
19 TraesCS6D01G012600 chrUn 320032588 320034817 2229 True 2427.000000 2427 86.448000 5868 8102 1 chrUn.!!$R6 2234
20 TraesCS6D01G012600 chrUn 345034608 345035903 1295 False 1303.000000 1303 85.323000 697 1969 1 chrUn.!!$F4 1272
21 TraesCS6D01G012600 chrUn 87336287 87344158 7871 False 1158.000000 3109 86.663400 815 9898 5 chrUn.!!$F7 9083
22 TraesCS6D01G012600 chrUn 305210889 305214018 3129 False 973.666667 2427 88.553333 5868 8993 3 chrUn.!!$F8 3125
23 TraesCS6D01G012600 chrUn 45207432 45208393 961 False 788.500000 1456 97.260000 2894 5215 2 chrUn.!!$F6 2321
24 TraesCS6D01G012600 chrUn 364737468 364738687 1219 False 579.000000 747 84.996500 133 1284 2 chrUn.!!$F9 1151
25 TraesCS6D01G012600 chr6B 10723095 10730958 7863 True 1323.000000 2970 89.116500 815 9918 4 chr6B.!!$R4 9103
26 TraesCS6D01G012600 chr6B 9784383 9792334 7951 True 1268.500000 2710 84.688250 1 9919 4 chr6B.!!$R3 9918
27 TraesCS6D01G012600 chr6B 10056903 10057897 994 False 494.500000 647 85.610000 8633 9912 2 chr6B.!!$F1 1279
28 TraesCS6D01G012600 chr2D 590973079 590974213 1134 False 1805.000000 1805 95.698000 3789 4901 1 chr2D.!!$F1 1112
29 TraesCS6D01G012600 chr2D 24907917 24909026 1109 True 1668.000000 1668 93.833000 3785 4901 1 chr2D.!!$R1 1116
30 TraesCS6D01G012600 chr2D 493076466 493077368 902 True 1443.000000 1443 95.590000 2888 3786 1 chr2D.!!$R2 898
31 TraesCS6D01G012600 chr3D 397749499 397750636 1137 False 1762.000000 1762 94.996000 3789 4901 1 chr3D.!!$F1 1112
32 TraesCS6D01G012600 chr3D 606822436 606823566 1130 False 1762.000000 1762 95.079000 3788 4901 1 chr3D.!!$F4 1113
33 TraesCS6D01G012600 chr3D 25940156 25941281 1125 True 1757.000000 1757 95.062000 3789 4901 1 chr3D.!!$R3 1112
34 TraesCS6D01G012600 chr3D 27872617 27873561 944 True 1386.000000 1386 93.565000 3981 4901 1 chr3D.!!$R4 920
35 TraesCS6D01G012600 chr3D 579607084 579607985 901 True 1214.000000 1214 91.438000 4022 4901 1 chr3D.!!$R6 879
36 TraesCS6D01G012600 chr7D 616433188 616434328 1140 True 1738.000000 1738 94.580000 3789 4901 1 chr7D.!!$R9 1112
37 TraesCS6D01G012600 chr7D 75295918 75297072 1154 True 1701.000000 1701 93.863000 3789 4901 1 chr7D.!!$R5 1112
38 TraesCS6D01G012600 chr7D 41385176 41386333 1157 False 1639.000000 1639 92.857000 3788 4901 1 chr7D.!!$F1 1113
39 TraesCS6D01G012600 chr7D 19661029 19662132 1103 True 1539.000000 1539 92.397000 3788 4859 1 chr7D.!!$R1 1071
40 TraesCS6D01G012600 chr7D 59887688 59888837 1149 False 1471.000000 1471 90.468000 3788 4901 1 chr7D.!!$F3 1113
41 TraesCS6D01G012600 chr7D 43789462 43790358 896 True 1450.000000 1450 95.884000 2895 3789 1 chr7D.!!$R4 894
42 TraesCS6D01G012600 chr7D 481609038 481609937 899 True 1432.000000 1432 95.364000 2887 3788 1 chr7D.!!$R6 901
43 TraesCS6D01G012600 chr7D 51233272 51234228 956 False 1343.000000 1343 92.604000 3978 4901 1 chr7D.!!$F2 923
44 TraesCS6D01G012600 chr1D 364611650 364612778 1128 True 1644.000000 1644 93.275000 3789 4901 1 chr1D.!!$R2 1112
45 TraesCS6D01G012600 chr1D 463249896 463250799 903 False 1506.000000 1506 96.796000 2888 3788 1 chr1D.!!$F5 900
46 TraesCS6D01G012600 chr1D 398983969 398984934 965 False 1474.000000 1474 94.450000 3789 4742 1 chr1D.!!$F1 953
47 TraesCS6D01G012600 chr1D 419978501 419979265 764 False 1182.000000 1182 94.902000 4153 4901 1 chr1D.!!$F2 748
48 TraesCS6D01G012600 chr4D 35123751 35124711 960 True 811.000000 1496 98.439000 2896 5215 2 chr4D.!!$R6 2319
49 TraesCS6D01G012600 chr4D 364025939 364026895 956 True 795.500000 1476 96.797500 2897 5215 2 chr4D.!!$R7 2318
50 TraesCS6D01G012600 chr4A 623989628 623990356 728 False 989.000000 989 91.240000 4170 4901 1 chr4A.!!$F2 731
51 TraesCS6D01G012600 chr4A 50576314 50576863 549 False 719.000000 719 90.433000 4590 5135 1 chr4A.!!$F1 545

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
220 244 0.167470 CTCGGTCTGCAGCAAACATG 59.833 55.000 9.47 0.0 0.00 3.21 F
276 300 0.179137 TGGCTAACATCGAGAGCACG 60.179 55.000 11.90 0.0 37.98 5.34 F
1179 1645 0.036010 CGCTGGATCAACTTGACCCT 60.036 55.000 3.68 0.0 28.81 4.34 F
1253 1719 0.605589 AGCCTCGACTCCTTTGTGAG 59.394 55.000 0.00 0.0 38.37 3.51 F
2874 8404 1.828660 CGGAGCTAGACGGGGATGT 60.829 63.158 0.00 0.0 0.00 3.06 F
5080 10941 0.911045 GAACCGGGACTAAAGGGGGA 60.911 60.000 6.32 0.0 0.00 4.81 F
5136 10998 0.039180 CCGGGACTAAAGGCCCTTTT 59.961 55.000 18.97 0.0 42.40 2.27 F
7242 15886 0.171903 GCAGTTGTGGATGATGGTGC 59.828 55.000 0.00 0.0 0.00 5.01 F
8067 16759 1.602851 CGACCAGGATGAGGTACGTAG 59.397 57.143 0.00 0.0 40.09 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1645 4.102210 TCATTTGCCCAAATTTTGACCTGA 59.898 37.500 10.72 2.71 38.84 3.86 R
1882 2518 9.554724 TGATACGAATCAAAAGCAAAGATAAAC 57.445 29.630 0.00 0.00 39.20 2.01 R
2940 8470 0.179121 GACGTGGATCCATGCGTGTA 60.179 55.000 28.96 0.00 37.71 2.90 R
3576 9119 2.545526 AGTTGTCATGTCGCTGAACTTG 59.454 45.455 0.00 0.00 0.00 3.16 R
5112 10974 0.392595 GGCCTTTAGTCCCGGTTCTG 60.393 60.000 0.00 0.00 0.00 3.02 R
7223 15867 0.171903 GCACCATCATCCACAACTGC 59.828 55.000 0.00 0.00 0.00 4.40 R
7263 15907 2.852449 TCTTCCAAGCTATGATTGGGGT 59.148 45.455 13.56 0.00 46.03 4.95 R
8481 17459 0.036306 GGACTAATGGGGGCGTATGG 59.964 60.000 0.00 0.00 0.00 2.74 R
9912 19247 4.311816 AGACAAATGAGTGGCAAAAGTG 57.688 40.909 0.00 0.00 0.00 3.16 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
156 157 4.086457 ACCAATGGAGGACATACCAAAAC 58.914 43.478 6.16 0.00 39.40 2.43
160 161 6.183360 CCAATGGAGGACATACCAAAACATAC 60.183 42.308 0.00 0.00 39.40 2.39
220 244 0.167470 CTCGGTCTGCAGCAAACATG 59.833 55.000 9.47 0.00 0.00 3.21
258 282 8.295288 AGATCTAAAGAAATTGTTTGTCTGCTG 58.705 33.333 0.00 0.00 0.00 4.41
264 288 3.923017 ATTGTTTGTCTGCTGGCTAAC 57.077 42.857 13.85 13.85 0.00 2.34
267 291 2.813754 TGTTTGTCTGCTGGCTAACATC 59.186 45.455 18.12 0.00 0.00 3.06
270 294 1.134995 TGTCTGCTGGCTAACATCGAG 60.135 52.381 0.00 0.00 0.00 4.04
276 300 0.179137 TGGCTAACATCGAGAGCACG 60.179 55.000 11.90 0.00 37.98 5.34
286 310 1.437772 CGAGAGCACGACCTCGGTAT 61.438 60.000 0.00 0.00 45.93 2.73
299 323 2.882137 CCTCGGTATCACCTCTTCTCTC 59.118 54.545 0.00 0.00 35.66 3.20
304 328 4.274147 GGTATCACCTCTTCTCTCACAGA 58.726 47.826 0.00 0.00 34.73 3.41
435 470 3.560636 AGCAAGTAACAACACTGTCCT 57.439 42.857 0.00 0.00 33.45 3.85
438 473 4.814771 AGCAAGTAACAACACTGTCCTTAC 59.185 41.667 0.00 2.60 33.45 2.34
439 474 4.814771 GCAAGTAACAACACTGTCCTTACT 59.185 41.667 5.95 5.95 33.45 2.24
440 475 5.050295 GCAAGTAACAACACTGTCCTTACTC 60.050 44.000 10.06 0.36 33.45 2.59
441 476 5.211174 AGTAACAACACTGTCCTTACTCC 57.789 43.478 5.95 0.00 33.45 3.85
442 477 3.487120 AACAACACTGTCCTTACTCCC 57.513 47.619 0.00 0.00 33.45 4.30
443 478 2.690840 ACAACACTGTCCTTACTCCCT 58.309 47.619 0.00 0.00 0.00 4.20
444 479 3.853207 ACAACACTGTCCTTACTCCCTA 58.147 45.455 0.00 0.00 0.00 3.53
465 500 1.590238 GTGCTCCGATGAGTTCAATCG 59.410 52.381 0.00 0.00 40.95 3.34
469 504 1.548719 TCCGATGAGTTCAATCGTGGT 59.451 47.619 5.24 0.00 36.21 4.16
549 596 2.486592 CGAAGCCGGTTTTGATTAACCT 59.513 45.455 12.75 0.00 44.38 3.50
642 725 1.091537 TGCGCACTAATTAAGCCACC 58.908 50.000 5.66 0.00 0.00 4.61
1179 1645 0.036010 CGCTGGATCAACTTGACCCT 60.036 55.000 3.68 0.00 28.81 4.34
1253 1719 0.605589 AGCCTCGACTCCTTTGTGAG 59.394 55.000 0.00 0.00 38.37 3.51
1882 2518 9.784531 ATGTCAACTAAGGAAGACAATATATGG 57.215 33.333 0.00 0.00 43.38 2.74
2874 8404 1.828660 CGGAGCTAGACGGGGATGT 60.829 63.158 0.00 0.00 0.00 3.06
3404 8946 4.756642 CACATGGCAACTCTCTCTTTTACA 59.243 41.667 0.00 0.00 37.61 2.41
3405 8947 5.413833 CACATGGCAACTCTCTCTTTTACAT 59.586 40.000 0.00 0.00 37.61 2.29
3576 9119 1.602323 TTGTCCGACATGGCAACCC 60.602 57.895 1.09 0.00 37.80 4.11
3646 9189 2.440796 CCATGGCAACTGCGGGAT 60.441 61.111 0.00 0.00 43.26 3.85
3726 9269 3.304659 GGCGTGTGGGCATTATCTATTTG 60.305 47.826 0.00 0.00 41.77 2.32
3801 9347 7.048512 GTGGGCATTACTCACTAGTAGAAAAT 58.951 38.462 3.59 0.00 39.36 1.82
3849 9395 3.067461 GCATTAATCCCGGTTGCATTACA 59.933 43.478 0.00 0.00 33.58 2.41
4369 10028 1.349688 AGATTTTGACACCCTACGGCA 59.650 47.619 0.00 0.00 0.00 5.69
4569 10243 6.882656 TGAATTTTGGTCAAATCTGGTCAAA 58.117 32.000 0.00 0.00 33.60 2.69
4570 10244 6.760770 TGAATTTTGGTCAAATCTGGTCAAAC 59.239 34.615 0.00 0.00 33.60 2.93
4572 10246 4.916983 TTGGTCAAATCTGGTCAAACTG 57.083 40.909 0.00 0.00 0.00 3.16
4574 10248 3.631686 TGGTCAAATCTGGTCAAACTGTG 59.368 43.478 0.00 0.00 0.00 3.66
4575 10249 3.004734 GGTCAAATCTGGTCAAACTGTGG 59.995 47.826 0.00 0.00 0.00 4.17
4577 10251 3.882888 TCAAATCTGGTCAAACTGTGGTC 59.117 43.478 0.00 0.00 0.00 4.02
4578 10252 3.576078 AATCTGGTCAAACTGTGGTCA 57.424 42.857 0.00 0.00 0.00 4.02
4581 10255 3.013921 TCTGGTCAAACTGTGGTCAAAC 58.986 45.455 0.00 0.00 0.00 2.93
4583 10257 3.157881 TGGTCAAACTGTGGTCAAACAA 58.842 40.909 0.00 0.00 0.00 2.83
4592 10266 4.111916 CTGTGGTCAAACAATGGTCAAAC 58.888 43.478 0.00 0.00 0.00 2.93
4593 10267 3.766591 TGTGGTCAAACAATGGTCAAACT 59.233 39.130 0.00 0.00 0.00 2.66
4769 10532 8.519526 AGTTTCAAACTCAAACAGTGAAATGTA 58.480 29.630 0.00 0.00 37.02 2.29
5049 10910 1.608154 GTGGAGGGCCTTTAGTCCC 59.392 63.158 7.89 3.10 42.94 4.46
5055 10916 1.449070 GGCCTTTAGTCCCGGTTCG 60.449 63.158 0.00 0.00 0.00 3.95
5056 10917 1.294459 GCCTTTAGTCCCGGTTCGT 59.706 57.895 0.00 0.00 0.00 3.85
5059 10920 1.545582 CCTTTAGTCCCGGTTCGTGTA 59.454 52.381 0.00 0.00 0.00 2.90
5060 10921 2.029110 CCTTTAGTCCCGGTTCGTGTAA 60.029 50.000 0.00 0.00 0.00 2.41
5078 10939 0.989602 AAGAACCGGGACTAAAGGGG 59.010 55.000 6.32 0.00 0.00 4.79
5079 10940 0.912968 AGAACCGGGACTAAAGGGGG 60.913 60.000 6.32 0.00 0.00 5.40
5080 10941 0.911045 GAACCGGGACTAAAGGGGGA 60.911 60.000 6.32 0.00 0.00 4.81
5084 10946 1.307953 GGGACTAAAGGGGGAGGCT 60.308 63.158 0.00 0.00 0.00 4.58
5091 10953 4.441757 ACTAAAGGGGGAGGCTTTAGTAA 58.558 43.478 5.23 0.00 46.00 2.24
5105 10967 5.473039 GCTTTAGTAACGACCCTTTAGTCA 58.527 41.667 0.00 0.00 36.52 3.41
5112 10974 1.670967 CGACCCTTTAGTCACGGTTCC 60.671 57.143 0.00 0.00 36.52 3.62
5135 10997 1.138228 ACCGGGACTAAAGGCCCTTT 61.138 55.000 18.97 14.26 42.40 3.11
5136 10998 0.039180 CCGGGACTAAAGGCCCTTTT 59.961 55.000 18.97 0.00 42.40 2.27
5137 10999 1.549265 CCGGGACTAAAGGCCCTTTTT 60.549 52.381 18.97 1.56 42.40 1.94
5138 11000 1.816835 CGGGACTAAAGGCCCTTTTTC 59.183 52.381 18.97 11.07 42.40 2.29
5139 11001 2.554564 CGGGACTAAAGGCCCTTTTTCT 60.555 50.000 18.97 0.00 42.40 2.52
5140 11002 3.307904 CGGGACTAAAGGCCCTTTTTCTA 60.308 47.826 18.97 0.00 42.40 2.10
5141 11003 4.015084 GGGACTAAAGGCCCTTTTTCTAC 58.985 47.826 15.13 5.73 41.31 2.59
5142 11004 4.263816 GGGACTAAAGGCCCTTTTTCTACT 60.264 45.833 15.13 0.00 41.31 2.57
5143 11005 5.045359 GGGACTAAAGGCCCTTTTTCTACTA 60.045 44.000 15.13 0.00 41.31 1.82
5144 11006 6.114089 GGACTAAAGGCCCTTTTTCTACTAG 58.886 44.000 15.13 6.21 35.21 2.57
5145 11007 6.296317 GGACTAAAGGCCCTTTTTCTACTAGT 60.296 42.308 15.13 9.58 35.21 2.57
5146 11008 6.473758 ACTAAAGGCCCTTTTTCTACTAGTG 58.526 40.000 15.13 0.00 35.21 2.74
5587 12051 3.213206 TGATGACTGGGTCCAATATGC 57.787 47.619 0.00 0.00 0.00 3.14
6082 13652 8.186821 CCACTTTCTGATGATTACTCCAAAATC 58.813 37.037 0.00 0.00 34.55 2.17
6664 14246 3.120199 CCAACAAGGTTCACAGATTAGCG 60.120 47.826 0.00 0.00 0.00 4.26
7181 15825 1.599047 GAGTCTGCAGGCAAGGCTA 59.401 57.895 22.50 0.00 0.00 3.93
7223 15867 3.875727 CCTGCACAAGATTCATACTCTGG 59.124 47.826 0.00 0.00 0.00 3.86
7242 15886 0.171903 GCAGTTGTGGATGATGGTGC 59.828 55.000 0.00 0.00 0.00 5.01
7263 15907 3.616560 GCTCAGACCAAGTATTCGGTTGA 60.617 47.826 0.00 0.00 34.99 3.18
8067 16759 1.602851 CGACCAGGATGAGGTACGTAG 59.397 57.143 0.00 0.00 40.09 3.51
8068 16760 2.652590 GACCAGGATGAGGTACGTAGT 58.347 52.381 0.00 0.00 42.94 2.73
8069 16761 3.742327 CGACCAGGATGAGGTACGTAGTA 60.742 52.174 0.00 0.00 40.30 1.82
8462 17440 6.488006 GTCCACTTCTTATATTGGCATCACAT 59.512 38.462 0.00 0.00 0.00 3.21
8481 17459 7.907214 TCACATTAGTAGAAAAAGAGGCTTC 57.093 36.000 0.00 0.00 0.00 3.86
8512 17490 3.130340 CCCATTAGTCCCCAAAACAATCG 59.870 47.826 0.00 0.00 0.00 3.34
8517 17495 1.957877 GTCCCCAAAACAATCGAACCA 59.042 47.619 0.00 0.00 0.00 3.67
9634 18965 8.447833 GTTGACTTAACGATCATGGTTGAAATA 58.552 33.333 0.00 0.00 34.96 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
239 263 3.385755 AGCCAGCAGACAAACAATTTCTT 59.614 39.130 0.00 0.00 0.00 2.52
247 271 2.159653 CGATGTTAGCCAGCAGACAAAC 60.160 50.000 2.86 0.00 0.00 2.93
249 273 1.275010 TCGATGTTAGCCAGCAGACAA 59.725 47.619 2.86 0.00 0.00 3.18
258 282 0.100682 TCGTGCTCTCGATGTTAGCC 59.899 55.000 6.71 0.00 35.33 3.93
264 288 4.700037 GAGGTCGTGCTCTCGATG 57.300 61.111 0.00 0.00 41.78 3.84
270 294 0.248539 GTGATACCGAGGTCGTGCTC 60.249 60.000 0.00 0.00 37.74 4.26
276 300 2.619646 GAGAAGAGGTGATACCGAGGTC 59.380 54.545 0.00 0.00 44.90 3.85
286 310 2.520069 GGTCTGTGAGAGAAGAGGTGA 58.480 52.381 0.00 0.00 30.26 4.02
299 323 0.744281 GTTTTGTGGGTGGGTCTGTG 59.256 55.000 0.00 0.00 0.00 3.66
304 328 2.239681 TCAAAGTTTTGTGGGTGGGT 57.760 45.000 4.67 0.00 39.18 4.51
381 406 2.170166 CAAAGTTGCCCAAGCCAGATA 58.830 47.619 0.00 0.00 38.69 1.98
435 470 2.092049 TCATCGGAGCACTAGGGAGTAA 60.092 50.000 0.00 0.00 33.32 2.24
438 473 0.958091 CTCATCGGAGCACTAGGGAG 59.042 60.000 0.00 0.00 33.67 4.30
439 474 0.259065 ACTCATCGGAGCACTAGGGA 59.741 55.000 0.00 0.00 45.42 4.20
440 475 1.067821 GAACTCATCGGAGCACTAGGG 59.932 57.143 0.00 0.00 45.42 3.53
441 476 1.751351 TGAACTCATCGGAGCACTAGG 59.249 52.381 0.00 0.00 45.42 3.02
442 477 3.510388 TTGAACTCATCGGAGCACTAG 57.490 47.619 0.00 0.00 45.42 2.57
443 478 3.489229 CGATTGAACTCATCGGAGCACTA 60.489 47.826 0.00 0.00 45.42 2.74
444 479 2.736719 CGATTGAACTCATCGGAGCACT 60.737 50.000 0.00 0.00 45.42 4.40
465 500 4.173256 CGGCAATTTGGATTTCTTACCAC 58.827 43.478 0.00 0.00 35.81 4.16
469 504 4.016444 AGAGCGGCAATTTGGATTTCTTA 58.984 39.130 1.45 0.00 0.00 2.10
549 596 4.141482 GCTTCAAAGAGATATACCCACCCA 60.141 45.833 0.00 0.00 0.00 4.51
615 693 5.028375 GCTTAATTAGTGCGCACTTTTAGG 58.972 41.667 44.31 35.33 42.54 2.69
618 696 3.254657 TGGCTTAATTAGTGCGCACTTTT 59.745 39.130 44.31 35.49 42.54 2.27
642 725 0.529337 TGCGCATGGTTTGTTGGTTG 60.529 50.000 5.66 0.00 0.00 3.77
861 1295 0.734889 GTTGCTGCCGCTTGTATGAT 59.265 50.000 0.70 0.00 36.97 2.45
1179 1645 4.102210 TCATTTGCCCAAATTTTGACCTGA 59.898 37.500 10.72 2.71 38.84 3.86
1882 2518 9.554724 TGATACGAATCAAAAGCAAAGATAAAC 57.445 29.630 0.00 0.00 39.20 2.01
2419 7935 6.670027 TGCTTTAAAAGATATTTGGGCCCTAA 59.330 34.615 25.70 23.40 0.00 2.69
2466 7984 4.533919 TGCATGACCCAATTGTTTTAGG 57.466 40.909 4.43 0.25 0.00 2.69
2850 8380 2.409651 CGTCTAGCTCCGCCACTC 59.590 66.667 0.00 0.00 0.00 3.51
2857 8387 0.831307 AAACATCCCCGTCTAGCTCC 59.169 55.000 0.00 0.00 0.00 4.70
2940 8470 0.179121 GACGTGGATCCATGCGTGTA 60.179 55.000 28.96 0.00 37.71 2.90
3576 9119 2.545526 AGTTGTCATGTCGCTGAACTTG 59.454 45.455 0.00 0.00 0.00 3.16
3646 9189 4.214327 TGTGACAGTCACCGCGCA 62.214 61.111 27.51 8.80 46.40 6.09
3801 9347 2.353573 GGCCGAACCAAAGCCCTA 59.646 61.111 0.00 0.00 41.00 3.53
3849 9395 1.349688 TGCTCACATTAGTCCCGGTTT 59.650 47.619 0.00 0.00 0.00 3.27
4369 10028 7.669427 TGAGGATTCTAAACATTTGCAAACAT 58.331 30.769 15.41 2.21 0.00 2.71
4542 10216 7.334090 TGACCAGATTTGACCAAAATTCAAAA 58.666 30.769 1.90 0.00 44.14 2.44
4545 10219 6.477053 TTGACCAGATTTGACCAAAATTCA 57.523 33.333 0.00 0.00 38.64 2.57
4547 10221 6.762661 CAGTTTGACCAGATTTGACCAAAATT 59.237 34.615 0.00 0.00 38.64 1.82
4548 10222 6.127083 ACAGTTTGACCAGATTTGACCAAAAT 60.127 34.615 0.00 0.00 41.33 1.82
4551 10225 4.097741 CACAGTTTGACCAGATTTGACCAA 59.902 41.667 0.00 0.00 0.00 3.67
4552 10226 3.631686 CACAGTTTGACCAGATTTGACCA 59.368 43.478 0.00 0.00 0.00 4.02
4553 10227 3.004734 CCACAGTTTGACCAGATTTGACC 59.995 47.826 0.00 0.00 0.00 4.02
4554 10228 3.632145 ACCACAGTTTGACCAGATTTGAC 59.368 43.478 0.00 0.00 0.00 3.18
4555 10229 3.882888 GACCACAGTTTGACCAGATTTGA 59.117 43.478 0.00 0.00 0.00 2.69
4556 10230 3.631686 TGACCACAGTTTGACCAGATTTG 59.368 43.478 0.00 0.00 0.00 2.32
4557 10231 3.897239 TGACCACAGTTTGACCAGATTT 58.103 40.909 0.00 0.00 0.00 2.17
4562 10236 2.796557 TGTTTGACCACAGTTTGACCA 58.203 42.857 0.00 0.00 0.00 4.02
4563 10237 3.859411 TTGTTTGACCACAGTTTGACC 57.141 42.857 0.00 0.00 0.00 4.02
4564 10238 4.111916 CCATTGTTTGACCACAGTTTGAC 58.888 43.478 0.00 0.00 0.00 3.18
4569 10243 3.011566 TGACCATTGTTTGACCACAGT 57.988 42.857 0.00 0.00 0.00 3.55
4570 10244 4.111916 GTTTGACCATTGTTTGACCACAG 58.888 43.478 0.00 0.00 0.00 3.66
4572 10246 4.385358 AGTTTGACCATTGTTTGACCAC 57.615 40.909 0.00 0.00 0.00 4.16
4574 10248 9.705290 AATAATTAGTTTGACCATTGTTTGACC 57.295 29.630 0.00 0.00 0.00 4.02
4769 10532 6.183360 GGAATTTAGCTTGAGCATGAAGTCAT 60.183 38.462 5.70 0.00 45.16 3.06
4970 10831 4.262420 GGTAACACCAACCGGTACTAAAGA 60.262 45.833 8.00 0.00 46.94 2.52
5055 10916 3.593096 CCTTTAGTCCCGGTTCTTACAC 58.407 50.000 0.00 0.00 0.00 2.90
5056 10917 2.568509 CCCTTTAGTCCCGGTTCTTACA 59.431 50.000 0.00 0.00 0.00 2.41
5059 10920 0.989602 CCCCTTTAGTCCCGGTTCTT 59.010 55.000 0.00 0.00 0.00 2.52
5060 10921 0.912968 CCCCCTTTAGTCCCGGTTCT 60.913 60.000 0.00 0.15 0.00 3.01
5078 10939 1.829849 AGGGTCGTTACTAAAGCCTCC 59.170 52.381 0.00 0.00 36.14 4.30
5079 10940 3.606595 AAGGGTCGTTACTAAAGCCTC 57.393 47.619 0.00 0.00 39.91 4.70
5080 10941 4.529769 ACTAAAGGGTCGTTACTAAAGCCT 59.470 41.667 0.00 0.00 42.52 4.58
5084 10946 5.460646 CGTGACTAAAGGGTCGTTACTAAA 58.539 41.667 0.00 0.00 38.91 1.85
5091 10953 1.000171 GAACCGTGACTAAAGGGTCGT 60.000 52.381 0.00 0.00 37.33 4.34
5112 10974 0.392595 GGCCTTTAGTCCCGGTTCTG 60.393 60.000 0.00 0.00 0.00 3.02
5307 11722 0.251634 GCCCTCCTTCCTCTCTTGTG 59.748 60.000 0.00 0.00 0.00 3.33
5587 12051 8.006298 TGGGTTAAAGTTAAGCATGATTATGG 57.994 34.615 3.91 0.00 41.56 2.74
5632 12098 4.414852 CCACAAGATGGTTTGCTATTTCG 58.585 43.478 0.00 0.00 44.46 3.46
5744 12218 6.665992 TTAGAAGTGTTCCTGTGATGTACT 57.334 37.500 0.00 0.00 0.00 2.73
6569 14151 8.564574 TGTGACAAAGTTTACCTCATTTGATAC 58.435 33.333 3.73 3.33 36.41 2.24
6664 14246 2.604139 TCCCCACTTTTTCCATGAACC 58.396 47.619 0.00 0.00 0.00 3.62
6825 15466 4.081420 ACAACTTACCGAGATGCTCAAGAT 60.081 41.667 0.00 0.00 31.75 2.40
7181 15825 3.053842 AGGTTGCACAGAGATTCCATCAT 60.054 43.478 0.00 0.00 0.00 2.45
7223 15867 0.171903 GCACCATCATCCACAACTGC 59.828 55.000 0.00 0.00 0.00 4.40
7242 15886 3.927142 GTCAACCGAATACTTGGTCTGAG 59.073 47.826 0.00 0.00 37.54 3.35
7263 15907 2.852449 TCTTCCAAGCTATGATTGGGGT 59.148 45.455 13.56 0.00 46.03 4.95
7316 15960 7.093902 CCTCGGTATAACTATGATAGGCAGAAA 60.094 40.741 4.27 0.00 0.00 2.52
8067 16759 3.795623 ACGATGGACAGTGGTATGTAC 57.204 47.619 0.00 0.00 34.35 2.90
8068 16760 4.521639 GGATACGATGGACAGTGGTATGTA 59.478 45.833 0.00 0.00 32.25 2.29
8069 16761 3.321111 GGATACGATGGACAGTGGTATGT 59.679 47.826 0.00 0.00 35.68 2.29
8462 17440 7.039882 CGTATGGAAGCCTCTTTTTCTACTAA 58.960 38.462 0.00 0.00 0.00 2.24
8481 17459 0.036306 GGACTAATGGGGGCGTATGG 59.964 60.000 0.00 0.00 0.00 2.74
8512 17490 1.100510 GGCCCCTTTTATCGTGGTTC 58.899 55.000 0.00 0.00 0.00 3.62
8517 17495 3.680754 CGACTAAAGGCCCCTTTTATCGT 60.681 47.826 23.46 14.83 42.93 3.73
8521 17499 1.676615 CGCGACTAAAGGCCCCTTTTA 60.677 52.381 16.74 0.00 42.93 1.52
8769 17819 7.223971 GTGAAACCGTACAGATGAATTGCTATA 59.776 37.037 0.00 0.00 0.00 1.31
8770 17820 6.037172 GTGAAACCGTACAGATGAATTGCTAT 59.963 38.462 0.00 0.00 0.00 2.97
9912 19247 4.311816 AGACAAATGAGTGGCAAAAGTG 57.688 40.909 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.