Multiple sequence alignment - TraesCS5B01G286600

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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 TraesCS5B01G286600 chr5B 100.000 6347 0 0 1 6347 472744368 472738022 0.000000e+00 11721.0
1 TraesCS5B01G286600 chr5B 98.540 137 2 0 5753 5889 472738485 472738349 6.360000e-60 243.0
2 TraesCS5B01G286600 chr5B 98.540 137 2 0 5884 6020 472738616 472738480 6.360000e-60 243.0
3 TraesCS5B01G286600 chr5B 90.816 98 5 2 5751 5847 51843391 51843297 1.860000e-25 128.0
4 TraesCS5B01G286600 chr5B 97.101 69 0 1 6281 6347 442396472 442396540 1.450000e-21 115.0
5 TraesCS5B01G286600 chr5B 93.151 73 4 1 6164 6236 705133011 705133082 8.700000e-19 106.0
6 TraesCS5B01G286600 chr5B 74.254 268 55 11 3440 3700 531642830 531643090 4.050000e-17 100.0
7 TraesCS5B01G286600 chr5B 80.952 126 18 4 3584 3706 531705356 531705234 1.880000e-15 95.3
8 TraesCS5B01G286600 chr5B 86.301 73 9 1 6164 6236 318405767 318405838 1.900000e-10 78.7
9 TraesCS5B01G286600 chr5B 84.848 66 7 3 6158 6222 30868236 30868173 5.310000e-06 63.9
10 TraesCS5B01G286600 chr5D 98.477 2954 17 7 1 2952 391981908 391978981 0.000000e+00 5180.0
11 TraesCS5B01G286600 chr5D 99.386 1792 11 0 2914 4705 391978981 391977190 0.000000e+00 3249.0
12 TraesCS5B01G286600 chr5D 98.203 946 13 2 4819 5760 391977189 391976244 0.000000e+00 1650.0
13 TraesCS5B01G286600 chr5D 88.978 372 20 4 5976 6342 391976196 391975841 2.100000e-119 440.0
14 TraesCS5B01G286600 chr5D 90.411 146 10 3 4688 4831 420228151 420228294 8.400000e-44 189.0
15 TraesCS5B01G286600 chr5D 73.743 358 73 18 3440 3788 437808996 437808651 3.110000e-23 121.0
16 TraesCS5B01G286600 chr5D 72.951 366 70 22 3440 3788 437696065 437696418 4.050000e-17 100.0
17 TraesCS5B01G286600 chr5D 86.301 73 9 1 6164 6236 280788348 280788419 1.900000e-10 78.7
18 TraesCS5B01G286600 chr5D 97.368 38 1 0 6160 6197 432925949 432925912 1.480000e-06 65.8
19 TraesCS5B01G286600 chr5A 91.020 3185 217 41 31 3176 495307853 495311007 0.000000e+00 4233.0
20 TraesCS5B01G286600 chr5A 93.553 1396 71 12 3145 4527 495311059 495312448 0.000000e+00 2061.0
21 TraesCS5B01G286600 chr5A 89.785 558 30 11 4819 5364 495312547 495313089 0.000000e+00 689.0
22 TraesCS5B01G286600 chr5A 91.975 162 11 2 4538 4697 320214405 320214244 6.400000e-55 226.0
23 TraesCS5B01G286600 chr5A 96.639 119 4 0 4704 4822 505594259 505594141 1.400000e-46 198.0
24 TraesCS5B01G286600 chr5A 80.952 126 18 4 3584 3706 552750004 552749882 1.880000e-15 95.3
25 TraesCS5B01G286600 chr5A 80.833 120 17 4 3584 3700 552676193 552676309 8.760000e-14 89.8
26 TraesCS5B01G286600 chr5A 86.301 73 9 1 6164 6236 371025733 371025662 1.900000e-10 78.7
27 TraesCS5B01G286600 chr6A 85.031 795 80 20 1439 2215 98904340 98905113 0.000000e+00 773.0
28 TraesCS5B01G286600 chr6A 89.109 101 5 5 5749 5846 147460794 147460891 3.110000e-23 121.0
29 TraesCS5B01G286600 chr3B 78.788 924 170 14 1236 2149 751109466 751108559 1.180000e-166 597.0
30 TraesCS5B01G286600 chr3B 91.667 96 4 2 5752 5846 380679455 380679547 5.160000e-26 130.0
31 TraesCS5B01G286600 chr4A 91.765 170 10 4 4531 4697 97529987 97530155 3.830000e-57 233.0
32 TraesCS5B01G286600 chr4A 92.553 94 4 1 5759 5849 236122216 236122123 1.440000e-26 132.0
33 TraesCS5B01G286600 chr4A 91.753 97 5 1 5756 5852 589013127 589013034 1.440000e-26 132.0
34 TraesCS5B01G286600 chr4A 90.099 101 5 5 5881 5978 195967841 195967939 6.680000e-25 126.0
35 TraesCS5B01G286600 chr4A 91.489 94 4 4 5757 5847 195967847 195967939 6.680000e-25 126.0
36 TraesCS5B01G286600 chr4A 90.426 94 6 3 5890 5980 236122216 236122123 3.110000e-23 121.0
37 TraesCS5B01G286600 chr4A 89.691 97 7 1 5887 5983 589013127 589013034 3.110000e-23 121.0
38 TraesCS5B01G286600 chr3D 91.515 165 12 2 4535 4697 87926164 87926000 6.400000e-55 226.0
39 TraesCS5B01G286600 chr3D 98.291 117 2 0 4704 4820 337959625 337959509 8.340000e-49 206.0
40 TraesCS5B01G286600 chr3D 92.308 91 7 0 5759 5849 528186792 528186702 5.160000e-26 130.0
41 TraesCS5B01G286600 chr3D 90.110 91 9 0 5890 5980 528186792 528186702 1.120000e-22 119.0
42 TraesCS5B01G286600 chr3D 90.217 92 7 1 5755 5846 537914043 537914132 1.120000e-22 119.0
43 TraesCS5B01G286600 chr3D 87.500 96 9 2 5882 5977 537914040 537914132 2.420000e-19 108.0
44 TraesCS5B01G286600 chr3D 84.286 70 8 2 6164 6232 428607420 428607353 1.480000e-06 65.8
45 TraesCS5B01G286600 chr3D 100.000 28 0 0 6164 6191 600598505 600598532 1.100000e-02 52.8
46 TraesCS5B01G286600 chr2D 91.018 167 13 2 4535 4699 387193692 387193858 2.300000e-54 224.0
47 TraesCS5B01G286600 chr2D 90.110 91 4 2 5889 5979 473096450 473096365 5.200000e-21 113.0
48 TraesCS5B01G286600 chr2D 85.841 113 5 7 5746 5855 310223452 310223556 6.730000e-20 110.0
49 TraesCS5B01G286600 chr2D 83.562 73 11 1 6164 6236 178868069 178868140 4.110000e-07 67.6
50 TraesCS5B01G286600 chr2D 83.077 65 8 3 6159 6222 603645697 603645759 8.890000e-04 56.5
51 TraesCS5B01G286600 chr3A 81.139 281 49 3 4538 4814 454163771 454163491 8.280000e-54 222.0
52 TraesCS5B01G286600 chr3A 89.655 174 16 2 4538 4709 93902622 93902795 2.980000e-53 220.0
53 TraesCS5B01G286600 chr2B 100.000 117 0 0 4704 4820 587232331 587232215 3.850000e-52 217.0
54 TraesCS5B01G286600 chr2B 89.205 176 15 4 4538 4710 740563570 740563396 3.850000e-52 217.0
55 TraesCS5B01G286600 chr6B 86.735 196 22 4 4538 4730 689088542 689088736 1.390000e-51 215.0
56 TraesCS5B01G286600 chr6B 75.155 483 104 12 3575 4048 411104373 411104848 4.980000e-51 213.0
57 TraesCS5B01G286600 chr6B 91.398 93 7 1 5756 5848 163967846 163967937 6.680000e-25 126.0
58 TraesCS5B01G286600 chr7D 78.638 323 61 7 2563 2884 25344998 25344683 2.320000e-49 207.0
59 TraesCS5B01G286600 chr7D 90.000 150 13 1 4675 4822 578069807 578069956 6.490000e-45 193.0
60 TraesCS5B01G286600 chr7D 88.043 92 7 2 5890 5980 264746831 264746919 8.700000e-19 106.0
61 TraesCS5B01G286600 chr6D 97.479 119 3 0 4704 4822 348647454 348647336 3.000000e-48 204.0
62 TraesCS5B01G286600 chr6D 96.000 125 4 1 4697 4821 9063568 9063691 1.080000e-47 202.0
63 TraesCS5B01G286600 chr6D 90.385 104 5 4 5751 5852 470574999 470575099 1.440000e-26 132.0
64 TraesCS5B01G286600 chr6D 89.583 96 6 3 5889 5983 470575007 470575099 1.120000e-22 119.0
65 TraesCS5B01G286600 chr6D 82.639 144 14 8 5843 5977 422327552 422327411 4.020000e-22 117.0
66 TraesCS5B01G286600 chr6D 88.235 102 3 4 5889 5981 200398713 200398814 5.200000e-21 113.0
67 TraesCS5B01G286600 chr6D 86.916 107 4 5 5889 5986 91559631 91559526 1.870000e-20 111.0
68 TraesCS5B01G286600 chr6D 93.333 75 3 1 5759 5833 91072612 91072540 6.730000e-20 110.0
69 TraesCS5B01G286600 chr6D 88.889 90 8 1 5758 5847 470575094 470575007 6.730000e-20 110.0
70 TraesCS5B01G286600 chr6D 87.000 100 4 7 5758 5851 436760914 436761010 3.130000e-18 104.0
71 TraesCS5B01G286600 chr6D 84.906 106 11 3 5745 5846 369858561 369858665 1.130000e-17 102.0
72 TraesCS5B01G286600 chr6D 87.778 90 7 2 5892 5977 369858576 369858665 1.130000e-17 102.0
73 TraesCS5B01G286600 chr6D 85.714 105 3 9 5756 5849 217918867 217918764 4.050000e-17 100.0
74 TraesCS5B01G286600 chr6D 89.286 84 3 5 5758 5839 469577297 469577218 4.050000e-17 100.0
75 TraesCS5B01G286600 chr6D 86.316 95 8 3 5758 5848 436761006 436760913 1.460000e-16 99.0
76 TraesCS5B01G286600 chr6D 86.000 100 5 8 5889 5982 436760914 436761010 1.460000e-16 99.0
77 TraesCS5B01G286600 chr6D 84.848 99 7 7 5889 5980 437956054 437955957 6.780000e-15 93.5
78 TraesCS5B01G286600 chr6D 86.905 84 7 3 5895 5977 91072532 91072612 2.440000e-14 91.6
79 TraesCS5B01G286600 chr6D 84.706 85 9 3 5897 5980 469577218 469577299 1.470000e-11 82.4
80 TraesCS5B01G286600 chr1B 89.262 149 12 3 4641 4788 204410308 204410453 3.910000e-42 183.0
81 TraesCS5B01G286600 chr1B 96.970 66 0 1 6281 6344 386539324 386539389 6.730000e-20 110.0
82 TraesCS5B01G286600 chr1B 96.970 66 0 1 6281 6344 386720069 386720134 6.730000e-20 110.0
83 TraesCS5B01G286600 chr1B 96.970 66 0 1 6281 6344 530076251 530076316 6.730000e-20 110.0
84 TraesCS5B01G286600 chr4D 94.444 90 3 2 5759 5846 401206912 401206823 3.090000e-28 137.0
85 TraesCS5B01G286600 chr4D 90.000 100 6 4 5881 5978 295575150 295575053 6.680000e-25 126.0
86 TraesCS5B01G286600 chr4D 92.222 90 5 2 5890 5977 401206912 401206823 6.680000e-25 126.0
87 TraesCS5B01G286600 chr4D 91.398 93 5 3 5757 5847 295575144 295575053 2.400000e-24 124.0
88 TraesCS5B01G286600 chr4D 89.362 94 7 1 5759 5852 303843553 303843463 1.450000e-21 115.0
89 TraesCS5B01G286600 chr4D 89.773 88 6 2 5759 5846 303843469 303843553 6.730000e-20 110.0
90 TraesCS5B01G286600 chr4D 84.956 113 12 3 5740 5850 397390686 397390795 6.730000e-20 110.0
91 TraesCS5B01G286600 chr4D 85.849 106 8 6 5748 5849 54683359 54683257 8.700000e-19 106.0
92 TraesCS5B01G286600 chr4D 87.234 94 9 2 5890 5983 303843553 303843463 3.130000e-18 104.0
93 TraesCS5B01G286600 chr4D 87.500 88 8 2 5890 5977 303843469 303843553 1.460000e-16 99.0
94 TraesCS5B01G286600 chr4D 86.316 95 6 5 5886 5978 93828286 93828197 5.240000e-16 97.1
95 TraesCS5B01G286600 chr4D 84.848 99 10 3 5885 5981 397390700 397390795 1.880000e-15 95.3
96 TraesCS5B01G286600 chr4B 91.089 101 5 2 5881 5978 364042116 364042215 3.990000e-27 134.0
97 TraesCS5B01G286600 chr4B 93.333 90 4 1 5758 5847 315723360 315723273 1.440000e-26 132.0
98 TraesCS5B01G286600 chr4B 92.553 94 4 2 5757 5847 364042122 364042215 1.440000e-26 132.0
99 TraesCS5B01G286600 chr4B 91.111 90 6 1 5889 5978 315723360 315723273 3.110000e-23 121.0
100 TraesCS5B01G286600 chr4B 87.879 99 10 1 5758 5856 315723273 315723369 1.450000e-21 115.0
101 TraesCS5B01G286600 chr4B 88.542 96 9 2 5759 5852 379084979 379084884 1.450000e-21 115.0
102 TraesCS5B01G286600 chr4B 96.970 66 0 1 6281 6344 472889055 472889120 6.730000e-20 110.0
103 TraesCS5B01G286600 chr4B 95.652 69 1 1 6281 6347 614152502 614152434 6.730000e-20 110.0
104 TraesCS5B01G286600 chr4B 87.500 96 8 3 5886 5980 432817288 432817380 2.420000e-19 108.0
105 TraesCS5B01G286600 chr4B 86.458 96 11 2 5890 5983 379084979 379084884 3.130000e-18 104.0
106 TraesCS5B01G286600 chr4B 100.000 29 0 0 6162 6190 169931520 169931548 3.000000e-03 54.7
107 TraesCS5B01G286600 chr4B 100.000 28 0 0 6163 6190 465454327 465454354 1.100000e-02 52.8
108 TraesCS5B01G286600 chr7A 91.489 94 6 1 5755 5848 475977273 475977182 1.860000e-25 128.0
109 TraesCS5B01G286600 chr2A 89.691 97 4 4 5887 5983 522505410 522505500 1.120000e-22 119.0
110 TraesCS5B01G286600 chr2A 88.889 99 7 3 5889 5987 654872303 654872209 1.120000e-22 119.0
111 TraesCS5B01G286600 chr2A 89.041 73 6 1 6164 6236 643485232 643485302 8.760000e-14 89.8
112 TraesCS5B01G286600 chrUn 84.553 123 7 7 5755 5867 348653273 348653153 1.870000e-20 111.0
113 TraesCS5B01G286600 chrUn 84.553 123 7 7 5755 5867 348655596 348655476 1.870000e-20 111.0
114 TraesCS5B01G286600 chrUn 84.553 123 7 7 5755 5867 415477409 415477289 1.870000e-20 111.0
115 TraesCS5B01G286600 chrUn 95.652 69 1 1 6281 6347 38180629 38180561 6.730000e-20 110.0
116 TraesCS5B01G286600 chrUn 89.130 92 4 5 5758 5847 92722825 92722738 6.730000e-20 110.0
117 TraesCS5B01G286600 chrUn 87.129 101 4 4 5758 5849 23574970 23574870 8.700000e-19 106.0
118 TraesCS5B01G286600 chrUn 94.203 69 2 1 6281 6347 37875001 37874933 3.130000e-18 104.0
119 TraesCS5B01G286600 chrUn 87.912 91 7 3 5889 5978 92722825 92722738 3.130000e-18 104.0
120 TraesCS5B01G286600 chrUn 94.203 69 2 1 6281 6347 289729942 289729874 3.130000e-18 104.0
121 TraesCS5B01G286600 chrUn 94.203 69 2 1 6281 6347 319330533 319330465 3.130000e-18 104.0
122 TraesCS5B01G286600 chrUn 95.385 65 1 1 6280 6342 40429997 40429933 1.130000e-17 102.0
123 TraesCS5B01G286600 chrUn 95.385 65 1 1 6280 6342 352530098 352530162 1.130000e-17 102.0
124 TraesCS5B01G286600 chrUn 86.735 98 4 4 5758 5846 27746662 27746565 4.050000e-17 100.0
125 TraesCS5B01G286600 chrUn 86.458 96 8 3 5887 5978 95593877 95593971 4.050000e-17 100.0
126 TraesCS5B01G286600 chrUn 88.043 92 2 5 5764 5846 302640136 302640045 4.050000e-17 100.0
127 TraesCS5B01G286600 chrUn 82.927 123 9 7 5886 5998 348653273 348653153 4.050000e-17 100.0
128 TraesCS5B01G286600 chrUn 82.927 123 9 7 5886 5998 348655596 348655476 4.050000e-17 100.0
129 TraesCS5B01G286600 chrUn 82.927 123 9 7 5886 5998 415477409 415477289 4.050000e-17 100.0
130 TraesCS5B01G286600 chrUn 85.149 101 10 4 5752 5850 92722731 92722828 1.460000e-16 99.0
131 TraesCS5B01G286600 chrUn 85.714 98 5 2 5890 5978 2713897 2713994 1.880000e-15 95.3
132 TraesCS5B01G286600 chrUn 85.714 98 5 2 5890 5978 2717499 2717596 1.880000e-15 95.3
133 TraesCS5B01G286600 chrUn 85.714 98 5 2 5890 5978 2780377 2780474 1.880000e-15 95.3
134 TraesCS5B01G286600 chrUn 85.149 101 6 4 5889 5980 23574970 23574870 1.880000e-15 95.3
135 TraesCS5B01G286600 chrUn 92.537 67 2 2 6281 6344 783927 783861 6.780000e-15 93.5
136 TraesCS5B01G286600 chrUn 85.567 97 5 2 5759 5846 155121189 155121093 6.780000e-15 93.5
137 TraesCS5B01G286600 chrUn 85.567 97 5 2 5759 5846 164263986 164264082 6.780000e-15 93.5
138 TraesCS5B01G286600 chrUn 92.537 67 2 2 6281 6344 253490065 253489999 6.780000e-15 93.5
139 TraesCS5B01G286600 chrUn 92.537 67 2 2 6281 6344 264414276 264414210 6.780000e-15 93.5
140 TraesCS5B01G286600 chrUn 84.466 103 7 4 5753 5846 371149022 371149124 6.780000e-15 93.5
141 TraesCS5B01G286600 chrUn 84.694 98 6 4 5889 5977 27746662 27746565 8.760000e-14 89.8
142 TraesCS5B01G286600 chrUn 98.039 51 1 0 5797 5847 48471430 48471380 8.760000e-14 89.8
143 TraesCS5B01G286600 chrUn 98.039 51 1 0 5797 5847 48498208 48498158 8.760000e-14 89.8
144 TraesCS5B01G286600 chrUn 84.694 98 6 2 5889 5977 79951804 79951901 8.760000e-14 89.8
145 TraesCS5B01G286600 chrUn 85.000 100 2 3 5760 5846 91247060 91246961 8.760000e-14 89.8
146 TraesCS5B01G286600 chrUn 98.039 51 1 0 5797 5847 235113531 235113481 8.760000e-14 89.8
147 TraesCS5B01G286600 chrUn 96.296 54 1 1 5793 5846 50416612 50416664 3.150000e-13 87.9
148 TraesCS5B01G286600 chrUn 83.495 103 5 6 5755 5847 12893995 12894095 1.130000e-12 86.1
149 TraesCS5B01G286600 chrUn 84.375 96 6 4 5893 5979 89396860 89396765 1.130000e-12 86.1
150 TraesCS5B01G286600 chrUn 81.982 111 9 6 5755 5855 2713997 2713888 4.080000e-12 84.2
151 TraesCS5B01G286600 chrUn 81.982 111 9 6 5755 5855 2717599 2717490 4.080000e-12 84.2
152 TraesCS5B01G286600 chrUn 81.982 111 9 6 5755 5855 2780477 2780368 4.080000e-12 84.2
153 TraesCS5B01G286600 chrUn 97.917 48 1 0 5931 5978 48471427 48471380 4.080000e-12 84.2
154 TraesCS5B01G286600 chrUn 97.917 48 1 0 5931 5978 48498205 48498158 4.080000e-12 84.2
155 TraesCS5B01G286600 chrUn 96.078 51 2 0 5927 5977 91247011 91246961 4.080000e-12 84.2
156 TraesCS5B01G286600 chrUn 83.168 101 8 5 5886 5977 102519288 102519388 4.080000e-12 84.2
157 TraesCS5B01G286600 chrUn 97.917 48 1 0 5931 5978 235113528 235113481 4.080000e-12 84.2
158 TraesCS5B01G286600 chrUn 96.078 51 2 0 5928 5978 237211131 237211181 4.080000e-12 84.2
159 TraesCS5B01G286600 chrUn 94.444 54 2 1 5924 5977 50416612 50416664 1.470000e-11 82.4
160 TraesCS5B01G286600 chrUn 81.905 105 8 6 5755 5849 27746561 27746664 1.900000e-10 78.7
161 TraesCS5B01G286600 chrUn 82.653 98 6 6 5890 5977 362465803 362465899 6.820000e-10 76.8
162 TraesCS5B01G286600 chrUn 83.721 86 8 5 5756 5839 389289577 389289496 6.820000e-10 76.8
163 TraesCS5B01G286600 chrUn 92.453 53 2 1 5755 5807 108661286 108661236 2.450000e-09 75.0
164 TraesCS5B01G286600 chrUn 81.553 103 7 7 5886 5977 124699918 124699817 2.450000e-09 75.0
165 TraesCS5B01G286600 chrUn 79.630 108 8 4 5755 5850 22130823 22130718 1.480000e-06 65.8
166 TraesCS5B01G286600 chrUn 88.679 53 4 1 5758 5810 48471380 48471430 5.310000e-06 63.9
167 TraesCS5B01G286600 chrUn 88.679 53 4 1 5758 5810 48498158 48498208 5.310000e-06 63.9
168 TraesCS5B01G286600 chrUn 86.667 60 5 2 5758 5816 267452864 267452921 5.310000e-06 63.9
169 TraesCS5B01G286600 chrUn 86.667 60 5 2 5758 5816 340256232 340256289 5.310000e-06 63.9
170 TraesCS5B01G286600 chr1D 95.652 69 1 1 6281 6347 37367701 37367633 6.730000e-20 110.0
171 TraesCS5B01G286600 chr1D 95.652 69 1 1 6281 6347 37414856 37414788 6.730000e-20 110.0
172 TraesCS5B01G286600 chr1D 87.755 98 6 5 5755 5849 120537706 120537612 6.730000e-20 110.0
173 TraesCS5B01G286600 chr1D 81.159 138 22 4 4269 4404 457936990 457936855 2.420000e-19 108.0
174 TraesCS5B01G286600 chr1D 94.203 69 2 1 6281 6347 37320293 37320225 3.130000e-18 104.0
175 TraesCS5B01G286600 chr1D 87.097 93 11 1 5757 5848 412026963 412027055 3.130000e-18 104.0
176 TraesCS5B01G286600 chr1D 88.462 78 6 3 6160 6236 444856710 444856785 2.440000e-14 91.6
177 TraesCS5B01G286600 chr1D 84.932 73 10 1 6164 6236 302671821 302671750 8.830000e-09 73.1
178 TraesCS5B01G286600 chr1A 85.859 99 9 5 5886 5982 8040593 8040688 4.050000e-17 100.0


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 TraesCS5B01G286600 chr5B 472738022 472744368 6346 True 11721.000000 11721 100.000000 1 6347 1 chr5B.!!$R3 6346
1 TraesCS5B01G286600 chr5D 391975841 391981908 6067 True 2629.750000 5180 96.261000 1 6342 4 chr5D.!!$R3 6341
2 TraesCS5B01G286600 chr5A 495307853 495313089 5236 False 2327.666667 4233 91.452667 31 5364 3 chr5A.!!$F2 5333
3 TraesCS5B01G286600 chr6A 98904340 98905113 773 False 773.000000 773 85.031000 1439 2215 1 chr6A.!!$F1 776
4 TraesCS5B01G286600 chr3B 751108559 751109466 907 True 597.000000 597 78.788000 1236 2149 1 chr3B.!!$R1 913

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
571 590 1.219664 CCACGCGAAATCCCCTGTA 59.780 57.895 15.93 0.00 0.00 2.74 F
1533 1559 0.780002 GCTGCAAATTTGTCTGCACG 59.220 50.000 24.95 13.15 43.44 5.34 F
2562 2617 2.046314 AATCAAGCGGTGGTCGGG 60.046 61.111 0.00 0.00 39.69 5.14 F
2867 2927 2.507471 AGGCAGTCCTGGGAAAGAATAG 59.493 50.000 0.00 0.00 42.34 1.73 F
4723 4919 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2257 3.733988 GCGAAAGGGCTTAAAGGTAATGC 60.734 47.826 0.00 0.00 0.00 3.56 R
2867 2927 5.408604 CACTTGGTCATGGTTACAGTAAGAC 59.591 44.000 0.00 0.00 0.00 3.01 R
3741 3932 5.407407 ACGATGAAGTGAGACTTAACCAT 57.593 39.130 0.00 0.00 38.80 3.55 R
4706 4902 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
5599 5810 0.247736 CTCGCAAGCTACCAAGAGGT 59.752 55.000 0.00 0.00 45.36 3.85 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
115 116 3.256631 GCTTTGGTTGGATGTGTTGATCT 59.743 43.478 0.00 0.00 0.00 2.75
235 236 2.743718 CAGGGGCACTCGTGACTT 59.256 61.111 2.53 0.00 39.02 3.01
305 309 5.484715 CAAATGAGTTCTAGGGGTCGTTTA 58.515 41.667 0.00 0.00 29.15 2.01
448 456 6.366340 TCATCGTATCTTACCTTCTCCTCTT 58.634 40.000 0.00 0.00 0.00 2.85
571 590 1.219664 CCACGCGAAATCCCCTGTA 59.780 57.895 15.93 0.00 0.00 2.74
1533 1559 0.780002 GCTGCAAATTTGTCTGCACG 59.220 50.000 24.95 13.15 43.44 5.34
1807 1849 3.076350 TGGATACACGTGGGGAACT 57.924 52.632 21.57 0.00 46.17 3.01
1895 1938 4.278419 GTGTGTTGTTTGCTTCCTCCTTAT 59.722 41.667 0.00 0.00 0.00 1.73
2204 2257 4.520111 TGTGGATGAAATGGAAGACTTGTG 59.480 41.667 0.00 0.00 0.00 3.33
2562 2617 2.046314 AATCAAGCGGTGGTCGGG 60.046 61.111 0.00 0.00 39.69 5.14
2599 2658 5.659440 AATAGGCGGTGTTTCATCAATTT 57.341 34.783 0.00 0.00 0.00 1.82
2600 2659 5.659440 ATAGGCGGTGTTTCATCAATTTT 57.341 34.783 0.00 0.00 0.00 1.82
2867 2927 2.507471 AGGCAGTCCTGGGAAAGAATAG 59.493 50.000 0.00 0.00 42.34 1.73
3116 3218 4.932799 TGCTTTTGATTTTGCTGATCATGG 59.067 37.500 0.00 0.00 33.82 3.66
3663 3854 5.437060 TCAGCAAGTTTGGTTAGAACTTCT 58.563 37.500 0.00 0.00 43.44 2.85
3741 3932 5.766670 ACTCTTTGCTTGTTCATTCAGATGA 59.233 36.000 0.00 0.00 40.46 2.92
4669 4865 9.932207 TGTAGTCCGTATTGAAATCTCTAAAAA 57.068 29.630 0.00 0.00 0.00 1.94
4705 4901 4.097135 GGAACGGAGGGAGTAGTTAGTTAC 59.903 50.000 0.00 0.00 0.00 2.50
4706 4902 4.582973 ACGGAGGGAGTAGTTAGTTACT 57.417 45.455 0.00 0.00 41.04 2.24
4707 4903 4.522114 ACGGAGGGAGTAGTTAGTTACTC 58.478 47.826 4.93 4.93 45.67 2.59
4714 4910 4.522114 GAGTAGTTAGTTACTCCCTCCGT 58.478 47.826 0.00 0.00 42.32 4.69
4715 4911 4.522114 AGTAGTTAGTTACTCCCTCCGTC 58.478 47.826 0.00 0.00 38.33 4.79
4716 4912 2.732763 AGTTAGTTACTCCCTCCGTCC 58.267 52.381 0.00 0.00 28.23 4.79
4717 4913 1.403323 GTTAGTTACTCCCTCCGTCCG 59.597 57.143 0.00 0.00 0.00 4.79
4718 4914 0.107017 TAGTTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
4719 4915 1.379044 GTTACTCCCTCCGTCCGGA 60.379 63.158 0.00 0.00 42.90 5.14
4720 4916 0.967380 GTTACTCCCTCCGTCCGGAA 60.967 60.000 5.23 0.00 44.66 4.30
4721 4917 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
4722 4918 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4723 4919 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4724 4920 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4725 4921 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4726 4922 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4727 4923 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4728 4924 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4729 4925 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4730 4926 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4731 4927 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
4732 4928 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
4733 4929 3.500982 CGTCCGGAAATACTTGTCGTAA 58.499 45.455 5.23 0.00 0.00 3.18
4734 4930 3.919804 CGTCCGGAAATACTTGTCGTAAA 59.080 43.478 5.23 0.00 0.00 2.01
4735 4931 4.385447 CGTCCGGAAATACTTGTCGTAAAA 59.615 41.667 5.23 0.00 0.00 1.52
4736 4932 5.107530 CGTCCGGAAATACTTGTCGTAAAAA 60.108 40.000 5.23 0.00 0.00 1.94
4737 4933 6.401367 CGTCCGGAAATACTTGTCGTAAAAAT 60.401 38.462 5.23 0.00 0.00 1.82
4738 4934 6.739550 GTCCGGAAATACTTGTCGTAAAAATG 59.260 38.462 5.23 0.00 0.00 2.32
4739 4935 6.649973 TCCGGAAATACTTGTCGTAAAAATGA 59.350 34.615 0.00 0.00 0.00 2.57
4740 4936 7.172875 TCCGGAAATACTTGTCGTAAAAATGAA 59.827 33.333 0.00 0.00 0.00 2.57
4741 4937 7.966204 CCGGAAATACTTGTCGTAAAAATGAAT 59.034 33.333 0.00 0.00 0.00 2.57
4742 4938 9.976255 CGGAAATACTTGTCGTAAAAATGAATA 57.024 29.630 0.00 0.00 0.00 1.75
4749 4945 9.405587 ACTTGTCGTAAAAATGAATACAAATGG 57.594 29.630 0.00 0.00 0.00 3.16
4750 4946 9.619316 CTTGTCGTAAAAATGAATACAAATGGA 57.381 29.630 0.00 0.00 0.00 3.41
4752 4948 9.566530 TGTCGTAAAAATGAATACAAATGGATG 57.433 29.630 0.00 0.00 0.00 3.51
4753 4949 9.567848 GTCGTAAAAATGAATACAAATGGATGT 57.432 29.630 0.00 0.00 37.32 3.06
4792 4988 6.522625 ACATCTAGATACATCCATTCCTCG 57.477 41.667 4.54 0.00 0.00 4.63
4793 4989 5.420421 ACATCTAGATACATCCATTCCTCGG 59.580 44.000 4.54 0.00 0.00 4.63
4794 4990 5.256806 TCTAGATACATCCATTCCTCGGA 57.743 43.478 0.00 0.00 36.84 4.55
4795 4991 5.010933 TCTAGATACATCCATTCCTCGGAC 58.989 45.833 0.00 0.00 34.69 4.79
4796 4992 3.576861 AGATACATCCATTCCTCGGACA 58.423 45.455 0.00 0.00 34.69 4.02
4797 4993 3.967326 AGATACATCCATTCCTCGGACAA 59.033 43.478 0.00 0.00 34.69 3.18
4798 4994 2.698855 ACATCCATTCCTCGGACAAG 57.301 50.000 0.00 0.00 34.69 3.16
4799 4995 1.909302 ACATCCATTCCTCGGACAAGT 59.091 47.619 0.00 0.00 34.69 3.16
4800 4996 3.104512 ACATCCATTCCTCGGACAAGTA 58.895 45.455 0.00 0.00 34.69 2.24
4801 4997 3.711704 ACATCCATTCCTCGGACAAGTAT 59.288 43.478 0.00 0.00 34.69 2.12
4802 4998 4.164221 ACATCCATTCCTCGGACAAGTATT 59.836 41.667 0.00 0.00 34.69 1.89
4803 4999 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
4804 5000 4.766375 TCCATTCCTCGGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
4805 5001 3.877508 CCATTCCTCGGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
4811 5007 1.648504 GGACAAGTATTTCCGGACGG 58.351 55.000 1.83 3.96 0.00 4.79
4812 5008 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
4813 5009 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4814 5010 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4815 5011 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4816 5012 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4817 5013 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
5222 5429 2.942376 TGTTTACTCTGGTTGCACACAG 59.058 45.455 9.92 9.92 36.07 3.66
5394 5601 4.245660 ACGTGATAATGGTGTTCAGTCAG 58.754 43.478 0.00 0.00 0.00 3.51
5417 5624 5.363580 AGAATTGTCTTGGAAATGTGGTGTT 59.636 36.000 0.00 0.00 0.00 3.32
5528 5736 9.667107 AAACGTTTAGGATGATTTGATCTCTAA 57.333 29.630 12.83 0.00 0.00 2.10
5675 5886 3.933332 AGGCTACAGCGAAGTATGAAAAC 59.067 43.478 0.00 0.00 43.26 2.43
5744 5955 3.197116 CCAACCCATTTACGGACTACTCT 59.803 47.826 0.00 0.00 0.00 3.24
5747 5958 4.351127 ACCCATTTACGGACTACTCTCTT 58.649 43.478 0.00 0.00 0.00 2.85
5758 5969 7.668492 ACGGACTACTCTCTTTGTTTCTAAAT 58.332 34.615 0.00 0.00 0.00 1.40
5759 5970 8.800332 ACGGACTACTCTCTTTGTTTCTAAATA 58.200 33.333 0.00 0.00 0.00 1.40
5760 5971 9.074443 CGGACTACTCTCTTTGTTTCTAAATAC 57.926 37.037 0.00 0.00 0.00 1.89
5764 5975 9.589111 CTACTCTCTTTGTTTCTAAATACTCCC 57.411 37.037 0.00 0.00 0.00 4.30
5765 5976 8.208575 ACTCTCTTTGTTTCTAAATACTCCCT 57.791 34.615 0.00 0.00 0.00 4.20
5766 5977 8.315482 ACTCTCTTTGTTTCTAAATACTCCCTC 58.685 37.037 0.00 0.00 0.00 4.30
5767 5978 7.621796 TCTCTTTGTTTCTAAATACTCCCTCC 58.378 38.462 0.00 0.00 0.00 4.30
5768 5979 6.403878 TCTTTGTTTCTAAATACTCCCTCCG 58.596 40.000 0.00 0.00 0.00 4.63
5769 5980 5.750352 TTGTTTCTAAATACTCCCTCCGT 57.250 39.130 0.00 0.00 0.00 4.69
5770 5981 5.334724 TGTTTCTAAATACTCCCTCCGTC 57.665 43.478 0.00 0.00 0.00 4.79
5771 5982 4.161001 TGTTTCTAAATACTCCCTCCGTCC 59.839 45.833 0.00 0.00 0.00 4.79
5772 5983 2.954792 TCTAAATACTCCCTCCGTCCC 58.045 52.381 0.00 0.00 0.00 4.46
5773 5984 2.245546 TCTAAATACTCCCTCCGTCCCA 59.754 50.000 0.00 0.00 0.00 4.37
5774 5985 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
5775 5986 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
5776 5987 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
5777 5988 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5778 5989 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5779 5990 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5780 5991 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5781 5992 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5782 5993 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5783 5994 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5784 5995 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5785 5996 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5786 5997 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5787 5998 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5788 5999 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5789 6000 4.700213 CCGTCCCAAAATAAGTGTCTCAAT 59.300 41.667 0.00 0.00 0.00 2.57
5790 6001 5.183140 CCGTCCCAAAATAAGTGTCTCAATT 59.817 40.000 0.00 0.00 0.00 2.32
5791 6002 6.294508 CCGTCCCAAAATAAGTGTCTCAATTT 60.295 38.462 0.00 0.00 0.00 1.82
5792 6003 7.145323 CGTCCCAAAATAAGTGTCTCAATTTT 58.855 34.615 0.00 0.00 33.07 1.82
5793 6004 7.651704 CGTCCCAAAATAAGTGTCTCAATTTTT 59.348 33.333 0.00 0.00 31.05 1.94
5821 6032 6.846325 ACAAAGTTGTACTAAGCTTGAGAC 57.154 37.500 9.86 4.39 40.16 3.36
5822 6033 6.346096 ACAAAGTTGTACTAAGCTTGAGACA 58.654 36.000 9.86 7.12 40.16 3.41
5823 6034 6.258068 ACAAAGTTGTACTAAGCTTGAGACAC 59.742 38.462 9.86 7.18 40.16 3.67
5824 6035 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
5825 6036 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
5826 6037 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
5827 6038 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
5828 6039 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
5829 6040 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
5830 6041 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
5831 6042 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
5832 6043 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
5833 6044 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
5834 6045 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
5835 6046 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
5836 6047 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
5837 6048 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5838 6049 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5839 6050 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5840 6051 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5841 6052 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5842 6053 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5843 6054 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5854 6065 4.446889 GGGACGGAGGGAGTATAAGACTAA 60.447 50.000 0.00 0.00 39.06 2.24
5884 6095 6.327279 AGCAAAATAAGTTAACCCACACTC 57.673 37.500 0.88 0.00 0.00 3.51
5886 6097 7.228590 AGCAAAATAAGTTAACCCACACTCTA 58.771 34.615 0.88 0.00 0.00 2.43
5887 6098 7.722285 AGCAAAATAAGTTAACCCACACTCTAA 59.278 33.333 0.88 0.00 0.00 2.10
5888 6099 8.354426 GCAAAATAAGTTAACCCACACTCTAAA 58.646 33.333 0.88 0.00 0.00 1.85
5894 6105 6.944096 AGTTAACCCACACTCTAAATACTCC 58.056 40.000 0.88 0.00 0.00 3.85
5895 6106 4.838904 AACCCACACTCTAAATACTCCC 57.161 45.455 0.00 0.00 0.00 4.30
5896 6107 4.076175 ACCCACACTCTAAATACTCCCT 57.924 45.455 0.00 0.00 0.00 4.20
5897 6108 4.031611 ACCCACACTCTAAATACTCCCTC 58.968 47.826 0.00 0.00 0.00 4.30
5898 6109 3.388350 CCCACACTCTAAATACTCCCTCC 59.612 52.174 0.00 0.00 0.00 4.30
5899 6110 3.068307 CCACACTCTAAATACTCCCTCCG 59.932 52.174 0.00 0.00 0.00 4.63
5900 6111 3.700038 CACACTCTAAATACTCCCTCCGT 59.300 47.826 0.00 0.00 0.00 4.69
5901 6112 3.952967 ACACTCTAAATACTCCCTCCGTC 59.047 47.826 0.00 0.00 0.00 4.79
5902 6113 4.208746 CACTCTAAATACTCCCTCCGTCT 58.791 47.826 0.00 0.00 0.00 4.18
5903 6114 4.276431 CACTCTAAATACTCCCTCCGTCTC 59.724 50.000 0.00 0.00 0.00 3.36
5904 6115 4.079901 ACTCTAAATACTCCCTCCGTCTCA 60.080 45.833 0.00 0.00 0.00 3.27
5905 6116 4.863548 TCTAAATACTCCCTCCGTCTCAA 58.136 43.478 0.00 0.00 0.00 3.02
5906 6117 5.266788 TCTAAATACTCCCTCCGTCTCAAA 58.733 41.667 0.00 0.00 0.00 2.69
5907 6118 4.903045 AAATACTCCCTCCGTCTCAAAA 57.097 40.909 0.00 0.00 0.00 2.44
5908 6119 5.437191 AAATACTCCCTCCGTCTCAAAAT 57.563 39.130 0.00 0.00 0.00 1.82
5909 6120 6.555463 AAATACTCCCTCCGTCTCAAAATA 57.445 37.500 0.00 0.00 0.00 1.40
5910 6121 6.555463 AATACTCCCTCCGTCTCAAAATAA 57.445 37.500 0.00 0.00 0.00 1.40
5911 6122 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
5912 6123 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
5913 6124 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
5914 6125 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
5915 6126 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
5916 6127 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
5917 6128 4.865365 CCTCCGTCTCAAAATAAGTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
5918 6129 5.462530 TCCGTCTCAAAATAAGTGTCTCA 57.537 39.130 0.00 0.00 0.00 3.27
5919 6130 5.849510 TCCGTCTCAAAATAAGTGTCTCAA 58.150 37.500 0.00 0.00 0.00 3.02
5920 6131 6.464222 TCCGTCTCAAAATAAGTGTCTCAAT 58.536 36.000 0.00 0.00 0.00 2.57
5921 6132 6.934645 TCCGTCTCAAAATAAGTGTCTCAATT 59.065 34.615 0.00 0.00 0.00 2.32
5922 6133 7.444183 TCCGTCTCAAAATAAGTGTCTCAATTT 59.556 33.333 0.00 0.00 0.00 1.82
5923 6134 8.076178 CCGTCTCAAAATAAGTGTCTCAATTTT 58.924 33.333 0.00 0.00 33.07 1.82
5924 6135 9.450807 CGTCTCAAAATAAGTGTCTCAATTTTT 57.549 29.630 0.00 0.00 31.05 1.94
5949 6160 5.418310 GTGCAAAGTTGTACTAAGCTTGA 57.582 39.130 9.86 0.00 40.10 3.02
5950 6161 5.444122 GTGCAAAGTTGTACTAAGCTTGAG 58.556 41.667 9.86 5.36 40.10 3.02
5951 6162 5.236478 GTGCAAAGTTGTACTAAGCTTGAGA 59.764 40.000 9.86 0.00 40.10 3.27
5952 6163 5.236478 TGCAAAGTTGTACTAAGCTTGAGAC 59.764 40.000 9.86 4.39 31.81 3.36
5953 6164 5.236478 GCAAAGTTGTACTAAGCTTGAGACA 59.764 40.000 9.86 7.12 0.00 3.41
5954 6165 6.650372 CAAAGTTGTACTAAGCTTGAGACAC 58.350 40.000 9.86 7.18 0.00 3.67
5955 6166 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
5956 6167 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
5957 6168 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
5958 6169 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
5959 6170 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
5960 6171 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
5961 6172 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
5962 6173 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
5963 6174 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
5964 6175 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
5965 6176 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
5966 6177 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
5967 6178 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
5968 6179 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5969 6180 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5970 6181 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5971 6182 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5972 6183 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5973 6184 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5974 6185 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5985 6196 4.446889 GGGACGGAGGGAGTATAAGACTAA 60.447 50.000 0.00 0.00 39.06 2.24
6029 6240 9.880157 TTAACCCACACTCTAAAATATGTCTAC 57.120 33.333 0.00 0.00 0.00 2.59
6031 6242 8.090788 ACCCACACTCTAAAATATGTCTACAT 57.909 34.615 0.63 0.63 40.22 2.29
6096 6309 8.992835 TTTTAGGAACGGAGAGAGTATTAAAC 57.007 34.615 0.00 0.00 0.00 2.01
6109 6322 9.911788 AGAGAGTATTAAACATGTCAATCCAAT 57.088 29.630 0.00 0.00 0.00 3.16
6110 6323 9.941664 GAGAGTATTAAACATGTCAATCCAATG 57.058 33.333 0.00 0.00 0.00 2.82
6145 6358 4.759205 GGCAGAACCCGCCCCAAT 62.759 66.667 0.00 0.00 44.22 3.16
6146 6359 3.140814 GCAGAACCCGCCCCAATC 61.141 66.667 0.00 0.00 0.00 2.67
6147 6360 2.440247 CAGAACCCGCCCCAATCC 60.440 66.667 0.00 0.00 0.00 3.01
6148 6361 2.938798 AGAACCCGCCCCAATCCA 60.939 61.111 0.00 0.00 0.00 3.41
6149 6362 2.036572 GAACCCGCCCCAATCCAA 59.963 61.111 0.00 0.00 0.00 3.53
6150 6363 2.283604 AACCCGCCCCAATCCAAC 60.284 61.111 0.00 0.00 0.00 3.77
6151 6364 3.897681 AACCCGCCCCAATCCAACC 62.898 63.158 0.00 0.00 0.00 3.77
6153 6366 4.374584 CCGCCCCAATCCAACCCA 62.375 66.667 0.00 0.00 0.00 4.51
6154 6367 2.043046 CGCCCCAATCCAACCCAT 60.043 61.111 0.00 0.00 0.00 4.00
6171 6384 3.858638 ACCCATGGATTTTCTACTCCCTT 59.141 43.478 15.22 0.00 0.00 3.95
6187 6400 3.364549 TCCCTTCGTCCGGAAATACTTA 58.635 45.455 5.23 0.00 33.34 2.24
6193 6406 5.247507 TCGTCCGGAAATACTTATCGAAA 57.752 39.130 5.23 0.00 0.00 3.46
6258 6471 3.548818 GCAAAGAACTCTTGCATCGTGTT 60.549 43.478 2.79 0.00 36.12 3.32
6271 6484 3.119849 GCATCGTGTTGGTCTTAAGCATT 60.120 43.478 0.00 0.00 31.86 3.56
6283 6496 5.048083 GGTCTTAAGCATTTCCATGTGACAA 60.048 40.000 0.00 0.00 32.28 3.18
6284 6497 6.088824 GTCTTAAGCATTTCCATGTGACAAG 58.911 40.000 0.00 0.00 32.28 3.16
6298 6511 4.081406 TGTGACAAGCAAGCAAAGGATAT 58.919 39.130 0.00 0.00 0.00 1.63
6302 6515 5.709631 TGACAAGCAAGCAAAGGATATAACA 59.290 36.000 0.00 0.00 0.00 2.41
6312 6528 7.934457 AGCAAAGGATATAACACAATAGCTTG 58.066 34.615 0.00 0.00 38.39 4.01
6342 6558 7.746703 AGTAAAGGTGAGAGATAACCAAAAGT 58.253 34.615 0.00 0.00 0.00 2.66
6343 6559 6.884280 AAAGGTGAGAGATAACCAAAAGTG 57.116 37.500 0.00 0.00 0.00 3.16
6344 6560 5.825593 AGGTGAGAGATAACCAAAAGTGA 57.174 39.130 0.00 0.00 0.00 3.41
6345 6561 6.187727 AGGTGAGAGATAACCAAAAGTGAA 57.812 37.500 0.00 0.00 0.00 3.18
6346 6562 6.601332 AGGTGAGAGATAACCAAAAGTGAAA 58.399 36.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.200483 ACAACAATTTTCCAGACTTCTCCA 58.800 37.500 0.00 0.00 0.00 3.86
235 236 1.304381 GCAATTGGGCACAGGGAGA 60.304 57.895 7.72 0.00 0.00 3.71
305 309 2.979678 ACCCACTACAGTCAATTCCACT 59.020 45.455 0.00 0.00 0.00 4.00
571 590 3.960102 CCTCACTCTAGCAGGAAGAGAAT 59.040 47.826 7.09 0.00 42.63 2.40
684 704 2.063266 CAAAGTTGATGGCATGCACAC 58.937 47.619 21.36 9.99 0.00 3.82
1070 1094 4.126437 GGTTCCCCACACAAGAAAAATTG 58.874 43.478 0.00 0.00 36.22 2.32
1533 1559 8.494016 ACCACTATCTTAAATAAGAGCAACAC 57.506 34.615 8.68 0.00 44.67 3.32
1660 1695 8.263940 TCTAGTTTCAATAACAACCATACTGC 57.736 34.615 0.00 0.00 0.00 4.40
1807 1849 4.371624 ACTTCACTTGGACCATCAATCA 57.628 40.909 0.00 0.00 0.00 2.57
2084 2137 8.796475 CATACCATAACCAAATATCCCTCAAAG 58.204 37.037 0.00 0.00 0.00 2.77
2204 2257 3.733988 GCGAAAGGGCTTAAAGGTAATGC 60.734 47.826 0.00 0.00 0.00 3.56
2867 2927 5.408604 CACTTGGTCATGGTTACAGTAAGAC 59.591 44.000 0.00 0.00 0.00 3.01
3116 3218 6.015688 AGGTGAATCAATCCATGAATATGCAC 60.016 38.462 0.00 0.00 42.54 4.57
3741 3932 5.407407 ACGATGAAGTGAGACTTAACCAT 57.593 39.130 0.00 0.00 38.80 3.55
4669 4865 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4705 4901 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4706 4902 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4707 4903 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4708 4904 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4709 4905 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4710 4906 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
4711 4907 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
4712 4908 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
4713 4909 5.844301 TTTTACGACAAGTATTTCCGGAC 57.156 39.130 1.83 0.00 34.88 4.79
4714 4910 6.649973 TCATTTTTACGACAAGTATTTCCGGA 59.350 34.615 0.00 0.00 34.88 5.14
4715 4911 6.833839 TCATTTTTACGACAAGTATTTCCGG 58.166 36.000 0.00 0.00 34.88 5.14
4716 4912 8.889849 ATTCATTTTTACGACAAGTATTTCCG 57.110 30.769 0.00 0.00 34.88 4.30
4723 4919 9.405587 CCATTTGTATTCATTTTTACGACAAGT 57.594 29.630 0.00 0.00 0.00 3.16
4724 4920 9.619316 TCCATTTGTATTCATTTTTACGACAAG 57.381 29.630 0.00 0.00 0.00 3.16
4726 4922 9.566530 CATCCATTTGTATTCATTTTTACGACA 57.433 29.630 0.00 0.00 0.00 4.35
4727 4923 9.567848 ACATCCATTTGTATTCATTTTTACGAC 57.432 29.630 0.00 0.00 0.00 4.34
4766 4962 8.690884 CGAGGAATGGATGTATCTAGATGTATT 58.309 37.037 15.79 6.57 0.00 1.89
4767 4963 7.286546 CCGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
4768 4964 6.603599 CCGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
4769 4965 5.420421 CCGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
4770 4966 5.654209 TCCGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
4771 4967 5.654650 GTCCGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 37.93 1.98
4772 4968 5.010933 GTCCGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 37.93 2.43
4773 4969 4.767409 TGTCCGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 37.93 2.43
4774 4970 4.736473 TGTCCGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 37.93 1.98
4775 4971 3.576861 TGTCCGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 37.93 1.98
4776 4972 4.202264 ACTTGTCCGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 37.93 2.24
4777 4973 3.711704 ACTTGTCCGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 37.93 2.29
4778 4974 3.104512 ACTTGTCCGAGGAATGGATGTA 58.895 45.455 0.00 0.00 37.93 2.29
4779 4975 1.909302 ACTTGTCCGAGGAATGGATGT 59.091 47.619 0.00 0.00 37.93 3.06
4780 4976 2.698855 ACTTGTCCGAGGAATGGATG 57.301 50.000 0.00 0.00 37.93 3.51
4781 4977 5.368989 GAAATACTTGTCCGAGGAATGGAT 58.631 41.667 0.00 0.00 37.93 3.41
4782 4978 4.383770 GGAAATACTTGTCCGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
4783 4979 3.877508 GGAAATACTTGTCCGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
4792 4988 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
4793 4989 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4794 4990 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4795 4991 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4796 4992 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4797 4993 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4798 4994 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4799 4995 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4800 4996 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4801 4997 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
4802 4998 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
4803 4999 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
4804 5000 1.679977 TTGTACTCCCTCCGTCCGG 60.680 63.158 0.00 0.00 0.00 5.14
4805 5001 1.246056 TGTTGTACTCCCTCCGTCCG 61.246 60.000 0.00 0.00 0.00 4.79
4806 5002 1.192428 ATGTTGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
4807 5003 3.329929 AAATGTTGTACTCCCTCCGTC 57.670 47.619 0.00 0.00 0.00 4.79
4808 5004 4.766375 CATAAATGTTGTACTCCCTCCGT 58.234 43.478 0.00 0.00 0.00 4.69
4809 5005 3.560068 GCATAAATGTTGTACTCCCTCCG 59.440 47.826 0.00 0.00 0.00 4.63
4810 5006 4.335594 GTGCATAAATGTTGTACTCCCTCC 59.664 45.833 0.00 0.00 0.00 4.30
4811 5007 4.335594 GGTGCATAAATGTTGTACTCCCTC 59.664 45.833 0.00 0.00 31.35 4.30
4812 5008 4.263727 TGGTGCATAAATGTTGTACTCCCT 60.264 41.667 0.00 0.00 31.35 4.20
4813 5009 4.013728 TGGTGCATAAATGTTGTACTCCC 58.986 43.478 0.00 0.00 31.35 4.30
4814 5010 4.700213 ACTGGTGCATAAATGTTGTACTCC 59.300 41.667 0.00 0.00 31.35 3.85
4815 5011 5.880054 ACTGGTGCATAAATGTTGTACTC 57.120 39.130 0.00 0.00 31.35 2.59
4816 5012 7.663905 TCTTTACTGGTGCATAAATGTTGTACT 59.336 33.333 0.00 0.00 31.35 2.73
4817 5013 7.812648 TCTTTACTGGTGCATAAATGTTGTAC 58.187 34.615 0.00 0.00 0.00 2.90
5222 5429 6.670077 AAAGAAGTCAGACACTGAAGAAAC 57.330 37.500 2.66 0.00 42.46 2.78
5394 5601 5.200368 ACACCACATTTCCAAGACAATTC 57.800 39.130 0.00 0.00 0.00 2.17
5538 5749 2.029828 TGTTTGTCCGGCGCAATTATTT 60.030 40.909 10.83 0.00 0.00 1.40
5541 5752 0.519519 CTGTTTGTCCGGCGCAATTA 59.480 50.000 10.83 4.41 0.00 1.40
5599 5810 0.247736 CTCGCAAGCTACCAAGAGGT 59.752 55.000 0.00 0.00 45.36 3.85
5610 5821 3.831715 AAAAACATAGACCTCGCAAGC 57.168 42.857 0.00 0.00 37.18 4.01
5675 5886 2.310233 CCAGGTTGACGTGTGCTCG 61.310 63.158 0.00 0.00 0.00 5.03
5744 5955 6.013984 ACGGAGGGAGTATTTAGAAACAAAGA 60.014 38.462 0.00 0.00 0.00 2.52
5747 5958 5.337813 GGACGGAGGGAGTATTTAGAAACAA 60.338 44.000 0.00 0.00 0.00 2.83
5758 5969 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
5759 5970 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
5760 5971 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5761 5972 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5762 5973 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5763 5974 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5764 5975 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5765 5976 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5766 5977 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5767 5978 5.880054 ATTGAGACACTTATTTTGGGACG 57.120 39.130 0.00 0.00 0.00 4.79
5768 5979 8.887036 AAAAATTGAGACACTTATTTTGGGAC 57.113 30.769 0.00 0.00 32.30 4.46
5797 6008 7.437267 GTGTCTCAAGCTTAGTACAACTTTGTA 59.563 37.037 0.00 0.00 42.35 2.41
5798 6009 6.258068 GTGTCTCAAGCTTAGTACAACTTTGT 59.742 38.462 0.00 0.00 44.86 2.83
5799 6010 6.480320 AGTGTCTCAAGCTTAGTACAACTTTG 59.520 38.462 0.00 0.00 0.00 2.77
5800 6011 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
5801 6012 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
5802 6013 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
5803 6014 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
5804 6015 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
5805 6016 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
5806 6017 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
5807 6018 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
5808 6019 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
5809 6020 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
5810 6021 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
5811 6022 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
5812 6023 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
5813 6024 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
5814 6025 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
5815 6026 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5816 6027 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5817 6028 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5818 6029 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5819 6030 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5820 6031 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5821 6032 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5822 6033 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5823 6034 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5824 6035 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5825 6036 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5826 6037 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5827 6038 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
5828 6039 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
5829 6040 2.245546 TCTTATACTCCCTCCGTCCCAA 59.754 50.000 0.00 0.00 0.00 4.12
5830 6041 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
5831 6042 2.158490 AGTCTTATACTCCCTCCGTCCC 60.158 54.545 0.00 0.00 30.33 4.46
5832 6043 3.226682 AGTCTTATACTCCCTCCGTCC 57.773 52.381 0.00 0.00 30.33 4.79
5833 6044 6.897706 ATTTAGTCTTATACTCCCTCCGTC 57.102 41.667 0.00 0.00 39.80 4.79
5873 6084 5.596763 AGGGAGTATTTAGAGTGTGGGTTA 58.403 41.667 0.00 0.00 0.00 2.85
5877 6088 3.068307 CGGAGGGAGTATTTAGAGTGTGG 59.932 52.174 0.00 0.00 0.00 4.17
5879 6090 3.952967 GACGGAGGGAGTATTTAGAGTGT 59.047 47.826 0.00 0.00 0.00 3.55
5881 6092 4.079901 TGAGACGGAGGGAGTATTTAGAGT 60.080 45.833 0.00 0.00 0.00 3.24
5884 6095 5.593679 TTTGAGACGGAGGGAGTATTTAG 57.406 43.478 0.00 0.00 0.00 1.85
5886 6097 4.903045 TTTTGAGACGGAGGGAGTATTT 57.097 40.909 0.00 0.00 0.00 1.40
5887 6098 6.156429 ACTTATTTTGAGACGGAGGGAGTATT 59.844 38.462 0.00 0.00 0.00 1.89
5888 6099 5.661759 ACTTATTTTGAGACGGAGGGAGTAT 59.338 40.000 0.00 0.00 0.00 2.12
5891 6102 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
5892 6103 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
5893 6104 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
5894 6105 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
5895 6106 5.470368 TGAGACACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
5896 6107 5.462530 TGAGACACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 0.00 4.69
5897 6108 6.727824 ATTGAGACACTTATTTTGAGACGG 57.272 37.500 0.00 0.00 0.00 4.79
5898 6109 9.450807 AAAAATTGAGACACTTATTTTGAGACG 57.549 29.630 0.00 0.00 32.30 4.18
5921 6132 7.992008 AGCTTAGTACAACTTTGCACTAAAAA 58.008 30.769 13.37 0.00 42.98 1.94
5922 6133 7.562454 AGCTTAGTACAACTTTGCACTAAAA 57.438 32.000 13.37 0.00 42.98 1.52
5923 6134 7.281324 TCAAGCTTAGTACAACTTTGCACTAAA 59.719 33.333 13.37 0.10 42.98 1.85
5924 6135 6.764085 TCAAGCTTAGTACAACTTTGCACTAA 59.236 34.615 12.27 12.27 42.00 2.24
5925 6136 6.285224 TCAAGCTTAGTACAACTTTGCACTA 58.715 36.000 0.00 0.00 36.29 2.74
5926 6137 5.123227 TCAAGCTTAGTACAACTTTGCACT 58.877 37.500 0.00 0.65 38.32 4.40
5927 6138 5.236478 TCTCAAGCTTAGTACAACTTTGCAC 59.764 40.000 0.00 0.00 31.06 4.57
5928 6139 5.236478 GTCTCAAGCTTAGTACAACTTTGCA 59.764 40.000 0.00 0.00 31.06 4.08
5929 6140 5.236478 TGTCTCAAGCTTAGTACAACTTTGC 59.764 40.000 0.00 0.00 0.00 3.68
5930 6141 6.480320 AGTGTCTCAAGCTTAGTACAACTTTG 59.520 38.462 0.00 0.00 0.00 2.77
5931 6142 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
5932 6143 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
5933 6144 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
5934 6145 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
5935 6146 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
5936 6147 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
5937 6148 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
5938 6149 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
5939 6150 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
5940 6151 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
5941 6152 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
5942 6153 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
5943 6154 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
5944 6155 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
5945 6156 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
5946 6157 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5947 6158 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5948 6159 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5949 6160 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5950 6161 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5951 6162 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5952 6163 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5953 6164 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5954 6165 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5955 6166 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5956 6167 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5957 6168 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5958 6169 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
5959 6170 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
5960 6171 2.245546 TCTTATACTCCCTCCGTCCCAA 59.754 50.000 0.00 0.00 0.00 4.12
5961 6172 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
5962 6173 2.158490 AGTCTTATACTCCCTCCGTCCC 60.158 54.545 0.00 0.00 30.33 4.46
5963 6174 3.226682 AGTCTTATACTCCCTCCGTCC 57.773 52.381 0.00 0.00 30.33 4.79
5964 6175 6.897706 ATTTAGTCTTATACTCCCTCCGTC 57.102 41.667 0.00 0.00 39.80 4.79
6004 6215 9.038072 TGTAGACATATTTTAGAGTGTGGGTTA 57.962 33.333 0.00 0.00 0.00 2.85
6096 6309 2.756207 TGGACTGCATTGGATTGACATG 59.244 45.455 0.00 0.00 0.00 3.21
6109 6322 6.600388 TCTGCCTAATTAATTATGGACTGCA 58.400 36.000 19.57 14.56 0.00 4.41
6110 6323 7.363431 GTTCTGCCTAATTAATTATGGACTGC 58.637 38.462 19.57 12.00 0.00 4.40
6147 6360 3.954258 GGGAGTAGAAAATCCATGGGTTG 59.046 47.826 12.04 0.00 37.33 3.77
6148 6361 3.858638 AGGGAGTAGAAAATCCATGGGTT 59.141 43.478 13.02 8.57 37.33 4.11
6149 6362 3.474920 AGGGAGTAGAAAATCCATGGGT 58.525 45.455 13.02 0.00 37.33 4.51
6150 6363 4.464947 GAAGGGAGTAGAAAATCCATGGG 58.535 47.826 13.02 0.00 37.33 4.00
6151 6364 4.130118 CGAAGGGAGTAGAAAATCCATGG 58.870 47.826 4.97 4.97 37.33 3.66
6152 6365 4.770795 ACGAAGGGAGTAGAAAATCCATG 58.229 43.478 0.00 0.00 37.33 3.66
6153 6366 4.141688 GGACGAAGGGAGTAGAAAATCCAT 60.142 45.833 0.00 0.00 37.33 3.41
6154 6367 3.197116 GGACGAAGGGAGTAGAAAATCCA 59.803 47.826 0.00 0.00 37.33 3.41
6171 6384 4.898829 TTCGATAAGTATTTCCGGACGA 57.101 40.909 1.83 3.31 0.00 4.20
6217 6430 8.462143 TCTTTGCAGACGTATTTTAGTTCTAG 57.538 34.615 0.00 0.00 0.00 2.43
6258 6471 4.458989 GTCACATGGAAATGCTTAAGACCA 59.541 41.667 6.67 7.35 0.00 4.02
6271 6484 1.689984 TGCTTGCTTGTCACATGGAA 58.310 45.000 0.00 0.00 0.00 3.53
6283 6496 6.780457 ATTGTGTTATATCCTTTGCTTGCT 57.220 33.333 0.00 0.00 0.00 3.91
6284 6497 6.638468 GCTATTGTGTTATATCCTTTGCTTGC 59.362 38.462 0.00 0.00 0.00 4.01
6298 6511 6.869315 TTACTTGTGCAAGCTATTGTGTTA 57.131 33.333 11.43 0.00 41.99 2.41
6302 6515 4.827284 ACCTTTACTTGTGCAAGCTATTGT 59.173 37.500 11.43 2.42 41.99 2.71
6312 6528 5.351740 GGTTATCTCTCACCTTTACTTGTGC 59.648 44.000 0.00 0.00 32.51 4.57


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

AutoCloner maintained by Alex Coulton.