Multiple sequence alignment - TraesCS2B01G163300
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 | TraesCS2B01G163300 | chr2B | 100.000 | 8187 | 0 | 0 | 1 | 8187 | 135698878 | 135690692 | 0.000000e+00 | 15119.0 |
1 | TraesCS2B01G163300 | chr2B | 81.020 | 1059 | 169 | 14 | 3038 | 4068 | 148250095 | 148249041 | 0.000000e+00 | 813.0 |
2 | TraesCS2B01G163300 | chr2B | 89.791 | 382 | 27 | 5 | 934 | 1310 | 135694334 | 135693960 | 5.750000e-131 | 479.0 |
3 | TraesCS2B01G163300 | chr2B | 89.791 | 382 | 27 | 5 | 4545 | 4919 | 135697945 | 135697569 | 5.750000e-131 | 479.0 |
4 | TraesCS2B01G163300 | chr2B | 78.581 | 733 | 136 | 18 | 3458 | 4178 | 160907007 | 160907730 | 1.610000e-126 | 464.0 |
5 | TraesCS2B01G163300 | chr2B | 80.307 | 391 | 74 | 2 | 3071 | 3458 | 100851664 | 100852054 | 8.040000e-75 | 292.0 |
6 | TraesCS2B01G163300 | chr2B | 91.304 | 46 | 2 | 2 | 4269 | 4313 | 539367056 | 539367012 | 2.470000e-05 | 62.1 |
7 | TraesCS2B01G163300 | chr2B | 90.909 | 44 | 1 | 3 | 4271 | 4313 | 22694159 | 22694118 | 1.000000e-03 | 56.5 |
8 | TraesCS2B01G163300 | chr2D | 88.562 | 4179 | 312 | 77 | 3461 | 7567 | 83825878 | 83821794 | 0.000000e+00 | 4916.0 |
9 | TraesCS2B01G163300 | chr2D | 90.975 | 831 | 44 | 11 | 1 | 830 | 83834982 | 83834182 | 0.000000e+00 | 1090.0 |
10 | TraesCS2B01G163300 | chr2D | 86.020 | 980 | 99 | 15 | 1361 | 2316 | 83832959 | 83831994 | 0.000000e+00 | 1016.0 |
11 | TraesCS2B01G163300 | chr2D | 87.393 | 698 | 68 | 11 | 2347 | 3029 | 83831994 | 83831302 | 0.000000e+00 | 784.0 |
12 | TraesCS2B01G163300 | chr2D | 92.608 | 487 | 24 | 7 | 821 | 1305 | 83833752 | 83833276 | 0.000000e+00 | 689.0 |
13 | TraesCS2B01G163300 | chr2D | 90.859 | 361 | 16 | 3 | 7565 | 7908 | 83821747 | 83821387 | 1.240000e-127 | 468.0 |
14 | TraesCS2B01G163300 | chr2D | 89.488 | 371 | 32 | 6 | 4545 | 4913 | 83833640 | 83833275 | 5.790000e-126 | 462.0 |
15 | TraesCS2B01G163300 | chr2D | 87.789 | 303 | 35 | 1 | 3094 | 3396 | 83826749 | 83826449 | 3.630000e-93 | 353.0 |
16 | TraesCS2B01G163300 | chr2D | 100.000 | 51 | 0 | 0 | 1315 | 1365 | 83833289 | 83833239 | 2.430000e-15 | 95.3 |
17 | TraesCS2B01G163300 | chr2A | 93.473 | 2436 | 122 | 17 | 4519 | 6933 | 84555192 | 84552773 | 0.000000e+00 | 3583.0 |
18 | TraesCS2B01G163300 | chr2A | 88.319 | 839 | 90 | 6 | 2563 | 3397 | 84557284 | 84556450 | 0.000000e+00 | 1000.0 |
19 | TraesCS2B01G163300 | chr2A | 82.823 | 1077 | 119 | 26 | 3403 | 4456 | 84556261 | 84555228 | 0.000000e+00 | 904.0 |
20 | TraesCS2B01G163300 | chr2A | 91.736 | 605 | 32 | 5 | 6964 | 7567 | 84552720 | 84552133 | 0.000000e+00 | 824.0 |
21 | TraesCS2B01G163300 | chr2A | 91.047 | 592 | 39 | 9 | 781 | 1365 | 84587028 | 84586444 | 0.000000e+00 | 787.0 |
22 | TraesCS2B01G163300 | chr2A | 89.144 | 654 | 34 | 18 | 7565 | 8187 | 84552024 | 84551377 | 0.000000e+00 | 780.0 |
23 | TraesCS2B01G163300 | chr2A | 84.771 | 742 | 89 | 16 | 1789 | 2514 | 84558339 | 84557606 | 0.000000e+00 | 723.0 |
24 | TraesCS2B01G163300 | chr2A | 78.354 | 984 | 172 | 21 | 3081 | 4032 | 65680778 | 65681752 | 4.230000e-167 | 599.0 |
25 | TraesCS2B01G163300 | chr2A | 89.791 | 382 | 27 | 7 | 4545 | 4919 | 84586877 | 84586501 | 5.750000e-131 | 479.0 |
26 | TraesCS2B01G163300 | chr2A | 89.751 | 361 | 30 | 4 | 934 | 1293 | 84555166 | 84554812 | 9.690000e-124 | 455.0 |
27 | TraesCS2B01G163300 | chr2A | 86.885 | 244 | 27 | 3 | 427 | 669 | 440944805 | 440944566 | 1.350000e-67 | 268.0 |
28 | TraesCS2B01G163300 | chr6D | 85.101 | 2074 | 204 | 60 | 5238 | 7260 | 435306174 | 435308193 | 0.000000e+00 | 2021.0 |
29 | TraesCS2B01G163300 | chr6D | 89.342 | 319 | 21 | 10 | 4596 | 4902 | 435300377 | 435300694 | 9.960000e-104 | 388.0 |
30 | TraesCS2B01G163300 | chr6D | 89.241 | 316 | 23 | 5 | 985 | 1292 | 435300377 | 435300689 | 1.290000e-102 | 385.0 |
31 | TraesCS2B01G163300 | chr6D | 86.800 | 250 | 27 | 4 | 422 | 668 | 13155569 | 13155323 | 2.910000e-69 | 274.0 |
32 | TraesCS2B01G163300 | chr6B | 86.451 | 1882 | 180 | 44 | 5415 | 7260 | 658295883 | 658297725 | 0.000000e+00 | 1993.0 |
33 | TraesCS2B01G163300 | chr6B | 89.728 | 331 | 26 | 6 | 963 | 1288 | 658275954 | 658276281 | 4.570000e-112 | 416.0 |
34 | TraesCS2B01G163300 | chr6B | 89.189 | 333 | 23 | 11 | 4582 | 4903 | 658275962 | 658276292 | 3.560000e-108 | 403.0 |
35 | TraesCS2B01G163300 | chr6B | 88.000 | 325 | 20 | 9 | 4604 | 4915 | 658291323 | 658291641 | 4.670000e-97 | 366.0 |
36 | TraesCS2B01G163300 | chr6B | 89.139 | 267 | 19 | 4 | 1036 | 1292 | 658291354 | 658291620 | 2.850000e-84 | 324.0 |
37 | TraesCS2B01G163300 | chr6A | 87.648 | 842 | 87 | 7 | 5385 | 6219 | 582252717 | 582253548 | 0.000000e+00 | 963.0 |
38 | TraesCS2B01G163300 | chr6A | 84.135 | 1040 | 95 | 35 | 6258 | 7260 | 582253554 | 582254560 | 0.000000e+00 | 942.0 |
39 | TraesCS2B01G163300 | chr6A | 88.272 | 324 | 18 | 11 | 4604 | 4915 | 582248688 | 582249003 | 3.610000e-98 | 370.0 |
40 | TraesCS2B01G163300 | chr6A | 86.885 | 305 | 23 | 7 | 1017 | 1306 | 582248701 | 582249003 | 7.920000e-85 | 326.0 |
41 | TraesCS2B01G163300 | chr6A | 81.569 | 255 | 41 | 3 | 3016 | 3265 | 585808047 | 585807794 | 1.080000e-48 | 206.0 |
42 | TraesCS2B01G163300 | chr6A | 86.905 | 84 | 9 | 2 | 1595 | 1678 | 562469415 | 562469334 | 8.750000e-15 | 93.5 |
43 | TraesCS2B01G163300 | chr7D | 80.078 | 1280 | 187 | 24 | 3018 | 4238 | 162198874 | 162200144 | 0.000000e+00 | 889.0 |
44 | TraesCS2B01G163300 | chr7D | 80.000 | 1175 | 182 | 32 | 3104 | 4241 | 579967009 | 579965851 | 0.000000e+00 | 819.0 |
45 | TraesCS2B01G163300 | chr7D | 78.447 | 1030 | 170 | 29 | 3015 | 4002 | 125911393 | 125910374 | 6.980000e-175 | 625.0 |
46 | TraesCS2B01G163300 | chr7D | 76.857 | 1171 | 203 | 32 | 3119 | 4238 | 270161313 | 270162466 | 4.230000e-167 | 599.0 |
47 | TraesCS2B01G163300 | chr5B | 80.338 | 1185 | 180 | 32 | 3094 | 4242 | 146905576 | 146906743 | 0.000000e+00 | 848.0 |
48 | TraesCS2B01G163300 | chr5B | 80.277 | 289 | 34 | 13 | 1979 | 2259 | 659989608 | 659989881 | 6.480000e-46 | 196.0 |
49 | TraesCS2B01G163300 | chr5B | 77.698 | 278 | 44 | 13 | 2012 | 2280 | 354728154 | 354728422 | 3.960000e-33 | 154.0 |
50 | TraesCS2B01G163300 | chr3B | 79.009 | 1272 | 213 | 23 | 3004 | 4238 | 228738549 | 228737295 | 0.000000e+00 | 821.0 |
51 | TraesCS2B01G163300 | chr3B | 88.571 | 245 | 23 | 3 | 426 | 668 | 353997184 | 353997425 | 8.040000e-75 | 292.0 |
52 | TraesCS2B01G163300 | chr3B | 86.420 | 243 | 28 | 3 | 427 | 667 | 595539542 | 595539303 | 2.270000e-65 | 261.0 |
53 | TraesCS2B01G163300 | chr3B | 91.304 | 46 | 1 | 3 | 4269 | 4313 | 592646780 | 592646737 | 8.870000e-05 | 60.2 |
54 | TraesCS2B01G163300 | chr1A | 80.202 | 1091 | 171 | 16 | 3015 | 4070 | 393508872 | 393509952 | 0.000000e+00 | 776.0 |
55 | TraesCS2B01G163300 | chr1A | 79.301 | 773 | 134 | 21 | 5411 | 6164 | 15345950 | 15345185 | 1.220000e-142 | 518.0 |
56 | TraesCS2B01G163300 | chr1A | 81.019 | 648 | 105 | 14 | 3461 | 4096 | 45788911 | 45789552 | 4.410000e-137 | 499.0 |
57 | TraesCS2B01G163300 | chr1A | 86.149 | 296 | 32 | 6 | 1013 | 1306 | 15348416 | 15348128 | 2.220000e-80 | 311.0 |
58 | TraesCS2B01G163300 | chr1A | 73.205 | 571 | 120 | 26 | 1712 | 2262 | 529315272 | 529315829 | 8.440000e-40 | 176.0 |
59 | TraesCS2B01G163300 | chr1A | 100.000 | 28 | 0 | 0 | 1379 | 1406 | 462035503 | 462035530 | 1.500000e-02 | 52.8 |
60 | TraesCS2B01G163300 | chr3A | 79.313 | 1107 | 181 | 29 | 3107 | 4186 | 398887513 | 398888598 | 0.000000e+00 | 732.0 |
61 | TraesCS2B01G163300 | chr7B | 78.245 | 1117 | 186 | 40 | 3068 | 4152 | 289195413 | 289194322 | 0.000000e+00 | 664.0 |
62 | TraesCS2B01G163300 | chr7B | 76.683 | 832 | 139 | 31 | 3032 | 3817 | 465598468 | 465599290 | 2.130000e-110 | 411.0 |
63 | TraesCS2B01G163300 | chr7B | 86.694 | 248 | 26 | 5 | 424 | 668 | 7711093 | 7711336 | 1.350000e-67 | 268.0 |
64 | TraesCS2B01G163300 | chr7B | 94.444 | 36 | 2 | 0 | 2644 | 2679 | 164099382 | 164099417 | 1.000000e-03 | 56.5 |
65 | TraesCS2B01G163300 | chr1D | 78.440 | 1141 | 151 | 38 | 3075 | 4185 | 449488104 | 449489179 | 0.000000e+00 | 656.0 |
66 | TraesCS2B01G163300 | chr1D | 76.710 | 1082 | 191 | 36 | 3153 | 4185 | 487775562 | 487776631 | 5.590000e-151 | 545.0 |
67 | TraesCS2B01G163300 | chr1D | 76.367 | 1024 | 188 | 27 | 3038 | 4026 | 305220177 | 305219173 | 1.230000e-137 | 501.0 |
68 | TraesCS2B01G163300 | chr4D | 77.632 | 1064 | 185 | 27 | 3008 | 4026 | 504565858 | 504564803 | 1.520000e-166 | 597.0 |
69 | TraesCS2B01G163300 | chr4D | 82.143 | 252 | 39 | 3 | 3094 | 3342 | 46189896 | 46189648 | 2.320000e-50 | 211.0 |
70 | TraesCS2B01G163300 | chr4D | 72.996 | 474 | 94 | 25 | 1823 | 2280 | 445089036 | 445089491 | 1.430000e-27 | 135.0 |
71 | TraesCS2B01G163300 | chr7A | 75.668 | 1122 | 196 | 42 | 3172 | 4238 | 299595536 | 299596635 | 9.550000e-134 | 488.0 |
72 | TraesCS2B01G163300 | chr7A | 78.072 | 830 | 133 | 36 | 3016 | 3819 | 485494046 | 485493240 | 5.750000e-131 | 479.0 |
73 | TraesCS2B01G163300 | chr7A | 88.889 | 63 | 6 | 1 | 4184 | 4245 | 50423426 | 50423488 | 8.810000e-10 | 76.8 |
74 | TraesCS2B01G163300 | chr4B | 76.010 | 817 | 132 | 40 | 1741 | 2532 | 609480315 | 609479538 | 1.680000e-96 | 364.0 |
75 | TraesCS2B01G163300 | chr4B | 80.751 | 213 | 37 | 3 | 3012 | 3220 | 656143808 | 656144020 | 6.570000e-36 | 163.0 |
76 | TraesCS2B01G163300 | chr5A | 75.502 | 747 | 136 | 32 | 1712 | 2441 | 662354455 | 662355171 | 1.030000e-83 | 322.0 |
77 | TraesCS2B01G163300 | chr5A | 86.066 | 244 | 28 | 4 | 427 | 668 | 69357495 | 69357256 | 2.930000e-64 | 257.0 |
78 | TraesCS2B01G163300 | chr5A | 82.222 | 90 | 9 | 5 | 4353 | 4436 | 76727963 | 76727875 | 4.100000e-08 | 71.3 |
79 | TraesCS2B01G163300 | chr3D | 88.980 | 245 | 22 | 3 | 426 | 668 | 236628801 | 236629042 | 1.730000e-76 | 298.0 |
80 | TraesCS2B01G163300 | chr3D | 87.243 | 243 | 27 | 2 | 427 | 668 | 251409156 | 251409395 | 2.910000e-69 | 274.0 |
81 | TraesCS2B01G163300 | chr5D | 72.968 | 566 | 122 | 22 | 1712 | 2261 | 315620859 | 315620309 | 1.410000e-37 | 169.0 |
82 | TraesCS2B01G163300 | chr5D | 80.255 | 157 | 16 | 8 | 1518 | 1661 | 397322826 | 397322672 | 4.040000e-18 | 104.0 |
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 | TraesCS2B01G163300 | chr2B | 135690692 | 135698878 | 8186 | True | 15119.000000 | 15119 | 100.000000 | 1 | 8187 | 1 | chr2B.!!$R2 | 8186 |
1 | TraesCS2B01G163300 | chr2B | 148249041 | 148250095 | 1054 | True | 813.000000 | 813 | 81.020000 | 3038 | 4068 | 1 | chr2B.!!$R3 | 1030 |
2 | TraesCS2B01G163300 | chr2B | 135693960 | 135697945 | 3985 | True | 479.000000 | 479 | 89.791000 | 934 | 4919 | 2 | chr2B.!!$R5 | 3985 |
3 | TraesCS2B01G163300 | chr2B | 160907007 | 160907730 | 723 | False | 464.000000 | 464 | 78.581000 | 3458 | 4178 | 1 | chr2B.!!$F2 | 720 |
4 | TraesCS2B01G163300 | chr2D | 83821387 | 83826749 | 5362 | True | 1912.333333 | 4916 | 89.070000 | 3094 | 7908 | 3 | chr2D.!!$R1 | 4814 |
5 | TraesCS2B01G163300 | chr2D | 83831302 | 83834982 | 3680 | True | 689.383333 | 1090 | 91.080667 | 1 | 4913 | 6 | chr2D.!!$R2 | 4912 |
6 | TraesCS2B01G163300 | chr2A | 84551377 | 84558339 | 6962 | True | 1181.285714 | 3583 | 88.573857 | 934 | 8187 | 7 | chr2A.!!$R2 | 7253 |
7 | TraesCS2B01G163300 | chr2A | 84586444 | 84587028 | 584 | True | 633.000000 | 787 | 90.419000 | 781 | 4919 | 2 | chr2A.!!$R3 | 4138 |
8 | TraesCS2B01G163300 | chr2A | 65680778 | 65681752 | 974 | False | 599.000000 | 599 | 78.354000 | 3081 | 4032 | 1 | chr2A.!!$F1 | 951 |
9 | TraesCS2B01G163300 | chr6D | 435306174 | 435308193 | 2019 | False | 2021.000000 | 2021 | 85.101000 | 5238 | 7260 | 1 | chr6D.!!$F1 | 2022 |
10 | TraesCS2B01G163300 | chr6B | 658295883 | 658297725 | 1842 | False | 1993.000000 | 1993 | 86.451000 | 5415 | 7260 | 1 | chr6B.!!$F1 | 1845 |
11 | TraesCS2B01G163300 | chr6A | 582248688 | 582254560 | 5872 | False | 650.250000 | 963 | 86.735000 | 1017 | 7260 | 4 | chr6A.!!$F1 | 6243 |
12 | TraesCS2B01G163300 | chr7D | 162198874 | 162200144 | 1270 | False | 889.000000 | 889 | 80.078000 | 3018 | 4238 | 1 | chr7D.!!$F1 | 1220 |
13 | TraesCS2B01G163300 | chr7D | 579965851 | 579967009 | 1158 | True | 819.000000 | 819 | 80.000000 | 3104 | 4241 | 1 | chr7D.!!$R2 | 1137 |
14 | TraesCS2B01G163300 | chr7D | 125910374 | 125911393 | 1019 | True | 625.000000 | 625 | 78.447000 | 3015 | 4002 | 1 | chr7D.!!$R1 | 987 |
15 | TraesCS2B01G163300 | chr7D | 270161313 | 270162466 | 1153 | False | 599.000000 | 599 | 76.857000 | 3119 | 4238 | 1 | chr7D.!!$F2 | 1119 |
16 | TraesCS2B01G163300 | chr5B | 146905576 | 146906743 | 1167 | False | 848.000000 | 848 | 80.338000 | 3094 | 4242 | 1 | chr5B.!!$F1 | 1148 |
17 | TraesCS2B01G163300 | chr3B | 228737295 | 228738549 | 1254 | True | 821.000000 | 821 | 79.009000 | 3004 | 4238 | 1 | chr3B.!!$R1 | 1234 |
18 | TraesCS2B01G163300 | chr1A | 393508872 | 393509952 | 1080 | False | 776.000000 | 776 | 80.202000 | 3015 | 4070 | 1 | chr1A.!!$F2 | 1055 |
19 | TraesCS2B01G163300 | chr1A | 45788911 | 45789552 | 641 | False | 499.000000 | 499 | 81.019000 | 3461 | 4096 | 1 | chr1A.!!$F1 | 635 |
20 | TraesCS2B01G163300 | chr1A | 15345185 | 15348416 | 3231 | True | 414.500000 | 518 | 82.725000 | 1013 | 6164 | 2 | chr1A.!!$R1 | 5151 |
21 | TraesCS2B01G163300 | chr3A | 398887513 | 398888598 | 1085 | False | 732.000000 | 732 | 79.313000 | 3107 | 4186 | 1 | chr3A.!!$F1 | 1079 |
22 | TraesCS2B01G163300 | chr7B | 289194322 | 289195413 | 1091 | True | 664.000000 | 664 | 78.245000 | 3068 | 4152 | 1 | chr7B.!!$R1 | 1084 |
23 | TraesCS2B01G163300 | chr7B | 465598468 | 465599290 | 822 | False | 411.000000 | 411 | 76.683000 | 3032 | 3817 | 1 | chr7B.!!$F3 | 785 |
24 | TraesCS2B01G163300 | chr1D | 449488104 | 449489179 | 1075 | False | 656.000000 | 656 | 78.440000 | 3075 | 4185 | 1 | chr1D.!!$F1 | 1110 |
25 | TraesCS2B01G163300 | chr1D | 487775562 | 487776631 | 1069 | False | 545.000000 | 545 | 76.710000 | 3153 | 4185 | 1 | chr1D.!!$F2 | 1032 |
26 | TraesCS2B01G163300 | chr1D | 305219173 | 305220177 | 1004 | True | 501.000000 | 501 | 76.367000 | 3038 | 4026 | 1 | chr1D.!!$R1 | 988 |
27 | TraesCS2B01G163300 | chr4D | 504564803 | 504565858 | 1055 | True | 597.000000 | 597 | 77.632000 | 3008 | 4026 | 1 | chr4D.!!$R2 | 1018 |
28 | TraesCS2B01G163300 | chr7A | 299595536 | 299596635 | 1099 | False | 488.000000 | 488 | 75.668000 | 3172 | 4238 | 1 | chr7A.!!$F2 | 1066 |
29 | TraesCS2B01G163300 | chr7A | 485493240 | 485494046 | 806 | True | 479.000000 | 479 | 78.072000 | 3016 | 3819 | 1 | chr7A.!!$R1 | 803 |
30 | TraesCS2B01G163300 | chr4B | 609479538 | 609480315 | 777 | True | 364.000000 | 364 | 76.010000 | 1741 | 2532 | 1 | chr4B.!!$R1 | 791 |
31 | TraesCS2B01G163300 | chr5A | 662354455 | 662355171 | 716 | False | 322.000000 | 322 | 75.502000 | 1712 | 2441 | 1 | chr5A.!!$F1 | 729 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
89 | 90 | 0.096628 | CCACTAGAAGGACGACGACG | 59.903 | 60.000 | 5.58 | 5.58 | 45.75 | 5.12 | F |
774 | 776 | 1.076332 | CACCACTCGTCGGAAAATCC | 58.924 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 | F |
827 | 832 | 3.430862 | CCACCACCATGCGTTCCG | 61.431 | 66.667 | 0.00 | 0.00 | 0.00 | 4.30 | F |
5149 | 8030 | 0.892814 | AGCTGCCTGAAACTGAAGCC | 60.893 | 55.000 | 0.00 | 0.00 | 0.00 | 4.35 | F |
5976 | 12035 | 0.964860 | TCCGCCATCATGGTTTGGTG | 60.965 | 55.000 | 5.31 | 13.60 | 40.46 | 4.17 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
5058 | 7455 | 3.633986 | AGAGATGTATCGATCACACAGCA | 59.366 | 43.478 | 15.28 | 1.08 | 31.16 | 4.41 | R |
5129 | 7532 | 0.240411 | GCTTCAGTTTCAGGCAGCTG | 59.760 | 55.000 | 10.11 | 10.11 | 0.00 | 4.24 | R |
5659 | 11718 | 1.130054 | ACTGCAGGAAGGAGAAGGCA | 61.130 | 55.000 | 19.93 | 0.00 | 38.04 | 4.75 | R |
6559 | 12699 | 0.035152 | ATTCTGCCGCAATCACCTCA | 60.035 | 50.000 | 0.00 | 0.00 | 0.00 | 3.86 | R |
7483 | 13686 | 0.334335 | TCCTGGTATTGGCATTGGCA | 59.666 | 50.000 | 9.11 | 9.11 | 43.71 | 4.92 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
29 | 30 | 6.206438 | TGCATAGCAGTTGACTCAATTTTACA | 59.794 | 34.615 | 0.00 | 0.00 | 33.32 | 2.41 |
31 | 32 | 7.573843 | GCATAGCAGTTGACTCAATTTTACAGT | 60.574 | 37.037 | 0.00 | 0.00 | 0.00 | 3.55 |
36 | 37 | 7.324616 | GCAGTTGACTCAATTTTACAGTGATTC | 59.675 | 37.037 | 0.00 | 0.00 | 0.00 | 2.52 |
68 | 69 | 7.840716 | TCCCAATGACAAAATAGGAGATTGATT | 59.159 | 33.333 | 0.00 | 0.00 | 0.00 | 2.57 |
89 | 90 | 0.096628 | CCACTAGAAGGACGACGACG | 59.903 | 60.000 | 5.58 | 5.58 | 45.75 | 5.12 |
92 | 93 | 1.297664 | CTAGAAGGACGACGACGGAT | 58.702 | 55.000 | 12.58 | 0.00 | 44.46 | 4.18 |
127 | 128 | 2.093106 | GGACATGTCTACGAGGTCACT | 58.907 | 52.381 | 24.50 | 0.00 | 0.00 | 3.41 |
194 | 195 | 3.680937 | CCAACTTGTTAAATAGCGTCCGA | 59.319 | 43.478 | 0.00 | 0.00 | 0.00 | 4.55 |
198 | 199 | 5.864986 | ACTTGTTAAATAGCGTCCGATTTG | 58.135 | 37.500 | 0.00 | 0.00 | 30.48 | 2.32 |
244 | 245 | 6.470877 | GCTTAAATTTTGTTCCGATTCGCATA | 59.529 | 34.615 | 0.00 | 0.00 | 0.00 | 3.14 |
245 | 246 | 7.513041 | GCTTAAATTTTGTTCCGATTCGCATAC | 60.513 | 37.037 | 0.00 | 0.00 | 0.00 | 2.39 |
250 | 251 | 5.365403 | TTGTTCCGATTCGCATACTTTTT | 57.635 | 34.783 | 0.00 | 0.00 | 0.00 | 1.94 |
251 | 252 | 4.965062 | TGTTCCGATTCGCATACTTTTTC | 58.035 | 39.130 | 0.00 | 0.00 | 0.00 | 2.29 |
252 | 253 | 4.693566 | TGTTCCGATTCGCATACTTTTTCT | 59.306 | 37.500 | 0.00 | 0.00 | 0.00 | 2.52 |
253 | 254 | 5.180492 | TGTTCCGATTCGCATACTTTTTCTT | 59.820 | 36.000 | 0.00 | 0.00 | 0.00 | 2.52 |
254 | 255 | 5.464965 | TCCGATTCGCATACTTTTTCTTC | 57.535 | 39.130 | 0.00 | 0.00 | 0.00 | 2.87 |
255 | 256 | 5.175859 | TCCGATTCGCATACTTTTTCTTCT | 58.824 | 37.500 | 0.00 | 0.00 | 0.00 | 2.85 |
256 | 257 | 5.642063 | TCCGATTCGCATACTTTTTCTTCTT | 59.358 | 36.000 | 0.00 | 0.00 | 0.00 | 2.52 |
257 | 258 | 5.960105 | CCGATTCGCATACTTTTTCTTCTTC | 59.040 | 40.000 | 0.00 | 0.00 | 0.00 | 2.87 |
258 | 259 | 6.183360 | CCGATTCGCATACTTTTTCTTCTTCT | 60.183 | 38.462 | 0.00 | 0.00 | 0.00 | 2.85 |
259 | 260 | 7.237173 | CGATTCGCATACTTTTTCTTCTTCTT | 58.763 | 34.615 | 0.00 | 0.00 | 0.00 | 2.52 |
290 | 291 | 7.962918 | CCCATTTATAATGTAGATTTAGTGCGC | 59.037 | 37.037 | 0.00 | 0.00 | 0.00 | 6.09 |
370 | 371 | 9.748708 | ATGAATTTTACGTATCCAATTTGATGG | 57.251 | 29.630 | 0.00 | 0.00 | 42.12 | 3.51 |
377 | 378 | 2.357575 | CCAATTTGATGGGCCGGCA | 61.358 | 57.895 | 30.85 | 9.36 | 36.79 | 5.69 |
393 | 394 | 3.393472 | GCACTGGAGATGCCCTAAG | 57.607 | 57.895 | 0.00 | 0.00 | 37.08 | 2.18 |
431 | 432 | 6.827586 | TTACCACCAAATGTTTGATACTCC | 57.172 | 37.500 | 7.04 | 0.00 | 40.55 | 3.85 |
438 | 439 | 8.210946 | CACCAAATGTTTGATACTCCCTCTATA | 58.789 | 37.037 | 7.04 | 0.00 | 40.55 | 1.31 |
452 | 453 | 5.767670 | TCCCTCTATACATCTATACAGGGC | 58.232 | 45.833 | 4.15 | 0.00 | 39.47 | 5.19 |
474 | 476 | 5.700373 | GGCCTAATGCATTTTTGAGACAAAA | 59.300 | 36.000 | 18.75 | 5.70 | 43.89 | 2.44 |
490 | 492 | 7.424803 | TGAGACAAAAATTGACCACATGTTAG | 58.575 | 34.615 | 0.00 | 0.00 | 0.00 | 2.34 |
526 | 528 | 6.875948 | TGACATGTAAGTTACACAAAGCAT | 57.124 | 33.333 | 17.79 | 0.00 | 42.23 | 3.79 |
645 | 647 | 2.432444 | CTCGAAAACACATTAGGCCCA | 58.568 | 47.619 | 0.00 | 0.00 | 0.00 | 5.36 |
646 | 648 | 2.420022 | CTCGAAAACACATTAGGCCCAG | 59.580 | 50.000 | 0.00 | 0.00 | 0.00 | 4.45 |
659 | 661 | 6.678411 | ACATTAGGCCCAGTATATATGGATGT | 59.322 | 38.462 | 0.00 | 6.85 | 40.51 | 3.06 |
690 | 692 | 3.125146 | TGACGTACTACTATTTCGCACGT | 59.875 | 43.478 | 0.00 | 0.00 | 43.11 | 4.49 |
693 | 695 | 4.201851 | ACGTACTACTATTTCGCACGTCAT | 60.202 | 41.667 | 0.00 | 0.00 | 36.51 | 3.06 |
700 | 702 | 6.274001 | ACTATTTCGCACGTCATGAATAAG | 57.726 | 37.500 | 0.00 | 0.00 | 0.00 | 1.73 |
701 | 703 | 5.810587 | ACTATTTCGCACGTCATGAATAAGT | 59.189 | 36.000 | 0.00 | 0.00 | 0.00 | 2.24 |
702 | 704 | 5.545658 | ATTTCGCACGTCATGAATAAGTT | 57.454 | 34.783 | 0.00 | 0.00 | 0.00 | 2.66 |
703 | 705 | 4.577687 | TTCGCACGTCATGAATAAGTTC | 57.422 | 40.909 | 0.00 | 0.00 | 34.85 | 3.01 |
704 | 706 | 2.596862 | TCGCACGTCATGAATAAGTTCG | 59.403 | 45.455 | 0.00 | 2.45 | 37.15 | 3.95 |
705 | 707 | 2.285026 | CGCACGTCATGAATAAGTTCGG | 60.285 | 50.000 | 0.00 | 0.00 | 37.15 | 4.30 |
706 | 708 | 2.927477 | GCACGTCATGAATAAGTTCGGA | 59.073 | 45.455 | 0.00 | 0.00 | 37.15 | 4.55 |
707 | 709 | 3.555956 | GCACGTCATGAATAAGTTCGGAT | 59.444 | 43.478 | 0.00 | 0.00 | 37.15 | 4.18 |
708 | 710 | 4.034048 | GCACGTCATGAATAAGTTCGGATT | 59.966 | 41.667 | 0.00 | 0.00 | 37.15 | 3.01 |
709 | 711 | 5.447279 | GCACGTCATGAATAAGTTCGGATTT | 60.447 | 40.000 | 0.00 | 0.00 | 37.15 | 2.17 |
710 | 712 | 5.959527 | CACGTCATGAATAAGTTCGGATTTG | 59.040 | 40.000 | 0.00 | 0.00 | 37.15 | 2.32 |
711 | 713 | 5.642063 | ACGTCATGAATAAGTTCGGATTTGT | 59.358 | 36.000 | 0.00 | 0.00 | 37.15 | 2.83 |
712 | 714 | 6.814644 | ACGTCATGAATAAGTTCGGATTTGTA | 59.185 | 34.615 | 0.00 | 0.00 | 37.15 | 2.41 |
713 | 715 | 7.117454 | CGTCATGAATAAGTTCGGATTTGTAC | 58.883 | 38.462 | 0.00 | 0.00 | 37.15 | 2.90 |
714 | 716 | 7.010183 | CGTCATGAATAAGTTCGGATTTGTACT | 59.990 | 37.037 | 0.00 | 0.00 | 37.15 | 2.73 |
715 | 717 | 9.309516 | GTCATGAATAAGTTCGGATTTGTACTA | 57.690 | 33.333 | 0.00 | 0.00 | 37.15 | 1.82 |
716 | 718 | 9.309516 | TCATGAATAAGTTCGGATTTGTACTAC | 57.690 | 33.333 | 0.00 | 0.00 | 37.15 | 2.73 |
717 | 719 | 9.093970 | CATGAATAAGTTCGGATTTGTACTACA | 57.906 | 33.333 | 0.00 | 0.00 | 37.15 | 2.74 |
718 | 720 | 9.661563 | ATGAATAAGTTCGGATTTGTACTACAA | 57.338 | 29.630 | 0.00 | 0.00 | 37.15 | 2.41 |
765 | 767 | 4.154195 | AGCATTAAATGTTCACCACTCGTC | 59.846 | 41.667 | 0.00 | 0.00 | 0.00 | 4.20 |
773 | 775 | 2.074547 | TCACCACTCGTCGGAAAATC | 57.925 | 50.000 | 0.00 | 0.00 | 0.00 | 2.17 |
774 | 776 | 1.076332 | CACCACTCGTCGGAAAATCC | 58.924 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 |
827 | 832 | 3.430862 | CCACCACCATGCGTTCCG | 61.431 | 66.667 | 0.00 | 0.00 | 0.00 | 4.30 |
5058 | 7455 | 7.919385 | ATTAATTAATTGCACCCCTTCAGAT | 57.081 | 32.000 | 11.05 | 0.00 | 0.00 | 2.90 |
5129 | 7532 | 5.047802 | TCTGCCAAAATTTTGAGATGGAGTC | 60.048 | 40.000 | 28.44 | 9.43 | 40.55 | 3.36 |
5149 | 8030 | 0.892814 | AGCTGCCTGAAACTGAAGCC | 60.893 | 55.000 | 0.00 | 0.00 | 0.00 | 4.35 |
5272 | 11018 | 8.732746 | AAACTAGAGTACAACACAATGAAAGT | 57.267 | 30.769 | 0.00 | 0.00 | 0.00 | 2.66 |
5315 | 11069 | 4.913335 | ATTCAGGCGACTTACGAATAGA | 57.087 | 40.909 | 0.61 | 0.00 | 45.77 | 1.98 |
5316 | 11070 | 3.687572 | TCAGGCGACTTACGAATAGAC | 57.312 | 47.619 | 0.00 | 0.00 | 45.77 | 2.59 |
5317 | 11071 | 3.276857 | TCAGGCGACTTACGAATAGACT | 58.723 | 45.455 | 0.00 | 0.00 | 45.77 | 3.24 |
5328 | 11082 | 4.715527 | ACGAATAGACTACTGTCCCAAC | 57.284 | 45.455 | 0.00 | 0.00 | 43.91 | 3.77 |
5362 | 11146 | 4.492791 | TGTTCTGCAGATGAACATTGTG | 57.507 | 40.909 | 19.04 | 0.00 | 45.77 | 3.33 |
5370 | 11154 | 1.921887 | GATGAACATTGTGGCATTGCG | 59.078 | 47.619 | 1.91 | 0.00 | 0.00 | 4.85 |
5374 | 11162 | 1.177895 | ACATTGTGGCATTGCGTCCA | 61.178 | 50.000 | 1.91 | 0.00 | 0.00 | 4.02 |
5659 | 11718 | 2.677228 | CAGATCCCCGGCCTGTTT | 59.323 | 61.111 | 0.00 | 0.00 | 0.00 | 2.83 |
5740 | 11799 | 2.126424 | GTCGTCTGCTCCGTGGTC | 60.126 | 66.667 | 0.00 | 0.00 | 0.00 | 4.02 |
5750 | 11809 | 2.435938 | CCGTGGTCCCATTCGTGG | 60.436 | 66.667 | 0.00 | 0.00 | 0.00 | 4.94 |
5953 | 12012 | 1.446099 | GACGATCAAGCTCGCCACA | 60.446 | 57.895 | 0.00 | 0.00 | 42.35 | 4.17 |
5976 | 12035 | 0.964860 | TCCGCCATCATGGTTTGGTG | 60.965 | 55.000 | 5.31 | 13.60 | 40.46 | 4.17 |
6164 | 12260 | 3.141398 | GTCATTGATCGCCATGTGGTAT | 58.859 | 45.455 | 0.35 | 0.00 | 37.57 | 2.73 |
6170 | 12266 | 1.732941 | TCGCCATGTGGTATGTTCAC | 58.267 | 50.000 | 0.35 | 0.00 | 37.57 | 3.18 |
6262 | 12373 | 5.704978 | TGATTCATGAACGAATGGACTTGAA | 59.295 | 36.000 | 11.07 | 0.00 | 35.74 | 2.69 |
6263 | 12374 | 5.356882 | TTCATGAACGAATGGACTTGAAC | 57.643 | 39.130 | 3.38 | 0.00 | 0.00 | 3.18 |
6265 | 12376 | 5.063204 | TCATGAACGAATGGACTTGAACTT | 58.937 | 37.500 | 0.00 | 0.00 | 0.00 | 2.66 |
6266 | 12377 | 5.179368 | TCATGAACGAATGGACTTGAACTTC | 59.821 | 40.000 | 0.00 | 0.00 | 0.00 | 3.01 |
6267 | 12378 | 4.703897 | TGAACGAATGGACTTGAACTTCT | 58.296 | 39.130 | 0.00 | 0.00 | 0.00 | 2.85 |
6276 | 12387 | 3.181516 | GGACTTGAACTTCTAATGCAGCG | 60.182 | 47.826 | 0.00 | 0.00 | 0.00 | 5.18 |
6380 | 12510 | 1.860676 | TGTTGTAAGCACGACCTGTC | 58.139 | 50.000 | 0.00 | 0.00 | 38.17 | 3.51 |
6442 | 12582 | 1.227002 | GATCGGAGCTGGGAACGTC | 60.227 | 63.158 | 0.00 | 0.00 | 0.00 | 4.34 |
6505 | 12645 | 2.028385 | GGTGTTCCTCGCTTTCTCCTTA | 60.028 | 50.000 | 0.00 | 0.00 | 0.00 | 2.69 |
6653 | 12793 | 1.581934 | CGTGCTGTCAGGTGAGAAAA | 58.418 | 50.000 | 1.14 | 0.00 | 0.00 | 2.29 |
6654 | 12794 | 1.939934 | CGTGCTGTCAGGTGAGAAAAA | 59.060 | 47.619 | 1.14 | 0.00 | 0.00 | 1.94 |
6700 | 12843 | 6.727824 | ACCAATCTTCAAGAATCACTTACG | 57.272 | 37.500 | 0.00 | 0.00 | 37.03 | 3.18 |
6724 | 12867 | 5.970023 | GTGCACTGAAGAGATAATTTCATGC | 59.030 | 40.000 | 10.32 | 11.27 | 37.78 | 4.06 |
6733 | 12876 | 6.715280 | AGAGATAATTTCATGCCACGGATAT | 58.285 | 36.000 | 0.00 | 0.00 | 0.00 | 1.63 |
6746 | 12889 | 8.501580 | CATGCCACGGATATGAAATCATATATC | 58.498 | 37.037 | 14.28 | 6.73 | 46.36 | 1.63 |
6749 | 12892 | 6.646653 | CCACGGATATGAAATCATATATCGGG | 59.353 | 42.308 | 25.27 | 23.40 | 46.36 | 5.14 |
6795 | 12942 | 7.449934 | AATTCCGCAAATTGACGAATAAATC | 57.550 | 32.000 | 10.41 | 0.00 | 36.20 | 2.17 |
6934 | 13082 | 4.021368 | GCTCAACTTCTACACCAAGGTAGA | 60.021 | 45.833 | 0.00 | 0.00 | 45.94 | 2.59 |
6978 | 13149 | 1.379710 | TCCATTGCGGAATGTGGGG | 60.380 | 57.895 | 25.30 | 12.37 | 42.52 | 4.96 |
7013 | 13192 | 6.237861 | GCTCGTACTCCATTCTGAAACATAAC | 60.238 | 42.308 | 0.00 | 0.00 | 0.00 | 1.89 |
7044 | 13223 | 2.082231 | GAGCACTGAACAGATGCACAT | 58.918 | 47.619 | 21.28 | 9.15 | 37.67 | 3.21 |
7045 | 13224 | 2.486982 | GAGCACTGAACAGATGCACATT | 59.513 | 45.455 | 21.28 | 8.92 | 37.67 | 2.71 |
7046 | 13225 | 2.889045 | AGCACTGAACAGATGCACATTT | 59.111 | 40.909 | 21.28 | 6.98 | 37.67 | 2.32 |
7222 | 13406 | 4.753516 | TGTGGCTAGCACTTGTATGTAT | 57.246 | 40.909 | 18.24 | 0.00 | 0.00 | 2.29 |
7316 | 13500 | 3.907894 | TTTGACCGTGTATTTCAAGGC | 57.092 | 42.857 | 0.24 | 0.00 | 46.93 | 4.35 |
7317 | 13501 | 2.552599 | TGACCGTGTATTTCAAGGCA | 57.447 | 45.000 | 0.24 | 0.00 | 46.93 | 4.75 |
7329 | 13513 | 8.243426 | GTGTATTTCAAGGCAATTTATGTCTCA | 58.757 | 33.333 | 0.00 | 0.00 | 45.30 | 3.27 |
7338 | 13522 | 7.114754 | AGGCAATTTATGTCTCAGAAAGATCA | 58.885 | 34.615 | 0.00 | 0.00 | 41.07 | 2.92 |
7342 | 13526 | 9.565213 | CAATTTATGTCTCAGAAAGATCAAACC | 57.435 | 33.333 | 0.00 | 0.00 | 36.11 | 3.27 |
7384 | 13568 | 5.703592 | AGAGAGTATACAGGAGAAGCATACG | 59.296 | 44.000 | 5.50 | 0.00 | 0.00 | 3.06 |
7392 | 13576 | 0.596859 | GAGAAGCATACGTACCGGGC | 60.597 | 60.000 | 6.32 | 0.00 | 0.00 | 6.13 |
7396 | 13580 | 2.026590 | CATACGTACCGGGCCGTC | 59.973 | 66.667 | 26.32 | 13.60 | 38.43 | 4.79 |
7424 | 13608 | 4.047125 | CCTCCCAACCGCACCCAT | 62.047 | 66.667 | 0.00 | 0.00 | 0.00 | 4.00 |
7425 | 13609 | 2.751436 | CTCCCAACCGCACCCATG | 60.751 | 66.667 | 0.00 | 0.00 | 0.00 | 3.66 |
7426 | 13610 | 4.358841 | TCCCAACCGCACCCATGG | 62.359 | 66.667 | 4.14 | 4.14 | 0.00 | 3.66 |
7562 | 13765 | 6.115448 | AGCTCAACTTGTAGTTAATCCAGT | 57.885 | 37.500 | 0.00 | 0.00 | 36.03 | 4.00 |
7584 | 13899 | 6.261826 | CAGTAAAGGAGGAGGCAATAGAAATG | 59.738 | 42.308 | 0.00 | 0.00 | 0.00 | 2.32 |
7642 | 13960 | 2.105134 | TCCTTACAAAGCAGGGACGAAA | 59.895 | 45.455 | 0.00 | 0.00 | 0.00 | 3.46 |
7775 | 14094 | 4.934001 | TGCTTTGTGTTGAAATTGCTTTCA | 59.066 | 33.333 | 0.00 | 0.00 | 46.92 | 2.69 |
7816 | 14152 | 1.632409 | AGCCACAAGGACATGATGACT | 59.368 | 47.619 | 0.00 | 0.00 | 36.89 | 3.41 |
7854 | 14190 | 1.727335 | GTCTGCTTCGCTGTTAACTCC | 59.273 | 52.381 | 7.22 | 0.00 | 0.00 | 3.85 |
7868 | 14204 | 6.260050 | GCTGTTAACTCCGGAAATGATAATCA | 59.740 | 38.462 | 5.23 | 1.13 | 0.00 | 2.57 |
7898 | 14234 | 5.698089 | ACTATTGGTAATCATCGAGCATGTG | 59.302 | 40.000 | 0.00 | 0.00 | 33.66 | 3.21 |
7951 | 14287 | 3.393426 | AGAAGTCATTGGCCATGGAAT | 57.607 | 42.857 | 18.40 | 3.34 | 33.07 | 3.01 |
7965 | 14301 | 8.579850 | TGGCCATGGAATATGTTTCTAATATC | 57.420 | 34.615 | 18.40 | 0.00 | 0.00 | 1.63 |
7985 | 14321 | 4.299586 | TCATGTCTGTATTGGGCTTGAA | 57.700 | 40.909 | 0.00 | 0.00 | 0.00 | 2.69 |
8011 | 14347 | 7.549134 | AGCAACTCAACGATGTCTATGAATTAA | 59.451 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
8092 | 14434 | 7.547370 | TGTTCTGTTGGGTTACAAAGAAATTTG | 59.453 | 33.333 | 0.00 | 0.00 | 41.58 | 2.32 |
8093 | 14435 | 7.411486 | TCTGTTGGGTTACAAAGAAATTTGA | 57.589 | 32.000 | 7.66 | 0.00 | 41.58 | 2.69 |
8094 | 14436 | 8.017418 | TCTGTTGGGTTACAAAGAAATTTGAT | 57.983 | 30.769 | 7.66 | 0.00 | 41.58 | 2.57 |
8136 | 14481 | 2.224209 | CCGGAAAATATGCCTACTCGGT | 60.224 | 50.000 | 0.00 | 0.00 | 34.25 | 4.69 |
8153 | 14498 | 6.510879 | ACTCGGTTTCAAAGAAGAAAAACT | 57.489 | 33.333 | 0.00 | 0.00 | 39.05 | 2.66 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
10 | 11 | 6.060028 | TCACTGTAAAATTGAGTCAACTGC | 57.940 | 37.500 | 7.96 | 0.44 | 0.00 | 4.40 |
11 | 12 | 7.805071 | GGAATCACTGTAAAATTGAGTCAACTG | 59.195 | 37.037 | 7.96 | 2.61 | 35.06 | 3.16 |
29 | 30 | 7.392766 | TTGTCATTGGGATATAGGAATCACT | 57.607 | 36.000 | 0.00 | 0.00 | 30.16 | 3.41 |
36 | 37 | 8.605947 | TCTCCTATTTTGTCATTGGGATATAGG | 58.394 | 37.037 | 0.00 | 0.00 | 0.00 | 2.57 |
43 | 44 | 7.592885 | ATCAATCTCCTATTTTGTCATTGGG | 57.407 | 36.000 | 0.00 | 0.00 | 0.00 | 4.12 |
57 | 58 | 4.141528 | CCTTCTAGTGGCAATCAATCTCCT | 60.142 | 45.833 | 0.00 | 0.00 | 0.00 | 3.69 |
63 | 64 | 2.565391 | TCGTCCTTCTAGTGGCAATCAA | 59.435 | 45.455 | 0.00 | 0.00 | 0.00 | 2.57 |
68 | 69 | 0.607217 | TCGTCGTCCTTCTAGTGGCA | 60.607 | 55.000 | 0.00 | 0.00 | 0.00 | 4.92 |
89 | 90 | 0.034616 | CCTCTGAGGCAATCCGATCC | 59.965 | 60.000 | 11.42 | 0.00 | 37.47 | 3.36 |
92 | 93 | 0.614697 | TGTCCTCTGAGGCAATCCGA | 60.615 | 55.000 | 19.08 | 0.00 | 34.61 | 4.55 |
127 | 128 | 5.948162 | ACTAAACTAAGTGAGATACCGGACA | 59.052 | 40.000 | 9.46 | 0.00 | 0.00 | 4.02 |
172 | 173 | 3.680937 | TCGGACGCTATTTAACAAGTTGG | 59.319 | 43.478 | 7.96 | 0.00 | 0.00 | 3.77 |
184 | 185 | 1.953559 | ATGTGCAAATCGGACGCTAT | 58.046 | 45.000 | 0.00 | 0.00 | 39.19 | 2.97 |
239 | 240 | 9.704098 | GGTATTAAGAAGAAGAAAAAGTATGCG | 57.296 | 33.333 | 0.00 | 0.00 | 0.00 | 4.73 |
264 | 265 | 7.962918 | GCGCACTAAATCTACATTATAAATGGG | 59.037 | 37.037 | 0.30 | 0.00 | 0.00 | 4.00 |
290 | 291 | 1.819632 | GGGCAGCCACATAACTCGG | 60.820 | 63.158 | 15.19 | 0.00 | 0.00 | 4.63 |
335 | 336 | 6.183360 | GGATACGTAAAATTCATGAGCACACA | 60.183 | 38.462 | 0.00 | 0.00 | 0.00 | 3.72 |
393 | 394 | 3.501062 | GGTGGTAAAAGTGTAGAGTTGCC | 59.499 | 47.826 | 0.00 | 0.00 | 0.00 | 4.52 |
431 | 432 | 5.772004 | AGGCCCTGTATAGATGTATAGAGG | 58.228 | 45.833 | 20.60 | 20.60 | 46.03 | 3.69 |
438 | 439 | 3.909995 | TGCATTAGGCCCTGTATAGATGT | 59.090 | 43.478 | 0.00 | 0.00 | 43.89 | 3.06 |
452 | 453 | 9.601971 | CAATTTTTGTCTCAAAAATGCATTAGG | 57.398 | 29.630 | 24.11 | 5.49 | 39.13 | 2.69 |
474 | 476 | 7.701539 | TTATTGCTCTAACATGTGGTCAATT | 57.298 | 32.000 | 0.00 | 0.00 | 0.00 | 2.32 |
513 | 515 | 9.124807 | GGAATTTAACTGTATGCTTTGTGTAAC | 57.875 | 33.333 | 0.00 | 0.00 | 37.35 | 2.50 |
524 | 526 | 7.896274 | CGTTTCACGTAGGAATTTAACTGTATG | 59.104 | 37.037 | 0.00 | 0.00 | 36.74 | 2.39 |
526 | 528 | 7.144661 | TCGTTTCACGTAGGAATTTAACTGTA | 58.855 | 34.615 | 0.00 | 0.00 | 43.14 | 2.74 |
620 | 622 | 3.500680 | GCCTAATGTGTTTTCGAGGTTGA | 59.499 | 43.478 | 0.00 | 0.00 | 0.00 | 3.18 |
645 | 647 | 9.869667 | GTCATACTCCCTACATCCATATATACT | 57.130 | 37.037 | 0.00 | 0.00 | 0.00 | 2.12 |
646 | 648 | 8.784994 | CGTCATACTCCCTACATCCATATATAC | 58.215 | 40.741 | 0.00 | 0.00 | 0.00 | 1.47 |
659 | 661 | 7.600375 | CGAAATAGTAGTACGTCATACTCCCTA | 59.400 | 40.741 | 14.03 | 7.13 | 43.47 | 3.53 |
690 | 692 | 9.309516 | GTAGTACAAATCCGAACTTATTCATGA | 57.690 | 33.333 | 0.00 | 0.00 | 34.14 | 3.07 |
693 | 695 | 9.661563 | ATTGTAGTACAAATCCGAACTTATTCA | 57.338 | 29.630 | 19.19 | 0.00 | 41.96 | 2.57 |
700 | 702 | 5.731263 | GCGAAATTGTAGTACAAATCCGAAC | 59.269 | 40.000 | 25.03 | 12.93 | 41.96 | 3.95 |
701 | 703 | 5.408909 | TGCGAAATTGTAGTACAAATCCGAA | 59.591 | 36.000 | 25.03 | 17.90 | 41.96 | 4.30 |
702 | 704 | 4.930405 | TGCGAAATTGTAGTACAAATCCGA | 59.070 | 37.500 | 25.03 | 14.38 | 41.96 | 4.55 |
703 | 705 | 5.211266 | TGCGAAATTGTAGTACAAATCCG | 57.789 | 39.130 | 19.19 | 19.91 | 41.96 | 4.18 |
704 | 706 | 7.027161 | ACAATGCGAAATTGTAGTACAAATCC | 58.973 | 34.615 | 19.19 | 13.59 | 41.96 | 3.01 |
705 | 707 | 7.218204 | GGACAATGCGAAATTGTAGTACAAATC | 59.782 | 37.037 | 19.19 | 17.61 | 41.96 | 2.17 |
706 | 708 | 7.027161 | GGACAATGCGAAATTGTAGTACAAAT | 58.973 | 34.615 | 19.19 | 8.79 | 41.96 | 2.32 |
707 | 709 | 6.205853 | AGGACAATGCGAAATTGTAGTACAAA | 59.794 | 34.615 | 19.19 | 2.70 | 41.96 | 2.83 |
708 | 710 | 5.703592 | AGGACAATGCGAAATTGTAGTACAA | 59.296 | 36.000 | 17.74 | 17.74 | 41.76 | 2.41 |
709 | 711 | 5.242434 | AGGACAATGCGAAATTGTAGTACA | 58.758 | 37.500 | 14.60 | 0.00 | 41.76 | 2.90 |
710 | 712 | 5.796350 | AGGACAATGCGAAATTGTAGTAC | 57.204 | 39.130 | 14.60 | 0.00 | 41.76 | 2.73 |
711 | 713 | 7.388224 | TGTTTAGGACAATGCGAAATTGTAGTA | 59.612 | 33.333 | 14.60 | 8.26 | 41.76 | 1.82 |
712 | 714 | 6.205853 | TGTTTAGGACAATGCGAAATTGTAGT | 59.794 | 34.615 | 14.60 | 9.01 | 41.76 | 2.73 |
713 | 715 | 6.523201 | GTGTTTAGGACAATGCGAAATTGTAG | 59.477 | 38.462 | 14.60 | 0.00 | 41.76 | 2.74 |
714 | 716 | 6.205853 | AGTGTTTAGGACAATGCGAAATTGTA | 59.794 | 34.615 | 14.60 | 0.60 | 41.76 | 2.41 |
715 | 717 | 5.009610 | AGTGTTTAGGACAATGCGAAATTGT | 59.990 | 36.000 | 14.54 | 14.54 | 44.08 | 2.71 |
716 | 718 | 5.343058 | CAGTGTTTAGGACAATGCGAAATTG | 59.657 | 40.000 | 9.08 | 9.08 | 45.88 | 2.32 |
717 | 719 | 5.460646 | CAGTGTTTAGGACAATGCGAAATT | 58.539 | 37.500 | 0.00 | 0.00 | 45.88 | 1.82 |
718 | 720 | 5.046910 | CAGTGTTTAGGACAATGCGAAAT | 57.953 | 39.130 | 0.00 | 0.00 | 45.88 | 2.17 |
765 | 767 | 8.552865 | TCGTACACATTTATATTGGATTTTCCG | 58.447 | 33.333 | 0.00 | 0.00 | 40.17 | 4.30 |
773 | 775 | 4.084223 | GGGCGTCGTACACATTTATATTGG | 60.084 | 45.833 | 0.00 | 0.00 | 0.00 | 3.16 |
774 | 776 | 4.748102 | AGGGCGTCGTACACATTTATATTG | 59.252 | 41.667 | 0.00 | 0.00 | 0.00 | 1.90 |
883 | 1327 | 4.021544 | GGGACTGGAGATTAGCAGATAGTG | 60.022 | 50.000 | 0.00 | 0.00 | 0.00 | 2.74 |
5058 | 7455 | 3.633986 | AGAGATGTATCGATCACACAGCA | 59.366 | 43.478 | 15.28 | 1.08 | 31.16 | 4.41 |
5103 | 7503 | 6.013984 | ACTCCATCTCAAAATTTTGGCAGAAT | 60.014 | 34.615 | 26.45 | 12.59 | 38.66 | 2.40 |
5129 | 7532 | 0.240411 | GCTTCAGTTTCAGGCAGCTG | 59.760 | 55.000 | 10.11 | 10.11 | 0.00 | 4.24 |
5170 | 8051 | 2.813754 | CACCTCGGAGCTTTTGAAATCA | 59.186 | 45.455 | 0.00 | 0.00 | 0.00 | 2.57 |
5315 | 11069 | 2.404559 | TGGACTTGTTGGGACAGTAGT | 58.595 | 47.619 | 0.00 | 0.00 | 42.39 | 2.73 |
5316 | 11070 | 3.703001 | ATGGACTTGTTGGGACAGTAG | 57.297 | 47.619 | 0.00 | 0.00 | 42.39 | 2.57 |
5317 | 11071 | 4.595781 | AGTTATGGACTTGTTGGGACAGTA | 59.404 | 41.667 | 0.00 | 0.00 | 35.15 | 2.74 |
5362 | 11146 | 1.212751 | GGAGTTTGGACGCAATGCC | 59.787 | 57.895 | 0.00 | 0.00 | 0.00 | 4.40 |
5370 | 11154 | 4.079253 | TGCTGGATTTTAGGAGTTTGGAC | 58.921 | 43.478 | 0.00 | 0.00 | 0.00 | 4.02 |
5374 | 11162 | 7.505923 | AGTTACTTTGCTGGATTTTAGGAGTTT | 59.494 | 33.333 | 0.00 | 0.00 | 0.00 | 2.66 |
5547 | 11606 | 2.969238 | GCCAGATGACGGCGATGG | 60.969 | 66.667 | 16.62 | 14.07 | 40.35 | 3.51 |
5659 | 11718 | 1.130054 | ACTGCAGGAAGGAGAAGGCA | 61.130 | 55.000 | 19.93 | 0.00 | 38.04 | 4.75 |
5809 | 11868 | 2.507944 | GTGGAGATGGCGGCAGAT | 59.492 | 61.111 | 19.29 | 8.27 | 0.00 | 2.90 |
5909 | 11968 | 0.734942 | ACATAGTTGAACGCGTCGGG | 60.735 | 55.000 | 14.44 | 7.88 | 0.00 | 5.14 |
5953 | 12012 | 1.863155 | AAACCATGATGGCGGAGGGT | 61.863 | 55.000 | 12.25 | 0.00 | 42.67 | 4.34 |
6164 | 12260 | 3.613193 | CGGACGGTATTGAAGAGTGAACA | 60.613 | 47.826 | 0.00 | 0.00 | 0.00 | 3.18 |
6170 | 12266 | 2.545952 | CCCATCGGACGGTATTGAAGAG | 60.546 | 54.545 | 0.00 | 0.00 | 0.00 | 2.85 |
6262 | 12373 | 1.424493 | GCTCGCGCTGCATTAGAAGT | 61.424 | 55.000 | 16.72 | 0.00 | 0.00 | 3.01 |
6263 | 12374 | 1.275066 | GCTCGCGCTGCATTAGAAG | 59.725 | 57.895 | 16.72 | 0.00 | 0.00 | 2.85 |
6265 | 12376 | 2.167219 | GTGCTCGCGCTGCATTAGA | 61.167 | 57.895 | 24.38 | 3.67 | 42.69 | 2.10 |
6266 | 12377 | 2.322422 | GTGCTCGCGCTGCATTAG | 59.678 | 61.111 | 24.38 | 7.08 | 42.69 | 1.73 |
6267 | 12378 | 3.553765 | CGTGCTCGCGCTGCATTA | 61.554 | 61.111 | 24.38 | 4.51 | 42.69 | 1.90 |
6351 | 12469 | 5.741982 | GTCGTGCTTACAACAACAAAGAAAT | 59.258 | 36.000 | 0.00 | 0.00 | 0.00 | 2.17 |
6442 | 12582 | 1.011904 | CGCATTCTTCGCCATGTCG | 60.012 | 57.895 | 0.00 | 0.00 | 0.00 | 4.35 |
6505 | 12645 | 3.255397 | AAGCCCAGCAGCAGGACT | 61.255 | 61.111 | 5.14 | 0.00 | 34.23 | 3.85 |
6559 | 12699 | 0.035152 | ATTCTGCCGCAATCACCTCA | 60.035 | 50.000 | 0.00 | 0.00 | 0.00 | 3.86 |
6653 | 12793 | 7.419172 | GGTTTAGGTAGTTAGCTGATGGATCTT | 60.419 | 40.741 | 0.00 | 0.00 | 35.39 | 2.40 |
6654 | 12794 | 6.042208 | GGTTTAGGTAGTTAGCTGATGGATCT | 59.958 | 42.308 | 0.00 | 0.00 | 35.39 | 2.75 |
6700 | 12843 | 5.970023 | GCATGAAATTATCTCTTCAGTGCAC | 59.030 | 40.000 | 9.40 | 9.40 | 36.79 | 4.57 |
6724 | 12867 | 6.646653 | CCCGATATATGATTTCATATCCGTGG | 59.353 | 42.308 | 14.69 | 15.91 | 43.91 | 4.94 |
6795 | 12942 | 2.738521 | CCCTGTCGTCACAAGCCG | 60.739 | 66.667 | 0.00 | 0.00 | 29.82 | 5.52 |
6848 | 12996 | 1.886886 | ACGCCACAAGGTTCGTTATT | 58.113 | 45.000 | 0.00 | 0.00 | 37.19 | 1.40 |
6993 | 13164 | 5.810587 | GCTCGTTATGTTTCAGAATGGAGTA | 59.189 | 40.000 | 0.00 | 0.00 | 36.16 | 2.59 |
7222 | 13406 | 0.541764 | GGCCATCTCACAAAACCCCA | 60.542 | 55.000 | 0.00 | 0.00 | 0.00 | 4.96 |
7308 | 13492 | 7.523293 | TTCTGAGACATAAATTGCCTTGAAA | 57.477 | 32.000 | 0.00 | 0.00 | 0.00 | 2.69 |
7312 | 13496 | 7.613022 | TGATCTTTCTGAGACATAAATTGCCTT | 59.387 | 33.333 | 0.00 | 0.00 | 37.17 | 4.35 |
7316 | 13500 | 9.565213 | GGTTTGATCTTTCTGAGACATAAATTG | 57.435 | 33.333 | 0.00 | 0.00 | 37.17 | 2.32 |
7317 | 13501 | 9.525826 | AGGTTTGATCTTTCTGAGACATAAATT | 57.474 | 29.630 | 0.00 | 0.00 | 37.17 | 1.82 |
7329 | 13513 | 5.324409 | TGCCATTACAGGTTTGATCTTTCT | 58.676 | 37.500 | 0.00 | 0.00 | 0.00 | 2.52 |
7338 | 13522 | 5.777732 | TCTGGTTAATTGCCATTACAGGTTT | 59.222 | 36.000 | 4.38 | 0.00 | 35.19 | 3.27 |
7342 | 13526 | 5.882557 | ACTCTCTGGTTAATTGCCATTACAG | 59.117 | 40.000 | 4.38 | 3.14 | 35.19 | 2.74 |
7392 | 13576 | 3.432051 | GAGGGTGGAGCATCGACGG | 62.432 | 68.421 | 0.00 | 0.00 | 45.51 | 4.79 |
7396 | 13580 | 2.669133 | TTGGGAGGGTGGAGCATCG | 61.669 | 63.158 | 0.00 | 0.00 | 34.37 | 3.84 |
7401 | 13585 | 4.410400 | GCGGTTGGGAGGGTGGAG | 62.410 | 72.222 | 0.00 | 0.00 | 0.00 | 3.86 |
7422 | 13606 | 7.718525 | TGAAAATATGAACATCCATGACCATG | 58.281 | 34.615 | 0.00 | 3.11 | 38.51 | 3.66 |
7423 | 13607 | 7.901283 | TGAAAATATGAACATCCATGACCAT | 57.099 | 32.000 | 0.00 | 0.00 | 0.00 | 3.55 |
7424 | 13608 | 7.147863 | CCTTGAAAATATGAACATCCATGACCA | 60.148 | 37.037 | 0.00 | 0.00 | 0.00 | 4.02 |
7425 | 13609 | 7.068593 | TCCTTGAAAATATGAACATCCATGACC | 59.931 | 37.037 | 0.00 | 0.00 | 0.00 | 4.02 |
7426 | 13610 | 7.917505 | GTCCTTGAAAATATGAACATCCATGAC | 59.082 | 37.037 | 0.00 | 0.00 | 0.00 | 3.06 |
7483 | 13686 | 0.334335 | TCCTGGTATTGGCATTGGCA | 59.666 | 50.000 | 9.11 | 9.11 | 43.71 | 4.92 |
7484 | 13687 | 0.746659 | GTCCTGGTATTGGCATTGGC | 59.253 | 55.000 | 2.73 | 2.73 | 40.13 | 4.52 |
7485 | 13688 | 2.142356 | TGTCCTGGTATTGGCATTGG | 57.858 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
7486 | 13689 | 3.289836 | TGATGTCCTGGTATTGGCATTG | 58.710 | 45.455 | 0.00 | 0.00 | 0.00 | 2.82 |
7487 | 13690 | 3.668141 | TGATGTCCTGGTATTGGCATT | 57.332 | 42.857 | 0.00 | 0.00 | 0.00 | 3.56 |
7488 | 13691 | 3.138839 | TGATGATGTCCTGGTATTGGCAT | 59.861 | 43.478 | 0.00 | 0.00 | 0.00 | 4.40 |
7562 | 13765 | 6.327386 | ACATTTCTATTGCCTCCTCCTTTA | 57.673 | 37.500 | 0.00 | 0.00 | 0.00 | 1.85 |
7584 | 13899 | 2.427095 | GTTAGCCACCATGGGAATGAAC | 59.573 | 50.000 | 18.09 | 10.65 | 38.19 | 3.18 |
7613 | 13928 | 3.947834 | CCTGCTTTGTAAGGAACCCATAG | 59.052 | 47.826 | 0.00 | 0.00 | 35.40 | 2.23 |
7666 | 13985 | 3.825143 | AATAATGAGGCAATTGGGCAC | 57.175 | 42.857 | 7.72 | 0.24 | 46.44 | 5.01 |
7775 | 14094 | 6.043590 | TGGCTCTGAAGTATTATGACCATCAT | 59.956 | 38.462 | 0.00 | 0.00 | 40.72 | 2.45 |
7776 | 14095 | 5.366477 | TGGCTCTGAAGTATTATGACCATCA | 59.634 | 40.000 | 0.00 | 0.00 | 0.00 | 3.07 |
7777 | 14096 | 5.698545 | GTGGCTCTGAAGTATTATGACCATC | 59.301 | 44.000 | 0.00 | 0.00 | 0.00 | 3.51 |
7778 | 14097 | 5.130975 | TGTGGCTCTGAAGTATTATGACCAT | 59.869 | 40.000 | 0.00 | 0.00 | 0.00 | 3.55 |
7779 | 14098 | 4.469586 | TGTGGCTCTGAAGTATTATGACCA | 59.530 | 41.667 | 0.00 | 0.00 | 0.00 | 4.02 |
7780 | 14099 | 5.023533 | TGTGGCTCTGAAGTATTATGACC | 57.976 | 43.478 | 0.00 | 0.00 | 0.00 | 4.02 |
7782 | 14101 | 5.425217 | TCCTTGTGGCTCTGAAGTATTATGA | 59.575 | 40.000 | 0.00 | 0.00 | 0.00 | 2.15 |
7816 | 14152 | 7.759489 | AGCAGACCTCATTGTAAATGTTTAA | 57.241 | 32.000 | 0.26 | 0.00 | 0.00 | 1.52 |
7878 | 14214 | 2.613595 | GCACATGCTCGATGATTACCAA | 59.386 | 45.455 | 0.00 | 0.00 | 38.21 | 3.67 |
7918 | 14254 | 6.088824 | CCAATGACTTCTTGTGTTATTGAGC | 58.911 | 40.000 | 11.24 | 0.00 | 41.12 | 4.26 |
7965 | 14301 | 3.181493 | GCTTCAAGCCCAATACAGACATG | 60.181 | 47.826 | 0.00 | 0.00 | 34.48 | 3.21 |
7972 | 14308 | 2.819608 | TGAGTTGCTTCAAGCCCAATAC | 59.180 | 45.455 | 7.01 | 0.00 | 41.51 | 1.89 |
7978 | 14314 | 0.944386 | TCGTTGAGTTGCTTCAAGCC | 59.056 | 50.000 | 7.01 | 0.00 | 41.51 | 4.35 |
7985 | 14321 | 4.456280 | TCATAGACATCGTTGAGTTGCT | 57.544 | 40.909 | 0.00 | 0.00 | 0.00 | 3.91 |
8050 | 14386 | 9.377312 | CCAACAGAACAAAAGAAGGATTTTAAA | 57.623 | 29.630 | 0.00 | 0.00 | 31.29 | 1.52 |
8053 | 14389 | 6.070251 | ACCCAACAGAACAAAAGAAGGATTTT | 60.070 | 34.615 | 0.00 | 0.00 | 32.65 | 1.82 |
8054 | 14390 | 5.425217 | ACCCAACAGAACAAAAGAAGGATTT | 59.575 | 36.000 | 0.00 | 0.00 | 0.00 | 2.17 |
8068 | 14410 | 7.841956 | TCAAATTTCTTTGTAACCCAACAGAA | 58.158 | 30.769 | 0.00 | 0.00 | 42.02 | 3.02 |
8124 | 14469 | 3.695830 | TCTTTGAAACCGAGTAGGCAT | 57.304 | 42.857 | 0.00 | 0.00 | 46.52 | 4.40 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.