Multiple sequence alignment - TraesCS6A01G152100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G152100 chr6A 100.000 4161 0 0 4273 8433 136657848 136662008 0.000000e+00 7685.0
1 TraesCS6A01G152100 chr6A 100.000 3908 0 0 1 3908 136653576 136657483 0.000000e+00 7217.0
2 TraesCS6A01G152100 chr6A 95.684 3499 131 6 4703 8184 11915100 11911605 0.000000e+00 5607.0
3 TraesCS6A01G152100 chr6A 94.091 1523 80 8 2336 3854 529363062 529364578 0.000000e+00 2305.0
4 TraesCS6A01G152100 chr6A 92.008 1001 39 4 1 1001 529358359 529359318 0.000000e+00 1367.0
5 TraesCS6A01G152100 chr6A 96.835 632 20 0 1690 2321 529359786 529360417 0.000000e+00 1057.0
6 TraesCS6A01G152100 chr6A 96.705 516 16 1 4300 4815 529364913 529365427 0.000000e+00 857.0
7 TraesCS6A01G152100 chr6A 94.455 523 21 6 990 1506 529359270 529359790 0.000000e+00 798.0
8 TraesCS6A01G152100 chr6A 97.041 338 10 0 1789 2126 401364219 401364556 3.420000e-158 569.0
9 TraesCS6A01G152100 chr6A 96.923 195 6 0 2127 2321 401364866 401365060 2.270000e-85 327.0
10 TraesCS6A01G152100 chr6A 100.000 29 0 0 1688 1716 136655207 136655235 4.000000e-03 54.7
11 TraesCS6A01G152100 chr3A 96.396 4134 134 5 4300 8433 733883067 733878949 0.000000e+00 6794.0
12 TraesCS6A01G152100 chr3A 94.784 4160 178 19 4273 8404 615140040 615135892 0.000000e+00 6444.0
13 TraesCS6A01G152100 chr3A 94.999 3499 155 6 4703 8184 233469815 233466320 0.000000e+00 5474.0
14 TraesCS6A01G152100 chr3A 94.455 2633 112 6 5803 8433 676001022 676003622 0.000000e+00 4023.0
15 TraesCS6A01G152100 chr3A 93.083 1200 56 6 7231 8404 702240299 702241497 0.000000e+00 1731.0
16 TraesCS6A01G152100 chr3A 92.179 1138 55 7 1 1136 513293508 513294613 0.000000e+00 1578.0
17 TraesCS6A01G152100 chr3A 95.625 640 20 1 1 640 733895841 733895210 0.000000e+00 1020.0
18 TraesCS6A01G152100 chr3A 96.061 330 12 1 1797 2126 733887617 733887289 3.460000e-148 536.0
19 TraesCS6A01G152100 chr3A 95.266 338 14 2 1789 2126 513294740 513295075 1.250000e-147 534.0
20 TraesCS6A01G152100 chr3A 91.553 367 18 4 1421 1787 5993187 5992834 2.110000e-135 494.0
21 TraesCS6A01G152100 chr3A 97.951 244 5 0 8190 8433 579910749 579910506 2.810000e-114 424.0
22 TraesCS6A01G152100 chr3A 94.297 263 14 1 8142 8404 706571667 706571406 1.320000e-107 401.0
23 TraesCS6A01G152100 chr3A 97.949 195 4 0 2127 2321 513295388 513295582 1.050000e-88 339.0
24 TraesCS6A01G152100 chr3A 91.393 244 4 2 8190 8433 153244259 153244033 1.370000e-82 318.0
25 TraesCS6A01G152100 chr3A 94.872 117 6 0 8190 8306 233466214 233466098 5.200000e-42 183.0
26 TraesCS6A01G152100 chr3A 97.030 101 3 0 8333 8433 233452484 233452384 4.050000e-38 171.0
27 TraesCS6A01G152100 chr2A 96.695 4055 127 5 4379 8433 605783138 605787185 0.000000e+00 6739.0
28 TraesCS6A01G152100 chr2A 95.351 2065 84 3 6369 8433 340611171 340609119 0.000000e+00 3271.0
29 TraesCS6A01G152100 chr2A 92.464 690 38 5 327 1015 605760738 605761414 0.000000e+00 974.0
30 TraesCS6A01G152100 chr2A 97.746 355 8 0 1 355 655911165 655910811 5.600000e-171 612.0
31 TraesCS6A01G152100 chr2A 95.139 288 12 1 8119 8404 259698518 259698805 3.590000e-123 453.0
32 TraesCS6A01G152100 chr2A 97.321 112 3 0 4273 4384 605774305 605774416 3.110000e-44 191.0
33 TraesCS6A01G152100 chr2A 100.000 29 0 0 4439 4467 605783161 605783189 4.000000e-03 54.7
34 TraesCS6A01G152100 chr5D 95.720 4112 151 10 4309 8404 384515403 384511301 0.000000e+00 6595.0
35 TraesCS6A01G152100 chr5D 95.205 4129 162 16 4303 8404 401777011 401781130 0.000000e+00 6495.0
36 TraesCS6A01G152100 chr5D 94.199 1017 39 3 1 1015 140962664 140961666 0.000000e+00 1533.0
37 TraesCS6A01G152100 chr5D 92.916 367 13 4 1421 1787 16496818 16496465 9.700000e-144 521.0
38 TraesCS6A01G152100 chr7D 95.362 3816 157 8 4301 8114 17940538 17936741 0.000000e+00 6048.0
39 TraesCS6A01G152100 chr7D 94.851 369 18 1 1036 1404 103531391 103531758 7.340000e-160 575.0
40 TraesCS6A01G152100 chr7D 93.733 367 10 4 1421 1787 103531931 103532284 9.630000e-149 538.0
41 TraesCS6A01G152100 chr7D 100.000 29 0 0 1688 1716 103532142 103532170 4.000000e-03 54.7
42 TraesCS6A01G152100 chr2B 94.329 3756 176 15 4700 8432 539883256 539886997 0.000000e+00 5722.0
43 TraesCS6A01G152100 chr2B 92.371 367 15 4 1421 1787 539865036 539865389 2.100000e-140 510.0
44 TraesCS6A01G152100 chr2B 87.121 396 26 13 4320 4707 539882845 539883223 7.820000e-115 425.0
45 TraesCS6A01G152100 chr2B 80.756 582 54 29 708 1269 539864376 539864919 1.320000e-107 401.0
46 TraesCS6A01G152100 chr5A 93.554 2746 128 11 5689 8433 530200071 530197374 0.000000e+00 4045.0
47 TraesCS6A01G152100 chr5A 94.440 2626 114 7 5808 8433 27045467 27042874 0.000000e+00 4012.0
48 TraesCS6A01G152100 chr5A 92.792 2192 133 10 6232 8404 235673726 235675911 0.000000e+00 3149.0
49 TraesCS6A01G152100 chr5A 92.520 1016 41 8 1 1015 168401575 168400594 0.000000e+00 1423.0
50 TraesCS6A01G152100 chr5A 92.224 1016 46 6 1 1015 133816320 133817303 0.000000e+00 1408.0
51 TraesCS6A01G152100 chr5A 90.253 554 35 9 7862 8403 178860401 178859855 0.000000e+00 706.0
52 TraesCS6A01G152100 chr5A 97.465 355 9 0 1 355 345674248 345673894 2.600000e-169 606.0
53 TraesCS6A01G152100 chr5A 96.942 327 10 0 1797 2123 133817533 133817859 4.450000e-152 549.0
54 TraesCS6A01G152100 chr5A 88.496 452 28 12 4273 4707 384026104 384026548 7.500000e-145 525.0
55 TraesCS6A01G152100 chr5A 92.361 288 20 1 8119 8404 384030044 384030331 7.880000e-110 409.0
56 TraesCS6A01G152100 chr5A 97.436 195 5 0 2127 2321 168399838 168399644 4.880000e-87 333.0
57 TraesCS6A01G152100 chr5A 96.923 195 6 0 2127 2321 133818175 133818369 2.270000e-85 327.0
58 TraesCS6A01G152100 chr3B 92.697 1780 92 13 6671 8433 753432208 753430450 0.000000e+00 2532.0
59 TraesCS6A01G152100 chr1D 93.385 1557 84 10 2336 3886 336735642 336734099 0.000000e+00 2287.0
60 TraesCS6A01G152100 chr7A 93.455 1528 74 15 2336 3840 579480625 579479101 0.000000e+00 2244.0
61 TraesCS6A01G152100 chr7A 97.746 355 8 0 1 355 644068067 644067713 5.600000e-171 612.0
62 TraesCS6A01G152100 chr7A 95.536 336 15 0 1789 2124 153040117 153039782 9.630000e-149 538.0
63 TraesCS6A01G152100 chr7A 95.139 288 12 1 8119 8404 220999905 221000192 3.590000e-123 453.0
64 TraesCS6A01G152100 chr7A 97.436 195 5 0 2127 2321 644066335 644066141 4.880000e-87 333.0
65 TraesCS6A01G152100 chr4B 91.860 1597 95 21 2336 3908 263065040 263063455 0.000000e+00 2196.0
66 TraesCS6A01G152100 chr4B 86.792 424 27 9 990 1404 343639256 343639659 6.010000e-121 446.0
67 TraesCS6A01G152100 chr4B 97.778 45 1 0 4273 4317 6833540 6833584 2.520000e-10 78.7
68 TraesCS6A01G152100 chr5B 93.003 1515 89 12 2336 3837 62363859 62362349 0.000000e+00 2194.0
69 TraesCS6A01G152100 chr7B 92.308 1547 94 17 2336 3865 689556258 689557796 0.000000e+00 2174.0
70 TraesCS6A01G152100 chr7B 92.056 1561 101 20 2336 3881 749268731 749270283 0.000000e+00 2174.0
71 TraesCS6A01G152100 chr6B 91.593 1582 105 21 2337 3908 518300138 518301701 0.000000e+00 2159.0
72 TraesCS6A01G152100 chr6B 91.688 397 25 5 1013 1402 518297109 518297504 2.070000e-150 544.0
73 TraesCS6A01G152100 chr6B 92.478 226 4 5 1562 1787 518297552 518297764 2.290000e-80 311.0
74 TraesCS6A01G152100 chr6B 100.000 29 0 0 1688 1716 518297622 518297650 4.000000e-03 54.7
75 TraesCS6A01G152100 chr4A 91.463 1593 103 23 2336 3908 660544478 660546057 0.000000e+00 2158.0
76 TraesCS6A01G152100 chr4A 93.333 420 21 2 990 1403 433611151 433610733 1.560000e-171 614.0
77 TraesCS6A01G152100 chr4A 97.746 355 8 0 1 355 490339552 490339906 5.600000e-171 612.0
78 TraesCS6A01G152100 chr4A 97.681 345 8 0 1421 1765 433610558 433610214 2.030000e-165 593.0
79 TraesCS6A01G152100 chr4A 96.154 338 13 0 1789 2126 429487912 429488249 3.440000e-153 553.0
80 TraesCS6A01G152100 chr4A 97.177 248 7 0 1879 2126 490340826 490341073 3.640000e-113 420.0
81 TraesCS6A01G152100 chr4A 97.436 195 5 0 2127 2321 429488562 429488756 4.880000e-87 333.0
82 TraesCS6A01G152100 chr4A 97.436 195 5 0 2127 2321 490341386 490341580 4.880000e-87 333.0
83 TraesCS6A01G152100 chr6D 95.084 1017 45 3 1 1015 297180920 297179907 0.000000e+00 1596.0
84 TraesCS6A01G152100 chr6D 94.505 364 7 4 1424 1787 46527841 46527491 4.450000e-152 549.0
85 TraesCS6A01G152100 chr6D 96.410 195 7 0 2127 2321 297179107 297178913 1.060000e-83 322.0
86 TraesCS6A01G152100 chr6D 96.875 32 1 0 1688 1719 46527633 46527602 4.000000e-03 54.7
87 TraesCS6A01G152100 chr1A 92.618 1016 42 6 1 1015 497973895 497974878 0.000000e+00 1430.0
88 TraesCS6A01G152100 chr1A 92.323 1016 41 10 1 1015 443852046 443853025 0.000000e+00 1410.0
89 TraesCS6A01G152100 chr1A 98.028 355 7 0 1 355 575417434 575417788 1.200000e-172 617.0
90 TraesCS6A01G152100 chr1A 97.041 338 9 1 1789 2126 580782891 580783227 1.230000e-157 568.0
91 TraesCS6A01G152100 chr1A 97.973 296 6 0 1789 2084 575418869 575419164 1.620000e-141 514.0
92 TraesCS6A01G152100 chr1A 97.436 195 5 0 2127 2321 575419439 575419633 4.880000e-87 333.0
93 TraesCS6A01G152100 chr4D 94.940 415 21 0 990 1404 125937677 125937263 0.000000e+00 651.0
94 TraesCS6A01G152100 chr4D 94.062 421 19 1 990 1404 125862089 125861669 1.190000e-177 634.0
95 TraesCS6A01G152100 chr4D 93.587 421 21 1 990 1404 125871899 125872319 2.580000e-174 623.0
96 TraesCS6A01G152100 chr4D 92.916 367 13 4 1421 1787 222630661 222630308 9.700000e-144 521.0
97 TraesCS6A01G152100 chr4D 96.875 32 1 0 1688 1719 222630450 222630419 4.000000e-03 54.7
98 TraesCS6A01G152100 chr3D 94.299 421 18 1 990 1404 57606019 57606439 2.570000e-179 640.0
99 TraesCS6A01G152100 chr3D 91.935 372 10 7 1421 1787 57606613 57606969 3.510000e-138 503.0
100 TraesCS6A01G152100 chr3D 98.630 73 1 0 1715 1787 330477564 330477492 6.870000e-26 130.0
101 TraesCS6A01G152100 chr3D 100.000 29 0 0 1688 1716 57606822 57606850 4.000000e-03 54.7
102 TraesCS6A01G152100 chr2D 93.733 367 10 4 1421 1787 397123120 397123473 9.630000e-149 538.0
103 TraesCS6A01G152100 chr2D 100.000 29 0 0 1688 1716 397123331 397123359 4.000000e-03 54.7


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 TraesCS6A01G152100 chr6A 136653576 136662008 8432 False 4985.566667 7685 100.000000 1 8433 3 chr6A.!!$F1 8432
1 TraesCS6A01G152100 chr6A 11911605 11915100 3495 True 5607.000000 5607 95.684000 4703 8184 1 chr6A.!!$R1 3481
2 TraesCS6A01G152100 chr6A 529358359 529365427 7068 False 1276.800000 2305 94.818800 1 4815 5 chr6A.!!$F3 4814
3 TraesCS6A01G152100 chr6A 401364219 401365060 841 False 448.000000 569 96.982000 1789 2321 2 chr6A.!!$F2 532
4 TraesCS6A01G152100 chr3A 733878949 733883067 4118 True 6794.000000 6794 96.396000 4300 8433 1 chr3A.!!$R7 4133
5 TraesCS6A01G152100 chr3A 615135892 615140040 4148 True 6444.000000 6444 94.784000 4273 8404 1 chr3A.!!$R5 4131
6 TraesCS6A01G152100 chr3A 676001022 676003622 2600 False 4023.000000 4023 94.455000 5803 8433 1 chr3A.!!$F1 2630
7 TraesCS6A01G152100 chr3A 233466098 233469815 3717 True 2828.500000 5474 94.935500 4703 8306 2 chr3A.!!$R10 3603
8 TraesCS6A01G152100 chr3A 702240299 702241497 1198 False 1731.000000 1731 93.083000 7231 8404 1 chr3A.!!$F2 1173
9 TraesCS6A01G152100 chr3A 733895210 733895841 631 True 1020.000000 1020 95.625000 1 640 1 chr3A.!!$R9 639
10 TraesCS6A01G152100 chr3A 513293508 513295582 2074 False 817.000000 1578 95.131333 1 2321 3 chr3A.!!$F3 2320
11 TraesCS6A01G152100 chr2A 605783138 605787185 4047 False 6739.000000 6739 96.695000 4379 8433 1 chr2A.!!$F4 4054
12 TraesCS6A01G152100 chr2A 340609119 340611171 2052 True 3271.000000 3271 95.351000 6369 8433 1 chr2A.!!$R1 2064
13 TraesCS6A01G152100 chr2A 605760738 605761414 676 False 974.000000 974 92.464000 327 1015 1 chr2A.!!$F2 688
14 TraesCS6A01G152100 chr5D 384511301 384515403 4102 True 6595.000000 6595 95.720000 4309 8404 1 chr5D.!!$R3 4095
15 TraesCS6A01G152100 chr5D 401777011 401781130 4119 False 6495.000000 6495 95.205000 4303 8404 1 chr5D.!!$F1 4101
16 TraesCS6A01G152100 chr5D 140961666 140962664 998 True 1533.000000 1533 94.199000 1 1015 1 chr5D.!!$R2 1014
17 TraesCS6A01G152100 chr7D 17936741 17940538 3797 True 6048.000000 6048 95.362000 4301 8114 1 chr7D.!!$R1 3813
18 TraesCS6A01G152100 chr7D 103531391 103532284 893 False 389.233333 575 96.194667 1036 1787 3 chr7D.!!$F1 751
19 TraesCS6A01G152100 chr2B 539882845 539886997 4152 False 3073.500000 5722 90.725000 4320 8432 2 chr2B.!!$F2 4112
20 TraesCS6A01G152100 chr2B 539864376 539865389 1013 False 455.500000 510 86.563500 708 1787 2 chr2B.!!$F1 1079
21 TraesCS6A01G152100 chr5A 530197374 530200071 2697 True 4045.000000 4045 93.554000 5689 8433 1 chr5A.!!$R4 2744
22 TraesCS6A01G152100 chr5A 27042874 27045467 2593 True 4012.000000 4012 94.440000 5808 8433 1 chr5A.!!$R1 2625
23 TraesCS6A01G152100 chr5A 235673726 235675911 2185 False 3149.000000 3149 92.792000 6232 8404 1 chr5A.!!$F1 2172
24 TraesCS6A01G152100 chr5A 168399644 168401575 1931 True 878.000000 1423 94.978000 1 2321 2 chr5A.!!$R5 2320
25 TraesCS6A01G152100 chr5A 133816320 133818369 2049 False 761.333333 1408 95.363000 1 2321 3 chr5A.!!$F2 2320
26 TraesCS6A01G152100 chr5A 178859855 178860401 546 True 706.000000 706 90.253000 7862 8403 1 chr5A.!!$R2 541
27 TraesCS6A01G152100 chr5A 384026104 384030331 4227 False 467.000000 525 90.428500 4273 8404 2 chr5A.!!$F3 4131
28 TraesCS6A01G152100 chr3B 753430450 753432208 1758 True 2532.000000 2532 92.697000 6671 8433 1 chr3B.!!$R1 1762
29 TraesCS6A01G152100 chr1D 336734099 336735642 1543 True 2287.000000 2287 93.385000 2336 3886 1 chr1D.!!$R1 1550
30 TraesCS6A01G152100 chr7A 579479101 579480625 1524 True 2244.000000 2244 93.455000 2336 3840 1 chr7A.!!$R2 1504
31 TraesCS6A01G152100 chr7A 644066141 644068067 1926 True 472.500000 612 97.591000 1 2321 2 chr7A.!!$R3 2320
32 TraesCS6A01G152100 chr4B 263063455 263065040 1585 True 2196.000000 2196 91.860000 2336 3908 1 chr4B.!!$R1 1572
33 TraesCS6A01G152100 chr5B 62362349 62363859 1510 True 2194.000000 2194 93.003000 2336 3837 1 chr5B.!!$R1 1501
34 TraesCS6A01G152100 chr7B 689556258 689557796 1538 False 2174.000000 2174 92.308000 2336 3865 1 chr7B.!!$F1 1529
35 TraesCS6A01G152100 chr7B 749268731 749270283 1552 False 2174.000000 2174 92.056000 2336 3881 1 chr7B.!!$F2 1545
36 TraesCS6A01G152100 chr6B 518297109 518301701 4592 False 767.175000 2159 93.939750 1013 3908 4 chr6B.!!$F1 2895
37 TraesCS6A01G152100 chr4A 660544478 660546057 1579 False 2158.000000 2158 91.463000 2336 3908 1 chr4A.!!$F1 1572
38 TraesCS6A01G152100 chr4A 433610214 433611151 937 True 603.500000 614 95.507000 990 1765 2 chr4A.!!$R1 775
39 TraesCS6A01G152100 chr4A 490339552 490341580 2028 False 455.000000 612 97.453000 1 2321 3 chr4A.!!$F3 2320
40 TraesCS6A01G152100 chr4A 429487912 429488756 844 False 443.000000 553 96.795000 1789 2321 2 chr4A.!!$F2 532
41 TraesCS6A01G152100 chr6D 297178913 297180920 2007 True 959.000000 1596 95.747000 1 2321 2 chr6D.!!$R2 2320
42 TraesCS6A01G152100 chr1A 497973895 497974878 983 False 1430.000000 1430 92.618000 1 1015 1 chr1A.!!$F2 1014
43 TraesCS6A01G152100 chr1A 443852046 443853025 979 False 1410.000000 1410 92.323000 1 1015 1 chr1A.!!$F1 1014
44 TraesCS6A01G152100 chr1A 575417434 575419633 2199 False 488.000000 617 97.812333 1 2321 3 chr1A.!!$F4 2320
45 TraesCS6A01G152100 chr3D 57606019 57606969 950 False 399.233333 640 95.411333 990 1787 3 chr3D.!!$F1 797

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
965 987 0.179000 CCCCTTCTCCTCCATCAACG 59.821 60.0 0.00 0.00 0.00 4.10 F
966 988 0.179000 CCCTTCTCCTCCATCAACGG 59.821 60.0 0.00 0.00 0.00 4.44 F
2324 3172 0.250640 GGGCAGATATGGTCCAGCTG 60.251 60.0 6.78 6.78 0.00 4.24 F
2329 3177 0.036022 GATATGGTCCAGCTGCTCCC 59.964 60.0 8.66 7.89 0.00 4.30 F
2330 3178 0.695462 ATATGGTCCAGCTGCTCCCA 60.695 55.0 16.50 16.50 0.00 4.37 F
2397 5215 0.745845 ATGCCTCCGTCTTGTGATGC 60.746 55.0 0.00 0.00 0.00 3.91 F
4398 8577 0.526524 CGTTGCTCTCCTCGATCCAC 60.527 60.0 0.00 0.00 0.00 4.02 F
4597 8785 0.034089 CCCTCTGGTTCATGGGGTTC 60.034 60.0 0.00 0.00 36.15 3.62 F
5105 9377 1.548357 GGAGGAGGAGCTCAAGCACA 61.548 60.0 17.19 0.00 45.16 4.57 F
6516 10789 0.481128 TGGAGGGTTGGGGTTCTTTC 59.519 55.0 0.00 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 3174 0.037447 TCAACGGATGCATTGTGGGA 59.963 50.000 0.00 2.45 0.00 4.37 R
2327 3175 0.887247 TTCAACGGATGCATTGTGGG 59.113 50.000 0.00 0.04 0.00 4.61 R
3307 6796 1.065709 GGAGGACCCGCAGTTCAAATA 60.066 52.381 0.00 0.00 0.00 1.40 R
4317 8487 1.335051 CGCCATCGTCGATGTAGTCAT 60.335 52.381 28.46 0.00 38.28 3.06 R
4333 8503 3.888930 TGATGTAGATGATGTAGTCGCCA 59.111 43.478 0.00 0.00 0.00 5.69 R
4592 8780 0.708209 AACCCTAACCCCATGAACCC 59.292 55.000 0.00 0.00 0.00 4.11 R
6220 10493 1.074752 GTGAGAGGCTCTTCTTTGCG 58.925 55.000 19.80 0.00 0.00 4.85 R
6516 10789 4.751060 AGCACAAGGAATAACATTGCATG 58.249 39.130 0.00 0.00 42.97 4.06 R
6660 10936 0.100682 GAGGCATTGCAGCAGATGTG 59.899 55.000 11.39 6.97 35.83 3.21 R
7540 11818 1.577328 ATCTTTGCACGCGGTCTTGG 61.577 55.000 12.47 0.00 0.00 3.61 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
26 27 4.196971 GTCTCCTTGGTAGTTGTTGTTGT 58.803 43.478 0.00 0.00 0.00 3.32
108 109 2.103373 TGTAGTGATGGAGAGGCAGAC 58.897 52.381 0.00 0.00 0.00 3.51
208 209 7.379750 TGAATGAAGATGCAAAATGATGAACA 58.620 30.769 0.00 0.00 0.00 3.18
449 451 4.129737 CCGTCTGATCCCACGCGT 62.130 66.667 5.58 5.58 34.58 6.01
538 541 4.331717 CGTTTCACTGTGTTTCTACCACTT 59.668 41.667 7.79 0.00 33.92 3.16
551 554 0.615850 ACCACTTGGCTAGGAAGAGC 59.384 55.000 0.20 0.00 42.05 4.09
625 628 3.762288 AGTATCAAACACAGACCTCGCTA 59.238 43.478 0.00 0.00 0.00 4.26
703 707 0.549169 TCGACCCTTTTCCCCCTGAT 60.549 55.000 0.00 0.00 0.00 2.90
828 833 6.322201 ACTCTATGCCAACCCTTTTCAATATG 59.678 38.462 0.00 0.00 0.00 1.78
829 834 3.608316 TGCCAACCCTTTTCAATATGC 57.392 42.857 0.00 0.00 0.00 3.14
854 860 1.137086 ACAGAACTCGCTGACAAGTGT 59.863 47.619 0.00 0.00 39.20 3.55
855 861 2.205074 CAGAACTCGCTGACAAGTGTT 58.795 47.619 0.00 0.00 38.14 3.32
938 960 3.151022 CACTCCTCCTCTCCGCCC 61.151 72.222 0.00 0.00 0.00 6.13
953 975 2.697644 CCCCTGGCATCCCCTTCT 60.698 66.667 0.00 0.00 0.00 2.85
954 976 2.761465 CCCCTGGCATCCCCTTCTC 61.761 68.421 0.00 0.00 0.00 2.87
955 977 2.761465 CCCTGGCATCCCCTTCTCC 61.761 68.421 0.00 0.00 0.00 3.71
956 978 1.695597 CCTGGCATCCCCTTCTCCT 60.696 63.158 0.00 0.00 0.00 3.69
957 979 1.704007 CCTGGCATCCCCTTCTCCTC 61.704 65.000 0.00 0.00 0.00 3.71
958 980 1.694169 TGGCATCCCCTTCTCCTCC 60.694 63.158 0.00 0.00 0.00 4.30
959 981 1.694169 GGCATCCCCTTCTCCTCCA 60.694 63.158 0.00 0.00 0.00 3.86
960 982 1.064824 GGCATCCCCTTCTCCTCCAT 61.065 60.000 0.00 0.00 0.00 3.41
961 983 0.399833 GCATCCCCTTCTCCTCCATC 59.600 60.000 0.00 0.00 0.00 3.51
962 984 1.811778 CATCCCCTTCTCCTCCATCA 58.188 55.000 0.00 0.00 0.00 3.07
963 985 2.130193 CATCCCCTTCTCCTCCATCAA 58.870 52.381 0.00 0.00 0.00 2.57
964 986 1.584724 TCCCCTTCTCCTCCATCAAC 58.415 55.000 0.00 0.00 0.00 3.18
965 987 0.179000 CCCCTTCTCCTCCATCAACG 59.821 60.000 0.00 0.00 0.00 4.10
966 988 0.179000 CCCTTCTCCTCCATCAACGG 59.821 60.000 0.00 0.00 0.00 4.44
967 989 0.462759 CCTTCTCCTCCATCAACGGC 60.463 60.000 0.00 0.00 0.00 5.68
968 990 0.807667 CTTCTCCTCCATCAACGGCG 60.808 60.000 4.80 4.80 0.00 6.46
969 991 1.254975 TTCTCCTCCATCAACGGCGA 61.255 55.000 16.62 0.00 0.00 5.54
970 992 1.043116 TCTCCTCCATCAACGGCGAT 61.043 55.000 16.62 0.00 0.00 4.58
971 993 0.877649 CTCCTCCATCAACGGCGATG 60.878 60.000 16.62 13.61 42.09 3.84
972 994 1.143838 CCTCCATCAACGGCGATGA 59.856 57.895 21.98 21.98 44.67 2.92
973 995 1.154205 CCTCCATCAACGGCGATGAC 61.154 60.000 22.16 0.00 44.67 3.06
974 996 1.153449 TCCATCAACGGCGATGACC 60.153 57.895 22.16 0.00 44.67 4.02
975 997 1.153369 CCATCAACGGCGATGACCT 60.153 57.895 22.16 4.64 44.67 3.85
976 998 1.154205 CCATCAACGGCGATGACCTC 61.154 60.000 22.16 0.00 44.67 3.85
977 999 1.144057 ATCAACGGCGATGACCTCC 59.856 57.895 22.16 0.00 0.00 4.30
978 1000 2.311688 ATCAACGGCGATGACCTCCC 62.312 60.000 22.16 0.00 0.00 4.30
979 1001 2.683933 AACGGCGATGACCTCCCT 60.684 61.111 16.62 0.00 0.00 4.20
980 1002 1.380785 AACGGCGATGACCTCCCTA 60.381 57.895 16.62 0.00 0.00 3.53
981 1003 1.392710 AACGGCGATGACCTCCCTAG 61.393 60.000 16.62 0.00 0.00 3.02
982 1004 2.737830 GGCGATGACCTCCCTAGC 59.262 66.667 0.00 0.00 0.00 3.42
983 1005 2.336809 GCGATGACCTCCCTAGCG 59.663 66.667 0.00 0.00 0.00 4.26
984 1006 2.194212 GCGATGACCTCCCTAGCGA 61.194 63.158 0.00 0.00 0.00 4.93
985 1007 1.655329 CGATGACCTCCCTAGCGAC 59.345 63.158 0.00 0.00 0.00 5.19
986 1008 1.797211 CGATGACCTCCCTAGCGACC 61.797 65.000 0.00 0.00 0.00 4.79
987 1009 1.457831 ATGACCTCCCTAGCGACCC 60.458 63.158 0.00 0.00 0.00 4.46
988 1010 2.043248 GACCTCCCTAGCGACCCA 60.043 66.667 0.00 0.00 0.00 4.51
1078 1149 1.639722 TGAATCCACCGACTCCTTCA 58.360 50.000 0.00 0.00 0.00 3.02
1150 1237 4.901927 AGGGTTCCTCTTCCTATTGATCT 58.098 43.478 0.00 0.00 0.00 2.75
1279 1382 7.543520 CAGATTAGGGTTCTTTGATTTGCTTTC 59.456 37.037 0.00 0.00 0.00 2.62
1623 2021 6.119536 AGTAGAAATGAGTGTGGTTTTGACA 58.880 36.000 0.00 0.00 0.00 3.58
1954 2357 3.131396 GTCGAGCGATTGGACCATATTT 58.869 45.455 0.00 0.00 0.00 1.40
1998 2401 5.782677 TTAGGCATTTAGGTTTAGGTCCA 57.217 39.130 0.00 0.00 0.00 4.02
2104 2507 8.585471 ATTCATCAGAAATAGAAAAGGCAGAA 57.415 30.769 0.00 0.00 37.29 3.02
2245 2961 9.104713 AGATATGGTTCATTGTAGATATGGTCA 57.895 33.333 0.00 0.00 0.00 4.02
2321 3169 1.422781 ACATGGGCAGATATGGTCCAG 59.577 52.381 0.00 0.10 44.46 3.86
2322 3170 0.403271 ATGGGCAGATATGGTCCAGC 59.597 55.000 0.00 0.00 44.46 4.85
2323 3171 0.695462 TGGGCAGATATGGTCCAGCT 60.695 55.000 0.00 0.00 34.48 4.24
2324 3172 0.250640 GGGCAGATATGGTCCAGCTG 60.251 60.000 6.78 6.78 0.00 4.24
2325 3173 2.626582 GCAGATATGGTCCAGCTGC 58.373 57.895 21.32 21.32 44.11 5.25
2326 3174 0.108207 GCAGATATGGTCCAGCTGCT 59.892 55.000 25.44 0.00 46.17 4.24
2327 3175 1.877258 GCAGATATGGTCCAGCTGCTC 60.877 57.143 25.44 2.83 46.17 4.26
2328 3176 1.055040 AGATATGGTCCAGCTGCTCC 58.945 55.000 8.66 13.00 0.00 4.70
2329 3177 0.036022 GATATGGTCCAGCTGCTCCC 59.964 60.000 8.66 7.89 0.00 4.30
2330 3178 0.695462 ATATGGTCCAGCTGCTCCCA 60.695 55.000 16.50 16.50 0.00 4.37
2331 3179 1.626356 TATGGTCCAGCTGCTCCCAC 61.626 60.000 16.51 4.42 0.00 4.61
2332 3180 3.640407 GGTCCAGCTGCTCCCACA 61.640 66.667 8.66 0.00 0.00 4.17
2333 3181 2.431683 GTCCAGCTGCTCCCACAA 59.568 61.111 8.66 0.00 0.00 3.33
2334 3182 1.001641 GTCCAGCTGCTCCCACAAT 60.002 57.895 8.66 0.00 0.00 2.71
2397 5215 0.745845 ATGCCTCCGTCTTGTGATGC 60.746 55.000 0.00 0.00 0.00 3.91
2489 5308 6.250527 GCTAAATACATGCGTTTTTCGTGAAT 59.749 34.615 0.00 0.00 42.13 2.57
2728 5547 5.699143 AGCTTCATAGGTAGGCATTTCATT 58.301 37.500 0.00 0.00 0.00 2.57
2805 5624 1.264826 ACGAAATCGACCGGTTTTTGG 59.735 47.619 9.42 13.01 43.02 3.28
2820 5639 6.201234 CCGGTTTTTGGAAACATCGTAAAAAT 59.799 34.615 0.00 0.00 45.52 1.82
2822 5641 7.790216 CGGTTTTTGGAAACATCGTAAAAATTC 59.210 33.333 4.64 0.00 45.52 2.17
2908 5732 7.817478 AGCAAAAATACTAAACTTGCAATACCC 59.183 33.333 0.00 0.00 43.77 3.69
3057 6542 0.745845 ATGCCTCCGTCTTGTGATGC 60.746 55.000 0.00 0.00 0.00 3.91
3148 6636 5.799542 AAATACATGCGTTTTTCGTGAAC 57.200 34.783 0.00 0.00 42.13 3.18
3151 6639 0.938713 ATGCGTTTTTCGTGAACCGA 59.061 45.000 0.00 0.00 45.66 4.69
3165 6653 2.225091 TGAACCGACTACAAGGAGGGTA 60.225 50.000 0.00 0.00 0.00 3.69
3193 6682 1.498865 CGGCGCCATTCCATGTCTAC 61.499 60.000 28.98 0.00 0.00 2.59
3218 6707 5.981174 TCAAAGTAGACCCTATTTTACGGG 58.019 41.667 0.00 0.00 46.26 5.28
3338 6827 1.348775 GGGTCCTCCATAGCTTGCCT 61.349 60.000 0.00 0.00 35.00 4.75
3429 6919 2.684927 GCATGACTCAAACCCTAGCCAT 60.685 50.000 0.00 0.00 0.00 4.40
3564 7062 3.067684 ACTAAACTTGCAATACCGGCT 57.932 42.857 0.00 0.00 0.00 5.52
3594 7747 9.697250 TTTGAGCTATTTCGTATGATTTTAACG 57.303 29.630 0.00 0.00 37.96 3.18
3693 7847 1.728323 CCACCCCACCAAAATTTCCT 58.272 50.000 0.00 0.00 0.00 3.36
3833 7996 1.209261 CCAAAATTTCCCCATTCCCCG 59.791 52.381 0.00 0.00 0.00 5.73
4398 8577 0.526524 CGTTGCTCTCCTCGATCCAC 60.527 60.000 0.00 0.00 0.00 4.02
4400 8579 1.330655 TTGCTCTCCTCGATCCACCC 61.331 60.000 0.00 0.00 0.00 4.61
4425 8604 5.770663 CCCCTCGATGTTTAGATCTTCTAGA 59.229 44.000 0.00 0.00 29.56 2.43
4431 8610 7.494952 TCGATGTTTAGATCTTCTAGAGTTCGA 59.505 37.037 0.00 3.35 32.36 3.71
4544 8723 1.070758 ACGTTGCTCTCTGGTTCATGT 59.929 47.619 0.00 0.00 0.00 3.21
4589 8777 2.402564 GGATGATCTCCCTCTGGTTCA 58.597 52.381 0.00 0.00 38.19 3.18
4590 8778 2.978278 GGATGATCTCCCTCTGGTTCAT 59.022 50.000 0.00 0.00 38.19 2.57
4591 8779 3.244491 GGATGATCTCCCTCTGGTTCATG 60.244 52.174 0.00 0.00 38.19 3.07
4592 8780 2.121948 TGATCTCCCTCTGGTTCATGG 58.878 52.381 0.00 0.00 0.00 3.66
4593 8781 1.419387 GATCTCCCTCTGGTTCATGGG 59.581 57.143 0.00 0.00 40.95 4.00
4594 8782 0.621571 TCTCCCTCTGGTTCATGGGG 60.622 60.000 0.00 0.00 40.05 4.96
4595 8783 0.916358 CTCCCTCTGGTTCATGGGGT 60.916 60.000 0.00 0.00 40.05 4.95
4596 8784 0.477597 TCCCTCTGGTTCATGGGGTT 60.478 55.000 0.00 0.00 40.05 4.11
4597 8785 0.034089 CCCTCTGGTTCATGGGGTTC 60.034 60.000 0.00 0.00 36.15 3.62
5048 9320 2.513204 CCTGTGGCAGCTCATCCG 60.513 66.667 0.00 0.00 0.00 4.18
5105 9377 1.548357 GGAGGAGGAGCTCAAGCACA 61.548 60.000 17.19 0.00 45.16 4.57
5244 9516 6.056090 TGTAGTTGTTGTTCCCATGCTATA 57.944 37.500 0.00 0.00 0.00 1.31
5495 9767 5.801380 TCTGGGTTGGTCTAGTTAATTCAC 58.199 41.667 0.00 0.00 0.00 3.18
5542 9814 1.948145 CATCTGCCATTTCTCTGAGCC 59.052 52.381 0.00 0.00 0.00 4.70
5553 9825 7.230309 GCCATTTCTCTGAGCCTTATTCTATTT 59.770 37.037 0.00 0.00 0.00 1.40
5950 10222 2.440627 CCACCTCAAGATCATCCATGGA 59.559 50.000 18.88 18.88 0.00 3.41
6220 10493 9.591792 ACCTAATAGTTACGTTTCCTTTATCAC 57.408 33.333 0.00 0.00 0.00 3.06
6299 10572 2.039746 ACAATCGAATGTTCCAGTCCCA 59.960 45.455 0.00 0.00 0.00 4.37
6359 10632 7.231467 ACAAATGGTGTACAAGAAGGTAGAAT 58.769 34.615 0.00 0.00 39.29 2.40
6516 10789 0.481128 TGGAGGGTTGGGGTTCTTTC 59.519 55.000 0.00 0.00 0.00 2.62
6521 10794 1.337118 GGTTGGGGTTCTTTCATGCA 58.663 50.000 0.00 0.00 0.00 3.96
6660 10936 3.679502 GCAAGAAGAAGAAGAGCTCAGAC 59.320 47.826 17.77 6.60 0.00 3.51
6680 10956 0.034380 ACATCTGCTGCAATGCCTCT 60.034 50.000 18.29 3.65 0.00 3.69
6832 11108 1.756430 CATGGACTCTGAGACCTCGA 58.244 55.000 23.09 7.32 31.23 4.04
6844 11120 1.837439 AGACCTCGATGCAAATGGGTA 59.163 47.619 0.00 0.00 0.00 3.69
6905 11181 1.555075 GGATGGAAGTGGCACTGTCTA 59.445 52.381 22.83 17.63 0.00 2.59
6987 11263 3.420893 CCCTGTTGCACCTTCTATTCAA 58.579 45.455 0.00 0.00 0.00 2.69
6988 11264 3.441572 CCCTGTTGCACCTTCTATTCAAG 59.558 47.826 0.00 0.00 0.00 3.02
7116 11392 6.345298 TCATGTATGCTTTTGTCGATTCCTA 58.655 36.000 0.00 0.00 0.00 2.94
7180 11456 6.839124 TTTTCAGATGCAATGACTACCAAT 57.161 33.333 4.57 0.00 0.00 3.16
7183 11459 5.368145 TCAGATGCAATGACTACCAATACC 58.632 41.667 0.00 0.00 0.00 2.73
7314 11590 2.338577 AAGCTTGCTTCTGAGTGTGT 57.661 45.000 0.00 0.00 0.00 3.72
7412 11690 6.877611 ACTACATTGGGAAAGTTGTTGTAG 57.122 37.500 0.00 0.00 40.37 2.74
7505 11783 2.949644 ACCTTGTTTGCTGTCTTGGTAC 59.050 45.455 0.00 0.00 0.00 3.34
7540 11818 1.803366 AACACGGACTCGGAGACCAC 61.803 60.000 22.87 7.32 41.39 4.16
7637 11915 2.429478 ACCGTAGCCGCAAATAAAGTT 58.571 42.857 0.00 0.00 0.00 2.66
7657 11935 0.905357 AGCATTAAGTCTCCCGTGCT 59.095 50.000 0.00 0.00 38.03 4.40
7790 12068 4.037803 AGTGCTAGATCATGCTGACAGTAG 59.962 45.833 3.99 0.00 0.00 2.57
7826 12105 3.194005 ACCTGTGTGTCGAACAAGATT 57.806 42.857 0.00 0.00 41.57 2.40
8011 12290 7.440523 AACATTTCAGAAAGAAGAGCGTAAT 57.559 32.000 1.28 0.00 37.57 1.89
8081 12360 1.141053 AGAAGCACGGGTTTTCAGAGT 59.859 47.619 6.79 0.00 0.00 3.24
8086 12365 2.561569 CACGGGTTTTCAGAGTCAGTT 58.438 47.619 0.00 0.00 0.00 3.16
8393 12855 6.143278 CGATCATATTGTTCCAATTGCATGTG 59.857 38.462 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.936847 AGTACAAAAACTACATCAGGATCACAA 59.063 33.333 0.00 0.00 0.00 3.33
108 109 4.880886 TGCATTGTATCTTCAACCATCG 57.119 40.909 0.00 0.00 0.00 3.84
208 209 7.573968 AACAGCTCTAAAAACAACATCTTCT 57.426 32.000 0.00 0.00 0.00 2.85
321 322 6.034898 CAGTTCACCAAAAACAACATCTTCAC 59.965 38.462 0.00 0.00 0.00 3.18
388 390 7.329226 CCCATGTAGTGCAAAATTCAGTTAAAG 59.671 37.037 0.00 0.00 0.00 1.85
449 451 1.820519 GCTCACAATGAAATGGAGCCA 59.179 47.619 0.00 0.00 43.87 4.75
625 628 1.227853 GTCGAGTGGCCCACTTGTT 60.228 57.895 26.80 1.72 45.44 2.83
828 833 0.944386 TCAGCGAGTTCTGTTTTGGC 59.056 50.000 0.00 0.00 35.63 4.52
829 834 1.939934 TGTCAGCGAGTTCTGTTTTGG 59.060 47.619 0.00 0.00 35.63 3.28
854 860 0.402861 AGTGGGGGAAAGAGTGGGAA 60.403 55.000 0.00 0.00 0.00 3.97
855 861 0.840722 GAGTGGGGGAAAGAGTGGGA 60.841 60.000 0.00 0.00 0.00 4.37
938 960 1.695597 AGGAGAAGGGGATGCCAGG 60.696 63.158 5.30 0.00 0.00 4.45
952 974 0.877649 CATCGCCGTTGATGGAGGAG 60.878 60.000 6.29 0.00 41.63 3.69
953 975 1.143838 CATCGCCGTTGATGGAGGA 59.856 57.895 6.29 0.00 41.63 3.71
954 976 1.143838 TCATCGCCGTTGATGGAGG 59.856 57.895 12.51 0.00 44.68 4.30
955 977 1.154205 GGTCATCGCCGTTGATGGAG 61.154 60.000 12.51 0.00 44.68 3.86
956 978 1.153449 GGTCATCGCCGTTGATGGA 60.153 57.895 12.51 0.29 44.68 3.41
957 979 1.153369 AGGTCATCGCCGTTGATGG 60.153 57.895 12.51 0.00 44.68 3.51
958 980 1.154205 GGAGGTCATCGCCGTTGATG 61.154 60.000 0.68 7.59 45.70 3.07
959 981 1.144057 GGAGGTCATCGCCGTTGAT 59.856 57.895 0.68 0.00 0.00 2.57
960 982 2.577059 GGAGGTCATCGCCGTTGA 59.423 61.111 0.00 0.00 0.00 3.18
961 983 1.672854 TAGGGAGGTCATCGCCGTTG 61.673 60.000 0.00 0.00 41.73 4.10
962 984 1.380785 TAGGGAGGTCATCGCCGTT 60.381 57.895 0.00 0.00 41.73 4.44
963 985 1.828660 CTAGGGAGGTCATCGCCGT 60.829 63.158 0.00 0.00 41.73 5.68
964 986 3.043419 CTAGGGAGGTCATCGCCG 58.957 66.667 0.00 0.00 41.73 6.46
965 987 2.737830 GCTAGGGAGGTCATCGCC 59.262 66.667 0.00 0.00 41.73 5.54
966 988 2.194212 TCGCTAGGGAGGTCATCGC 61.194 63.158 5.20 0.00 41.11 4.58
967 989 1.655329 GTCGCTAGGGAGGTCATCG 59.345 63.158 10.19 0.00 0.00 3.84
968 990 1.465200 GGGTCGCTAGGGAGGTCATC 61.465 65.000 10.19 0.00 0.00 2.92
969 991 1.457831 GGGTCGCTAGGGAGGTCAT 60.458 63.158 10.19 0.00 0.00 3.06
970 992 2.043248 GGGTCGCTAGGGAGGTCA 60.043 66.667 10.19 0.00 0.00 4.02
971 993 2.043248 TGGGTCGCTAGGGAGGTC 60.043 66.667 10.19 3.65 0.00 3.85
972 994 2.363925 GTGGGTCGCTAGGGAGGT 60.364 66.667 10.19 0.00 0.00 3.85
973 995 2.042843 AGTGGGTCGCTAGGGAGG 60.043 66.667 10.19 0.00 0.00 4.30
974 996 2.128507 GGAGTGGGTCGCTAGGGAG 61.129 68.421 10.19 0.00 0.00 4.30
975 997 2.043248 GGAGTGGGTCGCTAGGGA 60.043 66.667 5.20 5.20 0.00 4.20
976 998 2.042843 AGGAGTGGGTCGCTAGGG 60.043 66.667 0.00 0.00 0.00 3.53
977 999 2.128507 GGAGGAGTGGGTCGCTAGG 61.129 68.421 0.00 0.00 0.00 3.02
978 1000 0.757188 ATGGAGGAGTGGGTCGCTAG 60.757 60.000 0.00 0.00 0.00 3.42
979 1001 0.755698 GATGGAGGAGTGGGTCGCTA 60.756 60.000 0.00 0.00 0.00 4.26
980 1002 2.039624 ATGGAGGAGTGGGTCGCT 59.960 61.111 0.00 0.00 0.00 4.93
981 1003 2.501610 GATGGAGGAGTGGGTCGC 59.498 66.667 0.00 0.00 0.00 5.19
982 1004 1.109920 ATCGATGGAGGAGTGGGTCG 61.110 60.000 0.00 0.00 0.00 4.79
983 1005 0.390860 CATCGATGGAGGAGTGGGTC 59.609 60.000 17.96 0.00 0.00 4.46
984 1006 2.521103 CATCGATGGAGGAGTGGGT 58.479 57.895 17.96 0.00 0.00 4.51
1150 1237 0.171231 CTCGTGGATCTGCTTCGACA 59.829 55.000 0.00 0.00 0.00 4.35
1410 1513 6.614694 ACCAAAAATAACAATAGGAACCCC 57.385 37.500 0.00 0.00 0.00 4.95
1511 1909 3.568538 CAAGCTACATTGAGGCAAACAC 58.431 45.455 0.00 0.00 31.55 3.32
1595 1993 8.527810 TCAAAACCACACTCATTTCTACTTTTT 58.472 29.630 0.00 0.00 0.00 1.94
1858 2261 5.825679 GCCATGTAGTATACCACAATTCCAA 59.174 40.000 8.22 0.00 42.12 3.53
1954 2357 4.908601 TTCAGTCTGCAAAATCCCTCTA 57.091 40.909 0.00 0.00 0.00 2.43
1998 2401 4.040706 ACATCAACTGAACATGGCCAAAAT 59.959 37.500 10.96 0.00 0.00 1.82
2267 3013 9.019656 TCTACTATAAATGGCAAACACAACATT 57.980 29.630 0.00 0.00 35.24 2.71
2321 3169 1.436336 GATGCATTGTGGGAGCAGC 59.564 57.895 0.00 0.00 42.14 5.25
2322 3170 1.721664 CGGATGCATTGTGGGAGCAG 61.722 60.000 0.00 0.00 42.14 4.24
2323 3171 1.750018 CGGATGCATTGTGGGAGCA 60.750 57.895 0.00 0.00 43.14 4.26
2324 3172 1.315257 AACGGATGCATTGTGGGAGC 61.315 55.000 0.00 0.00 0.00 4.70
2325 3173 0.452987 CAACGGATGCATTGTGGGAG 59.547 55.000 0.00 0.00 0.00 4.30
2326 3174 0.037447 TCAACGGATGCATTGTGGGA 59.963 50.000 0.00 2.45 0.00 4.37
2327 3175 0.887247 TTCAACGGATGCATTGTGGG 59.113 50.000 0.00 0.04 0.00 4.61
2328 3176 2.945447 ATTCAACGGATGCATTGTGG 57.055 45.000 0.00 0.41 0.00 4.17
2329 3177 4.621068 ACTATTCAACGGATGCATTGTG 57.379 40.909 0.00 0.00 0.00 3.33
2330 3178 5.415701 AGAAACTATTCAACGGATGCATTGT 59.584 36.000 0.00 0.00 38.06 2.71
2331 3179 5.740569 CAGAAACTATTCAACGGATGCATTG 59.259 40.000 0.00 0.00 38.06 2.82
2332 3180 5.647658 TCAGAAACTATTCAACGGATGCATT 59.352 36.000 0.00 0.00 38.06 3.56
2333 3181 5.185454 TCAGAAACTATTCAACGGATGCAT 58.815 37.500 0.00 0.00 38.06 3.96
2334 3182 4.574892 TCAGAAACTATTCAACGGATGCA 58.425 39.130 0.00 0.00 38.06 3.96
2470 5289 3.423776 CCGATTCACGAAAAACGCATGTA 60.424 43.478 0.00 0.00 46.94 2.29
2489 5308 1.077805 TGACCCTCCTTGTAGCCGA 59.922 57.895 0.00 0.00 0.00 5.54
2712 5531 9.031537 TCGATTCTATAATGAAATGCCTACCTA 57.968 33.333 0.00 0.00 0.00 3.08
2728 5547 5.753438 GTGCCAATCTGTTGTCGATTCTATA 59.247 40.000 0.00 0.00 33.36 1.31
2783 5602 1.868469 AAAACCGGTCGATTTCGTCA 58.132 45.000 8.04 0.00 40.80 4.35
2908 5732 6.253298 TGAGAACACTTTTTCAAGAAAATGCG 59.747 34.615 16.44 11.87 39.69 4.73
3129 6617 3.256285 GGTTCACGAAAAACGCATGTA 57.744 42.857 0.00 0.00 46.94 2.29
3148 6636 1.479730 GGTTACCCTCCTTGTAGTCGG 59.520 57.143 0.00 0.00 0.00 4.79
3193 6682 6.047231 CCGTAAAATAGGGTCTACTTTGAGG 58.953 44.000 0.00 0.00 0.00 3.86
3218 6707 2.088178 CATGCTTTTTGGCGACCGC 61.088 57.895 5.75 5.75 41.06 5.68
3307 6796 1.065709 GGAGGACCCGCAGTTCAAATA 60.066 52.381 0.00 0.00 0.00 1.40
3429 6919 4.429212 CATCGCGGTGGTCGTCCA 62.429 66.667 12.68 0.00 42.05 4.02
3537 7035 7.969508 GCCGGTATTGCAAGTTTAGTATTTTTA 59.030 33.333 4.94 0.00 0.00 1.52
3693 7847 4.086457 GAGGGAAAATTTGGTGCTAGGAA 58.914 43.478 0.00 0.00 0.00 3.36
3833 7996 3.387947 TTCGTCGGGAAGAGGGGC 61.388 66.667 0.00 0.00 35.58 5.80
3890 8060 3.602030 AGGGGAGGGAGTGGTCGT 61.602 66.667 0.00 0.00 0.00 4.34
4317 8487 1.335051 CGCCATCGTCGATGTAGTCAT 60.335 52.381 28.46 0.00 38.28 3.06
4333 8503 3.888930 TGATGTAGATGATGTAGTCGCCA 59.111 43.478 0.00 0.00 0.00 5.69
4400 8579 3.643792 AGAAGATCTAAACATCGAGGGGG 59.356 47.826 0.69 0.00 0.00 5.40
4425 8604 3.784511 TCGAGGGGTATCTATCGAACT 57.215 47.619 0.00 0.00 40.88 3.01
4431 8610 7.415086 AGATCTAAACATCGAGGGGTATCTAT 58.585 38.462 0.69 0.00 0.00 1.98
4437 8616 4.290942 AGAAGATCTAAACATCGAGGGGT 58.709 43.478 0.69 0.00 0.00 4.95
4544 8723 2.257207 GAATCCCCATCGATCCTACCA 58.743 52.381 0.00 0.00 0.00 3.25
4589 8777 0.933700 CCTAACCCCATGAACCCCAT 59.066 55.000 0.00 0.00 35.44 4.00
4590 8778 1.218439 CCCTAACCCCATGAACCCCA 61.218 60.000 0.00 0.00 0.00 4.96
4591 8779 1.219131 ACCCTAACCCCATGAACCCC 61.219 60.000 0.00 0.00 0.00 4.95
4592 8780 0.708209 AACCCTAACCCCATGAACCC 59.292 55.000 0.00 0.00 0.00 4.11
4593 8781 1.356398 TGAACCCTAACCCCATGAACC 59.644 52.381 0.00 0.00 0.00 3.62
4594 8782 2.891191 TGAACCCTAACCCCATGAAC 57.109 50.000 0.00 0.00 0.00 3.18
4595 8783 3.565449 CCAATGAACCCTAACCCCATGAA 60.565 47.826 0.00 0.00 0.00 2.57
4596 8784 2.024464 CCAATGAACCCTAACCCCATGA 60.024 50.000 0.00 0.00 0.00 3.07
4597 8785 2.292192 ACCAATGAACCCTAACCCCATG 60.292 50.000 0.00 0.00 0.00 3.66
4858 9128 6.352910 CCATGAATCCAACCCCATACAAAATT 60.353 38.462 0.00 0.00 0.00 1.82
5001 9273 4.202000 ACATGACAACGCAAAACATCAAGA 60.202 37.500 0.00 0.00 0.00 3.02
5048 9320 1.363807 GCAGGACAAACAAGGCCAC 59.636 57.895 5.01 0.00 0.00 5.01
5105 9377 3.299977 TGGTGCGTCGTGGTAGCT 61.300 61.111 0.00 0.00 0.00 3.32
5446 9718 8.314751 AGAGCATATATCACACCTACATTAACC 58.685 37.037 0.00 0.00 0.00 2.85
5583 9855 8.574251 TTGGTGTCATTACATAAAAGTAGCAT 57.426 30.769 0.00 0.00 38.08 3.79
5950 10222 3.228188 TGCTTGACCTTGTCATCCTTT 57.772 42.857 0.00 0.00 42.40 3.11
6220 10493 1.074752 GTGAGAGGCTCTTCTTTGCG 58.925 55.000 19.80 0.00 0.00 4.85
6359 10632 5.513094 CCACTACCTTCTTGAACCTCATCAA 60.513 44.000 0.00 0.00 37.70 2.57
6516 10789 4.751060 AGCACAAGGAATAACATTGCATG 58.249 39.130 0.00 0.00 42.97 4.06
6521 10794 7.886629 ATATGTGAGCACAAGGAATAACATT 57.113 32.000 7.46 0.00 45.41 2.71
6660 10936 0.100682 GAGGCATTGCAGCAGATGTG 59.899 55.000 11.39 6.97 35.83 3.21
6832 11108 3.118665 GGCAACTCATTACCCATTTGCAT 60.119 43.478 6.46 0.00 40.88 3.96
6844 11120 2.053865 CCATGGGCGGCAACTCATT 61.054 57.895 12.47 0.00 0.00 2.57
6905 11181 4.965532 AGATGGTTGCTACTTCATCTAGGT 59.034 41.667 14.83 0.00 42.89 3.08
6987 11263 3.657398 TCATTGATGACAGCATTCCCT 57.343 42.857 0.00 0.00 34.11 4.20
6988 11264 3.949754 TCTTCATTGATGACAGCATTCCC 59.050 43.478 0.00 0.00 36.36 3.97
7033 11309 0.746659 GCAAAGGTCAACTTGCCTGT 59.253 50.000 5.76 0.00 39.96 4.00
7180 11456 4.263331 CCTTTGCCCTTTCTAAGTCTGGTA 60.263 45.833 0.00 0.00 0.00 3.25
7183 11459 3.084786 CCCTTTGCCCTTTCTAAGTCTG 58.915 50.000 0.00 0.00 0.00 3.51
7314 11590 4.226427 AGATGGCTTCTTGCAATGAGTA 57.774 40.909 0.00 0.00 45.15 2.59
7412 11690 6.967199 GCACATTAACTATGAAACAAGTAGCC 59.033 38.462 0.00 0.00 37.69 3.93
7505 11783 3.361644 CCGTGTTCATCTCAAAATTTGCG 59.638 43.478 0.00 0.00 0.00 4.85
7540 11818 1.577328 ATCTTTGCACGCGGTCTTGG 61.577 55.000 12.47 0.00 0.00 3.61
7637 11915 2.108168 AGCACGGGAGACTTAATGCTA 58.892 47.619 0.00 0.00 41.45 3.49
7657 11935 4.520179 CCATTCACCATCTGTCAGATCAA 58.480 43.478 12.62 4.31 31.32 2.57
7826 12105 7.595875 TGATTGTACACGACTTTTTCTCGATTA 59.404 33.333 0.00 0.00 35.08 1.75
8011 12290 2.935740 CGCAGACAGCTCCTCACCA 61.936 63.158 0.00 0.00 42.61 4.17
8086 12365 7.344134 TGGAGTGACTTACTATAGCAGTCTTA 58.656 38.462 23.61 9.85 40.53 2.10
8393 12855 3.957497 AGATGATGACTAGTGACCTGGAC 59.043 47.826 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.