Multiple sequence alignment - TraesCS5B01G208200
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 | TraesCS5B01G208200 | chr5B | 100.000 | 4217 | 0 | 0 | 1 | 4217 | 377697587 | 377701803 | 0.000000e+00 | 7788.0 |
1 | TraesCS5B01G208200 | chr5B | 85.964 | 2572 | 261 | 63 | 1001 | 3522 | 377843634 | 377846155 | 0.000000e+00 | 2658.0 |
2 | TraesCS5B01G208200 | chr5B | 83.645 | 642 | 66 | 24 | 1001 | 1608 | 378510565 | 378511201 | 6.120000e-158 | 568.0 |
3 | TraesCS5B01G208200 | chr5B | 86.837 | 509 | 52 | 10 | 1112 | 1608 | 377978340 | 377978845 | 4.760000e-154 | 555.0 |
4 | TraesCS5B01G208200 | chr5B | 86.154 | 520 | 50 | 13 | 1112 | 1609 | 378068455 | 378068974 | 3.710000e-150 | 542.0 |
5 | TraesCS5B01G208200 | chr5B | 93.567 | 171 | 10 | 1 | 532 | 702 | 102630143 | 102629974 | 1.950000e-63 | 254.0 |
6 | TraesCS5B01G208200 | chr5B | 84.979 | 233 | 30 | 5 | 1815 | 2045 | 378069267 | 378069496 | 9.120000e-57 | 231.0 |
7 | TraesCS5B01G208200 | chr5B | 81.673 | 251 | 42 | 4 | 1815 | 2064 | 377979110 | 377979357 | 5.530000e-49 | 206.0 |
8 | TraesCS5B01G208200 | chr5B | 94.792 | 96 | 3 | 2 | 3547 | 3641 | 290895025 | 290894931 | 9.450000e-32 | 148.0 |
9 | TraesCS5B01G208200 | chr5D | 94.492 | 2778 | 99 | 20 | 704 | 3470 | 325422428 | 325425162 | 0.000000e+00 | 4233.0 |
10 | TraesCS5B01G208200 | chr5D | 94.020 | 602 | 18 | 5 | 3631 | 4217 | 325425506 | 325426104 | 0.000000e+00 | 896.0 |
11 | TraesCS5B01G208200 | chr5D | 86.320 | 519 | 49 | 15 | 1112 | 1608 | 326118243 | 326118761 | 2.870000e-151 | 545.0 |
12 | TraesCS5B01G208200 | chr5D | 86.200 | 500 | 53 | 12 | 1112 | 1609 | 325663796 | 325664281 | 1.040000e-145 | 527.0 |
13 | TraesCS5B01G208200 | chr5D | 85.714 | 504 | 60 | 9 | 1112 | 1609 | 325646957 | 325647454 | 4.830000e-144 | 521.0 |
14 | TraesCS5B01G208200 | chr5D | 88.400 | 250 | 26 | 2 | 1815 | 2064 | 326119080 | 326119326 | 8.860000e-77 | 298.0 |
15 | TraesCS5B01G208200 | chr5D | 86.667 | 195 | 19 | 5 | 3961 | 4154 | 325374577 | 325374765 | 4.270000e-50 | 209.0 |
16 | TraesCS5B01G208200 | chr5D | 98.824 | 85 | 1 | 0 | 3467 | 3551 | 325425425 | 325425509 | 7.300000e-33 | 152.0 |
17 | TraesCS5B01G208200 | chr5D | 95.402 | 87 | 4 | 0 | 3546 | 3632 | 21789113 | 21789199 | 5.690000e-29 | 139.0 |
18 | TraesCS5B01G208200 | chr5D | 88.393 | 112 | 7 | 4 | 3524 | 3633 | 337703218 | 337703325 | 3.420000e-26 | 130.0 |
19 | TraesCS5B01G208200 | chr5A | 92.286 | 1750 | 108 | 7 | 1828 | 3551 | 423681159 | 423682907 | 0.000000e+00 | 2459.0 |
20 | TraesCS5B01G208200 | chr5A | 84.031 | 2605 | 265 | 77 | 1001 | 3535 | 423744978 | 423747501 | 0.000000e+00 | 2366.0 |
21 | TraesCS5B01G208200 | chr5A | 93.123 | 1047 | 47 | 12 | 704 | 1725 | 423680107 | 423681153 | 0.000000e+00 | 1511.0 |
22 | TraesCS5B01G208200 | chr5A | 87.525 | 505 | 49 | 12 | 1112 | 1608 | 430508317 | 430507819 | 4.730000e-159 | 571.0 |
23 | TraesCS5B01G208200 | chr5A | 83.798 | 574 | 68 | 20 | 3631 | 4199 | 423682904 | 423683457 | 4.830000e-144 | 521.0 |
24 | TraesCS5B01G208200 | chr5A | 85.772 | 492 | 50 | 11 | 1121 | 1609 | 430958477 | 430958003 | 1.750000e-138 | 503.0 |
25 | TraesCS5B01G208200 | chr5A | 93.985 | 133 | 7 | 1 | 4023 | 4154 | 423664071 | 423664203 | 2.570000e-47 | 200.0 |
26 | TraesCS5B01G208200 | chr5A | 87.302 | 63 | 6 | 2 | 2003 | 2064 | 666933475 | 666933414 | 2.100000e-08 | 71.3 |
27 | TraesCS5B01G208200 | chr2B | 93.384 | 529 | 35 | 0 | 1 | 529 | 374217763 | 374217235 | 0.000000e+00 | 784.0 |
28 | TraesCS5B01G208200 | chr2B | 92.030 | 527 | 42 | 0 | 1 | 527 | 94345870 | 94345344 | 0.000000e+00 | 741.0 |
29 | TraesCS5B01G208200 | chr2B | 85.938 | 192 | 21 | 5 | 519 | 707 | 797329985 | 797329797 | 2.570000e-47 | 200.0 |
30 | TraesCS5B01G208200 | chr7B | 92.453 | 530 | 39 | 1 | 1 | 529 | 284959235 | 284958706 | 0.000000e+00 | 756.0 |
31 | TraesCS5B01G208200 | chr7B | 92.075 | 530 | 39 | 3 | 1 | 529 | 194597118 | 194596591 | 0.000000e+00 | 743.0 |
32 | TraesCS5B01G208200 | chr3D | 91.871 | 529 | 43 | 0 | 1 | 529 | 28272520 | 28273048 | 0.000000e+00 | 739.0 |
33 | TraesCS5B01G208200 | chr3D | 93.293 | 164 | 11 | 0 | 540 | 703 | 459077268 | 459077431 | 4.210000e-60 | 243.0 |
34 | TraesCS5B01G208200 | chr3D | 91.279 | 172 | 15 | 0 | 535 | 706 | 6667270 | 6667441 | 7.050000e-58 | 235.0 |
35 | TraesCS5B01G208200 | chr3D | 95.556 | 90 | 3 | 1 | 3545 | 3634 | 296034413 | 296034501 | 4.400000e-30 | 143.0 |
36 | TraesCS5B01G208200 | chr3D | 93.750 | 96 | 5 | 1 | 3548 | 3642 | 505557393 | 505557298 | 4.400000e-30 | 143.0 |
37 | TraesCS5B01G208200 | chr6B | 91.698 | 530 | 43 | 1 | 1 | 529 | 21938517 | 21937988 | 0.000000e+00 | 734.0 |
38 | TraesCS5B01G208200 | chr6B | 91.682 | 529 | 44 | 0 | 1 | 529 | 714185330 | 714184802 | 0.000000e+00 | 734.0 |
39 | TraesCS5B01G208200 | chr6B | 92.941 | 170 | 10 | 2 | 537 | 705 | 314547152 | 314546984 | 3.260000e-61 | 246.0 |
40 | TraesCS5B01G208200 | chr6B | 92.398 | 171 | 12 | 1 | 537 | 706 | 119526975 | 119526805 | 4.210000e-60 | 243.0 |
41 | TraesCS5B01G208200 | chr6B | 92.073 | 164 | 13 | 0 | 541 | 704 | 98892445 | 98892608 | 9.120000e-57 | 231.0 |
42 | TraesCS5B01G208200 | chr6B | 87.097 | 186 | 19 | 5 | 524 | 705 | 656279215 | 656279399 | 5.530000e-49 | 206.0 |
43 | TraesCS5B01G208200 | chr6B | 96.774 | 93 | 3 | 0 | 3547 | 3639 | 68002400 | 68002308 | 5.650000e-34 | 156.0 |
44 | TraesCS5B01G208200 | chr6B | 92.929 | 99 | 6 | 1 | 3537 | 3635 | 38004042 | 38003945 | 4.400000e-30 | 143.0 |
45 | TraesCS5B01G208200 | chr3B | 91.682 | 529 | 43 | 1 | 1 | 529 | 242480663 | 242480136 | 0.000000e+00 | 732.0 |
46 | TraesCS5B01G208200 | chr3B | 85.484 | 186 | 23 | 3 | 522 | 704 | 456554366 | 456554182 | 1.550000e-44 | 191.0 |
47 | TraesCS5B01G208200 | chr3B | 96.809 | 94 | 3 | 0 | 3542 | 3635 | 748777085 | 748777178 | 1.570000e-34 | 158.0 |
48 | TraesCS5B01G208200 | chr1B | 91.493 | 529 | 45 | 0 | 1 | 529 | 645415369 | 645415897 | 0.000000e+00 | 728.0 |
49 | TraesCS5B01G208200 | chr1B | 86.857 | 175 | 23 | 0 | 528 | 702 | 687090925 | 687091099 | 3.330000e-46 | 196.0 |
50 | TraesCS5B01G208200 | chr1B | 85.915 | 142 | 20 | 0 | 1461 | 1602 | 121404862 | 121405003 | 7.300000e-33 | 152.0 |
51 | TraesCS5B01G208200 | chr1B | 95.604 | 91 | 4 | 0 | 3545 | 3635 | 234252677 | 234252587 | 3.400000e-31 | 147.0 |
52 | TraesCS5B01G208200 | chr1B | 93.684 | 95 | 6 | 0 | 3542 | 3636 | 28500414 | 28500508 | 4.400000e-30 | 143.0 |
53 | TraesCS5B01G208200 | chrUn | 93.976 | 166 | 10 | 0 | 537 | 702 | 141680742 | 141680907 | 7.000000e-63 | 252.0 |
54 | TraesCS5B01G208200 | chrUn | 94.444 | 90 | 5 | 0 | 3544 | 3633 | 244923808 | 244923897 | 5.690000e-29 | 139.0 |
55 | TraesCS5B01G208200 | chrUn | 94.444 | 90 | 5 | 0 | 3544 | 3633 | 287095696 | 287095785 | 5.690000e-29 | 139.0 |
56 | TraesCS5B01G208200 | chrUn | 93.407 | 91 | 6 | 0 | 3548 | 3638 | 371558133 | 371558043 | 7.350000e-28 | 135.0 |
57 | TraesCS5B01G208200 | chrUn | 93.407 | 91 | 6 | 0 | 3548 | 3638 | 371616940 | 371616850 | 7.350000e-28 | 135.0 |
58 | TraesCS5B01G208200 | chrUn | 92.473 | 93 | 7 | 0 | 3542 | 3634 | 27475949 | 27476041 | 2.650000e-27 | 134.0 |
59 | TraesCS5B01G208200 | chrUn | 93.333 | 90 | 6 | 0 | 3545 | 3634 | 55723609 | 55723698 | 2.650000e-27 | 134.0 |
60 | TraesCS5B01G208200 | chrUn | 88.596 | 114 | 7 | 5 | 3527 | 3639 | 335557631 | 335557739 | 2.650000e-27 | 134.0 |
61 | TraesCS5B01G208200 | chrUn | 93.258 | 89 | 6 | 0 | 3544 | 3632 | 2693318 | 2693230 | 9.510000e-27 | 132.0 |
62 | TraesCS5B01G208200 | chrUn | 94.118 | 85 | 5 | 0 | 3548 | 3632 | 13209427 | 13209343 | 3.420000e-26 | 130.0 |
63 | TraesCS5B01G208200 | chrUn | 93.182 | 88 | 6 | 0 | 3548 | 3635 | 16901709 | 16901622 | 3.420000e-26 | 130.0 |
64 | TraesCS5B01G208200 | chrUn | 87.302 | 63 | 6 | 2 | 2003 | 2064 | 30412927 | 30412866 | 2.100000e-08 | 71.3 |
65 | TraesCS5B01G208200 | chr2D | 93.902 | 164 | 10 | 0 | 540 | 703 | 87407526 | 87407363 | 9.050000e-62 | 248.0 |
66 | TraesCS5B01G208200 | chr2D | 88.506 | 174 | 14 | 4 | 526 | 697 | 565312765 | 565312596 | 5.530000e-49 | 206.0 |
67 | TraesCS5B01G208200 | chr2D | 93.617 | 94 | 6 | 0 | 3547 | 3640 | 572049125 | 572049218 | 1.580000e-29 | 141.0 |
68 | TraesCS5B01G208200 | chr4A | 92.857 | 168 | 11 | 1 | 537 | 703 | 517406637 | 517406470 | 4.210000e-60 | 243.0 |
69 | TraesCS5B01G208200 | chr4A | 87.931 | 116 | 11 | 3 | 3538 | 3653 | 34261960 | 34262072 | 2.650000e-27 | 134.0 |
70 | TraesCS5B01G208200 | chr4A | 88.034 | 117 | 8 | 5 | 3527 | 3642 | 632934475 | 632934364 | 2.650000e-27 | 134.0 |
71 | TraesCS5B01G208200 | chr4D | 89.831 | 177 | 15 | 3 | 528 | 703 | 23312045 | 23312219 | 1.530000e-54 | 224.0 |
72 | TraesCS5B01G208200 | chr4D | 94.444 | 90 | 5 | 0 | 3544 | 3633 | 436376805 | 436376716 | 5.690000e-29 | 139.0 |
73 | TraesCS5B01G208200 | chr1A | 87.912 | 182 | 21 | 1 | 522 | 702 | 139560037 | 139560218 | 3.300000e-51 | 213.0 |
74 | TraesCS5B01G208200 | chr1A | 96.512 | 86 | 3 | 0 | 3548 | 3633 | 542440397 | 542440312 | 4.400000e-30 | 143.0 |
75 | TraesCS5B01G208200 | chr1A | 93.548 | 93 | 6 | 0 | 3542 | 3634 | 498811738 | 498811646 | 5.690000e-29 | 139.0 |
76 | TraesCS5B01G208200 | chr1A | 91.919 | 99 | 6 | 2 | 3544 | 3642 | 551465803 | 551465707 | 2.040000e-28 | 137.0 |
77 | TraesCS5B01G208200 | chr1A | 77.253 | 233 | 49 | 3 | 1820 | 2052 | 50749026 | 50748798 | 2.650000e-27 | 134.0 |
78 | TraesCS5B01G208200 | chr1A | 89.524 | 105 | 9 | 2 | 3541 | 3643 | 448911830 | 448911934 | 9.510000e-27 | 132.0 |
79 | TraesCS5B01G208200 | chr1A | 87.719 | 114 | 8 | 5 | 3527 | 3639 | 555691336 | 555691444 | 1.230000e-25 | 128.0 |
80 | TraesCS5B01G208200 | chr3A | 87.709 | 179 | 21 | 1 | 528 | 706 | 659527403 | 659527226 | 1.540000e-49 | 207.0 |
81 | TraesCS5B01G208200 | chr3A | 91.429 | 105 | 7 | 2 | 3546 | 3648 | 709065498 | 709065602 | 4.400000e-30 | 143.0 |
82 | TraesCS5B01G208200 | chr7A | 86.932 | 176 | 23 | 0 | 527 | 702 | 727851110 | 727851285 | 9.250000e-47 | 198.0 |
83 | TraesCS5B01G208200 | chr6A | 84.868 | 152 | 21 | 2 | 1820 | 1971 | 57963272 | 57963123 | 7.300000e-33 | 152.0 |
84 | TraesCS5B01G208200 | chr6A | 95.556 | 90 | 4 | 0 | 3548 | 3637 | 439517401 | 439517312 | 1.220000e-30 | 145.0 |
85 | TraesCS5B01G208200 | chr6A | 94.505 | 91 | 5 | 0 | 3544 | 3634 | 7099612 | 7099702 | 1.580000e-29 | 141.0 |
86 | TraesCS5B01G208200 | chr6A | 92.708 | 96 | 6 | 1 | 3548 | 3643 | 89971069 | 89971163 | 2.040000e-28 | 137.0 |
87 | TraesCS5B01G208200 | chr4B | 97.701 | 87 | 2 | 0 | 3548 | 3634 | 248358333 | 248358247 | 2.630000e-32 | 150.0 |
88 | TraesCS5B01G208200 | chr2A | 89.256 | 121 | 8 | 4 | 3547 | 3667 | 386732356 | 386732241 | 3.400000e-31 | 147.0 |
89 | TraesCS5B01G208200 | chr7D | 90.826 | 109 | 8 | 2 | 3544 | 3650 | 53485498 | 53485606 | 1.220000e-30 | 145.0 |
90 | TraesCS5B01G208200 | chr7D | 93.684 | 95 | 6 | 0 | 3544 | 3638 | 511659434 | 511659528 | 4.400000e-30 | 143.0 |
91 | TraesCS5B01G208200 | chr7D | 86.066 | 122 | 14 | 3 | 3535 | 3653 | 37655966 | 37655845 | 1.230000e-25 | 128.0 |
92 | TraesCS5B01G208200 | chr6D | 96.512 | 86 | 3 | 0 | 3547 | 3632 | 36675481 | 36675396 | 4.400000e-30 | 143.0 |
93 | TraesCS5B01G208200 | chr6D | 94.565 | 92 | 4 | 1 | 3548 | 3638 | 157328025 | 157328116 | 1.580000e-29 | 141.0 |
94 | TraesCS5B01G208200 | chr6D | 94.444 | 90 | 5 | 0 | 3545 | 3634 | 31474853 | 31474942 | 5.690000e-29 | 139.0 |
95 | TraesCS5B01G208200 | chr6D | 92.784 | 97 | 6 | 1 | 3547 | 3642 | 206553954 | 206553858 | 5.690000e-29 | 139.0 |
96 | TraesCS5B01G208200 | chr6D | 94.382 | 89 | 5 | 0 | 3547 | 3635 | 199144927 | 199144839 | 2.040000e-28 | 137.0 |
97 | TraesCS5B01G208200 | chr6D | 94.382 | 89 | 5 | 0 | 3548 | 3636 | 380781868 | 380781780 | 2.040000e-28 | 137.0 |
98 | TraesCS5B01G208200 | chr6D | 91.000 | 100 | 7 | 2 | 3541 | 3639 | 58042851 | 58042753 | 2.650000e-27 | 134.0 |
99 | TraesCS5B01G208200 | chr1D | 92.929 | 99 | 5 | 2 | 3548 | 3646 | 234329042 | 234329138 | 4.400000e-30 | 143.0 |
100 | TraesCS5B01G208200 | chr1D | 95.455 | 88 | 4 | 0 | 3547 | 3634 | 85191512 | 85191599 | 1.580000e-29 | 141.0 |
101 | TraesCS5B01G208200 | chr1D | 92.708 | 96 | 6 | 1 | 3548 | 3642 | 200825983 | 200826078 | 2.040000e-28 | 137.0 |
102 | TraesCS5B01G208200 | chr1D | 88.785 | 107 | 10 | 2 | 3531 | 3636 | 253197637 | 253197532 | 3.420000e-26 | 130.0 |
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 | TraesCS5B01G208200 | chr5B | 377697587 | 377701803 | 4216 | False | 7788.000000 | 7788 | 100.000000 | 1 | 4217 | 1 | chr5B.!!$F1 | 4216 |
1 | TraesCS5B01G208200 | chr5B | 377843634 | 377846155 | 2521 | False | 2658.000000 | 2658 | 85.964000 | 1001 | 3522 | 1 | chr5B.!!$F2 | 2521 |
2 | TraesCS5B01G208200 | chr5B | 378510565 | 378511201 | 636 | False | 568.000000 | 568 | 83.645000 | 1001 | 1608 | 1 | chr5B.!!$F3 | 607 |
3 | TraesCS5B01G208200 | chr5B | 378068455 | 378069496 | 1041 | False | 386.500000 | 542 | 85.566500 | 1112 | 2045 | 2 | chr5B.!!$F5 | 933 |
4 | TraesCS5B01G208200 | chr5B | 377978340 | 377979357 | 1017 | False | 380.500000 | 555 | 84.255000 | 1112 | 2064 | 2 | chr5B.!!$F4 | 952 |
5 | TraesCS5B01G208200 | chr5D | 325422428 | 325426104 | 3676 | False | 1760.333333 | 4233 | 95.778667 | 704 | 4217 | 3 | chr5D.!!$F6 | 3513 |
6 | TraesCS5B01G208200 | chr5D | 326118243 | 326119326 | 1083 | False | 421.500000 | 545 | 87.360000 | 1112 | 2064 | 2 | chr5D.!!$F7 | 952 |
7 | TraesCS5B01G208200 | chr5A | 423744978 | 423747501 | 2523 | False | 2366.000000 | 2366 | 84.031000 | 1001 | 3535 | 1 | chr5A.!!$F2 | 2534 |
8 | TraesCS5B01G208200 | chr5A | 423680107 | 423683457 | 3350 | False | 1497.000000 | 2459 | 89.735667 | 704 | 4199 | 3 | chr5A.!!$F3 | 3495 |
9 | TraesCS5B01G208200 | chr2B | 374217235 | 374217763 | 528 | True | 784.000000 | 784 | 93.384000 | 1 | 529 | 1 | chr2B.!!$R2 | 528 |
10 | TraesCS5B01G208200 | chr2B | 94345344 | 94345870 | 526 | True | 741.000000 | 741 | 92.030000 | 1 | 527 | 1 | chr2B.!!$R1 | 526 |
11 | TraesCS5B01G208200 | chr7B | 284958706 | 284959235 | 529 | True | 756.000000 | 756 | 92.453000 | 1 | 529 | 1 | chr7B.!!$R2 | 528 |
12 | TraesCS5B01G208200 | chr7B | 194596591 | 194597118 | 527 | True | 743.000000 | 743 | 92.075000 | 1 | 529 | 1 | chr7B.!!$R1 | 528 |
13 | TraesCS5B01G208200 | chr3D | 28272520 | 28273048 | 528 | False | 739.000000 | 739 | 91.871000 | 1 | 529 | 1 | chr3D.!!$F2 | 528 |
14 | TraesCS5B01G208200 | chr6B | 21937988 | 21938517 | 529 | True | 734.000000 | 734 | 91.698000 | 1 | 529 | 1 | chr6B.!!$R1 | 528 |
15 | TraesCS5B01G208200 | chr6B | 714184802 | 714185330 | 528 | True | 734.000000 | 734 | 91.682000 | 1 | 529 | 1 | chr6B.!!$R6 | 528 |
16 | TraesCS5B01G208200 | chr3B | 242480136 | 242480663 | 527 | True | 732.000000 | 732 | 91.682000 | 1 | 529 | 1 | chr3B.!!$R1 | 528 |
17 | TraesCS5B01G208200 | chr1B | 645415369 | 645415897 | 528 | False | 728.000000 | 728 | 91.493000 | 1 | 529 | 1 | chr1B.!!$F3 | 528 |
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. |
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Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
522 | 525 | 0.608130 | ACCACAGAGTGCGCAATCTA | 59.392 | 50.0 | 36.48 | 0.0 | 33.56 | 1.98 | F |
752 | 756 | 0.877071 | GCAACCACATCAGACACCAG | 59.123 | 55.0 | 0.00 | 0.0 | 0.00 | 4.00 | F |
1697 | 1880 | 0.322008 | CTGTTCTTGTCCCCTGCCTC | 60.322 | 60.0 | 0.00 | 0.0 | 0.00 | 4.70 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1395 | 1428 | 1.258720 | TCGCAAGCATTTCATCGATCG | 59.741 | 47.619 | 9.36 | 9.36 | 37.18 | 3.69 | R |
2698 | 2976 | 1.004394 | TCGTCCTGAGAGTAGCTCCAA | 59.996 | 52.381 | 0.00 | 0.00 | 43.26 | 3.53 | R |
3224 | 3503 | 2.238898 | GCACACTTCCCCTACCATACTT | 59.761 | 50.000 | 0.00 | 0.00 | 0.00 | 2.24 | 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.