Multiple sequence alignment - TraesCS3A01G118000

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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 TraesCS3A01G118000 chr3A 100.000 9126 0 0 1 9126 89571967 89581092 0.000000e+00 16853.0
1 TraesCS3A01G118000 chr3A 96.080 3929 90 19 5199 9126 89665407 89669272 0.000000e+00 6344.0
2 TraesCS3A01G118000 chr3A 94.098 2050 102 7 1 2045 89662043 89664078 0.000000e+00 3097.0
3 TraesCS3A01G118000 chr3A 86.334 1683 188 20 1 1673 90115626 90117276 0.000000e+00 1796.0
4 TraesCS3A01G118000 chr3A 86.698 1278 152 9 1 1270 90061645 90060378 0.000000e+00 1402.0
5 TraesCS3A01G118000 chr3A 84.193 1493 180 26 566 2044 90125541 90126991 0.000000e+00 1399.0
6 TraesCS3A01G118000 chr3A 91.728 810 54 10 2043 2849 89664124 89664923 0.000000e+00 1112.0
7 TraesCS3A01G118000 chr3A 88.130 893 93 8 1 886 90077988 90078874 0.000000e+00 1050.0
8 TraesCS3A01G118000 chr3A 93.475 705 27 6 4288 4974 89575517 89574814 0.000000e+00 1029.0
9 TraesCS3A01G118000 chr3A 93.475 705 27 6 2848 3551 89576940 89576254 0.000000e+00 1029.0
10 TraesCS3A01G118000 chr3A 87.402 897 100 10 1 888 89970199 89971091 0.000000e+00 1018.0
11 TraesCS3A01G118000 chr3A 86.531 735 73 13 1309 2043 89984760 89984052 0.000000e+00 785.0
12 TraesCS3A01G118000 chr3A 81.047 860 92 35 4164 4981 640443896 640443066 3.620000e-173 619.0
13 TraesCS3A01G118000 chr3A 85.961 406 36 12 1640 2044 90065800 90066185 1.830000e-111 414.0
14 TraesCS3A01G118000 chr3A 91.011 178 12 3 2256 2433 90066486 90066659 4.260000e-58 237.0
15 TraesCS3A01G118000 chr3A 92.308 156 3 3 5001 5155 89665258 89665405 7.180000e-51 213.0
16 TraesCS3A01G118000 chr3A 92.920 113 7 1 1932 2044 90117322 90117433 7.330000e-36 163.0
17 TraesCS3A01G118000 chr3A 95.238 84 4 0 2043 2126 89983806 89983889 5.750000e-27 134.0
18 TraesCS3A01G118000 chr3D 95.152 3486 134 18 5159 8635 75543445 75546904 0.000000e+00 5469.0
19 TraesCS3A01G118000 chr3D 93.765 2053 106 12 1 2045 75538744 75540782 0.000000e+00 3062.0
20 TraesCS3A01G118000 chr3D 86.154 1820 190 33 1 1812 75655170 75656935 0.000000e+00 1908.0
21 TraesCS3A01G118000 chr3D 86.212 1494 151 31 563 2045 75664615 75666064 0.000000e+00 1567.0
22 TraesCS3A01G118000 chr3D 89.050 895 88 6 1 888 75637559 75638450 0.000000e+00 1101.0
23 TraesCS3A01G118000 chr3D 92.105 494 31 5 2043 2531 75540828 75541318 0.000000e+00 689.0
24 TraesCS3A01G118000 chr3D 89.631 434 36 3 8693 9124 75547055 75547481 2.240000e-150 544.0
25 TraesCS3A01G118000 chr3D 84.838 554 55 17 8578 9124 75667388 75667919 1.740000e-146 531.0
26 TraesCS3A01G118000 chr3D 86.553 409 32 12 2043 2433 75666110 75666513 6.550000e-116 429.0
27 TraesCS3A01G118000 chr3D 91.089 202 10 3 4978 5172 75543162 75543362 5.430000e-67 267.0
28 TraesCS3A01G118000 chr3D 100.000 35 0 0 2815 2849 75543131 75543165 2.130000e-06 65.8
29 TraesCS3A01G118000 chr3B 95.600 2682 107 6 5797 8476 121641676 121644348 0.000000e+00 4289.0
30 TraesCS3A01G118000 chr3B 86.884 2051 222 23 1 2045 122113528 122115537 0.000000e+00 2254.0
31 TraesCS3A01G118000 chr3B 86.728 2057 219 33 1 2044 121636946 121638961 0.000000e+00 2237.0
32 TraesCS3A01G118000 chr3B 86.139 1818 197 29 236 2044 122083083 122084854 0.000000e+00 1910.0
33 TraesCS3A01G118000 chr3B 86.488 1458 162 16 73 1523 122014137 122015566 0.000000e+00 1568.0
34 TraesCS3A01G118000 chr3B 88.923 659 52 8 8468 9124 121647590 121648229 0.000000e+00 793.0
35 TraesCS3A01G118000 chr3B 88.450 329 35 3 1708 2035 122015595 122015921 2.390000e-105 394.0
36 TraesCS3A01G118000 chr3B 82.927 410 60 7 8711 9118 122324411 122324812 2.420000e-95 361.0
37 TraesCS3A01G118000 chr3B 91.026 234 19 2 2043 2274 121638995 121639228 1.910000e-81 315.0
38 TraesCS3A01G118000 chr3B 79.780 455 50 23 4300 4721 342502196 342501751 8.960000e-75 292.0
39 TraesCS3A01G118000 chr3B 84.190 253 38 2 2257 2508 121639250 121639501 2.550000e-60 244.0
40 TraesCS3A01G118000 chr3B 88.265 196 21 2 2043 2236 122084901 122085096 5.510000e-57 233.0
41 TraesCS3A01G118000 chr3B 88.957 163 14 4 4978 5140 121641061 121641219 2.010000e-46 198.0
42 TraesCS3A01G118000 chr3B 92.623 122 6 2 2312 2433 122085285 122085403 1.220000e-38 172.0
43 TraesCS3A01G118000 chr3B 90.984 122 10 1 2312 2433 122115964 122116084 7.330000e-36 163.0
44 TraesCS3A01G118000 chrUn 91.154 1447 71 19 3568 4982 102524402 102522981 0.000000e+00 1910.0
45 TraesCS3A01G118000 chrUn 91.597 714 34 11 2848 3551 102522989 102523686 0.000000e+00 963.0
46 TraesCS3A01G118000 chrUn 82.353 884 92 36 3586 4434 346198817 346197963 0.000000e+00 710.0
47 TraesCS3A01G118000 chrUn 82.200 882 95 35 3586 4434 346321689 346322541 0.000000e+00 702.0
48 TraesCS3A01G118000 chrUn 78.852 331 66 4 7302 7630 334690501 334690829 4.290000e-53 220.0
49 TraesCS3A01G118000 chr2D 89.886 1404 66 24 3604 4981 523639033 523637680 0.000000e+00 1736.0
50 TraesCS3A01G118000 chr2D 91.561 711 29 13 2848 3551 523637687 523638373 0.000000e+00 952.0
51 TraesCS3A01G118000 chr4A 87.465 1412 101 28 3612 4981 120562843 120561466 0.000000e+00 1557.0
52 TraesCS3A01G118000 chr4A 87.184 1069 65 29 3603 4634 681891053 681890020 0.000000e+00 1149.0
53 TraesCS3A01G118000 chr4A 90.055 724 49 10 2848 3551 120561473 120562193 0.000000e+00 917.0
54 TraesCS3A01G118000 chr4A 79.742 1318 223 30 6871 8160 636314976 636313675 0.000000e+00 915.0
55 TraesCS3A01G118000 chr4A 77.688 1488 278 43 6638 8094 635960942 635959478 0.000000e+00 859.0
56 TraesCS3A01G118000 chr4A 77.108 1328 242 46 6813 8108 636084675 636083378 0.000000e+00 712.0
57 TraesCS3A01G118000 chr4A 85.575 617 73 12 5807 6413 635961750 635961140 4.650000e-177 632.0
58 TraesCS3A01G118000 chr4A 82.644 749 85 19 5683 6413 636044938 636044217 1.010000e-173 621.0
59 TraesCS3A01G118000 chr4A 79.237 944 126 42 5540 6457 636261569 636260670 2.190000e-165 593.0
60 TraesCS3A01G118000 chr4A 77.980 990 182 32 6814 7787 636101126 636100157 1.020000e-163 588.0
61 TraesCS3A01G118000 chr4A 80.724 773 126 20 6630 7390 636044030 636043269 1.710000e-161 580.0
62 TraesCS3A01G118000 chr4A 88.947 380 22 7 3191 3551 681890020 681890398 1.400000e-122 451.0
63 TraesCS3A01G118000 chr4A 90.541 296 26 2 2848 3143 681889720 681890013 3.090000e-104 390.0
64 TraesCS3A01G118000 chr4A 88.704 301 33 1 4682 4981 681890013 681889713 5.210000e-97 366.0
65 TraesCS3A01G118000 chr4A 72.373 923 211 36 7255 8151 636034728 636033824 1.520000e-62 252.0
66 TraesCS3A01G118000 chr4A 83.168 202 26 5 5497 5693 636047271 636047073 2.620000e-40 178.0
67 TraesCS3A01G118000 chr4A 79.528 254 40 12 7911 8157 636100018 636099770 4.380000e-38 171.0
68 TraesCS3A01G118000 chr5A 95.450 901 18 13 3288 4180 180342033 180341148 0.000000e+00 1415.0
69 TraesCS3A01G118000 chr5A 93.213 442 25 5 2848 3288 180346598 180346161 0.000000e+00 645.0
70 TraesCS3A01G118000 chr5A 92.617 447 29 4 4537 4981 180346161 180346605 2.780000e-179 640.0
71 TraesCS3A01G118000 chr5A 91.852 270 3 2 4287 4537 180341764 180342033 8.710000e-95 359.0
72 TraesCS3A01G118000 chr2B 82.983 1475 140 49 3573 4981 45643617 45645046 0.000000e+00 1230.0
73 TraesCS3A01G118000 chr2B 86.066 732 56 22 2848 3551 45645039 45644326 0.000000e+00 745.0
74 TraesCS3A01G118000 chr4D 82.473 1415 137 56 3642 4981 25434506 25435884 0.000000e+00 1136.0
75 TraesCS3A01G118000 chr4D 85.455 715 66 15 2848 3541 25435877 25435180 0.000000e+00 710.0
76 TraesCS3A01G118000 chr5D 79.909 1314 230 26 6871 8161 535643664 535644966 0.000000e+00 933.0
77 TraesCS3A01G118000 chr5D 89.362 329 25 6 6084 6404 535861919 535862245 1.100000e-108 405.0
78 TraesCS3A01G118000 chr5D 78.082 511 64 13 5497 5982 535861398 535861885 6.980000e-71 279.0
79 TraesCS3A01G118000 chr5D 78.638 426 83 8 7302 7725 499069513 499069094 9.030000e-70 276.0
80 TraesCS3A01G118000 chr5D 82.403 233 38 2 7911 8140 535817793 535818025 5.590000e-47 200.0
81 TraesCS3A01G118000 chr7D 79.125 1485 188 63 3570 4981 508830483 508829048 0.000000e+00 913.0
82 TraesCS3A01G118000 chr7D 82.889 900 85 38 3570 4434 380643 381508 0.000000e+00 745.0
83 TraesCS3A01G118000 chr7D 87.535 353 33 4 2848 3198 386627 386284 1.850000e-106 398.0
84 TraesCS3A01G118000 chr7D 83.889 360 44 7 4627 4981 386284 386634 1.900000e-86 331.0
85 TraesCS3A01G118000 chr5B 79.578 1327 223 31 6871 8161 676251104 676252418 0.000000e+00 905.0
86 TraesCS3A01G118000 chr5B 78.433 1289 218 29 6870 8132 676242499 676243753 0.000000e+00 785.0
87 TraesCS3A01G118000 chr5B 81.921 885 121 22 5548 6409 676271342 676272210 0.000000e+00 712.0
88 TraesCS3A01G118000 chr5B 78.958 998 144 39 5509 6467 676240821 676241791 3.620000e-173 619.0
89 TraesCS3A01G118000 chr5B 77.367 433 83 15 7302 7728 619112796 619112373 9.150000e-60 243.0
90 TraesCS3A01G118000 chr5B 76.581 427 90 10 7302 7725 619156587 619156168 9.220000e-55 226.0
91 TraesCS3A01G118000 chr5B 76.690 429 85 12 7302 7725 619279442 619279024 3.320000e-54 224.0
92 TraesCS3A01G118000 chr1A 79.410 1389 164 53 3678 4982 486958860 486960210 0.000000e+00 869.0
93 TraesCS3A01G118000 chr1A 83.426 718 75 22 2848 3541 486960202 486959505 2.160000e-175 627.0
94 TraesCS3A01G118000 chr7A 82.294 898 95 33 3570 4434 537104 537970 0.000000e+00 719.0
95 TraesCS3A01G118000 chr7A 83.277 592 56 24 4164 4732 139792091 139792662 1.060000e-138 505.0
96 TraesCS3A01G118000 chr7A 81.262 507 75 16 3570 4066 610273196 610273692 8.590000e-105 392.0
97 TraesCS3A01G118000 chr7A 81.172 478 37 25 3093 3550 139792662 139792218 1.470000e-87 335.0
98 TraesCS3A01G118000 chr1B 82.889 713 68 31 2848 3550 619385576 619386244 7.890000e-165 592.0


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 TraesCS3A01G118000 chr3A 89571967 89581092 9125 False 16853.000000 16853 100.000000 1 9126 1 chr3A.!!$F1 9125
1 TraesCS3A01G118000 chr3A 89662043 89669272 7229 False 2691.500000 6344 93.553500 1 9126 4 chr3A.!!$F6 9125
2 TraesCS3A01G118000 chr3A 90060378 90061645 1267 True 1402.000000 1402 86.698000 1 1270 1 chr3A.!!$R2 1269
3 TraesCS3A01G118000 chr3A 90125541 90126991 1450 False 1399.000000 1399 84.193000 566 2044 1 chr3A.!!$F5 1478
4 TraesCS3A01G118000 chr3A 90077988 90078874 886 False 1050.000000 1050 88.130000 1 886 1 chr3A.!!$F4 885
5 TraesCS3A01G118000 chr3A 89574814 89576940 2126 True 1029.000000 1029 93.475000 2848 4974 2 chr3A.!!$R4 2126
6 TraesCS3A01G118000 chr3A 89970199 89971091 892 False 1018.000000 1018 87.402000 1 888 1 chr3A.!!$F2 887
7 TraesCS3A01G118000 chr3A 90115626 90117433 1807 False 979.500000 1796 89.627000 1 2044 2 chr3A.!!$F8 2043
8 TraesCS3A01G118000 chr3A 89984052 89984760 708 True 785.000000 785 86.531000 1309 2043 1 chr3A.!!$R1 734
9 TraesCS3A01G118000 chr3A 640443066 640443896 830 True 619.000000 619 81.047000 4164 4981 1 chr3A.!!$R3 817
10 TraesCS3A01G118000 chr3A 90065800 90066659 859 False 325.500000 414 88.486000 1640 2433 2 chr3A.!!$F7 793
11 TraesCS3A01G118000 chr3D 75655170 75656935 1765 False 1908.000000 1908 86.154000 1 1812 1 chr3D.!!$F2 1811
12 TraesCS3A01G118000 chr3D 75538744 75547481 8737 False 1682.800000 5469 93.623667 1 9124 6 chr3D.!!$F3 9123
13 TraesCS3A01G118000 chr3D 75637559 75638450 891 False 1101.000000 1101 89.050000 1 888 1 chr3D.!!$F1 887
14 TraesCS3A01G118000 chr3D 75664615 75667919 3304 False 842.333333 1567 85.867667 563 9124 3 chr3D.!!$F4 8561
15 TraesCS3A01G118000 chr3B 121636946 121648229 11283 False 1346.000000 4289 89.237333 1 9124 6 chr3B.!!$F2 9123
16 TraesCS3A01G118000 chr3B 122113528 122116084 2556 False 1208.500000 2254 88.934000 1 2433 2 chr3B.!!$F5 2432
17 TraesCS3A01G118000 chr3B 122014137 122015921 1784 False 981.000000 1568 87.469000 73 2035 2 chr3B.!!$F3 1962
18 TraesCS3A01G118000 chr3B 122083083 122085403 2320 False 771.666667 1910 89.009000 236 2433 3 chr3B.!!$F4 2197
19 TraesCS3A01G118000 chrUn 102522981 102524402 1421 True 1910.000000 1910 91.154000 3568 4982 1 chrUn.!!$R1 1414
20 TraesCS3A01G118000 chrUn 102522989 102523686 697 False 963.000000 963 91.597000 2848 3551 1 chrUn.!!$F1 703
21 TraesCS3A01G118000 chrUn 346197963 346198817 854 True 710.000000 710 82.353000 3586 4434 1 chrUn.!!$R2 848
22 TraesCS3A01G118000 chrUn 346321689 346322541 852 False 702.000000 702 82.200000 3586 4434 1 chrUn.!!$F3 848
23 TraesCS3A01G118000 chr2D 523637680 523639033 1353 True 1736.000000 1736 89.886000 3604 4981 1 chr2D.!!$R1 1377
24 TraesCS3A01G118000 chr2D 523637687 523638373 686 False 952.000000 952 91.561000 2848 3551 1 chr2D.!!$F1 703
25 TraesCS3A01G118000 chr4A 120561466 120562843 1377 True 1557.000000 1557 87.465000 3612 4981 1 chr4A.!!$R1 1369
26 TraesCS3A01G118000 chr4A 120561473 120562193 720 False 917.000000 917 90.055000 2848 3551 1 chr4A.!!$F1 703
27 TraesCS3A01G118000 chr4A 636313675 636314976 1301 True 915.000000 915 79.742000 6871 8160 1 chr4A.!!$R5 1289
28 TraesCS3A01G118000 chr4A 681889713 681891053 1340 True 757.500000 1149 87.944000 3603 4981 2 chr4A.!!$R9 1378
29 TraesCS3A01G118000 chr4A 635959478 635961750 2272 True 745.500000 859 81.631500 5807 8094 2 chr4A.!!$R6 2287
30 TraesCS3A01G118000 chr4A 636083378 636084675 1297 True 712.000000 712 77.108000 6813 8108 1 chr4A.!!$R3 1295
31 TraesCS3A01G118000 chr4A 636260670 636261569 899 True 593.000000 593 79.237000 5540 6457 1 chr4A.!!$R4 917
32 TraesCS3A01G118000 chr4A 636043269 636047271 4002 True 459.666667 621 82.178667 5497 7390 3 chr4A.!!$R7 1893
33 TraesCS3A01G118000 chr4A 681889720 681890398 678 False 420.500000 451 89.744000 2848 3551 2 chr4A.!!$F2 703
34 TraesCS3A01G118000 chr4A 636099770 636101126 1356 True 379.500000 588 78.754000 6814 8157 2 chr4A.!!$R8 1343
35 TraesCS3A01G118000 chr4A 636033824 636034728 904 True 252.000000 252 72.373000 7255 8151 1 chr4A.!!$R2 896
36 TraesCS3A01G118000 chr5A 180341148 180342033 885 True 1415.000000 1415 95.450000 3288 4180 1 chr5A.!!$R1 892
37 TraesCS3A01G118000 chr2B 45643617 45645046 1429 False 1230.000000 1230 82.983000 3573 4981 1 chr2B.!!$F1 1408
38 TraesCS3A01G118000 chr2B 45644326 45645039 713 True 745.000000 745 86.066000 2848 3551 1 chr2B.!!$R1 703
39 TraesCS3A01G118000 chr4D 25434506 25435884 1378 False 1136.000000 1136 82.473000 3642 4981 1 chr4D.!!$F1 1339
40 TraesCS3A01G118000 chr4D 25435180 25435877 697 True 710.000000 710 85.455000 2848 3541 1 chr4D.!!$R1 693
41 TraesCS3A01G118000 chr5D 535643664 535644966 1302 False 933.000000 933 79.909000 6871 8161 1 chr5D.!!$F1 1290
42 TraesCS3A01G118000 chr5D 535861398 535862245 847 False 342.000000 405 83.722000 5497 6404 2 chr5D.!!$F3 907
43 TraesCS3A01G118000 chr7D 508829048 508830483 1435 True 913.000000 913 79.125000 3570 4981 1 chr7D.!!$R2 1411
44 TraesCS3A01G118000 chr7D 380643 381508 865 False 745.000000 745 82.889000 3570 4434 1 chr7D.!!$F1 864
45 TraesCS3A01G118000 chr5B 676251104 676252418 1314 False 905.000000 905 79.578000 6871 8161 1 chr5B.!!$F1 1290
46 TraesCS3A01G118000 chr5B 676271342 676272210 868 False 712.000000 712 81.921000 5548 6409 1 chr5B.!!$F2 861
47 TraesCS3A01G118000 chr5B 676240821 676243753 2932 False 702.000000 785 78.695500 5509 8132 2 chr5B.!!$F3 2623
48 TraesCS3A01G118000 chr1A 486958860 486960210 1350 False 869.000000 869 79.410000 3678 4982 1 chr1A.!!$F1 1304
49 TraesCS3A01G118000 chr1A 486959505 486960202 697 True 627.000000 627 83.426000 2848 3541 1 chr1A.!!$R1 693
50 TraesCS3A01G118000 chr7A 537104 537970 866 False 719.000000 719 82.294000 3570 4434 1 chr7A.!!$F1 864
51 TraesCS3A01G118000 chr7A 139792091 139792662 571 False 505.000000 505 83.277000 4164 4732 1 chr7A.!!$F2 568
52 TraesCS3A01G118000 chr1B 619385576 619386244 668 False 592.000000 592 82.889000 2848 3550 1 chr1B.!!$F1 702

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
908 936 0.909623 AAATCATCCCGGTCGACCTT 59.090 50.000 30.92 14.58 0.00 3.50 F
2735 4169 0.405585 CCACATCCACCCTTGTCCTT 59.594 55.000 0.00 0.00 0.00 3.36 F
2785 4220 1.267038 CGTTTGATCAGGTTCGCATCG 60.267 52.381 0.00 0.00 0.00 3.84 F
3634 6343 2.285889 TTTCCAAAGGCGGTCCACCA 62.286 55.000 0.00 0.00 35.14 4.17 F
4846 7978 0.899019 TATGCGGTGTGTAGAGCCAA 59.101 50.000 0.00 0.00 0.00 4.52 F
5549 9165 0.181350 CTATCCCCTGTCCCTGCAAC 59.819 60.000 0.00 0.00 0.00 4.17 F
5743 11510 2.227388 CCTGGTCAAGATTGCAGTGAAC 59.773 50.000 0.00 0.00 0.00 3.18 F
6185 12078 2.238353 TCTTGCTGCAAGAAGTCGC 58.762 52.632 35.50 0.00 45.84 5.19 F
6995 13259 3.382227 TCGACATCTTAATGGCTACCGAA 59.618 43.478 0.00 0.00 38.93 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2763 4197 0.034198 TGCGAACCTGATCAAACGGA 59.966 50.000 6.49 4.0 0.00 4.69 R
3555 5998 2.056577 GTATGCAATACGGCGGACTAC 58.943 52.381 13.24 0.0 40.43 2.73 R
4656 7778 3.056891 ACCAAGTGTGTGTTCTTGTTTGG 60.057 43.478 0.00 0.0 39.25 3.28 R
5107 8563 0.037303 ACGTCCTGGACCGTAAGAGA 59.963 55.000 20.68 0.0 43.02 3.10 R
5732 11499 5.600696 CCTTTTGTAAAGGTTCACTGCAAT 58.399 37.500 9.53 0.0 32.78 3.56 R
7239 13508 2.427812 TCATGCACATTACAATGGCCAG 59.572 45.455 13.05 0.0 40.70 4.85 R
7579 13863 3.308832 CCATCTGGGTTGGGTAAGCTTTA 60.309 47.826 3.20 0.0 34.76 1.85 R
7859 14157 4.104086 CCATATATCCCTAACCAGAGGCA 58.896 47.826 0.00 0.0 35.00 4.75 R
8510 18096 0.249868 CCTGAACCGCTGACTGTCAA 60.250 55.000 12.16 0.0 0.00 3.18 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
74 75 8.178313 TCATTAGTAGAAGTGTGAAGAAGTGA 57.822 34.615 0.00 0.00 0.00 3.41
351 356 4.441495 GCTTTGGCCTGTTTCTAACAACTT 60.441 41.667 3.32 0.00 41.61 2.66
352 357 5.660460 CTTTGGCCTGTTTCTAACAACTTT 58.340 37.500 3.32 0.00 41.61 2.66
382 388 7.631717 AAATCTCTACCCTGCATTACTTTTC 57.368 36.000 0.00 0.00 0.00 2.29
386 392 3.542969 ACCCTGCATTACTTTTCCCTT 57.457 42.857 0.00 0.00 0.00 3.95
613 632 1.929836 GATCACGCGAGAGAGCAAAAT 59.070 47.619 15.93 0.00 37.08 1.82
636 655 1.078891 TCAACGCCCACCTACCCTA 59.921 57.895 0.00 0.00 0.00 3.53
908 936 0.909623 AAATCATCCCGGTCGACCTT 59.090 50.000 30.92 14.58 0.00 3.50
986 1016 2.094762 ACGCGTGCTTCCTCTTTTAT 57.905 45.000 12.93 0.00 0.00 1.40
1024 1055 1.077645 CGGCGGCAAAAACATGATGG 61.078 55.000 10.53 0.00 0.00 3.51
1074 1105 4.399219 CCGAGATGGACCTAGAGTTATCA 58.601 47.826 0.00 0.00 42.00 2.15
1134 1168 3.053831 TCGGAGGTCTTTTCCAACATC 57.946 47.619 0.00 0.00 34.24 3.06
1220 1256 3.686016 ACAATAAGAAAGGTGCGTGGAT 58.314 40.909 0.00 0.00 0.00 3.41
1336 1374 5.228665 TGCGCTTGATTTGATTTGATTTGA 58.771 33.333 9.73 0.00 0.00 2.69
1344 1382 9.557061 TTGATTTGATTTGATTTGAAATGGTCA 57.443 25.926 0.00 0.00 0.00 4.02
1380 1418 2.016096 GCTCAGGCTGACCCTTCATTC 61.016 57.143 14.43 0.00 43.06 2.67
1546 1588 5.067936 TCGAAACATTTAGGCTTTGTTTGGA 59.932 36.000 20.49 20.44 42.07 3.53
1706 1751 4.129737 TCTAGCACAGACCGGCGC 62.130 66.667 0.00 0.00 34.54 6.53
1739 1784 0.969894 AGGAGTGCGCTAACTTGTCT 59.030 50.000 9.73 1.56 0.00 3.41
1823 1869 2.094417 GGGAATTCACGAGAAAGCGAAG 59.906 50.000 7.93 0.00 37.29 3.79
1824 1870 2.993899 GGAATTCACGAGAAAGCGAAGA 59.006 45.455 7.93 0.00 37.29 2.87
2202 2303 6.349611 CCTTTGTTTATCCAGGTTCATGTCAG 60.350 42.308 0.00 0.00 0.00 3.51
2221 2322 2.476619 CAGCAAGAAGGTGTAACACTCG 59.523 50.000 0.00 0.00 40.80 4.18
2440 2691 3.199071 AGGCACCGTGTATTTCATAGGAA 59.801 43.478 0.00 0.00 33.26 3.36
2471 2722 1.530013 GCCCTTCAGCAGTGCAATGT 61.530 55.000 19.20 0.00 0.00 2.71
2472 2723 0.963962 CCCTTCAGCAGTGCAATGTT 59.036 50.000 19.20 6.89 0.00 2.71
2514 2765 5.565592 TGAATCCATCCGTCATGAAAAAG 57.434 39.130 0.00 0.00 33.80 2.27
2516 2767 3.433306 TCCATCCGTCATGAAAAAGGT 57.567 42.857 0.00 0.00 33.80 3.50
2518 2769 2.164219 CCATCCGTCATGAAAAAGGTGG 59.836 50.000 0.00 0.00 33.80 4.61
2524 3955 3.505680 CGTCATGAAAAAGGTGGATGGAA 59.494 43.478 0.00 0.00 0.00 3.53
2576 4007 2.288334 GCATTTTGTCTGTGCATGTCCA 60.288 45.455 0.00 0.00 38.68 4.02
2637 4068 2.616842 GACACAAACAAACGACCATCCT 59.383 45.455 0.00 0.00 0.00 3.24
2643 4076 4.993029 AACAAACGACCATCCTTTTTCA 57.007 36.364 0.00 0.00 0.00 2.69
2682 4116 2.362375 GCCTGAATTTGGGCCGGA 60.362 61.111 5.05 0.00 42.30 5.14
2720 4154 3.975083 GATACGGACACGCGCCACA 62.975 63.158 5.73 0.00 46.04 4.17
2735 4169 0.405585 CCACATCCACCCTTGTCCTT 59.594 55.000 0.00 0.00 0.00 3.36
2742 4176 1.352083 CACCCTTGTCCTTCTCCTGA 58.648 55.000 0.00 0.00 0.00 3.86
2750 4184 3.787001 CTTCTCCTGACCCGCCCC 61.787 72.222 0.00 0.00 0.00 5.80
2763 4197 3.771160 GCCCCTCGGTGATGACGT 61.771 66.667 0.00 0.00 0.00 4.34
2776 4211 1.927174 GATGACGTCCGTTTGATCAGG 59.073 52.381 14.12 0.00 0.00 3.86
2785 4220 1.267038 CGTTTGATCAGGTTCGCATCG 60.267 52.381 0.00 0.00 0.00 3.84
2805 4591 2.672996 GCATGTTGGGGTCGCACT 60.673 61.111 0.00 0.00 0.00 4.40
2955 4764 4.931661 AATACGTGATCAATACGGTCCT 57.068 40.909 0.00 0.00 45.24 3.85
3371 5787 8.351461 CAACACAATGCTTGGGAATTTTAAAAT 58.649 29.630 7.64 7.64 37.55 1.82
3551 5994 9.353999 AGTTTCACAAAAATTCACTAACTTGTC 57.646 29.630 0.00 0.00 0.00 3.18
3553 5996 8.909708 TTCACAAAAATTCACTAACTTGTCAG 57.090 30.769 0.00 0.00 0.00 3.51
3554 5997 6.972328 TCACAAAAATTCACTAACTTGTCAGC 59.028 34.615 0.00 0.00 0.00 4.26
3555 5998 5.971202 ACAAAAATTCACTAACTTGTCAGCG 59.029 36.000 0.00 0.00 0.00 5.18
3556 5999 5.751243 AAAATTCACTAACTTGTCAGCGT 57.249 34.783 0.00 0.00 0.00 5.07
3557 6000 6.854496 AAAATTCACTAACTTGTCAGCGTA 57.146 33.333 0.00 0.00 0.00 4.42
3558 6001 6.467723 AAATTCACTAACTTGTCAGCGTAG 57.532 37.500 0.00 0.00 0.00 3.51
3592 6035 8.891671 ATTGCATACAGAAGTTTTGAAATTGT 57.108 26.923 0.00 0.00 0.00 2.71
3634 6343 2.285889 TTTCCAAAGGCGGTCCACCA 62.286 55.000 0.00 0.00 35.14 4.17
3654 6364 7.930865 TCCACCATTTTAAAAATTGGTCTGAAG 59.069 33.333 19.03 10.45 45.69 3.02
3673 6542 9.458374 GTCTGAAGGTTTTTCGAATTCAAATTA 57.542 29.630 11.18 0.00 30.10 1.40
4818 7950 4.250464 CGTGGCCTTCACTACAGAAATAA 58.750 43.478 3.32 0.00 43.94 1.40
4846 7978 0.899019 TATGCGGTGTGTAGAGCCAA 59.101 50.000 0.00 0.00 0.00 4.52
4857 7990 3.311596 GTGTAGAGCCAAACTGACGTTTT 59.688 43.478 0.00 0.00 41.23 2.43
4940 8074 4.083110 CGCAAATTCCAAGACTGAGTTGAT 60.083 41.667 0.00 0.00 0.00 2.57
5016 8466 1.874345 CGCCTAGTGTTGACGAGGGT 61.874 60.000 0.00 0.00 43.45 4.34
5019 8469 1.893801 CCTAGTGTTGACGAGGGTCTT 59.106 52.381 0.00 0.00 43.79 3.01
5107 8563 0.602905 CCTCGAAAGCGTTGGTTCCT 60.603 55.000 0.00 0.00 38.98 3.36
5394 9005 1.965935 CAACGATGTCCCATGCCATA 58.034 50.000 0.00 0.00 0.00 2.74
5483 9094 4.768448 GGGCATGGTTGATGATGATTGATA 59.232 41.667 0.00 0.00 33.31 2.15
5549 9165 0.181350 CTATCCCCTGTCCCTGCAAC 59.819 60.000 0.00 0.00 0.00 4.17
5552 9168 2.674380 CCCTGTCCCTGCAACAGC 60.674 66.667 10.90 0.00 42.26 4.40
5732 11499 5.875224 TCATGTTACAATTCCTGGTCAAGA 58.125 37.500 0.00 0.00 0.00 3.02
5743 11510 2.227388 CCTGGTCAAGATTGCAGTGAAC 59.773 50.000 0.00 0.00 0.00 3.18
5785 11554 4.749245 AAGTTCGGCTTGTGACAAATAG 57.251 40.909 0.00 0.00 35.80 1.73
6185 12078 2.238353 TCTTGCTGCAAGAAGTCGC 58.762 52.632 35.50 0.00 45.84 5.19
6905 13169 6.936900 TCATTCTACTTGGAACAGAGGAAAAG 59.063 38.462 0.00 0.00 42.39 2.27
6990 13254 3.636764 TCTGCTCGACATCTTAATGGCTA 59.363 43.478 0.00 0.00 38.93 3.93
6995 13259 3.382227 TCGACATCTTAATGGCTACCGAA 59.618 43.478 0.00 0.00 38.93 4.30
7239 13508 6.837992 TCATTTCGTAGAAAAATGTAGGCAC 58.162 36.000 8.06 0.00 45.90 5.01
7859 14157 4.101741 AGGAGACAGAGTTGTACAGCTTTT 59.898 41.667 13.87 2.99 37.76 2.27
8249 14585 5.705609 GGTAACCTGAATCATGTGTTGTT 57.294 39.130 0.00 0.00 0.00 2.83
8250 14586 5.460646 GGTAACCTGAATCATGTGTTGTTG 58.539 41.667 0.00 0.00 0.00 3.33
8251 14587 5.009610 GGTAACCTGAATCATGTGTTGTTGT 59.990 40.000 0.00 0.00 0.00 3.32
8387 14723 1.980765 TCTCTGTGCTGGGAAAGTGAT 59.019 47.619 0.00 0.00 0.00 3.06
8439 14775 1.678101 ACTTGGTGCTTCAACTGCTTC 59.322 47.619 0.00 0.00 0.00 3.86
8510 18096 4.999950 ACTTGCTGAATCTTGAATCTTCGT 59.000 37.500 0.00 0.00 0.00 3.85
8547 18133 0.174162 GGGCTTGCATTGCTACAAGG 59.826 55.000 10.49 0.00 42.82 3.61
8569 18155 2.439135 TCATCCGTCCCAATGATCACAT 59.561 45.455 0.00 0.00 38.50 3.21
8624 18211 2.828877 TGTCGACGGATTTGTGAAGTT 58.171 42.857 11.62 0.00 0.00 2.66
8691 18377 3.911698 ACACACACGAGCGCCAGA 61.912 61.111 2.29 0.00 0.00 3.86
8765 18462 0.251297 CCCCTCATGTCCTTGTTGCA 60.251 55.000 0.00 0.00 0.00 4.08
8829 18527 4.035102 GGGGTGCCTTCCTTCGCT 62.035 66.667 0.00 0.00 0.00 4.93
8935 18633 1.178534 CGGCATGAAAGGGTTGTGGT 61.179 55.000 0.00 0.00 0.00 4.16
8970 18668 2.511373 GCGCACCATGTCATCGGA 60.511 61.111 0.30 0.00 0.00 4.55
9062 18762 1.506718 CTCGGCTTGTCGCTAGTGA 59.493 57.895 0.70 0.70 39.13 3.41
9064 18764 1.333931 CTCGGCTTGTCGCTAGTGATA 59.666 52.381 9.64 3.61 39.13 2.15
9100 18800 1.258445 CCGGTCAGGCCTAGTCTTGT 61.258 60.000 3.98 0.00 34.25 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 8.211629 AGGGAGTAGTATTTTTCGCATATCTTT 58.788 33.333 0.00 0.00 0.00 2.52
351 356 5.708736 TGCAGGGTAGAGATTTTATCCAA 57.291 39.130 0.00 0.00 0.00 3.53
352 357 5.912149 ATGCAGGGTAGAGATTTTATCCA 57.088 39.130 0.00 0.00 0.00 3.41
366 371 3.542969 AAGGGAAAAGTAATGCAGGGT 57.457 42.857 0.00 0.00 0.00 4.34
382 388 9.639601 GACAAACAATAAAATTCCTTCTAAGGG 57.360 33.333 8.87 0.00 46.47 3.95
636 655 1.002900 CACTTGATTTGCGGTTCGTGT 60.003 47.619 0.00 0.00 0.00 4.49
908 936 5.515797 TTCTTCGAGAAGACAAGAGAACA 57.484 39.130 14.41 0.00 46.13 3.18
1012 1042 3.134442 ACCAACACAGCCATCATGTTTTT 59.866 39.130 0.00 0.00 34.36 1.94
1134 1168 3.005155 TGATGACCTCTATCTGCATCACG 59.995 47.826 0.00 0.00 40.05 4.35
1336 1374 6.705825 GCTGAAACAAAATTACCTGACCATTT 59.294 34.615 0.00 0.00 0.00 2.32
1344 1382 4.021981 GCCTGAGCTGAAACAAAATTACCT 60.022 41.667 0.00 0.00 35.50 3.08
1380 1418 2.478894 CACTAACACGGTAAACTGCCTG 59.521 50.000 0.00 0.00 0.00 4.85
1546 1588 1.005215 CGGGTCCTATATCCCCTACGT 59.995 57.143 0.00 0.00 40.54 3.57
1739 1784 4.309933 TCGTCTCTTACACGTTGTCTCTA 58.690 43.478 0.00 0.00 38.45 2.43
1823 1869 5.238650 TCGAGAGGTGGAACAGAAAAATTTC 59.761 40.000 0.00 0.00 41.80 2.17
1824 1870 5.008712 GTCGAGAGGTGGAACAGAAAAATTT 59.991 40.000 0.00 0.00 41.80 1.82
2202 2303 2.475487 GTCGAGTGTTACACCTTCTTGC 59.525 50.000 12.28 0.00 34.49 4.01
2221 2322 3.760537 CAAGAACTAGCACTAGGACGTC 58.239 50.000 7.13 7.13 37.49 4.34
2292 2443 0.401738 CAAACTGGAGCCTCAAGGGA 59.598 55.000 0.22 0.00 37.23 4.20
2410 2661 2.791613 TACACGGTGCCTAGGCTGGA 62.792 60.000 33.07 18.02 42.51 3.86
2458 2709 4.959596 AAGAGATAACATTGCACTGCTG 57.040 40.909 3.61 0.00 0.00 4.41
2462 2713 7.445402 ACACAGTTAAAGAGATAACATTGCACT 59.555 33.333 0.00 0.00 38.07 4.40
2471 2722 6.020971 TCAGCGACACAGTTAAAGAGATAA 57.979 37.500 0.00 0.00 0.00 1.75
2472 2723 5.638596 TCAGCGACACAGTTAAAGAGATA 57.361 39.130 0.00 0.00 0.00 1.98
2524 3955 6.293407 CGTGTTGAAGTTGTCATTAGATGGTT 60.293 38.462 0.00 0.00 35.70 3.67
2529 3960 3.496884 GGCGTGTTGAAGTTGTCATTAGA 59.503 43.478 0.00 0.00 35.70 2.10
2536 3967 1.758319 CGTCGGCGTGTTGAAGTTGT 61.758 55.000 6.85 0.00 0.00 3.32
2542 3973 1.777030 AAAATGCGTCGGCGTGTTGA 61.777 50.000 12.58 0.00 44.10 3.18
2576 4007 6.642707 TTTTGTGTCCATTTCGGTCTAAAT 57.357 33.333 0.00 0.00 35.57 1.40
2637 4068 1.271707 GGGTCCCGGACAGATGAAAAA 60.272 52.381 19.43 0.00 33.68 1.94
2643 4076 0.546598 GAAATGGGTCCCGGACAGAT 59.453 55.000 19.43 7.26 33.68 2.90
2682 4116 3.475774 GCGTGCGTCGACGGAAAT 61.476 61.111 36.13 0.00 42.34 2.17
2696 4130 1.876714 GCGTGTCCGTATCATGCGT 60.877 57.895 0.00 0.00 37.91 5.24
2720 4154 1.203492 AGGAGAAGGACAAGGGTGGAT 60.203 52.381 0.00 0.00 0.00 3.41
2735 4169 4.779733 GAGGGGCGGGTCAGGAGA 62.780 72.222 0.00 0.00 0.00 3.71
2763 4197 0.034198 TGCGAACCTGATCAAACGGA 59.966 50.000 6.49 4.00 0.00 4.69
2805 4591 0.821711 CCAGAACGGGCAACTCCAAA 60.822 55.000 0.00 0.00 36.21 3.28
2955 4764 2.169769 AGGACTGACGTTTCAACCTCAA 59.830 45.455 0.00 0.00 35.10 3.02
3084 4893 0.034477 TTCGAATCCCCCTTTGCCTC 60.034 55.000 0.00 0.00 0.00 4.70
3085 4894 0.323451 GTTCGAATCCCCCTTTGCCT 60.323 55.000 0.00 0.00 0.00 4.75
3443 5870 7.645058 TGAAAACCTTTTGAGAGTCAGAATT 57.355 32.000 0.00 0.00 0.00 2.17
3554 5997 3.478082 GTATGCAATACGGCGGACTACG 61.478 54.545 13.24 0.00 40.43 3.51
3555 5998 2.056577 GTATGCAATACGGCGGACTAC 58.943 52.381 13.24 0.00 40.43 2.73
3556 5999 2.427232 GTATGCAATACGGCGGACTA 57.573 50.000 13.24 0.00 40.43 2.59
3557 6000 3.284197 GTATGCAATACGGCGGACT 57.716 52.632 13.24 0.00 40.43 3.85
4351 7423 8.882736 GGTTTTCAAGAAATATTTTGCCTATGG 58.117 33.333 1.43 0.00 0.00 2.74
4656 7778 3.056891 ACCAAGTGTGTGTTCTTGTTTGG 60.057 43.478 0.00 0.00 39.25 3.28
4818 7950 2.022195 ACACACCGCATACGTATCTCT 58.978 47.619 4.74 0.00 37.70 3.10
4846 7978 5.059161 GTCCCTAAGGTTAAAACGTCAGTT 58.941 41.667 0.00 0.00 43.50 3.16
4857 7990 5.210430 TGATCAATACGGTCCCTAAGGTTA 58.790 41.667 0.00 0.00 0.00 2.85
4940 8074 0.108186 CTCGTACTTGCTGGCCATGA 60.108 55.000 5.51 0.00 0.00 3.07
4993 8127 2.434134 CGTCAACACTAGGCGTCGC 61.434 63.158 9.22 9.22 0.00 5.19
5016 8466 0.611714 GGACTGCCGGGAAGTTAAGA 59.388 55.000 9.60 0.00 0.00 2.10
5019 8469 1.601419 CGAGGACTGCCGGGAAGTTA 61.601 60.000 9.60 0.00 39.96 2.24
5107 8563 0.037303 ACGTCCTGGACCGTAAGAGA 59.963 55.000 20.68 0.00 43.02 3.10
5160 8616 3.508840 GAAATCGCAGGGCCCGTG 61.509 66.667 18.44 18.01 0.00 4.94
5163 8619 2.830370 CAGGAAATCGCAGGGCCC 60.830 66.667 16.46 16.46 0.00 5.80
5169 8779 0.461870 CGTGGATCCAGGAAATCGCA 60.462 55.000 26.94 0.00 34.13 5.10
5453 9064 2.270874 ATCAACCATGCCCTCCCGTC 62.271 60.000 0.00 0.00 0.00 4.79
5527 9141 0.689623 GCAGGGACAGGGGATAGATG 59.310 60.000 0.00 0.00 0.00 2.90
5531 9145 0.548926 TGTTGCAGGGACAGGGGATA 60.549 55.000 0.00 0.00 0.00 2.59
5549 9165 5.732528 GCAGTGGATTGATTGTATTCTGCTG 60.733 44.000 0.00 0.00 41.31 4.41
5552 9168 5.823209 TGCAGTGGATTGATTGTATTCTG 57.177 39.130 0.00 0.00 0.00 3.02
5701 11468 7.993183 ACCAGGAATTGTAACATGAATACTAGG 59.007 37.037 0.00 0.26 0.00 3.02
5732 11499 5.600696 CCTTTTGTAAAGGTTCACTGCAAT 58.399 37.500 9.53 0.00 32.78 3.56
6990 13254 6.465439 AGAAAGAACCTCAAATTTTTCGGT 57.535 33.333 0.00 0.00 31.67 4.69
6995 13259 7.274447 TCATGCAAGAAAGAACCTCAAATTTT 58.726 30.769 0.00 0.00 0.00 1.82
7239 13508 2.427812 TCATGCACATTACAATGGCCAG 59.572 45.455 13.05 0.00 40.70 4.85
7579 13863 3.308832 CCATCTGGGTTGGGTAAGCTTTA 60.309 47.826 3.20 0.00 34.76 1.85
7859 14157 4.104086 CCATATATCCCTAACCAGAGGCA 58.896 47.826 0.00 0.00 35.00 4.75
8249 14585 2.805671 CAGTAGCAACCGATCAACAACA 59.194 45.455 0.00 0.00 0.00 3.33
8250 14586 2.412847 GCAGTAGCAACCGATCAACAAC 60.413 50.000 0.00 0.00 41.58 3.32
8251 14587 1.804151 GCAGTAGCAACCGATCAACAA 59.196 47.619 0.00 0.00 41.58 2.83
8387 14723 3.747854 TGCATCATTCAGCCAACAAAA 57.252 38.095 0.00 0.00 0.00 2.44
8439 14775 7.657761 AGAAAAACACTACAGTAAGTCAGATGG 59.342 37.037 0.00 0.00 0.00 3.51
8510 18096 0.249868 CCTGAACCGCTGACTGTCAA 60.250 55.000 12.16 0.00 0.00 3.18
8547 18133 2.213499 GTGATCATTGGGACGGATGAC 58.787 52.381 0.00 0.00 36.58 3.06
8569 18155 2.094182 CGAAAAGAAGAGGGACGATCCA 60.094 50.000 6.41 0.00 38.64 3.41
8624 18211 2.938451 CAATCAGCATCCACGCTTAAGA 59.062 45.455 6.67 0.00 41.38 2.10
8665 18252 2.899838 CGTGTGTGTGGGTGGGTG 60.900 66.667 0.00 0.00 0.00 4.61
8666 18253 3.084646 TCGTGTGTGTGGGTGGGT 61.085 61.111 0.00 0.00 0.00 4.51
8667 18254 2.280797 CTCGTGTGTGTGGGTGGG 60.281 66.667 0.00 0.00 0.00 4.61
8668 18255 2.972505 GCTCGTGTGTGTGGGTGG 60.973 66.667 0.00 0.00 0.00 4.61
8669 18256 3.337889 CGCTCGTGTGTGTGGGTG 61.338 66.667 0.00 0.00 0.00 4.61
8738 18435 1.649271 GGACATGAGGGGGCAAGGAT 61.649 60.000 0.00 0.00 0.00 3.24
8796 18493 2.490148 CCCTCTGTCGCCGATGCTA 61.490 63.158 0.00 0.00 34.43 3.49
8851 18549 1.289066 CCACATCTCGTCCACACGT 59.711 57.895 0.00 0.00 46.76 4.49
8960 18658 0.767375 CCCATCCCTTCCGATGACAT 59.233 55.000 0.17 0.00 41.92 3.06
8970 18668 3.728373 GCACCCGTCCCATCCCTT 61.728 66.667 0.00 0.00 0.00 3.95
9100 18800 1.669440 GCACACCCTTGTCGGAGTA 59.331 57.895 0.00 0.00 31.66 2.59


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

AutoCloner maintained by Alex Coulton.