Multiple sequence alignment - TraesCS2D01G164600

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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 TraesCS2D01G164600 chr2D 100.000 5432 0 0 1 5432 109042489 109047920 0.000000e+00 10032
1 TraesCS2D01G164600 chr2D 85.846 1300 120 33 869 2156 109000814 109002061 0.000000e+00 1323
2 TraesCS2D01G164600 chr2D 93.757 865 47 2 1 860 277469507 277468645 0.000000e+00 1291
3 TraesCS2D01G164600 chr2D 96.990 764 21 2 3874 4636 109002057 109002819 0.000000e+00 1282
4 TraesCS2D01G164600 chr2D 93.526 865 46 4 1 860 116017668 116018527 0.000000e+00 1279
5 TraesCS2D01G164600 chr2D 91.265 767 58 8 3874 4636 109120583 109121344 0.000000e+00 1037
6 TraesCS2D01G164600 chr2D 95.118 594 17 6 4637 5218 109068472 109069065 0.000000e+00 926
7 TraesCS2D01G164600 chr2D 88.105 765 86 5 3874 4636 109392237 109392998 0.000000e+00 904
8 TraesCS2D01G164600 chr2D 93.814 582 34 2 4637 5218 82531123 82530544 0.000000e+00 874
9 TraesCS2D01G164600 chr2D 93.471 582 33 5 4637 5218 418960138 418960714 0.000000e+00 859
10 TraesCS2D01G164600 chr2D 93.299 582 37 2 4637 5218 535496157 535495578 0.000000e+00 857
11 TraesCS2D01G164600 chr2D 90.222 225 21 1 1647 1870 109113268 109113492 5.320000e-75 292
12 TraesCS2D01G164600 chr2D 92.529 174 13 0 1983 2156 109120414 109120587 3.250000e-62 250
13 TraesCS2D01G164600 chr2D 77.513 378 65 15 1201 1573 109107347 109107709 5.510000e-50 209
14 TraesCS2D01G164600 chr5D 97.908 1721 31 5 2156 3873 398879792 398878074 0.000000e+00 2974
15 TraesCS2D01G164600 chr5D 97.677 1722 34 6 2156 3873 122160379 122162098 0.000000e+00 2953
16 TraesCS2D01G164600 chr5D 97.619 1722 32 9 2156 3873 466623853 466622137 0.000000e+00 2944
17 TraesCS2D01G164600 chr5D 97.562 1723 35 5 2156 3873 468471251 468469531 0.000000e+00 2942
18 TraesCS2D01G164600 chr5D 93.757 865 46 4 1 860 206532323 206533184 0.000000e+00 1291
19 TraesCS2D01G164600 chr5D 94.567 589 19 7 4642 5218 108784267 108784854 0.000000e+00 898
20 TraesCS2D01G164600 chr5D 93.471 582 36 2 4637 5218 67996270 67996849 0.000000e+00 863
21 TraesCS2D01G164600 chr5D 92.955 582 39 2 4637 5218 415096212 415095633 0.000000e+00 846
22 TraesCS2D01G164600 chr5D 94.694 245 10 2 5188 5432 20116055 20116296 1.430000e-100 377
23 TraesCS2D01G164600 chr1D 97.796 1724 33 5 2153 3873 339269853 339271574 0.000000e+00 2968
24 TraesCS2D01G164600 chr1D 97.560 1721 36 6 2156 3873 105936980 105935263 0.000000e+00 2940
25 TraesCS2D01G164600 chr1D 94.340 583 31 2 4636 5218 38199000 38198420 0.000000e+00 893
26 TraesCS2D01G164600 chr1D 93.950 595 22 7 4637 5218 70985080 70985673 0.000000e+00 887
27 TraesCS2D01G164600 chr1D 92.845 587 39 3 4633 5218 319760504 319761088 0.000000e+00 848
28 TraesCS2D01G164600 chr1D 99.543 219 1 0 5214 5432 120511387 120511605 3.050000e-107 399
29 TraesCS2D01G164600 chr1D 98.661 224 2 1 5209 5432 318232759 318232981 3.940000e-106 396
30 TraesCS2D01G164600 chr1D 96.218 238 7 2 5195 5432 436079746 436079511 6.600000e-104 388
31 TraesCS2D01G164600 chr3D 97.791 1720 33 4 2157 3873 9407226 9405509 0.000000e+00 2961
32 TraesCS2D01G164600 chr3D 94.340 583 31 2 4636 5218 402261525 402262105 0.000000e+00 893
33 TraesCS2D01G164600 chr3D 92.979 584 39 2 4635 5218 451111701 451112282 0.000000e+00 850
34 TraesCS2D01G164600 chr3D 99.535 215 1 0 5218 5432 68244702 68244488 5.100000e-105 392
35 TraesCS2D01G164600 chr3D 97.403 231 3 3 5203 5432 12598347 12598575 1.830000e-104 390
36 TraesCS2D01G164600 chr7D 97.623 1725 30 9 2153 3873 84764024 84765741 0.000000e+00 2948
37 TraesCS2D01G164600 chr7D 93.410 865 50 2 1 860 266714915 266714053 0.000000e+00 1275
38 TraesCS2D01G164600 chr7D 93.410 865 50 2 1 860 305423441 305424303 0.000000e+00 1275
39 TraesCS2D01G164600 chr7D 93.410 865 49 3 1 860 520665969 520665108 0.000000e+00 1275
40 TraesCS2D01G164600 chr7D 94.511 583 30 2 4636 5218 558514462 558513882 0.000000e+00 898
41 TraesCS2D01G164600 chr7D 93.092 579 38 2 4637 5215 62805178 62805754 0.000000e+00 846
42 TraesCS2D01G164600 chr7D 97.009 234 5 2 5200 5432 580399295 580399527 5.100000e-105 392
43 TraesCS2D01G164600 chr6D 97.564 1724 32 10 2153 3871 171008788 171010506 0.000000e+00 2942
44 TraesCS2D01G164600 chr6D 93.410 865 50 2 1 860 322211515 322212377 0.000000e+00 1275
45 TraesCS2D01G164600 chr6D 93.844 601 23 7 4631 5218 418075869 418076468 0.000000e+00 893
46 TraesCS2D01G164600 chr6D 94.108 594 22 8 4637 5218 151178577 151179169 0.000000e+00 891
47 TraesCS2D01G164600 chr6D 93.771 594 24 7 4637 5218 418084922 418085514 0.000000e+00 880
48 TraesCS2D01G164600 chr6D 93.603 594 25 8 4637 5218 151145890 151146482 0.000000e+00 874
49 TraesCS2D01G164600 chr6D 92.955 582 38 3 4637 5218 113421386 113421964 0.000000e+00 845
50 TraesCS2D01G164600 chr6D 92.605 595 30 8 4637 5218 93858912 93858319 0.000000e+00 843
51 TraesCS2D01G164600 chr6D 92.612 582 41 2 4637 5218 305852180 305852759 0.000000e+00 835
52 TraesCS2D01G164600 chr6D 92.612 582 41 2 4637 5218 326267663 326267084 0.000000e+00 835
53 TraesCS2D01G164600 chr6D 92.721 577 40 2 4642 5218 41718569 41719143 0.000000e+00 832
54 TraesCS2D01G164600 chr6D 91.581 582 47 2 4637 5218 383992866 383992287 0.000000e+00 802
55 TraesCS2D01G164600 chr6D 99.545 220 0 1 5214 5432 331896043 331896262 3.050000e-107 399
56 TraesCS2D01G164600 chr6D 99.541 218 1 0 5215 5432 45308859 45308642 1.100000e-106 398
57 TraesCS2D01G164600 chr6D 99.541 218 1 0 5215 5432 47474988 47474771 1.100000e-106 398
58 TraesCS2D01G164600 chr6D 99.541 218 1 0 5215 5432 101771709 101771492 1.100000e-106 398
59 TraesCS2D01G164600 chr6D 99.541 218 1 0 5215 5432 302423120 302422903 1.100000e-106 398
60 TraesCS2D01G164600 chr6D 99.541 218 1 0 5215 5432 332986047 332986264 1.100000e-106 398
61 TraesCS2D01G164600 chr6D 99.541 218 1 0 5215 5432 332998576 332998793 1.100000e-106 398
62 TraesCS2D01G164600 chr2B 97.513 764 17 2 3874 4636 158643792 158644554 0.000000e+00 1304
63 TraesCS2D01G164600 chr2B 85.073 1293 171 18 869 2156 158642521 158643796 0.000000e+00 1299
64 TraesCS2D01G164600 chr2B 95.538 762 32 2 3876 4636 158781510 158782270 0.000000e+00 1218
65 TraesCS2D01G164600 chr2B 86.937 888 80 18 1274 2156 158780656 158781512 0.000000e+00 965
66 TraesCS2D01G164600 chr2B 88.602 658 63 6 3894 4548 159007082 159007730 0.000000e+00 789
67 TraesCS2D01G164600 chr7A 93.526 865 49 3 1 860 557913054 557913916 0.000000e+00 1280
68 TraesCS2D01G164600 chr4D 93.410 865 49 4 1 860 415124216 415123355 0.000000e+00 1275
69 TraesCS2D01G164600 chr4D 93.643 582 35 2 4637 5218 25924230 25924809 0.000000e+00 869
70 TraesCS2D01G164600 chr4D 92.496 613 29 11 4619 5218 496915866 496915258 0.000000e+00 861
71 TraesCS2D01G164600 chr4D 93.109 595 27 7 4637 5218 44265104 44265697 0.000000e+00 859
72 TraesCS2D01G164600 chr4D 100.000 218 0 0 5215 5432 116656595 116656378 2.360000e-108 403
73 TraesCS2D01G164600 chr4D 98.661 224 1 2 5209 5432 19388070 19388291 3.940000e-106 396
74 TraesCS2D01G164600 chr2A 84.467 1294 150 27 869 2156 104970072 104971320 0.000000e+00 1229
75 TraesCS2D01G164600 chr2A 95.550 764 32 2 3874 4636 104971316 104972078 0.000000e+00 1221
76 TraesCS2D01G164600 chr2A 83.302 1066 153 17 869 1929 105032709 105033754 0.000000e+00 959
77 TraesCS2D01G164600 chr2A 91.063 414 31 5 4225 4636 105045241 105045650 6.150000e-154 555
78 TraesCS2D01G164600 chr2A 91.329 173 14 1 4051 4222 105043393 105043565 9.100000e-58 235
79 TraesCS2D01G164600 chr2A 92.308 91 7 0 3874 3964 105034303 105034393 4.420000e-26 130
80 TraesCS2D01G164600 chrUn 89.863 582 57 2 4637 5218 102343147 102342568 0.000000e+00 747
81 TraesCS2D01G164600 chrUn 90.758 541 49 1 4634 5174 114701810 114702349 0.000000e+00 721
82 TraesCS2D01G164600 chrUn 88.739 595 53 8 4637 5218 80384274 80383681 0.000000e+00 715
83 TraesCS2D01G164600 chrUn 90.706 538 49 1 4637 5174 114743539 114744075 0.000000e+00 715
84 TraesCS2D01G164600 chrUn 90.317 537 51 1 4637 5173 127173882 127174417 0.000000e+00 702
85 TraesCS2D01G164600 chrUn 88.235 595 39 8 4637 5218 180559897 180559321 0.000000e+00 682
86 TraesCS2D01G164600 chrUn 84.615 598 70 15 4637 5218 103210148 103210739 4.720000e-160 575
87 TraesCS2D01G164600 chrUn 86.322 541 58 6 4637 5177 105592704 105592180 4.720000e-160 575
88 TraesCS2D01G164600 chrUn 85.273 550 79 2 4636 5185 68953059 68952512 2.840000e-157 566
89 TraesCS2D01G164600 chrUn 81.697 601 85 18 4637 5218 137685442 137684848 1.370000e-130 477
90 TraesCS2D01G164600 chrUn 82.625 541 86 8 4637 5174 19940310 19939775 6.370000e-129 472
91 TraesCS2D01G164600 chrUn 99.541 218 1 0 5215 5432 112046068 112046285 1.100000e-106 398
92 TraesCS2D01G164600 chrUn 99.537 216 1 0 5217 5432 97152704 97152489 1.420000e-105 394
93 TraesCS2D01G164600 chrUn 99.537 216 1 0 5217 5432 97168495 97168280 1.420000e-105 394
94 TraesCS2D01G164600 chrUn 99.083 218 2 0 5215 5432 27331469 27331686 5.100000e-105 392
95 TraesCS2D01G164600 chrUn 99.083 218 2 0 5215 5432 29925026 29924809 5.100000e-105 392
96 TraesCS2D01G164600 chrUn 99.083 218 2 0 5215 5432 97244918 97245135 5.100000e-105 392
97 TraesCS2D01G164600 chrUn 99.083 218 2 0 5215 5432 100522351 100522134 5.100000e-105 392
98 TraesCS2D01G164600 chrUn 99.083 218 2 0 5215 5432 103399276 103399493 5.100000e-105 392
99 TraesCS2D01G164600 chrUn 99.083 218 2 0 5215 5432 312741979 312742196 5.100000e-105 392
100 TraesCS2D01G164600 chrUn 98.222 225 3 1 5209 5432 316270693 316270469 5.100000e-105 392


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 TraesCS2D01G164600 chr2D 109042489 109047920 5431 False 10032.0 10032 100.0000 1 5432 1 chr2D.!!$F1 5431
1 TraesCS2D01G164600 chr2D 109000814 109002819 2005 False 1302.5 1323 91.4180 869 4636 2 chr2D.!!$F8 3767
2 TraesCS2D01G164600 chr2D 277468645 277469507 862 True 1291.0 1291 93.7570 1 860 1 chr2D.!!$R2 859
3 TraesCS2D01G164600 chr2D 116017668 116018527 859 False 1279.0 1279 93.5260 1 860 1 chr2D.!!$F6 859
4 TraesCS2D01G164600 chr2D 109068472 109069065 593 False 926.0 926 95.1180 4637 5218 1 chr2D.!!$F2 581
5 TraesCS2D01G164600 chr2D 109392237 109392998 761 False 904.0 904 88.1050 3874 4636 1 chr2D.!!$F5 762
6 TraesCS2D01G164600 chr2D 82530544 82531123 579 True 874.0 874 93.8140 4637 5218 1 chr2D.!!$R1 581
7 TraesCS2D01G164600 chr2D 418960138 418960714 576 False 859.0 859 93.4710 4637 5218 1 chr2D.!!$F7 581
8 TraesCS2D01G164600 chr2D 535495578 535496157 579 True 857.0 857 93.2990 4637 5218 1 chr2D.!!$R3 581
9 TraesCS2D01G164600 chr2D 109120414 109121344 930 False 643.5 1037 91.8970 1983 4636 2 chr2D.!!$F9 2653
10 TraesCS2D01G164600 chr5D 398878074 398879792 1718 True 2974.0 2974 97.9080 2156 3873 1 chr5D.!!$R1 1717
11 TraesCS2D01G164600 chr5D 122160379 122162098 1719 False 2953.0 2953 97.6770 2156 3873 1 chr5D.!!$F4 1717
12 TraesCS2D01G164600 chr5D 466622137 466623853 1716 True 2944.0 2944 97.6190 2156 3873 1 chr5D.!!$R3 1717
13 TraesCS2D01G164600 chr5D 468469531 468471251 1720 True 2942.0 2942 97.5620 2156 3873 1 chr5D.!!$R4 1717
14 TraesCS2D01G164600 chr5D 206532323 206533184 861 False 1291.0 1291 93.7570 1 860 1 chr5D.!!$F5 859
15 TraesCS2D01G164600 chr5D 108784267 108784854 587 False 898.0 898 94.5670 4642 5218 1 chr5D.!!$F3 576
16 TraesCS2D01G164600 chr5D 67996270 67996849 579 False 863.0 863 93.4710 4637 5218 1 chr5D.!!$F2 581
17 TraesCS2D01G164600 chr5D 415095633 415096212 579 True 846.0 846 92.9550 4637 5218 1 chr5D.!!$R2 581
18 TraesCS2D01G164600 chr1D 339269853 339271574 1721 False 2968.0 2968 97.7960 2153 3873 1 chr1D.!!$F5 1720
19 TraesCS2D01G164600 chr1D 105935263 105936980 1717 True 2940.0 2940 97.5600 2156 3873 1 chr1D.!!$R2 1717
20 TraesCS2D01G164600 chr1D 38198420 38199000 580 True 893.0 893 94.3400 4636 5218 1 chr1D.!!$R1 582
21 TraesCS2D01G164600 chr1D 70985080 70985673 593 False 887.0 887 93.9500 4637 5218 1 chr1D.!!$F1 581
22 TraesCS2D01G164600 chr1D 319760504 319761088 584 False 848.0 848 92.8450 4633 5218 1 chr1D.!!$F4 585
23 TraesCS2D01G164600 chr3D 9405509 9407226 1717 True 2961.0 2961 97.7910 2157 3873 1 chr3D.!!$R1 1716
24 TraesCS2D01G164600 chr3D 402261525 402262105 580 False 893.0 893 94.3400 4636 5218 1 chr3D.!!$F2 582
25 TraesCS2D01G164600 chr3D 451111701 451112282 581 False 850.0 850 92.9790 4635 5218 1 chr3D.!!$F3 583
26 TraesCS2D01G164600 chr7D 84764024 84765741 1717 False 2948.0 2948 97.6230 2153 3873 1 chr7D.!!$F2 1720
27 TraesCS2D01G164600 chr7D 266714053 266714915 862 True 1275.0 1275 93.4100 1 860 1 chr7D.!!$R1 859
28 TraesCS2D01G164600 chr7D 305423441 305424303 862 False 1275.0 1275 93.4100 1 860 1 chr7D.!!$F3 859
29 TraesCS2D01G164600 chr7D 520665108 520665969 861 True 1275.0 1275 93.4100 1 860 1 chr7D.!!$R2 859
30 TraesCS2D01G164600 chr7D 558513882 558514462 580 True 898.0 898 94.5110 4636 5218 1 chr7D.!!$R3 582
31 TraesCS2D01G164600 chr7D 62805178 62805754 576 False 846.0 846 93.0920 4637 5215 1 chr7D.!!$F1 578
32 TraesCS2D01G164600 chr6D 171008788 171010506 1718 False 2942.0 2942 97.5640 2153 3871 1 chr6D.!!$F5 1718
33 TraesCS2D01G164600 chr6D 322211515 322212377 862 False 1275.0 1275 93.4100 1 860 1 chr6D.!!$F7 859
34 TraesCS2D01G164600 chr6D 418075869 418076468 599 False 893.0 893 93.8440 4631 5218 1 chr6D.!!$F11 587
35 TraesCS2D01G164600 chr6D 151178577 151179169 592 False 891.0 891 94.1080 4637 5218 1 chr6D.!!$F4 581
36 TraesCS2D01G164600 chr6D 418084922 418085514 592 False 880.0 880 93.7710 4637 5218 1 chr6D.!!$F12 581
37 TraesCS2D01G164600 chr6D 151145890 151146482 592 False 874.0 874 93.6030 4637 5218 1 chr6D.!!$F3 581
38 TraesCS2D01G164600 chr6D 113421386 113421964 578 False 845.0 845 92.9550 4637 5218 1 chr6D.!!$F2 581
39 TraesCS2D01G164600 chr6D 93858319 93858912 593 True 843.0 843 92.6050 4637 5218 1 chr6D.!!$R3 581
40 TraesCS2D01G164600 chr6D 305852180 305852759 579 False 835.0 835 92.6120 4637 5218 1 chr6D.!!$F6 581
41 TraesCS2D01G164600 chr6D 326267084 326267663 579 True 835.0 835 92.6120 4637 5218 1 chr6D.!!$R6 581
42 TraesCS2D01G164600 chr6D 41718569 41719143 574 False 832.0 832 92.7210 4642 5218 1 chr6D.!!$F1 576
43 TraesCS2D01G164600 chr6D 383992287 383992866 579 True 802.0 802 91.5810 4637 5218 1 chr6D.!!$R7 581
44 TraesCS2D01G164600 chr2B 158642521 158644554 2033 False 1301.5 1304 91.2930 869 4636 2 chr2B.!!$F2 3767
45 TraesCS2D01G164600 chr2B 158780656 158782270 1614 False 1091.5 1218 91.2375 1274 4636 2 chr2B.!!$F3 3362
46 TraesCS2D01G164600 chr2B 159007082 159007730 648 False 789.0 789 88.6020 3894 4548 1 chr2B.!!$F1 654
47 TraesCS2D01G164600 chr7A 557913054 557913916 862 False 1280.0 1280 93.5260 1 860 1 chr7A.!!$F1 859
48 TraesCS2D01G164600 chr4D 415123355 415124216 861 True 1275.0 1275 93.4100 1 860 1 chr4D.!!$R2 859
49 TraesCS2D01G164600 chr4D 25924230 25924809 579 False 869.0 869 93.6430 4637 5218 1 chr4D.!!$F2 581
50 TraesCS2D01G164600 chr4D 496915258 496915866 608 True 861.0 861 92.4960 4619 5218 1 chr4D.!!$R3 599
51 TraesCS2D01G164600 chr4D 44265104 44265697 593 False 859.0 859 93.1090 4637 5218 1 chr4D.!!$F3 581
52 TraesCS2D01G164600 chr2A 104970072 104972078 2006 False 1225.0 1229 90.0085 869 4636 2 chr2A.!!$F1 3767
53 TraesCS2D01G164600 chr2A 105032709 105034393 1684 False 544.5 959 87.8050 869 3964 2 chr2A.!!$F2 3095
54 TraesCS2D01G164600 chr2A 105043393 105045650 2257 False 395.0 555 91.1960 4051 4636 2 chr2A.!!$F3 585
55 TraesCS2D01G164600 chrUn 102342568 102343147 579 True 747.0 747 89.8630 4637 5218 1 chrUn.!!$R8 581
56 TraesCS2D01G164600 chrUn 114701810 114702349 539 False 721.0 721 90.7580 4634 5174 1 chrUn.!!$F6 540
57 TraesCS2D01G164600 chrUn 80383681 80384274 593 True 715.0 715 88.7390 4637 5218 1 chrUn.!!$R4 581
58 TraesCS2D01G164600 chrUn 114743539 114744075 536 False 715.0 715 90.7060 4637 5174 1 chrUn.!!$F7 537
59 TraesCS2D01G164600 chrUn 127173882 127174417 535 False 702.0 702 90.3170 4637 5173 1 chrUn.!!$F8 536
60 TraesCS2D01G164600 chrUn 180559321 180559897 576 True 682.0 682 88.2350 4637 5218 1 chrUn.!!$R11 581
61 TraesCS2D01G164600 chrUn 103210148 103210739 591 False 575.0 575 84.6150 4637 5218 1 chrUn.!!$F3 581
62 TraesCS2D01G164600 chrUn 105592180 105592704 524 True 575.0 575 86.3220 4637 5177 1 chrUn.!!$R9 540
63 TraesCS2D01G164600 chrUn 68952512 68953059 547 True 566.0 566 85.2730 4636 5185 1 chrUn.!!$R3 549
64 TraesCS2D01G164600 chrUn 137684848 137685442 594 True 477.0 477 81.6970 4637 5218 1 chrUn.!!$R10 581
65 TraesCS2D01G164600 chrUn 19939775 19940310 535 True 472.0 472 82.6250 4637 5174 1 chrUn.!!$R1 537

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
61 62 0.034756 ATACAGTTGTCGTGGCTGCA 59.965 50.000 0.5 0.0 33.87 4.41 F
128 129 0.257039 GGATCCCTGCTGTGGTGAAT 59.743 55.000 0.0 0.0 0.00 2.57 F
1192 1208 0.901580 AGCCTGCTTTGGATGTTGGG 60.902 55.000 0.0 0.0 0.00 4.12 F
2142 2495 1.065564 GCTGAGGATGGAGCTTCAGTT 60.066 52.381 0.0 0.0 42.18 3.16 F
3596 3961 1.216444 GTCGTGCTGCTGGATCTCA 59.784 57.895 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1321 0.378257 GGCACCATGCGTGAGTATTG 59.622 55.0 7.72 0.0 46.21 1.90 R
1488 1514 1.552578 TGGCTTTACAGAGGCGACTA 58.447 50.0 0.00 0.0 44.43 2.59 R
3089 3443 0.824595 TTCCGGAACTCCTCGTGACA 60.825 55.0 14.35 0.0 0.00 3.58 R
3713 4079 0.393944 TGATGGAGTCGTACTCGCCT 60.394 55.0 8.33 0.0 45.96 5.52 R
5405 7487 0.036164 TGTCCATGGTCAGGAAACCG 59.964 55.0 12.58 0.0 42.62 4.44 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
44 45 6.484364 TCTGCTCAGTTGATGATGGTAATA 57.516 37.500 0.00 0.00 37.28 0.98
61 62 0.034756 ATACAGTTGTCGTGGCTGCA 59.965 50.000 0.50 0.00 33.87 4.41
128 129 0.257039 GGATCCCTGCTGTGGTGAAT 59.743 55.000 0.00 0.00 0.00 2.57
182 183 1.179174 ACACAGCGCAGTAGGAGTGA 61.179 55.000 11.47 0.00 0.00 3.41
196 197 2.439507 AGGAGTGAGACAAACCACACAT 59.560 45.455 0.00 0.00 35.84 3.21
241 242 8.644216 TCTGTAACAGAAGTAATTGTGTAAGGA 58.356 33.333 6.10 1.14 37.57 3.36
252 253 8.962679 AGTAATTGTGTAAGGACTTGTTTGAAA 58.037 29.630 0.00 0.00 0.00 2.69
312 313 4.348168 AGGAATAGGATAGGAATGCACGTT 59.652 41.667 0.00 0.00 0.00 3.99
395 396 3.765381 TGGAAGATCACAGGATGCAAAA 58.235 40.909 0.00 0.00 42.53 2.44
438 444 9.275398 AGTCACAAGAAAATGTACGGTTATAAA 57.725 29.630 0.00 0.00 30.84 1.40
523 529 7.501225 ACAAGTGGATATTAAAATTCCTACGGG 59.499 37.037 0.00 0.00 0.00 5.28
607 613 6.311935 CCTTTGAACCAAATGCATGAATAGTG 59.688 38.462 0.00 0.00 32.70 2.74
625 631 8.387813 TGAATAGTGGTACCATAGGAAACTTTT 58.612 33.333 19.72 9.57 43.67 2.27
756 762 1.072266 ACTTTGGACCCATGCCACTA 58.928 50.000 0.00 0.00 34.56 2.74
831 837 6.566564 CGCAGAGATAAATAATGATGGCGTTT 60.567 38.462 0.00 0.00 35.41 3.60
861 867 5.449107 TCCATCACGGATAGCTAAGTTAC 57.551 43.478 0.00 0.00 39.64 2.50
862 868 4.891168 TCCATCACGGATAGCTAAGTTACA 59.109 41.667 0.00 0.00 39.64 2.41
863 869 5.009710 TCCATCACGGATAGCTAAGTTACAG 59.990 44.000 0.00 0.00 39.64 2.74
864 870 4.303086 TCACGGATAGCTAAGTTACAGC 57.697 45.455 0.00 0.00 39.41 4.40
865 871 3.043586 CACGGATAGCTAAGTTACAGCG 58.956 50.000 0.00 0.00 43.97 5.18
866 872 2.947652 ACGGATAGCTAAGTTACAGCGA 59.052 45.455 0.00 0.00 43.97 4.93
867 873 3.379372 ACGGATAGCTAAGTTACAGCGAA 59.621 43.478 0.00 0.00 43.97 4.70
873 879 7.437267 GGATAGCTAAGTTACAGCGAAATGTTA 59.563 37.037 0.00 0.00 43.97 2.41
944 951 3.935203 CTCATCCTGTTACAGCGAAATGT 59.065 43.478 6.88 0.00 37.19 2.71
950 957 4.320667 TGTTACAGCGAAATGTTGATCG 57.679 40.909 0.00 0.00 41.81 3.69
959 966 4.707563 CGAAATGTTGATCGTTTGTGCTA 58.292 39.130 0.00 0.00 35.66 3.49
967 974 2.677003 CGTTTGTGCTAGCCACCCG 61.677 63.158 13.29 10.06 44.01 5.28
985 992 1.090052 CGGCTCCTTCGGTTCATTCC 61.090 60.000 0.00 0.00 0.00 3.01
1018 1025 2.840038 TGGATGGCTATCACTCAACAGT 59.160 45.455 12.54 0.00 34.90 3.55
1019 1026 3.264193 TGGATGGCTATCACTCAACAGTT 59.736 43.478 12.54 0.00 34.90 3.16
1048 1055 3.084786 GCCTTACCATTTGAGCTCAACT 58.915 45.455 28.46 20.65 35.28 3.16
1058 1065 3.117888 TTTGAGCTCAACTGGAAGGAACT 60.118 43.478 28.46 0.00 39.30 3.01
1083 1090 3.005155 AGAAAGCAAAACAGACATCAGCC 59.995 43.478 0.00 0.00 0.00 4.85
1084 1091 1.985473 AGCAAAACAGACATCAGCCA 58.015 45.000 0.00 0.00 0.00 4.75
1114 1121 6.667007 ACCTTTGCAAAAAGTTCTTCATTG 57.333 33.333 13.84 0.00 0.00 2.82
1115 1122 5.585844 ACCTTTGCAAAAAGTTCTTCATTGG 59.414 36.000 13.84 8.36 0.00 3.16
1156 1168 6.753744 GGAATTAAGCAAACCATCTCATTCAC 59.246 38.462 0.00 0.00 0.00 3.18
1161 1173 3.063997 GCAAACCATCTCATTCACTACCG 59.936 47.826 0.00 0.00 0.00 4.02
1170 1182 7.169982 CCATCTCATTCACTACCGAAATTAGAC 59.830 40.741 0.00 0.00 0.00 2.59
1172 1184 8.515695 TCTCATTCACTACCGAAATTAGACTA 57.484 34.615 0.00 0.00 0.00 2.59
1173 1185 8.963725 TCTCATTCACTACCGAAATTAGACTAA 58.036 33.333 0.00 0.00 0.00 2.24
1188 1203 2.307098 AGACTAAGCCTGCTTTGGATGT 59.693 45.455 10.01 2.46 37.47 3.06
1192 1208 0.901580 AGCCTGCTTTGGATGTTGGG 60.902 55.000 0.00 0.00 0.00 4.12
1199 1215 3.390639 TGCTTTGGATGTTGGGAATTTGT 59.609 39.130 0.00 0.00 0.00 2.83
1203 1219 5.720371 TTGGATGTTGGGAATTTGTAGTG 57.280 39.130 0.00 0.00 0.00 2.74
1271 1288 4.620589 TGTGGTCGTAATGGGAGTAAAA 57.379 40.909 0.00 0.00 0.00 1.52
1272 1289 4.970711 TGTGGTCGTAATGGGAGTAAAAA 58.029 39.130 0.00 0.00 0.00 1.94
1335 1357 1.565156 GCCACGCATTCTGAACGTCA 61.565 55.000 3.44 0.00 38.09 4.35
1345 1369 5.554636 CATTCTGAACGTCAAGCTGAATAC 58.445 41.667 0.00 0.00 31.71 1.89
1350 1374 1.336887 ACGTCAAGCTGAATACGCTGT 60.337 47.619 9.48 0.00 38.87 4.40
1395 1419 7.934855 AATATATGCCCTCTGTGATGATTTC 57.065 36.000 0.00 0.00 0.00 2.17
1404 1428 6.320171 CCTCTGTGATGATTTCAATTGTGAC 58.680 40.000 5.13 0.00 35.70 3.67
1425 1449 5.815740 TGACTTTGTCACTGAACCTAAACTC 59.184 40.000 0.00 0.00 37.67 3.01
1476 1502 4.562082 TCTGAATTGCTGCCTTCATTTTG 58.438 39.130 13.08 4.70 31.39 2.44
1488 1514 5.163322 TGCCTTCATTTTGTTGTCCAGATTT 60.163 36.000 0.00 0.00 0.00 2.17
1492 1518 7.809806 CCTTCATTTTGTTGTCCAGATTTAGTC 59.190 37.037 0.00 0.00 0.00 2.59
1522 1549 1.219124 GCCATCTCGTCTTCTGCCA 59.781 57.895 0.00 0.00 0.00 4.92
1524 1551 1.945819 GCCATCTCGTCTTCTGCCAAA 60.946 52.381 0.00 0.00 0.00 3.28
1581 1608 8.373981 CCCTGATGAGATACTATCAAAACTCAT 58.626 37.037 0.00 0.00 44.24 2.90
1694 1721 7.763985 TCTTAATCTGCTTAATCGATGTTGACA 59.236 33.333 0.00 0.00 0.00 3.58
1709 1736 3.243873 TGTTGACAGTGACTCCTTGCTAG 60.244 47.826 0.00 0.00 0.00 3.42
1787 1814 2.944129 TCCTTCCCTTTCAAAGTGGTG 58.056 47.619 0.00 0.00 0.00 4.17
1824 1851 4.890158 CCTTTAAAGGTCCCAAATTGCT 57.110 40.909 23.89 0.00 41.41 3.91
1879 1906 5.586877 TCAGGTACACTATCCACCTAGTTT 58.413 41.667 0.00 0.00 40.77 2.66
1888 1915 6.814146 CACTATCCACCTAGTTTTCTGTTCTC 59.186 42.308 0.00 0.00 29.41 2.87
1900 1927 7.945134 AGTTTTCTGTTCTCTGCAAATATGTT 58.055 30.769 0.00 0.00 0.00 2.71
1904 1931 6.182627 TCTGTTCTCTGCAAATATGTTCCAT 58.817 36.000 0.00 0.00 0.00 3.41
1910 1937 6.012337 TCTGCAAATATGTTCCATTCCCTA 57.988 37.500 0.00 0.00 0.00 3.53
1930 1957 8.162848 TCCCTATACTATACTAACGTACCCAT 57.837 38.462 0.00 0.00 0.00 4.00
1942 2295 1.757118 CGTACCCATCTCACCTGATGT 59.243 52.381 0.00 0.00 41.47 3.06
1979 2332 7.700656 CCCTTCATTTTCACAATATTACCGTTC 59.299 37.037 0.00 0.00 0.00 3.95
1992 2345 2.080286 ACCGTTCAAGATCAGGTTCG 57.920 50.000 0.00 0.00 0.00 3.95
2014 2367 6.570692 TCGTGGAGATTAGATGGTTTAAGTC 58.429 40.000 0.00 0.00 0.00 3.01
2036 2389 2.306805 TGAAAGTGATCCATGGAGCACT 59.693 45.455 45.04 45.04 46.93 4.40
2040 2393 2.012673 GTGATCCATGGAGCACTGAAC 58.987 52.381 42.14 24.48 46.93 3.18
2047 2400 1.419381 TGGAGCACTGAACACACCTA 58.581 50.000 0.00 0.00 0.00 3.08
2093 2446 3.537580 TCAAGTTCAGCGGTTTACAGTT 58.462 40.909 0.00 0.00 0.00 3.16
2097 2450 2.870411 GTTCAGCGGTTTACAGTTCACT 59.130 45.455 0.00 0.00 0.00 3.41
2123 2476 4.395583 GCTCGGTGTGCTGCTTGC 62.396 66.667 0.00 0.00 43.25 4.01
2142 2495 1.065564 GCTGAGGATGGAGCTTCAGTT 60.066 52.381 0.00 0.00 42.18 3.16
2481 2835 4.216257 TGCTAGAGCTTTTCCAATGTCAAC 59.784 41.667 2.72 0.00 42.66 3.18
2690 3044 1.299541 CCCACTCGGTAATGCATCAC 58.700 55.000 0.00 0.00 0.00 3.06
3506 3870 4.741239 GTGCCTCCCTCTCCCCCA 62.741 72.222 0.00 0.00 0.00 4.96
3554 3919 2.187946 CGAAGCCCTGCCGAGAAT 59.812 61.111 0.00 0.00 0.00 2.40
3557 3922 1.977293 GAAGCCCTGCCGAGAATCCT 61.977 60.000 0.00 0.00 0.00 3.24
3596 3961 1.216444 GTCGTGCTGCTGGATCTCA 59.784 57.895 0.00 0.00 0.00 3.27
3713 4079 3.278574 GGTCATCGGTGATTTGGATCAA 58.721 45.455 0.00 0.00 43.58 2.57
3801 4167 1.281419 TGCATTCCTTTCCCCTCGTA 58.719 50.000 0.00 0.00 0.00 3.43
3848 4214 5.242838 TCTTGGTGATGCGTAGGAAATTTTT 59.757 36.000 0.00 0.00 0.00 1.94
3886 4252 1.004277 CCCAACAAAGGCCTACTGCTA 59.996 52.381 5.16 0.00 40.92 3.49
4107 4474 1.023513 CCTACTCGTTCCTCGTCGGT 61.024 60.000 0.00 0.00 40.80 4.69
4122 4489 1.378514 CGGTGGGATTGGAGGGTTG 60.379 63.158 0.00 0.00 0.00 3.77
4336 6377 2.076100 CGACTGAGCTATTTGTTGGCA 58.924 47.619 0.00 0.00 33.47 4.92
4442 6483 1.762370 TGTGGACTGAGCTTCTTGACA 59.238 47.619 0.00 0.00 0.00 3.58
4504 6550 7.342769 GGGGGTAAAATTTAACAGATGTAGG 57.657 40.000 3.01 0.00 0.00 3.18
4522 6568 7.613801 AGATGTAGGATTTCATAGTAGCTCGAT 59.386 37.037 0.00 0.00 0.00 3.59
4523 6569 6.914259 TGTAGGATTTCATAGTAGCTCGATG 58.086 40.000 0.00 0.00 0.00 3.84
5056 7107 2.737359 GCGCTACACAGTAGCCATGTTA 60.737 50.000 19.96 0.00 37.26 2.41
5224 7306 7.776618 TCATTAAGGAGACAAGACTGTTAGA 57.223 36.000 0.00 0.00 35.30 2.10
5225 7307 8.190326 TCATTAAGGAGACAAGACTGTTAGAA 57.810 34.615 0.00 0.00 35.30 2.10
5226 7308 8.647796 TCATTAAGGAGACAAGACTGTTAGAAA 58.352 33.333 0.00 0.00 35.30 2.52
5227 7309 9.442047 CATTAAGGAGACAAGACTGTTAGAAAT 57.558 33.333 0.00 0.00 35.30 2.17
5231 7313 7.044798 AGGAGACAAGACTGTTAGAAATATGC 58.955 38.462 0.00 0.00 35.30 3.14
5232 7314 6.258947 GGAGACAAGACTGTTAGAAATATGCC 59.741 42.308 0.00 0.00 35.30 4.40
5233 7315 6.116126 AGACAAGACTGTTAGAAATATGCCC 58.884 40.000 0.00 0.00 35.30 5.36
5234 7316 6.067217 ACAAGACTGTTAGAAATATGCCCT 57.933 37.500 0.00 0.00 28.57 5.19
5235 7317 7.125811 AGACAAGACTGTTAGAAATATGCCCTA 59.874 37.037 0.00 0.00 35.30 3.53
5236 7318 7.275920 ACAAGACTGTTAGAAATATGCCCTAG 58.724 38.462 0.00 0.00 28.57 3.02
5237 7319 7.125811 ACAAGACTGTTAGAAATATGCCCTAGA 59.874 37.037 0.00 0.00 28.57 2.43
5238 7320 7.296628 AGACTGTTAGAAATATGCCCTAGAG 57.703 40.000 0.00 0.00 0.00 2.43
5239 7321 6.268847 AGACTGTTAGAAATATGCCCTAGAGG 59.731 42.308 0.00 0.00 39.47 3.69
5255 7337 7.839680 CCCTAGAGGCAATAATAAATTGGTT 57.160 36.000 0.00 0.00 0.00 3.67
5256 7338 8.934023 CCCTAGAGGCAATAATAAATTGGTTA 57.066 34.615 0.00 0.00 0.00 2.85
5257 7339 9.533831 CCCTAGAGGCAATAATAAATTGGTTAT 57.466 33.333 0.00 0.00 33.58 1.89
5318 7400 9.812347 ATCCATGCTAAAATTGTATTGATAGGA 57.188 29.630 0.00 0.00 0.00 2.94
5319 7401 9.639563 TCCATGCTAAAATTGTATTGATAGGAA 57.360 29.630 0.00 0.00 0.00 3.36
5332 7414 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
5333 7415 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
5334 7416 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
5335 7417 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
5336 7418 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
5337 7419 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
5338 7420 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
5339 7421 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
5340 7422 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
5341 7423 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
5357 7439 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
5358 7440 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
5359 7441 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
5360 7442 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
5366 7448 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
5367 7449 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
5368 7450 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
5369 7451 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
5370 7452 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
5371 7453 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
5372 7454 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
5373 7455 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
5374 7456 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
5375 7457 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
5376 7458 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
5377 7459 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
5378 7460 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
5379 7461 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
5380 7462 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
5381 7463 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
5382 7464 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
5383 7465 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
5384 7466 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
5385 7467 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
5386 7468 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
5387 7469 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
5388 7470 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
5389 7471 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
5390 7472 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
5391 7473 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
5392 7474 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
5393 7475 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
5394 7476 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
5395 7477 5.078411 AGTTGACTAGCTCGTTGATCAAT 57.922 39.130 12.12 0.00 0.00 2.57
5396 7478 6.208988 AGTTGACTAGCTCGTTGATCAATA 57.791 37.500 12.12 2.38 0.00 1.90
5397 7479 6.269315 AGTTGACTAGCTCGTTGATCAATAG 58.731 40.000 12.12 13.07 0.00 1.73
5398 7480 6.095580 AGTTGACTAGCTCGTTGATCAATAGA 59.904 38.462 19.51 16.55 0.00 1.98
5399 7481 6.641169 TGACTAGCTCGTTGATCAATAGAT 57.359 37.500 19.51 16.66 37.13 1.98
5400 7482 6.442112 TGACTAGCTCGTTGATCAATAGATG 58.558 40.000 19.51 12.48 33.72 2.90
5401 7483 5.777802 ACTAGCTCGTTGATCAATAGATGG 58.222 41.667 19.51 17.62 33.72 3.51
5402 7484 4.679373 AGCTCGTTGATCAATAGATGGT 57.321 40.909 19.51 14.02 33.72 3.55
5403 7485 5.028549 AGCTCGTTGATCAATAGATGGTT 57.971 39.130 19.51 6.05 33.72 3.67
5404 7486 6.161855 AGCTCGTTGATCAATAGATGGTTA 57.838 37.500 19.51 0.00 33.72 2.85
5405 7487 5.986135 AGCTCGTTGATCAATAGATGGTTAC 59.014 40.000 19.51 1.79 33.72 2.50
5406 7488 5.107837 GCTCGTTGATCAATAGATGGTTACG 60.108 44.000 19.51 12.22 33.72 3.18
5407 7489 5.286438 TCGTTGATCAATAGATGGTTACGG 58.714 41.667 12.12 0.00 33.72 4.02
5408 7490 5.047847 CGTTGATCAATAGATGGTTACGGT 58.952 41.667 12.12 0.00 33.72 4.83
5409 7491 5.522460 CGTTGATCAATAGATGGTTACGGTT 59.478 40.000 12.12 0.00 33.72 4.44
5410 7492 6.036735 CGTTGATCAATAGATGGTTACGGTTT 59.963 38.462 12.12 0.00 33.72 3.27
5411 7493 7.407337 GTTGATCAATAGATGGTTACGGTTTC 58.593 38.462 12.12 0.00 33.72 2.78
5412 7494 6.053005 TGATCAATAGATGGTTACGGTTTCC 58.947 40.000 0.00 0.00 33.72 3.13
5413 7495 5.687166 TCAATAGATGGTTACGGTTTCCT 57.313 39.130 0.00 0.00 0.00 3.36
5414 7496 5.424757 TCAATAGATGGTTACGGTTTCCTG 58.575 41.667 0.00 0.00 0.00 3.86
5415 7497 5.188163 TCAATAGATGGTTACGGTTTCCTGA 59.812 40.000 0.00 0.00 0.00 3.86
5416 7498 3.329929 AGATGGTTACGGTTTCCTGAC 57.670 47.619 0.00 0.00 0.00 3.51
5417 7499 2.027469 AGATGGTTACGGTTTCCTGACC 60.027 50.000 0.00 0.00 36.31 4.02
5418 7500 1.129917 TGGTTACGGTTTCCTGACCA 58.870 50.000 0.00 0.00 39.78 4.02
5419 7501 1.700739 TGGTTACGGTTTCCTGACCAT 59.299 47.619 0.00 0.00 39.78 3.55
5420 7502 2.081462 GGTTACGGTTTCCTGACCATG 58.919 52.381 0.00 0.00 39.78 3.66
5421 7503 2.081462 GTTACGGTTTCCTGACCATGG 58.919 52.381 11.19 11.19 39.78 3.66
5422 7504 1.646912 TACGGTTTCCTGACCATGGA 58.353 50.000 21.47 0.00 39.78 3.41
5423 7505 0.036306 ACGGTTTCCTGACCATGGAC 59.964 55.000 21.47 13.94 39.78 4.02
5424 7506 0.036164 CGGTTTCCTGACCATGGACA 59.964 55.000 21.47 18.47 39.78 4.02
5425 7507 1.340017 CGGTTTCCTGACCATGGACAT 60.340 52.381 21.47 0.00 39.78 3.06
5426 7508 2.807676 GGTTTCCTGACCATGGACATT 58.192 47.619 21.47 0.00 39.57 2.71
5427 7509 2.493278 GGTTTCCTGACCATGGACATTG 59.507 50.000 21.47 12.72 39.57 2.82
5428 7510 2.493278 GTTTCCTGACCATGGACATTGG 59.507 50.000 21.47 16.85 32.65 3.16
5429 7511 1.667595 TCCTGACCATGGACATTGGA 58.332 50.000 21.47 18.93 0.00 3.53
5430 7512 2.207988 TCCTGACCATGGACATTGGAT 58.792 47.619 21.47 0.00 0.00 3.41
5431 7513 2.092267 TCCTGACCATGGACATTGGATG 60.092 50.000 21.47 5.31 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.889105 CTGCAGCCACGACAACTGT 60.889 57.895 0.00 0.00 33.87 3.55
128 129 0.250234 CTGCTCCAATGACGGAAGGA 59.750 55.000 0.00 0.00 33.65 3.36
156 157 1.754380 TACTGCGCTGTGTTCCACCT 61.754 55.000 27.70 2.00 32.73 4.00
174 175 3.035363 TGTGTGGTTTGTCTCACTCCTA 58.965 45.455 0.00 0.00 35.15 2.94
196 197 8.564574 GTTACAGATATGTGTCAAAGAAAACCA 58.435 33.333 9.06 0.00 31.46 3.67
241 242 8.912988 TGTTAGAATCCTCAATTTCAAACAAGT 58.087 29.630 0.00 0.00 0.00 3.16
252 253 4.891756 CCCTGCATTGTTAGAATCCTCAAT 59.108 41.667 0.00 0.00 0.00 2.57
312 313 9.364989 CCTGTGTTTTTAAATTCTCTGTTTTGA 57.635 29.630 0.00 0.00 0.00 2.69
395 396 9.288576 TCTTGTGACTTAATCTCATCATGTTTT 57.711 29.630 0.00 0.00 31.07 2.43
398 399 8.853077 TTTCTTGTGACTTAATCTCATCATGT 57.147 30.769 0.00 0.00 31.07 3.21
530 536 5.768164 TGTTCCTTTAGTGCCTCCTTAAAAG 59.232 40.000 0.00 0.00 0.00 2.27
531 537 5.697067 TGTTCCTTTAGTGCCTCCTTAAAA 58.303 37.500 0.00 0.00 0.00 1.52
534 540 4.986054 TTGTTCCTTTAGTGCCTCCTTA 57.014 40.909 0.00 0.00 0.00 2.69
570 576 7.425224 TTTGGTTCAAAGGAATGGAGTAAAA 57.575 32.000 0.00 0.00 35.05 1.52
574 580 4.262592 GCATTTGGTTCAAAGGAATGGAGT 60.263 41.667 8.87 0.00 37.32 3.85
607 613 7.396339 AGGAATTGAAAAGTTTCCTATGGTACC 59.604 37.037 4.43 4.43 42.07 3.34
625 631 8.477419 AAGTGAAGGAAAAACATAGGAATTGA 57.523 30.769 0.00 0.00 0.00 2.57
726 732 6.826741 GCATGGGTCCAAAGTAGTAGAAATAA 59.173 38.462 0.00 0.00 0.00 1.40
729 735 4.566907 GGCATGGGTCCAAAGTAGTAGAAA 60.567 45.833 0.00 0.00 0.00 2.52
756 762 1.361543 TGGGAGTTGAGCTAGTAGGGT 59.638 52.381 0.00 0.00 0.00 4.34
860 866 2.738846 CTGTCTGCTAACATTTCGCTGT 59.261 45.455 0.00 0.00 0.00 4.40
861 867 2.475187 GCTGTCTGCTAACATTTCGCTG 60.475 50.000 0.00 0.00 38.95 5.18
862 868 1.734465 GCTGTCTGCTAACATTTCGCT 59.266 47.619 0.00 0.00 38.95 4.93
863 869 1.202076 GGCTGTCTGCTAACATTTCGC 60.202 52.381 1.44 0.00 42.39 4.70
864 870 2.350522 AGGCTGTCTGCTAACATTTCG 58.649 47.619 1.44 0.00 42.39 3.46
865 871 4.022849 ACAAAGGCTGTCTGCTAACATTTC 60.023 41.667 1.44 0.00 42.39 2.17
866 872 3.891366 ACAAAGGCTGTCTGCTAACATTT 59.109 39.130 1.44 0.00 42.39 2.32
867 873 3.254166 CACAAAGGCTGTCTGCTAACATT 59.746 43.478 1.44 0.00 42.39 2.71
873 879 0.107017 ACACACAAAGGCTGTCTGCT 60.107 50.000 1.44 0.00 42.39 4.24
886 892 6.986904 TGTGTTACACAAATAAGACACACA 57.013 33.333 16.40 0.00 41.69 3.72
944 951 1.804151 GTGGCTAGCACAAACGATCAA 59.196 47.619 18.24 0.00 0.00 2.57
950 957 2.332654 CCGGGTGGCTAGCACAAAC 61.333 63.158 18.24 8.67 0.00 2.93
985 992 2.704572 AGCCATCCAGAAAGAAACTCG 58.295 47.619 0.00 0.00 0.00 4.18
988 995 5.189180 AGTGATAGCCATCCAGAAAGAAAC 58.811 41.667 0.00 0.00 0.00 2.78
994 1001 3.519107 TGTTGAGTGATAGCCATCCAGAA 59.481 43.478 0.00 0.00 0.00 3.02
1018 1025 4.671831 TCAAATGGTAAGGCATTCTGGAA 58.328 39.130 0.00 0.00 0.00 3.53
1019 1026 4.272489 CTCAAATGGTAAGGCATTCTGGA 58.728 43.478 0.00 0.00 0.00 3.86
1048 1055 3.576078 TGCTTTCTGAAGTTCCTTCCA 57.424 42.857 0.00 0.00 39.51 3.53
1058 1065 5.734220 GCTGATGTCTGTTTTGCTTTCTGAA 60.734 40.000 0.00 0.00 0.00 3.02
1083 1090 4.298332 ACTTTTTGCAAAGGTAATCGCTG 58.702 39.130 12.41 0.00 43.47 5.18
1084 1091 4.584327 ACTTTTTGCAAAGGTAATCGCT 57.416 36.364 12.41 0.00 43.47 4.93
1114 1121 7.604545 GCTTAATTCCTATGAGACATACCTTCC 59.395 40.741 0.00 0.00 0.00 3.46
1115 1122 8.150945 TGCTTAATTCCTATGAGACATACCTTC 58.849 37.037 0.00 0.00 0.00 3.46
1156 1168 4.745620 GCAGGCTTAGTCTAATTTCGGTAG 59.254 45.833 0.00 0.00 0.00 3.18
1161 1173 5.648092 TCCAAAGCAGGCTTAGTCTAATTTC 59.352 40.000 6.99 0.00 34.84 2.17
1170 1182 2.165030 CCAACATCCAAAGCAGGCTTAG 59.835 50.000 6.99 2.49 34.84 2.18
1172 1184 0.971386 CCAACATCCAAAGCAGGCTT 59.029 50.000 0.00 0.00 37.98 4.35
1173 1185 0.901580 CCCAACATCCAAAGCAGGCT 60.902 55.000 0.00 0.00 0.00 4.58
1188 1203 4.463050 AGGAACCACTACAAATTCCCAA 57.537 40.909 0.00 0.00 41.39 4.12
1192 1208 6.399639 TTCCAAAGGAACCACTACAAATTC 57.600 37.500 0.00 0.00 36.71 2.17
1199 1215 3.586470 TTGCTTCCAAAGGAACCACTA 57.414 42.857 0.00 0.00 36.71 2.74
1203 1219 7.588497 AGAATATATTGCTTCCAAAGGAACC 57.412 36.000 1.78 0.00 41.75 3.62
1299 1321 0.378257 GGCACCATGCGTGAGTATTG 59.622 55.000 7.72 0.00 46.21 1.90
1323 1345 4.327357 CGTATTCAGCTTGACGTTCAGAAT 59.673 41.667 0.00 0.00 0.00 2.40
1335 1357 1.827969 AGAGGACAGCGTATTCAGCTT 59.172 47.619 0.00 0.00 44.06 3.74
1369 1393 9.624373 GAAATCATCACAGAGGGCATATATTAT 57.376 33.333 0.00 0.00 0.00 1.28
1404 1428 5.368989 AGGAGTTTAGGTTCAGTGACAAAG 58.631 41.667 0.00 0.00 0.00 2.77
1454 1479 4.039488 ACAAAATGAAGGCAGCAATTCAGA 59.961 37.500 15.28 0.00 38.72 3.27
1476 1502 2.930682 GAGGCGACTAAATCTGGACAAC 59.069 50.000 0.00 0.00 44.43 3.32
1488 1514 1.552578 TGGCTTTACAGAGGCGACTA 58.447 50.000 0.00 0.00 44.43 2.59
1492 1518 1.576356 GAGATGGCTTTACAGAGGCG 58.424 55.000 0.00 0.00 44.53 5.52
1522 1549 5.650266 GGGAAATGTTTTTGGTTCCACTTTT 59.350 36.000 3.87 0.00 41.17 2.27
1524 1551 4.226168 TGGGAAATGTTTTTGGTTCCACTT 59.774 37.500 3.87 0.00 41.17 3.16
1581 1608 5.441718 AAAGGCATCAGACTCTTCCAATA 57.558 39.130 0.00 0.00 27.72 1.90
1591 1618 6.422400 GCTCTAGTATGTAAAAGGCATCAGAC 59.578 42.308 0.00 0.00 0.00 3.51
1646 1673 6.514947 AGATTGCAGAGTTCTTATCTAGCAG 58.485 40.000 0.00 0.00 34.58 4.24
1694 1721 4.156477 ACTCTTTCTAGCAAGGAGTCACT 58.844 43.478 2.17 0.00 0.00 3.41
1709 1736 5.059833 CCCATAGATTGCTGGTACTCTTTC 58.940 45.833 0.00 0.00 0.00 2.62
1824 1851 5.355071 CCGATCCAGATTTCTTTGATTGTCA 59.645 40.000 0.00 0.00 0.00 3.58
1879 1906 6.003326 TGGAACATATTTGCAGAGAACAGAA 58.997 36.000 0.00 0.00 0.00 3.02
1900 1927 9.672673 GTACGTTAGTATAGTATAGGGAATGGA 57.327 37.037 0.00 0.00 35.01 3.41
1904 1931 7.984475 TGGGTACGTTAGTATAGTATAGGGAA 58.016 38.462 0.00 0.00 35.01 3.97
1910 1937 7.609532 GGTGAGATGGGTACGTTAGTATAGTAT 59.390 40.741 0.00 0.00 35.01 2.12
1922 1949 2.515926 CATCAGGTGAGATGGGTACG 57.484 55.000 0.00 0.00 41.29 3.67
1930 1957 6.173339 GGAAGAACATTTACATCAGGTGAGA 58.827 40.000 0.00 0.00 0.00 3.27
1942 2295 8.243961 TGTGAAAATGAAGGGAAGAACATTTA 57.756 30.769 0.00 0.00 40.48 1.40
1979 2332 3.533606 ATCTCCACGAACCTGATCTTG 57.466 47.619 0.00 0.00 0.00 3.02
1992 2345 7.556844 TCAGACTTAAACCATCTAATCTCCAC 58.443 38.462 0.00 0.00 0.00 4.02
2014 2367 2.681848 GTGCTCCATGGATCACTTTCAG 59.318 50.000 32.14 13.23 38.00 3.02
2036 2389 5.513094 CCCTCAAGATCTTTAGGTGTGTTCA 60.513 44.000 26.75 0.00 33.25 3.18
2040 2393 4.826274 TCCCTCAAGATCTTTAGGTGTG 57.174 45.455 26.75 15.90 33.25 3.82
2047 2400 5.310409 TCAAGTGTTCCCTCAAGATCTTT 57.690 39.130 4.86 0.00 0.00 2.52
2123 2476 2.027377 ACAACTGAAGCTCCATCCTCAG 60.027 50.000 8.90 8.90 0.00 3.35
2142 2495 1.108727 CCAACAGCCTTGCTTCCACA 61.109 55.000 0.00 0.00 36.40 4.17
2151 2504 2.110578 GGGCATATTTCCAACAGCCTT 58.889 47.619 0.00 0.00 41.71 4.35
2154 2507 3.817647 CTCTAGGGCATATTTCCAACAGC 59.182 47.826 0.00 0.00 0.00 4.40
2481 2835 7.812191 CGATCTCATGGTCTAAGGAAAAGATAG 59.188 40.741 0.00 0.00 0.00 2.08
2690 3044 6.204301 CCTTAGTCACATTGAGCTCATTATGG 59.796 42.308 25.13 16.75 0.00 2.74
2810 3164 4.827692 TGTCAATCGGTATGTTACTTGCT 58.172 39.130 0.00 0.00 0.00 3.91
3089 3443 0.824595 TTCCGGAACTCCTCGTGACA 60.825 55.000 14.35 0.00 0.00 3.58
3506 3870 1.254284 CGAGAGGGAGAGGTGTTGCT 61.254 60.000 0.00 0.00 0.00 3.91
3553 3917 0.912486 GGTGGTGGAAGTAGCAGGAT 59.088 55.000 0.00 0.00 0.00 3.24
3554 3919 0.472925 TGGTGGTGGAAGTAGCAGGA 60.473 55.000 0.00 0.00 0.00 3.86
3557 3922 1.369692 CGTGGTGGTGGAAGTAGCA 59.630 57.895 0.00 0.00 0.00 3.49
3596 3961 1.203622 AGGGGGAAGGAGAGGTTGATT 60.204 52.381 0.00 0.00 0.00 2.57
3713 4079 0.393944 TGATGGAGTCGTACTCGCCT 60.394 55.000 8.33 0.00 45.96 5.52
3786 4152 2.292061 ACTAGCTACGAGGGGAAAGGAA 60.292 50.000 0.00 0.00 0.00 3.36
3848 4214 4.764050 TGGGGATCGTAGCAGAATTTAA 57.236 40.909 0.00 0.00 0.00 1.52
3849 4215 4.080807 TGTTGGGGATCGTAGCAGAATTTA 60.081 41.667 0.00 0.00 0.00 1.40
4107 4474 1.383799 CAGCAACCCTCCAATCCCA 59.616 57.895 0.00 0.00 0.00 4.37
4122 4489 3.117491 TGGAGCAGCAATAGATACAGC 57.883 47.619 0.00 0.00 0.00 4.40
4504 6550 4.560128 TGCCATCGAGCTACTATGAAATC 58.440 43.478 0.00 0.00 0.00 2.17
4522 6568 8.623903 CATACTTAGCTTAAATCTTGAATGCCA 58.376 33.333 0.00 0.00 0.00 4.92
4523 6569 8.078596 CCATACTTAGCTTAAATCTTGAATGCC 58.921 37.037 0.00 0.00 0.00 4.40
5039 7090 4.381185 CGAGGTTAACATGGCTACTGTGTA 60.381 45.833 8.10 0.00 0.00 2.90
5044 7095 3.451178 ACATCGAGGTTAACATGGCTACT 59.549 43.478 8.10 0.00 0.00 2.57
5056 7107 1.183030 TCGTGGGTGACATCGAGGTT 61.183 55.000 3.38 0.00 32.00 3.50
5186 7268 3.181497 CCTTAATGAGGCACATGTTTCGG 60.181 47.826 0.00 0.00 39.09 4.30
5231 7313 7.839680 AACCAATTTATTATTGCCTCTAGGG 57.160 36.000 0.00 0.00 35.18 3.53
5292 7374 9.812347 TCCTATCAATACAATTTTAGCATGGAT 57.188 29.630 0.00 0.00 0.00 3.41
5293 7375 9.639563 TTCCTATCAATACAATTTTAGCATGGA 57.360 29.630 0.00 0.00 0.00 3.41
5306 7388 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
5307 7389 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
5308 7390 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
5309 7391 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
5310 7392 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
5311 7393 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
5312 7394 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
5313 7395 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
5314 7396 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
5315 7397 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
5316 7398 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
5317 7399 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
5318 7400 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
5319 7401 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
5320 7402 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
5321 7403 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
5322 7404 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
5323 7405 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
5324 7406 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
5325 7407 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
5326 7408 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
5327 7409 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
5328 7410 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
5329 7411 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
5330 7412 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
5331 7413 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
5332 7414 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
5333 7415 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
5334 7416 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
5335 7417 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
5336 7418 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
5337 7419 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
5338 7420 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
5339 7421 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
5340 7422 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
5341 7423 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
5342 7424 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
5343 7425 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
5344 7426 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
5345 7427 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
5346 7428 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
5347 7429 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
5348 7430 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
5349 7431 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
5350 7432 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
5351 7433 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
5352 7434 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
5353 7435 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
5354 7436 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
5355 7437 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
5356 7438 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
5357 7439 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
5358 7440 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
5359 7441 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
5360 7442 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
5361 7443 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
5362 7444 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
5363 7445 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
5364 7446 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
5365 7447 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
5366 7448 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
5367 7449 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
5368 7450 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
5369 7451 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
5370 7452 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
5371 7453 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
5372 7454 5.638596 TTGATCAACGAGCTAGTCAACTA 57.361 39.130 3.38 0.00 0.00 2.24
5373 7455 4.521130 TTGATCAACGAGCTAGTCAACT 57.479 40.909 3.38 0.00 0.00 3.16
5374 7456 6.266323 TCTATTGATCAACGAGCTAGTCAAC 58.734 40.000 11.07 0.00 0.00 3.18
5375 7457 6.451064 TCTATTGATCAACGAGCTAGTCAA 57.549 37.500 11.07 0.55 0.00 3.18
5376 7458 6.442112 CATCTATTGATCAACGAGCTAGTCA 58.558 40.000 11.07 0.00 0.00 3.41
5377 7459 5.861251 CCATCTATTGATCAACGAGCTAGTC 59.139 44.000 11.07 0.00 0.00 2.59
5378 7460 5.303078 ACCATCTATTGATCAACGAGCTAGT 59.697 40.000 11.07 6.23 0.00 2.57
5379 7461 5.777802 ACCATCTATTGATCAACGAGCTAG 58.222 41.667 11.07 8.38 0.00 3.42
5380 7462 5.791336 ACCATCTATTGATCAACGAGCTA 57.209 39.130 11.07 0.00 0.00 3.32
5381 7463 4.679373 ACCATCTATTGATCAACGAGCT 57.321 40.909 11.07 0.00 0.00 4.09
5382 7464 5.107837 CGTAACCATCTATTGATCAACGAGC 60.108 44.000 11.07 0.00 0.00 5.03
5383 7465 5.402568 CCGTAACCATCTATTGATCAACGAG 59.597 44.000 11.07 11.28 0.00 4.18
5384 7466 5.163488 ACCGTAACCATCTATTGATCAACGA 60.163 40.000 11.07 10.80 0.00 3.85
5385 7467 5.047847 ACCGTAACCATCTATTGATCAACG 58.952 41.667 11.07 6.28 0.00 4.10
5386 7468 6.920569 AACCGTAACCATCTATTGATCAAC 57.079 37.500 11.07 0.00 0.00 3.18
5387 7469 6.540914 GGAAACCGTAACCATCTATTGATCAA 59.459 38.462 11.26 11.26 0.00 2.57
5388 7470 6.053005 GGAAACCGTAACCATCTATTGATCA 58.947 40.000 0.00 0.00 0.00 2.92
5389 7471 6.202954 CAGGAAACCGTAACCATCTATTGATC 59.797 42.308 0.00 0.00 0.00 2.92
5390 7472 6.055588 CAGGAAACCGTAACCATCTATTGAT 58.944 40.000 0.00 0.00 0.00 2.57
5391 7473 5.188163 TCAGGAAACCGTAACCATCTATTGA 59.812 40.000 0.00 0.00 0.00 2.57
5392 7474 5.293569 GTCAGGAAACCGTAACCATCTATTG 59.706 44.000 0.00 0.00 0.00 1.90
5393 7475 5.425630 GTCAGGAAACCGTAACCATCTATT 58.574 41.667 0.00 0.00 0.00 1.73
5394 7476 4.141779 GGTCAGGAAACCGTAACCATCTAT 60.142 45.833 0.00 0.00 0.00 1.98
5395 7477 3.196254 GGTCAGGAAACCGTAACCATCTA 59.804 47.826 0.00 0.00 0.00 1.98
5396 7478 2.027469 GGTCAGGAAACCGTAACCATCT 60.027 50.000 0.00 0.00 0.00 2.90
5397 7479 2.289819 TGGTCAGGAAACCGTAACCATC 60.290 50.000 0.00 0.00 42.62 3.51
5398 7480 1.700739 TGGTCAGGAAACCGTAACCAT 59.299 47.619 0.00 0.00 42.62 3.55
5399 7481 1.129917 TGGTCAGGAAACCGTAACCA 58.870 50.000 0.00 0.00 42.62 3.67
5400 7482 2.081462 CATGGTCAGGAAACCGTAACC 58.919 52.381 0.00 0.00 42.62 2.85
5401 7483 2.081462 CCATGGTCAGGAAACCGTAAC 58.919 52.381 2.57 0.00 42.62 2.50
5402 7484 1.979308 TCCATGGTCAGGAAACCGTAA 59.021 47.619 12.58 0.00 42.62 3.18
5403 7485 1.276989 GTCCATGGTCAGGAAACCGTA 59.723 52.381 12.58 0.00 42.62 4.02
5404 7486 0.036306 GTCCATGGTCAGGAAACCGT 59.964 55.000 12.58 0.00 42.62 4.83
5405 7487 0.036164 TGTCCATGGTCAGGAAACCG 59.964 55.000 12.58 0.00 42.62 4.44
5406 7488 2.493278 CAATGTCCATGGTCAGGAAACC 59.507 50.000 16.79 0.00 36.80 3.27
5407 7489 2.493278 CCAATGTCCATGGTCAGGAAAC 59.507 50.000 16.79 4.30 36.80 2.78
5408 7490 2.378208 TCCAATGTCCATGGTCAGGAAA 59.622 45.455 16.79 1.08 39.09 3.13
5409 7491 1.991813 TCCAATGTCCATGGTCAGGAA 59.008 47.619 16.79 0.75 39.09 3.36
5410 7492 1.667595 TCCAATGTCCATGGTCAGGA 58.332 50.000 16.79 15.06 39.09 3.86
5411 7493 2.304092 CATCCAATGTCCATGGTCAGG 58.696 52.381 16.79 13.14 39.09 3.86


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

AutoCloner maintained by Alex Coulton.