Multiple sequence alignment - TraesCS7D01G327300

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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 TraesCS7D01G327300 chr7D 100.000 6683 0 0 1 6683 418057924 418051242 0.000000e+00 12342.0
1 TraesCS7D01G327300 chr7D 98.701 2848 21 6 3847 6683 417929071 417926229 0.000000e+00 5040.0
2 TraesCS7D01G327300 chr7D 98.695 2145 15 3 745 2877 417931208 417929065 0.000000e+00 3794.0
3 TraesCS7D01G327300 chr7D 92.976 1438 86 7 3858 5284 418902206 418900773 0.000000e+00 2082.0
4 TraesCS7D01G327300 chr7D 92.768 1438 88 8 3858 5284 418614364 418612932 0.000000e+00 2065.0
5 TraesCS7D01G327300 chr7D 97.936 969 16 4 2879 3846 577791444 577790479 0.000000e+00 1676.0
6 TraesCS7D01G327300 chr7D 98.414 883 13 1 745 1626 418616899 418616017 0.000000e+00 1552.0
7 TraesCS7D01G327300 chr7D 90.095 1161 57 22 1684 2794 418903361 418902209 0.000000e+00 1454.0
8 TraesCS7D01G327300 chr7D 96.032 882 29 3 745 1626 418904235 418903360 0.000000e+00 1430.0
9 TraesCS7D01G327300 chr7D 98.798 749 9 0 1 749 418069136 418068388 0.000000e+00 1334.0
10 TraesCS7D01G327300 chr7D 91.487 787 53 8 4504 5284 418394478 418393700 0.000000e+00 1070.0
11 TraesCS7D01G327300 chr7D 90.090 777 48 14 5268 6021 418900758 418899988 0.000000e+00 981.0
12 TraesCS7D01G327300 chr7D 89.935 775 52 12 5268 6021 418612917 418612148 0.000000e+00 976.0
13 TraesCS7D01G327300 chr7D 88.035 794 62 17 5268 6040 418393685 418392904 0.000000e+00 909.0
14 TraesCS7D01G327300 chr7D 86.839 737 76 6 2912 3630 30000415 29999682 0.000000e+00 804.0
15 TraesCS7D01G327300 chr7D 91.404 570 39 6 3953 4516 418396271 418395706 0.000000e+00 773.0
16 TraesCS7D01G327300 chr7D 90.034 592 34 9 1684 2258 418616018 418615435 0.000000e+00 743.0
17 TraesCS7D01G327300 chr7D 89.081 577 28 14 2251 2794 418614941 418614367 0.000000e+00 684.0
18 TraesCS7D01G327300 chr7D 83.903 497 66 9 5257 5746 449543340 449542851 4.720000e-126 462.0
19 TraesCS7D01G327300 chr7D 94.872 234 9 1 6448 6681 418899542 418899312 4.930000e-96 363.0
20 TraesCS7D01G327300 chr7D 94.444 234 10 1 6448 6681 418390028 418389798 2.290000e-94 357.0
21 TraesCS7D01G327300 chr7D 95.000 220 8 1 6448 6667 418611659 418611443 6.420000e-90 342.0
22 TraesCS7D01G327300 chr7D 87.500 216 27 0 6466 6681 449508685 449508470 4.000000e-62 250.0
23 TraesCS7D01G327300 chr7B 93.482 2424 120 16 3847 6249 433869688 433867282 0.000000e+00 3567.0
24 TraesCS7D01G327300 chr7B 95.109 2147 72 19 745 2881 433871801 433869678 0.000000e+00 3352.0
25 TraesCS7D01G327300 chr7B 93.790 2190 68 17 745 2877 434364715 434362537 0.000000e+00 3229.0
26 TraesCS7D01G327300 chr7B 94.297 1999 78 9 3847 5827 434362543 434360563 0.000000e+00 3027.0
27 TraesCS7D01G327300 chr7B 91.097 1449 79 19 745 2172 212776095 212777514 0.000000e+00 1916.0
28 TraesCS7D01G327300 chr7B 78.753 1139 184 38 4091 5185 212778618 212779742 0.000000e+00 710.0
29 TraesCS7D01G327300 chr7B 79.594 985 129 40 5306 6249 212779783 212780736 2.030000e-179 640.0
30 TraesCS7D01G327300 chr7B 95.406 283 10 3 6403 6683 433866714 433866433 1.320000e-121 448.0
31 TraesCS7D01G327300 chr7B 93.590 234 12 1 6448 6681 434358581 434358351 4.960000e-91 346.0
32 TraesCS7D01G327300 chr7B 85.294 340 29 11 2174 2492 212777600 212777939 1.390000e-86 331.0
33 TraesCS7D01G327300 chr7B 89.451 237 23 1 6445 6681 212781003 212781237 1.410000e-76 298.0
34 TraesCS7D01G327300 chr7B 92.771 166 8 1 6448 6613 434166257 434166096 3.120000e-58 237.0
35 TraesCS7D01G327300 chr7B 81.784 269 34 12 5763 6021 434360561 434360298 1.890000e-50 211.0
36 TraesCS7D01G327300 chr7B 83.721 86 9 4 3885 3965 212778020 212778105 7.190000e-10 76.8
37 TraesCS7D01G327300 chr7A 95.314 2134 71 8 4133 6249 483488808 483486687 0.000000e+00 3360.0
38 TraesCS7D01G327300 chr7A 93.995 2115 97 13 3847 5941 483944901 483942797 0.000000e+00 3175.0
39 TraesCS7D01G327300 chr7A 91.131 1432 65 22 1476 2881 483946286 483944891 0.000000e+00 1884.0
40 TraesCS7D01G327300 chr7A 96.135 1035 30 7 1857 2881 483494288 483493254 0.000000e+00 1681.0
41 TraesCS7D01G327300 chr7A 92.165 970 42 18 2883 3848 13775321 13774382 0.000000e+00 1339.0
42 TraesCS7D01G327300 chr7A 96.035 681 24 1 745 1422 483946965 483946285 0.000000e+00 1105.0
43 TraesCS7D01G327300 chr7A 95.888 681 25 1 745 1422 483495532 483494852 0.000000e+00 1099.0
44 TraesCS7D01G327300 chr7A 89.580 643 57 5 3879 4516 483746833 483746196 0.000000e+00 808.0
45 TraesCS7D01G327300 chr7A 91.045 603 41 7 4501 5097 483744968 483744373 0.000000e+00 802.0
46 TraesCS7D01G327300 chr7A 83.926 815 82 10 2912 3700 30258402 30257611 0.000000e+00 734.0
47 TraesCS7D01G327300 chr7A 90.674 386 21 9 1476 1861 483494853 483494483 3.600000e-137 499.0
48 TraesCS7D01G327300 chr7A 94.178 292 15 2 3847 4137 483493264 483492974 1.710000e-120 444.0
49 TraesCS7D01G327300 chr7A 94.094 254 14 1 6428 6681 483486188 483485936 1.050000e-102 385.0
50 TraesCS7D01G327300 chr7A 89.474 304 18 4 5537 5827 483654903 483654601 8.180000e-99 372.0
51 TraesCS7D01G327300 chr7A 92.511 227 14 1 6438 6664 483757775 483757552 8.360000e-84 322.0
52 TraesCS7D01G327300 chr7A 89.394 66 7 0 6184 6249 514706529 514706594 4.290000e-12 84.2
53 TraesCS7D01G327300 chr5D 98.020 909 13 1 2927 3835 335957535 335958438 0.000000e+00 1574.0
54 TraesCS7D01G327300 chr5D 99.355 155 1 0 6248 6402 3146905 3146751 1.420000e-71 281.0
55 TraesCS7D01G327300 chr3D 96.667 750 24 1 1 750 516681964 516682712 0.000000e+00 1245.0
56 TraesCS7D01G327300 chr3D 98.065 155 3 0 6248 6402 154712388 154712542 3.070000e-68 270.0
57 TraesCS7D01G327300 chr3D 98.065 155 3 0 6248 6402 213394012 213393858 3.070000e-68 270.0
58 TraesCS7D01G327300 chr3D 90.141 71 7 0 3776 3846 157344208 157344138 7.140000e-15 93.5
59 TraesCS7D01G327300 chr6D 96.529 749 24 1 3 749 85682987 85682239 0.000000e+00 1238.0
60 TraesCS7D01G327300 chr6D 96.405 751 25 1 1 749 85678342 85677592 0.000000e+00 1236.0
61 TraesCS7D01G327300 chr6D 96.386 747 26 1 3 749 267867002 267867747 0.000000e+00 1229.0
62 TraesCS7D01G327300 chr6D 96.252 747 28 0 3 749 131318244 131317498 0.000000e+00 1225.0
63 TraesCS7D01G327300 chr6D 95.984 747 28 1 3 749 103446145 103446889 0.000000e+00 1212.0
64 TraesCS7D01G327300 chr1A 95.490 776 31 1 3062 3833 516707498 516708273 0.000000e+00 1236.0
65 TraesCS7D01G327300 chr1A 95.385 195 8 1 2879 3073 516702198 516702391 6.510000e-80 309.0
66 TraesCS7D01G327300 chr1A 93.011 186 13 0 1300 1485 158972676 158972861 8.540000e-69 272.0
67 TraesCS7D01G327300 chr1A 97.419 155 4 0 6248 6402 115746485 115746331 1.430000e-66 265.0
68 TraesCS7D01G327300 chr1A 96.795 156 4 1 6248 6402 16392168 16392013 6.650000e-65 259.0
69 TraesCS7D01G327300 chr1A 92.188 64 2 3 1624 1685 53412015 53412077 3.320000e-13 87.9
70 TraesCS7D01G327300 chr2D 96.519 747 24 2 3 749 116196396 116197140 0.000000e+00 1234.0
71 TraesCS7D01G327300 chr4D 96.272 751 27 1 1 751 421948175 421948924 0.000000e+00 1230.0
72 TraesCS7D01G327300 chr4D 99.355 155 1 0 6248 6402 123627423 123627577 1.420000e-71 281.0
73 TraesCS7D01G327300 chr4D 99.355 155 1 0 6248 6402 135017481 135017327 1.420000e-71 281.0
74 TraesCS7D01G327300 chr4D 96.341 82 3 0 6248 6329 109653666 109653585 1.170000e-27 135.0
75 TraesCS7D01G327300 chrUn 95.041 363 11 2 2878 3239 10359459 10359103 1.260000e-156 564.0
76 TraesCS7D01G327300 chrUn 95.041 363 11 2 2878 3239 222282929 222282573 1.260000e-156 564.0
77 TraesCS7D01G327300 chrUn 94.809 366 12 2 2875 3239 239193571 239193930 1.260000e-156 564.0
78 TraesCS7D01G327300 chrUn 99.355 155 1 0 6248 6402 40097882 40097728 1.420000e-71 281.0
79 TraesCS7D01G327300 chrUn 99.355 155 1 0 6248 6402 399744423 399744269 1.420000e-71 281.0
80 TraesCS7D01G327300 chr5B 92.767 318 20 2 970 1284 101893622 101893939 2.200000e-124 457.0
81 TraesCS7D01G327300 chr5B 94.652 187 10 0 1300 1486 290922982 290922796 2.360000e-74 291.0
82 TraesCS7D01G327300 chr4A 83.709 399 44 11 3079 3458 687506554 687506158 2.290000e-94 357.0
83 TraesCS7D01G327300 chr2B 92.653 245 18 0 745 989 42564805 42565049 2.960000e-93 353.0
84 TraesCS7D01G327300 chr3B 86.728 324 33 8 3541 3856 749654544 749654223 1.070000e-92 351.0
85 TraesCS7D01G327300 chr5A 99.363 157 1 0 6246 6402 31738902 31739058 1.100000e-72 285.0
86 TraesCS7D01G327300 chr5A 99.363 157 1 0 6246 6402 31828107 31828263 1.100000e-72 285.0
87 TraesCS7D01G327300 chr5A 99.363 157 1 0 6246 6402 31919506 31919662 1.100000e-72 285.0
88 TraesCS7D01G327300 chr6B 94.086 186 11 0 1300 1485 576310343 576310528 3.950000e-72 283.0
89 TraesCS7D01G327300 chr6B 95.000 180 9 0 1307 1486 704982549 704982728 3.950000e-72 283.0
90 TraesCS7D01G327300 chr6B 99.355 155 1 0 6248 6402 388192137 388191983 1.420000e-71 281.0
91 TraesCS7D01G327300 chr6B 99.355 155 1 0 6248 6402 388309365 388309211 1.420000e-71 281.0
92 TraesCS7D01G327300 chr1D 99.355 155 1 0 6248 6402 185752390 185752544 1.420000e-71 281.0
93 TraesCS7D01G327300 chr1D 96.800 125 3 1 6248 6372 461637151 461637274 2.440000e-49 207.0
94 TraesCS7D01G327300 chr1D 98.039 102 1 1 6301 6402 141337274 141337174 6.890000e-40 176.0
95 TraesCS7D01G327300 chr4B 93.583 187 12 0 1300 1486 236138901 236139087 5.100000e-71 279.0
96 TraesCS7D01G327300 chr4B 98.710 155 2 0 6248 6402 209173553 209173707 6.600000e-70 276.0
97 TraesCS7D01G327300 chr4B 92.513 187 14 0 1300 1486 294102545 294102731 1.100000e-67 268.0
98 TraesCS7D01G327300 chr4B 90.909 187 16 1 1300 1486 628839312 628839127 4.000000e-62 250.0
99 TraesCS7D01G327300 chr4B 91.837 147 12 0 3701 3847 37526433 37526579 8.780000e-49 206.0
100 TraesCS7D01G327300 chr4B 98.058 103 2 0 6293 6395 658524293 658524191 5.320000e-41 180.0
101 TraesCS7D01G327300 chr1B 98.710 155 2 0 6248 6402 338961172 338961018 6.600000e-70 276.0
102 TraesCS7D01G327300 chr1B 98.710 155 2 0 6248 6402 583524748 583524902 6.600000e-70 276.0
103 TraesCS7D01G327300 chr1B 98.101 158 2 1 6248 6405 338904444 338904288 2.370000e-69 274.0


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 TraesCS7D01G327300 chr7D 418051242 418057924 6682 True 12342.000000 12342 100.000000 1 6683 1 chr7D.!!$R2 6682
1 TraesCS7D01G327300 chr7D 417926229 417931208 4979 True 4417.000000 5040 98.698000 745 6683 2 chr7D.!!$R7 5938
2 TraesCS7D01G327300 chr7D 577790479 577791444 965 True 1676.000000 1676 97.936000 2879 3846 1 chr7D.!!$R6 967
3 TraesCS7D01G327300 chr7D 418068388 418069136 748 True 1334.000000 1334 98.798000 1 749 1 chr7D.!!$R3 748
4 TraesCS7D01G327300 chr7D 418899312 418904235 4923 True 1262.000000 2082 92.813000 745 6681 5 chr7D.!!$R10 5936
5 TraesCS7D01G327300 chr7D 418611443 418616899 5456 True 1060.333333 2065 92.538667 745 6667 6 chr7D.!!$R9 5922
6 TraesCS7D01G327300 chr7D 29999682 30000415 733 True 804.000000 804 86.839000 2912 3630 1 chr7D.!!$R1 718
7 TraesCS7D01G327300 chr7D 418389798 418396271 6473 True 777.250000 1070 91.342500 3953 6681 4 chr7D.!!$R8 2728
8 TraesCS7D01G327300 chr7B 433866433 433871801 5368 True 2455.666667 3567 94.665667 745 6683 3 chr7B.!!$R2 5938
9 TraesCS7D01G327300 chr7B 434358351 434364715 6364 True 1703.250000 3229 90.865250 745 6681 4 chr7B.!!$R3 5936
10 TraesCS7D01G327300 chr7B 212776095 212781237 5142 False 661.966667 1916 84.651667 745 6681 6 chr7B.!!$F1 5936
11 TraesCS7D01G327300 chr7A 483942797 483946965 4168 True 2054.666667 3175 93.720333 745 5941 3 chr7A.!!$R8 5196
12 TraesCS7D01G327300 chr7A 483485936 483488808 2872 True 1872.500000 3360 94.704000 4133 6681 2 chr7A.!!$R5 2548
13 TraesCS7D01G327300 chr7A 13774382 13775321 939 True 1339.000000 1339 92.165000 2883 3848 1 chr7A.!!$R1 965
14 TraesCS7D01G327300 chr7A 483492974 483495532 2558 True 930.750000 1681 94.218750 745 4137 4 chr7A.!!$R6 3392
15 TraesCS7D01G327300 chr7A 483744373 483746833 2460 True 805.000000 808 90.312500 3879 5097 2 chr7A.!!$R7 1218
16 TraesCS7D01G327300 chr7A 30257611 30258402 791 True 734.000000 734 83.926000 2912 3700 1 chr7A.!!$R2 788
17 TraesCS7D01G327300 chr5D 335957535 335958438 903 False 1574.000000 1574 98.020000 2927 3835 1 chr5D.!!$F1 908
18 TraesCS7D01G327300 chr3D 516681964 516682712 748 False 1245.000000 1245 96.667000 1 750 1 chr3D.!!$F2 749
19 TraesCS7D01G327300 chr6D 85677592 85682987 5395 True 1237.000000 1238 96.467000 1 749 2 chr6D.!!$R2 748
20 TraesCS7D01G327300 chr6D 267867002 267867747 745 False 1229.000000 1229 96.386000 3 749 1 chr6D.!!$F2 746
21 TraesCS7D01G327300 chr6D 131317498 131318244 746 True 1225.000000 1225 96.252000 3 749 1 chr6D.!!$R1 746
22 TraesCS7D01G327300 chr6D 103446145 103446889 744 False 1212.000000 1212 95.984000 3 749 1 chr6D.!!$F1 746
23 TraesCS7D01G327300 chr1A 516707498 516708273 775 False 1236.000000 1236 95.490000 3062 3833 1 chr1A.!!$F4 771
24 TraesCS7D01G327300 chr2D 116196396 116197140 744 False 1234.000000 1234 96.519000 3 749 1 chr2D.!!$F1 746
25 TraesCS7D01G327300 chr4D 421948175 421948924 749 False 1230.000000 1230 96.272000 1 751 1 chr4D.!!$F2 750

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
491 5137 0.038744 GCCACTAGCATGCCCCATAT 59.961 55.000 15.66 0.00 42.97 1.78 F
802 5450 0.985490 GCCCTCCAGGACTCCTCAAT 60.985 60.000 0.00 0.00 38.24 2.57 F
1864 6743 1.206132 CTTGGACGTGTACATAGCCCA 59.794 52.381 0.00 1.78 0.00 5.36 F
2870 8401 3.130340 TGCTTTCTCAAGTTTCCGCTTTT 59.870 39.130 0.00 0.00 31.86 2.27 F
2871 8402 3.731216 GCTTTCTCAAGTTTCCGCTTTTC 59.269 43.478 0.00 0.00 31.86 2.29 F
3947 9530 1.610522 GCATCCTGCAAACTGTTCACT 59.389 47.619 0.00 0.00 44.26 3.41 F
5048 13603 6.425417 TGCGAACAGTGAGAATATACAACAAA 59.575 34.615 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 6743 1.477295 GCTACACTCTAAAGACGGCCT 59.523 52.381 0.00 0.00 0.00 5.19 R
2870 8401 8.693625 GGGTACTGTAAAAGAGCTCTTATAAGA 58.306 37.037 28.67 14.42 34.61 2.10 R
3702 9267 1.969923 CTTGATCCAAGGGGCAAAACA 59.030 47.619 0.00 0.00 37.77 2.83 R
3906 9488 4.246458 GCCTAGTTTCAATCTGAGTTCGT 58.754 43.478 0.00 0.00 0.00 3.85 R
4850 13404 4.340617 TCCAGTATAAAGCCCACAAAAGG 58.659 43.478 0.00 0.00 0.00 3.11 R
5582 14190 6.096282 TGACTCGTAGATGATGTGGATGTTAA 59.904 38.462 0.00 0.00 33.89 2.01 R
6544 19400 5.640147 TGAGTTCATTTGGAGGTTTATGGT 58.360 37.500 0.00 0.00 0.00 3.55 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
491 5137 0.038744 GCCACTAGCATGCCCCATAT 59.961 55.000 15.66 0.00 42.97 1.78
614 5260 3.917324 AGGGGTATTATCTCTCCGGAA 57.083 47.619 5.23 0.00 0.00 4.30
754 5402 1.250328 AGAATACCACGACACCGACA 58.750 50.000 0.00 0.00 39.50 4.35
802 5450 0.985490 GCCCTCCAGGACTCCTCAAT 60.985 60.000 0.00 0.00 38.24 2.57
1864 6743 1.206132 CTTGGACGTGTACATAGCCCA 59.794 52.381 0.00 1.78 0.00 5.36
2259 7747 8.925161 TGTTAAATATTAGATTTGTTGCCAGC 57.075 30.769 0.00 0.00 0.00 4.85
2870 8401 3.130340 TGCTTTCTCAAGTTTCCGCTTTT 59.870 39.130 0.00 0.00 31.86 2.27
2871 8402 3.731216 GCTTTCTCAAGTTTCCGCTTTTC 59.269 43.478 0.00 0.00 31.86 2.29
2872 8403 4.498177 GCTTTCTCAAGTTTCCGCTTTTCT 60.498 41.667 0.00 0.00 31.86 2.52
2873 8404 5.576447 TTTCTCAAGTTTCCGCTTTTCTT 57.424 34.783 0.00 0.00 0.00 2.52
2874 8405 6.687081 TTTCTCAAGTTTCCGCTTTTCTTA 57.313 33.333 0.00 0.00 0.00 2.10
2875 8406 6.877611 TTCTCAAGTTTCCGCTTTTCTTAT 57.122 33.333 0.00 0.00 0.00 1.73
2876 8407 7.972832 TTCTCAAGTTTCCGCTTTTCTTATA 57.027 32.000 0.00 0.00 0.00 0.98
2877 8408 7.972832 TCTCAAGTTTCCGCTTTTCTTATAA 57.027 32.000 0.00 0.00 0.00 0.98
2902 8433 5.030820 AGCTCTTTTACAGTACCCTGGTAT 58.969 41.667 0.00 0.00 43.36 2.73
3906 9488 7.360522 CCGCAATTGTAAACAGTGACTACAATA 60.361 37.037 23.00 8.25 42.57 1.90
3947 9530 1.610522 GCATCCTGCAAACTGTTCACT 59.389 47.619 0.00 0.00 44.26 3.41
5048 13603 6.425417 TGCGAACAGTGAGAATATACAACAAA 59.575 34.615 0.00 0.00 0.00 2.83
5087 13642 7.672983 TGCCAACTTACTCTAATTTTCTGAG 57.327 36.000 0.00 0.00 0.00 3.35
5582 14190 1.673033 CGTTTCACCGATTGAGGAGCT 60.673 52.381 0.00 0.00 34.94 4.09
6076 16043 2.860735 GTCAGTCTGATGCCGTTATGAC 59.139 50.000 5.68 0.00 0.00 3.06
6119 16089 9.767684 TTTGTATGCTATTTAATCGTTGTTGAG 57.232 29.630 0.00 0.00 0.00 3.02
6544 19400 2.685388 CTGAGCCTCTTCAGATACACGA 59.315 50.000 0.00 0.00 45.95 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 4762 4.025858 GGCCAGGCAGAGCAGTCA 62.026 66.667 15.19 0.00 0.00 3.41
491 5137 6.070653 TGCATCTGATCTGGTATATGCATGTA 60.071 38.462 17.28 3.81 43.32 2.29
620 5266 2.010544 GCGCTAGTTTACCCAGGTTCC 61.011 57.143 0.00 0.00 0.00 3.62
734 5382 1.614903 TGTCGGTGTCGTGGTATTCTT 59.385 47.619 0.00 0.00 37.69 2.52
754 5402 2.044451 TCCGCCGCAATTGGGATT 60.044 55.556 22.97 0.00 0.00 3.01
802 5450 2.804572 CGGAGTAGAGGTCGTCGGATTA 60.805 54.545 0.00 0.00 0.00 1.75
1864 6743 1.477295 GCTACACTCTAAAGACGGCCT 59.523 52.381 0.00 0.00 0.00 5.19
2870 8401 8.693625 GGGTACTGTAAAAGAGCTCTTATAAGA 58.306 37.037 28.67 14.42 34.61 2.10
2871 8402 8.697292 AGGGTACTGTAAAAGAGCTCTTATAAG 58.303 37.037 28.67 22.89 34.61 1.73
2872 8403 8.475639 CAGGGTACTGTAAAAGAGCTCTTATAA 58.524 37.037 28.67 14.37 39.92 0.98
2873 8404 7.069578 CCAGGGTACTGTAAAAGAGCTCTTATA 59.930 40.741 28.67 11.97 43.36 0.98
2874 8405 6.127026 CCAGGGTACTGTAAAAGAGCTCTTAT 60.127 42.308 28.67 15.90 43.36 1.73
2875 8406 5.187186 CCAGGGTACTGTAAAAGAGCTCTTA 59.813 44.000 28.67 12.17 43.36 2.10
2876 8407 4.020128 CCAGGGTACTGTAAAAGAGCTCTT 60.020 45.833 23.49 23.49 43.36 2.85
2877 8408 3.515901 CCAGGGTACTGTAAAAGAGCTCT 59.484 47.826 11.45 11.45 43.36 4.09
2902 8433 2.106857 ACTCCGGTGTATGGTTTTGGAA 59.893 45.455 7.54 0.00 0.00 3.53
3702 9267 1.969923 CTTGATCCAAGGGGCAAAACA 59.030 47.619 0.00 0.00 37.77 2.83
3906 9488 4.246458 GCCTAGTTTCAATCTGAGTTCGT 58.754 43.478 0.00 0.00 0.00 3.85
4850 13404 4.340617 TCCAGTATAAAGCCCACAAAAGG 58.659 43.478 0.00 0.00 0.00 3.11
5048 13603 9.740710 AGTAAGTTGGCAAGATAACTAAGAAAT 57.259 29.630 0.00 0.00 36.19 2.17
5582 14190 6.096282 TGACTCGTAGATGATGTGGATGTTAA 59.904 38.462 0.00 0.00 33.89 2.01
6076 16043 6.195244 GCATACAAAGCAGAATTATCACAACG 59.805 38.462 0.00 0.00 0.00 4.10
6077 16044 7.253422 AGCATACAAAGCAGAATTATCACAAC 58.747 34.615 0.00 0.00 0.00 3.32
6078 16045 7.395190 AGCATACAAAGCAGAATTATCACAA 57.605 32.000 0.00 0.00 0.00 3.33
6544 19400 5.640147 TGAGTTCATTTGGAGGTTTATGGT 58.360 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.