Multiple sequence alignment - TraesCS5D01G083100

Loading Multiple Alignment...

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 TraesCS5D01G083100 chr5D 100.000 4347 0 0 2471 6817 84903402 84899056 0.000000e+00 8028.0
1 TraesCS5D01G083100 chr5D 100.000 2303 0 0 1 2303 84905872 84903570 0.000000e+00 4253.0
2 TraesCS5D01G083100 chr5D 74.302 681 148 16 85 750 406322413 406323081 5.240000e-66 263.0
3 TraesCS5D01G083100 chr5D 83.486 109 16 2 6479 6587 328435784 328435678 4.350000e-17 100.0
4 TraesCS5D01G083100 chr5A 97.665 3640 68 6 2898 6525 79287160 79283526 0.000000e+00 6235.0
5 TraesCS5D01G083100 chr5A 96.600 2294 54 10 1 2280 79290438 79288155 0.000000e+00 3783.0
6 TraesCS5D01G083100 chr5A 95.778 379 5 1 2534 2901 79287843 79287465 9.780000e-168 601.0
7 TraesCS5D01G083100 chr5A 91.667 432 15 9 6387 6817 79283526 79283115 4.580000e-161 579.0
8 TraesCS5D01G083100 chr5B 95.258 1687 53 13 4230 5896 92234689 92233010 0.000000e+00 2647.0
9 TraesCS5D01G083100 chr5B 93.274 1338 58 13 966 2282 92238048 92236722 0.000000e+00 1943.0
10 TraesCS5D01G083100 chr5B 93.466 1056 41 13 2471 3511 92236424 92235382 0.000000e+00 1543.0
11 TraesCS5D01G083100 chr5B 96.564 291 10 0 3555 3845 92235388 92235098 3.700000e-132 483.0
12 TraesCS5D01G083100 chr5B 94.012 167 9 1 817 983 92238516 92238351 1.130000e-62 252.0
13 TraesCS5D01G083100 chr5B 96.026 151 6 0 4088 4238 92235023 92234873 5.280000e-61 246.0
14 TraesCS5D01G083100 chr5B 94.366 142 7 1 3832 3972 483709682 483709823 4.140000e-52 217.0
15 TraesCS5D01G083100 chr5B 89.437 142 9 4 6677 6817 92232832 92232696 2.530000e-39 174.0
16 TraesCS5D01G083100 chr5B 93.913 115 4 2 3972 4086 92235096 92234985 3.270000e-38 171.0
17 TraesCS5D01G083100 chr5B 85.849 106 14 1 6479 6584 618158225 618158329 2.010000e-20 111.0
18 TraesCS5D01G083100 chr5B 85.185 108 15 1 6479 6586 129721887 129721781 7.230000e-20 110.0
19 TraesCS5D01G083100 chr5B 98.113 53 1 0 5966 6018 553341865 553341813 7.280000e-15 93.5
20 TraesCS5D01G083100 chr5B 97.917 48 1 0 5970 6017 566976191 566976238 4.380000e-12 84.2
21 TraesCS5D01G083100 chr5B 94.000 50 3 0 6635 6684 92232941 92232892 7.330000e-10 76.8
22 TraesCS5D01G083100 chr5B 90.909 55 5 0 5906 5960 264910485 264910431 2.640000e-09 75.0
23 TraesCS5D01G083100 chr5B 88.136 59 7 0 5903 5961 316708984 316709042 3.410000e-08 71.3
24 TraesCS5D01G083100 chr1B 89.263 1900 135 38 3972 5827 579790417 579788543 0.000000e+00 2314.0
25 TraesCS5D01G083100 chr1B 84.856 1182 100 32 2685 3839 579791549 579790420 0.000000e+00 1118.0
26 TraesCS5D01G083100 chr1B 86.681 916 93 19 4268 5169 662545232 662546132 0.000000e+00 989.0
27 TraesCS5D01G083100 chr1B 85.551 699 67 21 4268 4951 662550591 662551270 0.000000e+00 701.0
28 TraesCS5D01G083100 chr1B 89.474 190 14 6 1435 1620 579792439 579792252 1.140000e-57 235.0
29 TraesCS5D01G083100 chr1B 94.631 149 8 0 3248 3396 662549431 662549579 1.480000e-56 231.0
30 TraesCS5D01G083100 chr1B 92.617 149 11 0 3248 3396 662537211 662537359 1.490000e-51 215.0
31 TraesCS5D01G083100 chr1B 88.372 129 9 4 3708 3831 662545003 662545130 4.260000e-32 150.0
32 TraesCS5D01G083100 chr1B 83.810 105 15 2 6479 6583 286356513 286356615 1.560000e-16 99.0
33 TraesCS5D01G083100 chr1A 88.621 1863 148 40 3987 5823 522956340 522954516 0.000000e+00 2207.0
34 TraesCS5D01G083100 chr1A 85.251 1173 91 31 2685 3843 522957450 522956346 0.000000e+00 1133.0
35 TraesCS5D01G083100 chr1A 85.387 917 105 19 4268 5169 572013712 572014614 0.000000e+00 924.0
36 TraesCS5D01G083100 chr1A 85.154 357 47 3 5181 5531 572014777 572015133 1.810000e-95 361.0
37 TraesCS5D01G083100 chr1A 82.880 368 45 13 3438 3792 572004950 572005312 1.430000e-81 315.0
38 TraesCS5D01G083100 chr1A 84.039 307 41 8 1389 1691 522958303 522958001 8.650000e-74 289.0
39 TraesCS5D01G083100 chr1A 93.793 145 9 0 3252 3396 572004728 572004872 1.150000e-52 219.0
40 TraesCS5D01G083100 chr1D 90.860 1674 111 22 4180 5827 427620418 427618761 0.000000e+00 2206.0
41 TraesCS5D01G083100 chr1D 86.713 1144 98 29 2719 3848 427621641 427620538 0.000000e+00 1221.0
42 TraesCS5D01G083100 chr1D 85.125 921 100 21 4268 5169 476229630 476230532 0.000000e+00 907.0
43 TraesCS5D01G083100 chr1D 82.198 455 50 18 3248 3675 476227495 476227945 5.030000e-96 363.0
44 TraesCS5D01G083100 chr1D 86.000 300 34 8 1394 1692 427622430 427622138 1.430000e-81 315.0
45 TraesCS5D01G083100 chr1D 88.112 143 13 2 3672 3810 476229254 476229396 4.230000e-37 167.0
46 TraesCS5D01G083100 chr1D 96.429 56 1 1 3972 4027 427620542 427620488 2.620000e-14 91.6
47 TraesCS5D01G083100 chr4B 84.615 546 59 13 1235 1768 577022635 577022103 2.820000e-143 520.0
48 TraesCS5D01G083100 chr4B 85.526 152 21 1 2471 2621 488891784 488891935 2.550000e-34 158.0
49 TraesCS5D01G083100 chr4B 86.441 59 8 0 5903 5961 553247961 553248019 1.590000e-06 65.8
50 TraesCS5D01G083100 chr4B 100.000 28 0 0 581 608 88398793 88398766 1.200000e-02 52.8
51 TraesCS5D01G083100 chr6B 83.889 360 43 9 1158 1517 27703421 27703077 5.100000e-86 329.0
52 TraesCS5D01G083100 chr6B 93.525 139 8 1 3835 3972 207510889 207511027 8.960000e-49 206.0
53 TraesCS5D01G083100 chr6B 81.068 206 27 3 2477 2672 11468789 11468586 3.290000e-33 154.0
54 TraesCS5D01G083100 chr7D 85.000 300 40 3 1218 1517 445146852 445146558 4.000000e-77 300.0
55 TraesCS5D01G083100 chr7D 93.525 139 8 1 3840 3978 150359296 150359433 8.960000e-49 206.0
56 TraesCS5D01G083100 chr7D 73.077 442 87 24 71 502 137554346 137554765 2.000000e-25 128.0
57 TraesCS5D01G083100 chr7D 86.607 112 13 2 6474 6584 83654314 83654424 9.280000e-24 122.0
58 TraesCS5D01G083100 chr7D 85.586 111 15 1 6474 6584 565129548 565129657 1.550000e-21 115.0
59 TraesCS5D01G083100 chr7D 87.342 79 9 1 2195 2272 511225721 511225643 9.420000e-14 89.8
60 TraesCS5D01G083100 chr7D 91.667 48 4 0 2213 2260 85228082 85228035 4.410000e-07 67.6
61 TraesCS5D01G083100 chr3A 84.758 269 26 9 1157 1425 11822173 11821920 8.770000e-64 255.0
62 TraesCS5D01G083100 chr3A 83.111 225 23 7 2471 2681 451672923 451673146 2.510000e-44 191.0
63 TraesCS5D01G083100 chr3A 81.043 211 40 0 2471 2681 455236919 455236709 1.180000e-37 169.0
64 TraesCS5D01G083100 chr3A 94.444 54 2 1 5966 6018 735552969 735552916 1.580000e-11 82.4
65 TraesCS5D01G083100 chr3A 86.957 69 7 2 1 68 496547205 496547138 7.330000e-10 76.8
66 TraesCS5D01G083100 chr2B 84.015 269 28 9 1157 1425 106129766 106130019 1.900000e-60 244.0
67 TraesCS5D01G083100 chr2B 91.489 141 10 2 3835 3974 186880652 186880513 6.980000e-45 193.0
68 TraesCS5D01G083100 chr2B 96.154 52 2 0 5966 6017 461094568 461094619 1.220000e-12 86.1
69 TraesCS5D01G083100 chr2B 91.071 56 5 0 5906 5961 45785918 45785973 7.330000e-10 76.8
70 TraesCS5D01G083100 chr4A 86.730 211 28 0 2471 2681 1525635 1525845 1.140000e-57 235.0
71 TraesCS5D01G083100 chr2D 93.617 141 8 1 3836 3975 186642116 186641976 6.930000e-50 209.0
72 TraesCS5D01G083100 chr2D 97.917 48 1 0 5971 6018 78687901 78687948 4.380000e-12 84.2
73 TraesCS5D01G083100 chr2D 92.857 56 4 0 5906 5961 617215346 617215291 1.580000e-11 82.4
74 TraesCS5D01G083100 chrUn 92.361 144 11 0 3832 3975 150797777 150797920 8.960000e-49 206.0
75 TraesCS5D01G083100 chrUn 75.909 220 45 8 158 375 70161137 70160924 9.350000e-19 106.0
76 TraesCS5D01G083100 chr7B 92.908 141 10 0 3832 3972 401136674 401136814 8.960000e-49 206.0
77 TraesCS5D01G083100 chr7B 91.275 149 10 3 3830 3976 540780767 540780620 4.170000e-47 200.0
78 TraesCS5D01G083100 chr7B 85.938 64 7 2 1 63 551191739 551191801 4.410000e-07 67.6
79 TraesCS5D01G083100 chr7A 92.857 140 9 1 3841 3980 231553498 231553636 1.160000e-47 202.0
80 TraesCS5D01G083100 chr3B 93.233 133 9 0 3840 3972 426308876 426308744 5.390000e-46 196.0
81 TraesCS5D01G083100 chr3B 89.474 152 13 3 2471 2621 35973898 35974047 9.030000e-44 189.0
82 TraesCS5D01G083100 chr3B 85.047 107 13 3 6494 6599 474408621 474408517 9.350000e-19 106.0
83 TraesCS5D01G083100 chr6A 89.032 155 12 4 3820 3973 6860120 6859970 3.250000e-43 187.0
84 TraesCS5D01G083100 chr4D 84.071 113 16 2 6474 6586 466839101 466838991 2.600000e-19 108.0
85 TraesCS5D01G083100 chr4D 96.154 52 2 0 5966 6017 21147738 21147789 1.220000e-12 86.1
86 TraesCS5D01G083100 chr4D 97.917 48 1 0 5970 6017 18724433 18724480 4.380000e-12 84.2
87 TraesCS5D01G083100 chr4D 86.441 59 8 0 5903 5961 163791050 163791108 1.590000e-06 65.8
88 TraesCS5D01G083100 chr3D 97.917 48 1 0 5970 6017 539119781 539119734 4.380000e-12 84.2
89 TraesCS5D01G083100 chr2A 91.379 58 5 0 5906 5963 776929525 776929468 5.670000e-11 80.5
90 TraesCS5D01G083100 chr6D 89.091 55 6 0 5903 5957 455971475 455971529 1.230000e-07 69.4


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 TraesCS5D01G083100 chr5D 84899056 84905872 6816 True 6140.500000 8028 100.000000 1 6817 2 chr5D.!!$R2 6816
1 TraesCS5D01G083100 chr5D 406322413 406323081 668 False 263.000000 263 74.302000 85 750 1 chr5D.!!$F1 665
2 TraesCS5D01G083100 chr5A 79283115 79290438 7323 True 2799.500000 6235 95.427500 1 6817 4 chr5A.!!$R1 6816
3 TraesCS5D01G083100 chr5B 92232696 92238516 5820 True 837.311111 2647 93.994444 817 6817 9 chr5B.!!$R4 6000
4 TraesCS5D01G083100 chr1B 579788543 579792439 3896 True 1222.333333 2314 87.864333 1435 5827 3 chr1B.!!$R1 4392
5 TraesCS5D01G083100 chr1B 662545003 662551270 6267 False 517.750000 989 88.808750 3248 5169 4 chr1B.!!$F3 1921
6 TraesCS5D01G083100 chr1A 522954516 522958303 3787 True 1209.666667 2207 85.970333 1389 5823 3 chr1A.!!$R1 4434
7 TraesCS5D01G083100 chr1A 572013712 572015133 1421 False 642.500000 924 85.270500 4268 5531 2 chr1A.!!$F2 1263
8 TraesCS5D01G083100 chr1A 572004728 572005312 584 False 267.000000 315 88.336500 3252 3792 2 chr1A.!!$F1 540
9 TraesCS5D01G083100 chr1D 427618761 427622430 3669 True 958.400000 2206 90.000500 1394 5827 4 chr1D.!!$R1 4433
10 TraesCS5D01G083100 chr1D 476227495 476230532 3037 False 479.000000 907 85.145000 3248 5169 3 chr1D.!!$F1 1921
11 TraesCS5D01G083100 chr4B 577022103 577022635 532 True 520.000000 520 84.615000 1235 1768 1 chr4B.!!$R2 533

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
554 568 1.686355 TTTTCCTTCAAGGCAGCGAA 58.314 45.000 0.00 0.00 34.61 4.70 F
677 691 2.584608 CGGAGGCCCAAAGACGAT 59.415 61.111 0.00 0.00 0.00 3.73 F
1415 1753 0.550914 TCCTGCAACTGGTCTTTGGT 59.449 50.000 0.00 0.00 0.00 3.67 F
2216 2743 1.202830 TCAAAAAGGCGTTCCTAGGCA 60.203 47.619 2.96 0.00 43.40 4.75 F
2514 3297 1.399440 TCAGTCGACTGTACCATACGC 59.601 52.381 37.21 0.00 44.12 4.42 F
3966 6981 2.165030 GACAAGTATTTCCGGACGGAGA 59.835 50.000 13.64 10.06 46.06 3.71 F
5124 8407 2.103263 CAGGTTCTAGGAGAAATCGGGG 59.897 54.545 0.00 0.00 35.75 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1753 1.371267 CCGACTCGCGTTCACTGAA 60.371 57.895 5.77 0.00 38.67 3.02 R
2523 3306 2.505819 GCCCATCTTCCTGTTCTCCTAA 59.494 50.000 0.00 0.00 0.00 2.69 R
2731 3525 1.821759 CCACCGCACAAAGTCACCA 60.822 57.895 0.00 0.00 0.00 4.17 R
3966 6981 2.174210 TGGTCGGGCTATGTACTACTCT 59.826 50.000 0.00 0.00 0.00 3.24 R
4459 7718 1.134818 CATGCTGGTTCATTGCTGCAT 60.135 47.619 1.84 0.00 41.08 3.96 R
5384 8832 1.519246 CTGGAGCTTGGCGAGATCA 59.481 57.895 20.82 7.07 42.62 2.92 R
6362 9837 0.108662 CGTTACCCACCTTACCGGTC 60.109 60.000 12.40 0.00 44.93 4.79 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
27 28 1.905512 CCCGAACCTCCTAGTTGGG 59.094 63.158 0.00 0.00 43.20 4.12
267 271 2.031870 CAGACCTGTCATACATCGGGA 58.968 52.381 0.00 0.00 34.49 5.14
530 544 4.141251 TCTCTACAAGCTCTTTTTGGGGTT 60.141 41.667 0.00 0.00 0.00 4.11
531 545 4.542697 TCTACAAGCTCTTTTTGGGGTTT 58.457 39.130 0.00 0.00 0.00 3.27
554 568 1.686355 TTTTCCTTCAAGGCAGCGAA 58.314 45.000 0.00 0.00 34.61 4.70
655 669 4.155826 GGGTTTCAAAAAGTTTGCTTTGCT 59.844 37.500 0.00 0.00 43.52 3.91
677 691 2.584608 CGGAGGCCCAAAGACGAT 59.415 61.111 0.00 0.00 0.00 3.73
742 757 5.337330 GGAAGAAGAGTTCGACATCCCTAAA 60.337 44.000 0.00 0.00 34.02 1.85
842 857 2.600470 GCCCTTGGGCCTTTTCGT 60.600 61.111 19.46 0.00 0.00 3.85
1415 1753 0.550914 TCCTGCAACTGGTCTTTGGT 59.449 50.000 0.00 0.00 0.00 3.67
1775 2218 7.797617 TCTGGTGGTCCCTATTATATTACCTTT 59.202 37.037 0.00 0.00 0.00 3.11
2216 2743 1.202830 TCAAAAAGGCGTTCCTAGGCA 60.203 47.619 2.96 0.00 43.40 4.75
2488 3270 3.434053 GGCGTGAGGAGGATACCTA 57.566 57.895 0.00 0.00 40.73 3.08
2514 3297 1.399440 TCAGTCGACTGTACCATACGC 59.601 52.381 37.21 0.00 44.12 4.42
2523 3306 2.484651 CTGTACCATACGCGAGCTCTAT 59.515 50.000 15.93 0.00 0.00 1.98
2731 3525 6.048509 GCATTTGGGTCATATCCGAATTTTT 58.951 36.000 0.00 0.00 36.51 1.94
3966 6981 2.165030 GACAAGTATTTCCGGACGGAGA 59.835 50.000 13.64 10.06 46.06 3.71
5124 8407 2.103263 CAGGTTCTAGGAGAAATCGGGG 59.897 54.545 0.00 0.00 35.75 5.73
5209 8501 5.819901 AGCCAAACAGAGACAGCTATTAATC 59.180 40.000 0.00 0.00 0.00 1.75
5384 8832 0.949105 GTGTGGTCGCCGTGAAGAAT 60.949 55.000 0.00 0.00 0.00 2.40
5531 8979 2.112297 GAAGTTCCACCGTGCCCA 59.888 61.111 0.00 0.00 0.00 5.36
5659 9109 5.355350 GGTGGAGGAGAAAACATTATGAGTG 59.645 44.000 0.00 0.00 0.00 3.51
5668 9118 9.387123 GAGAAAACATTATGAGTGTGAAAGTTC 57.613 33.333 0.00 0.00 0.00 3.01
5671 9121 9.736023 AAAACATTATGAGTGTGAAAGTTCTTC 57.264 29.630 0.00 0.00 0.00 2.87
5788 9253 6.328410 ACCTACTACTTTGGTTCAGGTTTACT 59.672 38.462 0.00 0.00 30.61 2.24
5912 9381 2.415857 AGTTGTAGTACGTGCTCTCTCG 59.584 50.000 10.21 0.00 35.54 4.04
5921 9390 2.295349 ACGTGCTCTCTCGGTTTCTAAA 59.705 45.455 0.00 0.00 33.90 1.85
5936 9405 9.683870 TCGGTTTCTAAATATAAGCCCTTTTAA 57.316 29.630 0.00 0.00 0.00 1.52
5967 9441 3.829728 AGGGACTATATACGAGGGCTT 57.170 47.619 0.00 0.00 36.02 4.35
6039 9514 1.686115 GGCTGGCAATGTGGATTACCT 60.686 52.381 0.00 0.00 37.04 3.08
6065 9540 4.969484 AGGTATCTCCGTGACAACTTTTT 58.031 39.130 0.00 0.00 41.99 1.94
6073 9548 2.223688 CGTGACAACTTTTTCATGCCCA 60.224 45.455 0.00 0.00 0.00 5.36
6090 9565 2.482494 CCCATCCCCATCCCTATACTC 58.518 57.143 0.00 0.00 0.00 2.59
6097 9572 1.200252 CCATCCCTATACTCGTCTGCG 59.800 57.143 0.00 0.00 39.92 5.18
6117 9592 6.208599 TCTGCGGGGATAAAAATATTTCCATC 59.791 38.462 0.10 7.19 0.00 3.51
6125 9600 2.971901 AATATTTCCATCCCCGTCCC 57.028 50.000 0.00 0.00 0.00 4.46
6126 9601 1.827792 ATATTTCCATCCCCGTCCCA 58.172 50.000 0.00 0.00 0.00 4.37
6160 9635 2.148768 CCCGTGGAAAAACCTAGACAC 58.851 52.381 0.00 0.00 39.86 3.67
6182 9657 6.922957 ACACGCAATTAACAACAATCTTCAAT 59.077 30.769 0.00 0.00 0.00 2.57
6306 9781 1.428869 TGGGTGAAAATTTGGGTGGG 58.571 50.000 0.00 0.00 0.00 4.61
6362 9837 0.537188 AGCCCACATCTACGTCCTTG 59.463 55.000 0.00 0.00 0.00 3.61
6365 9840 1.134788 CCCACATCTACGTCCTTGACC 60.135 57.143 0.00 0.00 0.00 4.02
6398 9873 0.896923 ACGGTTACGGGTAATGCTGA 59.103 50.000 0.00 0.00 46.48 4.26
6452 10065 4.639135 GGTATTTGACCCATCAGCTTTC 57.361 45.455 0.00 0.00 43.25 2.62
6476 10089 4.037923 CCGTGGGCATTAAAGCTTGAATAT 59.962 41.667 8.81 0.00 34.17 1.28
6492 10105 9.416794 AGCTTGAATATAGATGCATATATACGC 57.583 33.333 20.39 15.71 29.96 4.42
6506 10119 9.262358 TGCATATATACGCATTTTAGTGTGTAA 57.738 29.630 0.00 0.00 45.12 2.41
6525 10138 5.239525 GTGTAAACTCACTCATTTTGCTCCT 59.760 40.000 0.00 0.00 35.68 3.69
6531 10144 5.413833 ACTCACTCATTTTGCTCCTTATGTG 59.586 40.000 0.00 0.00 0.00 3.21
6540 10153 9.754382 CATTTTGCTCCTTATGTGCTTTATATT 57.246 29.630 0.00 0.00 34.56 1.28
6604 10218 5.886960 ATTACTCACAGATGCCAAGAAAC 57.113 39.130 0.00 0.00 0.00 2.78
6787 10480 2.230508 CTCAGCATGTGCCTTGTTTGAT 59.769 45.455 0.57 0.00 43.38 2.57
6788 10481 2.629137 TCAGCATGTGCCTTGTTTGATT 59.371 40.909 0.57 0.00 43.38 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.955461 ATCTCCCAACTAGGAGGTTCGG 60.955 54.545 7.70 0.00 45.61 4.30
27 28 3.068873 GGGAGTACTCACCATGTCATCTC 59.931 52.174 23.91 2.11 0.00 2.75
554 568 1.672881 GGCTGCGATCTACAAAGCAAT 59.327 47.619 0.00 0.00 39.26 3.56
853 869 0.253327 GTAGCCTCCTTGAACCCCTG 59.747 60.000 0.00 0.00 0.00 4.45
854 870 1.265454 CGTAGCCTCCTTGAACCCCT 61.265 60.000 0.00 0.00 0.00 4.79
856 872 0.175989 CTCGTAGCCTCCTTGAACCC 59.824 60.000 0.00 0.00 0.00 4.11
857 873 1.183549 TCTCGTAGCCTCCTTGAACC 58.816 55.000 0.00 0.00 0.00 3.62
1361 1699 1.575922 CGCAGCTGCAGCAGTAAAA 59.424 52.632 38.24 0.00 45.16 1.52
1415 1753 1.371267 CCGACTCGCGTTCACTGAA 60.371 57.895 5.77 0.00 38.67 3.02
1775 2218 6.121776 ACATAGACACAGTAATTTGGGACA 57.878 37.500 0.00 0.00 0.00 4.02
2488 3270 4.866508 TGGTACAGTCGACTGAAAATCT 57.133 40.909 43.55 26.37 46.59 2.40
2514 3297 4.138290 TCCTGTTCTCCTAATAGAGCTCG 58.862 47.826 8.37 0.00 33.66 5.03
2523 3306 2.505819 GCCCATCTTCCTGTTCTCCTAA 59.494 50.000 0.00 0.00 0.00 2.69
2731 3525 1.821759 CCACCGCACAAAGTCACCA 60.822 57.895 0.00 0.00 0.00 4.17
3183 4291 6.778834 ATGAGCACATCAACATCCATTTAA 57.221 33.333 0.00 0.00 42.53 1.52
3966 6981 2.174210 TGGTCGGGCTATGTACTACTCT 59.826 50.000 0.00 0.00 0.00 3.24
4253 7512 5.297029 GCCCTGTTCAACAAGGTAGATATTC 59.703 44.000 7.04 0.00 32.28 1.75
4459 7718 1.134818 CATGCTGGTTCATTGCTGCAT 60.135 47.619 1.84 0.00 41.08 3.96
4669 7935 2.733956 TCCGGAATGGGGATTTTCTTG 58.266 47.619 0.00 0.00 38.76 3.02
5124 8407 1.944676 CGAATACGTCAGGGAGCGC 60.945 63.158 0.00 0.00 34.56 5.92
5209 8501 3.947910 AAGCAATGTCCAAGGATTGTG 57.052 42.857 4.81 0.00 46.99 3.33
5384 8832 1.519246 CTGGAGCTTGGCGAGATCA 59.481 57.895 20.82 7.07 42.62 2.92
5531 8979 2.031163 GCGGGTGTGCTTCAGAGT 59.969 61.111 0.00 0.00 0.00 3.24
5659 9109 4.000988 TCCCGCAATAGAAGAACTTTCAC 58.999 43.478 0.00 0.00 0.00 3.18
5668 9118 4.209288 CGTAGACAAATCCCGCAATAGAAG 59.791 45.833 0.00 0.00 0.00 2.85
5671 9121 2.221055 GCGTAGACAAATCCCGCAATAG 59.779 50.000 0.00 0.00 42.36 1.73
5788 9253 8.397906 CAATGAAAAATAGGCAAGACGATTAGA 58.602 33.333 0.00 0.00 0.00 2.10
5945 9414 5.469210 AAGCCCTCGTATATAGTCCCTAT 57.531 43.478 0.00 0.00 0.00 2.57
5947 9416 3.829728 AAGCCCTCGTATATAGTCCCT 57.170 47.619 0.00 0.00 0.00 4.20
5948 9417 3.577415 ACAAAGCCCTCGTATATAGTCCC 59.423 47.826 0.00 0.00 0.00 4.46
5949 9418 4.868314 ACAAAGCCCTCGTATATAGTCC 57.132 45.455 0.00 0.00 0.00 3.85
5992 9466 7.883217 TCGTATGTAGTCCCTATTGAAATCTC 58.117 38.462 0.00 0.00 0.00 2.75
6050 9525 2.034053 GGCATGAAAAAGTTGTCACGGA 59.966 45.455 0.00 0.00 0.00 4.69
6065 9540 2.472463 GGGATGGGGATGGGCATGA 61.472 63.158 0.00 0.00 0.00 3.07
6073 9548 2.655407 AGACGAGTATAGGGATGGGGAT 59.345 50.000 0.00 0.00 0.00 3.85
6090 9565 5.432885 AAATATTTTTATCCCCGCAGACG 57.567 39.130 0.00 0.00 39.67 4.18
6117 9592 0.251608 AAAAACCTGATGGGACGGGG 60.252 55.000 0.00 0.00 40.34 5.73
6141 9616 1.796459 CGTGTCTAGGTTTTTCCACGG 59.204 52.381 0.00 0.00 41.24 4.94
6160 9635 7.273164 TGCTATTGAAGATTGTTGTTAATTGCG 59.727 33.333 0.00 0.00 31.01 4.85
6229 9704 6.017357 GCCCTAACCTAGCAACAACATATTAC 60.017 42.308 0.00 0.00 0.00 1.89
6230 9705 6.059484 GCCCTAACCTAGCAACAACATATTA 58.941 40.000 0.00 0.00 0.00 0.98
6231 9706 4.887655 GCCCTAACCTAGCAACAACATATT 59.112 41.667 0.00 0.00 0.00 1.28
6277 9752 0.863956 TTTTCACCCATCCCACCCTT 59.136 50.000 0.00 0.00 0.00 3.95
6278 9753 1.092549 ATTTTCACCCATCCCACCCT 58.907 50.000 0.00 0.00 0.00 4.34
6306 9781 4.813027 TCACGTGTAATTCCTGTCCTTAC 58.187 43.478 16.51 0.00 0.00 2.34
6362 9837 0.108662 CGTTACCCACCTTACCGGTC 60.109 60.000 12.40 0.00 44.93 4.79
6365 9840 0.321346 AACCGTTACCCACCTTACCG 59.679 55.000 0.00 0.00 0.00 4.02
6398 9873 1.766461 GACGGGGATGAGGATGGGT 60.766 63.158 0.00 0.00 0.00 4.51
6444 10057 2.424842 AATGCCCACGGGAAAGCTGA 62.425 55.000 6.21 0.00 37.50 4.26
6452 10065 0.173255 CAAGCTTTAATGCCCACGGG 59.827 55.000 9.56 0.00 38.57 5.28
6492 10105 9.950680 AAATGAGTGAGTTTACACACTAAAATG 57.049 29.630 11.97 0.00 45.42 2.32
6506 10119 6.006449 ACATAAGGAGCAAAATGAGTGAGTT 58.994 36.000 0.00 0.00 0.00 3.01
6573 10187 5.011533 GGCATCTGTGAGTAATACTCCATCT 59.988 44.000 16.89 3.71 44.44 2.90
6574 10188 5.221521 TGGCATCTGTGAGTAATACTCCATC 60.222 44.000 16.89 8.66 44.44 3.51
6575 10189 4.655649 TGGCATCTGTGAGTAATACTCCAT 59.344 41.667 16.89 2.46 44.44 3.41
6576 10190 4.030216 TGGCATCTGTGAGTAATACTCCA 58.970 43.478 16.89 12.92 44.44 3.86
6577 10191 4.672587 TGGCATCTGTGAGTAATACTCC 57.327 45.455 16.89 9.37 44.44 3.85
6578 10192 5.907207 TCTTGGCATCTGTGAGTAATACTC 58.093 41.667 13.20 13.20 45.26 2.59
6579 10193 5.939764 TCTTGGCATCTGTGAGTAATACT 57.060 39.130 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.