Multiple sequence alignment - TraesCS3D01G488700

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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 TraesCS3D01G488700 chr3D 100.000 8695 0 0 1 8695 583188300 583179606 0.000000e+00 16057.0
1 TraesCS3D01G488700 chr3D 94.616 4123 178 19 449 4562 583284706 583280619 0.000000e+00 6344.0
2 TraesCS3D01G488700 chr3D 92.895 2801 163 18 5225 8016 583279666 583276893 0.000000e+00 4037.0
3 TraesCS3D01G488700 chr3D 94.081 2534 130 13 136 2659 583182174 583179651 0.000000e+00 3831.0
4 TraesCS3D01G488700 chr3D 94.081 2534 130 13 6127 8650 583188165 583185642 0.000000e+00 3831.0
5 TraesCS3D01G488700 chr3D 95.660 2212 68 7 6440 8650 583284706 583282522 0.000000e+00 3528.0
6 TraesCS3D01G488700 chr3D 92.052 2164 128 16 2424 4553 583223355 583221202 0.000000e+00 3003.0
7 TraesCS3D01G488700 chr3D 94.030 1876 101 6 136 2011 583278779 583276915 0.000000e+00 2833.0
8 TraesCS3D01G488700 chr3D 88.983 2115 150 50 5930 8016 583170819 583168760 0.000000e+00 2538.0
9 TraesCS3D01G488700 chr3D 88.000 1875 166 35 136 2004 583170610 583168789 0.000000e+00 2161.0
10 TraesCS3D01G488700 chr3D 86.335 2049 169 65 5941 7952 583225657 583223683 0.000000e+00 2130.0
11 TraesCS3D01G488700 chr3D 85.978 1840 177 50 136 1964 583225452 583223683 0.000000e+00 1893.0
12 TraesCS3D01G488700 chr3D 89.832 1249 87 17 4685 5923 583190130 583188912 0.000000e+00 1567.0
13 TraesCS3D01G488700 chr3D 93.082 318 20 2 4840 5155 583280441 583280124 1.710000e-126 464.0
14 TraesCS3D01G488700 chr3D 82.878 549 59 18 5060 5601 599351149 599351669 2.210000e-125 460.0
15 TraesCS3D01G488700 chr3D 82.847 548 61 18 5060 5601 599363444 599363964 2.210000e-125 460.0
16 TraesCS3D01G488700 chr3D 95.911 269 8 3 8168 8434 583188904 583188637 4.820000e-117 433.0
17 TraesCS3D01G488700 chr3D 94.815 270 11 3 2175 2443 583188904 583188637 1.350000e-112 418.0
18 TraesCS3D01G488700 chr3D 86.972 284 32 3 4236 4519 583188629 583188351 1.820000e-81 315.0
19 TraesCS3D01G488700 chr3D 85.772 246 25 3 8415 8650 583223355 583223110 1.450000e-62 252.0
20 TraesCS3D01G488700 chr3B 93.090 3835 198 27 136 3957 780302615 780298835 0.000000e+00 5552.0
21 TraesCS3D01G488700 chr3B 91.286 4005 240 53 4675 8650 780304053 780300129 0.000000e+00 5361.0
22 TraesCS3D01G488700 chr3B 89.414 2749 228 25 5209 7952 780331304 780328614 0.000000e+00 3406.0
23 TraesCS3D01G488700 chr3B 86.169 2639 286 43 5228 7842 780297262 780294679 0.000000e+00 2778.0
24 TraesCS3D01G488700 chr3B 89.767 2101 168 30 5862 7952 780326943 780324880 0.000000e+00 2645.0
25 TraesCS3D01G488700 chr3B 89.719 2101 169 30 5862 7952 780322338 780320275 0.000000e+00 2639.0
26 TraesCS3D01G488700 chr3B 89.624 2101 171 29 5862 7952 780316964 780314901 0.000000e+00 2628.0
27 TraesCS3D01G488700 chr3B 88.575 2162 160 27 2407 4519 780339427 780337304 0.000000e+00 2543.0
28 TraesCS3D01G488700 chr3B 90.795 1836 141 17 136 1964 780330428 780328614 0.000000e+00 2429.0
29 TraesCS3D01G488700 chr3B 89.450 1962 129 33 2601 4519 780314286 780312360 0.000000e+00 2405.0
30 TraesCS3D01G488700 chr3B 89.455 1963 128 26 2601 4519 780324265 780322338 0.000000e+00 2405.0
31 TraesCS3D01G488700 chr3B 90.196 1836 139 23 136 1964 780322076 780320275 0.000000e+00 2355.0
32 TraesCS3D01G488700 chr3B 90.142 1836 140 23 136 1964 780326681 780324880 0.000000e+00 2350.0
33 TraesCS3D01G488700 chr3B 90.087 1836 141 23 136 1964 780316702 780314901 0.000000e+00 2344.0
34 TraesCS3D01G488700 chr3B 85.240 1748 196 45 136 1854 780296393 780294679 0.000000e+00 1742.0
35 TraesCS3D01G488700 chr3B 89.354 1099 95 13 4055 5137 780298825 780297733 0.000000e+00 1362.0
36 TraesCS3D01G488700 chr3B 91.600 881 63 3 4148 5019 780332516 780331638 0.000000e+00 1206.0
37 TraesCS3D01G488700 chr3B 83.886 1266 120 30 5052 6309 780307296 780306107 0.000000e+00 1131.0
38 TraesCS3D01G488700 chr3B 90.701 785 61 4 4148 4923 780308093 780307312 0.000000e+00 1035.0
39 TraesCS3D01G488700 chr3B 83.179 1082 119 26 4713 5782 780310002 780308972 0.000000e+00 931.0
40 TraesCS3D01G488700 chr3B 86.716 813 54 15 3728 4519 780317743 780316964 0.000000e+00 854.0
41 TraesCS3D01G488700 chr3B 86.716 813 54 15 3728 4519 780327722 780326943 0.000000e+00 854.0
42 TraesCS3D01G488700 chr3B 85.190 817 92 16 4769 5574 426822556 426823354 0.000000e+00 811.0
43 TraesCS3D01G488700 chr3B 83.416 808 85 22 4978 5782 780334171 780333410 0.000000e+00 704.0
44 TraesCS3D01G488700 chr3B 85.882 425 24 17 1543 1964 780340174 780339783 3.750000e-113 420.0
45 TraesCS3D01G488700 chr3B 85.445 371 36 10 306 672 780085267 780084911 3.830000e-98 370.0
46 TraesCS3D01G488700 chr3B 89.669 242 21 4 2601 2839 780327999 780327759 1.100000e-78 305.0
47 TraesCS3D01G488700 chr3B 85.496 262 29 3 8398 8650 780339427 780339166 1.860000e-66 265.0
48 TraesCS3D01G488700 chrUn 90.521 1688 105 19 2848 4513 352585812 352587466 0.000000e+00 2180.0
49 TraesCS3D01G488700 chrUn 90.103 485 33 9 5862 6343 352587472 352587944 4.460000e-172 616.0
50 TraesCS3D01G488700 chrUn 91.244 217 13 1 136 352 352587734 352587944 3.070000e-74 291.0
51 TraesCS3D01G488700 chr6A 88.274 1228 108 24 2834 4046 34278094 34276888 0.000000e+00 1437.0
52 TraesCS3D01G488700 chr6A 88.144 1223 114 19 2834 4045 34273292 34272090 0.000000e+00 1426.0
53 TraesCS3D01G488700 chr6A 82.022 1474 183 39 2456 3883 34280563 34279126 0.000000e+00 1179.0
54 TraesCS3D01G488700 chr6A 80.586 1638 216 45 2292 3882 34282693 34281111 0.000000e+00 1170.0
55 TraesCS3D01G488700 chr6A 81.684 1485 188 45 2456 3883 34393150 34391693 0.000000e+00 1158.0
56 TraesCS3D01G488700 chr6A 75.526 380 47 18 8282 8650 34282693 34282349 2.530000e-30 145.0
57 TraesCS3D01G488700 chr6A 79.147 211 32 8 8447 8650 34393150 34392945 1.520000e-27 135.0
58 TraesCS3D01G488700 chr6A 79.227 207 26 3 8447 8650 34280563 34280371 2.550000e-25 128.0
59 TraesCS3D01G488700 chr7D 82.971 1104 145 22 4517 5601 2221246 2222325 0.000000e+00 957.0
60 TraesCS3D01G488700 chr7D 92.500 40 3 0 5702 5741 631322050 631322089 3.390000e-04 58.4
61 TraesCS3D01G488700 chr3A 80.841 1070 124 34 4777 5831 626033291 626034294 0.000000e+00 765.0
62 TraesCS3D01G488700 chr3A 81.543 661 93 17 4521 5162 519205902 519206552 1.290000e-142 518.0
63 TraesCS3D01G488700 chr3A 82.973 370 46 13 4521 4883 443143 442784 1.410000e-82 318.0
64 TraesCS3D01G488700 chr4D 83.942 548 60 12 5060 5601 401794812 401794287 4.690000e-137 499.0
65 TraesCS3D01G488700 chr1A 86.461 421 45 5 5185 5601 566570133 566570545 1.330000e-122 451.0
66 TraesCS3D01G488700 chr7A 77.570 642 134 9 4520 5155 36556406 36557043 6.370000e-101 379.0
67 TraesCS3D01G488700 chr7A 100.000 33 0 0 8000 8032 287849856 287849888 2.620000e-05 62.1
68 TraesCS3D01G488700 chr1B 83.333 372 49 11 4517 4883 593010777 593010414 1.810000e-86 331.0
69 TraesCS3D01G488700 chr5D 81.795 390 58 11 4518 4904 3250768 3251147 1.820000e-81 315.0
70 TraesCS3D01G488700 chr6D 81.141 403 57 14 4518 4913 458747950 458748340 1.100000e-78 305.0
71 TraesCS3D01G488700 chr2D 87.097 93 8 4 5701 5792 522996572 522996483 1.540000e-17 102.0
72 TraesCS3D01G488700 chr7B 95.238 42 2 0 8414 8455 244635311 244635352 5.630000e-07 67.6
73 TraesCS3D01G488700 chr7B 92.857 42 3 0 2423 2464 244635311 244635352 2.620000e-05 62.1


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 TraesCS3D01G488700 chr3D 583179606 583188300 8694 True 16057.000000 16057 100.000000 1 8695 1 chr3D.!!$R1 8694
1 TraesCS3D01G488700 chr3D 583276893 583284706 7813 True 3441.200000 6344 94.056600 136 8650 5 chr3D.!!$R5 8514
2 TraesCS3D01G488700 chr3D 583168760 583170819 2059 True 2349.500000 2538 88.491500 136 8016 2 chr3D.!!$R2 7880
3 TraesCS3D01G488700 chr3D 583221202 583225657 4455 True 1819.500000 3003 87.534250 136 8650 4 chr3D.!!$R4 8514
4 TraesCS3D01G488700 chr3D 583179651 583190130 10479 True 1732.500000 3831 92.615333 136 8650 6 chr3D.!!$R3 8514
5 TraesCS3D01G488700 chr3D 599351149 599351669 520 False 460.000000 460 82.878000 5060 5601 1 chr3D.!!$F1 541
6 TraesCS3D01G488700 chr3D 599363444 599363964 520 False 460.000000 460 82.847000 5060 5601 1 chr3D.!!$F2 541
7 TraesCS3D01G488700 chr3B 780294679 780340174 45495 True 2024.961538 5552 88.447077 136 8650 26 chr3B.!!$R2 8514
8 TraesCS3D01G488700 chr3B 426822556 426823354 798 False 811.000000 811 85.190000 4769 5574 1 chr3B.!!$F1 805
9 TraesCS3D01G488700 chrUn 352585812 352587944 2132 False 1029.000000 2180 90.622667 136 6343 3 chrUn.!!$F1 6207
10 TraesCS3D01G488700 chr6A 34272090 34282693 10603 True 914.166667 1437 82.296500 2292 8650 6 chr6A.!!$R1 6358
11 TraesCS3D01G488700 chr6A 34391693 34393150 1457 True 646.500000 1158 80.415500 2456 8650 2 chr6A.!!$R2 6194
12 TraesCS3D01G488700 chr7D 2221246 2222325 1079 False 957.000000 957 82.971000 4517 5601 1 chr7D.!!$F1 1084
13 TraesCS3D01G488700 chr3A 626033291 626034294 1003 False 765.000000 765 80.841000 4777 5831 1 chr3A.!!$F2 1054
14 TraesCS3D01G488700 chr3A 519205902 519206552 650 False 518.000000 518 81.543000 4521 5162 1 chr3A.!!$F1 641
15 TraesCS3D01G488700 chr4D 401794287 401794812 525 True 499.000000 499 83.942000 5060 5601 1 chr4D.!!$R1 541
16 TraesCS3D01G488700 chr7A 36556406 36557043 637 False 379.000000 379 77.570000 4520 5155 1 chr7A.!!$F1 635

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
132 133 1.798223 CTTTTCACTCAATGGCGACGA 59.202 47.619 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
8650 51565 1.97064 TGAGTAGCATGACCACTGTGT 59.029 47.619 7.08 0.0 0.0 3.72 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
46 47 8.809468 AATATACTTCTGTTTCTTTCTTCCCC 57.191 34.615 0.00 0.00 0.00 4.81
47 48 3.833732 ACTTCTGTTTCTTTCTTCCCCC 58.166 45.455 0.00 0.00 0.00 5.40
48 49 3.463704 ACTTCTGTTTCTTTCTTCCCCCT 59.536 43.478 0.00 0.00 0.00 4.79
50 51 2.783510 TCTGTTTCTTTCTTCCCCCTGT 59.216 45.455 0.00 0.00 0.00 4.00
51 52 3.204382 TCTGTTTCTTTCTTCCCCCTGTT 59.796 43.478 0.00 0.00 0.00 3.16
52 53 4.414182 TCTGTTTCTTTCTTCCCCCTGTTA 59.586 41.667 0.00 0.00 0.00 2.41
53 54 4.466827 TGTTTCTTTCTTCCCCCTGTTAC 58.533 43.478 0.00 0.00 0.00 2.50
55 56 5.077564 GTTTCTTTCTTCCCCCTGTTACAT 58.922 41.667 0.00 0.00 0.00 2.29
56 57 5.333566 TTCTTTCTTCCCCCTGTTACATT 57.666 39.130 0.00 0.00 0.00 2.71
57 58 4.662278 TCTTTCTTCCCCCTGTTACATTG 58.338 43.478 0.00 0.00 0.00 2.82
59 60 5.311121 TCTTTCTTCCCCCTGTTACATTGTA 59.689 40.000 0.00 0.00 0.00 2.41
61 62 3.054655 TCTTCCCCCTGTTACATTGTAGC 60.055 47.826 3.91 3.91 0.00 3.58
62 63 2.557869 TCCCCCTGTTACATTGTAGCT 58.442 47.619 11.30 0.00 0.00 3.32
63 64 3.726790 TCCCCCTGTTACATTGTAGCTA 58.273 45.455 11.30 0.00 0.00 3.32
64 65 4.105577 TCCCCCTGTTACATTGTAGCTAA 58.894 43.478 11.30 0.00 0.00 3.09
65 66 4.163458 TCCCCCTGTTACATTGTAGCTAAG 59.837 45.833 11.30 2.57 0.00 2.18
66 67 4.163458 CCCCCTGTTACATTGTAGCTAAGA 59.837 45.833 11.30 0.00 0.00 2.10
67 68 5.338871 CCCCCTGTTACATTGTAGCTAAGAA 60.339 44.000 11.30 0.00 0.00 2.52
69 70 6.828785 CCCCTGTTACATTGTAGCTAAGAATT 59.171 38.462 11.30 0.00 0.00 2.17
70 71 7.339466 CCCCTGTTACATTGTAGCTAAGAATTT 59.661 37.037 11.30 0.00 0.00 1.82
71 72 8.184192 CCCTGTTACATTGTAGCTAAGAATTTG 58.816 37.037 11.30 0.00 0.00 2.32
73 74 9.546909 CTGTTACATTGTAGCTAAGAATTTGTG 57.453 33.333 11.30 0.00 0.00 3.33
74 75 9.278978 TGTTACATTGTAGCTAAGAATTTGTGA 57.721 29.630 11.30 0.00 0.00 3.58
75 76 9.760660 GTTACATTGTAGCTAAGAATTTGTGAG 57.239 33.333 0.00 0.00 0.00 3.51
77 78 8.621532 ACATTGTAGCTAAGAATTTGTGAGAA 57.378 30.769 0.00 0.00 0.00 2.87
78 79 9.066892 ACATTGTAGCTAAGAATTTGTGAGAAA 57.933 29.630 0.00 0.00 0.00 2.52
79 80 9.552114 CATTGTAGCTAAGAATTTGTGAGAAAG 57.448 33.333 0.00 0.00 0.00 2.62
81 82 8.677148 TGTAGCTAAGAATTTGTGAGAAAGTT 57.323 30.769 0.00 0.00 0.00 2.66
82 83 9.120538 TGTAGCTAAGAATTTGTGAGAAAGTTT 57.879 29.630 0.00 0.00 0.00 2.66
85 86 8.568794 AGCTAAGAATTTGTGAGAAAGTTTACC 58.431 33.333 0.00 0.00 0.00 2.85
89 90 8.062065 AGAATTTGTGAGAAAGTTTACCAACA 57.938 30.769 0.00 0.00 35.05 3.33
91 92 9.959749 GAATTTGTGAGAAAGTTTACCAACATA 57.040 29.630 0.00 0.00 35.05 2.29
96 97 7.865385 TGTGAGAAAGTTTACCAACATATTTGC 59.135 33.333 0.00 0.00 35.05 3.68
97 98 7.328493 GTGAGAAAGTTTACCAACATATTTGCC 59.672 37.037 0.00 0.00 35.05 4.52
98 99 7.232534 TGAGAAAGTTTACCAACATATTTGCCT 59.767 33.333 0.00 0.00 35.05 4.75
99 100 7.602753 AGAAAGTTTACCAACATATTTGCCTC 58.397 34.615 0.00 0.00 35.05 4.70
100 101 7.451566 AGAAAGTTTACCAACATATTTGCCTCT 59.548 33.333 0.00 0.00 35.05 3.69
101 102 7.539034 AAGTTTACCAACATATTTGCCTCTT 57.461 32.000 0.00 0.00 35.05 2.85
102 103 7.158099 AGTTTACCAACATATTTGCCTCTTC 57.842 36.000 0.00 0.00 35.05 2.87
103 104 6.719370 AGTTTACCAACATATTTGCCTCTTCA 59.281 34.615 0.00 0.00 35.05 3.02
104 105 7.232534 AGTTTACCAACATATTTGCCTCTTCAA 59.767 33.333 0.00 0.00 35.05 2.69
105 106 5.391312 ACCAACATATTTGCCTCTTCAAC 57.609 39.130 0.00 0.00 0.00 3.18
106 107 5.079643 ACCAACATATTTGCCTCTTCAACT 58.920 37.500 0.00 0.00 0.00 3.16
109 110 8.052748 ACCAACATATTTGCCTCTTCAACTATA 58.947 33.333 0.00 0.00 0.00 1.31
110 111 8.902806 CCAACATATTTGCCTCTTCAACTATAA 58.097 33.333 0.00 0.00 0.00 0.98
119 120 8.268850 TGCCTCTTCAACTATAATCTTTTCAC 57.731 34.615 0.00 0.00 0.00 3.18
120 121 8.103305 TGCCTCTTCAACTATAATCTTTTCACT 58.897 33.333 0.00 0.00 0.00 3.41
121 122 8.608317 GCCTCTTCAACTATAATCTTTTCACTC 58.392 37.037 0.00 0.00 0.00 3.51
122 123 9.658799 CCTCTTCAACTATAATCTTTTCACTCA 57.341 33.333 0.00 0.00 0.00 3.41
128 129 7.251704 ACTATAATCTTTTCACTCAATGGCG 57.748 36.000 0.00 0.00 0.00 5.69
129 130 7.047891 ACTATAATCTTTTCACTCAATGGCGA 58.952 34.615 0.00 0.00 0.00 5.54
130 131 4.425577 AATCTTTTCACTCAATGGCGAC 57.574 40.909 0.00 0.00 0.00 5.19
132 133 1.798223 CTTTTCACTCAATGGCGACGA 59.202 47.619 0.00 0.00 0.00 4.20
133 134 2.093306 TTTCACTCAATGGCGACGAT 57.907 45.000 0.00 0.00 0.00 3.73
134 135 2.093306 TTCACTCAATGGCGACGATT 57.907 45.000 0.00 0.00 0.00 3.34
135 136 2.093306 TCACTCAATGGCGACGATTT 57.907 45.000 0.00 0.00 0.00 2.17
136 137 3.239587 TCACTCAATGGCGACGATTTA 57.760 42.857 0.00 0.00 0.00 1.40
138 139 3.802139 TCACTCAATGGCGACGATTTATC 59.198 43.478 0.00 0.00 0.00 1.75
675 14107 4.997395 GCTTGAACTGACAAGATTCCACTA 59.003 41.667 17.72 0.00 46.85 2.74
8655 51570 2.464865 GCTAGGTTAGCGATCACACAG 58.535 52.381 0.00 0.00 42.62 3.66
8667 52362 2.455674 TCACACAGTGGTCATGCTAC 57.544 50.000 5.31 0.00 33.87 3.58
8669 52364 2.029020 TCACACAGTGGTCATGCTACTC 60.029 50.000 5.31 0.00 36.75 2.59
8672 52367 1.970640 ACAGTGGTCATGCTACTCACA 59.029 47.619 0.00 0.00 36.75 3.58
8673 52368 2.289072 ACAGTGGTCATGCTACTCACAC 60.289 50.000 0.00 0.00 36.75 3.82
8675 52370 2.028658 AGTGGTCATGCTACTCACACAG 60.029 50.000 0.00 0.00 33.33 3.66
8676 52371 1.970640 TGGTCATGCTACTCACACAGT 59.029 47.619 0.00 0.00 39.41 3.55
8677 52372 2.289010 TGGTCATGCTACTCACACAGTG 60.289 50.000 0.00 0.00 36.43 3.66
8678 52373 2.341257 GTCATGCTACTCACACAGTGG 58.659 52.381 5.31 0.00 36.43 4.00
8679 52374 1.970640 TCATGCTACTCACACAGTGGT 59.029 47.619 5.31 0.00 35.98 4.16
8680 52375 2.368548 TCATGCTACTCACACAGTGGTT 59.631 45.455 5.31 0.00 35.98 3.67
8681 52376 2.238942 TGCTACTCACACAGTGGTTG 57.761 50.000 5.31 0.00 35.98 3.77
8683 52378 1.512926 CTACTCACACAGTGGTTGGC 58.487 55.000 5.31 0.00 36.43 4.52
8684 52379 1.070758 CTACTCACACAGTGGTTGGCT 59.929 52.381 5.31 0.00 36.43 4.75
8685 52380 0.464373 ACTCACACAGTGGTTGGCTG 60.464 55.000 5.31 0.00 39.67 4.85
8686 52381 0.179048 CTCACACAGTGGTTGGCTGA 60.179 55.000 5.31 0.00 37.40 4.26
8688 52383 1.102154 CACACAGTGGTTGGCTGAAA 58.898 50.000 5.31 0.00 37.40 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.184753 AGGGGGAAGAAAGAAACAGAAGTATAT 59.815 37.037 0.00 0.0 0.00 0.86
23 24 6.504279 AGGGGGAAGAAAGAAACAGAAGTATA 59.496 38.462 0.00 0.0 0.00 1.47
24 25 5.313506 AGGGGGAAGAAAGAAACAGAAGTAT 59.686 40.000 0.00 0.0 0.00 2.12
25 26 4.663592 AGGGGGAAGAAAGAAACAGAAGTA 59.336 41.667 0.00 0.0 0.00 2.24
28 29 3.204382 ACAGGGGGAAGAAAGAAACAGAA 59.796 43.478 0.00 0.0 0.00 3.02
29 30 2.783510 ACAGGGGGAAGAAAGAAACAGA 59.216 45.455 0.00 0.0 0.00 3.41
30 31 3.229697 ACAGGGGGAAGAAAGAAACAG 57.770 47.619 0.00 0.0 0.00 3.16
31 32 3.680777 AACAGGGGGAAGAAAGAAACA 57.319 42.857 0.00 0.0 0.00 2.83
32 33 4.466827 TGTAACAGGGGGAAGAAAGAAAC 58.533 43.478 0.00 0.0 0.00 2.78
33 34 4.799715 TGTAACAGGGGGAAGAAAGAAA 57.200 40.909 0.00 0.0 0.00 2.52
34 35 5.076873 CAATGTAACAGGGGGAAGAAAGAA 58.923 41.667 0.00 0.0 0.00 2.52
35 36 4.105697 ACAATGTAACAGGGGGAAGAAAGA 59.894 41.667 0.00 0.0 0.00 2.52
36 37 4.407365 ACAATGTAACAGGGGGAAGAAAG 58.593 43.478 0.00 0.0 0.00 2.62
37 38 4.463050 ACAATGTAACAGGGGGAAGAAA 57.537 40.909 0.00 0.0 0.00 2.52
40 41 3.054361 AGCTACAATGTAACAGGGGGAAG 60.054 47.826 0.00 0.0 0.00 3.46
43 44 4.163458 TCTTAGCTACAATGTAACAGGGGG 59.837 45.833 0.00 0.0 0.00 5.40
44 45 5.353394 TCTTAGCTACAATGTAACAGGGG 57.647 43.478 0.00 0.0 0.00 4.79
45 46 7.865706 AATTCTTAGCTACAATGTAACAGGG 57.134 36.000 0.00 0.0 0.00 4.45
46 47 8.730680 ACAAATTCTTAGCTACAATGTAACAGG 58.269 33.333 0.00 0.0 0.00 4.00
47 48 9.546909 CACAAATTCTTAGCTACAATGTAACAG 57.453 33.333 0.00 0.0 0.00 3.16
48 49 9.278978 TCACAAATTCTTAGCTACAATGTAACA 57.721 29.630 0.00 0.0 0.00 2.41
50 51 9.719355 TCTCACAAATTCTTAGCTACAATGTAA 57.281 29.630 0.00 0.0 0.00 2.41
51 52 9.719355 TTCTCACAAATTCTTAGCTACAATGTA 57.281 29.630 0.00 0.0 0.00 2.29
52 53 8.621532 TTCTCACAAATTCTTAGCTACAATGT 57.378 30.769 0.00 0.0 0.00 2.71
53 54 9.552114 CTTTCTCACAAATTCTTAGCTACAATG 57.448 33.333 0.00 0.0 0.00 2.82
55 56 8.677148 ACTTTCTCACAAATTCTTAGCTACAA 57.323 30.769 0.00 0.0 0.00 2.41
56 57 8.677148 AACTTTCTCACAAATTCTTAGCTACA 57.323 30.769 0.00 0.0 0.00 2.74
59 60 8.568794 GGTAAACTTTCTCACAAATTCTTAGCT 58.431 33.333 0.00 0.0 0.00 3.32
63 64 8.527810 TGTTGGTAAACTTTCTCACAAATTCTT 58.472 29.630 0.00 0.0 37.19 2.52
64 65 8.062065 TGTTGGTAAACTTTCTCACAAATTCT 57.938 30.769 0.00 0.0 37.19 2.40
65 66 8.871686 ATGTTGGTAAACTTTCTCACAAATTC 57.128 30.769 0.00 0.0 37.19 2.17
69 70 9.743057 CAAATATGTTGGTAAACTTTCTCACAA 57.257 29.630 0.00 0.0 37.19 3.33
70 71 7.865385 GCAAATATGTTGGTAAACTTTCTCACA 59.135 33.333 0.00 0.0 37.19 3.58
71 72 7.328493 GGCAAATATGTTGGTAAACTTTCTCAC 59.672 37.037 0.00 0.0 37.19 3.51
73 74 7.602753 AGGCAAATATGTTGGTAAACTTTCTC 58.397 34.615 0.00 0.0 37.19 2.87
74 75 7.451566 AGAGGCAAATATGTTGGTAAACTTTCT 59.548 33.333 0.00 0.0 37.19 2.52
75 76 7.602753 AGAGGCAAATATGTTGGTAAACTTTC 58.397 34.615 0.00 0.0 37.19 2.62
77 78 7.232534 TGAAGAGGCAAATATGTTGGTAAACTT 59.767 33.333 0.00 0.0 37.19 2.66
78 79 6.719370 TGAAGAGGCAAATATGTTGGTAAACT 59.281 34.615 0.00 0.0 37.19 2.66
79 80 6.919721 TGAAGAGGCAAATATGTTGGTAAAC 58.080 36.000 0.00 0.0 36.78 2.01
81 82 6.719370 AGTTGAAGAGGCAAATATGTTGGTAA 59.281 34.615 0.00 0.0 0.00 2.85
82 83 6.245408 AGTTGAAGAGGCAAATATGTTGGTA 58.755 36.000 0.00 0.0 0.00 3.25
83 84 5.079643 AGTTGAAGAGGCAAATATGTTGGT 58.920 37.500 0.00 0.0 0.00 3.67
84 85 5.649782 AGTTGAAGAGGCAAATATGTTGG 57.350 39.130 0.00 0.0 0.00 3.77
92 93 9.295825 TGAAAAGATTATAGTTGAAGAGGCAAA 57.704 29.630 0.00 0.0 0.00 3.68
93 94 8.730680 GTGAAAAGATTATAGTTGAAGAGGCAA 58.269 33.333 0.00 0.0 0.00 4.52
94 95 8.103305 AGTGAAAAGATTATAGTTGAAGAGGCA 58.897 33.333 0.00 0.0 0.00 4.75
96 97 9.658799 TGAGTGAAAAGATTATAGTTGAAGAGG 57.341 33.333 0.00 0.0 0.00 3.69
101 102 8.677300 GCCATTGAGTGAAAAGATTATAGTTGA 58.323 33.333 0.00 0.0 0.00 3.18
102 103 7.641411 CGCCATTGAGTGAAAAGATTATAGTTG 59.359 37.037 0.00 0.0 0.00 3.16
103 104 7.552687 TCGCCATTGAGTGAAAAGATTATAGTT 59.447 33.333 0.00 0.0 0.00 2.24
104 105 7.011482 GTCGCCATTGAGTGAAAAGATTATAGT 59.989 37.037 0.00 0.0 0.00 2.12
105 106 7.348201 GTCGCCATTGAGTGAAAAGATTATAG 58.652 38.462 0.00 0.0 0.00 1.31
106 107 6.019075 CGTCGCCATTGAGTGAAAAGATTATA 60.019 38.462 0.00 0.0 0.00 0.98
109 110 3.120199 CGTCGCCATTGAGTGAAAAGATT 60.120 43.478 0.00 0.0 0.00 2.40
110 111 2.416547 CGTCGCCATTGAGTGAAAAGAT 59.583 45.455 0.00 0.0 0.00 2.40
111 112 1.798223 CGTCGCCATTGAGTGAAAAGA 59.202 47.619 0.00 0.0 0.00 2.52
112 113 1.798223 TCGTCGCCATTGAGTGAAAAG 59.202 47.619 0.00 0.0 0.00 2.27
114 115 2.093306 ATCGTCGCCATTGAGTGAAA 57.907 45.000 0.00 0.0 0.00 2.69
115 116 2.093306 AATCGTCGCCATTGAGTGAA 57.907 45.000 0.00 0.0 0.00 3.18
116 117 2.093306 AAATCGTCGCCATTGAGTGA 57.907 45.000 0.00 0.0 0.00 3.41
117 118 3.804325 AGATAAATCGTCGCCATTGAGTG 59.196 43.478 0.00 0.0 0.00 3.51
119 120 6.366061 TGAATAGATAAATCGTCGCCATTGAG 59.634 38.462 0.00 0.0 0.00 3.02
120 121 6.145534 GTGAATAGATAAATCGTCGCCATTGA 59.854 38.462 0.00 0.0 0.00 2.57
121 122 6.073819 TGTGAATAGATAAATCGTCGCCATTG 60.074 38.462 0.00 0.0 0.00 2.82
122 123 5.989168 TGTGAATAGATAAATCGTCGCCATT 59.011 36.000 0.00 0.0 0.00 3.16
124 125 4.939271 TGTGAATAGATAAATCGTCGCCA 58.061 39.130 0.00 0.0 0.00 5.69
125 126 5.220381 TCTGTGAATAGATAAATCGTCGCC 58.780 41.667 0.00 0.0 0.00 5.54
126 127 6.749216 TTCTGTGAATAGATAAATCGTCGC 57.251 37.500 0.00 0.0 0.00 5.19
128 129 8.592998 ACGTTTTCTGTGAATAGATAAATCGTC 58.407 33.333 0.00 0.0 0.00 4.20
129 130 8.475331 ACGTTTTCTGTGAATAGATAAATCGT 57.525 30.769 0.00 0.0 0.00 3.73
133 134 9.210329 TGCTTACGTTTTCTGTGAATAGATAAA 57.790 29.630 0.00 0.0 0.00 1.40
134 135 8.766000 TGCTTACGTTTTCTGTGAATAGATAA 57.234 30.769 0.00 0.0 0.00 1.75
135 136 8.942338 ATGCTTACGTTTTCTGTGAATAGATA 57.058 30.769 0.00 0.0 0.00 1.98
136 137 7.849804 ATGCTTACGTTTTCTGTGAATAGAT 57.150 32.000 0.00 0.0 0.00 1.98
138 139 8.728088 AAAATGCTTACGTTTTCTGTGAATAG 57.272 30.769 0.00 0.0 40.21 1.73
8650 51565 1.970640 TGAGTAGCATGACCACTGTGT 59.029 47.619 7.08 0.0 0.00 3.72
8651 51566 2.289010 TGTGAGTAGCATGACCACTGTG 60.289 50.000 0.00 0.0 0.00 3.66
8652 51567 1.970640 TGTGAGTAGCATGACCACTGT 59.029 47.619 0.00 0.0 0.00 3.55
8653 51568 2.289010 TGTGTGAGTAGCATGACCACTG 60.289 50.000 0.00 0.0 0.00 3.66
8655 51570 2.289072 ACTGTGTGAGTAGCATGACCAC 60.289 50.000 0.00 0.0 30.86 4.16
8667 52362 0.179048 TCAGCCAACCACTGTGTGAG 60.179 55.000 7.08 0.0 35.23 3.51
8669 52364 1.066002 CTTTCAGCCAACCACTGTGTG 59.934 52.381 7.08 0.0 36.50 3.82
8672 52367 2.419057 GCTTTCAGCCAACCACTGT 58.581 52.632 0.00 0.0 34.48 3.55


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

AutoCloner maintained by Alex Coulton.