Multiple sequence alignment - TraesCS3D01G408500

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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 TraesCS3D01G408500 chr3D 100.000 6316 0 0 1 6316 522957280 522950965 0.000000e+00 11664
1 TraesCS3D01G408500 chr3D 97.110 865 25 0 5452 6316 603319158 603318294 0.000000e+00 1459
2 TraesCS3D01G408500 chr3A 93.486 4590 192 56 1 4568 657621755 657617251 0.000000e+00 6721
3 TraesCS3D01G408500 chr3A 88.792 919 57 20 4564 5443 657616948 657616037 0.000000e+00 1085
4 TraesCS3D01G408500 chr3B 92.605 4341 184 56 1071 5349 689427697 689423432 0.000000e+00 6111
5 TraesCS3D01G408500 chr3B 96.412 864 29 2 5453 6316 168701539 168700678 0.000000e+00 1423
6 TraesCS3D01G408500 chr3B 93.838 714 41 3 1 714 689428925 689428215 0.000000e+00 1072
7 TraesCS3D01G408500 chr3B 90.256 195 9 4 747 940 689428217 689428032 4.890000e-61 246
8 TraesCS3D01G408500 chr5D 97.474 871 22 0 5446 6316 413676696 413675826 0.000000e+00 1487
9 TraesCS3D01G408500 chr5D 96.339 874 28 2 5446 6316 510558396 510557524 0.000000e+00 1434
10 TraesCS3D01G408500 chr2D 96.904 872 26 1 5446 6316 102292437 102291566 0.000000e+00 1459
11 TraesCS3D01G408500 chr2D 91.870 369 30 0 1713 2081 467630896 467630528 3.380000e-142 516
12 TraesCS3D01G408500 chr1D 96.647 865 29 0 5452 6316 58118479 58117615 0.000000e+00 1437
13 TraesCS3D01G408500 chr4A 96.647 865 28 1 5452 6316 652091591 652092454 0.000000e+00 1435
14 TraesCS3D01G408500 chr4A 96.420 866 29 2 5452 6316 724797308 724796444 0.000000e+00 1426
15 TraesCS3D01G408500 chr7B 96.420 866 29 2 5451 6316 9677601 9678464 0.000000e+00 1426
16 TraesCS3D01G408500 chrUn 94.920 374 19 0 1399 1772 71035816 71035443 2.540000e-163 586
17 TraesCS3D01G408500 chrUn 90.968 310 28 0 1772 2081 71030299 71029990 9.790000e-113 418
18 TraesCS3D01G408500 chrUn 90.968 310 28 0 1772 2081 408523804 408524113 9.790000e-113 418
19 TraesCS3D01G408500 chr4D 94.851 369 19 0 1713 2081 12844001 12844369 1.530000e-160 577
20 TraesCS3D01G408500 chr4D 92.935 368 26 0 1714 2081 197324233 197323866 2.590000e-148 536
21 TraesCS3D01G408500 chr7A 94.038 369 22 0 1713 2081 337925086 337925454 1.540000e-155 560
22 TraesCS3D01G408500 chr7A 82.353 119 17 4 1336 1452 694018867 694018751 4.030000e-17 100
23 TraesCS3D01G408500 chr2B 93.478 368 24 0 1713 2080 703575425 703575792 1.200000e-151 547
24 TraesCS3D01G408500 chr4B 90.515 369 33 1 1713 2081 509258071 509258437 2.650000e-133 486
25 TraesCS3D01G408500 chr7D 82.353 119 17 4 1336 1452 602189551 602189435 4.030000e-17 100


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 TraesCS3D01G408500 chr3D 522950965 522957280 6315 True 11664.000000 11664 100.000 1 6316 1 chr3D.!!$R1 6315
1 TraesCS3D01G408500 chr3D 603318294 603319158 864 True 1459.000000 1459 97.110 5452 6316 1 chr3D.!!$R2 864
2 TraesCS3D01G408500 chr3A 657616037 657621755 5718 True 3903.000000 6721 91.139 1 5443 2 chr3A.!!$R1 5442
3 TraesCS3D01G408500 chr3B 689423432 689428925 5493 True 2476.333333 6111 92.233 1 5349 3 chr3B.!!$R2 5348
4 TraesCS3D01G408500 chr3B 168700678 168701539 861 True 1423.000000 1423 96.412 5453 6316 1 chr3B.!!$R1 863
5 TraesCS3D01G408500 chr5D 413675826 413676696 870 True 1487.000000 1487 97.474 5446 6316 1 chr5D.!!$R1 870
6 TraesCS3D01G408500 chr5D 510557524 510558396 872 True 1434.000000 1434 96.339 5446 6316 1 chr5D.!!$R2 870
7 TraesCS3D01G408500 chr2D 102291566 102292437 871 True 1459.000000 1459 96.904 5446 6316 1 chr2D.!!$R1 870
8 TraesCS3D01G408500 chr1D 58117615 58118479 864 True 1437.000000 1437 96.647 5452 6316 1 chr1D.!!$R1 864
9 TraesCS3D01G408500 chr4A 652091591 652092454 863 False 1435.000000 1435 96.647 5452 6316 1 chr4A.!!$F1 864
10 TraesCS3D01G408500 chr4A 724796444 724797308 864 True 1426.000000 1426 96.420 5452 6316 1 chr4A.!!$R1 864
11 TraesCS3D01G408500 chr7B 9677601 9678464 863 False 1426.000000 1426 96.420 5451 6316 1 chr7B.!!$F1 865

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
92 93 0.248417 CTCTCATCTCCGTCAGTGCG 60.248 60.000 0.71 0.71 0.00 5.34 F
1099 1312 0.395311 CGTACCTCCACCTCCAGCTA 60.395 60.000 0.00 0.00 0.00 3.32 F
2236 2495 0.251341 TCTTTCCAAAGGGAGCTGCC 60.251 55.000 18.04 18.04 46.01 4.85 F
2620 2880 2.311462 CTTGAAGTGTGTCTCGAGTCG 58.689 52.381 13.13 6.09 0.00 4.18 F
2635 2895 3.132160 CGAGTCGGCTTGTAGATCTCTA 58.868 50.000 4.10 0.00 0.00 2.43 F
3409 3669 3.374988 TGCTGGCTACTTTTGAATGATCG 59.625 43.478 0.00 0.00 0.00 3.69 F
4107 4373 2.362169 AAGCGTTCTTCTCTCTCTGC 57.638 50.000 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 1748 0.747255 TGAATCGGCAGAGAGGTAGC 59.253 55.000 0.00 0.00 0.00 3.58 R
2590 2850 1.082756 CACTTCAAGCGCACGGAAC 60.083 57.895 11.47 0.00 0.00 3.62 R
3409 3669 0.108138 ATAGAGGTCGCACAAGCACC 60.108 55.000 0.00 0.00 42.27 5.01 R
3492 3752 3.403051 AGATATAGAGGTAGGTGGTGGCT 59.597 47.826 0.00 0.00 0.00 4.75 R
3551 3811 4.292186 AGGAGTGCAGAAGATTTAAGCA 57.708 40.909 0.00 0.00 0.00 3.91 R
4669 5248 0.982852 TCGAGAGCATGACCCCCATT 60.983 55.000 0.00 0.00 31.94 3.16 R
5759 6382 1.349688 TCCATGAACCCTAACGCTGTT 59.650 47.619 0.00 0.02 0.00 3.16 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
36 37 1.067250 ATGCCAACACCAACGCAAC 59.933 52.632 0.00 0.00 34.38 4.17
92 93 0.248417 CTCTCATCTCCGTCAGTGCG 60.248 60.000 0.71 0.71 0.00 5.34
112 113 2.474816 GATCGGCAACCTCATCACTAC 58.525 52.381 0.00 0.00 0.00 2.73
207 208 1.884579 GGCTATGCTGATGGTTCCATG 59.115 52.381 9.21 0.00 0.00 3.66
268 269 3.455910 TGTTGCCAGTAGATAGCCAATCT 59.544 43.478 4.70 4.70 46.95 2.40
269 270 4.061596 GTTGCCAGTAGATAGCCAATCTC 58.938 47.826 2.56 0.00 44.17 2.75
275 276 5.221342 CCAGTAGATAGCCAATCTCGACTTT 60.221 44.000 2.56 0.00 44.17 2.66
320 321 4.341366 TCACACTGTCATGATCACACTT 57.659 40.909 0.00 0.00 0.00 3.16
401 402 4.080863 GTCCTTTGGTCTACACTCCATGAT 60.081 45.833 0.00 0.00 33.50 2.45
404 405 5.994054 CCTTTGGTCTACACTCCATGATATG 59.006 44.000 0.00 0.00 33.50 1.78
499 500 6.450545 TCTCGGCTCTTGAATATTATCACAG 58.549 40.000 0.00 0.00 0.00 3.66
578 579 0.554792 CAATCTTGCCCCTCCTCCAT 59.445 55.000 0.00 0.00 0.00 3.41
589 590 2.203394 CCTCCATCCCATTGCCCG 60.203 66.667 0.00 0.00 0.00 6.13
664 665 4.808895 TGATGAATCTACCGTTCGAAATGG 59.191 41.667 14.45 14.45 43.45 3.16
737 738 1.741028 TGGGAGTGAATGACTTGGGA 58.259 50.000 0.00 0.00 33.83 4.37
849 850 9.396022 GAGATTATTGATGTCCAAACCTTTAGA 57.604 33.333 0.00 0.00 38.43 2.10
855 856 2.304761 TGTCCAAACCTTTAGATCGCCT 59.695 45.455 0.00 0.00 0.00 5.52
861 862 0.931005 CCTTTAGATCGCCTTGTCGC 59.069 55.000 0.00 0.00 0.00 5.19
898 901 0.901124 TTTGCCGCTGCCCAAAATAT 59.099 45.000 9.73 0.00 36.33 1.28
1064 1067 1.814169 GTCGGAAACCCGCATCTCC 60.814 63.158 0.00 0.00 46.35 3.71
1090 1303 2.126189 GACCACGCGTACCTCCAC 60.126 66.667 13.44 0.00 0.00 4.02
1099 1312 0.395311 CGTACCTCCACCTCCAGCTA 60.395 60.000 0.00 0.00 0.00 3.32
1100 1313 1.112950 GTACCTCCACCTCCAGCTAC 58.887 60.000 0.00 0.00 0.00 3.58
1101 1314 0.708209 TACCTCCACCTCCAGCTACA 59.292 55.000 0.00 0.00 0.00 2.74
1102 1315 0.616111 ACCTCCACCTCCAGCTACAG 60.616 60.000 0.00 0.00 0.00 2.74
1103 1316 1.519719 CTCCACCTCCAGCTACAGC 59.480 63.158 0.00 0.00 42.49 4.40
1104 1317 1.965754 CTCCACCTCCAGCTACAGCC 61.966 65.000 0.00 0.00 43.38 4.85
1523 1739 0.895530 CTTCCGCAGACCAGGTCTTA 59.104 55.000 20.57 3.03 41.37 2.10
1524 1740 1.482593 CTTCCGCAGACCAGGTCTTAT 59.517 52.381 20.57 0.00 41.37 1.73
1529 1745 2.932614 CGCAGACCAGGTCTTATTTGAG 59.067 50.000 20.57 7.23 41.37 3.02
1530 1746 3.617531 CGCAGACCAGGTCTTATTTGAGT 60.618 47.826 20.57 0.00 41.37 3.41
1532 1748 4.177026 CAGACCAGGTCTTATTTGAGTCG 58.823 47.826 20.57 0.44 41.37 4.18
1539 1755 4.098196 AGGTCTTATTTGAGTCGCTACCTC 59.902 45.833 0.00 0.00 28.80 3.85
1544 1760 0.811915 TTGAGTCGCTACCTCTCTGC 59.188 55.000 0.00 0.00 0.00 4.26
1566 1785 3.611113 CCGATTCATTTTGCTTGCTTCTG 59.389 43.478 0.00 0.00 0.00 3.02
1570 1789 0.322648 ATTTTGCTTGCTTCTGGGCC 59.677 50.000 0.00 0.00 0.00 5.80
1589 1808 3.099267 CCTGTGATTTAGGCTAGTCCG 57.901 52.381 0.00 0.00 40.77 4.79
1590 1809 2.474816 CTGTGATTTAGGCTAGTCCGC 58.525 52.381 0.00 0.00 40.77 5.54
1591 1810 2.101582 CTGTGATTTAGGCTAGTCCGCT 59.898 50.000 0.00 0.00 40.77 5.52
1592 1811 2.159099 TGTGATTTAGGCTAGTCCGCTG 60.159 50.000 0.00 0.00 40.77 5.18
1593 1812 1.412710 TGATTTAGGCTAGTCCGCTGG 59.587 52.381 0.00 0.00 40.77 4.85
1594 1813 1.413077 GATTTAGGCTAGTCCGCTGGT 59.587 52.381 0.00 0.00 40.77 4.00
1595 1814 0.535335 TTTAGGCTAGTCCGCTGGTG 59.465 55.000 0.00 0.00 40.77 4.17
1596 1815 1.327690 TTAGGCTAGTCCGCTGGTGG 61.328 60.000 0.00 0.00 40.77 4.61
1598 1817 2.656069 GGCTAGTCCGCTGGTGGAA 61.656 63.158 4.33 0.00 40.44 3.53
1655 1875 8.880750 GGATATTACAGTTAAGTGGAAACAGTC 58.119 37.037 11.98 7.70 45.37 3.51
1689 1915 5.852827 TCGAGTCATATGTAATGCCAATCA 58.147 37.500 1.90 0.00 0.00 2.57
1690 1916 6.287525 TCGAGTCATATGTAATGCCAATCAA 58.712 36.000 1.90 0.00 0.00 2.57
1691 1917 6.424812 TCGAGTCATATGTAATGCCAATCAAG 59.575 38.462 1.90 0.00 0.00 3.02
1704 1930 6.135290 TGCCAATCAAGTTATATTGTGCTC 57.865 37.500 16.02 0.00 33.83 4.26
1707 1933 6.694411 GCCAATCAAGTTATATTGTGCTCAAG 59.306 38.462 7.35 0.00 36.97 3.02
1708 1934 7.415541 GCCAATCAAGTTATATTGTGCTCAAGA 60.416 37.037 7.35 2.65 36.97 3.02
1709 1935 8.127327 CCAATCAAGTTATATTGTGCTCAAGAG 58.873 37.037 7.35 0.00 36.97 2.85
1723 1949 5.050490 TGCTCAAGAGTAAGACACTGAAAC 58.950 41.667 0.00 0.00 37.72 2.78
1803 2030 6.127451 TGACAGATCTATATCGTTGGTGTGTT 60.127 38.462 0.00 0.00 37.19 3.32
1810 2037 0.321741 TCGTTGGTGTGTTGTGTGGT 60.322 50.000 0.00 0.00 0.00 4.16
1811 2038 0.523966 CGTTGGTGTGTTGTGTGGTT 59.476 50.000 0.00 0.00 0.00 3.67
1931 2167 5.234543 GTCTTCAGACTTGTCTAAACACCAC 59.765 44.000 2.72 0.00 41.65 4.16
1933 2169 4.693283 TCAGACTTGTCTAAACACCACAG 58.307 43.478 2.72 0.00 34.35 3.66
1953 2189 3.057315 CAGGGTGCCAAGAATACAAGTTG 60.057 47.826 0.00 0.00 0.00 3.16
2035 2271 4.134379 ACAGCATCAGACCTTCATACAG 57.866 45.455 0.00 0.00 0.00 2.74
2122 2362 3.333680 AGGACATGGGTGGTCAAATAGTT 59.666 43.478 0.00 0.00 37.00 2.24
2225 2484 5.243730 GTCCACATTCCTTCATTCTTTCCAA 59.756 40.000 0.00 0.00 0.00 3.53
2236 2495 0.251341 TCTTTCCAAAGGGAGCTGCC 60.251 55.000 18.04 18.04 46.01 4.85
2276 2535 7.057894 AGGAACTATGGTTTACACAGTTTGAA 58.942 34.615 0.00 0.00 36.02 2.69
2363 2623 3.553096 GGCGATACTGTGATAAGGGACTG 60.553 52.174 0.00 0.00 40.86 3.51
2385 2645 5.674525 TGTGAGGGATATGTGACATTTCTC 58.325 41.667 14.14 11.12 0.00 2.87
2422 2682 4.453819 GCAGAGTTTACTGATATGGATGGC 59.546 45.833 0.00 0.00 39.94 4.40
2590 2850 3.243737 GCACCAAGGTTTTACCCTTTGAG 60.244 47.826 0.00 0.00 42.24 3.02
2620 2880 2.311462 CTTGAAGTGTGTCTCGAGTCG 58.689 52.381 13.13 6.09 0.00 4.18
2635 2895 3.132160 CGAGTCGGCTTGTAGATCTCTA 58.868 50.000 4.10 0.00 0.00 2.43
2805 3065 7.888250 TTGTTATTACATATGATGTTGGGCA 57.112 32.000 10.38 0.00 41.63 5.36
2841 3101 6.721318 TCTGCTTATTGGATAAACTTGAGGT 58.279 36.000 0.00 0.00 0.00 3.85
3284 3544 3.761752 TGCAGAAGGTAGGCAATTTAACC 59.238 43.478 0.00 0.00 34.05 2.85
3297 3557 5.364778 GCAATTTAACCTGTTTGAGGGTTT 58.635 37.500 2.69 0.00 39.70 3.27
3409 3669 3.374988 TGCTGGCTACTTTTGAATGATCG 59.625 43.478 0.00 0.00 0.00 3.69
3458 3718 4.875536 GTGAAAGAACTTTGCCAAACCATT 59.124 37.500 4.48 0.00 32.11 3.16
3492 3752 6.821160 CACCATACAAGTATACAACACATCCA 59.179 38.462 5.50 0.00 0.00 3.41
3520 3780 9.716556 CCACCACCTACCTCTATATCTATTATT 57.283 37.037 0.00 0.00 0.00 1.40
3607 3867 4.163458 ACTCCGCAGAATAATTCCACCTTA 59.837 41.667 0.00 0.00 0.00 2.69
3941 4207 4.989797 TGTGGAATCATTTCATTTGTGTGC 59.010 37.500 0.00 0.00 33.23 4.57
4107 4373 2.362169 AAGCGTTCTTCTCTCTCTGC 57.638 50.000 0.00 0.00 0.00 4.26
4118 4384 6.013379 TCTTCTCTCTCTGCTTTTCTCCTTA 58.987 40.000 0.00 0.00 0.00 2.69
4152 4418 4.222366 TGCACCATTCCAAATATTGCTGAA 59.778 37.500 0.00 0.00 0.00 3.02
4309 4580 6.538381 AGAAAACAAGGTTATGGCAAAAGTTG 59.462 34.615 0.00 0.00 0.00 3.16
4453 4724 4.906618 ACCCTCGATTGATTTTACTGTGT 58.093 39.130 0.00 0.00 0.00 3.72
4456 4727 5.163854 CCCTCGATTGATTTTACTGTGTGTC 60.164 44.000 0.00 0.00 0.00 3.67
4462 4733 7.492669 CGATTGATTTTACTGTGTGTCCTCTAT 59.507 37.037 0.00 0.00 0.00 1.98
4747 5326 3.343617 TGGTCTTTTCGGGATGAACATC 58.656 45.455 6.28 6.28 35.97 3.06
4956 5535 1.672356 CTTCGCTGGACAACCCCTG 60.672 63.158 0.00 0.00 34.81 4.45
4994 5573 4.392138 GCGCTTGGAATATATTGGTACCTC 59.608 45.833 14.36 0.00 0.00 3.85
5004 5583 9.630098 GAATATATTGGTACCTCAAAATGCATG 57.370 33.333 14.36 0.00 0.00 4.06
5015 5594 3.577848 TCAAAATGCATGCCTGTAACCTT 59.422 39.130 16.68 0.00 0.00 3.50
5029 5608 4.595986 TGTAACCTTATCCCTTGAAAGCC 58.404 43.478 0.00 0.00 0.00 4.35
5083 5662 2.973945 AGACAATGGGTAGTTCGAAGC 58.026 47.619 0.00 0.00 0.00 3.86
5097 5676 2.942710 TCGAAGCGAAGAAGATCGTTT 58.057 42.857 0.00 0.00 46.61 3.60
5157 5736 3.211963 GCTATTGCACCTGCGGGG 61.212 66.667 18.00 4.25 45.83 5.73
5182 5775 2.744741 GCAGTTGCTTAAACCCTCTCTC 59.255 50.000 0.00 0.00 39.85 3.20
5259 5855 5.683876 ATCACTGTAGAAATGCTGGTACT 57.316 39.130 0.00 0.00 0.00 2.73
5260 5856 4.820897 TCACTGTAGAAATGCTGGTACTG 58.179 43.478 0.00 0.00 0.00 2.74
5291 5887 3.074857 TGGCCAGGGGAGAGTTATTAT 57.925 47.619 0.00 0.00 0.00 1.28
5319 5915 4.452114 TGTGATATTGTTGACAGTGTGAGC 59.548 41.667 0.00 0.00 0.00 4.26
5321 5917 1.953559 ATTGTTGACAGTGTGAGCGT 58.046 45.000 0.00 0.00 0.00 5.07
5327 5923 5.234752 TGTTGACAGTGTGAGCGTATATTT 58.765 37.500 0.00 0.00 0.00 1.40
5329 5925 5.778161 TGACAGTGTGAGCGTATATTTTG 57.222 39.130 0.00 0.00 0.00 2.44
5331 5927 5.699001 TGACAGTGTGAGCGTATATTTTGTT 59.301 36.000 0.00 0.00 0.00 2.83
5332 5928 5.927030 ACAGTGTGAGCGTATATTTTGTTG 58.073 37.500 0.00 0.00 0.00 3.33
5333 5929 5.106712 ACAGTGTGAGCGTATATTTTGTTGG 60.107 40.000 0.00 0.00 0.00 3.77
5337 5944 6.304683 GTGTGAGCGTATATTTTGTTGGTTTC 59.695 38.462 0.00 0.00 0.00 2.78
5356 5963 3.510388 TCTACTCTGATCGCTGGTTTG 57.490 47.619 0.00 0.00 0.00 2.93
5358 5965 0.674895 ACTCTGATCGCTGGTTTGGC 60.675 55.000 0.00 0.00 0.00 4.52
5371 5991 1.063469 GGTTTGGCCATCGTTGTATCG 59.937 52.381 6.09 0.00 37.17 2.92
5375 5995 4.587584 TTGGCCATCGTTGTATCGTATA 57.412 40.909 6.09 0.00 0.00 1.47
5436 6056 7.104043 TGCGTCACTACTAATAATAACCTGT 57.896 36.000 0.00 0.00 0.00 4.00
6128 6751 2.901839 ACTTTGGAGGTCCGTAAAGCTA 59.098 45.455 12.57 0.00 39.43 3.32
6244 6867 2.294233 CAGGCGCTGGTATTTTGCATAT 59.706 45.455 7.64 0.00 0.00 1.78
6284 6907 3.388024 AGTCATGTATGGTCGGTGCTTAT 59.612 43.478 0.00 0.00 0.00 1.73
6302 6925 6.093495 GTGCTTATGTGCCTTGTAACTTGATA 59.907 38.462 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 2.474816 GTAGTGATGAGGTTGCCGATC 58.525 52.381 0.00 0.00 0.00 3.69
161 162 2.435586 CTTGAGCACAGAGGGCGG 60.436 66.667 0.00 0.00 36.08 6.13
195 196 0.462581 GCGCTCTCATGGAACCATCA 60.463 55.000 0.00 0.00 33.90 3.07
207 208 3.418068 GTGTGTGGCAGCGCTCTC 61.418 66.667 7.13 2.67 0.00 3.20
268 269 1.270550 GGTACCACCGAAGAAAGTCGA 59.729 52.381 7.15 0.00 43.86 4.20
269 270 1.000060 TGGTACCACCGAAGAAAGTCG 60.000 52.381 11.60 0.00 42.58 4.18
275 276 0.034337 GTTGCTGGTACCACCGAAGA 59.966 55.000 11.60 0.00 42.58 2.87
320 321 2.762887 CTCCTCAGTCATGTAGCCAAGA 59.237 50.000 0.00 0.00 0.00 3.02
401 402 0.393808 GCCCTTGGAAGGCGAACATA 60.394 55.000 0.00 0.00 45.10 2.29
499 500 2.094417 GCGGCAACAAGACTCTTCATAC 59.906 50.000 0.00 0.00 0.00 2.39
578 579 1.003839 GATATCGCGGGCAATGGGA 60.004 57.895 6.13 0.00 0.00 4.37
589 590 6.874134 AGAAACTATACAATGGTGGATATCGC 59.126 38.462 0.00 0.00 29.75 4.58
664 665 4.033587 GCACAATCAACATGATGGCAATTC 59.966 41.667 0.00 0.00 37.15 2.17
721 722 4.338118 TGTGTTTTCCCAAGTCATTCACTC 59.662 41.667 0.00 0.00 32.30 3.51
737 738 3.316308 GTGCACCTCATCTTCTGTGTTTT 59.684 43.478 5.22 0.00 0.00 2.43
778 779 8.477419 TTCAAAGTCAATCTAAAGGTTTGGAT 57.523 30.769 0.00 0.00 39.63 3.41
817 818 7.718753 GGTTTGGACATCAATAATCTCTCAGAT 59.281 37.037 0.00 0.00 34.03 2.90
975 978 1.145598 CGCACTCATGGGCTGATCT 59.854 57.895 0.00 0.00 32.10 2.75
1030 1033 1.546773 CCGACTGAAAATTGTGGGGGA 60.547 52.381 0.00 0.00 0.00 4.81
1081 1288 1.112950 GTAGCTGGAGGTGGAGGTAC 58.887 60.000 0.00 0.00 36.36 3.34
1090 1303 2.688666 TGGGGCTGTAGCTGGAGG 60.689 66.667 0.00 0.00 41.70 4.30
1100 1313 4.899239 GATCGTCGGCTGGGGCTG 62.899 72.222 0.00 0.00 45.61 4.85
1343 1556 1.681327 GGACGGGTAGGACAGCAGA 60.681 63.158 0.00 0.00 0.00 4.26
1503 1716 1.122019 AAGACCTGGTCTGCGGAAGT 61.122 55.000 28.96 9.56 42.59 3.01
1511 1727 3.368531 GCGACTCAAATAAGACCTGGTCT 60.369 47.826 23.49 23.49 45.64 3.85
1523 1739 2.159170 GCAGAGAGGTAGCGACTCAAAT 60.159 50.000 18.71 2.41 37.43 2.32
1524 1740 1.202582 GCAGAGAGGTAGCGACTCAAA 59.797 52.381 18.71 0.00 37.43 2.69
1529 1745 1.448922 ATCGGCAGAGAGGTAGCGAC 61.449 60.000 0.00 0.00 0.00 5.19
1530 1746 0.752009 AATCGGCAGAGAGGTAGCGA 60.752 55.000 0.00 0.00 0.00 4.93
1532 1748 0.747255 TGAATCGGCAGAGAGGTAGC 59.253 55.000 0.00 0.00 0.00 3.58
1539 1755 3.176708 CAAGCAAAATGAATCGGCAGAG 58.823 45.455 0.00 0.00 0.00 3.35
1544 1760 3.611113 CAGAAGCAAGCAAAATGAATCGG 59.389 43.478 0.00 0.00 0.00 4.18
1570 1789 2.101582 AGCGGACTAGCCTAAATCACAG 59.898 50.000 0.00 0.00 38.01 3.66
1595 1814 5.700832 TCAGATATCGTGCAATGGTTATTCC 59.299 40.000 0.00 0.00 0.00 3.01
1596 1815 6.785488 TCAGATATCGTGCAATGGTTATTC 57.215 37.500 0.00 0.00 0.00 1.75
1598 1817 6.203530 CAGTTCAGATATCGTGCAATGGTTAT 59.796 38.462 0.00 0.00 0.00 1.89
1689 1915 9.372369 GTCTTACTCTTGAGCACAATATAACTT 57.628 33.333 0.00 0.00 35.37 2.66
1690 1916 8.531982 TGTCTTACTCTTGAGCACAATATAACT 58.468 33.333 0.00 0.00 35.37 2.24
1691 1917 8.596380 GTGTCTTACTCTTGAGCACAATATAAC 58.404 37.037 0.00 0.00 35.37 1.89
1704 1930 6.436261 TCTACGTTTCAGTGTCTTACTCTTG 58.564 40.000 0.00 0.00 37.60 3.02
1707 1933 6.694411 TGTTTCTACGTTTCAGTGTCTTACTC 59.306 38.462 0.00 0.00 37.60 2.59
1708 1934 6.567050 TGTTTCTACGTTTCAGTGTCTTACT 58.433 36.000 0.00 0.00 41.36 2.24
1709 1935 6.817270 TGTTTCTACGTTTCAGTGTCTTAC 57.183 37.500 0.00 0.00 0.00 2.34
1723 1949 8.141909 TCCTAATCCAGATGTTATGTTTCTACG 58.858 37.037 0.00 0.00 0.00 3.51
1793 2020 2.029828 TGAAACCACACAACACACCAAC 60.030 45.455 0.00 0.00 0.00 3.77
1803 2030 5.651387 TGAAAAACATCTGAAACCACACA 57.349 34.783 0.00 0.00 0.00 3.72
1810 2037 7.780064 TGAGAAACCATGAAAAACATCTGAAA 58.220 30.769 0.00 0.00 37.07 2.69
1811 2038 7.345422 TGAGAAACCATGAAAAACATCTGAA 57.655 32.000 0.00 0.00 37.07 3.02
1931 2167 2.795329 ACTTGTATTCTTGGCACCCTG 58.205 47.619 0.00 0.00 0.00 4.45
1933 2169 3.153919 TCAACTTGTATTCTTGGCACCC 58.846 45.455 0.00 0.00 0.00 4.61
1953 2189 8.183830 TCTCAAAACATGACAACAAACAAATC 57.816 30.769 0.00 0.00 33.47 2.17
2035 2271 6.144080 GTCAGCAGAACATATATTGTACCGAC 59.856 42.308 0.00 0.00 37.68 4.79
2276 2535 6.774656 AGTCAGAATTCAAGAATGGTTTGAGT 59.225 34.615 8.44 0.00 36.07 3.41
2285 2544 6.070309 AGCCTACAGAGTCAGAATTCAAGAAT 60.070 38.462 8.44 4.41 0.00 2.40
2363 2623 5.674525 TGAGAAATGTCACATATCCCTCAC 58.325 41.667 0.00 0.00 0.00 3.51
2385 2645 4.510038 AACTCTGCAGCCTGTTAAAATG 57.490 40.909 9.47 0.00 0.00 2.32
2422 2682 3.789756 GTGAAGCAATTGCAGATGATTCG 59.210 43.478 30.89 0.00 43.08 3.34
2590 2850 1.082756 CACTTCAAGCGCACGGAAC 60.083 57.895 11.47 0.00 0.00 3.62
2620 2880 5.381757 TCCTCTTCTAGAGATCTACAAGCC 58.618 45.833 0.00 0.00 45.07 4.35
2635 2895 5.723887 AGATGAAACACATACCTCCTCTTCT 59.276 40.000 0.00 0.00 39.56 2.85
2805 3065 6.248433 TCCAATAAGCAGAGGTGAAGAAATT 58.752 36.000 0.00 0.00 0.00 1.82
2841 3101 6.721318 ACTTCTATAAATTGCTCCAACCAGA 58.279 36.000 0.00 0.00 0.00 3.86
2959 3219 1.896465 ACTCCAGACAGACCAGCTTAC 59.104 52.381 0.00 0.00 0.00 2.34
3031 3291 9.444600 TCTCAAAAGTAGTTTGTAAACTTGACT 57.555 29.630 14.47 10.32 46.52 3.41
3409 3669 0.108138 ATAGAGGTCGCACAAGCACC 60.108 55.000 0.00 0.00 42.27 5.01
3458 3718 7.681679 TGTATACTTGTATGGTGAAGGTTTGA 58.318 34.615 4.17 0.00 0.00 2.69
3492 3752 3.403051 AGATATAGAGGTAGGTGGTGGCT 59.597 47.826 0.00 0.00 0.00 4.75
3520 3780 4.415881 TTGCGAGGAAATTATAGCAGGA 57.584 40.909 0.00 0.00 35.95 3.86
3551 3811 4.292186 AGGAGTGCAGAAGATTTAAGCA 57.708 40.909 0.00 0.00 0.00 3.91
3915 4181 6.479331 CACACAAATGAAATGATTCCACACAA 59.521 34.615 0.00 0.00 34.49 3.33
3941 4207 4.464244 TCGCTTCTATAATCCTCATCCCTG 59.536 45.833 0.00 0.00 0.00 4.45
4107 4373 7.965107 GTGCAAGTAACATGATAAGGAGAAAAG 59.035 37.037 0.00 0.00 0.00 2.27
4118 4384 4.343231 TGGAATGGTGCAAGTAACATGAT 58.657 39.130 0.00 0.00 0.00 2.45
4152 4418 7.617723 TGTTAACAATAATAAGTGGGCAGGATT 59.382 33.333 5.64 0.00 0.00 3.01
4283 4554 6.280643 ACTTTTGCCATAACCTTGTTTTCTC 58.719 36.000 0.00 0.00 0.00 2.87
4293 4564 6.426633 AGCATTTTACAACTTTTGCCATAACC 59.573 34.615 0.00 0.00 0.00 2.85
4309 4580 6.668541 TGAGAGTGAAGCATAGCATTTTAC 57.331 37.500 0.00 0.00 0.00 2.01
4669 5248 0.982852 TCGAGAGCATGACCCCCATT 60.983 55.000 0.00 0.00 31.94 3.16
4747 5326 3.654414 GGGAGTGTAAAGAGATATGCCG 58.346 50.000 0.00 0.00 0.00 5.69
4956 5535 3.423154 CGCACACCGCCCTCTTTC 61.423 66.667 0.00 0.00 37.30 2.62
4968 5547 3.550820 ACCAATATATTCCAAGCGCACA 58.449 40.909 11.47 0.00 0.00 4.57
4975 5554 8.637986 GCATTTTGAGGTACCAATATATTCCAA 58.362 33.333 15.94 0.00 0.00 3.53
4980 5559 7.309990 GGCATGCATTTTGAGGTACCAATATAT 60.310 37.037 21.36 0.00 0.00 0.86
4994 5573 3.598019 AGGTTACAGGCATGCATTTTG 57.402 42.857 21.36 13.80 0.00 2.44
5004 5583 3.926058 TCAAGGGATAAGGTTACAGGC 57.074 47.619 0.00 0.00 0.00 4.85
5015 5594 5.373812 CCTTCTAAGGCTTTCAAGGGATA 57.626 43.478 21.26 0.00 39.76 2.59
5029 5608 5.506730 AACTTTCTTCCCTCCCTTCTAAG 57.493 43.478 0.00 0.00 0.00 2.18
5083 5662 7.050281 ACACTTTATGAAACGATCTTCTTCG 57.950 36.000 0.00 0.00 44.56 3.79
5097 5676 3.573538 AGCATTGTGCCAACACTTTATGA 59.426 39.130 0.00 0.00 46.52 2.15
5182 5775 5.040635 ACAATGGCAAGACAAACTTTTACG 58.959 37.500 0.00 0.00 36.61 3.18
5291 5887 5.997129 ACACTGTCAACAATATCACACATGA 59.003 36.000 0.00 0.00 39.83 3.07
5306 5902 5.699001 ACAAAATATACGCTCACACTGTCAA 59.301 36.000 0.00 0.00 0.00 3.18
5319 5915 9.146984 TCAGAGTAGAAACCAACAAAATATACG 57.853 33.333 0.00 0.00 0.00 3.06
5327 5923 3.994392 GCGATCAGAGTAGAAACCAACAA 59.006 43.478 0.00 0.00 0.00 2.83
5329 5925 3.614616 CAGCGATCAGAGTAGAAACCAAC 59.385 47.826 0.00 0.00 0.00 3.77
5331 5927 2.166459 CCAGCGATCAGAGTAGAAACCA 59.834 50.000 0.00 0.00 0.00 3.67
5332 5928 2.166664 ACCAGCGATCAGAGTAGAAACC 59.833 50.000 0.00 0.00 0.00 3.27
5333 5929 3.512033 ACCAGCGATCAGAGTAGAAAC 57.488 47.619 0.00 0.00 0.00 2.78
5337 5944 2.544685 CCAAACCAGCGATCAGAGTAG 58.455 52.381 0.00 0.00 0.00 2.57
5356 5963 5.260027 GTTTATACGATACAACGATGGCC 57.740 43.478 0.00 0.00 37.03 5.36
5391 6011 8.044060 ACGCAAATCTATCTTGATTCAAAAGA 57.956 30.769 0.01 4.73 35.82 2.52
5392 6012 7.964559 TGACGCAAATCTATCTTGATTCAAAAG 59.035 33.333 0.01 0.00 35.82 2.27
5393 6013 7.750458 GTGACGCAAATCTATCTTGATTCAAAA 59.250 33.333 0.01 0.00 35.82 2.44
5443 6063 4.100498 CGGCTAGGGTAGGAAAACAGATAA 59.900 45.833 0.00 0.00 0.00 1.75
5444 6064 3.640029 CGGCTAGGGTAGGAAAACAGATA 59.360 47.826 0.00 0.00 0.00 1.98
5759 6382 1.349688 TCCATGAACCCTAACGCTGTT 59.650 47.619 0.00 0.02 0.00 3.16
5808 6431 2.612285 AGGAGAGACACACCTGATGA 57.388 50.000 0.00 0.00 38.14 2.92
6104 6727 3.259902 CTTTACGGACCTCCAAAGTAGC 58.740 50.000 0.00 0.00 35.14 3.58
6128 6751 1.445095 GGCTCCATCGCTGATCAGT 59.555 57.895 23.38 1.24 0.00 3.41
6196 6819 2.816012 TTCGACACCACCGAAGCA 59.184 55.556 0.00 0.00 40.56 3.91
6244 6867 8.868522 ACATGACTGAAAAGATAGGAAAATCA 57.131 30.769 0.00 0.00 0.00 2.57
6284 6907 9.461312 AGAATAAATATCAAGTTACAAGGCACA 57.539 29.630 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.