Multiple sequence alignment - TraesCS7D01G264000

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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 TraesCS7D01G264000 chr7D 100.000 6890 0 0 1 6890 244768271 244775160 0.000000e+00 12724.0
1 TraesCS7D01G264000 chr7D 84.722 72 4 6 6057 6126 172110633 172110699 1.600000e-06 65.8
2 TraesCS7D01G264000 chr7B 91.820 6015 305 81 388 6300 220129513 220135442 0.000000e+00 8209.0
3 TraesCS7D01G264000 chr7B 88.098 857 60 15 6059 6890 220140871 220141710 0.000000e+00 979.0
4 TraesCS7D01G264000 chr7B 90.210 286 17 7 1 280 220129096 220129376 5.080000e-96 363.0
5 TraesCS7D01G264000 chr7A 96.059 4238 128 19 1773 5984 260903806 260908030 0.000000e+00 6865.0
6 TraesCS7D01G264000 chr7A 90.055 1810 102 38 1 1774 260902129 260903896 0.000000e+00 2274.0
7 TraesCS7D01G264000 chr7A 87.282 401 25 16 6057 6453 260908016 260908394 1.060000e-117 435.0
8 TraesCS7D01G264000 chr5B 90.698 86 6 2 5982 6065 466779844 466779759 5.650000e-21 113.0
9 TraesCS7D01G264000 chr5B 90.476 84 6 2 5982 6063 466779763 466779846 7.310000e-20 110.0
10 TraesCS7D01G264000 chr5B 87.234 94 4 4 5983 6068 138777619 138777526 4.400000e-17 100.0
11 TraesCS7D01G264000 chr5B 93.846 65 4 0 5681 5745 476802508 476802572 1.580000e-16 99.0
12 TraesCS7D01G264000 chr4B 90.361 83 6 2 5982 6062 25847311 25847393 2.630000e-19 108.0
13 TraesCS7D01G264000 chr4B 90.244 82 6 2 5982 6061 25847392 25847311 9.450000e-19 106.0
14 TraesCS7D01G264000 chr4B 93.878 49 2 1 6078 6125 450911743 450911791 9.590000e-09 73.1
15 TraesCS7D01G264000 chr2A 88.636 88 7 3 5983 6068 667018451 667018365 3.400000e-18 104.0
16 TraesCS7D01G264000 chr2A 88.000 75 5 4 6054 6126 52122854 52122926 1.230000e-12 86.1
17 TraesCS7D01G264000 chr5D 89.286 84 6 2 5982 6065 330704965 330704885 1.220000e-17 102.0
18 TraesCS7D01G264000 chr5D 90.769 65 6 0 5681 5745 396806764 396806828 3.420000e-13 87.9
19 TraesCS7D01G264000 chr2D 86.316 95 9 3 5983 6076 642198717 642198808 4.400000e-17 100.0
20 TraesCS7D01G264000 chr3B 86.022 93 10 2 5974 6063 703659139 703659047 5.690000e-16 97.1
21 TraesCS7D01G264000 chr6D 96.078 51 1 1 6083 6132 462207613 462207563 1.590000e-11 82.4
22 TraesCS7D01G264000 chr5A 89.231 65 7 0 5681 5745 502376912 502376976 1.590000e-11 82.4
23 TraesCS7D01G264000 chr4A 97.727 44 0 1 6078 6120 171606590 171606633 2.670000e-09 75.0
24 TraesCS7D01G264000 chr4D 93.878 49 2 1 6078 6125 366320088 366320136 9.590000e-09 73.1


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 TraesCS7D01G264000 chr7D 244768271 244775160 6889 False 12724.000000 12724 100.000 1 6890 1 chr7D.!!$F2 6889
1 TraesCS7D01G264000 chr7B 220129096 220135442 6346 False 4286.000000 8209 91.015 1 6300 2 chr7B.!!$F2 6299
2 TraesCS7D01G264000 chr7B 220140871 220141710 839 False 979.000000 979 88.098 6059 6890 1 chr7B.!!$F1 831
3 TraesCS7D01G264000 chr7A 260902129 260908394 6265 False 3191.333333 6865 91.132 1 6453 3 chr7A.!!$F1 6452

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
47 48 0.528684 GCAGTCCATCGCTCAGGTAC 60.529 60.000 0.00 0.00 0.00 3.34 F
1916 2027 0.036952 CAGGGCTGTGACGTGATCTT 60.037 55.000 0.00 0.00 0.00 2.40 F
2716 2830 0.038801 GGCAAGGAAAAGACTGCTGC 60.039 55.000 0.00 0.00 0.00 5.25 F
2895 3009 1.188219 AGTCACAGGCATGTCCGACT 61.188 55.000 16.16 16.16 37.68 4.18 F
3643 3757 2.906389 TCTTGCTGGTAGATTGTCCACT 59.094 45.455 0.00 0.00 0.00 4.00 F
3650 3764 3.195610 TGGTAGATTGTCCACTAGTGCAG 59.804 47.826 17.86 5.06 0.00 4.41 F
5501 5646 1.486310 TGCAGATGAAGGCGAGGTAAT 59.514 47.619 0.00 0.00 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2143 0.108585 TCAGACCCACTGGAAGCAAC 59.891 55.000 0.00 0.0 45.76 4.17 R
3650 3764 0.607620 TTTGGGCTATTGCTGTTGGC 59.392 50.000 0.00 0.0 39.59 4.52 R
3733 3847 1.213537 CAGTTGAATGCGCCCCTTG 59.786 57.895 4.18 0.0 0.00 3.61 R
4622 4766 1.344065 TCTCAAACTTAGGCGACCCA 58.656 50.000 0.00 0.0 0.00 4.51 R
5235 5380 1.734465 GATTTCTTCGCACCTGAGTGG 59.266 52.381 0.00 0.0 44.69 4.00 R
5523 5668 4.081198 CCTGGAAGAAAGCTGTCACTAGAT 60.081 45.833 6.68 0.0 34.07 1.98 R
6686 6883 0.322456 CATCGGCACCAGGAAAGGAA 60.322 55.000 0.00 0.0 0.00 3.36 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
47 48 0.528684 GCAGTCCATCGCTCAGGTAC 60.529 60.000 0.00 0.00 0.00 3.34
178 181 7.093201 ACCGGTCTTAGATTTGATACCAAAGTA 60.093 37.037 0.00 0.00 44.53 2.24
239 245 6.708054 CAGTCCACTGTTTTGAATCTAGTCTT 59.292 38.462 0.00 0.00 39.09 3.01
251 258 7.897575 TGAATCTAGTCTTCTTTTCTTCTGC 57.102 36.000 8.55 0.00 0.00 4.26
256 263 5.411083 AGTCTTCTTTTCTTCTGCGAAAC 57.589 39.130 0.00 0.00 32.99 2.78
259 266 6.931840 AGTCTTCTTTTCTTCTGCGAAACTAT 59.068 34.615 0.00 0.00 32.99 2.12
270 277 2.026636 TGCGAAACTATAAACAGGCCCT 60.027 45.455 0.00 0.00 0.00 5.19
296 303 5.804692 AAAGATGTGTTTTCGTGTGTACA 57.195 34.783 0.00 0.00 0.00 2.90
301 308 2.931325 GTGTTTTCGTGTGTACAGGTCA 59.069 45.455 0.00 0.00 33.80 4.02
337 364 2.725221 AGACGGAGGTTCGGTATAGT 57.275 50.000 0.00 0.00 29.69 2.12
345 372 4.445448 GGAGGTTCGGTATAGTCTCCTACA 60.445 50.000 0.00 0.00 38.13 2.74
347 374 4.886489 AGGTTCGGTATAGTCTCCTACAAC 59.114 45.833 0.00 0.00 0.00 3.32
348 375 4.886489 GGTTCGGTATAGTCTCCTACAACT 59.114 45.833 0.00 0.00 0.00 3.16
352 379 4.608951 GGTATAGTCTCCTACAACTTGCG 58.391 47.826 0.00 0.00 0.00 4.85
358 385 1.204062 CCTACAACTTGCGTGCGTG 59.796 57.895 0.00 0.00 0.00 5.34
362 389 1.206325 CAACTTGCGTGCGTGCATA 59.794 52.632 3.33 0.00 45.78 3.14
367 394 0.658829 TTGCGTGCGTGCATAACAAC 60.659 50.000 3.33 0.00 45.78 3.32
394 430 7.271511 AGATCTGATGTCAGGTGTTTTAGATC 58.728 38.462 9.94 0.00 43.91 2.75
399 435 6.878923 TGATGTCAGGTGTTTTAGATCGATTT 59.121 34.615 0.00 0.00 0.00 2.17
402 438 8.786826 TGTCAGGTGTTTTAGATCGATTTAAT 57.213 30.769 9.02 0.00 0.00 1.40
415 451 8.259049 AGATCGATTTAATGGTTTAACAACGA 57.741 30.769 0.00 0.00 34.34 3.85
428 465 2.450609 ACAACGACGACTATGGCTTT 57.549 45.000 0.00 0.00 0.00 3.51
481 521 7.432252 GTGAAAACTTTTCAACTGTCATCGATT 59.568 33.333 16.79 0.00 0.00 3.34
497 537 1.723288 GATTAGGCTAGGCTGGGTCT 58.277 55.000 27.95 8.17 0.00 3.85
509 549 0.689623 CTGGGTCTGATATGGGAGCC 59.310 60.000 13.00 13.00 46.60 4.70
530 571 1.137404 GACAATGGCATGTCGGTGC 59.863 57.895 0.00 0.61 40.23 5.01
747 820 1.611977 ACCGAATCTGTGAGACGTGAA 59.388 47.619 0.00 0.00 0.00 3.18
924 1009 0.691904 TACTAACCCAACCCAACCCG 59.308 55.000 0.00 0.00 0.00 5.28
1064 1156 1.447489 CAGCCAGAGGAGAACGCAG 60.447 63.158 0.00 0.00 0.00 5.18
1193 1299 4.918201 GCGGCCCTCAATCTCGGG 62.918 72.222 0.00 0.00 43.60 5.14
1282 1388 6.335781 TGGATAGGCAGGTAAACCTTTATT 57.664 37.500 0.00 0.00 46.09 1.40
1283 1389 7.454553 TGGATAGGCAGGTAAACCTTTATTA 57.545 36.000 0.00 0.00 46.09 0.98
1284 1390 7.284820 TGGATAGGCAGGTAAACCTTTATTAC 58.715 38.462 0.00 0.00 46.09 1.89
1418 1525 4.934797 ATTTGGGTCTCTCATTTCCTCA 57.065 40.909 0.00 0.00 0.00 3.86
1484 1591 0.738412 GCCCATGCATGTCTGTTTGC 60.738 55.000 24.58 11.36 39.33 3.68
1489 1596 1.154150 GCATGTCTGTTTGCTCGGC 60.154 57.895 0.00 0.00 35.95 5.54
1494 1601 0.179215 GTCTGTTTGCTCGGCGATTG 60.179 55.000 11.27 0.00 0.00 2.67
1495 1602 1.135315 CTGTTTGCTCGGCGATTGG 59.865 57.895 11.27 0.00 0.00 3.16
1622 1730 4.764172 GCATCAGGCGGAAGATATAGAAT 58.236 43.478 0.00 0.00 0.00 2.40
1689 1797 5.276584 GCACGTAGTATTGATTGAGCTTCTG 60.277 44.000 0.00 0.00 41.61 3.02
1697 1805 5.618056 TTGATTGAGCTTCTGTTCATCAC 57.382 39.130 0.00 0.00 33.55 3.06
1802 1913 6.828273 TCTTGGTCATGTAGTGGGATTAATTG 59.172 38.462 0.00 0.00 0.00 2.32
1803 1914 6.320434 TGGTCATGTAGTGGGATTAATTGA 57.680 37.500 0.00 0.00 0.00 2.57
1826 1937 3.265737 ACTTGTATTCATGGGTGTAGCCA 59.734 43.478 5.14 5.14 39.65 4.75
1916 2027 0.036952 CAGGGCTGTGACGTGATCTT 60.037 55.000 0.00 0.00 0.00 2.40
1934 2045 3.031013 TCTTCTCGCATGGTTCATCCTA 58.969 45.455 0.00 0.00 37.07 2.94
1938 2049 0.886490 CGCATGGTTCATCCTAGGCC 60.886 60.000 2.96 0.00 37.07 5.19
1957 2068 2.991540 GGTCCCTGGTTGCTTGCC 60.992 66.667 0.00 0.00 0.00 4.52
1971 2082 1.530013 CTTGCCCAGCCTCCAAGTTG 61.530 60.000 0.00 0.00 33.17 3.16
2030 2143 3.247006 AGTAGTGGCAAGATGGTAACG 57.753 47.619 0.00 0.00 42.51 3.18
2040 2153 2.699954 AGATGGTAACGTTGCTTCCAG 58.300 47.619 16.07 0.00 42.51 3.86
2051 2164 0.108585 TGCTTCCAGTGGGTCTGAAC 59.891 55.000 9.92 0.00 46.27 3.18
2072 2185 1.209127 GAAATGCCGGTGTGGTTCG 59.791 57.895 1.90 0.00 41.21 3.95
2102 2215 3.005261 CGGTGGTGATTGGTTTCAATTGA 59.995 43.478 3.38 3.38 43.08 2.57
2159 2273 1.115467 AAGATACTGAGAGGGCCGTG 58.885 55.000 0.65 0.00 0.00 4.94
2292 2406 3.437198 GGGAGGATGTCTCTACAGGATCA 60.437 52.174 0.00 0.00 42.10 2.92
2313 2427 3.660724 ACACCTGTGTCAAGCCCT 58.339 55.556 0.00 0.00 40.24 5.19
2316 2430 0.179020 CACCTGTGTCAAGCCCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
2349 2463 1.523154 TTGGTGCCTGCGATTTGGAC 61.523 55.000 0.00 0.00 0.00 4.02
2368 2482 1.450491 GGGCTTCCTCGAGAAAGCC 60.450 63.158 39.00 39.00 42.96 4.35
2417 2531 5.295292 CGATTGGCAATTTCAGTAGACAGAT 59.705 40.000 14.93 0.00 0.00 2.90
2432 2546 3.458857 AGACAGATTGCATCAGATTCCCT 59.541 43.478 0.00 0.00 0.00 4.20
2552 2666 7.503549 TCTAGATCTTCTCATAAATTGCAGCA 58.496 34.615 0.00 0.00 0.00 4.41
2553 2667 6.621316 AGATCTTCTCATAAATTGCAGCAG 57.379 37.500 0.00 0.00 0.00 4.24
2554 2668 4.627611 TCTTCTCATAAATTGCAGCAGC 57.372 40.909 0.00 0.00 42.57 5.25
2577 2691 1.954733 GCTGTCCATATGCCCACAACA 60.955 52.381 0.00 0.00 0.00 3.33
2716 2830 0.038801 GGCAAGGAAAAGACTGCTGC 60.039 55.000 0.00 0.00 0.00 5.25
2744 2858 6.074005 CGTTGAAAAATGTGCTCTCTAGAAC 58.926 40.000 0.00 0.00 0.00 3.01
2828 2942 6.015350 CCAGGTAAGAAACTCTACAGTTCTGA 60.015 42.308 6.83 0.00 42.45 3.27
2895 3009 1.188219 AGTCACAGGCATGTCCGACT 61.188 55.000 16.16 16.16 37.68 4.18
2940 3054 8.900781 ACTTCAGAATTTGATGTCAATAGGATG 58.099 33.333 0.00 0.00 39.27 3.51
3277 3391 4.398319 TCAAAACTGGGGTTCTGAATCTC 58.602 43.478 0.02 0.00 30.51 2.75
3472 3586 7.543172 CAGGGTATTGACTGTTGAATTTGATTG 59.457 37.037 0.00 0.00 0.00 2.67
3532 3646 4.307032 AGCTGTCCTGAATATTGTTGGT 57.693 40.909 0.00 0.00 0.00 3.67
3563 3677 3.583086 CTCTCCCCCAACTCAGAAACTTA 59.417 47.826 0.00 0.00 0.00 2.24
3643 3757 2.906389 TCTTGCTGGTAGATTGTCCACT 59.094 45.455 0.00 0.00 0.00 4.00
3650 3764 3.195610 TGGTAGATTGTCCACTAGTGCAG 59.804 47.826 17.86 5.06 0.00 4.41
3733 3847 3.272334 CGCTTACGCATCCCTGCC 61.272 66.667 0.00 0.00 46.07 4.85
3857 3971 7.286775 ACCACTCCATCTTTTCTCTATCTAGTC 59.713 40.741 0.00 0.00 0.00 2.59
3978 4115 4.946157 TGTTTCAATGTGCCAAACCAAATT 59.054 33.333 0.00 0.00 30.32 1.82
4250 4387 9.233232 CTTTATATATTGACGAAAACCAAAGGC 57.767 33.333 0.00 0.00 0.00 4.35
4599 4743 7.723616 TCCTGAGTAATATCTCTCTCTTCCTTG 59.276 40.741 8.06 0.00 35.68 3.61
4704 4848 8.928270 ACCTTAACTTAAGAAGTATCATGTCG 57.072 34.615 10.09 0.00 41.91 4.35
4730 4874 8.703336 GTGCACAGAGAAATATTTTCCTTTTTC 58.297 33.333 13.17 0.00 0.00 2.29
4788 4932 5.416013 CCACCTTTTGTTTTCTCTATCCCTC 59.584 44.000 0.00 0.00 0.00 4.30
5501 5646 1.486310 TGCAGATGAAGGCGAGGTAAT 59.514 47.619 0.00 0.00 0.00 1.89
5748 5894 6.560253 ACTTCGACATAAGCAACTGAAAAT 57.440 33.333 0.00 0.00 0.00 1.82
5808 5954 6.090358 CACACCGATAAACGAAAACTCTGTAT 59.910 38.462 0.00 0.00 45.77 2.29
5943 6089 6.057321 ACTTTTTAGGGTCATCGTCCATAA 57.943 37.500 0.00 0.00 30.91 1.90
5950 6096 3.322254 GGGTCATCGTCCATAAGTCTGAT 59.678 47.826 0.00 0.00 0.00 2.90
5955 6101 4.913335 TCGTCCATAAGTCTGATGTACC 57.087 45.455 0.00 0.00 0.00 3.34
5988 6134 7.927092 GTCCTGAATTACTTGTCTTATACTCCC 59.073 40.741 0.00 0.00 0.00 4.30
5991 6137 8.840200 TGAATTACTTGTCTTATACTCCCTCT 57.160 34.615 0.00 0.00 0.00 3.69
6007 6153 3.913799 TCCCTCTGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
6010 6156 4.938226 CCTCTGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
6013 6159 5.997746 TCTGTCCCAAAATAAGTGACTCAAG 59.002 40.000 0.00 0.00 0.00 3.02
6017 6163 6.918022 GTCCCAAAATAAGTGACTCAAGTTTG 59.082 38.462 11.50 11.50 0.00 2.93
6057 6222 2.850568 ACTTATTTTGGGACGGAGGGAT 59.149 45.455 0.00 0.00 0.00 3.85
6059 6224 4.475747 ACTTATTTTGGGACGGAGGGATTA 59.524 41.667 0.00 0.00 0.00 1.75
6060 6225 5.133830 ACTTATTTTGGGACGGAGGGATTAT 59.866 40.000 0.00 0.00 0.00 1.28
6061 6226 4.536295 ATTTTGGGACGGAGGGATTATT 57.464 40.909 0.00 0.00 0.00 1.40
6062 6227 4.325084 TTTTGGGACGGAGGGATTATTT 57.675 40.909 0.00 0.00 0.00 1.40
6063 6228 3.290948 TTGGGACGGAGGGATTATTTG 57.709 47.619 0.00 0.00 0.00 2.32
6133 6298 7.931015 TGGGACAGAGGTAATACAATATTCT 57.069 36.000 0.00 0.00 0.00 2.40
6340 6527 6.566197 ACAAAGACAAATCTGGAGATGAAC 57.434 37.500 0.00 0.00 34.48 3.18
6356 6543 6.238130 GGAGATGAACGGTAGCTAATTCAAAC 60.238 42.308 16.18 13.64 34.88 2.93
6367 6554 1.928868 AATTCAAACTGGGCTGGGAG 58.071 50.000 0.00 0.00 0.00 4.30
6383 6570 2.369394 GGGAGTTCAGCCCATTTACAG 58.631 52.381 0.00 0.00 45.31 2.74
6399 6586 7.703621 CCCATTTACAGTATCAGCTTGAATTTG 59.296 37.037 0.00 0.00 0.00 2.32
6563 6753 2.046314 AAGCGTGGGCGTATTGCT 60.046 55.556 0.00 0.00 46.35 3.91
6567 6757 1.934463 CGTGGGCGTATTGCTGATC 59.066 57.895 0.00 0.00 45.43 2.92
6578 6768 3.207669 GCTGATCGGCTTGCCAGG 61.208 66.667 19.63 0.00 0.00 4.45
6579 6769 3.207669 CTGATCGGCTTGCCAGGC 61.208 66.667 3.66 3.66 42.39 4.85
6580 6770 3.982316 CTGATCGGCTTGCCAGGCA 62.982 63.158 11.22 11.22 46.30 4.75
6581 6771 3.512516 GATCGGCTTGCCAGGCAC 61.513 66.667 15.89 2.97 46.30 5.01
6628 6825 1.131638 TTCTGTGTGACCAAGAGCCT 58.868 50.000 0.00 0.00 0.00 4.58
6634 6831 0.972883 GTGACCAAGAGCCTGAGAGT 59.027 55.000 0.00 0.00 0.00 3.24
6656 6853 1.599047 CACCACCTGCTCTTCGGAT 59.401 57.895 0.00 0.00 0.00 4.18
6665 6862 0.463620 GCTCTTCGGATGCTCCTTCT 59.536 55.000 1.51 0.00 33.30 2.85
6676 6873 1.340114 TGCTCCTTCTCGAGACAGCTA 60.340 52.381 27.89 17.73 34.13 3.32
6686 6883 0.457851 GAGACAGCTATGGCACGAGT 59.542 55.000 3.10 0.00 36.64 4.18
6715 6912 3.381983 TGCCGATGCACCTCGAGT 61.382 61.111 12.31 0.00 44.23 4.18
6730 6927 1.079750 GAGTCCACCAAGGCGAGAC 60.080 63.158 0.00 0.00 37.29 3.36
6731 6928 1.534235 AGTCCACCAAGGCGAGACT 60.534 57.895 0.00 1.65 37.29 3.24
6811 7022 0.689412 AGGGCTCTCCTCCTTGCTAC 60.689 60.000 0.00 0.00 44.06 3.58
6859 7070 3.315765 TGGGACAACATCGTGTTCC 57.684 52.632 0.00 0.00 46.25 3.62
6883 7094 2.889200 GAGGCTCCCTCTCTTTCGA 58.111 57.895 2.15 0.00 46.41 3.71
6884 7095 1.187087 GAGGCTCCCTCTCTTTCGAA 58.813 55.000 2.15 0.00 46.41 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.528684 GTACCTGAGCGATGGACTGC 60.529 60.000 0.00 0.00 0.00 4.40
47 48 0.108138 CCCTCGGAGTAGCTTTGTGG 60.108 60.000 4.02 0.00 0.00 4.17
89 91 3.069586 CCTGCCATGATGCATCATCTTTT 59.930 43.478 34.17 15.85 45.23 2.27
178 181 0.953003 GGCTAAGATCCGTACGCTCT 59.047 55.000 10.49 11.09 0.00 4.09
239 245 8.373048 TGTTTATAGTTTCGCAGAAGAAAAGA 57.627 30.769 0.00 0.00 45.90 2.52
251 258 4.258543 TCAAGGGCCTGTTTATAGTTTCG 58.741 43.478 6.92 0.00 0.00 3.46
256 263 6.378280 ACATCTTTTCAAGGGCCTGTTTATAG 59.622 38.462 6.92 0.82 0.00 1.31
259 266 4.280677 CACATCTTTTCAAGGGCCTGTTTA 59.719 41.667 6.92 0.00 0.00 2.01
270 277 5.704888 ACACACGAAAACACATCTTTTCAA 58.295 33.333 0.00 0.00 39.26 2.69
286 293 2.228103 GACTGATGACCTGTACACACGA 59.772 50.000 0.00 0.00 0.00 4.35
292 299 1.202154 CGGACGACTGATGACCTGTAC 60.202 57.143 0.00 0.00 0.00 2.90
296 303 0.322636 AGACGGACGACTGATGACCT 60.323 55.000 0.00 0.00 0.00 3.85
301 308 3.761311 GTCTTAAGACGGACGACTGAT 57.239 47.619 19.39 0.00 35.12 2.90
326 353 6.264088 CAAGTTGTAGGAGACTATACCGAAC 58.736 44.000 0.00 0.00 46.56 3.95
347 374 0.385348 TTGTTATGCACGCACGCAAG 60.385 50.000 0.60 0.00 46.87 4.01
348 375 0.658829 GTTGTTATGCACGCACGCAA 60.659 50.000 0.60 0.00 46.87 4.85
352 379 2.679355 TCTTGTTGTTATGCACGCAC 57.321 45.000 0.00 0.00 0.00 5.34
358 385 6.426980 TGACATCAGATCTTGTTGTTATGC 57.573 37.500 1.65 0.00 39.28 3.14
362 389 4.758674 CACCTGACATCAGATCTTGTTGTT 59.241 41.667 10.55 0.00 46.59 2.83
367 394 5.954296 AAAACACCTGACATCAGATCTTG 57.046 39.130 10.55 4.74 46.59 3.02
394 430 6.244883 GTCGTCGTTGTTAAACCATTAAATCG 59.755 38.462 0.00 0.00 32.98 3.34
399 435 6.310956 CCATAGTCGTCGTTGTTAAACCATTA 59.689 38.462 0.00 0.00 32.23 1.90
402 438 3.989167 CCATAGTCGTCGTTGTTAAACCA 59.011 43.478 0.00 0.00 32.23 3.67
415 451 2.170607 AGCACCATAAAGCCATAGTCGT 59.829 45.455 0.00 0.00 0.00 4.34
428 465 2.557869 ACCCTAAAGACCAGCACCATA 58.442 47.619 0.00 0.00 0.00 2.74
455 493 6.255215 TCGATGACAGTTGAAAAGTTTTCAC 58.745 36.000 26.72 20.88 0.00 3.18
481 521 0.563173 ATCAGACCCAGCCTAGCCTA 59.437 55.000 0.00 0.00 0.00 3.93
497 537 1.681486 TTGTCGCGGCTCCCATATCA 61.681 55.000 13.81 0.00 0.00 2.15
522 563 1.532604 ATCAGAACGAGGCACCGACA 61.533 55.000 6.32 0.00 0.00 4.35
530 571 2.926200 CACTACTGCAATCAGAACGAGG 59.074 50.000 0.00 0.00 42.95 4.63
633 702 6.547510 GCCCAGAGGACATATATTTCTTTTGT 59.452 38.462 0.00 0.00 33.47 2.83
645 714 0.253044 GTTGCTGCCCAGAGGACATA 59.747 55.000 0.00 0.00 33.47 2.29
653 722 1.342174 ACAAATTCTGTTGCTGCCCAG 59.658 47.619 9.42 9.42 32.99 4.45
678 747 2.011947 GGTGGTTAATGTACCGGCTTC 58.988 52.381 0.00 0.00 41.28 3.86
716 785 3.923461 CACAGATTCGGTTTCTGAGACTC 59.077 47.826 14.37 0.00 42.63 3.36
747 820 3.330701 TCTGTTTCTAACATTCAGGCCCT 59.669 43.478 0.00 0.00 41.26 5.19
900 985 0.326927 TGGGTTGGGTTAGTAGCAGC 59.673 55.000 0.00 0.00 0.00 5.25
901 986 2.433436 GTTGGGTTGGGTTAGTAGCAG 58.567 52.381 0.00 0.00 0.00 4.24
902 987 1.074244 GGTTGGGTTGGGTTAGTAGCA 59.926 52.381 0.00 0.00 0.00 3.49
903 988 1.615116 GGGTTGGGTTGGGTTAGTAGC 60.615 57.143 0.00 0.00 0.00 3.58
904 989 1.339342 CGGGTTGGGTTGGGTTAGTAG 60.339 57.143 0.00 0.00 0.00 2.57
924 1009 2.484742 TTTTCTAGAGGGGAAACGCC 57.515 50.000 0.00 0.00 46.15 5.68
1064 1156 2.428085 GCCGGACCTTCTCCTCTCC 61.428 68.421 5.05 0.00 36.80 3.71
1193 1299 2.244651 CGAATCGAATCGGGGTGCC 61.245 63.158 15.07 0.00 39.12 5.01
1282 1388 0.538118 AGAAATACAAGCCGGCGGTA 59.462 50.000 28.19 28.19 0.00 4.02
1283 1389 1.024579 CAGAAATACAAGCCGGCGGT 61.025 55.000 28.82 26.13 0.00 5.68
1284 1390 1.721487 CAGAAATACAAGCCGGCGG 59.279 57.895 24.35 24.35 0.00 6.13
1484 1591 2.892425 GGTCAGCCAATCGCCGAG 60.892 66.667 0.00 0.00 38.78 4.63
1508 1615 1.252904 CCCAGACCAGGCACAAATGG 61.253 60.000 0.00 0.00 42.60 3.16
1530 1637 4.082463 GCTATCTACTCCACTCCATACTGC 60.082 50.000 0.00 0.00 0.00 4.40
1531 1638 5.073428 TGCTATCTACTCCACTCCATACTG 58.927 45.833 0.00 0.00 0.00 2.74
1532 1639 5.326283 TGCTATCTACTCCACTCCATACT 57.674 43.478 0.00 0.00 0.00 2.12
1622 1730 3.876914 CAGGAGCAACAAACTTGTCAGTA 59.123 43.478 0.00 0.00 41.31 2.74
1689 1797 6.537301 TCAATTAATCCCACTACGTGATGAAC 59.463 38.462 0.00 0.00 35.23 3.18
1697 1805 5.671493 AGGAGTTCAATTAATCCCACTACG 58.329 41.667 0.00 0.00 31.86 3.51
1713 1821 7.339482 ACTAAACCCATGAATAGAAGGAGTTC 58.661 38.462 0.00 0.00 0.00 3.01
1802 1913 4.335594 GGCTACACCCATGAATACAAGTTC 59.664 45.833 0.00 0.00 0.00 3.01
1803 1914 4.263727 TGGCTACACCCATGAATACAAGTT 60.264 41.667 0.00 0.00 37.83 2.66
1826 1937 5.369110 AGAGGCTCAATTGATCCTATCACTT 59.631 40.000 26.73 7.19 40.47 3.16
1881 1992 1.428448 CCTGCAGAAACGAATCGACA 58.572 50.000 17.39 0.00 0.00 4.35
1882 1993 0.721718 CCCTGCAGAAACGAATCGAC 59.278 55.000 17.39 0.26 0.00 4.20
1916 2027 1.688735 CCTAGGATGAACCATGCGAGA 59.311 52.381 1.05 0.00 37.17 4.04
1938 2049 2.270986 GCAAGCAACCAGGGACCTG 61.271 63.158 11.44 11.44 43.26 4.00
1957 2068 0.466189 ACACACAACTTGGAGGCTGG 60.466 55.000 0.00 0.00 0.00 4.85
1961 2072 3.070018 GAGATGACACACAACTTGGAGG 58.930 50.000 0.00 0.00 31.86 4.30
1971 2082 2.146342 CCACAACTGGAGATGACACAC 58.854 52.381 0.00 0.00 40.55 3.82
2030 2143 0.108585 TCAGACCCACTGGAAGCAAC 59.891 55.000 0.00 0.00 45.76 4.17
2040 2153 1.541588 GCATTTCTGGTTCAGACCCAC 59.458 52.381 0.00 0.00 45.92 4.61
2053 2166 1.234615 CGAACCACACCGGCATTTCT 61.235 55.000 0.00 0.00 39.03 2.52
2102 2215 5.240183 CCAAATCGATGCCTAGACAAATCAT 59.760 40.000 0.00 0.00 0.00 2.45
2159 2273 4.470304 AGTACACCTATCCAGTTCCTTTCC 59.530 45.833 0.00 0.00 0.00 3.13
2313 2427 2.222886 CCAACACCATTGGTACGTGAA 58.777 47.619 8.31 0.00 32.11 3.18
2349 2463 1.811679 GCTTTCTCGAGGAAGCCCG 60.812 63.158 38.12 15.43 37.58 6.13
2368 2482 3.551454 CGATATGAAGCCTTGCCATTTGG 60.551 47.826 0.00 0.00 38.53 3.28
2417 2531 2.510800 TCATCCAGGGAATCTGATGCAA 59.489 45.455 0.00 0.00 46.18 4.08
2432 2546 7.113437 TCTAAAATACCCGTTTGATTCATCCA 58.887 34.615 0.00 0.00 0.00 3.41
2552 2666 1.150081 GGCATATGGACAGCAGGCT 59.850 57.895 4.56 0.00 0.00 4.58
2553 2667 1.900498 GGGCATATGGACAGCAGGC 60.900 63.158 4.56 0.00 0.00 4.85
2554 2668 0.820891 GTGGGCATATGGACAGCAGG 60.821 60.000 4.56 0.00 0.00 4.85
2577 2691 1.970640 GATTCAAAGCCCACAACCCTT 59.029 47.619 0.00 0.00 0.00 3.95
2716 2830 2.554032 AGAGCACATTTTTCAACGGAGG 59.446 45.455 0.00 0.00 0.00 4.30
2744 2858 2.698803 TCAGTGAATCACCATGGAACG 58.301 47.619 21.47 6.49 34.49 3.95
2895 3009 0.924090 TCCGACTGGACCATCTAGGA 59.076 55.000 0.00 0.00 40.17 2.94
2940 3054 7.144000 GGCCATCAGTGAAATGATTAGAATTC 58.856 38.462 0.00 0.00 37.84 2.17
3434 3548 8.502738 ACAGTCAATACCCTGGAATTGTAATAT 58.497 33.333 16.40 3.72 35.16 1.28
3435 3549 7.867921 ACAGTCAATACCCTGGAATTGTAATA 58.132 34.615 16.40 1.38 35.16 0.98
3436 3550 6.731467 ACAGTCAATACCCTGGAATTGTAAT 58.269 36.000 16.40 6.19 35.16 1.89
3437 3551 6.134535 ACAGTCAATACCCTGGAATTGTAA 57.865 37.500 16.40 2.17 35.16 2.41
3472 3586 4.034975 GTCTGCATCCACAGAGAATTAAGC 59.965 45.833 0.00 0.00 47.00 3.09
3643 3757 2.358957 CTATTGCTGTTGGCTGCACTA 58.641 47.619 0.50 0.00 46.65 2.74
3650 3764 0.607620 TTTGGGCTATTGCTGTTGGC 59.392 50.000 0.00 0.00 39.59 4.52
3733 3847 1.213537 CAGTTGAATGCGCCCCTTG 59.786 57.895 4.18 0.00 0.00 3.61
3745 3859 5.472137 GGTCAAGCAATTTAGTACCAGTTGA 59.528 40.000 2.96 0.00 0.00 3.18
3884 4021 5.347012 CAATCCAAAATGGCTTGTCAAAC 57.653 39.130 5.10 0.00 38.47 2.93
3978 4115 3.788227 AACCTAGCCATCACAAGTGAA 57.212 42.857 7.02 0.00 43.58 3.18
4064 4201 6.061441 TCAAGATGGGAACGCATATAACAAT 58.939 36.000 4.45 0.00 0.00 2.71
4250 4387 7.326789 CACATTTGTGTTTTGGTGCTAGAATAG 59.673 37.037 2.48 0.00 40.44 1.73
4613 4757 3.194329 ACTTAGGCGACCCACTTAGTTAC 59.806 47.826 0.00 0.00 0.00 2.50
4622 4766 1.344065 TCTCAAACTTAGGCGACCCA 58.656 50.000 0.00 0.00 0.00 4.51
4627 4771 3.190874 GTCCTGATCTCAAACTTAGGCG 58.809 50.000 0.00 0.00 0.00 5.52
4702 4846 5.245531 AGGAAAATATTTCTCTGTGCACGA 58.754 37.500 13.13 11.42 0.00 4.35
4704 4848 8.593492 AAAAAGGAAAATATTTCTCTGTGCAC 57.407 30.769 10.75 10.75 0.00 4.57
4788 4932 8.915057 ATACACAAGGGAAATAAGATGAGATG 57.085 34.615 0.00 0.00 0.00 2.90
5082 5227 3.617284 TGATTCATCAGCTGAGTTGCAT 58.383 40.909 22.96 12.12 34.68 3.96
5231 5376 3.858868 TTCGCACCTGAGTGGACGC 62.859 63.158 0.00 0.00 44.69 5.19
5235 5380 1.734465 GATTTCTTCGCACCTGAGTGG 59.266 52.381 0.00 0.00 44.69 4.00
5523 5668 4.081198 CCTGGAAGAAAGCTGTCACTAGAT 60.081 45.833 6.68 0.00 34.07 1.98
5566 5711 5.065218 ACATAGGTCTTCTAAATTGCAAGCG 59.935 40.000 4.94 0.00 0.00 4.68
5702 5848 1.144936 GGGATCAGCAGGGAAGTCG 59.855 63.158 0.00 0.00 0.00 4.18
5748 5894 5.401550 GCTATACATGACAGCAAAAGCAAA 58.598 37.500 0.00 0.00 35.35 3.68
5780 5926 1.880271 TTTCGTTTATCGGTGTGCCA 58.120 45.000 0.00 0.00 40.32 4.92
5808 5954 9.360901 TGCTGGCAAATTAGTGGAATAAATATA 57.639 29.630 0.00 0.00 0.00 0.86
5832 5978 1.818674 CCTGTACATTTTGGGGACTGC 59.181 52.381 0.00 0.00 0.00 4.40
5943 6089 0.397254 CGGAGGGGGTACATCAGACT 60.397 60.000 0.00 0.00 0.00 3.24
5950 6096 2.038329 CAGGACGGAGGGGGTACA 59.962 66.667 0.00 0.00 0.00 2.90
5955 6101 1.497161 AGTAATTCAGGACGGAGGGG 58.503 55.000 0.00 0.00 0.00 4.79
5988 6134 5.551233 TGAGTCACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
5991 6137 5.690865 ACTTGAGTCACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
6024 6170 6.935208 GTCCCAAAATAAGTGACTCAAGTAGT 59.065 38.462 0.00 0.00 42.80 2.73
6025 6171 6.090898 CGTCCCAAAATAAGTGACTCAAGTAG 59.909 42.308 0.00 0.00 0.00 2.57
6026 6172 5.929992 CGTCCCAAAATAAGTGACTCAAGTA 59.070 40.000 0.00 0.00 0.00 2.24
6027 6173 4.755123 CGTCCCAAAATAAGTGACTCAAGT 59.245 41.667 0.00 0.00 0.00 3.16
6028 6174 4.154195 CCGTCCCAAAATAAGTGACTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
6031 6196 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
6034 6199 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
6037 6202 3.577805 ATCCCTCCGTCCCAAAATAAG 57.422 47.619 0.00 0.00 0.00 1.73
6133 6298 7.216494 ACACGATACACAATATTCATGATCCA 58.784 34.615 0.00 0.00 0.00 3.41
6286 6473 9.739276 AGATATGTGTTTTAGTCTTGGATTCAA 57.261 29.630 0.00 0.00 0.00 2.69
6340 6527 2.354821 GCCCAGTTTGAATTAGCTACCG 59.645 50.000 0.00 0.00 0.00 4.02
6367 6554 4.035675 GCTGATACTGTAAATGGGCTGAAC 59.964 45.833 0.00 0.00 0.00 3.18
6383 6570 7.147976 ACAAAAGGACAAATTCAAGCTGATAC 58.852 34.615 0.00 0.00 0.00 2.24
6399 6586 5.751243 TGTAGCTTGAGAAACAAAAGGAC 57.249 39.130 0.00 0.00 38.08 3.85
6469 6658 9.758651 TTCATGTCTAATACTAATATTGCACGT 57.241 29.630 0.00 0.00 32.98 4.49
6508 6697 3.117776 ACCCTGTCCTTACGGTTTTCTTT 60.118 43.478 0.00 0.00 0.00 2.52
6519 6708 0.911769 CCTGATGCACCCTGTCCTTA 59.088 55.000 0.00 0.00 0.00 2.69
6563 6753 4.032452 TGCCTGGCAAGCCGATCA 62.032 61.111 21.08 0.95 39.42 2.92
6656 6853 0.610509 AGCTGTCTCGAGAAGGAGCA 60.611 55.000 29.71 18.81 34.83 4.26
6665 6862 1.029947 TCGTGCCATAGCTGTCTCGA 61.030 55.000 0.00 0.00 40.80 4.04
6676 6873 0.693049 AGGAAAGGAACTCGTGCCAT 59.307 50.000 0.00 0.00 38.49 4.40
6686 6883 0.322456 CATCGGCACCAGGAAAGGAA 60.322 55.000 0.00 0.00 0.00 3.36
6710 6907 2.599281 TCGCCTTGGTGGACTCGA 60.599 61.111 0.00 0.00 38.35 4.04
6712 6909 1.079750 GTCTCGCCTTGGTGGACTC 60.080 63.158 11.74 0.00 38.35 3.36
6715 6912 1.533033 TCAGTCTCGCCTTGGTGGA 60.533 57.895 0.00 0.00 38.35 4.02
6730 6927 4.726416 CACCAATCTTGAAAATCGGTCAG 58.274 43.478 0.00 0.00 0.00 3.51
6731 6928 3.057596 GCACCAATCTTGAAAATCGGTCA 60.058 43.478 0.00 0.00 0.00 4.02
6811 7022 2.072298 GAGAAGCCATGCGCCTATAAG 58.928 52.381 4.18 0.00 38.78 1.73
6841 7052 0.470341 TGGAACACGATGTTGTCCCA 59.530 50.000 7.89 6.82 41.28 4.37
6842 7053 1.600023 TTGGAACACGATGTTGTCCC 58.400 50.000 7.89 4.76 41.28 4.46


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

AutoCloner maintained by Alex Coulton.