Multiple sequence alignment - TraesCS5A01G179000

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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 TraesCS5A01G179000 chr5A 100.000 2883 0 0 1 2883 377118825 377121707 0.000000e+00 5325.0
1 TraesCS5A01G179000 chr5A 100.000 30 0 0 788 817 118671135 118671106 4.010000e-04 56.5
2 TraesCS5A01G179000 chr5B 94.139 1672 85 9 339 2004 322858269 322859933 0.000000e+00 2532.0
3 TraesCS5A01G179000 chr5B 90.698 516 33 11 2340 2845 322860305 322860815 0.000000e+00 673.0
4 TraesCS5A01G179000 chr5B 94.488 381 8 4 2027 2398 322859926 322860302 2.490000e-160 575.0
5 TraesCS5A01G179000 chr5B 85.490 510 40 17 25 530 322858025 322858504 4.290000e-138 501.0
6 TraesCS5A01G179000 chr5D 93.512 1680 76 25 340 2004 285246997 285248658 0.000000e+00 2468.0
7 TraesCS5A01G179000 chr5D 93.437 838 35 12 2025 2845 285248649 285249483 0.000000e+00 1225.0
8 TraesCS5A01G179000 chr5D 83.333 552 56 25 1 530 285246694 285247231 7.230000e-131 477.0
9 TraesCS5A01G179000 chr3D 96.552 58 0 2 777 833 252334793 252334849 8.500000e-16 95.3
10 TraesCS5A01G179000 chr3D 94.444 36 2 0 2244 2279 591123639 591123604 4.010000e-04 56.5
11 TraesCS5A01G179000 chr3B 96.491 57 2 0 777 833 313808026 313808082 8.500000e-16 95.3
12 TraesCS5A01G179000 chr3A 100.000 51 0 0 783 833 332220139 332220089 8.500000e-16 95.3
13 TraesCS5A01G179000 chr6D 98.039 51 1 0 783 833 52724695 52724645 3.960000e-14 89.8
14 TraesCS5A01G179000 chr6D 97.059 34 1 0 2244 2277 58701995 58701962 1.120000e-04 58.4
15 TraesCS5A01G179000 chr6D 94.595 37 1 1 2244 2280 58702031 58701996 4.010000e-04 56.5
16 TraesCS5A01G179000 chr6B 98.039 51 1 0 783 833 119849607 119849557 3.960000e-14 89.8
17 TraesCS5A01G179000 chr6A 98.039 51 1 0 783 833 63610635 63610585 3.960000e-14 89.8
18 TraesCS5A01G179000 chr7A 94.872 39 2 0 2239 2277 717088985 717088947 8.630000e-06 62.1
19 TraesCS5A01G179000 chr1A 94.737 38 2 0 2239 2276 83823608 83823645 3.100000e-05 60.2
20 TraesCS5A01G179000 chr1A 94.737 38 2 0 2240 2277 508556829 508556792 3.100000e-05 60.2
21 TraesCS5A01G179000 chr7B 94.595 37 2 0 2239 2275 718359806 718359842 1.120000e-04 58.4


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 TraesCS5A01G179000 chr5A 377118825 377121707 2882 False 5325.00 5325 100.00000 1 2883 1 chr5A.!!$F1 2882
1 TraesCS5A01G179000 chr5B 322858025 322860815 2790 False 1070.25 2532 91.20375 25 2845 4 chr5B.!!$F1 2820
2 TraesCS5A01G179000 chr5D 285246694 285249483 2789 False 1390.00 2468 90.09400 1 2845 3 chr5D.!!$F1 2844

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
169 170 0.179108 CTAGGTTTCCTTCCGCTCCG 60.179 60.0 0.0 0.0 34.61 4.63 F
390 410 0.262876 ATCCATTTCCCAGGGAAGGC 59.737 55.0 20.9 0.0 43.06 4.35 F
708 733 0.319125 GATAGAGCCGCAGTAGCACC 60.319 60.0 0.0 0.0 42.27 5.01 F
1021 1049 0.391597 GTCAAGTGGGACCTCGTTCA 59.608 55.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1375 0.474184 AGCAGATATTTCGGGTGGGG 59.526 55.000 0.00 0.0 0.00 4.96 R
1765 1804 1.136305 GGGTTCGCTGTGCTAGTGATA 59.864 52.381 5.80 0.0 44.85 2.15 R
1822 1861 2.647875 CCGGCGCCAAAAATGTCA 59.352 55.556 28.98 0.0 0.00 3.58 R
2806 2928 0.847373 TCCTTAGGTGGGTTTGTGCA 59.153 50.000 0.00 0.0 0.00 4.57 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
48 49 4.082245 CACCACCACCATTACCAATTTCTC 60.082 45.833 0.00 0.00 0.00 2.87
68 69 0.796312 TCGCAATTGTTTCTCTCGCC 59.204 50.000 7.40 0.00 0.00 5.54
72 73 2.726241 GCAATTGTTTCTCTCGCCAAAC 59.274 45.455 7.40 0.00 33.78 2.93
83 84 4.351938 GCCAAACCCGCCCGTTTC 62.352 66.667 0.00 0.00 33.69 2.78
84 85 3.676605 CCAAACCCGCCCGTTTCC 61.677 66.667 0.00 0.00 33.69 3.13
105 106 1.160137 GGCTATAAATGCCGCCTCTG 58.840 55.000 0.00 0.00 41.03 3.35
164 165 1.679032 CCCTTGCTAGGTTTCCTTCCG 60.679 57.143 13.38 0.00 40.19 4.30
165 166 1.087501 CTTGCTAGGTTTCCTTCCGC 58.912 55.000 0.00 0.00 34.61 5.54
166 167 0.690762 TTGCTAGGTTTCCTTCCGCT 59.309 50.000 0.00 0.00 34.61 5.52
168 169 0.462225 GCTAGGTTTCCTTCCGCTCC 60.462 60.000 0.00 0.00 34.61 4.70
169 170 0.179108 CTAGGTTTCCTTCCGCTCCG 60.179 60.000 0.00 0.00 34.61 4.63
172 173 4.752879 TTTCCTTCCGCTCCGCCG 62.753 66.667 0.00 0.00 0.00 6.46
200 201 1.735360 GCCAAACAGCAGAGCACAA 59.265 52.632 0.00 0.00 0.00 3.33
219 220 2.283145 ATCTGTTTCTTGGCTGCTGT 57.717 45.000 0.00 0.00 0.00 4.40
221 222 0.595095 CTGTTTCTTGGCTGCTGTCC 59.405 55.000 0.00 0.00 0.00 4.02
327 347 1.201414 CCAAATTTTCTTCCCCGGTCG 59.799 52.381 0.00 0.00 0.00 4.79
380 400 2.713167 TCTCCCCTCATCATCCATTTCC 59.287 50.000 0.00 0.00 0.00 3.13
381 401 1.782752 TCCCCTCATCATCCATTTCCC 59.217 52.381 0.00 0.00 0.00 3.97
382 402 1.500303 CCCCTCATCATCCATTTCCCA 59.500 52.381 0.00 0.00 0.00 4.37
383 403 2.490351 CCCCTCATCATCCATTTCCCAG 60.490 54.545 0.00 0.00 0.00 4.45
384 404 2.490351 CCCTCATCATCCATTTCCCAGG 60.490 54.545 0.00 0.00 0.00 4.45
385 405 2.490351 CCTCATCATCCATTTCCCAGGG 60.490 54.545 0.00 0.00 0.00 4.45
386 406 2.444388 CTCATCATCCATTTCCCAGGGA 59.556 50.000 3.01 3.01 34.70 4.20
387 407 2.858133 TCATCATCCATTTCCCAGGGAA 59.142 45.455 18.05 18.05 40.27 3.97
388 408 3.117398 TCATCATCCATTTCCCAGGGAAG 60.117 47.826 20.90 10.58 43.06 3.46
389 409 1.570501 TCATCCATTTCCCAGGGAAGG 59.429 52.381 20.90 19.03 43.06 3.46
390 410 0.262876 ATCCATTTCCCAGGGAAGGC 59.737 55.000 20.90 0.00 43.06 4.35
391 411 0.850883 TCCATTTCCCAGGGAAGGCT 60.851 55.000 20.90 7.55 43.06 4.58
392 412 0.396278 CCATTTCCCAGGGAAGGCTC 60.396 60.000 20.90 0.00 43.06 4.70
393 413 0.627986 CATTTCCCAGGGAAGGCTCT 59.372 55.000 20.90 2.64 43.06 4.09
394 414 0.627986 ATTTCCCAGGGAAGGCTCTG 59.372 55.000 20.90 0.00 43.06 3.35
395 415 2.142292 TTTCCCAGGGAAGGCTCTGC 62.142 60.000 20.90 0.00 43.06 4.26
409 429 3.665745 GCTCTGCCAAAAATTCCTTCA 57.334 42.857 0.00 0.00 0.00 3.02
410 430 3.320626 GCTCTGCCAAAAATTCCTTCAC 58.679 45.455 0.00 0.00 0.00 3.18
411 431 3.006217 GCTCTGCCAAAAATTCCTTCACT 59.994 43.478 0.00 0.00 0.00 3.41
412 432 4.553323 CTCTGCCAAAAATTCCTTCACTG 58.447 43.478 0.00 0.00 0.00 3.66
413 433 4.214310 TCTGCCAAAAATTCCTTCACTGA 58.786 39.130 0.00 0.00 0.00 3.41
414 434 4.834496 TCTGCCAAAAATTCCTTCACTGAT 59.166 37.500 0.00 0.00 0.00 2.90
415 435 5.047802 TCTGCCAAAAATTCCTTCACTGATC 60.048 40.000 0.00 0.00 0.00 2.92
416 436 4.588106 TGCCAAAAATTCCTTCACTGATCA 59.412 37.500 0.00 0.00 0.00 2.92
417 437 5.246656 TGCCAAAAATTCCTTCACTGATCAT 59.753 36.000 0.00 0.00 0.00 2.45
418 438 5.809051 GCCAAAAATTCCTTCACTGATCATC 59.191 40.000 0.00 0.00 0.00 2.92
419 439 6.335777 CCAAAAATTCCTTCACTGATCATCC 58.664 40.000 0.00 0.00 0.00 3.51
420 440 6.071221 CCAAAAATTCCTTCACTGATCATCCA 60.071 38.462 0.00 0.00 0.00 3.41
421 441 7.364408 CCAAAAATTCCTTCACTGATCATCCAT 60.364 37.037 0.00 0.00 0.00 3.41
422 442 7.729124 AAAATTCCTTCACTGATCATCCATT 57.271 32.000 0.00 0.00 0.00 3.16
423 443 7.729124 AAATTCCTTCACTGATCATCCATTT 57.271 32.000 0.00 0.00 0.00 2.32
424 444 6.956202 ATTCCTTCACTGATCATCCATTTC 57.044 37.500 0.00 0.00 0.00 2.17
454 474 2.599659 GCTCTGCCAAAAATTCCTTCG 58.400 47.619 0.00 0.00 0.00 3.79
648 670 8.777865 TCTGAAAACAGAACAGATCGATAATT 57.222 30.769 0.00 0.00 36.04 1.40
650 672 9.483062 CTGAAAACAGAACAGATCGATAATTTC 57.517 33.333 0.00 0.98 34.07 2.17
651 673 8.998377 TGAAAACAGAACAGATCGATAATTTCA 58.002 29.630 0.00 3.01 31.66 2.69
655 680 7.923888 ACAGAACAGATCGATAATTTCATTGG 58.076 34.615 0.00 0.00 0.00 3.16
708 733 0.319125 GATAGAGCCGCAGTAGCACC 60.319 60.000 0.00 0.00 42.27 5.01
709 734 1.043116 ATAGAGCCGCAGTAGCACCA 61.043 55.000 0.00 0.00 42.27 4.17
710 735 1.667154 TAGAGCCGCAGTAGCACCAG 61.667 60.000 0.00 0.00 42.27 4.00
731 756 2.884639 GGTGTAGATGTTGTTGCTGGTT 59.115 45.455 0.00 0.00 0.00 3.67
840 865 3.726557 TCTACGTCTTCTCCCTAACCA 57.273 47.619 0.00 0.00 0.00 3.67
945 973 4.219725 AGTGCTGTTACAAGGTGTGTTTTT 59.780 37.500 0.00 0.00 41.98 1.94
1021 1049 0.391597 GTCAAGTGGGACCTCGTTCA 59.608 55.000 0.00 0.00 0.00 3.18
1110 1138 3.078305 AGAAGAGGAGGAAGAGGAGGAAA 59.922 47.826 0.00 0.00 0.00 3.13
1178 1206 0.961358 CACCTCGACGACCTCTCCTT 60.961 60.000 0.00 0.00 0.00 3.36
1333 1361 4.261114 CCCAAGCATGCGAAAACAAAAATT 60.261 37.500 13.01 0.00 0.00 1.82
1347 1375 8.599876 AAAACAAAAATTGATGAAAACGAAGC 57.400 26.923 0.00 0.00 0.00 3.86
1348 1376 6.285790 ACAAAAATTGATGAAAACGAAGCC 57.714 33.333 0.00 0.00 0.00 4.35
1378 1407 6.017933 CGAAATATCTGCTCAGACAAAACAC 58.982 40.000 1.15 0.00 40.75 3.32
1430 1459 2.355818 GCCCCCTACCTAACACTTTGAG 60.356 54.545 0.00 0.00 0.00 3.02
1540 1577 9.273016 TCTACATGAAAGAAAACCTAACAAGAG 57.727 33.333 0.00 0.00 0.00 2.85
1765 1804 3.134985 AGATCATCTGCTGCATGAACTCT 59.865 43.478 9.72 6.75 33.94 3.24
1771 1810 3.450096 TCTGCTGCATGAACTCTATCACT 59.550 43.478 1.31 0.00 30.82 3.41
1773 1812 4.941657 TGCTGCATGAACTCTATCACTAG 58.058 43.478 0.00 0.00 30.82 2.57
1777 1816 4.160252 TGCATGAACTCTATCACTAGCACA 59.840 41.667 0.00 0.00 33.08 4.57
1788 1827 3.296709 CTAGCACAGCGAACCCCGT 62.297 63.158 0.00 0.00 41.15 5.28
1822 1861 1.538047 CCACAACAAGCAGTGCCTAT 58.462 50.000 12.58 0.00 34.48 2.57
1882 1921 6.351033 CCATAGACTTGTACCAGTGCTTCTAA 60.351 42.308 3.99 0.00 0.00 2.10
1884 1923 4.021016 AGACTTGTACCAGTGCTTCTAAGG 60.021 45.833 3.99 0.00 0.00 2.69
1885 1924 3.901844 ACTTGTACCAGTGCTTCTAAGGA 59.098 43.478 0.00 0.00 0.00 3.36
1886 1925 4.347000 ACTTGTACCAGTGCTTCTAAGGAA 59.653 41.667 0.00 0.00 0.00 3.36
2011 2053 1.522900 CCCCCTCTCTCTCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
2012 2054 1.421646 CCCCCTCTCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
2013 2055 2.412591 CCCCTCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
2014 2056 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
2015 2057 3.312890 CCCTCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
2016 2058 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
2017 2059 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
2018 2060 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
2019 2061 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2020 2062 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2021 2063 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2022 2064 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2023 2065 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2024 2066 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2025 2067 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2026 2068 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2027 2069 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2028 2070 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2029 2071 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2030 2072 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2031 2073 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2032 2074 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2033 2075 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2240 2284 5.403558 TCTCCATCTTCATGTACTCCCTA 57.596 43.478 0.00 0.00 0.00 3.53
2242 2286 5.835819 TCTCCATCTTCATGTACTCCCTAAG 59.164 44.000 0.00 0.00 0.00 2.18
2295 2348 5.337009 GGGACGAATAATTATCTCCGCCTAA 60.337 44.000 0.00 0.00 0.00 2.69
2349 2402 8.754773 TCCTCTTGGTTAGGCTCAAGTATTGC 62.755 46.154 12.50 0.00 38.93 3.56
2362 2474 4.236935 CAAGTATTGCGCTCCAACATTTT 58.763 39.130 9.73 0.00 40.39 1.82
2414 2526 7.885297 TGCCCATAAGTTATATTTTGCAGATC 58.115 34.615 0.00 0.00 0.00 2.75
2415 2527 7.505248 TGCCCATAAGTTATATTTTGCAGATCA 59.495 33.333 0.00 0.00 0.00 2.92
2430 2542 6.286240 TGCAGATCAGTGTAGATGTAAGTT 57.714 37.500 0.00 0.00 0.00 2.66
2444 2556 4.488126 TGTAAGTTCAGAAGCATGCAAC 57.512 40.909 21.98 14.73 0.00 4.17
2643 2765 6.381498 TTTGAACCCTAATGGATACTGTCA 57.619 37.500 0.00 0.00 38.00 3.58
2661 2783 3.324846 TGTCATGCCTCAACAACTCTACT 59.675 43.478 0.00 0.00 0.00 2.57
2714 2836 3.428045 GCATTGTTCAATGTACAGAGCCC 60.428 47.826 21.38 3.80 32.87 5.19
2717 2839 2.290260 TGTTCAATGTACAGAGCCCCAG 60.290 50.000 0.33 0.00 0.00 4.45
2744 2866 2.601905 ACAGAGCCTTGCAAAATCCTT 58.398 42.857 0.00 0.00 0.00 3.36
2806 2928 1.286553 TCCCGGCCAAAACAGGATAAT 59.713 47.619 2.24 0.00 0.00 1.28
2845 2967 5.792741 AGGATAGAGCATGCAAGAGATTAC 58.207 41.667 21.98 1.36 0.00 1.89
2846 2968 5.306419 AGGATAGAGCATGCAAGAGATTACA 59.694 40.000 21.98 0.00 0.00 2.41
2847 2969 5.994054 GGATAGAGCATGCAAGAGATTACAA 59.006 40.000 21.98 0.00 0.00 2.41
2848 2970 6.484643 GGATAGAGCATGCAAGAGATTACAAA 59.515 38.462 21.98 0.00 0.00 2.83
2849 2971 7.012704 GGATAGAGCATGCAAGAGATTACAAAA 59.987 37.037 21.98 0.00 0.00 2.44
2850 2972 6.579666 AGAGCATGCAAGAGATTACAAAAA 57.420 33.333 21.98 0.00 0.00 1.94
2851 2973 6.385033 AGAGCATGCAAGAGATTACAAAAAC 58.615 36.000 21.98 0.00 0.00 2.43
2852 2974 6.016024 AGAGCATGCAAGAGATTACAAAAACA 60.016 34.615 21.98 0.00 0.00 2.83
2853 2975 6.694447 AGCATGCAAGAGATTACAAAAACAT 58.306 32.000 21.98 0.00 0.00 2.71
2854 2976 6.810182 AGCATGCAAGAGATTACAAAAACATC 59.190 34.615 21.98 0.00 0.00 3.06
2855 2977 6.587226 GCATGCAAGAGATTACAAAAACATCA 59.413 34.615 14.21 0.00 0.00 3.07
2856 2978 7.277098 GCATGCAAGAGATTACAAAAACATCAT 59.723 33.333 14.21 0.00 0.00 2.45
2857 2979 9.146984 CATGCAAGAGATTACAAAAACATCATT 57.853 29.630 0.00 0.00 0.00 2.57
2858 2980 8.523523 TGCAAGAGATTACAAAAACATCATTG 57.476 30.769 0.00 0.00 0.00 2.82
2859 2981 7.116662 TGCAAGAGATTACAAAAACATCATTGC 59.883 33.333 11.46 11.46 39.70 3.56
2860 2982 7.412237 GCAAGAGATTACAAAAACATCATTGCC 60.412 37.037 0.00 0.00 36.67 4.52
2861 2983 7.230849 AGAGATTACAAAAACATCATTGCCA 57.769 32.000 0.00 0.00 0.00 4.92
2862 2984 7.092716 AGAGATTACAAAAACATCATTGCCAC 58.907 34.615 0.00 0.00 0.00 5.01
2863 2985 5.863397 AGATTACAAAAACATCATTGCCACG 59.137 36.000 0.00 0.00 0.00 4.94
2864 2986 3.724508 ACAAAAACATCATTGCCACGA 57.275 38.095 0.00 0.00 0.00 4.35
2865 2987 4.052159 ACAAAAACATCATTGCCACGAA 57.948 36.364 0.00 0.00 0.00 3.85
2866 2988 4.050553 ACAAAAACATCATTGCCACGAAG 58.949 39.130 0.00 0.00 0.00 3.79
2868 2990 3.559238 AAACATCATTGCCACGAAGTC 57.441 42.857 0.00 0.00 41.61 3.01
2869 2991 2.183478 ACATCATTGCCACGAAGTCA 57.817 45.000 0.00 0.00 41.61 3.41
2870 2992 1.806542 ACATCATTGCCACGAAGTCAC 59.193 47.619 0.00 0.00 41.61 3.67
2871 2993 1.805943 CATCATTGCCACGAAGTCACA 59.194 47.619 0.00 0.00 41.61 3.58
2872 2994 2.183478 TCATTGCCACGAAGTCACAT 57.817 45.000 0.00 0.00 41.61 3.21
2873 2995 3.326836 TCATTGCCACGAAGTCACATA 57.673 42.857 0.00 0.00 41.61 2.29
2874 2996 3.669536 TCATTGCCACGAAGTCACATAA 58.330 40.909 0.00 0.00 41.61 1.90
2875 2997 3.435327 TCATTGCCACGAAGTCACATAAC 59.565 43.478 0.00 0.00 41.61 1.89
2876 2998 2.831685 TGCCACGAAGTCACATAACT 57.168 45.000 0.00 0.00 41.61 2.24
2877 2999 2.683968 TGCCACGAAGTCACATAACTC 58.316 47.619 0.00 0.00 41.61 3.01
2878 3000 2.036604 TGCCACGAAGTCACATAACTCA 59.963 45.455 0.00 0.00 41.61 3.41
2879 3001 3.064207 GCCACGAAGTCACATAACTCAA 58.936 45.455 0.00 0.00 41.61 3.02
2880 3002 3.120649 GCCACGAAGTCACATAACTCAAC 60.121 47.826 0.00 0.00 41.61 3.18
2881 3003 3.121279 CCACGAAGTCACATAACTCAACG 59.879 47.826 0.00 0.00 41.61 4.10
2882 3004 3.734231 CACGAAGTCACATAACTCAACGT 59.266 43.478 0.00 0.00 41.61 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.201965 GGCGAGAGAAACAATTGCGAG 60.202 52.381 5.05 0.00 0.00 5.03
68 69 3.676605 GGGAAACGGGCGGGTTTG 61.677 66.667 9.60 0.00 40.05 2.93
105 106 1.260544 AGGGAATTGAAGCTTGGTGC 58.739 50.000 2.10 0.00 43.29 5.01
172 173 1.571460 CTGTTTGGCGTGCTCTCAC 59.429 57.895 0.00 0.00 39.78 3.51
173 174 2.253758 GCTGTTTGGCGTGCTCTCA 61.254 57.895 0.00 0.00 0.00 3.27
175 176 2.203195 TGCTGTTTGGCGTGCTCT 60.203 55.556 0.00 0.00 34.52 4.09
176 177 2.180131 CTCTGCTGTTTGGCGTGCTC 62.180 60.000 0.00 0.00 34.52 4.26
177 178 2.203195 TCTGCTGTTTGGCGTGCT 60.203 55.556 0.00 0.00 34.52 4.40
178 179 2.253452 CTCTGCTGTTTGGCGTGC 59.747 61.111 0.00 0.00 34.52 5.34
179 180 2.253452 GCTCTGCTGTTTGGCGTG 59.747 61.111 0.00 0.00 34.52 5.34
180 181 2.203195 TGCTCTGCTGTTTGGCGT 60.203 55.556 0.00 0.00 34.52 5.68
181 182 2.062361 TTGTGCTCTGCTGTTTGGCG 62.062 55.000 0.00 0.00 34.52 5.69
183 184 1.884579 AGATTGTGCTCTGCTGTTTGG 59.115 47.619 0.00 0.00 0.00 3.28
184 185 2.292569 ACAGATTGTGCTCTGCTGTTTG 59.707 45.455 0.83 0.00 45.37 2.93
185 186 2.579873 ACAGATTGTGCTCTGCTGTTT 58.420 42.857 0.83 0.00 45.37 2.83
186 187 2.267174 ACAGATTGTGCTCTGCTGTT 57.733 45.000 0.83 0.00 45.37 3.16
187 188 2.267174 AACAGATTGTGCTCTGCTGT 57.733 45.000 0.83 0.00 45.37 4.40
200 201 2.157738 GACAGCAGCCAAGAAACAGAT 58.842 47.619 0.00 0.00 0.00 2.90
219 220 4.954118 ACTGTGGACGGGGCTGGA 62.954 66.667 0.00 0.00 0.00 3.86
221 222 4.704833 CCACTGTGGACGGGGCTG 62.705 72.222 22.33 0.00 40.96 4.85
239 240 3.373565 GAGGTGGCGGGCTTTTGG 61.374 66.667 2.38 0.00 0.00 3.28
327 347 0.704664 AACCTCCCCTGGAAATGGAC 59.295 55.000 0.00 0.00 0.00 4.02
389 409 3.006217 AGTGAAGGAATTTTTGGCAGAGC 59.994 43.478 0.00 0.00 0.00 4.09
390 410 4.279169 TCAGTGAAGGAATTTTTGGCAGAG 59.721 41.667 0.00 0.00 0.00 3.35
391 411 4.214310 TCAGTGAAGGAATTTTTGGCAGA 58.786 39.130 0.00 0.00 0.00 4.26
392 412 4.589216 TCAGTGAAGGAATTTTTGGCAG 57.411 40.909 0.00 0.00 0.00 4.85
393 413 4.588106 TGATCAGTGAAGGAATTTTTGGCA 59.412 37.500 0.00 0.00 0.00 4.92
394 414 5.138125 TGATCAGTGAAGGAATTTTTGGC 57.862 39.130 0.00 0.00 0.00 4.52
395 415 6.071221 TGGATGATCAGTGAAGGAATTTTTGG 60.071 38.462 0.09 0.00 0.00 3.28
396 416 6.927416 TGGATGATCAGTGAAGGAATTTTTG 58.073 36.000 0.09 0.00 0.00 2.44
397 417 7.729124 ATGGATGATCAGTGAAGGAATTTTT 57.271 32.000 0.09 0.00 0.00 1.94
398 418 7.729124 AATGGATGATCAGTGAAGGAATTTT 57.271 32.000 0.09 0.00 0.00 1.82
399 419 7.147776 GGAAATGGATGATCAGTGAAGGAATTT 60.148 37.037 0.09 0.00 0.00 1.82
400 420 6.323225 GGAAATGGATGATCAGTGAAGGAATT 59.677 38.462 0.09 0.00 0.00 2.17
401 421 5.832060 GGAAATGGATGATCAGTGAAGGAAT 59.168 40.000 0.09 0.00 0.00 3.01
402 422 5.195940 GGAAATGGATGATCAGTGAAGGAA 58.804 41.667 0.09 0.00 0.00 3.36
403 423 4.385643 GGGAAATGGATGATCAGTGAAGGA 60.386 45.833 0.09 0.00 0.00 3.36
404 424 3.887716 GGGAAATGGATGATCAGTGAAGG 59.112 47.826 0.09 0.00 0.00 3.46
405 425 4.529897 TGGGAAATGGATGATCAGTGAAG 58.470 43.478 0.09 0.00 0.00 3.02
406 426 4.529897 CTGGGAAATGGATGATCAGTGAA 58.470 43.478 0.09 0.00 0.00 3.18
407 427 3.117776 CCTGGGAAATGGATGATCAGTGA 60.118 47.826 0.09 0.00 0.00 3.41
408 428 3.220110 CCTGGGAAATGGATGATCAGTG 58.780 50.000 0.09 0.00 0.00 3.66
409 429 2.176364 CCCTGGGAAATGGATGATCAGT 59.824 50.000 7.01 0.00 0.00 3.41
410 430 2.490351 CCCCTGGGAAATGGATGATCAG 60.490 54.545 16.20 0.00 37.50 2.90
411 431 1.500303 CCCCTGGGAAATGGATGATCA 59.500 52.381 16.20 0.00 37.50 2.92
412 432 1.782752 TCCCCTGGGAAATGGATGATC 59.217 52.381 16.20 0.00 42.05 2.92
413 433 1.785208 CTCCCCTGGGAAATGGATGAT 59.215 52.381 16.20 0.00 44.66 2.45
414 434 1.225373 CTCCCCTGGGAAATGGATGA 58.775 55.000 16.20 0.00 44.66 2.92
415 435 0.186873 CCTCCCCTGGGAAATGGATG 59.813 60.000 16.20 0.00 44.66 3.51
416 436 1.659035 GCCTCCCCTGGGAAATGGAT 61.659 60.000 16.20 0.00 44.66 3.41
417 437 2.316586 GCCTCCCCTGGGAAATGGA 61.317 63.158 16.20 0.82 44.66 3.41
418 438 2.280079 GCCTCCCCTGGGAAATGG 59.720 66.667 16.20 11.23 44.66 3.16
419 439 1.228510 GAGCCTCCCCTGGGAAATG 59.771 63.158 16.20 0.00 44.66 2.32
420 440 1.085605 AGAGCCTCCCCTGGGAAAT 59.914 57.895 16.20 0.00 44.66 2.17
421 441 1.925455 CAGAGCCTCCCCTGGGAAA 60.925 63.158 16.20 0.31 44.66 3.13
422 442 2.285668 CAGAGCCTCCCCTGGGAA 60.286 66.667 16.20 0.00 44.66 3.97
454 474 1.242076 CCTGGAAATGGATGATCGGC 58.758 55.000 0.00 0.00 0.00 5.54
589 609 2.230992 TGCTGTGCGGCAAGAAAAATAT 59.769 40.909 3.23 0.00 39.43 1.28
593 615 1.065600 GTGCTGTGCGGCAAGAAAA 59.934 52.632 3.23 0.00 44.18 2.29
603 625 0.459934 TGCAAGTTTTGGTGCTGTGC 60.460 50.000 0.00 0.00 41.48 4.57
648 670 7.998964 AGACTCTTTTCTTTACCTTCCAATGAA 59.001 33.333 0.00 0.00 0.00 2.57
650 672 7.229506 ACAGACTCTTTTCTTTACCTTCCAATG 59.770 37.037 0.00 0.00 0.00 2.82
651 673 7.290813 ACAGACTCTTTTCTTTACCTTCCAAT 58.709 34.615 0.00 0.00 0.00 3.16
655 680 7.065923 ACACAACAGACTCTTTTCTTTACCTTC 59.934 37.037 0.00 0.00 0.00 3.46
708 733 2.485426 CCAGCAACAACATCTACACCTG 59.515 50.000 0.00 0.00 0.00 4.00
709 734 2.106511 ACCAGCAACAACATCTACACCT 59.893 45.455 0.00 0.00 0.00 4.00
710 735 2.504367 ACCAGCAACAACATCTACACC 58.496 47.619 0.00 0.00 0.00 4.16
731 756 1.004745 GAAAGGGGATGCTCCAACAGA 59.995 52.381 4.85 0.00 38.64 3.41
749 774 0.531090 CGCCGACCATAAATCCGGAA 60.531 55.000 9.01 0.00 44.29 4.30
965 993 6.526674 CCAACAACTTACAACAGTTTCACTTC 59.473 38.462 0.00 0.00 34.60 3.01
977 1005 3.547746 GTCACCTCCCAACAACTTACAA 58.452 45.455 0.00 0.00 0.00 2.41
990 1018 1.611673 CCACTTGACATGGTCACCTCC 60.612 57.143 0.00 0.00 42.60 4.30
1021 1049 3.692406 GGTCCCTTGGCTCGACGT 61.692 66.667 0.00 0.00 0.00 4.34
1110 1138 1.977544 CGACTCCCGGTTGGACTCT 60.978 63.158 0.00 0.00 38.61 3.24
1178 1206 2.303175 GAAGGGTGTAACAAACCTGCA 58.697 47.619 0.00 0.00 39.98 4.41
1297 1325 2.747460 TTGGGCGCATGCTCTCAC 60.747 61.111 10.39 3.16 44.15 3.51
1320 1348 8.798640 TTCGTTTTCATCAATTTTTGTTTTCG 57.201 26.923 0.00 0.00 0.00 3.46
1333 1361 1.243902 GTGGGGCTTCGTTTTCATCA 58.756 50.000 0.00 0.00 0.00 3.07
1347 1375 0.474184 AGCAGATATTTCGGGTGGGG 59.526 55.000 0.00 0.00 0.00 4.96
1348 1376 1.140852 TGAGCAGATATTTCGGGTGGG 59.859 52.381 0.00 0.00 0.00 4.61
1378 1407 4.441913 GGGGCATGGAAATCACAATAACTG 60.442 45.833 0.00 0.00 0.00 3.16
1430 1459 3.383620 TGGATGAATTTGTGGTGTTGC 57.616 42.857 0.00 0.00 0.00 4.17
1502 1532 6.408869 TCTTTCATGTAGAAGATGTGATGCA 58.591 36.000 0.00 0.00 37.57 3.96
1583 1621 5.215252 TCCACCTGTTTTTGTCACAAAAA 57.785 34.783 22.01 22.01 0.00 1.94
1765 1804 1.136305 GGGTTCGCTGTGCTAGTGATA 59.864 52.381 5.80 0.00 44.85 2.15
1771 1810 3.291101 GACGGGGTTCGCTGTGCTA 62.291 63.158 6.09 0.00 43.89 3.49
1808 1847 2.795231 ATGTCATAGGCACTGCTTGT 57.205 45.000 0.00 0.00 41.52 3.16
1822 1861 2.647875 CCGGCGCCAAAAATGTCA 59.352 55.556 28.98 0.00 0.00 3.58
1882 1921 5.014544 TCAACCATCCATTCTTCTTCTTCCT 59.985 40.000 0.00 0.00 0.00 3.36
1884 1923 6.376581 ACATCAACCATCCATTCTTCTTCTTC 59.623 38.462 0.00 0.00 0.00 2.87
1885 1924 6.251471 ACATCAACCATCCATTCTTCTTCTT 58.749 36.000 0.00 0.00 0.00 2.52
1886 1925 5.824421 ACATCAACCATCCATTCTTCTTCT 58.176 37.500 0.00 0.00 0.00 2.85
2004 2046 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2005 2047 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2006 2048 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2007 2049 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2008 2050 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2009 2051 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2010 2052 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2011 2053 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2012 2054 5.362143 TCAAGAGAGAGAGAGAGAGAGAGAG 59.638 48.000 0.00 0.00 0.00 3.20
2013 2055 5.272402 TCAAGAGAGAGAGAGAGAGAGAGA 58.728 45.833 0.00 0.00 0.00 3.10
2014 2056 5.604758 TCAAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.00 0.00 3.20
2015 2057 6.070021 ACAATCAAGAGAGAGAGAGAGAGAGA 60.070 42.308 0.00 0.00 0.00 3.10
2016 2058 6.118170 ACAATCAAGAGAGAGAGAGAGAGAG 58.882 44.000 0.00 0.00 0.00 3.20
2017 2059 6.065976 ACAATCAAGAGAGAGAGAGAGAGA 57.934 41.667 0.00 0.00 0.00 3.10
2018 2060 6.764308 AACAATCAAGAGAGAGAGAGAGAG 57.236 41.667 0.00 0.00 0.00 3.20
2019 2061 8.821686 ATAAACAATCAAGAGAGAGAGAGAGA 57.178 34.615 0.00 0.00 0.00 3.10
2020 2062 9.874205 AAATAAACAATCAAGAGAGAGAGAGAG 57.126 33.333 0.00 0.00 0.00 3.20
2023 2065 9.784531 ACAAAATAAACAATCAAGAGAGAGAGA 57.215 29.630 0.00 0.00 0.00 3.10
2024 2066 9.823098 CACAAAATAAACAATCAAGAGAGAGAG 57.177 33.333 0.00 0.00 0.00 3.20
2025 2067 9.559732 TCACAAAATAAACAATCAAGAGAGAGA 57.440 29.630 0.00 0.00 0.00 3.10
2026 2068 9.823098 CTCACAAAATAAACAATCAAGAGAGAG 57.177 33.333 0.00 0.00 0.00 3.20
2027 2069 8.786898 CCTCACAAAATAAACAATCAAGAGAGA 58.213 33.333 0.00 0.00 0.00 3.10
2028 2070 8.571336 ACCTCACAAAATAAACAATCAAGAGAG 58.429 33.333 0.00 0.00 0.00 3.20
2029 2071 8.463930 ACCTCACAAAATAAACAATCAAGAGA 57.536 30.769 0.00 0.00 0.00 3.10
2030 2072 8.971321 CAACCTCACAAAATAAACAATCAAGAG 58.029 33.333 0.00 0.00 0.00 2.85
2031 2073 7.925483 CCAACCTCACAAAATAAACAATCAAGA 59.075 33.333 0.00 0.00 0.00 3.02
2032 2074 7.171337 CCCAACCTCACAAAATAAACAATCAAG 59.829 37.037 0.00 0.00 0.00 3.02
2033 2075 6.989169 CCCAACCTCACAAAATAAACAATCAA 59.011 34.615 0.00 0.00 0.00 2.57
2258 2302 7.931578 ATTATTCGTCCCAAAATAAGTGTCA 57.068 32.000 0.00 0.00 32.50 3.58
2295 2348 3.119101 ACACGTGCGATAAGAGAAGGATT 60.119 43.478 17.22 0.00 0.00 3.01
2362 2474 4.777896 ACCTACCTAGCTTCACATCTCAAA 59.222 41.667 0.00 0.00 0.00 2.69
2414 2526 6.159293 TGCTTCTGAACTTACATCTACACTG 58.841 40.000 0.00 0.00 0.00 3.66
2415 2527 6.346477 TGCTTCTGAACTTACATCTACACT 57.654 37.500 0.00 0.00 0.00 3.55
2430 2542 3.119884 CCGTAAATGTTGCATGCTTCTGA 60.120 43.478 20.33 0.00 0.00 3.27
2444 2556 9.103048 GCAATATTCGACTTTTATCCGTAAATG 57.897 33.333 0.00 0.00 33.49 2.32
2612 2728 4.141251 TCCATTAGGGTTCAAATCCTAGCC 60.141 45.833 2.18 0.00 42.49 3.93
2643 2765 4.323562 GGGTTAGTAGAGTTGTTGAGGCAT 60.324 45.833 0.00 0.00 0.00 4.40
2720 2842 3.119708 GGATTTTGCAAGGCTCTGTAGTG 60.120 47.826 0.00 0.00 0.00 2.74
2806 2928 0.847373 TCCTTAGGTGGGTTTGTGCA 59.153 50.000 0.00 0.00 0.00 4.57
2845 2967 4.050553 ACTTCGTGGCAATGATGTTTTTG 58.949 39.130 0.00 0.00 0.00 2.44
2846 2968 4.202101 TGACTTCGTGGCAATGATGTTTTT 60.202 37.500 3.50 0.00 31.65 1.94
2847 2969 3.317711 TGACTTCGTGGCAATGATGTTTT 59.682 39.130 3.50 0.00 31.65 2.43
2848 2970 2.884012 TGACTTCGTGGCAATGATGTTT 59.116 40.909 3.50 0.00 31.65 2.83
2849 2971 2.226437 GTGACTTCGTGGCAATGATGTT 59.774 45.455 3.50 0.00 34.07 2.71
2850 2972 1.806542 GTGACTTCGTGGCAATGATGT 59.193 47.619 1.53 1.53 34.07 3.06
2851 2973 1.805943 TGTGACTTCGTGGCAATGATG 59.194 47.619 0.00 0.00 34.07 3.07
2852 2974 2.183478 TGTGACTTCGTGGCAATGAT 57.817 45.000 0.00 0.00 34.07 2.45
2853 2975 2.183478 ATGTGACTTCGTGGCAATGA 57.817 45.000 0.00 0.00 34.07 2.57
2854 2976 3.436704 AGTTATGTGACTTCGTGGCAATG 59.563 43.478 0.00 0.00 34.07 2.82
2855 2977 3.674997 AGTTATGTGACTTCGTGGCAAT 58.325 40.909 0.00 0.00 34.07 3.56
2856 2978 3.064207 GAGTTATGTGACTTCGTGGCAA 58.936 45.455 0.00 0.00 34.07 4.52
2857 2979 2.036604 TGAGTTATGTGACTTCGTGGCA 59.963 45.455 0.00 0.00 0.00 4.92
2858 2980 2.683968 TGAGTTATGTGACTTCGTGGC 58.316 47.619 0.00 0.00 0.00 5.01
2859 2981 3.121279 CGTTGAGTTATGTGACTTCGTGG 59.879 47.826 0.00 0.00 0.00 4.94
2860 2982 3.734231 ACGTTGAGTTATGTGACTTCGTG 59.266 43.478 0.00 0.00 33.86 4.35
2861 2983 3.973657 ACGTTGAGTTATGTGACTTCGT 58.026 40.909 0.00 0.00 32.00 3.85


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

AutoCloner maintained by Alex Coulton.