Multiple sequence alignment - TraesCS5D01G060500

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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 TraesCS5D01G060500 chr5D 100.000 2174 0 0 906 3079 57370671 57368498 0.000000e+00 4015.0
1 TraesCS5D01G060500 chr5D 100.000 619 0 0 1 619 57371576 57370958 0.000000e+00 1144.0
2 TraesCS5D01G060500 chr5D 84.428 411 43 6 2056 2453 57216386 57215984 4.820000e-103 385.0
3 TraesCS5D01G060500 chr5D 96.667 60 2 0 2002 2061 57226923 57226864 1.950000e-17 100.0
4 TraesCS5D01G060500 chr5B 91.037 993 43 14 925 1899 60903749 60904713 0.000000e+00 1299.0
5 TraesCS5D01G060500 chr5B 95.046 545 24 3 65 606 60903199 60903743 0.000000e+00 854.0
6 TraesCS5D01G060500 chr5B 92.000 375 30 0 1308 1682 61061626 61062000 7.560000e-146 527.0
7 TraesCS5D01G060500 chr5B 81.002 479 41 18 2002 2463 61066115 61066560 4.920000e-88 335.0
8 TraesCS5D01G060500 chr5B 80.556 180 13 7 1677 1854 61065911 61066070 5.390000e-23 119.0
9 TraesCS5D01G060500 chr5B 94.595 74 3 1 1 74 60902817 60902889 2.510000e-21 113.0
10 TraesCS5D01G060500 chr5B 90.411 73 7 0 1 73 641921982 641922054 2.530000e-16 97.1
11 TraesCS5D01G060500 chr5A 93.560 823 35 8 909 1724 45527869 45527058 0.000000e+00 1210.0
12 TraesCS5D01G060500 chr5A 83.688 423 47 11 2056 2464 45450397 45449983 2.240000e-101 379.0
13 TraesCS5D01G060500 chr5A 95.745 94 4 0 513 606 45527957 45527864 5.320000e-33 152.0
14 TraesCS5D01G060500 chr5A 100.000 28 0 0 308 335 709611113 709611140 6.000000e-03 52.8
15 TraesCS5D01G060500 chr2D 96.367 578 21 0 2462 3039 95504992 95504415 0.000000e+00 952.0
16 TraesCS5D01G060500 chr2D 95.675 578 25 0 2461 3038 35246589 35247166 0.000000e+00 929.0
17 TraesCS5D01G060500 chr2D 95.189 582 27 1 2462 3042 559316396 559315815 0.000000e+00 918.0
18 TraesCS5D01G060500 chr2D 93.151 73 5 0 1 73 194452273 194452345 1.170000e-19 108.0
19 TraesCS5D01G060500 chr2D 93.151 73 5 0 1 73 587115290 587115362 1.170000e-19 108.0
20 TraesCS5D01G060500 chr2D 97.674 43 1 0 3037 3079 154190062 154190020 1.180000e-09 75.0
21 TraesCS5D01G060500 chr1D 96.034 580 21 2 2464 3042 30587758 30588336 0.000000e+00 942.0
22 TraesCS5D01G060500 chr1D 91.781 73 6 0 1 73 255495129 255495201 5.430000e-18 102.0
23 TraesCS5D01G060500 chr1D 88.608 79 7 2 1 77 441035350 441035428 9.090000e-16 95.3
24 TraesCS5D01G060500 chr1D 97.674 43 1 0 3037 3079 59511760 59511718 1.180000e-09 75.0
25 TraesCS5D01G060500 chr4D 95.400 587 23 2 2460 3042 66298009 66298595 0.000000e+00 931.0
26 TraesCS5D01G060500 chr4D 95.222 586 23 3 2461 3042 487284281 487284865 0.000000e+00 922.0
27 TraesCS5D01G060500 chr6D 95.392 586 22 3 2462 3042 107938741 107938156 0.000000e+00 928.0
28 TraesCS5D01G060500 chr6D 88.462 78 6 3 1 76 216866023 216866099 1.180000e-14 91.6
29 TraesCS5D01G060500 chr6D 97.674 43 1 0 3037 3079 411184994 411185036 1.180000e-09 75.0
30 TraesCS5D01G060500 chr6D 97.619 42 1 0 3038 3079 68858195 68858154 4.260000e-09 73.1
31 TraesCS5D01G060500 chr6D 97.619 42 1 0 3038 3079 424818605 424818564 4.260000e-09 73.1
32 TraesCS5D01G060500 chr6D 97.619 42 1 0 3038 3079 446607863 446607904 4.260000e-09 73.1
33 TraesCS5D01G060500 chr6D 97.619 42 1 0 3038 3079 457743577 457743618 4.260000e-09 73.1
34 TraesCS5D01G060500 chr7D 94.234 607 31 4 2438 3042 527732877 527732273 0.000000e+00 924.0
35 TraesCS5D01G060500 chr7D 95.197 583 25 3 2462 3042 168499958 168499377 0.000000e+00 918.0
36 TraesCS5D01G060500 chr7D 100.000 31 0 0 307 337 615961789 615961819 1.190000e-04 58.4
37 TraesCS5D01G060500 chr7D 100.000 31 0 0 307 337 615962888 615962918 1.190000e-04 58.4
38 TraesCS5D01G060500 chr3B 89.474 76 7 1 3 77 81971225 81971150 9.090000e-16 95.3
39 TraesCS5D01G060500 chr1B 89.474 76 7 1 3 77 634801721 634801796 9.090000e-16 95.3
40 TraesCS5D01G060500 chr1B 97.674 43 1 0 3037 3079 540141366 540141324 1.180000e-09 75.0
41 TraesCS5D01G060500 chr2A 97.674 43 1 0 3037 3079 707208752 707208794 1.180000e-09 75.0
42 TraesCS5D01G060500 chr4A 100.000 28 0 0 417 444 739863850 739863877 6.000000e-03 52.8


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 TraesCS5D01G060500 chr5D 57368498 57371576 3078 True 2579.500000 4015 100.000000 1 3079 2 chr5D.!!$R3 3078
1 TraesCS5D01G060500 chr5B 60902817 60904713 1896 False 755.333333 1299 93.559333 1 1899 3 chr5B.!!$F2 1898
2 TraesCS5D01G060500 chr5B 61061626 61066560 4934 False 327.000000 527 84.519333 1308 2463 3 chr5B.!!$F3 1155
3 TraesCS5D01G060500 chr5A 45527058 45527957 899 True 681.000000 1210 94.652500 513 1724 2 chr5A.!!$R2 1211
4 TraesCS5D01G060500 chr2D 95504415 95504992 577 True 952.000000 952 96.367000 2462 3039 1 chr2D.!!$R1 577
5 TraesCS5D01G060500 chr2D 35246589 35247166 577 False 929.000000 929 95.675000 2461 3038 1 chr2D.!!$F1 577
6 TraesCS5D01G060500 chr2D 559315815 559316396 581 True 918.000000 918 95.189000 2462 3042 1 chr2D.!!$R3 580
7 TraesCS5D01G060500 chr1D 30587758 30588336 578 False 942.000000 942 96.034000 2464 3042 1 chr1D.!!$F1 578
8 TraesCS5D01G060500 chr4D 66298009 66298595 586 False 931.000000 931 95.400000 2460 3042 1 chr4D.!!$F1 582
9 TraesCS5D01G060500 chr4D 487284281 487284865 584 False 922.000000 922 95.222000 2461 3042 1 chr4D.!!$F2 581
10 TraesCS5D01G060500 chr6D 107938156 107938741 585 True 928.000000 928 95.392000 2462 3042 1 chr6D.!!$R2 580
11 TraesCS5D01G060500 chr7D 527732273 527732877 604 True 924.000000 924 94.234000 2438 3042 1 chr7D.!!$R2 604
12 TraesCS5D01G060500 chr7D 168499377 168499958 581 True 918.000000 918 95.197000 2462 3042 1 chr7D.!!$R1 580

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
608 931 0.035458 AAGCACTGGTGAGCAGTACC 59.965 55.0 17.66 11.25 38.71 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 6555 0.107508 CCATTGGCATCCTCGACAGT 60.108 55.0 0.0 0.0 0.0 3.55 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 8.966155 AAAAATCCCAAGAATTCTAACCCTTA 57.034 30.769 8.75 0.00 0.00 2.69
86 406 3.876309 AGGAGCCTAAACCAGTTTTGA 57.124 42.857 0.37 0.00 34.23 2.69
197 517 6.530019 AAATTTATGCGGAAGAAGGAACAT 57.470 33.333 0.00 0.00 0.00 2.71
224 545 6.345093 CGAACTTGAACTCTCGTAACAGAAAG 60.345 42.308 0.00 0.00 0.00 2.62
238 559 7.330208 TCGTAACAGAAAGTAAACTAGGCAATC 59.670 37.037 0.00 0.00 0.00 2.67
267 588 8.773645 CATATAACAAGTTAATCTGATTCGGCA 58.226 33.333 6.10 0.00 0.00 5.69
277 598 4.944962 TCTGATTCGGCATGTTTTACAG 57.055 40.909 0.00 0.00 0.00 2.74
498 821 4.216708 AGAGTATTTAGGAACGGAGGGAG 58.783 47.826 0.00 0.00 0.00 4.30
499 822 2.699321 AGTATTTAGGAACGGAGGGAGC 59.301 50.000 0.00 0.00 0.00 4.70
606 929 1.047801 TCAAGCACTGGTGAGCAGTA 58.952 50.000 17.66 0.00 32.15 2.74
607 930 1.151668 CAAGCACTGGTGAGCAGTAC 58.848 55.000 17.66 12.10 32.15 2.73
608 931 0.035458 AAGCACTGGTGAGCAGTACC 59.965 55.000 17.66 11.25 38.71 3.34
610 933 1.079819 CACTGGTGAGCAGTACCCG 60.080 63.158 17.66 0.99 37.40 5.28
611 934 2.125512 CTGGTGAGCAGTACCCGC 60.126 66.667 2.99 0.00 37.40 6.13
612 935 2.920384 TGGTGAGCAGTACCCGCA 60.920 61.111 7.55 0.00 37.40 5.69
613 936 2.345991 GGTGAGCAGTACCCGCAA 59.654 61.111 7.55 0.00 31.89 4.85
614 937 1.302192 GGTGAGCAGTACCCGCAAA 60.302 57.895 7.55 0.00 31.89 3.68
615 938 0.887387 GGTGAGCAGTACCCGCAAAA 60.887 55.000 7.55 0.00 31.89 2.44
616 939 0.948678 GTGAGCAGTACCCGCAAAAA 59.051 50.000 7.55 0.00 0.00 1.94
935 1258 1.901464 CTCCCCACCCCAACAAACG 60.901 63.158 0.00 0.00 0.00 3.60
964 1292 1.912001 TGCGTATGTAGCGTACAACC 58.088 50.000 0.00 0.00 42.76 3.77
972 1300 1.532437 GTAGCGTACAACCACAAACCC 59.468 52.381 0.00 0.00 0.00 4.11
974 1302 1.943293 CGTACAACCACAAACCCCG 59.057 57.895 0.00 0.00 0.00 5.73
975 1303 0.814812 CGTACAACCACAAACCCCGT 60.815 55.000 0.00 0.00 0.00 5.28
1497 1836 3.998672 GGCGTGACCCGACAGGAA 61.999 66.667 0.00 0.00 46.74 3.36
1742 6000 8.744652 GCTTAATTAGCTACTCCATATCTCTCA 58.255 37.037 0.00 0.00 46.77 3.27
1745 6003 8.719645 AATTAGCTACTCCATATCTCTCAACT 57.280 34.615 0.00 0.00 0.00 3.16
1746 6004 7.753309 TTAGCTACTCCATATCTCTCAACTC 57.247 40.000 0.00 0.00 0.00 3.01
1747 6005 5.952387 AGCTACTCCATATCTCTCAACTCT 58.048 41.667 0.00 0.00 0.00 3.24
1748 6006 6.003950 AGCTACTCCATATCTCTCAACTCTC 58.996 44.000 0.00 0.00 0.00 3.20
1749 6007 5.767665 GCTACTCCATATCTCTCAACTCTCA 59.232 44.000 0.00 0.00 0.00 3.27
1750 6008 6.264292 GCTACTCCATATCTCTCAACTCTCAA 59.736 42.308 0.00 0.00 0.00 3.02
1751 6009 6.713762 ACTCCATATCTCTCAACTCTCAAG 57.286 41.667 0.00 0.00 0.00 3.02
1752 6010 5.598005 ACTCCATATCTCTCAACTCTCAAGG 59.402 44.000 0.00 0.00 0.00 3.61
1753 6011 4.343526 TCCATATCTCTCAACTCTCAAGGC 59.656 45.833 0.00 0.00 0.00 4.35
1754 6012 4.502950 CCATATCTCTCAACTCTCAAGGCC 60.503 50.000 0.00 0.00 0.00 5.19
1755 6013 1.270907 TCTCTCAACTCTCAAGGCCC 58.729 55.000 0.00 0.00 0.00 5.80
1756 6014 0.251634 CTCTCAACTCTCAAGGCCCC 59.748 60.000 0.00 0.00 0.00 5.80
1757 6015 1.078848 CTCAACTCTCAAGGCCCCG 60.079 63.158 0.00 0.00 0.00 5.73
1758 6016 1.831652 CTCAACTCTCAAGGCCCCGT 61.832 60.000 0.00 0.00 0.00 5.28
1759 6017 1.672356 CAACTCTCAAGGCCCCGTG 60.672 63.158 0.00 0.00 0.00 4.94
1760 6018 3.553095 AACTCTCAAGGCCCCGTGC 62.553 63.158 0.00 0.00 40.16 5.34
1856 6125 7.761038 GAAGGAACCTTCTTTTTGGAGATTA 57.239 36.000 21.88 0.00 46.38 1.75
1857 6126 8.354711 GAAGGAACCTTCTTTTTGGAGATTAT 57.645 34.615 21.88 0.00 46.38 1.28
1858 6127 7.946381 AGGAACCTTCTTTTTGGAGATTATC 57.054 36.000 0.00 0.00 0.00 1.75
1859 6128 7.470192 AGGAACCTTCTTTTTGGAGATTATCA 58.530 34.615 0.00 0.00 0.00 2.15
1860 6129 8.118600 AGGAACCTTCTTTTTGGAGATTATCAT 58.881 33.333 0.00 0.00 0.00 2.45
1861 6130 8.753133 GGAACCTTCTTTTTGGAGATTATCATT 58.247 33.333 0.00 0.00 0.00 2.57
1862 6131 9.578439 GAACCTTCTTTTTGGAGATTATCATTG 57.422 33.333 0.00 0.00 0.00 2.82
1863 6132 8.884124 ACCTTCTTTTTGGAGATTATCATTGA 57.116 30.769 0.00 0.00 0.00 2.57
1864 6133 8.743714 ACCTTCTTTTTGGAGATTATCATTGAC 58.256 33.333 0.00 0.00 0.00 3.18
1865 6134 8.964772 CCTTCTTTTTGGAGATTATCATTGACT 58.035 33.333 0.00 0.00 0.00 3.41
1917 6187 3.936902 TTGCAACGTAGTGAAGTGTTC 57.063 42.857 0.00 0.00 45.00 3.18
1918 6188 3.173668 TGCAACGTAGTGAAGTGTTCT 57.826 42.857 0.00 0.00 45.00 3.01
1919 6189 4.310357 TGCAACGTAGTGAAGTGTTCTA 57.690 40.909 0.00 0.00 45.00 2.10
1920 6190 4.295870 TGCAACGTAGTGAAGTGTTCTAG 58.704 43.478 0.00 0.00 45.00 2.43
1921 6191 4.037089 TGCAACGTAGTGAAGTGTTCTAGA 59.963 41.667 0.00 0.00 45.00 2.43
1922 6192 5.162075 GCAACGTAGTGAAGTGTTCTAGAT 58.838 41.667 0.00 0.00 45.00 1.98
1923 6193 6.072342 TGCAACGTAGTGAAGTGTTCTAGATA 60.072 38.462 0.00 0.00 45.00 1.98
1924 6194 6.469595 GCAACGTAGTGAAGTGTTCTAGATAG 59.530 42.308 0.00 0.00 45.00 2.08
1925 6195 7.625817 GCAACGTAGTGAAGTGTTCTAGATAGA 60.626 40.741 0.00 0.00 45.00 1.98
1926 6196 7.918536 ACGTAGTGAAGTGTTCTAGATAGAA 57.081 36.000 0.00 0.00 42.51 2.10
1939 6209 7.749377 TTCTAGATAGAACAAAAGATCCCCA 57.251 36.000 0.00 0.00 37.40 4.96
1940 6210 7.125792 TCTAGATAGAACAAAAGATCCCCAC 57.874 40.000 0.00 0.00 0.00 4.61
1941 6211 5.779241 AGATAGAACAAAAGATCCCCACA 57.221 39.130 0.00 0.00 0.00 4.17
1942 6212 6.139679 AGATAGAACAAAAGATCCCCACAA 57.860 37.500 0.00 0.00 0.00 3.33
1943 6213 6.552008 AGATAGAACAAAAGATCCCCACAAA 58.448 36.000 0.00 0.00 0.00 2.83
1944 6214 7.010160 AGATAGAACAAAAGATCCCCACAAAA 58.990 34.615 0.00 0.00 0.00 2.44
1945 6215 5.948742 AGAACAAAAGATCCCCACAAAAA 57.051 34.783 0.00 0.00 0.00 1.94
2048 6318 5.759506 TGGCACGATTGAAAAAGAAGTTA 57.240 34.783 0.00 0.00 0.00 2.24
2049 6319 6.137794 TGGCACGATTGAAAAAGAAGTTAA 57.862 33.333 0.00 0.00 0.00 2.01
2051 6321 7.206687 TGGCACGATTGAAAAAGAAGTTAATT 58.793 30.769 0.00 0.00 0.00 1.40
2053 6323 8.003784 GGCACGATTGAAAAAGAAGTTAATTTG 58.996 33.333 0.00 0.00 0.00 2.32
2054 6324 8.539674 GCACGATTGAAAAAGAAGTTAATTTGT 58.460 29.630 0.00 0.00 0.00 2.83
2099 6369 9.651913 GATTATTCTTTGTAAATTGGCCTCAAA 57.348 29.630 3.32 5.61 36.36 2.69
2110 6380 7.902920 AAATTGGCCTCAAAGTATGATGTAT 57.097 32.000 3.32 0.00 37.44 2.29
2111 6381 7.516198 AATTGGCCTCAAAGTATGATGTATC 57.484 36.000 3.32 0.00 37.44 2.24
2112 6382 5.628797 TGGCCTCAAAGTATGATGTATCA 57.371 39.130 3.32 0.00 41.70 2.15
2113 6383 7.236529 ATTGGCCTCAAAGTATGATGTATCAT 58.763 34.615 3.32 11.69 42.02 2.45
2114 6384 5.999600 TGGCCTCAAAGTATGATGTATCATG 59.000 40.000 15.72 2.58 46.34 3.07
2115 6385 6.000219 GGCCTCAAAGTATGATGTATCATGT 59.000 40.000 15.72 2.54 46.34 3.21
2116 6386 7.161404 GGCCTCAAAGTATGATGTATCATGTA 58.839 38.462 15.72 0.00 46.34 2.29
2117 6387 7.826252 GGCCTCAAAGTATGATGTATCATGTAT 59.174 37.037 15.72 1.31 46.34 2.29
2118 6388 8.663025 GCCTCAAAGTATGATGTATCATGTATG 58.337 37.037 15.72 10.04 46.34 2.39
2119 6389 9.716531 CCTCAAAGTATGATGTATCATGTATGT 57.283 33.333 15.72 0.00 46.34 2.29
2127 6397 8.768957 ATGATGTATCATGTATGTAGAGTTGC 57.231 34.615 6.56 0.00 45.27 4.17
2130 6400 7.346751 TGTATCATGTATGTAGAGTTGCAGA 57.653 36.000 0.00 0.00 0.00 4.26
2135 6405 0.108138 ATGTAGAGTTGCAGACCGCC 60.108 55.000 0.00 0.00 41.33 6.13
2139 6409 1.375908 GAGTTGCAGACCGCCATCA 60.376 57.895 0.00 0.00 41.33 3.07
2146 6416 3.023119 TGCAGACCGCCATCATAATTTT 58.977 40.909 0.00 0.00 41.33 1.82
2155 6425 4.856487 CGCCATCATAATTTTCAACACGTT 59.144 37.500 0.00 0.00 0.00 3.99
2159 6434 7.540745 GCCATCATAATTTTCAACACGTTAAGT 59.459 33.333 0.00 0.00 0.00 2.24
2199 6474 2.037208 CCACCTTTTGGCGGGGAT 59.963 61.111 0.00 0.00 45.59 3.85
2200 6475 2.052104 CCACCTTTTGGCGGGGATC 61.052 63.158 0.00 0.00 45.59 3.36
2253 6528 0.110192 GCTACAAGGCGTTGCTGAAC 60.110 55.000 18.61 1.30 42.30 3.18
2259 6534 2.665185 GCGTTGCTGAACTCCGGT 60.665 61.111 0.00 0.00 0.00 5.28
2279 6554 1.153349 GGACCTTGCCCTCGATCAC 60.153 63.158 0.00 0.00 0.00 3.06
2280 6555 1.596934 GACCTTGCCCTCGATCACA 59.403 57.895 0.00 0.00 0.00 3.58
2282 6557 1.194781 ACCTTGCCCTCGATCACACT 61.195 55.000 0.00 0.00 0.00 3.55
2286 6561 1.517257 GCCCTCGATCACACTGTCG 60.517 63.158 0.00 0.00 39.11 4.35
2295 6570 1.184970 TCACACTGTCGAGGATGCCA 61.185 55.000 0.00 0.00 0.00 4.92
2297 6572 0.615331 ACACTGTCGAGGATGCCAAT 59.385 50.000 0.00 0.00 0.00 3.16
2344 6620 4.038883 TGGTGACATGATCTGCTATCTCTG 59.961 45.833 0.00 2.74 33.40 3.35
2358 6634 5.240623 TGCTATCTCTGAAGAACTAGCTAGC 59.759 44.000 20.91 6.62 36.18 3.42
2372 6656 5.174395 ACTAGCTAGCAGAACAAACATCAG 58.826 41.667 20.91 0.00 0.00 2.90
2374 6658 4.252073 AGCTAGCAGAACAAACATCAGAG 58.748 43.478 18.83 0.00 0.00 3.35
2378 6662 5.474578 AGCAGAACAAACATCAGAGAGTA 57.525 39.130 0.00 0.00 0.00 2.59
2379 6663 5.477510 AGCAGAACAAACATCAGAGAGTAG 58.522 41.667 0.00 0.00 0.00 2.57
2380 6664 4.092675 GCAGAACAAACATCAGAGAGTAGC 59.907 45.833 0.00 0.00 0.00 3.58
2381 6665 5.477510 CAGAACAAACATCAGAGAGTAGCT 58.522 41.667 0.00 0.00 0.00 3.32
2395 6681 8.322828 TCAGAGAGTAGCTAACTTAGAGAGAAA 58.677 37.037 0.00 0.00 39.07 2.52
2399 6685 8.617809 AGAGTAGCTAACTTAGAGAGAAAATCG 58.382 37.037 0.00 0.00 39.07 3.34
2410 6696 5.810095 AGAGAGAAAATCGTGAGGGAATTT 58.190 37.500 0.00 0.00 0.00 1.82
2411 6697 5.645497 AGAGAGAAAATCGTGAGGGAATTTG 59.355 40.000 0.00 0.00 0.00 2.32
2413 6699 4.662278 AGAAAATCGTGAGGGAATTTGGA 58.338 39.130 0.00 0.00 0.00 3.53
2415 6701 3.433306 AATCGTGAGGGAATTTGGACA 57.567 42.857 0.00 0.00 0.00 4.02
2436 6722 1.722011 ATTTCAGGTACGCCTTCACG 58.278 50.000 0.00 0.00 44.18 4.35
2447 6733 1.244019 GCCTTCACGCCAACCAGAAT 61.244 55.000 0.00 0.00 0.00 2.40
2532 6819 2.281276 GTTCGTTTGGGTCGGCCT 60.281 61.111 5.77 0.00 34.45 5.19
2533 6820 1.895231 GTTCGTTTGGGTCGGCCTT 60.895 57.895 5.77 0.00 34.45 4.35
2631 6918 1.138671 CTGGCCGCCCAATTTTACG 59.861 57.895 7.03 0.00 41.58 3.18
2762 7053 9.302345 TCACATAGTTTTGCAAACGAATAAAAA 57.698 25.926 12.39 0.00 0.00 1.94
2893 7184 1.200020 GCTCAAATGTTGCCGCTACTT 59.800 47.619 6.52 0.00 0.00 2.24
2998 7289 1.955080 TGTGCATGATCACACAAGCAA 59.045 42.857 14.82 3.12 43.48 3.91
3039 7333 0.577269 GCGTGCTCCAAGTATTAGCG 59.423 55.000 0.00 0.00 39.14 4.26
3041 7335 1.202371 CGTGCTCCAAGTATTAGCGGA 60.202 52.381 0.00 0.00 39.14 5.54
3043 7337 3.467803 GTGCTCCAAGTATTAGCGGAAT 58.532 45.455 0.00 0.00 39.14 3.01
3044 7338 3.877508 GTGCTCCAAGTATTAGCGGAATT 59.122 43.478 0.00 0.00 39.14 2.17
3045 7339 4.335594 GTGCTCCAAGTATTAGCGGAATTT 59.664 41.667 0.00 0.00 39.14 1.82
3046 7340 4.335315 TGCTCCAAGTATTAGCGGAATTTG 59.665 41.667 0.00 0.00 39.14 2.32
3047 7341 4.335594 GCTCCAAGTATTAGCGGAATTTGT 59.664 41.667 0.00 0.00 0.00 2.83
3048 7342 5.730568 GCTCCAAGTATTAGCGGAATTTGTG 60.731 44.000 0.00 0.00 0.00 3.33
3049 7343 5.492895 TCCAAGTATTAGCGGAATTTGTGA 58.507 37.500 0.00 0.00 0.00 3.58
3050 7344 6.119536 TCCAAGTATTAGCGGAATTTGTGAT 58.880 36.000 0.00 0.00 0.00 3.06
3051 7345 6.038161 TCCAAGTATTAGCGGAATTTGTGATG 59.962 38.462 0.00 0.00 0.00 3.07
3052 7346 6.183360 CCAAGTATTAGCGGAATTTGTGATGT 60.183 38.462 0.00 0.00 0.00 3.06
3053 7347 7.250569 CAAGTATTAGCGGAATTTGTGATGTT 58.749 34.615 0.00 0.00 0.00 2.71
3054 7348 7.391148 AGTATTAGCGGAATTTGTGATGTTT 57.609 32.000 0.00 0.00 0.00 2.83
3055 7349 7.250569 AGTATTAGCGGAATTTGTGATGTTTG 58.749 34.615 0.00 0.00 0.00 2.93
3056 7350 5.697473 TTAGCGGAATTTGTGATGTTTGA 57.303 34.783 0.00 0.00 0.00 2.69
3057 7351 4.582701 AGCGGAATTTGTGATGTTTGAA 57.417 36.364 0.00 0.00 0.00 2.69
3058 7352 4.298332 AGCGGAATTTGTGATGTTTGAAC 58.702 39.130 0.00 0.00 0.00 3.18
3059 7353 4.047822 GCGGAATTTGTGATGTTTGAACA 58.952 39.130 0.00 0.00 44.06 3.18
3060 7354 4.505922 GCGGAATTTGTGATGTTTGAACAA 59.494 37.500 0.10 0.00 43.03 2.83
3061 7355 5.556194 GCGGAATTTGTGATGTTTGAACAAC 60.556 40.000 0.10 0.00 43.03 3.32
3062 7356 5.331458 CGGAATTTGTGATGTTTGAACAACG 60.331 40.000 0.10 0.00 43.03 4.10
3063 7357 5.051106 GGAATTTGTGATGTTTGAACAACGG 60.051 40.000 0.10 0.00 43.03 4.44
3064 7358 3.428746 TTGTGATGTTTGAACAACGGG 57.571 42.857 0.10 0.00 43.03 5.28
3065 7359 2.370349 TGTGATGTTTGAACAACGGGT 58.630 42.857 0.10 0.00 43.03 5.28
3066 7360 2.755655 TGTGATGTTTGAACAACGGGTT 59.244 40.909 0.10 0.00 43.03 4.11
3067 7361 3.193691 TGTGATGTTTGAACAACGGGTTT 59.806 39.130 0.10 0.00 43.03 3.27
3068 7362 3.549873 GTGATGTTTGAACAACGGGTTTG 59.450 43.478 0.10 0.00 43.03 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.966155 AAGGGTTAGAATTCTTGGGATTTTTA 57.034 30.769 14.36 0.00 0.00 1.52
12 13 8.966155 TTAAGGGTTAGAATTCTTGGGATTTT 57.034 30.769 14.36 3.42 0.00 1.82
86 406 6.635030 AAAGCCGTTCTTTGAGAAATACTT 57.365 33.333 0.00 0.00 43.04 2.24
197 517 3.316029 TGTTACGAGAGTTCAAGTTCGGA 59.684 43.478 0.00 0.00 46.40 4.55
200 521 6.476053 ACTTTCTGTTACGAGAGTTCAAGTTC 59.524 38.462 0.00 0.00 46.40 3.01
224 545 8.378172 TGTTATATGCAGATTGCCTAGTTTAC 57.622 34.615 0.00 0.00 44.23 2.01
238 559 9.803130 CGAATCAGATTAACTTGTTATATGCAG 57.197 33.333 0.00 0.00 0.00 4.41
258 579 2.816672 TGCTGTAAAACATGCCGAATCA 59.183 40.909 0.00 0.00 0.00 2.57
267 588 4.753233 TGCAGTTGTTTGCTGTAAAACAT 58.247 34.783 10.25 0.00 46.44 2.71
476 798 4.216708 CTCCCTCCGTTCCTAAATACTCT 58.783 47.826 0.00 0.00 0.00 3.24
909 1232 4.416738 GGGTGGGGAGCTGACTGC 62.417 72.222 0.00 0.00 43.29 4.40
910 1233 3.721706 GGGGTGGGGAGCTGACTG 61.722 72.222 0.00 0.00 0.00 3.51
911 1234 3.810687 TTGGGGTGGGGAGCTGACT 62.811 63.158 0.00 0.00 0.00 3.41
912 1235 3.256960 TTGGGGTGGGGAGCTGAC 61.257 66.667 0.00 0.00 0.00 3.51
913 1236 3.256960 GTTGGGGTGGGGAGCTGA 61.257 66.667 0.00 0.00 0.00 4.26
914 1237 2.655077 TTTGTTGGGGTGGGGAGCTG 62.655 60.000 0.00 0.00 0.00 4.24
915 1238 2.399607 TTTGTTGGGGTGGGGAGCT 61.400 57.895 0.00 0.00 0.00 4.09
916 1239 2.200092 TTTGTTGGGGTGGGGAGC 59.800 61.111 0.00 0.00 0.00 4.70
917 1240 1.901464 CGTTTGTTGGGGTGGGGAG 60.901 63.158 0.00 0.00 0.00 4.30
918 1241 2.196229 CGTTTGTTGGGGTGGGGA 59.804 61.111 0.00 0.00 0.00 4.81
919 1242 1.758906 AACGTTTGTTGGGGTGGGG 60.759 57.895 0.00 0.00 36.81 4.96
920 1243 3.942601 AACGTTTGTTGGGGTGGG 58.057 55.556 0.00 0.00 36.81 4.61
950 1278 2.809696 GGTTTGTGGTTGTACGCTACAT 59.190 45.455 7.14 0.00 38.68 2.29
953 1281 1.542987 GGGGTTTGTGGTTGTACGCTA 60.543 52.381 0.00 0.00 0.00 4.26
964 1292 2.153645 GGTTTAGGTACGGGGTTTGTG 58.846 52.381 0.00 0.00 0.00 3.33
972 1300 1.140252 CATGGGGAGGTTTAGGTACGG 59.860 57.143 0.00 0.00 0.00 4.02
974 1302 2.158798 GCTCATGGGGAGGTTTAGGTAC 60.159 54.545 0.00 0.00 44.22 3.34
975 1303 2.124411 GCTCATGGGGAGGTTTAGGTA 58.876 52.381 0.00 0.00 44.22 3.08
1053 1387 3.808771 CGTCGATCTCTTCGCCGGG 62.809 68.421 2.18 0.00 44.77 5.73
1497 1836 4.996434 GCCCACACGCTGAGCTGT 62.996 66.667 1.78 3.20 0.00 4.40
1515 1854 1.161563 GGAACGGGTTGAACAGCGAA 61.162 55.000 0.00 0.00 0.00 4.70
1740 5998 1.841556 ACGGGGCCTTGAGAGTTGA 60.842 57.895 0.84 0.00 0.00 3.18
1741 5999 1.672356 CACGGGGCCTTGAGAGTTG 60.672 63.158 0.84 0.00 0.00 3.16
1742 6000 2.750350 CACGGGGCCTTGAGAGTT 59.250 61.111 0.84 0.00 0.00 3.01
1743 6001 4.021925 GCACGGGGCCTTGAGAGT 62.022 66.667 0.84 0.00 36.11 3.24
1760 6018 2.798009 CTTATTTGGCCACGGCGG 59.202 61.111 3.88 0.00 43.06 6.13
1826 6084 9.243105 CTCCAAAAAGAAGGTTCCTTCATATAA 57.757 33.333 26.74 10.09 43.38 0.98
1917 6187 6.889198 TGTGGGGATCTTTTGTTCTATCTAG 58.111 40.000 0.00 0.00 0.00 2.43
1918 6188 6.884472 TGTGGGGATCTTTTGTTCTATCTA 57.116 37.500 0.00 0.00 0.00 1.98
1919 6189 5.779241 TGTGGGGATCTTTTGTTCTATCT 57.221 39.130 0.00 0.00 0.00 1.98
1920 6190 6.834168 TTTGTGGGGATCTTTTGTTCTATC 57.166 37.500 0.00 0.00 0.00 2.08
1921 6191 7.610580 TTTTTGTGGGGATCTTTTGTTCTAT 57.389 32.000 0.00 0.00 0.00 1.98
1923 6193 5.948742 TTTTTGTGGGGATCTTTTGTTCT 57.051 34.783 0.00 0.00 0.00 3.01
2002 6272 9.806203 CCATGAATGATTGCTAGTTCAAAATAA 57.194 29.630 0.00 0.00 34.62 1.40
2015 6285 2.787601 ATCGTGCCATGAATGATTGC 57.212 45.000 0.00 0.00 0.00 3.56
2022 6292 4.844998 TCTTTTTCAATCGTGCCATGAA 57.155 36.364 0.00 0.00 0.00 2.57
2093 6363 9.716531 ACATACATGATACATCATACTTTGAGG 57.283 33.333 0.00 0.00 45.23 3.86
2110 6380 4.440112 CGGTCTGCAACTCTACATACATGA 60.440 45.833 0.00 0.00 0.00 3.07
2111 6381 3.798878 CGGTCTGCAACTCTACATACATG 59.201 47.826 0.00 0.00 0.00 3.21
2112 6382 3.738281 GCGGTCTGCAACTCTACATACAT 60.738 47.826 0.00 0.00 45.45 2.29
2113 6383 2.416836 GCGGTCTGCAACTCTACATACA 60.417 50.000 0.00 0.00 45.45 2.29
2114 6384 2.194271 GCGGTCTGCAACTCTACATAC 58.806 52.381 0.00 0.00 45.45 2.39
2115 6385 2.579207 GCGGTCTGCAACTCTACATA 57.421 50.000 0.00 0.00 45.45 2.29
2116 6386 3.442996 GCGGTCTGCAACTCTACAT 57.557 52.632 0.00 0.00 45.45 2.29
2117 6387 4.988065 GCGGTCTGCAACTCTACA 57.012 55.556 0.00 0.00 45.45 2.74
2126 6396 3.066621 TGAAAATTATGATGGCGGTCTGC 59.933 43.478 0.00 0.00 45.38 4.26
2127 6397 4.898829 TGAAAATTATGATGGCGGTCTG 57.101 40.909 0.00 0.00 0.00 3.51
2130 6400 4.674101 CGTGTTGAAAATTATGATGGCGGT 60.674 41.667 0.00 0.00 0.00 5.68
2139 6409 8.234546 CCAGCTACTTAACGTGTTGAAAATTAT 58.765 33.333 0.00 0.00 0.00 1.28
2146 6416 3.305813 CCTCCAGCTACTTAACGTGTTGA 60.306 47.826 0.00 0.00 0.00 3.18
2183 6458 2.406616 CGATCCCCGCCAAAAGGTG 61.407 63.158 0.00 0.00 0.00 4.00
2195 6470 1.745489 GACAACCTGGCACGATCCC 60.745 63.158 0.00 0.00 0.00 3.85
2196 6471 2.100631 CGACAACCTGGCACGATCC 61.101 63.158 0.00 0.00 0.00 3.36
2197 6472 2.100631 CCGACAACCTGGCACGATC 61.101 63.158 0.00 0.00 0.00 3.69
2198 6473 2.047274 CCGACAACCTGGCACGAT 60.047 61.111 0.00 0.00 0.00 3.73
2199 6474 3.220999 CTCCGACAACCTGGCACGA 62.221 63.158 0.00 0.00 0.00 4.35
2200 6475 2.738521 CTCCGACAACCTGGCACG 60.739 66.667 0.00 0.00 0.00 5.34
2207 6482 1.507174 CTCGACCTCTCCGACAACC 59.493 63.158 0.00 0.00 32.18 3.77
2238 6513 1.576421 GGAGTTCAGCAACGCCTTG 59.424 57.895 2.91 0.00 46.28 3.61
2253 6528 4.410400 GGCAAGGTCCCACCGGAG 62.410 72.222 9.46 0.00 44.90 4.63
2276 6551 1.184970 TGGCATCCTCGACAGTGTGA 61.185 55.000 0.00 0.00 0.00 3.58
2279 6554 1.012086 CATTGGCATCCTCGACAGTG 58.988 55.000 0.00 0.00 0.00 3.66
2280 6555 0.107508 CCATTGGCATCCTCGACAGT 60.108 55.000 0.00 0.00 0.00 3.55
2282 6557 4.961637 CCATTGGCATCCTCGACA 57.038 55.556 0.00 0.00 0.00 4.35
2295 6570 1.613255 CGGTACCTTGACCTTGCCATT 60.613 52.381 10.90 0.00 37.34 3.16
2297 6572 1.373435 CGGTACCTTGACCTTGCCA 59.627 57.895 10.90 0.00 37.34 4.92
2301 6576 0.178912 ACCTCCGGTACCTTGACCTT 60.179 55.000 10.90 0.00 37.34 3.50
2307 6582 0.472352 TCACCAACCTCCGGTACCTT 60.472 55.000 10.90 0.00 33.12 3.50
2319 6595 4.701765 AGATAGCAGATCATGTCACCAAC 58.298 43.478 0.00 0.00 0.00 3.77
2329 6605 6.016360 GCTAGTTCTTCAGAGATAGCAGATCA 60.016 42.308 13.56 0.00 38.60 2.92
2344 6620 5.696724 TGTTTGTTCTGCTAGCTAGTTCTTC 59.303 40.000 21.62 10.58 0.00 2.87
2358 6634 5.477510 AGCTACTCTCTGATGTTTGTTCTG 58.522 41.667 0.00 0.00 0.00 3.02
2372 6656 9.946165 GATTTTCTCTCTAAGTTAGCTACTCTC 57.054 37.037 4.93 0.00 35.54 3.20
2374 6658 8.400186 ACGATTTTCTCTCTAAGTTAGCTACTC 58.600 37.037 4.93 0.00 35.54 2.59
2378 6662 7.159322 TCACGATTTTCTCTCTAAGTTAGCT 57.841 36.000 4.93 0.00 0.00 3.32
2379 6663 6.474102 CCTCACGATTTTCTCTCTAAGTTAGC 59.526 42.308 4.93 0.00 0.00 3.09
2380 6664 6.975772 CCCTCACGATTTTCTCTCTAAGTTAG 59.024 42.308 3.29 3.29 0.00 2.34
2381 6665 6.662234 TCCCTCACGATTTTCTCTCTAAGTTA 59.338 38.462 0.00 0.00 0.00 2.24
2395 6681 3.433306 TGTCCAAATTCCCTCACGATT 57.567 42.857 0.00 0.00 0.00 3.34
2399 6685 5.852827 TGAAATTTGTCCAAATTCCCTCAC 58.147 37.500 16.05 6.95 46.76 3.51
2410 6696 2.156098 GGCGTACCTGAAATTTGTCCA 58.844 47.619 0.00 0.00 0.00 4.02
2411 6697 2.913777 GGCGTACCTGAAATTTGTCC 57.086 50.000 0.00 0.00 0.00 4.02
2447 6733 1.629043 CTCTAACCCTAGCCGCCATA 58.371 55.000 0.00 0.00 0.00 2.74
2546 6833 3.096092 GACCCATATGAAAAACAGGGCA 58.904 45.455 3.65 0.00 35.63 5.36
2631 6918 8.710551 TCACAATATGTTTGAATGCAAATCAAC 58.289 29.630 15.51 11.92 45.01 3.18
2762 7053 7.112122 TGCTGACAACCAATAGATGTATCTTT 58.888 34.615 0.00 0.00 38.32 2.52
2782 7073 2.842457 GCATATGTGGACTCATGCTGA 58.158 47.619 4.29 0.00 40.46 4.26
2785 7076 2.842457 TGAGCATATGTGGACTCATGC 58.158 47.619 4.29 7.63 43.24 4.06
2998 7289 4.445448 GCAGAAACTATGGGAGGTGATGAT 60.445 45.833 0.00 0.00 0.00 2.45
3039 7333 5.051106 CCGTTGTTCAAACATCACAAATTCC 60.051 40.000 0.00 0.00 38.95 3.01
3041 7335 4.808364 CCCGTTGTTCAAACATCACAAATT 59.192 37.500 0.00 0.00 38.95 1.82
3043 7337 3.193691 ACCCGTTGTTCAAACATCACAAA 59.806 39.130 0.00 0.00 38.95 2.83
3044 7338 2.755655 ACCCGTTGTTCAAACATCACAA 59.244 40.909 0.00 0.00 38.95 3.33
3045 7339 2.370349 ACCCGTTGTTCAAACATCACA 58.630 42.857 0.00 0.00 38.95 3.58
3046 7340 3.430333 AACCCGTTGTTCAAACATCAC 57.570 42.857 0.00 0.00 38.95 3.06
3047 7341 3.775202 CAAACCCGTTGTTCAAACATCA 58.225 40.909 0.00 0.00 38.95 3.07


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

AutoCloner maintained by Alex Coulton.