Multiple sequence alignment - TraesCS2D01G257100

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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 TraesCS2D01G257100 chr2D 100.000 1754 0 0 673 2426 312447364 312449117 0.000000e+00 3240.0
1 TraesCS2D01G257100 chr2D 100.000 471 0 0 1 471 312446692 312447162 0.000000e+00 870.0
2 TraesCS2D01G257100 chr2B 95.775 1065 33 3 674 1731 380258681 380259740 0.000000e+00 1707.0
3 TraesCS2D01G257100 chr2B 90.446 314 24 4 1 312 380251435 380251744 2.250000e-110 409.0
4 TraesCS2D01G257100 chr2B 96.023 176 6 1 297 471 380258496 380258671 3.950000e-73 285.0
5 TraesCS2D01G257100 chr2B 84.914 232 32 3 1999 2229 380263315 380263544 5.220000e-57 231.0
6 TraesCS2D01G257100 chr2A 94.363 887 36 3 674 1548 424444377 424443493 0.000000e+00 1349.0
7 TraesCS2D01G257100 chr2A 84.008 494 41 20 1 471 424444865 424444387 7.960000e-120 440.0
8 TraesCS2D01G257100 chr2A 93.382 136 4 2 1595 1730 424443500 424443370 1.900000e-46 196.0
9 TraesCS2D01G257100 chrUn 83.568 213 28 5 1 207 92702163 92701952 2.460000e-45 193.0
10 TraesCS2D01G257100 chr7B 83.810 210 23 6 4 203 654972632 654972840 3.180000e-44 189.0
11 TraesCS2D01G257100 chr5D 89.333 150 14 2 1 150 61793796 61793649 1.150000e-43 187.0
12 TraesCS2D01G257100 chr4D 82.464 211 29 6 2 207 504326562 504326769 6.890000e-41 178.0
13 TraesCS2D01G257100 chr3B 86.667 165 17 4 1 162 519860696 519860858 6.890000e-41 178.0
14 TraesCS2D01G257100 chr3B 82.160 213 29 6 1 207 354001694 354001485 8.920000e-40 174.0
15 TraesCS2D01G257100 chr4A 82.297 209 26 7 4 203 718416198 718416404 1.150000e-38 171.0
16 TraesCS2D01G257100 chr7D 81.221 213 31 6 1 207 606706469 606706678 1.930000e-36 163.0
17 TraesCS2D01G257100 chr7A 80.000 175 23 11 2015 2187 230304856 230304692 4.240000e-23 119.0
18 TraesCS2D01G257100 chr5B 97.222 36 1 0 1886 1921 648285418 648285453 7.240000e-06 62.1
19 TraesCS2D01G257100 chr5B 91.111 45 3 1 2032 2076 682817267 682817310 2.600000e-05 60.2


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 TraesCS2D01G257100 chr2D 312446692 312449117 2425 False 2055.000000 3240 100.000000 1 2426 2 chr2D.!!$F1 2425
1 TraesCS2D01G257100 chr2B 380258496 380263544 5048 False 741.000000 1707 92.237333 297 2229 3 chr2B.!!$F2 1932
2 TraesCS2D01G257100 chr2A 424443370 424444865 1495 True 661.666667 1349 90.584333 1 1730 3 chr2A.!!$R1 1729

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
351 376 0.597637 ACTGTTCACCGAGCTCGTTG 60.598 55.0 32.41 29.19 37.74 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 5673 0.107214 AATACCCACCGCCATCAGTG 60.107 55.0 0.0 0.0 0.0 3.66 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
27 28 6.625873 AGTCAAACCTCAGAAACTTTGATC 57.374 37.500 0.00 0.00 35.61 2.92
37 38 7.922278 CCTCAGAAACTTTGATCAAATTTGTGA 59.078 33.333 28.75 28.75 34.39 3.58
46 47 9.525409 CTTTGATCAAATTTGTGAAGAGAAACT 57.475 29.630 20.76 0.00 0.00 2.66
47 48 9.874205 TTTGATCAAATTTGTGAAGAGAAACTT 57.126 25.926 16.91 0.00 42.03 2.66
64 65 7.117956 AGAGAAACTTTTTACGTCTAGAATGCC 59.882 37.037 0.00 0.00 0.00 4.40
69 70 6.261381 ACTTTTTACGTCTAGAATGCCAAACA 59.739 34.615 0.00 0.00 0.00 2.83
70 71 6.811253 TTTTACGTCTAGAATGCCAAACAT 57.189 33.333 0.00 0.00 42.30 2.71
216 233 8.335532 TGTAATGAAGGGAGTAACATTTTCAG 57.664 34.615 0.00 0.00 35.19 3.02
222 239 8.383175 TGAAGGGAGTAACATTTTCAGAGTATT 58.617 33.333 0.00 0.00 0.00 1.89
223 240 8.567285 AAGGGAGTAACATTTTCAGAGTATTG 57.433 34.615 0.00 0.00 0.00 1.90
249 272 3.604875 TCTTTTACCACGCCTTCTAGG 57.395 47.619 0.00 0.00 38.80 3.02
259 282 4.881850 CCACGCCTTCTAGGAATGTTATTT 59.118 41.667 0.00 0.00 37.67 1.40
295 318 8.773404 TTTTAGAAGCTCCTAGTACATTTGTC 57.227 34.615 0.00 0.00 0.00 3.18
351 376 0.597637 ACTGTTCACCGAGCTCGTTG 60.598 55.000 32.41 29.19 37.74 4.10
452 477 1.421410 CGGTGCCTCGATAACAGTGC 61.421 60.000 0.00 0.00 0.00 4.40
792 817 2.415512 GCACTCACCTAAAGCTAAACCG 59.584 50.000 0.00 0.00 0.00 4.44
915 953 2.949644 GCGCCCAAAGTCATAAATACCT 59.050 45.455 0.00 0.00 0.00 3.08
1048 1086 4.067512 TCCTCCTGCTCGCCCTCT 62.068 66.667 0.00 0.00 0.00 3.69
1071 1109 2.035155 TCCTTCGTCCTCGCCTCA 59.965 61.111 0.00 0.00 36.96 3.86
1101 1139 1.990060 GAGCTACCCAGAGCACCCA 60.990 63.158 0.00 0.00 45.43 4.51
1469 1511 0.827368 GGAGATGGGTGACTGGAGAC 59.173 60.000 0.00 0.00 0.00 3.36
1480 1522 3.068064 TGGAGACGGATCGCTGCA 61.068 61.111 0.00 0.00 32.11 4.41
1556 1598 3.753294 AGTTGTACTTGTAGCAGCAGT 57.247 42.857 0.00 0.00 0.00 4.40
1673 1715 1.064505 CTTTGAGCGTGCATATGGTGG 59.935 52.381 4.56 0.00 0.00 4.61
1740 4294 1.497991 TGTTCAGAACACAGTAGCGC 58.502 50.000 12.24 0.00 36.25 5.92
1743 4467 3.056821 TGTTCAGAACACAGTAGCGCTAT 60.057 43.478 21.96 2.45 36.25 2.97
1745 4469 4.288670 TCAGAACACAGTAGCGCTATAC 57.711 45.455 21.96 11.72 0.00 1.47
1747 4471 4.038361 CAGAACACAGTAGCGCTATACAG 58.962 47.826 21.96 10.84 0.00 2.74
1748 4472 3.945921 AGAACACAGTAGCGCTATACAGA 59.054 43.478 21.96 0.00 0.00 3.41
1752 4476 6.576662 ACACAGTAGCGCTATACAGATAAT 57.423 37.500 21.96 0.00 0.00 1.28
1783 4885 2.938451 ACAGTAGCGCTATACGTACACA 59.062 45.455 21.96 0.00 46.11 3.72
1788 4890 1.254570 GCGCTATACGTACACACTTGC 59.745 52.381 0.00 0.00 46.11 4.01
1790 4892 2.782192 CGCTATACGTACACACTTGCTC 59.218 50.000 0.00 0.00 36.87 4.26
1793 4895 0.726787 TACGTACACACTTGCTCGCG 60.727 55.000 0.00 0.00 0.00 5.87
1795 4897 1.665544 CGTACACACTTGCTCGCGAG 61.666 60.000 31.37 31.37 0.00 5.03
1810 4912 0.319125 GCGAGAGATAAAGCCTCGGG 60.319 60.000 12.04 0.00 46.82 5.14
1811 4913 1.319541 CGAGAGATAAAGCCTCGGGA 58.680 55.000 0.00 0.00 44.11 5.14
1812 4914 1.268352 CGAGAGATAAAGCCTCGGGAG 59.732 57.143 0.00 0.00 44.11 4.30
1814 4916 0.034198 GAGATAAAGCCTCGGGAGCC 59.966 60.000 0.00 0.00 0.00 4.70
1815 4917 0.399233 AGATAAAGCCTCGGGAGCCT 60.399 55.000 0.00 0.00 0.00 4.58
1816 4918 0.034198 GATAAAGCCTCGGGAGCCTC 59.966 60.000 0.00 0.00 0.00 4.70
1817 4919 0.399233 ATAAAGCCTCGGGAGCCTCT 60.399 55.000 0.00 0.00 0.00 3.69
1818 4920 0.260816 TAAAGCCTCGGGAGCCTCTA 59.739 55.000 0.00 0.00 0.00 2.43
1819 4921 0.617820 AAAGCCTCGGGAGCCTCTAA 60.618 55.000 0.00 0.00 0.00 2.10
1820 4922 1.331399 AAGCCTCGGGAGCCTCTAAC 61.331 60.000 0.00 0.00 0.00 2.34
1822 4924 2.022240 GCCTCGGGAGCCTCTAACTG 62.022 65.000 0.00 0.00 0.00 3.16
1869 4982 6.401047 TCTTATATGAACCGTCCGATCTTT 57.599 37.500 0.00 0.00 0.00 2.52
1877 4990 3.528532 ACCGTCCGATCTTTATTCAACC 58.471 45.455 0.00 0.00 0.00 3.77
1894 5037 2.294078 CCGCACCTCCCTTCCTTCT 61.294 63.158 0.00 0.00 0.00 2.85
1903 5046 1.208706 CCCTTCCTTCTTCCTCCTCC 58.791 60.000 0.00 0.00 0.00 4.30
1904 5047 1.208706 CCTTCCTTCTTCCTCCTCCC 58.791 60.000 0.00 0.00 0.00 4.30
1905 5048 0.827368 CTTCCTTCTTCCTCCTCCCG 59.173 60.000 0.00 0.00 0.00 5.14
1906 5049 0.412244 TTCCTTCTTCCTCCTCCCGA 59.588 55.000 0.00 0.00 0.00 5.14
1907 5050 0.324460 TCCTTCTTCCTCCTCCCGAC 60.324 60.000 0.00 0.00 0.00 4.79
1908 5051 1.331399 CCTTCTTCCTCCTCCCGACC 61.331 65.000 0.00 0.00 0.00 4.79
1909 5052 1.305887 TTCTTCCTCCTCCCGACCC 60.306 63.158 0.00 0.00 0.00 4.46
1910 5053 2.764547 CTTCCTCCTCCCGACCCC 60.765 72.222 0.00 0.00 0.00 4.95
1911 5054 4.410033 TTCCTCCTCCCGACCCCC 62.410 72.222 0.00 0.00 0.00 5.40
1917 5060 4.475444 CTCCCGACCCCCAGCCTA 62.475 72.222 0.00 0.00 0.00 3.93
1918 5061 4.791069 TCCCGACCCCCAGCCTAC 62.791 72.222 0.00 0.00 0.00 3.18
1922 5065 4.752594 GACCCCCAGCCTACCCCA 62.753 72.222 0.00 0.00 0.00 4.96
1923 5066 4.052833 ACCCCCAGCCTACCCCAT 62.053 66.667 0.00 0.00 0.00 4.00
1924 5067 3.178611 CCCCCAGCCTACCCCATC 61.179 72.222 0.00 0.00 0.00 3.51
1925 5068 3.178611 CCCCAGCCTACCCCATCC 61.179 72.222 0.00 0.00 0.00 3.51
1926 5069 3.178611 CCCAGCCTACCCCATCCC 61.179 72.222 0.00 0.00 0.00 3.85
1927 5070 2.368192 CCAGCCTACCCCATCCCA 60.368 66.667 0.00 0.00 0.00 4.37
1928 5071 1.775877 CCAGCCTACCCCATCCCAT 60.776 63.158 0.00 0.00 0.00 4.00
1929 5072 1.457604 CAGCCTACCCCATCCCATG 59.542 63.158 0.00 0.00 0.00 3.66
1930 5073 2.116125 GCCTACCCCATCCCATGC 59.884 66.667 0.00 0.00 0.00 4.06
1934 5301 2.715532 CTACCCCATCCCATGCGTCG 62.716 65.000 0.00 0.00 0.00 5.12
2061 5428 2.061790 GCCCCAGCCATCCCTCTAAG 62.062 65.000 0.00 0.00 0.00 2.18
2065 5432 1.772156 AGCCATCCCTCTAAGCCCC 60.772 63.158 0.00 0.00 0.00 5.80
2066 5433 3.151906 CCATCCCTCTAAGCCCCG 58.848 66.667 0.00 0.00 0.00 5.73
2067 5434 2.427753 CATCCCTCTAAGCCCCGC 59.572 66.667 0.00 0.00 0.00 6.13
2078 5445 2.829914 GCCCCGCTGCATCAATGA 60.830 61.111 0.00 0.00 0.00 2.57
2087 5454 2.751259 GCTGCATCAATGAAGAACTCCA 59.249 45.455 1.94 0.00 35.32 3.86
2088 5455 3.181499 GCTGCATCAATGAAGAACTCCAG 60.181 47.826 1.94 0.00 35.32 3.86
2089 5456 4.259356 CTGCATCAATGAAGAACTCCAGA 58.741 43.478 0.00 0.00 35.32 3.86
2095 5462 4.163078 TCAATGAAGAACTCCAGAGATCCC 59.837 45.833 0.70 0.00 31.43 3.85
2100 5467 0.252881 AACTCCAGAGATCCCCTGCA 60.253 55.000 0.70 0.00 0.00 4.41
2104 5471 2.367512 AGAGATCCCCTGCACCCC 60.368 66.667 0.00 0.00 0.00 4.95
2125 5492 4.207165 CCCTCCACCCACATGTAAAATAG 58.793 47.826 0.00 0.00 0.00 1.73
2200 5567 2.481449 GGCGAGCTTATTTCTTCTCCGA 60.481 50.000 0.00 0.00 0.00 4.55
2215 5582 2.101770 CGACGAGGTCCGGCTAAC 59.898 66.667 0.00 0.00 46.22 2.34
2222 5589 1.221021 GGTCCGGCTAACAGGGAAG 59.779 63.158 0.00 0.00 0.00 3.46
2224 5591 1.079621 TCCGGCTAACAGGGAAGGA 59.920 57.895 0.00 0.00 0.00 3.36
2229 5596 2.488153 CGGCTAACAGGGAAGGAAAAAG 59.512 50.000 0.00 0.00 0.00 2.27
2230 5597 2.826128 GGCTAACAGGGAAGGAAAAAGG 59.174 50.000 0.00 0.00 0.00 3.11
2231 5598 3.499745 GGCTAACAGGGAAGGAAAAAGGA 60.500 47.826 0.00 0.00 0.00 3.36
2232 5599 4.149598 GCTAACAGGGAAGGAAAAAGGAA 58.850 43.478 0.00 0.00 0.00 3.36
2233 5600 4.587262 GCTAACAGGGAAGGAAAAAGGAAA 59.413 41.667 0.00 0.00 0.00 3.13
2234 5601 5.279006 GCTAACAGGGAAGGAAAAAGGAAAG 60.279 44.000 0.00 0.00 0.00 2.62
2235 5602 4.536295 ACAGGGAAGGAAAAAGGAAAGA 57.464 40.909 0.00 0.00 0.00 2.52
2236 5603 4.878968 ACAGGGAAGGAAAAAGGAAAGAA 58.121 39.130 0.00 0.00 0.00 2.52
2237 5604 4.895889 ACAGGGAAGGAAAAAGGAAAGAAG 59.104 41.667 0.00 0.00 0.00 2.85
2238 5605 4.895889 CAGGGAAGGAAAAAGGAAAGAAGT 59.104 41.667 0.00 0.00 0.00 3.01
2239 5606 4.895889 AGGGAAGGAAAAAGGAAAGAAGTG 59.104 41.667 0.00 0.00 0.00 3.16
2240 5607 4.893524 GGGAAGGAAAAAGGAAAGAAGTGA 59.106 41.667 0.00 0.00 0.00 3.41
2241 5608 5.221263 GGGAAGGAAAAAGGAAAGAAGTGAC 60.221 44.000 0.00 0.00 0.00 3.67
2242 5609 5.594725 GGAAGGAAAAAGGAAAGAAGTGACT 59.405 40.000 0.00 0.00 0.00 3.41
2243 5610 6.456795 AAGGAAAAAGGAAAGAAGTGACTG 57.543 37.500 0.00 0.00 0.00 3.51
2244 5611 5.755849 AGGAAAAAGGAAAGAAGTGACTGA 58.244 37.500 0.00 0.00 0.00 3.41
2245 5612 6.187682 AGGAAAAAGGAAAGAAGTGACTGAA 58.812 36.000 0.00 0.00 0.00 3.02
2246 5613 6.319911 AGGAAAAAGGAAAGAAGTGACTGAAG 59.680 38.462 0.00 0.00 0.00 3.02
2247 5614 5.506686 AAAAGGAAAGAAGTGACTGAAGC 57.493 39.130 0.00 0.00 0.00 3.86
2248 5615 2.760374 AGGAAAGAAGTGACTGAAGCG 58.240 47.619 0.00 0.00 0.00 4.68
2249 5616 1.801178 GGAAAGAAGTGACTGAAGCGG 59.199 52.381 0.00 0.00 0.00 5.52
2250 5617 2.548067 GGAAAGAAGTGACTGAAGCGGA 60.548 50.000 0.00 0.00 0.00 5.54
2251 5618 2.910688 AAGAAGTGACTGAAGCGGAA 57.089 45.000 0.00 0.00 0.00 4.30
2252 5619 2.910688 AGAAGTGACTGAAGCGGAAA 57.089 45.000 0.00 0.00 0.00 3.13
2253 5620 3.194005 AGAAGTGACTGAAGCGGAAAA 57.806 42.857 0.00 0.00 0.00 2.29
2254 5621 3.541632 AGAAGTGACTGAAGCGGAAAAA 58.458 40.909 0.00 0.00 0.00 1.94
2279 5646 3.303049 TCAGGCATCTGAGAGAATAGCA 58.697 45.455 0.00 0.00 44.39 3.49
2280 5647 3.708121 TCAGGCATCTGAGAGAATAGCAA 59.292 43.478 0.00 0.00 44.39 3.91
2281 5648 4.162888 TCAGGCATCTGAGAGAATAGCAAA 59.837 41.667 0.00 0.00 44.39 3.68
2282 5649 5.064558 CAGGCATCTGAGAGAATAGCAAAT 58.935 41.667 0.00 0.00 43.49 2.32
2283 5650 5.179742 CAGGCATCTGAGAGAATAGCAAATC 59.820 44.000 0.00 0.00 43.49 2.17
2284 5651 4.455190 GGCATCTGAGAGAATAGCAAATCC 59.545 45.833 0.00 0.00 0.00 3.01
2285 5652 5.061853 GCATCTGAGAGAATAGCAAATCCA 58.938 41.667 0.00 0.00 0.00 3.41
2286 5653 5.706369 GCATCTGAGAGAATAGCAAATCCAT 59.294 40.000 0.00 0.00 0.00 3.41
2287 5654 6.877855 GCATCTGAGAGAATAGCAAATCCATA 59.122 38.462 0.00 0.00 0.00 2.74
2288 5655 7.389884 GCATCTGAGAGAATAGCAAATCCATAA 59.610 37.037 0.00 0.00 0.00 1.90
2289 5656 9.281371 CATCTGAGAGAATAGCAAATCCATAAA 57.719 33.333 0.00 0.00 0.00 1.40
2290 5657 9.857656 ATCTGAGAGAATAGCAAATCCATAAAA 57.142 29.630 0.00 0.00 0.00 1.52
2291 5658 9.113838 TCTGAGAGAATAGCAAATCCATAAAAC 57.886 33.333 0.00 0.00 0.00 2.43
2292 5659 8.225603 TGAGAGAATAGCAAATCCATAAAACC 57.774 34.615 0.00 0.00 0.00 3.27
2293 5660 8.055181 TGAGAGAATAGCAAATCCATAAAACCT 58.945 33.333 0.00 0.00 0.00 3.50
2294 5661 8.457238 AGAGAATAGCAAATCCATAAAACCTC 57.543 34.615 0.00 0.00 0.00 3.85
2295 5662 8.055181 AGAGAATAGCAAATCCATAAAACCTCA 58.945 33.333 0.00 0.00 0.00 3.86
2296 5663 8.000780 AGAATAGCAAATCCATAAAACCTCAC 57.999 34.615 0.00 0.00 0.00 3.51
2297 5664 4.701956 AGCAAATCCATAAAACCTCACG 57.298 40.909 0.00 0.00 0.00 4.35
2298 5665 4.079253 AGCAAATCCATAAAACCTCACGT 58.921 39.130 0.00 0.00 0.00 4.49
2299 5666 4.522789 AGCAAATCCATAAAACCTCACGTT 59.477 37.500 0.00 0.00 35.70 3.99
2300 5667 5.010617 AGCAAATCCATAAAACCTCACGTTT 59.989 36.000 0.00 0.00 46.92 3.60
2301 5668 5.118510 GCAAATCCATAAAACCTCACGTTTG 59.881 40.000 0.00 0.00 44.09 2.93
2302 5669 5.385509 AATCCATAAAACCTCACGTTTGG 57.614 39.130 2.33 2.33 44.09 3.28
2303 5670 3.822940 TCCATAAAACCTCACGTTTGGT 58.177 40.909 3.59 3.59 44.09 3.67
2304 5671 3.816523 TCCATAAAACCTCACGTTTGGTC 59.183 43.478 9.37 0.00 44.09 4.02
2305 5672 3.818773 CCATAAAACCTCACGTTTGGTCT 59.181 43.478 9.37 3.85 44.09 3.85
2306 5673 4.083484 CCATAAAACCTCACGTTTGGTCTC 60.083 45.833 9.37 0.00 44.09 3.36
2307 5674 2.702592 AAACCTCACGTTTGGTCTCA 57.297 45.000 9.37 0.00 43.21 3.27
2308 5675 1.949465 AACCTCACGTTTGGTCTCAC 58.051 50.000 9.37 0.00 35.17 3.51
2309 5676 1.120530 ACCTCACGTTTGGTCTCACT 58.879 50.000 3.59 0.00 29.18 3.41
2310 5677 1.202533 ACCTCACGTTTGGTCTCACTG 60.203 52.381 3.59 0.00 29.18 3.66
2311 5678 1.068588 CCTCACGTTTGGTCTCACTGA 59.931 52.381 0.00 0.00 0.00 3.41
2312 5679 2.289072 CCTCACGTTTGGTCTCACTGAT 60.289 50.000 0.00 0.00 0.00 2.90
2313 5680 2.733552 CTCACGTTTGGTCTCACTGATG 59.266 50.000 0.00 0.00 0.00 3.07
2314 5681 1.800586 CACGTTTGGTCTCACTGATGG 59.199 52.381 0.00 0.00 0.00 3.51
2315 5682 0.798776 CGTTTGGTCTCACTGATGGC 59.201 55.000 0.00 0.00 0.00 4.40
2316 5683 0.798776 GTTTGGTCTCACTGATGGCG 59.201 55.000 0.00 0.00 0.00 5.69
2317 5684 0.321564 TTTGGTCTCACTGATGGCGG 60.322 55.000 0.00 0.00 0.00 6.13
2318 5685 1.480212 TTGGTCTCACTGATGGCGGT 61.480 55.000 0.00 0.00 0.00 5.68
2323 5690 2.986290 CACTGATGGCGGTGGGTA 59.014 61.111 0.00 0.00 45.65 3.69
2324 5691 1.526887 CACTGATGGCGGTGGGTAT 59.473 57.895 0.00 0.00 45.65 2.73
2325 5692 0.107214 CACTGATGGCGGTGGGTATT 60.107 55.000 0.00 0.00 45.65 1.89
2326 5693 0.107214 ACTGATGGCGGTGGGTATTG 60.107 55.000 0.00 0.00 30.79 1.90
2327 5694 0.107214 CTGATGGCGGTGGGTATTGT 60.107 55.000 0.00 0.00 0.00 2.71
2328 5695 0.393673 TGATGGCGGTGGGTATTGTG 60.394 55.000 0.00 0.00 0.00 3.33
2329 5696 1.724582 GATGGCGGTGGGTATTGTGC 61.725 60.000 0.00 0.00 0.00 4.57
2330 5697 2.360600 GGCGGTGGGTATTGTGCA 60.361 61.111 0.00 0.00 0.00 4.57
2331 5698 2.696759 GGCGGTGGGTATTGTGCAC 61.697 63.158 10.75 10.75 0.00 4.57
2332 5699 1.674322 GCGGTGGGTATTGTGCACT 60.674 57.895 19.41 0.28 0.00 4.40
2333 5700 1.241315 GCGGTGGGTATTGTGCACTT 61.241 55.000 19.41 8.24 0.00 3.16
2334 5701 1.243902 CGGTGGGTATTGTGCACTTT 58.756 50.000 19.41 7.86 0.00 2.66
2335 5702 1.611491 CGGTGGGTATTGTGCACTTTT 59.389 47.619 19.41 5.22 0.00 2.27
2336 5703 2.606795 CGGTGGGTATTGTGCACTTTTG 60.607 50.000 19.41 0.00 0.00 2.44
2337 5704 2.364002 GGTGGGTATTGTGCACTTTTGT 59.636 45.455 19.41 2.03 0.00 2.83
2338 5705 3.181470 GGTGGGTATTGTGCACTTTTGTT 60.181 43.478 19.41 0.00 0.00 2.83
2339 5706 3.801594 GTGGGTATTGTGCACTTTTGTTG 59.198 43.478 19.41 0.00 0.00 3.33
2340 5707 3.181471 TGGGTATTGTGCACTTTTGTTGG 60.181 43.478 19.41 0.00 0.00 3.77
2341 5708 3.068873 GGGTATTGTGCACTTTTGTTGGA 59.931 43.478 19.41 0.00 0.00 3.53
2342 5709 4.442192 GGGTATTGTGCACTTTTGTTGGAA 60.442 41.667 19.41 0.20 0.00 3.53
2343 5710 4.744631 GGTATTGTGCACTTTTGTTGGAAG 59.255 41.667 19.41 0.00 0.00 3.46
2344 5711 3.951775 TTGTGCACTTTTGTTGGAAGT 57.048 38.095 19.41 0.00 37.82 3.01
2351 5718 5.782893 CACTTTTGTTGGAAGTGGGATAA 57.217 39.130 8.68 0.00 46.37 1.75
2352 5719 6.345096 CACTTTTGTTGGAAGTGGGATAAT 57.655 37.500 8.68 0.00 46.37 1.28
2353 5720 7.461182 CACTTTTGTTGGAAGTGGGATAATA 57.539 36.000 8.68 0.00 46.37 0.98
2354 5721 7.538575 CACTTTTGTTGGAAGTGGGATAATAG 58.461 38.462 8.68 0.00 46.37 1.73
2355 5722 6.152831 ACTTTTGTTGGAAGTGGGATAATAGC 59.847 38.462 0.00 0.00 36.08 2.97
2356 5723 3.804036 TGTTGGAAGTGGGATAATAGCG 58.196 45.455 0.00 0.00 0.00 4.26
2357 5724 3.139077 GTTGGAAGTGGGATAATAGCGG 58.861 50.000 0.00 0.00 0.00 5.52
2358 5725 2.404559 TGGAAGTGGGATAATAGCGGT 58.595 47.619 0.00 0.00 0.00 5.68
2359 5726 2.367567 TGGAAGTGGGATAATAGCGGTC 59.632 50.000 0.00 0.00 0.00 4.79
2360 5727 2.633481 GGAAGTGGGATAATAGCGGTCT 59.367 50.000 0.00 0.00 0.00 3.85
2361 5728 3.306156 GGAAGTGGGATAATAGCGGTCTC 60.306 52.174 0.00 0.00 0.00 3.36
2362 5729 2.249139 AGTGGGATAATAGCGGTCTCC 58.751 52.381 0.00 0.00 0.00 3.71
2363 5730 1.968493 GTGGGATAATAGCGGTCTCCA 59.032 52.381 0.00 0.00 0.00 3.86
2364 5731 2.028930 GTGGGATAATAGCGGTCTCCAG 60.029 54.545 0.00 0.00 0.00 3.86
2365 5732 2.158370 TGGGATAATAGCGGTCTCCAGA 60.158 50.000 0.00 0.00 0.00 3.86
2366 5733 2.494073 GGGATAATAGCGGTCTCCAGAG 59.506 54.545 0.00 0.00 0.00 3.35
2367 5734 3.422796 GGATAATAGCGGTCTCCAGAGA 58.577 50.000 0.00 0.00 34.56 3.10
2368 5735 3.827302 GGATAATAGCGGTCTCCAGAGAA 59.173 47.826 0.00 0.00 39.48 2.87
2369 5736 4.082463 GGATAATAGCGGTCTCCAGAGAAG 60.082 50.000 0.00 0.00 39.48 2.85
2370 5737 2.738587 ATAGCGGTCTCCAGAGAAGA 57.261 50.000 0.00 0.00 39.48 2.87
2371 5738 2.045561 TAGCGGTCTCCAGAGAAGAG 57.954 55.000 0.00 0.00 39.48 2.85
2372 5739 0.329931 AGCGGTCTCCAGAGAAGAGA 59.670 55.000 0.00 0.00 39.48 3.10
2373 5740 1.064017 AGCGGTCTCCAGAGAAGAGAT 60.064 52.381 0.00 0.00 42.16 2.75
2374 5741 1.754226 GCGGTCTCCAGAGAAGAGATT 59.246 52.381 0.00 0.00 42.16 2.40
2375 5742 2.952978 GCGGTCTCCAGAGAAGAGATTA 59.047 50.000 0.00 0.00 42.16 1.75
2376 5743 3.572255 GCGGTCTCCAGAGAAGAGATTAT 59.428 47.826 0.00 0.00 42.16 1.28
2377 5744 4.762765 GCGGTCTCCAGAGAAGAGATTATA 59.237 45.833 0.00 0.00 42.16 0.98
2378 5745 5.106317 GCGGTCTCCAGAGAAGAGATTATAG 60.106 48.000 0.00 0.00 42.16 1.31
2379 5746 6.234920 CGGTCTCCAGAGAAGAGATTATAGA 58.765 44.000 0.00 0.00 42.16 1.98
2380 5747 6.712998 CGGTCTCCAGAGAAGAGATTATAGAA 59.287 42.308 0.00 0.00 42.16 2.10
2381 5748 7.229707 CGGTCTCCAGAGAAGAGATTATAGAAA 59.770 40.741 0.00 0.00 42.16 2.52
2382 5749 8.919145 GGTCTCCAGAGAAGAGATTATAGAAAA 58.081 37.037 0.00 0.00 42.16 2.29
2403 5770 9.639601 AGAAAAAGAAGAACGAAAGAACAAAAT 57.360 25.926 0.00 0.00 0.00 1.82
2404 5771 9.675553 GAAAAAGAAGAACGAAAGAACAAAATG 57.324 29.630 0.00 0.00 0.00 2.32
2405 5772 8.757164 AAAAGAAGAACGAAAGAACAAAATGT 57.243 26.923 0.00 0.00 0.00 2.71
2406 5773 9.849166 AAAAGAAGAACGAAAGAACAAAATGTA 57.151 25.926 0.00 0.00 0.00 2.29
2407 5774 9.849166 AAAGAAGAACGAAAGAACAAAATGTAA 57.151 25.926 0.00 0.00 0.00 2.41
2412 5779 9.450807 AGAACGAAAGAACAAAATGTAATTCTG 57.549 29.630 0.00 0.00 33.67 3.02
2413 5780 8.574196 AACGAAAGAACAAAATGTAATTCTGG 57.426 30.769 0.00 0.00 33.67 3.86
2414 5781 7.936584 ACGAAAGAACAAAATGTAATTCTGGA 58.063 30.769 0.00 0.00 33.67 3.86
2415 5782 8.410141 ACGAAAGAACAAAATGTAATTCTGGAA 58.590 29.630 0.00 0.00 33.67 3.53
2416 5783 9.410556 CGAAAGAACAAAATGTAATTCTGGAAT 57.589 29.630 0.00 0.00 33.67 3.01
2423 5790 9.480053 ACAAAATGTAATTCTGGAATCAAAGTG 57.520 29.630 0.00 0.00 33.67 3.16
2424 5791 9.695526 CAAAATGTAATTCTGGAATCAAAGTGA 57.304 29.630 0.00 0.00 33.67 3.41
2425 5792 9.696917 AAAATGTAATTCTGGAATCAAAGTGAC 57.303 29.630 0.00 0.00 33.67 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.885743 CGTAAAAAGTTTCTCTTCACAAATTTG 57.114 29.630 16.67 16.67 35.02 2.32
37 38 8.496751 GCATTCTAGACGTAAAAAGTTTCTCTT 58.503 33.333 0.00 0.00 38.10 2.85
46 47 6.621316 TGTTTGGCATTCTAGACGTAAAAA 57.379 33.333 0.00 0.00 0.00 1.94
47 48 6.811253 ATGTTTGGCATTCTAGACGTAAAA 57.189 33.333 0.00 0.00 33.14 1.52
52 53 7.889589 TGATATATGTTTGGCATTCTAGACG 57.110 36.000 0.00 0.00 38.94 4.18
180 197 8.090788 ACTCCCTTCATTACATAATGTAGTGT 57.909 34.615 13.84 8.83 40.23 3.55
193 210 8.383175 ACTCTGAAAATGTTACTCCCTTCATTA 58.617 33.333 0.00 0.00 31.54 1.90
194 211 7.234355 ACTCTGAAAATGTTACTCCCTTCATT 58.766 34.615 0.00 0.00 32.86 2.57
216 233 7.272731 GGCGTGGTAAAAGAAAAATCAATACTC 59.727 37.037 0.00 0.00 0.00 2.59
222 239 5.300792 AGAAGGCGTGGTAAAAGAAAAATCA 59.699 36.000 0.00 0.00 0.00 2.57
223 240 5.769367 AGAAGGCGTGGTAAAAGAAAAATC 58.231 37.500 0.00 0.00 0.00 2.17
229 246 3.167485 TCCTAGAAGGCGTGGTAAAAGA 58.833 45.455 0.00 0.00 34.61 2.52
230 247 3.604875 TCCTAGAAGGCGTGGTAAAAG 57.395 47.619 0.00 0.00 34.61 2.27
239 262 6.867662 ATGAAATAACATTCCTAGAAGGCG 57.132 37.500 0.00 0.00 34.61 5.52
270 293 8.372459 TGACAAATGTACTAGGAGCTTCTAAAA 58.628 33.333 2.64 0.00 0.00 1.52
274 297 6.360370 TTGACAAATGTACTAGGAGCTTCT 57.640 37.500 0.00 0.00 0.00 2.85
275 298 7.435068 TTTTGACAAATGTACTAGGAGCTTC 57.565 36.000 0.50 0.00 0.00 3.86
351 376 0.108567 GAGTTTCTCAGCCCGAGTCC 60.109 60.000 1.01 0.00 42.88 3.85
672 697 0.676184 ACTGATGTCGATCCATCCGG 59.324 55.000 12.10 0.00 40.43 5.14
792 817 1.139520 GCGATTCCATGTGGTTGCC 59.860 57.895 0.00 0.00 36.34 4.52
837 862 2.553247 GGAAGGAAGAAAGGTGGTGAGG 60.553 54.545 0.00 0.00 0.00 3.86
838 863 2.553247 GGGAAGGAAGAAAGGTGGTGAG 60.553 54.545 0.00 0.00 0.00 3.51
839 864 1.423921 GGGAAGGAAGAAAGGTGGTGA 59.576 52.381 0.00 0.00 0.00 4.02
840 865 1.547901 GGGGAAGGAAGAAAGGTGGTG 60.548 57.143 0.00 0.00 0.00 4.17
841 866 0.778083 GGGGAAGGAAGAAAGGTGGT 59.222 55.000 0.00 0.00 0.00 4.16
915 953 0.325296 AGATTGGTGCGGAGGAGGTA 60.325 55.000 0.00 0.00 0.00 3.08
1048 1086 1.874345 GCGAGGACGAAGGACAGGAA 61.874 60.000 0.00 0.00 42.66 3.36
1080 1118 2.679996 TGCTCTGGGTAGCTCGCA 60.680 61.111 0.00 0.00 43.19 5.10
1082 1120 2.496817 GGTGCTCTGGGTAGCTCG 59.503 66.667 0.00 0.00 43.19 5.03
1469 1511 2.125952 TGAGTGTGCAGCGATCCG 60.126 61.111 0.00 0.00 0.00 4.18
1480 1522 3.055819 GTCCTGGATGTGTATGTGAGTGT 60.056 47.826 0.00 0.00 0.00 3.55
1673 1715 7.197071 TCACAAACAGTTATAACATGGTCAC 57.803 36.000 17.65 0.00 0.00 3.67
1745 4469 9.370126 GCGCTACTGTGTTTTTATTATTATCTG 57.630 33.333 0.00 0.00 0.00 2.90
1752 4476 7.701924 ACGTATAGCGCTACTGTGTTTTTATTA 59.298 33.333 21.49 0.00 46.11 0.98
1759 4483 3.374988 TGTACGTATAGCGCTACTGTGTT 59.625 43.478 21.49 5.11 46.11 3.32
1761 4485 3.242511 TGTGTACGTATAGCGCTACTGTG 60.243 47.826 21.49 12.41 46.11 3.66
1763 4487 3.002042 AGTGTGTACGTATAGCGCTACTG 59.998 47.826 21.49 14.64 46.11 2.74
1765 4489 3.599046 AGTGTGTACGTATAGCGCTAC 57.401 47.619 21.49 10.10 46.11 3.58
1777 4879 0.386858 TCTCGCGAGCAAGTGTGTAC 60.387 55.000 30.97 0.00 0.00 2.90
1783 4885 2.803451 CTTTATCTCTCGCGAGCAAGT 58.197 47.619 30.97 17.83 37.19 3.16
1788 4890 1.661743 CGAGGCTTTATCTCTCGCGAG 60.662 57.143 30.03 30.03 42.70 5.03
1790 4892 0.661780 CCGAGGCTTTATCTCTCGCG 60.662 60.000 0.00 0.00 46.08 5.87
1793 4895 1.000394 GCTCCCGAGGCTTTATCTCTC 60.000 57.143 0.00 0.00 0.00 3.20
1795 4897 3.597550 GCTCCCGAGGCTTTATCTC 57.402 57.895 0.00 0.00 0.00 2.75
1838 4951 6.479001 CGGACGGTTCATATAAGAAGTGATTT 59.521 38.462 0.00 0.00 0.00 2.17
1847 4960 8.758633 AATAAAGATCGGACGGTTCATATAAG 57.241 34.615 0.00 0.00 0.00 1.73
1857 4970 2.538449 CGGTTGAATAAAGATCGGACGG 59.462 50.000 0.00 0.00 0.00 4.79
1861 4974 2.031683 GGTGCGGTTGAATAAAGATCGG 59.968 50.000 0.00 0.00 0.00 4.18
1869 4982 0.988832 AAGGGAGGTGCGGTTGAATA 59.011 50.000 0.00 0.00 0.00 1.75
1877 4990 0.391793 GAAGAAGGAAGGGAGGTGCG 60.392 60.000 0.00 0.00 0.00 5.34
1894 5037 4.410033 GGGGGTCGGGAGGAGGAA 62.410 72.222 0.00 0.00 0.00 3.36
1905 5048 4.752594 TGGGGTAGGCTGGGGGTC 62.753 72.222 0.00 0.00 0.00 4.46
1906 5049 4.052833 ATGGGGTAGGCTGGGGGT 62.053 66.667 0.00 0.00 0.00 4.95
1907 5050 3.178611 GATGGGGTAGGCTGGGGG 61.179 72.222 0.00 0.00 0.00 5.40
1908 5051 3.178611 GGATGGGGTAGGCTGGGG 61.179 72.222 0.00 0.00 0.00 4.96
1909 5052 3.178611 GGGATGGGGTAGGCTGGG 61.179 72.222 0.00 0.00 0.00 4.45
1910 5053 1.775877 ATGGGATGGGGTAGGCTGG 60.776 63.158 0.00 0.00 0.00 4.85
1911 5054 1.457604 CATGGGATGGGGTAGGCTG 59.542 63.158 0.00 0.00 0.00 4.85
1912 5055 2.464403 GCATGGGATGGGGTAGGCT 61.464 63.158 0.00 0.00 0.00 4.58
1913 5056 2.116125 GCATGGGATGGGGTAGGC 59.884 66.667 0.00 0.00 0.00 3.93
1914 5057 2.397413 GACGCATGGGATGGGGTAGG 62.397 65.000 17.76 0.00 46.33 3.18
1915 5058 1.071471 GACGCATGGGATGGGGTAG 59.929 63.158 17.76 0.00 46.33 3.18
1916 5059 2.802724 CGACGCATGGGATGGGGTA 61.803 63.158 17.76 0.00 46.33 3.69
1917 5060 4.175337 CGACGCATGGGATGGGGT 62.175 66.667 17.76 0.00 46.33 4.95
1918 5061 4.935495 CCGACGCATGGGATGGGG 62.935 72.222 17.76 7.65 46.33 4.96
1921 5064 4.552365 AGGCCGACGCATGGGATG 62.552 66.667 17.76 7.83 36.38 3.51
1922 5065 4.241555 GAGGCCGACGCATGGGAT 62.242 66.667 17.76 0.37 36.38 3.85
1959 5326 4.373116 AGGTGGCGCACGGTACTG 62.373 66.667 10.83 0.00 34.83 2.74
1960 5327 4.065281 GAGGTGGCGCACGGTACT 62.065 66.667 10.83 0.00 34.83 2.73
1986 5353 4.176752 GATGGTCGTGGGGAGGGC 62.177 72.222 0.00 0.00 0.00 5.19
1987 5354 3.480133 GGATGGTCGTGGGGAGGG 61.480 72.222 0.00 0.00 0.00 4.30
2047 5414 1.772156 GGGGCTTAGAGGGATGGCT 60.772 63.158 0.00 0.00 0.00 4.75
2048 5415 2.839836 GGGGCTTAGAGGGATGGC 59.160 66.667 0.00 0.00 0.00 4.40
2050 5417 2.143419 AGCGGGGCTTAGAGGGATG 61.143 63.158 0.00 0.00 33.89 3.51
2061 5428 2.345880 CTTCATTGATGCAGCGGGGC 62.346 60.000 0.00 0.00 0.00 5.80
2065 5432 2.223203 GGAGTTCTTCATTGATGCAGCG 60.223 50.000 0.00 0.00 0.00 5.18
2066 5433 2.751259 TGGAGTTCTTCATTGATGCAGC 59.249 45.455 0.00 0.00 0.00 5.25
2067 5434 4.259356 TCTGGAGTTCTTCATTGATGCAG 58.741 43.478 0.00 0.71 0.00 4.41
2078 5445 2.476199 CAGGGGATCTCTGGAGTTCTT 58.524 52.381 0.00 0.00 0.00 2.52
2087 5454 2.367512 GGGGTGCAGGGGATCTCT 60.368 66.667 0.00 0.00 0.00 3.10
2088 5455 3.493303 GGGGGTGCAGGGGATCTC 61.493 72.222 0.00 0.00 0.00 2.75
2089 5456 4.044390 AGGGGGTGCAGGGGATCT 62.044 66.667 0.00 0.00 0.00 2.75
2100 5467 2.424989 TACATGTGGGTGGAGGGGGT 62.425 60.000 9.11 0.00 0.00 4.95
2104 5471 5.110814 TCTATTTTACATGTGGGTGGAGG 57.889 43.478 9.11 0.00 0.00 4.30
2109 5476 7.010160 CCCCATTATCTATTTTACATGTGGGT 58.990 38.462 9.11 0.00 40.69 4.51
2125 5492 5.070685 GGGTGAAGTAATGACCCCATTATC 58.929 45.833 0.00 0.00 44.37 1.75
2149 5516 0.181350 CAGCCCCACCATCTACCTTC 59.819 60.000 0.00 0.00 0.00 3.46
2200 5567 2.348888 CCTGTTAGCCGGACCTCGT 61.349 63.158 5.05 0.00 37.11 4.18
2212 5579 6.020881 TCTTTCCTTTTTCCTTCCCTGTTA 57.979 37.500 0.00 0.00 0.00 2.41
2215 5582 4.895889 ACTTCTTTCCTTTTTCCTTCCCTG 59.104 41.667 0.00 0.00 0.00 4.45
2222 5589 6.451064 TTCAGTCACTTCTTTCCTTTTTCC 57.549 37.500 0.00 0.00 0.00 3.13
2224 5591 5.449177 CGCTTCAGTCACTTCTTTCCTTTTT 60.449 40.000 0.00 0.00 0.00 1.94
2229 5596 1.801178 CCGCTTCAGTCACTTCTTTCC 59.199 52.381 0.00 0.00 0.00 3.13
2230 5597 2.755650 TCCGCTTCAGTCACTTCTTTC 58.244 47.619 0.00 0.00 0.00 2.62
2231 5598 2.910688 TCCGCTTCAGTCACTTCTTT 57.089 45.000 0.00 0.00 0.00 2.52
2232 5599 2.910688 TTCCGCTTCAGTCACTTCTT 57.089 45.000 0.00 0.00 0.00 2.52
2233 5600 2.910688 TTTCCGCTTCAGTCACTTCT 57.089 45.000 0.00 0.00 0.00 2.85
2234 5601 3.963383 TTTTTCCGCTTCAGTCACTTC 57.037 42.857 0.00 0.00 0.00 3.01
2258 5625 3.303049 TGCTATTCTCTCAGATGCCTGA 58.697 45.455 0.00 0.00 46.48 3.86
2259 5626 3.747854 TGCTATTCTCTCAGATGCCTG 57.252 47.619 0.00 0.00 41.74 4.85
2260 5627 4.767578 TTTGCTATTCTCTCAGATGCCT 57.232 40.909 0.00 0.00 0.00 4.75
2261 5628 4.455190 GGATTTGCTATTCTCTCAGATGCC 59.545 45.833 0.00 0.00 0.00 4.40
2262 5629 5.061853 TGGATTTGCTATTCTCTCAGATGC 58.938 41.667 0.00 0.00 0.00 3.91
2263 5630 8.843885 TTATGGATTTGCTATTCTCTCAGATG 57.156 34.615 0.00 0.00 0.00 2.90
2264 5631 9.857656 TTTTATGGATTTGCTATTCTCTCAGAT 57.142 29.630 0.00 0.00 0.00 2.90
2265 5632 9.113838 GTTTTATGGATTTGCTATTCTCTCAGA 57.886 33.333 0.00 0.00 0.00 3.27
2266 5633 8.348507 GGTTTTATGGATTTGCTATTCTCTCAG 58.651 37.037 0.00 0.00 0.00 3.35
2267 5634 8.055181 AGGTTTTATGGATTTGCTATTCTCTCA 58.945 33.333 0.00 0.00 0.00 3.27
2268 5635 8.457238 AGGTTTTATGGATTTGCTATTCTCTC 57.543 34.615 0.00 0.00 0.00 3.20
2269 5636 8.055181 TGAGGTTTTATGGATTTGCTATTCTCT 58.945 33.333 0.00 0.00 0.00 3.10
2270 5637 8.131731 GTGAGGTTTTATGGATTTGCTATTCTC 58.868 37.037 0.00 0.00 0.00 2.87
2271 5638 7.201732 CGTGAGGTTTTATGGATTTGCTATTCT 60.202 37.037 0.00 0.00 0.00 2.40
2272 5639 6.912591 CGTGAGGTTTTATGGATTTGCTATTC 59.087 38.462 0.00 0.00 0.00 1.75
2273 5640 6.377146 ACGTGAGGTTTTATGGATTTGCTATT 59.623 34.615 0.00 0.00 0.00 1.73
2274 5641 5.885912 ACGTGAGGTTTTATGGATTTGCTAT 59.114 36.000 0.00 0.00 0.00 2.97
2275 5642 5.250200 ACGTGAGGTTTTATGGATTTGCTA 58.750 37.500 0.00 0.00 0.00 3.49
2276 5643 4.079253 ACGTGAGGTTTTATGGATTTGCT 58.921 39.130 0.00 0.00 0.00 3.91
2277 5644 4.434713 ACGTGAGGTTTTATGGATTTGC 57.565 40.909 0.00 0.00 0.00 3.68
2278 5645 5.633182 CCAAACGTGAGGTTTTATGGATTTG 59.367 40.000 0.00 0.00 46.52 2.32
2279 5646 5.303333 ACCAAACGTGAGGTTTTATGGATTT 59.697 36.000 12.57 0.00 46.52 2.17
2280 5647 4.830600 ACCAAACGTGAGGTTTTATGGATT 59.169 37.500 12.57 0.00 46.52 3.01
2281 5648 4.403734 ACCAAACGTGAGGTTTTATGGAT 58.596 39.130 12.57 0.00 46.52 3.41
2282 5649 3.816523 GACCAAACGTGAGGTTTTATGGA 59.183 43.478 12.83 0.00 46.52 3.41
2283 5650 3.818773 AGACCAAACGTGAGGTTTTATGG 59.181 43.478 12.83 3.34 46.52 2.74
2284 5651 4.513692 TGAGACCAAACGTGAGGTTTTATG 59.486 41.667 12.83 0.00 46.52 1.90
2285 5652 4.514066 GTGAGACCAAACGTGAGGTTTTAT 59.486 41.667 12.83 1.63 46.52 1.40
2286 5653 3.872771 GTGAGACCAAACGTGAGGTTTTA 59.127 43.478 12.83 2.66 46.52 1.52
2287 5654 2.681344 GTGAGACCAAACGTGAGGTTTT 59.319 45.455 12.83 5.69 46.52 2.43
2289 5656 1.485066 AGTGAGACCAAACGTGAGGTT 59.515 47.619 12.83 4.39 45.95 3.50
2290 5657 1.120530 AGTGAGACCAAACGTGAGGT 58.879 50.000 11.59 11.59 41.83 3.85
2291 5658 1.068588 TCAGTGAGACCAAACGTGAGG 59.931 52.381 5.07 5.07 0.00 3.86
2292 5659 2.509052 TCAGTGAGACCAAACGTGAG 57.491 50.000 0.00 0.00 0.00 3.51
2293 5660 2.547855 CCATCAGTGAGACCAAACGTGA 60.548 50.000 0.00 0.00 0.00 4.35
2294 5661 1.800586 CCATCAGTGAGACCAAACGTG 59.199 52.381 0.00 0.00 0.00 4.49
2295 5662 1.878102 GCCATCAGTGAGACCAAACGT 60.878 52.381 0.00 0.00 0.00 3.99
2296 5663 0.798776 GCCATCAGTGAGACCAAACG 59.201 55.000 0.00 0.00 0.00 3.60
2297 5664 0.798776 CGCCATCAGTGAGACCAAAC 59.201 55.000 0.00 0.00 0.00 2.93
2298 5665 0.321564 CCGCCATCAGTGAGACCAAA 60.322 55.000 0.00 0.00 0.00 3.28
2299 5666 1.296392 CCGCCATCAGTGAGACCAA 59.704 57.895 0.00 0.00 0.00 3.67
2300 5667 1.913262 ACCGCCATCAGTGAGACCA 60.913 57.895 0.00 0.00 0.00 4.02
2301 5668 1.448540 CACCGCCATCAGTGAGACC 60.449 63.158 0.00 0.00 36.01 3.85
2302 5669 1.448540 CCACCGCCATCAGTGAGAC 60.449 63.158 0.00 0.00 36.01 3.36
2303 5670 2.659063 CCCACCGCCATCAGTGAGA 61.659 63.158 0.00 0.00 36.01 3.27
2304 5671 1.613317 TACCCACCGCCATCAGTGAG 61.613 60.000 0.00 0.00 36.01 3.51
2305 5672 0.980754 ATACCCACCGCCATCAGTGA 60.981 55.000 0.00 0.00 36.01 3.41
2306 5673 0.107214 AATACCCACCGCCATCAGTG 60.107 55.000 0.00 0.00 0.00 3.66
2307 5674 0.107214 CAATACCCACCGCCATCAGT 60.107 55.000 0.00 0.00 0.00 3.41
2308 5675 0.107214 ACAATACCCACCGCCATCAG 60.107 55.000 0.00 0.00 0.00 2.90
2309 5676 0.393673 CACAATACCCACCGCCATCA 60.394 55.000 0.00 0.00 0.00 3.07
2310 5677 1.724582 GCACAATACCCACCGCCATC 61.725 60.000 0.00 0.00 0.00 3.51
2311 5678 1.752694 GCACAATACCCACCGCCAT 60.753 57.895 0.00 0.00 0.00 4.40
2312 5679 2.360600 GCACAATACCCACCGCCA 60.361 61.111 0.00 0.00 0.00 5.69
2313 5680 2.360600 TGCACAATACCCACCGCC 60.361 61.111 0.00 0.00 0.00 6.13
2314 5681 1.241315 AAGTGCACAATACCCACCGC 61.241 55.000 21.04 0.00 0.00 5.68
2315 5682 1.243902 AAAGTGCACAATACCCACCG 58.756 50.000 21.04 0.00 0.00 4.94
2316 5683 2.364002 ACAAAAGTGCACAATACCCACC 59.636 45.455 21.04 0.00 0.00 4.61
2317 5684 3.726291 ACAAAAGTGCACAATACCCAC 57.274 42.857 21.04 0.00 0.00 4.61
2318 5685 3.181471 CCAACAAAAGTGCACAATACCCA 60.181 43.478 21.04 0.00 0.00 4.51
2319 5686 3.068873 TCCAACAAAAGTGCACAATACCC 59.931 43.478 21.04 0.00 0.00 3.69
2320 5687 4.314740 TCCAACAAAAGTGCACAATACC 57.685 40.909 21.04 0.00 0.00 2.73
2321 5688 5.231991 CACTTCCAACAAAAGTGCACAATAC 59.768 40.000 21.04 0.00 44.94 1.89
2322 5689 5.347342 CACTTCCAACAAAAGTGCACAATA 58.653 37.500 21.04 0.00 44.94 1.90
2323 5690 4.183101 CACTTCCAACAAAAGTGCACAAT 58.817 39.130 21.04 4.21 44.94 2.71
2324 5691 3.583806 CACTTCCAACAAAAGTGCACAA 58.416 40.909 21.04 0.00 44.94 3.33
2325 5692 3.229276 CACTTCCAACAAAAGTGCACA 57.771 42.857 21.04 0.00 44.94 4.57
2330 5697 6.152831 GCTATTATCCCACTTCCAACAAAAGT 59.847 38.462 0.00 0.00 37.44 2.66
2331 5698 6.564328 GCTATTATCCCACTTCCAACAAAAG 58.436 40.000 0.00 0.00 0.00 2.27
2332 5699 5.124776 CGCTATTATCCCACTTCCAACAAAA 59.875 40.000 0.00 0.00 0.00 2.44
2333 5700 4.638421 CGCTATTATCCCACTTCCAACAAA 59.362 41.667 0.00 0.00 0.00 2.83
2334 5701 4.196193 CGCTATTATCCCACTTCCAACAA 58.804 43.478 0.00 0.00 0.00 2.83
2335 5702 3.433031 CCGCTATTATCCCACTTCCAACA 60.433 47.826 0.00 0.00 0.00 3.33
2336 5703 3.139077 CCGCTATTATCCCACTTCCAAC 58.861 50.000 0.00 0.00 0.00 3.77
2337 5704 2.775384 ACCGCTATTATCCCACTTCCAA 59.225 45.455 0.00 0.00 0.00 3.53
2338 5705 2.367567 GACCGCTATTATCCCACTTCCA 59.632 50.000 0.00 0.00 0.00 3.53
2339 5706 2.633481 AGACCGCTATTATCCCACTTCC 59.367 50.000 0.00 0.00 0.00 3.46
2340 5707 3.306156 GGAGACCGCTATTATCCCACTTC 60.306 52.174 0.00 0.00 0.00 3.01
2341 5708 2.633481 GGAGACCGCTATTATCCCACTT 59.367 50.000 0.00 0.00 0.00 3.16
2342 5709 2.249139 GGAGACCGCTATTATCCCACT 58.751 52.381 0.00 0.00 0.00 4.00
2343 5710 1.968493 TGGAGACCGCTATTATCCCAC 59.032 52.381 0.00 0.00 0.00 4.61
2344 5711 2.158370 TCTGGAGACCGCTATTATCCCA 60.158 50.000 0.00 0.00 0.00 4.37
2345 5712 2.494073 CTCTGGAGACCGCTATTATCCC 59.506 54.545 0.00 0.00 0.00 3.85
2346 5713 3.422796 TCTCTGGAGACCGCTATTATCC 58.577 50.000 0.00 0.00 31.41 2.59
2347 5714 4.762765 TCTTCTCTGGAGACCGCTATTATC 59.237 45.833 0.00 0.00 37.14 1.75
2348 5715 4.730966 TCTTCTCTGGAGACCGCTATTAT 58.269 43.478 0.00 0.00 37.14 1.28
2349 5716 4.138290 CTCTTCTCTGGAGACCGCTATTA 58.862 47.826 0.00 0.00 37.14 0.98
2350 5717 2.955660 CTCTTCTCTGGAGACCGCTATT 59.044 50.000 0.00 0.00 37.14 1.73
2351 5718 2.173782 TCTCTTCTCTGGAGACCGCTAT 59.826 50.000 0.00 0.00 37.14 2.97
2352 5719 1.560146 TCTCTTCTCTGGAGACCGCTA 59.440 52.381 0.00 0.00 37.14 4.26
2353 5720 0.329931 TCTCTTCTCTGGAGACCGCT 59.670 55.000 0.00 0.00 37.14 5.52
2354 5721 1.398692 ATCTCTTCTCTGGAGACCGC 58.601 55.000 0.00 0.00 41.76 5.68
2355 5722 6.234920 TCTATAATCTCTTCTCTGGAGACCG 58.765 44.000 0.00 0.00 41.76 4.79
2356 5723 8.472007 TTTCTATAATCTCTTCTCTGGAGACC 57.528 38.462 0.00 0.00 41.76 3.85
2377 5744 9.639601 ATTTTGTTCTTTCGTTCTTCTTTTTCT 57.360 25.926 0.00 0.00 0.00 2.52
2378 5745 9.675553 CATTTTGTTCTTTCGTTCTTCTTTTTC 57.324 29.630 0.00 0.00 0.00 2.29
2379 5746 9.203421 ACATTTTGTTCTTTCGTTCTTCTTTTT 57.797 25.926 0.00 0.00 0.00 1.94
2380 5747 8.757164 ACATTTTGTTCTTTCGTTCTTCTTTT 57.243 26.923 0.00 0.00 0.00 2.27
2381 5748 9.849166 TTACATTTTGTTCTTTCGTTCTTCTTT 57.151 25.926 0.00 0.00 0.00 2.52
2386 5753 9.450807 CAGAATTACATTTTGTTCTTTCGTTCT 57.549 29.630 0.00 0.00 0.00 3.01
2387 5754 8.690840 CCAGAATTACATTTTGTTCTTTCGTTC 58.309 33.333 0.00 0.00 0.00 3.95
2388 5755 8.410141 TCCAGAATTACATTTTGTTCTTTCGTT 58.590 29.630 0.00 0.00 0.00 3.85
2389 5756 7.936584 TCCAGAATTACATTTTGTTCTTTCGT 58.063 30.769 0.00 0.00 0.00 3.85
2390 5757 8.795786 TTCCAGAATTACATTTTGTTCTTTCG 57.204 30.769 0.00 0.00 0.00 3.46
2397 5764 9.480053 CACTTTGATTCCAGAATTACATTTTGT 57.520 29.630 0.00 0.00 0.00 2.83
2398 5765 9.695526 TCACTTTGATTCCAGAATTACATTTTG 57.304 29.630 0.00 0.00 0.00 2.44
2399 5766 9.696917 GTCACTTTGATTCCAGAATTACATTTT 57.303 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.