Multiple sequence alignment - TraesCS6A01G226000

Loading Multiple Alignment...

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 TraesCS6A01G226000 chr6A 100.000 2453 0 0 1 2453 425656575 425659027 0.000000e+00 4530.0
1 TraesCS6A01G226000 chr6A 94.872 39 2 0 1767 1805 126353242 126353280 7.320000e-06 62.1
2 TraesCS6A01G226000 chr6B 92.500 1720 86 17 17 1709 459603562 459601859 0.000000e+00 2422.0
3 TraesCS6A01G226000 chr6B 93.836 292 12 3 1848 2139 459601640 459601355 3.750000e-118 435.0
4 TraesCS6A01G226000 chr6B 92.958 142 5 1 2312 2453 459601363 459601227 4.140000e-48 202.0
5 TraesCS6A01G226000 chr6B 96.667 60 2 0 1710 1769 459601800 459601741 1.550000e-17 100.0
6 TraesCS6A01G226000 chr6D 93.029 1162 45 11 554 1695 295355464 295354319 0.000000e+00 1664.0
7 TraesCS6A01G226000 chr6D 90.586 563 43 7 2 561 295356160 295355605 0.000000e+00 737.0
8 TraesCS6A01G226000 chr6D 95.185 270 10 1 1835 2101 295354188 295353919 8.110000e-115 424.0
9 TraesCS6A01G226000 chr6D 87.413 143 9 4 2312 2453 295306657 295306523 3.270000e-34 156.0
10 TraesCS6A01G226000 chr6D 98.214 56 1 0 1710 1765 295354239 295354184 5.580000e-17 99.0
11 TraesCS6A01G226000 chr7D 85.315 143 19 2 2165 2307 406338877 406339017 1.970000e-31 147.0
12 TraesCS6A01G226000 chr7D 80.982 163 29 2 2153 2314 125907603 125907764 7.120000e-26 128.0
13 TraesCS6A01G226000 chr7D 97.436 39 1 0 1770 1808 625036373 625036411 1.570000e-07 67.6
14 TraesCS6A01G226000 chr2B 80.556 180 33 2 2153 2332 495146717 495146540 1.180000e-28 137.0
15 TraesCS6A01G226000 chr2B 87.156 109 13 1 2206 2314 760299930 760300037 3.310000e-24 122.0
16 TraesCS6A01G226000 chr5A 80.892 157 24 5 2153 2308 374665794 374665643 4.280000e-23 119.0
17 TraesCS6A01G226000 chr5A 78.981 157 32 1 2159 2315 491750337 491750182 3.340000e-19 106.0
18 TraesCS6A01G226000 chr3A 80.255 157 28 2 2153 2307 522063835 522063680 5.540000e-22 115.0
19 TraesCS6A01G226000 chr3A 94.737 38 2 0 1771 1808 712148087 712148050 2.630000e-05 60.2
20 TraesCS6A01G226000 chr3A 94.737 38 2 0 1768 1805 750540959 750540996 2.630000e-05 60.2
21 TraesCS6A01G226000 chr3B 79.114 158 26 6 2154 2308 670028781 670028628 4.320000e-18 102.0
22 TraesCS6A01G226000 chr3B 92.308 39 3 0 1770 1808 221753059 221753021 3.410000e-04 56.5
23 TraesCS6A01G226000 chrUn 78.146 151 27 4 2159 2307 126990371 126990225 9.340000e-15 91.6
24 TraesCS6A01G226000 chr2D 92.308 39 3 0 1770 1808 155114465 155114427 3.410000e-04 56.5


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 TraesCS6A01G226000 chr6A 425656575 425659027 2452 False 4530.00 4530 100.00000 1 2453 1 chr6A.!!$F2 2452
1 TraesCS6A01G226000 chr6B 459601227 459603562 2335 True 789.75 2422 93.99025 17 2453 4 chr6B.!!$R1 2436
2 TraesCS6A01G226000 chr6D 295353919 295356160 2241 True 731.00 1664 94.25350 2 2101 4 chr6D.!!$R2 2099

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
115 116 0.253160 AGTACTCCCCAATGAGCCCA 60.253 55.0 0.00 0.0 35.72 5.36 F
155 156 0.878416 GTTGTAGGCCGTGCAATTCA 59.122 50.0 11.64 0.0 32.88 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1599 0.533755 CTTAATCCGGAGCCAGCAGG 60.534 60.000 11.34 0.0 38.23 4.85 R
2138 2462 1.007721 AGTCTCATCTAGCCACACCCT 59.992 52.381 0.00 0.0 0.00 4.34 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
49 50 3.750599 GCCTTTAGCTGGGGCATACATAA 60.751 47.826 17.56 0.00 44.69 1.90
94 95 4.844420 CCATCACGAGGGAAGAGC 57.156 61.111 0.00 0.00 33.27 4.09
114 115 0.470341 GAGTACTCCCCAATGAGCCC 59.530 60.000 12.13 0.00 35.72 5.19
115 116 0.253160 AGTACTCCCCAATGAGCCCA 60.253 55.000 0.00 0.00 35.72 5.36
155 156 0.878416 GTTGTAGGCCGTGCAATTCA 59.122 50.000 11.64 0.00 32.88 2.57
173 174 2.072487 AGTGCTCCGCCCCACATAT 61.072 57.895 0.00 0.00 34.48 1.78
183 184 1.134670 GCCCCACATATCTATCGCCTC 60.135 57.143 0.00 0.00 0.00 4.70
230 235 1.066071 GGAGAAAAAGGGAGGAGACGG 60.066 57.143 0.00 0.00 0.00 4.79
256 261 1.308047 AGCAAACTTCGCACATGTGA 58.692 45.000 29.80 6.58 0.00 3.58
285 290 9.638239 GTATGAAAAATTGATAAAGAAGGCACA 57.362 29.630 0.00 0.00 0.00 4.57
287 292 8.761575 TGAAAAATTGATAAAGAAGGCACATC 57.238 30.769 0.00 0.00 0.00 3.06
288 293 8.366401 TGAAAAATTGATAAAGAAGGCACATCA 58.634 29.630 0.00 0.00 0.00 3.07
295 300 7.512130 TGATAAAGAAGGCACATCATCATACT 58.488 34.615 0.00 0.00 0.00 2.12
361 366 1.344114 GCATGGGAAAACAAAGGAGCA 59.656 47.619 0.00 0.00 0.00 4.26
407 413 3.321968 CACTATCCCATCACCGAGATTCA 59.678 47.826 0.00 0.00 33.72 2.57
419 425 2.220363 CCGAGATTCATGCAAGTCATCG 59.780 50.000 0.00 0.00 31.79 3.84
420 426 3.118542 CGAGATTCATGCAAGTCATCGA 58.881 45.455 0.00 0.00 31.79 3.59
423 429 3.624861 AGATTCATGCAAGTCATCGAACC 59.375 43.478 0.00 0.00 31.79 3.62
426 432 1.464608 CATGCAAGTCATCGAACCGTT 59.535 47.619 0.00 0.00 31.79 4.44
440 446 3.978764 CGTTGTCGTTGCGTCGCA 61.979 61.111 17.58 17.58 36.47 5.10
444 450 2.429571 GTCGTTGCGTCGCACCTA 60.430 61.111 21.61 1.15 38.71 3.08
445 451 2.126618 TCGTTGCGTCGCACCTAG 60.127 61.111 21.61 11.43 38.71 3.02
448 454 1.373748 GTTGCGTCGCACCTAGGAA 60.374 57.895 21.61 0.00 38.71 3.36
455 461 2.798499 CGTCGCACCTAGGAAGTAATGG 60.798 54.545 17.98 0.00 0.00 3.16
469 475 6.717084 AGGAAGTAATGGGAGAACTTTCTTTG 59.283 38.462 0.00 0.00 35.92 2.77
481 487 7.434013 GGAGAACTTTCTTTGACGCAATTTTTA 59.566 33.333 0.00 0.00 37.73 1.52
491 497 8.664211 TTTGACGCAATTTTTAAGGGTAATTT 57.336 26.923 0.00 0.00 0.00 1.82
596 750 6.800408 CGTATACAATGACAACTATACCCTCG 59.200 42.308 3.32 0.00 0.00 4.63
670 824 6.403636 CGATGGCATTCCTGTTATTTATAGCC 60.404 42.308 0.00 0.00 38.82 3.93
718 872 5.106673 GCTTGAATATAAATAGACCACCGCC 60.107 44.000 0.00 0.00 0.00 6.13
721 875 1.513858 ATAAATAGACCACCGCCCCA 58.486 50.000 0.00 0.00 0.00 4.96
803 957 3.092301 CCCTCTCTTTCCACCAAAATCC 58.908 50.000 0.00 0.00 0.00 3.01
807 961 1.146152 TCTTTCCACCAAAATCCCCGT 59.854 47.619 0.00 0.00 0.00 5.28
809 963 1.623163 TTCCACCAAAATCCCCGTTC 58.377 50.000 0.00 0.00 0.00 3.95
853 1007 1.038280 CCCCCTGTGATAGTACGGAC 58.962 60.000 0.00 0.00 0.00 4.79
1182 1354 4.383602 CGGTTCGCCAACAAGCCG 62.384 66.667 0.00 0.00 37.00 5.52
1184 1356 4.700365 GTTCGCCAACAAGCCGCC 62.700 66.667 0.00 0.00 32.14 6.13
1185 1357 4.947147 TTCGCCAACAAGCCGCCT 62.947 61.111 0.00 0.00 0.00 5.52
1186 1358 3.538785 TTCGCCAACAAGCCGCCTA 62.539 57.895 0.00 0.00 0.00 3.93
1200 1372 4.155733 CCTACCATGCCGACGCCA 62.156 66.667 0.00 0.00 0.00 5.69
1463 1636 1.949847 AAGGAGTGATGGAGGACGCG 61.950 60.000 3.53 3.53 0.00 6.01
1550 1723 1.818674 GACGAACCCATGCTTTTGGAT 59.181 47.619 0.00 0.00 39.25 3.41
1569 1742 3.371595 GGATATAGCAAGTGGTGGTGGTT 60.372 47.826 0.00 0.00 38.75 3.67
1697 1877 8.314751 CACTAGAATTTCATGGGGGTAGTATAG 58.685 40.741 0.00 0.00 0.00 1.31
1765 2003 5.679734 ATCCTTCGCTTGCATATGTTTAG 57.320 39.130 4.29 0.99 0.00 1.85
1769 2007 5.383984 TTCGCTTGCATATGTTTAGTACG 57.616 39.130 4.29 0.57 0.00 3.67
1770 2008 4.426416 TCGCTTGCATATGTTTAGTACGT 58.574 39.130 4.29 0.00 0.00 3.57
1771 2009 5.580661 TCGCTTGCATATGTTTAGTACGTA 58.419 37.500 4.29 0.00 32.93 3.57
1772 2010 5.456497 TCGCTTGCATATGTTTAGTACGTAC 59.544 40.000 18.10 18.10 31.22 3.67
1773 2011 5.457799 CGCTTGCATATGTTTAGTACGTACT 59.542 40.000 29.62 29.62 40.24 2.73
1774 2012 6.344780 CGCTTGCATATGTTTAGTACGTACTC 60.345 42.308 30.53 17.41 37.73 2.59
1775 2013 6.074463 GCTTGCATATGTTTAGTACGTACTCC 60.074 42.308 30.53 19.37 37.73 3.85
1776 2014 6.704289 TGCATATGTTTAGTACGTACTCCT 57.296 37.500 30.53 11.22 37.73 3.69
1777 2015 7.104043 TGCATATGTTTAGTACGTACTCCTT 57.896 36.000 30.53 18.51 37.73 3.36
1778 2016 7.198390 TGCATATGTTTAGTACGTACTCCTTC 58.802 38.462 30.53 18.77 37.73 3.46
1779 2017 6.640092 GCATATGTTTAGTACGTACTCCTTCC 59.360 42.308 30.53 15.51 37.73 3.46
1780 2018 4.685169 TGTTTAGTACGTACTCCTTCCG 57.315 45.455 30.53 0.00 37.73 4.30
1781 2019 4.072131 TGTTTAGTACGTACTCCTTCCGT 58.928 43.478 30.53 8.23 37.73 4.69
1782 2020 4.518970 TGTTTAGTACGTACTCCTTCCGTT 59.481 41.667 30.53 7.49 37.73 4.44
1783 2021 5.009610 TGTTTAGTACGTACTCCTTCCGTTT 59.990 40.000 30.53 6.75 37.73 3.60
1784 2022 3.839051 AGTACGTACTCCTTCCGTTTC 57.161 47.619 22.45 0.00 36.12 2.78
1785 2023 3.149196 AGTACGTACTCCTTCCGTTTCA 58.851 45.455 22.45 0.00 36.12 2.69
1786 2024 3.569701 AGTACGTACTCCTTCCGTTTCAA 59.430 43.478 22.45 0.00 36.12 2.69
1787 2025 3.457610 ACGTACTCCTTCCGTTTCAAA 57.542 42.857 0.00 0.00 0.00 2.69
1788 2026 3.795877 ACGTACTCCTTCCGTTTCAAAA 58.204 40.909 0.00 0.00 0.00 2.44
1789 2027 4.383173 ACGTACTCCTTCCGTTTCAAAAT 58.617 39.130 0.00 0.00 0.00 1.82
1790 2028 5.540911 ACGTACTCCTTCCGTTTCAAAATA 58.459 37.500 0.00 0.00 0.00 1.40
1791 2029 5.636543 ACGTACTCCTTCCGTTTCAAAATAG 59.363 40.000 0.00 0.00 0.00 1.73
1792 2030 5.865552 CGTACTCCTTCCGTTTCAAAATAGA 59.134 40.000 0.00 0.00 0.00 1.98
1793 2031 6.183360 CGTACTCCTTCCGTTTCAAAATAGAC 60.183 42.308 0.00 0.00 0.00 2.59
1794 2032 4.689345 ACTCCTTCCGTTTCAAAATAGACG 59.311 41.667 0.00 0.00 35.44 4.18
1795 2033 4.885413 TCCTTCCGTTTCAAAATAGACGA 58.115 39.130 0.00 0.00 37.69 4.20
1796 2034 4.687483 TCCTTCCGTTTCAAAATAGACGAC 59.313 41.667 0.00 0.00 37.69 4.34
1797 2035 4.142966 CCTTCCGTTTCAAAATAGACGACC 60.143 45.833 0.00 0.00 37.69 4.79
1798 2036 3.328505 TCCGTTTCAAAATAGACGACCC 58.671 45.455 0.00 0.00 37.69 4.46
1799 2037 3.068560 CCGTTTCAAAATAGACGACCCA 58.931 45.455 0.00 0.00 37.69 4.51
1800 2038 3.499157 CCGTTTCAAAATAGACGACCCAA 59.501 43.478 0.00 0.00 37.69 4.12
1801 2039 4.460505 CGTTTCAAAATAGACGACCCAAC 58.539 43.478 0.00 0.00 37.69 3.77
1802 2040 4.212636 CGTTTCAAAATAGACGACCCAACT 59.787 41.667 0.00 0.00 37.69 3.16
1803 2041 5.277634 CGTTTCAAAATAGACGACCCAACTT 60.278 40.000 0.00 0.00 37.69 2.66
1804 2042 6.500910 GTTTCAAAATAGACGACCCAACTTT 58.499 36.000 0.00 0.00 0.00 2.66
1805 2043 7.518689 CGTTTCAAAATAGACGACCCAACTTTA 60.519 37.037 0.00 0.00 37.69 1.85
1806 2044 7.989416 TTCAAAATAGACGACCCAACTTTAT 57.011 32.000 0.00 0.00 0.00 1.40
1807 2045 9.504708 TTTCAAAATAGACGACCCAACTTTATA 57.495 29.630 0.00 0.00 0.00 0.98
1808 2046 8.712285 TCAAAATAGACGACCCAACTTTATAG 57.288 34.615 0.00 0.00 0.00 1.31
1809 2047 8.533657 TCAAAATAGACGACCCAACTTTATAGA 58.466 33.333 0.00 0.00 0.00 1.98
1810 2048 8.818057 CAAAATAGACGACCCAACTTTATAGAG 58.182 37.037 0.00 0.00 0.00 2.43
1811 2049 7.657023 AATAGACGACCCAACTTTATAGAGT 57.343 36.000 0.00 0.00 0.00 3.24
1812 2050 5.579564 AGACGACCCAACTTTATAGAGTC 57.420 43.478 0.00 0.00 0.00 3.36
1813 2051 5.014858 AGACGACCCAACTTTATAGAGTCA 58.985 41.667 0.00 0.00 0.00 3.41
1814 2052 5.657302 AGACGACCCAACTTTATAGAGTCAT 59.343 40.000 0.00 0.00 0.00 3.06
1815 2053 5.903810 ACGACCCAACTTTATAGAGTCATC 58.096 41.667 0.00 0.00 0.00 2.92
1816 2054 5.657302 ACGACCCAACTTTATAGAGTCATCT 59.343 40.000 0.00 0.00 39.75 2.90
1817 2055 5.980116 CGACCCAACTTTATAGAGTCATCTG 59.020 44.000 0.00 0.00 36.96 2.90
1818 2056 6.405953 CGACCCAACTTTATAGAGTCATCTGT 60.406 42.308 0.00 0.00 36.96 3.41
1819 2057 7.259088 ACCCAACTTTATAGAGTCATCTGTT 57.741 36.000 0.00 0.00 36.96 3.16
1820 2058 7.690256 ACCCAACTTTATAGAGTCATCTGTTT 58.310 34.615 0.00 0.00 36.96 2.83
1821 2059 8.164070 ACCCAACTTTATAGAGTCATCTGTTTT 58.836 33.333 0.00 0.00 36.96 2.43
1822 2060 8.454106 CCCAACTTTATAGAGTCATCTGTTTTG 58.546 37.037 0.00 0.00 36.96 2.44
1823 2061 8.454106 CCAACTTTATAGAGTCATCTGTTTTGG 58.546 37.037 0.00 0.00 36.96 3.28
1824 2062 9.219603 CAACTTTATAGAGTCATCTGTTTTGGA 57.780 33.333 0.00 0.00 36.96 3.53
1825 2063 9.793259 AACTTTATAGAGTCATCTGTTTTGGAA 57.207 29.630 0.00 0.00 36.96 3.53
1826 2064 9.793259 ACTTTATAGAGTCATCTGTTTTGGAAA 57.207 29.630 0.00 0.00 36.96 3.13
1828 2066 8.792830 TTATAGAGTCATCTGTTTTGGAAAGG 57.207 34.615 0.00 0.00 36.96 3.11
1829 2067 5.310409 AGAGTCATCTGTTTTGGAAAGGA 57.690 39.130 0.00 0.00 33.30 3.36
1830 2068 5.312079 AGAGTCATCTGTTTTGGAAAGGAG 58.688 41.667 0.00 0.00 33.30 3.69
1831 2069 4.401925 AGTCATCTGTTTTGGAAAGGAGG 58.598 43.478 0.00 0.00 0.00 4.30
1832 2070 3.507622 GTCATCTGTTTTGGAAAGGAGGG 59.492 47.826 0.00 0.00 0.00 4.30
1836 2074 3.977999 TCTGTTTTGGAAAGGAGGGAGTA 59.022 43.478 0.00 0.00 0.00 2.59
1837 2075 4.072839 CTGTTTTGGAAAGGAGGGAGTAC 58.927 47.826 0.00 0.00 0.00 2.73
1963 2287 5.316770 GTTCAACGATTGTTCTAGTGATGC 58.683 41.667 0.00 0.00 35.72 3.91
1997 2321 4.887748 ACTACTAGGCGATTTGATCCATG 58.112 43.478 0.00 0.00 0.00 3.66
2043 2367 2.615493 CCTCCCACATTGTACTGTGTCC 60.615 54.545 12.67 0.00 44.04 4.02
2103 2427 2.239400 CTATCAGGGCGATGTACTGGA 58.761 52.381 0.00 0.00 35.39 3.86
2112 2436 3.485216 GGCGATGTACTGGAATGTTTTCG 60.485 47.826 0.00 0.00 32.28 3.46
2127 2451 5.694674 TGTTTTCGTGACTGAAATTTTGC 57.305 34.783 0.00 0.00 37.66 3.68
2137 2461 7.951565 CGTGACTGAAATTTTGCCATTTTATTC 59.048 33.333 0.00 0.00 0.00 1.75
2138 2462 8.772705 GTGACTGAAATTTTGCCATTTTATTCA 58.227 29.630 0.00 0.00 0.00 2.57
2139 2463 8.991026 TGACTGAAATTTTGCCATTTTATTCAG 58.009 29.630 9.84 9.84 44.87 3.02
2140 2464 8.326680 ACTGAAATTTTGCCATTTTATTCAGG 57.673 30.769 14.44 0.00 44.09 3.86
2141 2465 7.391275 ACTGAAATTTTGCCATTTTATTCAGGG 59.609 33.333 14.44 0.00 44.09 4.45
2142 2466 7.230027 TGAAATTTTGCCATTTTATTCAGGGT 58.770 30.769 0.00 0.00 0.00 4.34
2143 2467 7.174599 TGAAATTTTGCCATTTTATTCAGGGTG 59.825 33.333 0.00 0.00 0.00 4.61
2144 2468 5.559148 TTTTGCCATTTTATTCAGGGTGT 57.441 34.783 0.00 0.00 0.00 4.16
2145 2469 4.533919 TTGCCATTTTATTCAGGGTGTG 57.466 40.909 0.00 0.00 0.00 3.82
2146 2470 2.830923 TGCCATTTTATTCAGGGTGTGG 59.169 45.455 0.00 0.00 0.00 4.17
2147 2471 2.418609 GCCATTTTATTCAGGGTGTGGC 60.419 50.000 0.00 0.00 43.29 5.01
2148 2472 3.099141 CCATTTTATTCAGGGTGTGGCT 58.901 45.455 0.00 0.00 0.00 4.75
2149 2473 4.277476 CCATTTTATTCAGGGTGTGGCTA 58.723 43.478 0.00 0.00 0.00 3.93
2150 2474 4.339247 CCATTTTATTCAGGGTGTGGCTAG 59.661 45.833 0.00 0.00 0.00 3.42
2151 2475 4.919774 TTTTATTCAGGGTGTGGCTAGA 57.080 40.909 0.00 0.00 0.00 2.43
2152 2476 5.450818 TTTTATTCAGGGTGTGGCTAGAT 57.549 39.130 0.00 0.00 0.00 1.98
2153 2477 4.422073 TTATTCAGGGTGTGGCTAGATG 57.578 45.455 0.00 0.00 0.00 2.90
2154 2478 1.951209 TTCAGGGTGTGGCTAGATGA 58.049 50.000 0.00 0.00 0.00 2.92
2155 2479 1.489481 TCAGGGTGTGGCTAGATGAG 58.511 55.000 0.00 0.00 0.00 2.90
2156 2480 1.007118 TCAGGGTGTGGCTAGATGAGA 59.993 52.381 0.00 0.00 0.00 3.27
2157 2481 1.137872 CAGGGTGTGGCTAGATGAGAC 59.862 57.143 0.00 0.00 0.00 3.36
2158 2482 1.007721 AGGGTGTGGCTAGATGAGACT 59.992 52.381 0.00 0.00 32.36 3.24
2159 2483 1.834263 GGGTGTGGCTAGATGAGACTT 59.166 52.381 0.00 0.00 32.36 3.01
2160 2484 3.031736 GGGTGTGGCTAGATGAGACTTA 58.968 50.000 0.00 0.00 32.36 2.24
2161 2485 3.451178 GGGTGTGGCTAGATGAGACTTAA 59.549 47.826 0.00 0.00 32.36 1.85
2162 2486 4.434520 GGTGTGGCTAGATGAGACTTAAC 58.565 47.826 0.00 0.00 32.36 2.01
2163 2487 4.081642 GGTGTGGCTAGATGAGACTTAACA 60.082 45.833 0.00 0.00 32.36 2.41
2164 2488 5.479306 GTGTGGCTAGATGAGACTTAACAA 58.521 41.667 0.00 0.00 32.36 2.83
2165 2489 5.932303 GTGTGGCTAGATGAGACTTAACAAA 59.068 40.000 0.00 0.00 32.36 2.83
2166 2490 6.091441 GTGTGGCTAGATGAGACTTAACAAAG 59.909 42.308 0.00 0.00 32.36 2.77
2167 2491 6.166982 GTGGCTAGATGAGACTTAACAAAGT 58.833 40.000 0.00 0.00 32.36 2.66
2168 2492 6.651225 GTGGCTAGATGAGACTTAACAAAGTT 59.349 38.462 0.00 0.00 32.36 2.66
2169 2493 7.173390 GTGGCTAGATGAGACTTAACAAAGTTT 59.827 37.037 0.00 0.00 32.36 2.66
2170 2494 7.387948 TGGCTAGATGAGACTTAACAAAGTTTC 59.612 37.037 0.00 2.73 35.26 2.78
2171 2495 7.387948 GGCTAGATGAGACTTAACAAAGTTTCA 59.612 37.037 12.21 12.21 44.52 2.69
2172 2496 8.439286 GCTAGATGAGACTTAACAAAGTTTCAG 58.561 37.037 14.36 5.17 43.94 3.02
2173 2497 7.195839 AGATGAGACTTAACAAAGTTTCAGC 57.804 36.000 15.27 15.27 45.16 4.26
2174 2498 5.751243 TGAGACTTAACAAAGTTTCAGCC 57.249 39.130 7.24 0.00 38.49 4.85
2175 2499 5.189928 TGAGACTTAACAAAGTTTCAGCCA 58.810 37.500 7.24 0.00 38.49 4.75
2176 2500 5.650266 TGAGACTTAACAAAGTTTCAGCCAA 59.350 36.000 7.24 0.00 38.49 4.52
2177 2501 6.136541 AGACTTAACAAAGTTTCAGCCAAG 57.863 37.500 0.00 0.00 32.22 3.61
2178 2502 5.652452 AGACTTAACAAAGTTTCAGCCAAGT 59.348 36.000 0.00 0.00 32.22 3.16
2179 2503 5.650543 ACTTAACAAAGTTTCAGCCAAGTG 58.349 37.500 0.00 0.00 0.00 3.16
2180 2504 5.417580 ACTTAACAAAGTTTCAGCCAAGTGA 59.582 36.000 0.00 0.00 0.00 3.41
2181 2505 6.096846 ACTTAACAAAGTTTCAGCCAAGTGAT 59.903 34.615 0.00 0.00 0.00 3.06
2182 2506 7.284489 ACTTAACAAAGTTTCAGCCAAGTGATA 59.716 33.333 0.00 0.00 0.00 2.15
2183 2507 5.695851 ACAAAGTTTCAGCCAAGTGATAG 57.304 39.130 0.00 0.00 0.00 2.08
2184 2508 5.376625 ACAAAGTTTCAGCCAAGTGATAGA 58.623 37.500 0.00 0.00 0.00 1.98
2185 2509 5.827797 ACAAAGTTTCAGCCAAGTGATAGAA 59.172 36.000 0.00 0.00 0.00 2.10
2186 2510 5.948992 AAGTTTCAGCCAAGTGATAGAAC 57.051 39.130 0.00 0.00 0.00 3.01
2187 2511 4.973168 AGTTTCAGCCAAGTGATAGAACA 58.027 39.130 0.00 0.00 0.00 3.18
2188 2512 5.564550 AGTTTCAGCCAAGTGATAGAACAT 58.435 37.500 0.00 0.00 0.00 2.71
2189 2513 6.711277 AGTTTCAGCCAAGTGATAGAACATA 58.289 36.000 0.00 0.00 0.00 2.29
2190 2514 7.341805 AGTTTCAGCCAAGTGATAGAACATAT 58.658 34.615 0.00 0.00 0.00 1.78
2191 2515 8.486210 AGTTTCAGCCAAGTGATAGAACATATA 58.514 33.333 0.00 0.00 0.00 0.86
2192 2516 9.109393 GTTTCAGCCAAGTGATAGAACATATAA 57.891 33.333 0.00 0.00 0.00 0.98
2193 2517 9.679661 TTTCAGCCAAGTGATAGAACATATAAA 57.320 29.630 0.00 0.00 0.00 1.40
2194 2518 9.679661 TTCAGCCAAGTGATAGAACATATAAAA 57.320 29.630 0.00 0.00 0.00 1.52
2195 2519 9.330063 TCAGCCAAGTGATAGAACATATAAAAG 57.670 33.333 0.00 0.00 0.00 2.27
2196 2520 8.562892 CAGCCAAGTGATAGAACATATAAAAGG 58.437 37.037 0.00 0.00 0.00 3.11
2197 2521 8.494433 AGCCAAGTGATAGAACATATAAAAGGA 58.506 33.333 0.00 0.00 0.00 3.36
2198 2522 9.120538 GCCAAGTGATAGAACATATAAAAGGAA 57.879 33.333 0.00 0.00 0.00 3.36
2237 2561 9.902196 TTTAAAGAAAATTTTACACGGATCTCC 57.098 29.630 2.75 0.00 0.00 3.71
2238 2562 7.519032 AAAGAAAATTTTACACGGATCTCCA 57.481 32.000 2.75 0.00 35.14 3.86
2239 2563 6.496338 AGAAAATTTTACACGGATCTCCAC 57.504 37.500 2.75 0.00 35.14 4.02
2240 2564 6.001460 AGAAAATTTTACACGGATCTCCACA 58.999 36.000 2.75 0.00 35.14 4.17
2241 2565 5.622770 AAATTTTACACGGATCTCCACAC 57.377 39.130 0.00 0.00 35.14 3.82
2242 2566 3.755112 TTTTACACGGATCTCCACACA 57.245 42.857 0.00 0.00 35.14 3.72
2243 2567 3.755112 TTTACACGGATCTCCACACAA 57.245 42.857 0.00 0.00 35.14 3.33
2244 2568 3.313012 TTACACGGATCTCCACACAAG 57.687 47.619 0.00 0.00 35.14 3.16
2245 2569 1.338107 ACACGGATCTCCACACAAGA 58.662 50.000 0.00 0.00 35.14 3.02
2246 2570 1.902508 ACACGGATCTCCACACAAGAT 59.097 47.619 0.00 0.00 36.19 2.40
2247 2571 2.093973 ACACGGATCTCCACACAAGATC 60.094 50.000 4.85 4.85 45.54 2.75
2248 2572 2.167281 CACGGATCTCCACACAAGATCT 59.833 50.000 11.66 0.00 45.56 2.75
2249 2573 3.381590 CACGGATCTCCACACAAGATCTA 59.618 47.826 11.66 0.00 45.56 1.98
2250 2574 4.023980 ACGGATCTCCACACAAGATCTAA 58.976 43.478 11.66 0.00 45.56 2.10
2251 2575 4.142138 ACGGATCTCCACACAAGATCTAAC 60.142 45.833 11.66 0.00 45.56 2.34
2252 2576 4.363999 GGATCTCCACACAAGATCTAACG 58.636 47.826 11.66 0.00 45.56 3.18
2253 2577 4.098044 GGATCTCCACACAAGATCTAACGA 59.902 45.833 11.66 0.00 45.56 3.85
2254 2578 5.394224 GGATCTCCACACAAGATCTAACGAA 60.394 44.000 11.66 0.00 45.56 3.85
2255 2579 5.661056 TCTCCACACAAGATCTAACGAAT 57.339 39.130 0.00 0.00 0.00 3.34
2256 2580 6.769134 TCTCCACACAAGATCTAACGAATA 57.231 37.500 0.00 0.00 0.00 1.75
2257 2581 7.348080 TCTCCACACAAGATCTAACGAATAT 57.652 36.000 0.00 0.00 0.00 1.28
2258 2582 7.203218 TCTCCACACAAGATCTAACGAATATG 58.797 38.462 0.00 0.00 0.00 1.78
2259 2583 6.280643 TCCACACAAGATCTAACGAATATGG 58.719 40.000 0.00 0.00 0.00 2.74
2260 2584 5.050091 CCACACAAGATCTAACGAATATGGC 60.050 44.000 0.00 0.00 0.00 4.40
2261 2585 5.523552 CACACAAGATCTAACGAATATGGCA 59.476 40.000 0.00 0.00 0.00 4.92
2262 2586 6.203530 CACACAAGATCTAACGAATATGGCAT 59.796 38.462 4.88 4.88 0.00 4.40
2263 2587 6.425114 ACACAAGATCTAACGAATATGGCATC 59.575 38.462 1.65 0.00 0.00 3.91
2264 2588 5.635280 ACAAGATCTAACGAATATGGCATCG 59.365 40.000 1.65 5.15 44.33 3.84
2265 2589 5.644977 AGATCTAACGAATATGGCATCGA 57.355 39.130 15.19 0.00 41.43 3.59
2266 2590 5.645624 AGATCTAACGAATATGGCATCGAG 58.354 41.667 15.19 4.06 41.43 4.04
2267 2591 4.848562 TCTAACGAATATGGCATCGAGT 57.151 40.909 15.19 4.27 41.43 4.18
2268 2592 4.546570 TCTAACGAATATGGCATCGAGTG 58.453 43.478 15.19 5.16 41.43 3.51
2269 2593 3.452755 AACGAATATGGCATCGAGTGA 57.547 42.857 15.19 0.00 41.43 3.41
2270 2594 3.018598 ACGAATATGGCATCGAGTGAG 57.981 47.619 15.19 0.21 41.43 3.51
2271 2595 2.623416 ACGAATATGGCATCGAGTGAGA 59.377 45.455 15.19 0.00 41.43 3.27
2272 2596 2.983136 CGAATATGGCATCGAGTGAGAC 59.017 50.000 1.65 0.00 41.43 3.36
2273 2597 3.304996 CGAATATGGCATCGAGTGAGACT 60.305 47.826 1.65 0.00 41.43 3.24
2274 2598 4.626042 GAATATGGCATCGAGTGAGACTT 58.374 43.478 1.65 0.00 0.00 3.01
2275 2599 5.562890 CGAATATGGCATCGAGTGAGACTTA 60.563 44.000 1.65 0.00 41.43 2.24
2276 2600 5.791336 ATATGGCATCGAGTGAGACTTAA 57.209 39.130 1.65 0.00 0.00 1.85
2277 2601 4.679373 ATGGCATCGAGTGAGACTTAAT 57.321 40.909 0.00 0.00 0.00 1.40
2278 2602 3.785486 TGGCATCGAGTGAGACTTAATG 58.215 45.455 0.00 0.00 0.00 1.90
2279 2603 3.447229 TGGCATCGAGTGAGACTTAATGA 59.553 43.478 0.00 0.00 0.00 2.57
2280 2604 4.081697 TGGCATCGAGTGAGACTTAATGAA 60.082 41.667 0.00 0.00 0.00 2.57
2281 2605 4.505922 GGCATCGAGTGAGACTTAATGAAG 59.494 45.833 0.00 0.00 38.76 3.02
2293 2617 5.968528 ACTTAATGAAGTCTCAGTCGACT 57.031 39.130 13.58 13.58 42.50 4.18
2294 2618 5.704888 ACTTAATGAAGTCTCAGTCGACTG 58.295 41.667 34.76 34.76 42.50 3.51
2295 2619 5.473846 ACTTAATGAAGTCTCAGTCGACTGA 59.526 40.000 38.24 38.24 45.19 3.41
2307 2631 5.633996 CAGTCGACTGAGATTTAGCAATC 57.366 43.478 36.73 0.00 46.59 2.67
2329 2653 9.123902 CAATCTTGTTTTATCCATGATGAGGTA 57.876 33.333 0.00 0.00 29.98 3.08
2423 2747 5.622914 GCACACCATTATGCATTTCTCAAGT 60.623 40.000 3.54 0.00 41.65 3.16
2424 2748 6.032094 CACACCATTATGCATTTCTCAAGTC 58.968 40.000 3.54 0.00 0.00 3.01
2425 2749 5.711506 ACACCATTATGCATTTCTCAAGTCA 59.288 36.000 3.54 0.00 0.00 3.41
2426 2750 6.209192 ACACCATTATGCATTTCTCAAGTCAA 59.791 34.615 3.54 0.00 0.00 3.18
2427 2751 6.750501 CACCATTATGCATTTCTCAAGTCAAG 59.249 38.462 3.54 0.00 0.00 3.02
2443 2767 6.094048 TCAAGTCAAGGAAACAAAAGAGTGAG 59.906 38.462 0.00 0.00 0.00 3.51
2446 2770 5.354234 GTCAAGGAAACAAAAGAGTGAGACA 59.646 40.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.498481 GCCCATGTAGATTAGCCCATGAA 60.498 47.826 0.00 0.00 37.47 2.57
37 38 2.247358 CCCCACAATTATGTATGCCCC 58.753 52.381 0.00 0.00 37.82 5.80
49 50 0.345502 TAGGAGGTAGGCCCCACAAT 59.654 55.000 0.00 0.00 34.57 2.71
92 93 1.115467 CTCATTGGGGAGTACTCGCT 58.885 55.000 31.60 15.31 41.61 4.93
94 95 0.105039 GGCTCATTGGGGAGTACTCG 59.895 60.000 16.56 1.97 37.24 4.18
173 174 1.048601 GAACATGGGGAGGCGATAGA 58.951 55.000 0.00 0.00 39.76 1.98
183 184 4.636249 GCATACTAAGAGAGAACATGGGG 58.364 47.826 0.00 0.00 0.00 4.96
230 235 1.725973 GCGAAGTTTGCTTCCACGC 60.726 57.895 7.92 0.00 46.24 5.34
285 290 4.344968 TCGATGTTGACCCAGTATGATGAT 59.655 41.667 0.00 0.00 39.69 2.45
286 291 3.704061 TCGATGTTGACCCAGTATGATGA 59.296 43.478 0.00 0.00 39.69 2.92
287 292 4.058721 TCGATGTTGACCCAGTATGATG 57.941 45.455 0.00 0.00 39.69 3.07
288 293 4.963318 ATCGATGTTGACCCAGTATGAT 57.037 40.909 0.00 0.00 39.69 2.45
295 300 3.201045 TCCCAATAATCGATGTTGACCCA 59.799 43.478 19.73 3.87 0.00 4.51
347 352 4.222114 CAATCGTCTGCTCCTTTGTTTTC 58.778 43.478 0.00 0.00 0.00 2.29
380 385 0.532862 GGTGATGGGATAGTGTGGCG 60.533 60.000 0.00 0.00 0.00 5.69
407 413 1.464608 CAACGGTTCGATGACTTGCAT 59.535 47.619 0.00 0.00 40.77 3.96
419 425 1.083847 GACGCAACGACAACGGTTC 60.084 57.895 0.00 0.00 44.46 3.62
420 426 2.862776 CGACGCAACGACAACGGTT 61.863 57.895 0.00 0.00 44.46 4.44
423 429 3.978764 TGCGACGCAACGACAACG 61.979 61.111 22.24 0.00 38.50 4.10
440 446 4.961585 AGTTCTCCCATTACTTCCTAGGT 58.038 43.478 9.08 0.00 0.00 3.08
444 450 6.455690 AAGAAAGTTCTCCCATTACTTCCT 57.544 37.500 0.00 0.00 36.28 3.36
445 451 6.715264 TCAAAGAAAGTTCTCCCATTACTTCC 59.285 38.462 0.00 0.00 36.28 3.46
448 454 5.701290 CGTCAAAGAAAGTTCTCCCATTACT 59.299 40.000 0.00 0.00 36.28 2.24
455 461 3.963383 TTGCGTCAAAGAAAGTTCTCC 57.037 42.857 0.00 0.00 36.28 3.71
497 503 5.689068 GCAGTAATTAGCTCATTCAATTGCC 59.311 40.000 0.00 0.00 0.00 4.52
596 750 5.163447 GGTAATTAATGGTTCTGGAAAGGCC 60.163 44.000 0.00 0.00 37.10 5.19
656 810 6.106673 CCATCGGGTAGGCTATAAATAACAG 58.893 44.000 0.00 0.00 0.00 3.16
670 824 3.813596 GCAGTTGCCATCGGGTAG 58.186 61.111 0.00 0.00 36.17 3.18
807 961 3.927163 GAGAAGGCGCCGAACGGAA 62.927 63.158 23.20 0.00 43.93 4.30
809 963 4.436998 AGAGAAGGCGCCGAACGG 62.437 66.667 23.20 9.00 43.93 4.44
845 999 1.178276 CTGGAGAGCAAGTCCGTACT 58.822 55.000 0.00 0.00 36.82 2.73
853 1007 2.045536 GGCCCACTGGAGAGCAAG 60.046 66.667 0.00 0.00 0.00 4.01
1184 1356 2.890474 GTGGCGTCGGCATGGTAG 60.890 66.667 25.14 0.00 40.92 3.18
1185 1357 4.460683 GGTGGCGTCGGCATGGTA 62.461 66.667 25.14 0.00 40.92 3.25
1338 1510 4.051167 TACCTCCTCGCGGGGTCA 62.051 66.667 27.35 5.35 35.97 4.02
1427 1599 0.533755 CTTAATCCGGAGCCAGCAGG 60.534 60.000 11.34 0.00 38.23 4.85
1535 1708 4.183223 TGCTATATCCAAAAGCATGGGT 57.817 40.909 0.00 0.00 41.15 4.51
1550 1723 2.373836 ACAACCACCACCACTTGCTATA 59.626 45.455 0.00 0.00 0.00 1.31
1569 1742 2.554344 GGATCTGGGCAAAGTAACCACA 60.554 50.000 0.00 0.00 0.00 4.17
1619 1792 9.284594 TGAAATTCTTAAAACGAAACAACTGAG 57.715 29.630 0.00 0.00 0.00 3.35
1620 1793 9.796120 ATGAAATTCTTAAAACGAAACAACTGA 57.204 25.926 0.00 0.00 0.00 3.41
1621 1794 9.833894 CATGAAATTCTTAAAACGAAACAACTG 57.166 29.630 0.00 0.00 0.00 3.16
1659 1832 2.273370 TTCTAGTGCCGCTAGTTTCG 57.727 50.000 11.83 0.00 45.65 3.46
1697 1877 7.068692 AGCATACTCGGTACATGTTAAAAAC 57.931 36.000 2.30 0.00 0.00 2.43
1765 2003 3.559238 TGAAACGGAAGGAGTACGTAC 57.441 47.619 18.10 18.10 40.31 3.67
1769 2007 6.183360 CGTCTATTTTGAAACGGAAGGAGTAC 60.183 42.308 0.00 0.00 0.00 2.73
1770 2008 5.865552 CGTCTATTTTGAAACGGAAGGAGTA 59.134 40.000 0.00 0.00 0.00 2.59
1771 2009 4.689345 CGTCTATTTTGAAACGGAAGGAGT 59.311 41.667 0.00 0.00 0.00 3.85
1772 2010 4.927425 TCGTCTATTTTGAAACGGAAGGAG 59.073 41.667 0.00 0.00 35.89 3.69
1773 2011 4.687483 GTCGTCTATTTTGAAACGGAAGGA 59.313 41.667 0.00 0.00 35.89 3.36
1774 2012 4.142966 GGTCGTCTATTTTGAAACGGAAGG 60.143 45.833 0.00 0.00 35.89 3.46
1775 2013 4.142966 GGGTCGTCTATTTTGAAACGGAAG 60.143 45.833 0.00 0.00 35.89 3.46
1776 2014 3.747529 GGGTCGTCTATTTTGAAACGGAA 59.252 43.478 0.00 0.00 35.89 4.30
1777 2015 3.244146 TGGGTCGTCTATTTTGAAACGGA 60.244 43.478 0.00 0.00 35.89 4.69
1778 2016 3.068560 TGGGTCGTCTATTTTGAAACGG 58.931 45.455 0.00 0.00 35.89 4.44
1779 2017 4.212636 AGTTGGGTCGTCTATTTTGAAACG 59.787 41.667 0.00 0.00 36.50 3.60
1780 2018 5.684550 AGTTGGGTCGTCTATTTTGAAAC 57.315 39.130 0.00 0.00 0.00 2.78
1781 2019 6.702716 AAAGTTGGGTCGTCTATTTTGAAA 57.297 33.333 0.00 0.00 0.00 2.69
1782 2020 7.989416 ATAAAGTTGGGTCGTCTATTTTGAA 57.011 32.000 0.00 0.00 0.00 2.69
1783 2021 8.533657 TCTATAAAGTTGGGTCGTCTATTTTGA 58.466 33.333 0.00 0.00 0.00 2.69
1784 2022 8.712285 TCTATAAAGTTGGGTCGTCTATTTTG 57.288 34.615 0.00 0.00 0.00 2.44
1785 2023 8.537858 ACTCTATAAAGTTGGGTCGTCTATTTT 58.462 33.333 0.00 0.00 0.00 1.82
1786 2024 8.075761 ACTCTATAAAGTTGGGTCGTCTATTT 57.924 34.615 0.00 0.00 0.00 1.40
1787 2025 7.341256 TGACTCTATAAAGTTGGGTCGTCTATT 59.659 37.037 0.00 0.00 0.00 1.73
1788 2026 6.832384 TGACTCTATAAAGTTGGGTCGTCTAT 59.168 38.462 0.00 0.00 0.00 1.98
1789 2027 6.182627 TGACTCTATAAAGTTGGGTCGTCTA 58.817 40.000 0.00 0.00 0.00 2.59
1790 2028 5.014858 TGACTCTATAAAGTTGGGTCGTCT 58.985 41.667 0.00 0.00 0.00 4.18
1791 2029 5.320549 TGACTCTATAAAGTTGGGTCGTC 57.679 43.478 0.00 0.00 0.00 4.20
1792 2030 5.657302 AGATGACTCTATAAAGTTGGGTCGT 59.343 40.000 0.00 0.00 0.00 4.34
1793 2031 5.980116 CAGATGACTCTATAAAGTTGGGTCG 59.020 44.000 0.00 0.00 0.00 4.79
1794 2032 6.879400 ACAGATGACTCTATAAAGTTGGGTC 58.121 40.000 0.00 0.00 0.00 4.46
1795 2033 6.875972 ACAGATGACTCTATAAAGTTGGGT 57.124 37.500 0.00 0.00 0.00 4.51
1796 2034 8.454106 CAAAACAGATGACTCTATAAAGTTGGG 58.546 37.037 0.00 0.00 0.00 4.12
1797 2035 8.454106 CCAAAACAGATGACTCTATAAAGTTGG 58.546 37.037 0.00 0.00 0.00 3.77
1798 2036 9.219603 TCCAAAACAGATGACTCTATAAAGTTG 57.780 33.333 0.00 0.00 0.00 3.16
1799 2037 9.793259 TTCCAAAACAGATGACTCTATAAAGTT 57.207 29.630 0.00 0.00 0.00 2.66
1800 2038 9.793259 TTTCCAAAACAGATGACTCTATAAAGT 57.207 29.630 0.00 0.00 0.00 2.66
1802 2040 9.231297 CCTTTCCAAAACAGATGACTCTATAAA 57.769 33.333 0.00 0.00 0.00 1.40
1803 2041 8.602424 TCCTTTCCAAAACAGATGACTCTATAA 58.398 33.333 0.00 0.00 0.00 0.98
1804 2042 8.146053 TCCTTTCCAAAACAGATGACTCTATA 57.854 34.615 0.00 0.00 0.00 1.31
1805 2043 7.020827 TCCTTTCCAAAACAGATGACTCTAT 57.979 36.000 0.00 0.00 0.00 1.98
1806 2044 6.433847 TCCTTTCCAAAACAGATGACTCTA 57.566 37.500 0.00 0.00 0.00 2.43
1807 2045 5.310409 TCCTTTCCAAAACAGATGACTCT 57.690 39.130 0.00 0.00 0.00 3.24
1808 2046 4.457257 CCTCCTTTCCAAAACAGATGACTC 59.543 45.833 0.00 0.00 0.00 3.36
1809 2047 4.401925 CCTCCTTTCCAAAACAGATGACT 58.598 43.478 0.00 0.00 0.00 3.41
1810 2048 3.507622 CCCTCCTTTCCAAAACAGATGAC 59.492 47.826 0.00 0.00 0.00 3.06
1811 2049 3.397618 TCCCTCCTTTCCAAAACAGATGA 59.602 43.478 0.00 0.00 0.00 2.92
1812 2050 3.760684 CTCCCTCCTTTCCAAAACAGATG 59.239 47.826 0.00 0.00 0.00 2.90
1813 2051 3.399305 ACTCCCTCCTTTCCAAAACAGAT 59.601 43.478 0.00 0.00 0.00 2.90
1814 2052 2.783510 ACTCCCTCCTTTCCAAAACAGA 59.216 45.455 0.00 0.00 0.00 3.41
1815 2053 3.229697 ACTCCCTCCTTTCCAAAACAG 57.770 47.619 0.00 0.00 0.00 3.16
1816 2054 3.460340 TGTACTCCCTCCTTTCCAAAACA 59.540 43.478 0.00 0.00 0.00 2.83
1817 2055 4.094830 TGTACTCCCTCCTTTCCAAAAC 57.905 45.455 0.00 0.00 0.00 2.43
1818 2056 4.799715 TTGTACTCCCTCCTTTCCAAAA 57.200 40.909 0.00 0.00 0.00 2.44
1819 2057 5.333566 AATTGTACTCCCTCCTTTCCAAA 57.666 39.130 0.00 0.00 0.00 3.28
1820 2058 5.333566 AAATTGTACTCCCTCCTTTCCAA 57.666 39.130 0.00 0.00 0.00 3.53
1821 2059 5.333566 AAAATTGTACTCCCTCCTTTCCA 57.666 39.130 0.00 0.00 0.00 3.53
1822 2060 6.946583 AGTTAAAATTGTACTCCCTCCTTTCC 59.053 38.462 0.00 0.00 0.00 3.13
1823 2061 7.997773 AGTTAAAATTGTACTCCCTCCTTTC 57.002 36.000 0.00 0.00 0.00 2.62
1824 2062 8.442374 TGTAGTTAAAATTGTACTCCCTCCTTT 58.558 33.333 0.00 0.00 0.00 3.11
1825 2063 7.981142 TGTAGTTAAAATTGTACTCCCTCCTT 58.019 34.615 0.00 0.00 0.00 3.36
1826 2064 7.563724 TGTAGTTAAAATTGTACTCCCTCCT 57.436 36.000 0.00 0.00 0.00 3.69
1827 2065 8.803397 AATGTAGTTAAAATTGTACTCCCTCC 57.197 34.615 0.00 0.00 0.00 4.30
1832 2070 9.968743 CGGAGAAATGTAGTTAAAATTGTACTC 57.031 33.333 0.00 0.00 0.00 2.59
1836 2074 8.842358 TCTCGGAGAAATGTAGTTAAAATTGT 57.158 30.769 4.96 0.00 34.09 2.71
1963 2287 8.976986 AATCGCCTAGTAGTAATTAATAACGG 57.023 34.615 0.00 0.00 0.00 4.44
1997 2321 2.350772 CGGTGCAAAATCAGAGTTGGAC 60.351 50.000 11.02 11.02 43.14 4.02
2043 2367 1.210478 ACCAGATGAAGGGACAATCGG 59.790 52.381 0.00 0.00 0.00 4.18
2103 2427 6.238076 GGCAAAATTTCAGTCACGAAAACATT 60.238 34.615 0.00 0.00 38.33 2.71
2112 2436 8.772705 TGAATAAAATGGCAAAATTTCAGTCAC 58.227 29.630 0.00 0.00 0.00 3.67
2127 2451 3.099141 AGCCACACCCTGAATAAAATGG 58.901 45.455 0.00 0.00 0.00 3.16
2137 2461 1.137872 GTCTCATCTAGCCACACCCTG 59.862 57.143 0.00 0.00 0.00 4.45
2138 2462 1.007721 AGTCTCATCTAGCCACACCCT 59.992 52.381 0.00 0.00 0.00 4.34
2139 2463 1.490574 AGTCTCATCTAGCCACACCC 58.509 55.000 0.00 0.00 0.00 4.61
2140 2464 4.081642 TGTTAAGTCTCATCTAGCCACACC 60.082 45.833 0.00 0.00 0.00 4.16
2141 2465 5.073311 TGTTAAGTCTCATCTAGCCACAC 57.927 43.478 0.00 0.00 0.00 3.82
2142 2466 5.738619 TTGTTAAGTCTCATCTAGCCACA 57.261 39.130 0.00 0.00 0.00 4.17
2143 2467 6.166982 ACTTTGTTAAGTCTCATCTAGCCAC 58.833 40.000 0.00 0.00 40.60 5.01
2144 2468 6.360370 ACTTTGTTAAGTCTCATCTAGCCA 57.640 37.500 0.00 0.00 40.60 4.75
2145 2469 7.387948 TGAAACTTTGTTAAGTCTCATCTAGCC 59.612 37.037 0.00 0.00 43.74 3.93
2146 2470 8.311650 TGAAACTTTGTTAAGTCTCATCTAGC 57.688 34.615 0.00 0.00 43.74 3.42
2147 2471 8.439286 GCTGAAACTTTGTTAAGTCTCATCTAG 58.561 37.037 0.00 0.00 43.74 2.43
2148 2472 7.387948 GGCTGAAACTTTGTTAAGTCTCATCTA 59.612 37.037 0.00 0.00 43.74 1.98
2149 2473 6.205658 GGCTGAAACTTTGTTAAGTCTCATCT 59.794 38.462 0.00 0.00 43.74 2.90
2150 2474 6.017109 TGGCTGAAACTTTGTTAAGTCTCATC 60.017 38.462 0.00 0.00 43.74 2.92
2151 2475 5.827797 TGGCTGAAACTTTGTTAAGTCTCAT 59.172 36.000 0.00 0.00 43.74 2.90
2152 2476 5.189928 TGGCTGAAACTTTGTTAAGTCTCA 58.810 37.500 0.00 0.00 43.74 3.27
2153 2477 5.751243 TGGCTGAAACTTTGTTAAGTCTC 57.249 39.130 0.00 0.00 43.74 3.36
2154 2478 5.652452 ACTTGGCTGAAACTTTGTTAAGTCT 59.348 36.000 0.00 0.00 43.74 3.24
2155 2479 5.743872 CACTTGGCTGAAACTTTGTTAAGTC 59.256 40.000 0.00 0.00 43.74 3.01
2156 2480 5.417580 TCACTTGGCTGAAACTTTGTTAAGT 59.582 36.000 0.00 0.00 46.44 2.24
2157 2481 5.890334 TCACTTGGCTGAAACTTTGTTAAG 58.110 37.500 0.00 0.00 37.40 1.85
2158 2482 5.906113 TCACTTGGCTGAAACTTTGTTAA 57.094 34.783 0.00 0.00 0.00 2.01
2159 2483 6.995686 TCTATCACTTGGCTGAAACTTTGTTA 59.004 34.615 0.00 0.00 0.00 2.41
2160 2484 5.827797 TCTATCACTTGGCTGAAACTTTGTT 59.172 36.000 0.00 0.00 0.00 2.83
2161 2485 5.376625 TCTATCACTTGGCTGAAACTTTGT 58.623 37.500 0.00 0.00 0.00 2.83
2162 2486 5.947228 TCTATCACTTGGCTGAAACTTTG 57.053 39.130 0.00 0.00 0.00 2.77
2163 2487 5.827797 TGTTCTATCACTTGGCTGAAACTTT 59.172 36.000 0.00 0.00 0.00 2.66
2164 2488 5.376625 TGTTCTATCACTTGGCTGAAACTT 58.623 37.500 0.00 0.00 0.00 2.66
2165 2489 4.973168 TGTTCTATCACTTGGCTGAAACT 58.027 39.130 0.00 0.00 0.00 2.66
2166 2490 5.886960 ATGTTCTATCACTTGGCTGAAAC 57.113 39.130 0.00 0.00 0.00 2.78
2167 2491 9.679661 TTTATATGTTCTATCACTTGGCTGAAA 57.320 29.630 0.00 0.00 0.00 2.69
2168 2492 9.679661 TTTTATATGTTCTATCACTTGGCTGAA 57.320 29.630 0.00 0.00 0.00 3.02
2169 2493 9.330063 CTTTTATATGTTCTATCACTTGGCTGA 57.670 33.333 0.00 0.00 0.00 4.26
2170 2494 8.562892 CCTTTTATATGTTCTATCACTTGGCTG 58.437 37.037 0.00 0.00 0.00 4.85
2171 2495 8.494433 TCCTTTTATATGTTCTATCACTTGGCT 58.506 33.333 0.00 0.00 0.00 4.75
2172 2496 8.677148 TCCTTTTATATGTTCTATCACTTGGC 57.323 34.615 0.00 0.00 0.00 4.52
2211 2535 9.902196 GGAGATCCGTGTAAAATTTTCTTTAAA 57.098 29.630 6.72 0.00 0.00 1.52
2212 2536 9.069082 TGGAGATCCGTGTAAAATTTTCTTTAA 57.931 29.630 6.72 0.00 39.43 1.52
2213 2537 8.508875 GTGGAGATCCGTGTAAAATTTTCTTTA 58.491 33.333 6.72 0.00 39.43 1.85
2214 2538 7.013846 TGTGGAGATCCGTGTAAAATTTTCTTT 59.986 33.333 6.72 0.00 39.43 2.52
2215 2539 6.488683 TGTGGAGATCCGTGTAAAATTTTCTT 59.511 34.615 6.72 0.00 39.43 2.52
2216 2540 6.001460 TGTGGAGATCCGTGTAAAATTTTCT 58.999 36.000 6.72 0.00 39.43 2.52
2217 2541 6.084277 GTGTGGAGATCCGTGTAAAATTTTC 58.916 40.000 6.72 0.37 39.43 2.29
2218 2542 5.533154 TGTGTGGAGATCCGTGTAAAATTTT 59.467 36.000 8.75 8.75 39.43 1.82
2219 2543 5.067273 TGTGTGGAGATCCGTGTAAAATTT 58.933 37.500 0.00 0.00 39.43 1.82
2220 2544 4.647611 TGTGTGGAGATCCGTGTAAAATT 58.352 39.130 0.00 0.00 39.43 1.82
2221 2545 4.280436 TGTGTGGAGATCCGTGTAAAAT 57.720 40.909 0.00 0.00 39.43 1.82
2222 2546 3.755112 TGTGTGGAGATCCGTGTAAAA 57.245 42.857 0.00 0.00 39.43 1.52
2223 2547 3.322541 TCTTGTGTGGAGATCCGTGTAAA 59.677 43.478 0.00 0.00 39.43 2.01
2224 2548 2.894765 TCTTGTGTGGAGATCCGTGTAA 59.105 45.455 0.00 0.00 39.43 2.41
2225 2549 2.521126 TCTTGTGTGGAGATCCGTGTA 58.479 47.619 0.00 0.00 39.43 2.90
2226 2550 1.338107 TCTTGTGTGGAGATCCGTGT 58.662 50.000 0.00 0.00 39.43 4.49
2227 2551 2.167281 AGATCTTGTGTGGAGATCCGTG 59.833 50.000 9.76 0.00 46.88 4.94
2228 2552 2.461695 AGATCTTGTGTGGAGATCCGT 58.538 47.619 9.76 0.00 46.88 4.69
2229 2553 4.363999 GTTAGATCTTGTGTGGAGATCCG 58.636 47.826 0.00 0.00 46.88 4.18
2230 2554 4.098044 TCGTTAGATCTTGTGTGGAGATCC 59.902 45.833 0.00 0.00 46.88 3.36
2231 2555 5.250235 TCGTTAGATCTTGTGTGGAGATC 57.750 43.478 0.00 6.09 46.32 2.75
2232 2556 5.661056 TTCGTTAGATCTTGTGTGGAGAT 57.339 39.130 0.00 0.00 36.60 2.75
2233 2557 5.661056 ATTCGTTAGATCTTGTGTGGAGA 57.339 39.130 0.00 0.00 0.00 3.71
2234 2558 6.422100 CCATATTCGTTAGATCTTGTGTGGAG 59.578 42.308 0.00 0.00 0.00 3.86
2235 2559 6.280643 CCATATTCGTTAGATCTTGTGTGGA 58.719 40.000 0.00 0.00 0.00 4.02
2236 2560 5.050091 GCCATATTCGTTAGATCTTGTGTGG 60.050 44.000 0.00 0.82 0.00 4.17
2237 2561 5.523552 TGCCATATTCGTTAGATCTTGTGTG 59.476 40.000 0.00 0.00 0.00 3.82
2238 2562 5.670485 TGCCATATTCGTTAGATCTTGTGT 58.330 37.500 0.00 0.00 0.00 3.72
2239 2563 6.400409 CGATGCCATATTCGTTAGATCTTGTG 60.400 42.308 0.00 0.00 0.00 3.33
2240 2564 5.635280 CGATGCCATATTCGTTAGATCTTGT 59.365 40.000 0.00 0.00 0.00 3.16
2241 2565 5.863935 TCGATGCCATATTCGTTAGATCTTG 59.136 40.000 0.00 0.00 36.74 3.02
2242 2566 6.025749 TCGATGCCATATTCGTTAGATCTT 57.974 37.500 0.00 0.00 36.74 2.40
2243 2567 5.184096 ACTCGATGCCATATTCGTTAGATCT 59.816 40.000 0.00 0.00 36.74 2.75
2244 2568 5.287274 CACTCGATGCCATATTCGTTAGATC 59.713 44.000 0.00 0.00 36.74 2.75
2245 2569 5.048013 TCACTCGATGCCATATTCGTTAGAT 60.048 40.000 0.00 0.00 36.74 1.98
2246 2570 4.277423 TCACTCGATGCCATATTCGTTAGA 59.723 41.667 0.00 0.00 36.74 2.10
2247 2571 4.546570 TCACTCGATGCCATATTCGTTAG 58.453 43.478 0.00 0.00 36.74 2.34
2248 2572 4.277423 TCTCACTCGATGCCATATTCGTTA 59.723 41.667 0.00 0.00 36.74 3.18
2249 2573 3.068165 TCTCACTCGATGCCATATTCGTT 59.932 43.478 0.00 0.00 36.74 3.85
2250 2574 2.623416 TCTCACTCGATGCCATATTCGT 59.377 45.455 0.00 0.00 36.74 3.85
2251 2575 2.983136 GTCTCACTCGATGCCATATTCG 59.017 50.000 0.00 0.00 36.72 3.34
2252 2576 4.250116 AGTCTCACTCGATGCCATATTC 57.750 45.455 0.00 0.00 0.00 1.75
2253 2577 4.679373 AAGTCTCACTCGATGCCATATT 57.321 40.909 0.00 0.00 0.00 1.28
2254 2578 5.791336 TTAAGTCTCACTCGATGCCATAT 57.209 39.130 0.00 0.00 0.00 1.78
2255 2579 5.301805 TCATTAAGTCTCACTCGATGCCATA 59.698 40.000 0.00 0.00 0.00 2.74
2256 2580 4.100035 TCATTAAGTCTCACTCGATGCCAT 59.900 41.667 0.00 0.00 0.00 4.40
2257 2581 3.447229 TCATTAAGTCTCACTCGATGCCA 59.553 43.478 0.00 0.00 0.00 4.92
2258 2582 4.046938 TCATTAAGTCTCACTCGATGCC 57.953 45.455 0.00 0.00 0.00 4.40
2259 2583 5.105752 ACTTCATTAAGTCTCACTCGATGC 58.894 41.667 0.00 0.00 42.42 3.91
2285 2609 5.633996 GATTGCTAAATCTCAGTCGACTG 57.366 43.478 34.76 34.76 39.36 3.51
2298 2622 9.806203 CATCATGGATAAAACAAGATTGCTAAA 57.194 29.630 0.00 0.00 0.00 1.85
2299 2623 9.187996 TCATCATGGATAAAACAAGATTGCTAA 57.812 29.630 0.00 0.00 0.00 3.09
2300 2624 8.750515 TCATCATGGATAAAACAAGATTGCTA 57.249 30.769 0.00 0.00 0.00 3.49
2301 2625 7.201884 CCTCATCATGGATAAAACAAGATTGCT 60.202 37.037 0.00 0.00 0.00 3.91
2302 2626 6.921857 CCTCATCATGGATAAAACAAGATTGC 59.078 38.462 0.00 0.00 0.00 3.56
2303 2627 8.004087 ACCTCATCATGGATAAAACAAGATTG 57.996 34.615 0.00 0.00 0.00 2.67
2304 2628 9.699410 TTACCTCATCATGGATAAAACAAGATT 57.301 29.630 0.00 0.00 0.00 2.40
2305 2629 9.872684 ATTACCTCATCATGGATAAAACAAGAT 57.127 29.630 0.00 0.00 0.00 2.40
2306 2630 9.699410 AATTACCTCATCATGGATAAAACAAGA 57.301 29.630 0.00 0.00 0.00 3.02
2307 2631 9.740239 CAATTACCTCATCATGGATAAAACAAG 57.260 33.333 0.00 0.00 0.00 3.16
2308 2632 8.196771 GCAATTACCTCATCATGGATAAAACAA 58.803 33.333 0.00 0.00 0.00 2.83
2309 2633 7.341512 TGCAATTACCTCATCATGGATAAAACA 59.658 33.333 0.00 0.00 0.00 2.83
2310 2634 7.715657 TGCAATTACCTCATCATGGATAAAAC 58.284 34.615 0.00 0.00 0.00 2.43
2311 2635 7.894753 TGCAATTACCTCATCATGGATAAAA 57.105 32.000 0.00 0.00 0.00 1.52
2312 2636 7.506599 ACATGCAATTACCTCATCATGGATAAA 59.493 33.333 0.00 0.00 36.54 1.40
2313 2637 7.005902 ACATGCAATTACCTCATCATGGATAA 58.994 34.615 0.00 0.00 36.54 1.75
2314 2638 6.545567 ACATGCAATTACCTCATCATGGATA 58.454 36.000 0.00 0.00 36.54 2.59
2315 2639 5.391256 ACATGCAATTACCTCATCATGGAT 58.609 37.500 0.00 0.00 36.54 3.41
2316 2640 4.795469 ACATGCAATTACCTCATCATGGA 58.205 39.130 0.00 0.00 36.54 3.41
2317 2641 5.301045 AGAACATGCAATTACCTCATCATGG 59.699 40.000 0.00 0.00 36.54 3.66
2329 2653 9.985730 TTCTTTTTCTGATAAGAACATGCAATT 57.014 25.926 9.91 0.00 35.93 2.32
2384 2708 2.776526 TGCCCAGGTGACCAGGTT 60.777 61.111 12.38 0.00 0.00 3.50
2423 2747 5.496556 TGTCTCACTCTTTTGTTTCCTTGA 58.503 37.500 0.00 0.00 0.00 3.02
2424 2748 5.818136 TGTCTCACTCTTTTGTTTCCTTG 57.182 39.130 0.00 0.00 0.00 3.61
2425 2749 5.300286 CCATGTCTCACTCTTTTGTTTCCTT 59.700 40.000 0.00 0.00 0.00 3.36
2426 2750 4.823989 CCATGTCTCACTCTTTTGTTTCCT 59.176 41.667 0.00 0.00 0.00 3.36
2427 2751 4.557496 GCCATGTCTCACTCTTTTGTTTCC 60.557 45.833 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.