Multiple sequence alignment - TraesCS1D01G023200

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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 TraesCS1D01G023200 chr1D 100.000 2255 0 0 1 2255 9856891 9859145 0.000000e+00 4165.0
1 TraesCS1D01G023200 chr1D 85.922 206 23 3 848 1047 9823626 9823831 4.880000e-52 215.0
2 TraesCS1D01G023200 chr1B 92.732 853 50 7 1 851 14169199 14170041 0.000000e+00 1221.0
3 TraesCS1D01G023200 chr1B 91.425 898 54 8 848 1725 14170094 14170988 0.000000e+00 1210.0
4 TraesCS1D01G023200 chr1B 89.659 822 49 11 8 819 14464830 14465625 0.000000e+00 1014.0
5 TraesCS1D01G023200 chr1B 90.251 718 50 6 1019 1721 14665591 14666303 0.000000e+00 920.0
6 TraesCS1D01G023200 chr1B 88.440 718 63 6 1015 1718 14783187 14783898 0.000000e+00 848.0
7 TraesCS1D01G023200 chr1B 92.414 290 15 3 1 290 14659158 14659440 7.500000e-110 407.0
8 TraesCS1D01G023200 chr1B 88.816 304 18 9 725 1023 14662646 14662938 2.130000e-95 359.0
9 TraesCS1D01G023200 chr1B 84.444 315 34 7 999 1303 14465630 14465939 1.690000e-76 296.0
10 TraesCS1D01G023200 chr1B 88.739 222 19 5 2037 2253 14666498 14666718 1.330000e-67 267.0
11 TraesCS1D01G023200 chr1B 86.301 219 20 5 2038 2255 14171383 14171592 1.740000e-56 230.0
12 TraesCS1D01G023200 chr1B 83.761 234 32 2 848 1075 14510383 14510616 1.360000e-52 217.0
13 TraesCS1D01G023200 chr1B 87.283 173 12 1 287 459 14659942 14660104 2.960000e-44 189.0
14 TraesCS1D01G023200 chr1B 81.218 197 24 10 1546 1730 14171040 14171235 1.800000e-31 147.0
15 TraesCS1D01G023200 chr1B 82.550 149 19 2 11 159 14509493 14509634 8.460000e-25 124.0
16 TraesCS1D01G023200 chr1B 89.394 66 5 2 1667 1730 14783898 14783963 5.160000e-12 82.4
17 TraesCS1D01G023200 chr1B 93.617 47 3 0 1667 1713 14170979 14171025 1.120000e-08 71.3
18 TraesCS1D01G023200 chr4D 92.790 319 21 2 1727 2043 486181399 486181717 5.670000e-126 460.0
19 TraesCS1D01G023200 chr4D 92.971 313 21 1 1726 2037 221433910 221433598 2.640000e-124 455.0
20 TraesCS1D01G023200 chr3D 93.791 306 19 0 1732 2037 301849557 301849252 5.670000e-126 460.0
21 TraesCS1D01G023200 chr6A 93.226 310 21 0 1730 2039 524364318 524364627 7.340000e-125 457.0
22 TraesCS1D01G023200 chr7A 92.949 312 22 0 1730 2041 209519939 209519628 2.640000e-124 455.0
23 TraesCS1D01G023200 chr7A 92.926 311 22 0 1730 2040 248333517 248333207 9.500000e-124 453.0
24 TraesCS1D01G023200 chr7A 91.925 322 24 2 1721 2040 570272649 570272328 1.230000e-122 449.0
25 TraesCS1D01G023200 chr7A 91.925 322 24 2 1721 2040 570284274 570283953 1.230000e-122 449.0
26 TraesCS1D01G023200 chr2D 92.903 310 22 0 1730 2039 585641510 585641819 3.420000e-123 451.0
27 TraesCS1D01G023200 chr1A 89.238 223 19 4 2037 2255 11638632 11638853 7.930000e-70 274.0
28 TraesCS1D01G023200 chr1A 89.189 222 12 5 1 217 11637984 11638198 1.330000e-67 267.0
29 TraesCS1D01G023200 chr1A 89.655 145 13 2 1496 1640 11638268 11638410 1.380000e-42 183.0
30 TraesCS1D01G023200 chr1A 96.721 61 2 0 1451 1511 11638188 11638248 3.960000e-18 102.0
31 TraesCS1D01G023200 chr1A 95.349 43 2 0 1667 1709 11638447 11638489 4.020000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G023200 chr1D 9856891 9859145 2254 False 4165.00 4165 100.0000 1 2255 1 chr1D.!!$F2 2254
1 TraesCS1D01G023200 chr1B 14464830 14465939 1109 False 655.00 1014 87.0515 8 1303 2 chr1B.!!$F2 1295
2 TraesCS1D01G023200 chr1B 14169199 14171592 2393 False 575.86 1221 89.0586 1 2255 5 chr1B.!!$F1 2254
3 TraesCS1D01G023200 chr1B 14783187 14783963 776 False 465.20 848 88.9170 1015 1730 2 chr1B.!!$F5 715
4 TraesCS1D01G023200 chr1B 14659158 14666718 7560 False 428.40 920 89.5006 1 2253 5 chr1B.!!$F4 2252

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
979 3867 0.75085 TCCATAGCACGCTAGAACCC 59.249 55.0 4.87 0.0 31.45 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 7920 0.106066 TGGCATGTCCATTGGATCCC 60.106 55.0 9.9 7.65 40.72 3.85 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
40 41 6.649141 CCAGTAGTGTTACACAAAGCAATAGA 59.351 38.462 18.19 0.00 36.74 1.98
41 42 7.360101 CCAGTAGTGTTACACAAAGCAATAGAC 60.360 40.741 18.19 0.42 36.74 2.59
42 43 7.170828 CAGTAGTGTTACACAAAGCAATAGACA 59.829 37.037 18.19 0.00 36.74 3.41
43 44 6.545504 AGTGTTACACAAAGCAATAGACAG 57.454 37.500 18.19 0.00 36.74 3.51
44 45 5.049405 AGTGTTACACAAAGCAATAGACAGC 60.049 40.000 18.19 0.00 36.74 4.40
45 46 5.049405 GTGTTACACAAAGCAATAGACAGCT 60.049 40.000 10.96 0.00 37.19 4.24
46 47 5.179368 TGTTACACAAAGCAATAGACAGCTC 59.821 40.000 0.00 0.00 40.90 4.09
53 54 1.396301 GCAATAGACAGCTCACAGCAC 59.604 52.381 0.00 0.00 45.56 4.40
54 55 2.005451 CAATAGACAGCTCACAGCACC 58.995 52.381 0.00 0.00 45.56 5.01
57 58 2.280389 ACAGCTCACAGCACCGTG 60.280 61.111 0.00 0.00 45.56 4.94
115 116 4.334203 AGAGTCTCTGCAATACTACTCACG 59.666 45.833 0.18 0.00 36.63 4.35
116 117 4.262617 AGTCTCTGCAATACTACTCACGA 58.737 43.478 0.00 0.00 0.00 4.35
241 242 6.097129 GGTCTACTCCAAAGATGCTACTAGTT 59.903 42.308 0.00 0.00 0.00 2.24
264 265 5.070001 TGGAAAACCGATGATTTGACTTCT 58.930 37.500 0.00 0.00 0.00 2.85
404 910 5.447624 ACACTTATTTTTGAACGAAGGGG 57.552 39.130 0.00 0.00 0.00 4.79
499 2868 6.879458 AGTTTTGATCGTGTTTAGCTAAGGAT 59.121 34.615 6.24 8.37 0.00 3.24
619 2997 4.260985 ACAAAAACCCAGCCTTTTCAAAG 58.739 39.130 0.00 0.00 35.79 2.77
622 3000 5.887214 AAAACCCAGCCTTTTCAAAGTAT 57.113 34.783 0.00 0.00 34.20 2.12
702 3533 6.220201 GTGGGCAATTTGCTAGTTTTCTAAA 58.780 36.000 20.06 0.00 44.28 1.85
749 3580 1.669779 CATGTGCAAGGAAGCTCTAGC 59.330 52.381 0.00 0.00 42.49 3.42
813 3644 5.684704 AGTCTCTTCCAGTCAAATCAACAA 58.315 37.500 0.00 0.00 0.00 2.83
843 3674 9.178758 ACTTTGTCAATAAACTTCCATCCTATC 57.821 33.333 0.00 0.00 0.00 2.08
858 3745 7.062322 TCCATCCTATCGGTGTACTTTACTTA 58.938 38.462 0.00 0.00 0.00 2.24
979 3867 0.750850 TCCATAGCACGCTAGAACCC 59.249 55.000 4.87 0.00 31.45 4.11
1092 6640 1.227383 CATTGGGGTAGTCCAGGGC 59.773 63.158 0.00 0.00 38.17 5.19
1293 6847 2.274542 TCACCTGCTATTTCCTTCCCA 58.725 47.619 0.00 0.00 0.00 4.37
1382 6950 4.814771 GGTTGGTCCTGTAATATGTAGTGC 59.185 45.833 0.00 0.00 0.00 4.40
1408 6976 3.061322 TCTGAATTTCGTACGGTGTTGG 58.939 45.455 16.52 1.37 0.00 3.77
1446 7015 4.657436 AGGATATGTGTCGAGTTCCTTC 57.343 45.455 0.00 0.00 29.33 3.46
1448 7017 3.385111 GGATATGTGTCGAGTTCCTTCCT 59.615 47.826 0.00 0.00 0.00 3.36
1535 7104 1.933247 CAAAACAACCCGTGCATTGT 58.067 45.000 0.00 0.00 40.76 2.71
1536 7105 1.592081 CAAAACAACCCGTGCATTGTG 59.408 47.619 4.26 0.00 39.00 3.33
1541 7110 1.250154 AACCCGTGCATTGTGATGGG 61.250 55.000 11.58 11.58 42.50 4.00
1542 7111 1.378382 CCCGTGCATTGTGATGGGA 60.378 57.895 8.67 0.00 39.03 4.37
1570 7142 3.753294 AATACCATGCTCTCCTAACCG 57.247 47.619 0.00 0.00 0.00 4.44
1573 7145 1.906574 ACCATGCTCTCCTAACCGAAA 59.093 47.619 0.00 0.00 0.00 3.46
1592 7164 5.750067 CCGAAAAATCATGATTCAACATCCC 59.250 40.000 20.95 4.87 0.00 3.85
1623 7195 1.271379 CCAGGGTGGACTTGTAACTGG 60.271 57.143 0.00 0.00 40.96 4.00
1626 7198 1.271217 GGGTGGACTTGTAACTGGGAC 60.271 57.143 0.00 0.00 0.00 4.46
1736 7700 2.492019 GCGGATTGCAAATAAGGGTC 57.508 50.000 1.71 0.00 45.45 4.46
1737 7701 2.024414 GCGGATTGCAAATAAGGGTCT 58.976 47.619 1.71 0.00 45.45 3.85
1738 7702 2.033424 GCGGATTGCAAATAAGGGTCTC 59.967 50.000 1.71 0.00 45.45 3.36
1739 7703 3.545703 CGGATTGCAAATAAGGGTCTCT 58.454 45.455 1.71 0.00 0.00 3.10
1740 7704 3.947834 CGGATTGCAAATAAGGGTCTCTT 59.052 43.478 1.71 0.00 39.40 2.85
1741 7705 4.399303 CGGATTGCAAATAAGGGTCTCTTT 59.601 41.667 1.71 0.00 36.93 2.52
1742 7706 5.654497 GGATTGCAAATAAGGGTCTCTTTG 58.346 41.667 1.71 0.00 36.93 2.77
1743 7707 5.418840 GGATTGCAAATAAGGGTCTCTTTGA 59.581 40.000 1.71 0.00 36.93 2.69
1744 7708 6.097412 GGATTGCAAATAAGGGTCTCTTTGAT 59.903 38.462 1.71 0.00 36.93 2.57
1745 7709 6.916360 TTGCAAATAAGGGTCTCTTTGATT 57.084 33.333 0.00 0.00 36.93 2.57
1746 7710 6.515272 TGCAAATAAGGGTCTCTTTGATTC 57.485 37.500 0.00 0.00 36.93 2.52
1747 7711 6.009589 TGCAAATAAGGGTCTCTTTGATTCA 58.990 36.000 0.00 0.00 36.93 2.57
1748 7712 6.493115 TGCAAATAAGGGTCTCTTTGATTCAA 59.507 34.615 0.00 0.00 36.93 2.69
1749 7713 6.808704 GCAAATAAGGGTCTCTTTGATTCAAC 59.191 38.462 0.00 0.00 36.93 3.18
1750 7714 6.743575 AATAAGGGTCTCTTTGATTCAACG 57.256 37.500 0.00 0.00 36.93 4.10
1751 7715 3.059352 AGGGTCTCTTTGATTCAACGG 57.941 47.619 0.00 0.00 0.00 4.44
1752 7716 2.637872 AGGGTCTCTTTGATTCAACGGA 59.362 45.455 0.00 0.42 0.00 4.69
1753 7717 3.264450 AGGGTCTCTTTGATTCAACGGAT 59.736 43.478 0.00 0.00 0.00 4.18
1754 7718 4.010349 GGGTCTCTTTGATTCAACGGATT 58.990 43.478 0.00 0.00 0.00 3.01
1755 7719 4.459337 GGGTCTCTTTGATTCAACGGATTT 59.541 41.667 0.00 0.00 0.00 2.17
1756 7720 5.048013 GGGTCTCTTTGATTCAACGGATTTT 60.048 40.000 0.00 0.00 0.00 1.82
1757 7721 6.086871 GGTCTCTTTGATTCAACGGATTTTC 58.913 40.000 0.00 0.00 0.00 2.29
1758 7722 6.293955 GGTCTCTTTGATTCAACGGATTTTCA 60.294 38.462 0.00 0.00 0.00 2.69
1759 7723 7.308435 GTCTCTTTGATTCAACGGATTTTCAT 58.692 34.615 0.00 0.00 0.00 2.57
1760 7724 8.450964 GTCTCTTTGATTCAACGGATTTTCATA 58.549 33.333 0.00 0.00 0.00 2.15
1761 7725 8.668353 TCTCTTTGATTCAACGGATTTTCATAG 58.332 33.333 0.00 0.00 0.00 2.23
1762 7726 7.761409 TCTTTGATTCAACGGATTTTCATAGG 58.239 34.615 0.00 0.00 0.00 2.57
1763 7727 7.609918 TCTTTGATTCAACGGATTTTCATAGGA 59.390 33.333 0.00 0.00 0.00 2.94
1764 7728 7.880160 TTGATTCAACGGATTTTCATAGGAT 57.120 32.000 0.00 0.00 0.00 3.24
1765 7729 7.496529 TGATTCAACGGATTTTCATAGGATC 57.503 36.000 0.00 0.00 0.00 3.36
1766 7730 7.282585 TGATTCAACGGATTTTCATAGGATCT 58.717 34.615 0.00 0.00 0.00 2.75
1767 7731 7.775093 TGATTCAACGGATTTTCATAGGATCTT 59.225 33.333 0.00 0.00 0.00 2.40
1768 7732 7.938140 TTCAACGGATTTTCATAGGATCTTT 57.062 32.000 0.00 0.00 0.00 2.52
1769 7733 7.320443 TCAACGGATTTTCATAGGATCTTTG 57.680 36.000 0.00 0.00 0.00 2.77
1770 7734 7.109501 TCAACGGATTTTCATAGGATCTTTGA 58.890 34.615 0.00 0.00 0.00 2.69
1771 7735 7.609918 TCAACGGATTTTCATAGGATCTTTGAA 59.390 33.333 0.00 0.00 31.64 2.69
1772 7736 7.559590 ACGGATTTTCATAGGATCTTTGAAG 57.440 36.000 0.00 0.00 34.19 3.02
1773 7737 6.543831 ACGGATTTTCATAGGATCTTTGAAGG 59.456 38.462 0.00 0.00 34.19 3.46
1774 7738 6.767902 CGGATTTTCATAGGATCTTTGAAGGA 59.232 38.462 0.00 0.00 34.19 3.36
1775 7739 7.446625 CGGATTTTCATAGGATCTTTGAAGGAT 59.553 37.037 0.00 0.00 34.19 3.24
1776 7740 9.140874 GGATTTTCATAGGATCTTTGAAGGATT 57.859 33.333 0.00 0.00 34.19 3.01
1779 7743 9.973661 TTTTCATAGGATCTTTGAAGGATTACA 57.026 29.630 0.00 0.00 34.19 2.41
1780 7744 9.973661 TTTCATAGGATCTTTGAAGGATTACAA 57.026 29.630 0.00 0.00 34.19 2.41
1782 7746 9.565090 TCATAGGATCTTTGAAGGATTACAATG 57.435 33.333 0.00 0.00 0.00 2.82
1783 7747 6.705863 AGGATCTTTGAAGGATTACAATGC 57.294 37.500 0.00 0.00 0.00 3.56
1784 7748 6.430007 AGGATCTTTGAAGGATTACAATGCT 58.570 36.000 0.00 0.00 38.86 3.79
1786 7750 8.055181 AGGATCTTTGAAGGATTACAATGCTTA 58.945 33.333 8.47 0.00 45.40 3.09
1787 7751 8.348507 GGATCTTTGAAGGATTACAATGCTTAG 58.651 37.037 8.47 4.06 45.40 2.18
1788 7752 7.630242 TCTTTGAAGGATTACAATGCTTAGG 57.370 36.000 8.47 0.00 45.40 2.69
1789 7753 7.402054 TCTTTGAAGGATTACAATGCTTAGGA 58.598 34.615 8.47 0.00 45.40 2.94
1790 7754 7.888021 TCTTTGAAGGATTACAATGCTTAGGAA 59.112 33.333 8.47 4.31 45.40 3.36
1791 7755 8.415950 TTTGAAGGATTACAATGCTTAGGAAA 57.584 30.769 8.47 6.21 45.40 3.13
1792 7756 8.593945 TTGAAGGATTACAATGCTTAGGAAAT 57.406 30.769 8.47 0.00 45.40 2.17
1793 7757 8.593945 TGAAGGATTACAATGCTTAGGAAATT 57.406 30.769 8.47 0.00 45.40 1.82
1794 7758 9.034800 TGAAGGATTACAATGCTTAGGAAATTT 57.965 29.630 8.47 0.00 45.40 1.82
1795 7759 9.875691 GAAGGATTACAATGCTTAGGAAATTTT 57.124 29.630 8.47 0.00 45.40 1.82
1796 7760 9.875691 AAGGATTACAATGCTTAGGAAATTTTC 57.124 29.630 6.90 0.24 43.91 2.29
1797 7761 8.478066 AGGATTACAATGCTTAGGAAATTTTCC 58.522 33.333 18.71 18.71 41.11 3.13
1809 7773 5.638596 GGAAATTTTCCTACATTGGTCGT 57.361 39.130 19.01 0.00 46.57 4.34
1810 7774 6.020971 GGAAATTTTCCTACATTGGTCGTT 57.979 37.500 19.01 0.00 46.57 3.85
1811 7775 6.452242 GGAAATTTTCCTACATTGGTCGTTT 58.548 36.000 19.01 0.00 46.57 3.60
1812 7776 6.364976 GGAAATTTTCCTACATTGGTCGTTTG 59.635 38.462 19.01 0.00 46.57 2.93
1813 7777 6.642707 AATTTTCCTACATTGGTCGTTTGA 57.357 33.333 0.00 0.00 0.00 2.69
1814 7778 6.834168 ATTTTCCTACATTGGTCGTTTGAT 57.166 33.333 0.00 0.00 0.00 2.57
1815 7779 6.642707 TTTTCCTACATTGGTCGTTTGATT 57.357 33.333 0.00 0.00 0.00 2.57
1816 7780 5.873179 TTCCTACATTGGTCGTTTGATTC 57.127 39.130 0.00 0.00 0.00 2.52
1817 7781 3.930229 TCCTACATTGGTCGTTTGATTCG 59.070 43.478 0.00 0.00 0.00 3.34
1818 7782 3.682858 CCTACATTGGTCGTTTGATTCGT 59.317 43.478 0.00 0.00 0.00 3.85
1819 7783 4.865925 CCTACATTGGTCGTTTGATTCGTA 59.134 41.667 0.00 0.00 0.00 3.43
1820 7784 4.921470 ACATTGGTCGTTTGATTCGTAG 57.079 40.909 0.00 0.00 0.00 3.51
1821 7785 3.682858 ACATTGGTCGTTTGATTCGTAGG 59.317 43.478 0.00 0.00 0.00 3.18
1822 7786 3.663995 TTGGTCGTTTGATTCGTAGGA 57.336 42.857 0.00 0.00 0.00 2.94
1823 7787 3.880047 TGGTCGTTTGATTCGTAGGAT 57.120 42.857 0.00 0.00 0.00 3.24
1824 7788 4.196626 TGGTCGTTTGATTCGTAGGATT 57.803 40.909 0.00 0.00 0.00 3.01
1825 7789 3.930229 TGGTCGTTTGATTCGTAGGATTG 59.070 43.478 0.00 0.00 0.00 2.67
1826 7790 4.178540 GGTCGTTTGATTCGTAGGATTGA 58.821 43.478 0.00 0.00 0.00 2.57
1827 7791 4.628333 GGTCGTTTGATTCGTAGGATTGAA 59.372 41.667 0.00 0.00 0.00 2.69
1828 7792 5.293569 GGTCGTTTGATTCGTAGGATTGAAT 59.706 40.000 0.00 0.00 37.52 2.57
1829 7793 6.411652 GTCGTTTGATTCGTAGGATTGAATC 58.588 40.000 7.76 7.76 46.77 2.52
1830 7794 5.522460 TCGTTTGATTCGTAGGATTGAATCC 59.478 40.000 16.35 16.35 46.29 3.01
1865 7829 9.444600 TTTTTCCTAAGGATTCATGTGTACTAC 57.555 33.333 0.00 0.00 0.00 2.73
1866 7830 7.727578 TTCCTAAGGATTCATGTGTACTACA 57.272 36.000 0.00 0.00 44.87 2.74
1876 7840 3.945981 TGTGTACTACATTTCGCAGGA 57.054 42.857 0.00 0.00 33.42 3.86
1877 7841 4.260139 TGTGTACTACATTTCGCAGGAA 57.740 40.909 0.00 0.00 33.42 3.36
1878 7842 4.827692 TGTGTACTACATTTCGCAGGAAT 58.172 39.130 0.00 0.00 33.42 3.01
1879 7843 5.242434 TGTGTACTACATTTCGCAGGAATT 58.758 37.500 0.00 0.00 33.42 2.17
1880 7844 5.350365 TGTGTACTACATTTCGCAGGAATTC 59.650 40.000 0.00 0.00 33.42 2.17
1881 7845 5.581085 GTGTACTACATTTCGCAGGAATTCT 59.419 40.000 5.23 0.00 30.88 2.40
1882 7846 6.755141 GTGTACTACATTTCGCAGGAATTCTA 59.245 38.462 5.23 0.00 30.88 2.10
1883 7847 7.277098 GTGTACTACATTTCGCAGGAATTCTAA 59.723 37.037 5.23 0.00 30.88 2.10
1884 7848 6.663944 ACTACATTTCGCAGGAATTCTAAC 57.336 37.500 5.23 0.00 30.88 2.34
1885 7849 6.170506 ACTACATTTCGCAGGAATTCTAACA 58.829 36.000 5.23 0.00 30.88 2.41
1886 7850 6.823689 ACTACATTTCGCAGGAATTCTAACAT 59.176 34.615 5.23 0.00 30.88 2.71
1887 7851 6.124088 ACATTTCGCAGGAATTCTAACATC 57.876 37.500 5.23 0.00 30.88 3.06
1888 7852 5.066505 ACATTTCGCAGGAATTCTAACATCC 59.933 40.000 5.23 0.00 30.88 3.51
1889 7853 3.904800 TCGCAGGAATTCTAACATCCA 57.095 42.857 5.23 0.00 35.62 3.41
1890 7854 3.531538 TCGCAGGAATTCTAACATCCAC 58.468 45.455 5.23 0.00 35.62 4.02
1891 7855 3.197766 TCGCAGGAATTCTAACATCCACT 59.802 43.478 5.23 0.00 35.62 4.00
1892 7856 3.557595 CGCAGGAATTCTAACATCCACTC 59.442 47.826 5.23 0.00 35.62 3.51
1893 7857 3.879892 GCAGGAATTCTAACATCCACTCC 59.120 47.826 5.23 0.00 35.62 3.85
1894 7858 4.626287 GCAGGAATTCTAACATCCACTCCA 60.626 45.833 5.23 0.00 35.62 3.86
1895 7859 5.500234 CAGGAATTCTAACATCCACTCCAA 58.500 41.667 5.23 0.00 35.62 3.53
1896 7860 5.355350 CAGGAATTCTAACATCCACTCCAAC 59.645 44.000 5.23 0.00 35.62 3.77
1897 7861 4.640647 GGAATTCTAACATCCACTCCAACC 59.359 45.833 5.23 0.00 33.30 3.77
1898 7862 5.501156 GAATTCTAACATCCACTCCAACCT 58.499 41.667 0.00 0.00 0.00 3.50
1899 7863 4.553330 TTCTAACATCCACTCCAACCTC 57.447 45.455 0.00 0.00 0.00 3.85
1900 7864 3.791320 TCTAACATCCACTCCAACCTCT 58.209 45.455 0.00 0.00 0.00 3.69
1901 7865 4.168101 TCTAACATCCACTCCAACCTCTT 58.832 43.478 0.00 0.00 0.00 2.85
1902 7866 2.867109 ACATCCACTCCAACCTCTTG 57.133 50.000 0.00 0.00 0.00 3.02
1903 7867 1.271597 ACATCCACTCCAACCTCTTGC 60.272 52.381 0.00 0.00 0.00 4.01
1904 7868 1.067295 ATCCACTCCAACCTCTTGCA 58.933 50.000 0.00 0.00 0.00 4.08
1905 7869 0.843309 TCCACTCCAACCTCTTGCAA 59.157 50.000 0.00 0.00 0.00 4.08
1906 7870 1.202806 TCCACTCCAACCTCTTGCAAG 60.203 52.381 20.81 20.81 0.00 4.01
1907 7871 1.202806 CCACTCCAACCTCTTGCAAGA 60.203 52.381 26.87 26.87 0.00 3.02
1908 7872 2.575532 CACTCCAACCTCTTGCAAGAA 58.424 47.619 28.16 12.73 34.03 2.52
1909 7873 2.951642 CACTCCAACCTCTTGCAAGAAA 59.048 45.455 28.16 9.08 34.03 2.52
1910 7874 3.571401 CACTCCAACCTCTTGCAAGAAAT 59.429 43.478 28.16 17.01 34.03 2.17
1911 7875 3.823304 ACTCCAACCTCTTGCAAGAAATC 59.177 43.478 28.16 0.00 34.03 2.17
1912 7876 3.157087 TCCAACCTCTTGCAAGAAATCC 58.843 45.455 28.16 0.00 34.03 3.01
1913 7877 3.160269 CCAACCTCTTGCAAGAAATCCT 58.840 45.455 28.16 9.94 34.03 3.24
1914 7878 3.575687 CCAACCTCTTGCAAGAAATCCTT 59.424 43.478 28.16 12.74 34.03 3.36
1915 7879 4.039609 CCAACCTCTTGCAAGAAATCCTTT 59.960 41.667 28.16 12.73 34.03 3.11
1916 7880 4.861102 ACCTCTTGCAAGAAATCCTTTG 57.139 40.909 28.16 14.55 34.03 2.77
1917 7881 3.006217 ACCTCTTGCAAGAAATCCTTTGC 59.994 43.478 28.16 2.47 34.03 3.68
1918 7882 3.257624 CCTCTTGCAAGAAATCCTTTGCT 59.742 43.478 28.16 0.00 34.03 3.91
1919 7883 4.262335 CCTCTTGCAAGAAATCCTTTGCTT 60.262 41.667 28.16 0.00 34.03 3.91
1920 7884 5.280654 TCTTGCAAGAAATCCTTTGCTTT 57.719 34.783 26.61 0.00 33.25 3.51
1921 7885 5.673514 TCTTGCAAGAAATCCTTTGCTTTT 58.326 33.333 26.61 0.00 33.25 2.27
1922 7886 5.754890 TCTTGCAAGAAATCCTTTGCTTTTC 59.245 36.000 26.61 0.00 33.25 2.29
1923 7887 4.379652 TGCAAGAAATCCTTTGCTTTTCC 58.620 39.130 10.13 0.00 33.25 3.13
1924 7888 3.748048 GCAAGAAATCCTTTGCTTTTCCC 59.252 43.478 2.22 0.00 31.42 3.97
1925 7889 3.942130 AGAAATCCTTTGCTTTTCCCG 57.058 42.857 0.00 0.00 31.25 5.14
1926 7890 3.230976 AGAAATCCTTTGCTTTTCCCGT 58.769 40.909 0.00 0.00 31.25 5.28
1927 7891 3.005791 AGAAATCCTTTGCTTTTCCCGTG 59.994 43.478 0.00 0.00 31.25 4.94
1928 7892 2.286365 ATCCTTTGCTTTTCCCGTGA 57.714 45.000 0.00 0.00 0.00 4.35
1929 7893 1.314730 TCCTTTGCTTTTCCCGTGAC 58.685 50.000 0.00 0.00 0.00 3.67
1930 7894 1.028905 CCTTTGCTTTTCCCGTGACA 58.971 50.000 0.00 0.00 0.00 3.58
1931 7895 1.269051 CCTTTGCTTTTCCCGTGACAC 60.269 52.381 0.00 0.00 0.00 3.67
1932 7896 1.403679 CTTTGCTTTTCCCGTGACACA 59.596 47.619 6.37 0.00 0.00 3.72
1933 7897 1.021202 TTGCTTTTCCCGTGACACAG 58.979 50.000 6.37 0.00 0.00 3.66
1934 7898 0.107410 TGCTTTTCCCGTGACACAGT 60.107 50.000 6.37 0.00 0.00 3.55
1935 7899 0.586802 GCTTTTCCCGTGACACAGTC 59.413 55.000 6.37 0.00 0.00 3.51
1936 7900 1.948104 CTTTTCCCGTGACACAGTCA 58.052 50.000 6.37 0.00 40.50 3.41
1937 7901 2.285083 CTTTTCCCGTGACACAGTCAA 58.715 47.619 6.37 0.00 44.49 3.18
1938 7902 2.404923 TTTCCCGTGACACAGTCAAA 57.595 45.000 6.37 0.00 44.49 2.69
1939 7903 1.658994 TTCCCGTGACACAGTCAAAC 58.341 50.000 6.37 0.00 44.49 2.93
1940 7904 0.537653 TCCCGTGACACAGTCAAACA 59.462 50.000 6.37 0.00 44.49 2.83
1941 7905 1.066071 TCCCGTGACACAGTCAAACAA 60.066 47.619 6.37 0.00 44.49 2.83
1942 7906 1.740585 CCCGTGACACAGTCAAACAAA 59.259 47.619 6.37 0.00 44.49 2.83
1943 7907 2.477189 CCCGTGACACAGTCAAACAAAC 60.477 50.000 6.37 0.00 44.49 2.93
1944 7908 2.418628 CCGTGACACAGTCAAACAAACT 59.581 45.455 6.37 0.00 44.49 2.66
1945 7909 3.485216 CCGTGACACAGTCAAACAAACTC 60.485 47.826 6.37 0.00 44.49 3.01
1946 7910 3.124466 CGTGACACAGTCAAACAAACTCA 59.876 43.478 6.37 0.00 44.49 3.41
1947 7911 4.377943 CGTGACACAGTCAAACAAACTCAA 60.378 41.667 6.37 0.00 44.49 3.02
1948 7912 5.457140 GTGACACAGTCAAACAAACTCAAA 58.543 37.500 0.00 0.00 44.49 2.69
1949 7913 6.092748 GTGACACAGTCAAACAAACTCAAAT 58.907 36.000 0.00 0.00 44.49 2.32
1950 7914 6.251376 GTGACACAGTCAAACAAACTCAAATC 59.749 38.462 0.00 0.00 44.49 2.17
1951 7915 5.650543 ACACAGTCAAACAAACTCAAATCC 58.349 37.500 0.00 0.00 0.00 3.01
1952 7916 5.418840 ACACAGTCAAACAAACTCAAATCCT 59.581 36.000 0.00 0.00 0.00 3.24
1953 7917 6.601613 ACACAGTCAAACAAACTCAAATCCTA 59.398 34.615 0.00 0.00 0.00 2.94
1954 7918 7.285401 ACACAGTCAAACAAACTCAAATCCTAT 59.715 33.333 0.00 0.00 0.00 2.57
1955 7919 8.783093 CACAGTCAAACAAACTCAAATCCTATA 58.217 33.333 0.00 0.00 0.00 1.31
1956 7920 9.003658 ACAGTCAAACAAACTCAAATCCTATAG 57.996 33.333 0.00 0.00 0.00 1.31
1957 7921 8.454106 CAGTCAAACAAACTCAAATCCTATAGG 58.546 37.037 13.07 13.07 0.00 2.57
1958 7922 7.611855 AGTCAAACAAACTCAAATCCTATAGGG 59.388 37.037 18.97 4.00 35.41 3.53
1970 7934 4.502036 TCCTATAGGGATCCAATGGACA 57.498 45.455 18.97 0.00 39.58 4.02
1971 7935 5.041695 TCCTATAGGGATCCAATGGACAT 57.958 43.478 18.97 0.00 39.58 3.06
1972 7936 4.784838 TCCTATAGGGATCCAATGGACATG 59.215 45.833 18.97 0.00 39.58 3.21
1973 7937 2.957402 TAGGGATCCAATGGACATGC 57.043 50.000 15.23 0.00 32.98 4.06
1974 7938 0.186873 AGGGATCCAATGGACATGCC 59.813 55.000 15.23 4.48 32.98 4.40
1985 7949 3.104519 TGGACATGCCATTTCAATCCT 57.895 42.857 4.93 0.00 43.33 3.24
1986 7950 4.248174 TGGACATGCCATTTCAATCCTA 57.752 40.909 4.93 0.00 43.33 2.94
1987 7951 3.953612 TGGACATGCCATTTCAATCCTAC 59.046 43.478 4.93 0.00 43.33 3.18
1988 7952 3.003689 GGACATGCCATTTCAATCCTACG 59.996 47.826 0.00 0.00 36.34 3.51
1989 7953 2.951642 ACATGCCATTTCAATCCTACGG 59.048 45.455 0.00 0.00 0.00 4.02
1990 7954 2.799126 TGCCATTTCAATCCTACGGT 57.201 45.000 0.00 0.00 0.00 4.83
1991 7955 3.080300 TGCCATTTCAATCCTACGGTT 57.920 42.857 0.00 0.00 0.00 4.44
1992 7956 3.426615 TGCCATTTCAATCCTACGGTTT 58.573 40.909 0.00 0.00 0.00 3.27
1993 7957 3.442273 TGCCATTTCAATCCTACGGTTTC 59.558 43.478 0.00 0.00 0.00 2.78
1994 7958 3.181490 GCCATTTCAATCCTACGGTTTCC 60.181 47.826 0.00 0.00 0.00 3.13
1995 7959 3.380320 CCATTTCAATCCTACGGTTTCCC 59.620 47.826 0.00 0.00 0.00 3.97
1996 7960 4.270008 CATTTCAATCCTACGGTTTCCCT 58.730 43.478 0.00 0.00 0.00 4.20
1997 7961 5.433526 CATTTCAATCCTACGGTTTCCCTA 58.566 41.667 0.00 0.00 0.00 3.53
1998 7962 5.703730 TTTCAATCCTACGGTTTCCCTAT 57.296 39.130 0.00 0.00 0.00 2.57
1999 7963 5.703730 TTCAATCCTACGGTTTCCCTATT 57.296 39.130 0.00 0.00 0.00 1.73
2000 7964 5.703730 TCAATCCTACGGTTTCCCTATTT 57.296 39.130 0.00 0.00 0.00 1.40
2001 7965 6.069705 TCAATCCTACGGTTTCCCTATTTT 57.930 37.500 0.00 0.00 0.00 1.82
2002 7966 6.486941 TCAATCCTACGGTTTCCCTATTTTT 58.513 36.000 0.00 0.00 0.00 1.94
2003 7967 6.376018 TCAATCCTACGGTTTCCCTATTTTTG 59.624 38.462 0.00 0.00 0.00 2.44
2004 7968 5.245584 TCCTACGGTTTCCCTATTTTTGT 57.754 39.130 0.00 0.00 0.00 2.83
2005 7969 5.005094 TCCTACGGTTTCCCTATTTTTGTG 58.995 41.667 0.00 0.00 0.00 3.33
2006 7970 4.763279 CCTACGGTTTCCCTATTTTTGTGT 59.237 41.667 0.00 0.00 0.00 3.72
2007 7971 5.242171 CCTACGGTTTCCCTATTTTTGTGTT 59.758 40.000 0.00 0.00 0.00 3.32
2008 7972 5.601583 ACGGTTTCCCTATTTTTGTGTTT 57.398 34.783 0.00 0.00 0.00 2.83
2009 7973 5.979993 ACGGTTTCCCTATTTTTGTGTTTT 58.020 33.333 0.00 0.00 0.00 2.43
2010 7974 6.408035 ACGGTTTCCCTATTTTTGTGTTTTT 58.592 32.000 0.00 0.00 0.00 1.94
2011 7975 6.314152 ACGGTTTCCCTATTTTTGTGTTTTTG 59.686 34.615 0.00 0.00 0.00 2.44
2012 7976 6.491394 GGTTTCCCTATTTTTGTGTTTTTGC 58.509 36.000 0.00 0.00 0.00 3.68
2013 7977 6.094186 GGTTTCCCTATTTTTGTGTTTTTGCA 59.906 34.615 0.00 0.00 0.00 4.08
2014 7978 6.917217 TTCCCTATTTTTGTGTTTTTGCAG 57.083 33.333 0.00 0.00 0.00 4.41
2015 7979 5.983540 TCCCTATTTTTGTGTTTTTGCAGT 58.016 33.333 0.00 0.00 0.00 4.40
2016 7980 6.045955 TCCCTATTTTTGTGTTTTTGCAGTC 58.954 36.000 0.00 0.00 0.00 3.51
2017 7981 5.236263 CCCTATTTTTGTGTTTTTGCAGTCC 59.764 40.000 0.00 0.00 0.00 3.85
2018 7982 6.048509 CCTATTTTTGTGTTTTTGCAGTCCT 58.951 36.000 0.00 0.00 0.00 3.85
2019 7983 7.206687 CCTATTTTTGTGTTTTTGCAGTCCTA 58.793 34.615 0.00 0.00 0.00 2.94
2020 7984 7.872483 CCTATTTTTGTGTTTTTGCAGTCCTAT 59.128 33.333 0.00 0.00 0.00 2.57
2021 7985 6.900568 TTTTTGTGTTTTTGCAGTCCTATG 57.099 33.333 0.00 0.00 0.00 2.23
2022 7986 5.843673 TTTGTGTTTTTGCAGTCCTATGA 57.156 34.783 0.00 0.00 0.00 2.15
2023 7987 5.843673 TTGTGTTTTTGCAGTCCTATGAA 57.156 34.783 0.00 0.00 0.00 2.57
2024 7988 6.403866 TTGTGTTTTTGCAGTCCTATGAAT 57.596 33.333 0.00 0.00 0.00 2.57
2025 7989 6.012658 TGTGTTTTTGCAGTCCTATGAATC 57.987 37.500 0.00 0.00 0.00 2.52
2026 7990 5.534278 TGTGTTTTTGCAGTCCTATGAATCA 59.466 36.000 0.00 0.00 0.00 2.57
2027 7991 6.040278 TGTGTTTTTGCAGTCCTATGAATCAA 59.960 34.615 0.00 0.00 0.00 2.57
2028 7992 6.922957 GTGTTTTTGCAGTCCTATGAATCAAA 59.077 34.615 0.00 0.00 0.00 2.69
2029 7993 7.115378 GTGTTTTTGCAGTCCTATGAATCAAAG 59.885 37.037 0.00 0.00 0.00 2.77
2030 7994 7.014134 TGTTTTTGCAGTCCTATGAATCAAAGA 59.986 33.333 0.00 0.00 0.00 2.52
2031 7995 6.748333 TTTGCAGTCCTATGAATCAAAGAG 57.252 37.500 0.00 0.00 0.00 2.85
2032 7996 4.774124 TGCAGTCCTATGAATCAAAGAGG 58.226 43.478 3.58 3.58 0.00 3.69
2033 7997 3.563390 GCAGTCCTATGAATCAAAGAGGC 59.437 47.826 4.80 1.85 0.00 4.70
2034 7998 4.133078 CAGTCCTATGAATCAAAGAGGCC 58.867 47.826 0.00 0.00 0.00 5.19
2035 7999 3.137360 AGTCCTATGAATCAAAGAGGCCC 59.863 47.826 0.00 0.00 0.00 5.80
2036 8000 3.137360 GTCCTATGAATCAAAGAGGCCCT 59.863 47.826 0.00 0.00 0.00 5.19
2116 8080 1.012841 GTGAGCCTCTAGTTGCATGC 58.987 55.000 11.82 11.82 0.00 4.06
2173 8139 1.452110 CAATTGCGTGTGGAGGATGA 58.548 50.000 0.00 0.00 0.00 2.92
2184 8150 3.640498 TGTGGAGGATGAACATGCAAAAA 59.360 39.130 8.79 0.00 31.83 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.280389 CACGGTGCTGTGAGCTGT 60.280 61.111 5.26 0.00 42.97 4.40
41 42 2.029518 TCACGGTGCTGTGAGCTG 59.970 61.111 9.55 0.00 43.62 4.24
45 46 2.734591 GAGGTCACGGTGCTGTGA 59.265 61.111 9.55 9.55 46.15 3.58
46 47 2.357517 GGAGGTCACGGTGCTGTG 60.358 66.667 2.51 4.86 41.28 3.66
57 58 2.154462 CAAGTGGTTGTGATGGAGGTC 58.846 52.381 0.00 0.00 0.00 3.85
115 116 4.581824 TGGAGCTTCCTTGCATATGAAATC 59.418 41.667 6.97 0.00 37.46 2.17
116 117 4.539726 TGGAGCTTCCTTGCATATGAAAT 58.460 39.130 6.97 0.00 37.46 2.17
167 168 1.566018 CGGAGACTTGGAACCAACGC 61.566 60.000 1.83 0.00 0.00 4.84
241 242 5.070001 AGAAGTCAAATCATCGGTTTTCCA 58.930 37.500 0.00 0.00 40.70 3.53
264 265 5.399113 AGTAAACTTTCCCCAAGGCAATTA 58.601 37.500 0.00 0.00 36.72 1.40
315 821 7.289310 TGCAACATTTATTATGGATCAGAGGA 58.711 34.615 0.00 0.00 0.00 3.71
320 826 9.752961 CAAATCTGCAACATTTATTATGGATCA 57.247 29.630 0.00 0.00 0.00 2.92
370 876 4.759516 AAATAAGTGTCGCGGTTTTGAT 57.240 36.364 6.13 0.00 0.00 2.57
499 2868 2.722094 ACTCCTTTTTCACTGTGCACA 58.278 42.857 20.37 20.37 0.00 4.57
600 2978 5.508994 CGATACTTTGAAAAGGCTGGGTTTT 60.509 40.000 7.65 0.00 40.31 2.43
707 3538 6.783708 TGAAATCACTTGGGTTAACAGTTT 57.216 33.333 8.10 0.00 0.00 2.66
749 3580 1.970114 CCAAGTGGTGCTCTGGCTG 60.970 63.158 0.00 0.00 39.59 4.85
843 3674 8.746922 TGAAATGTAGTAAGTAAAGTACACCG 57.253 34.615 0.00 0.00 37.93 4.94
858 3745 2.420129 GCATCGGACCCTGAAATGTAGT 60.420 50.000 0.00 0.00 0.00 2.73
904 3791 5.911178 TGCTATTTATATAGGGGCTGCCTAT 59.089 40.000 19.68 11.84 35.31 2.57
905 3792 5.285401 TGCTATTTATATAGGGGCTGCCTA 58.715 41.667 19.68 4.18 35.31 3.93
979 3867 8.812147 TTCATATCTAATGCAAGTAGTTACCG 57.188 34.615 0.00 0.00 35.67 4.02
1056 6604 2.125552 TTCACGGCGCAGAGGATG 60.126 61.111 16.26 1.51 0.00 3.51
1092 6640 2.255252 CGCCAAAACCTTCTGCCG 59.745 61.111 0.00 0.00 0.00 5.69
1293 6847 0.951558 AAAGCCGACGAAGCACATTT 59.048 45.000 0.00 0.00 0.00 2.32
1339 6907 9.729281 ACCAACCGAATAGAGAAAGTATAAAAA 57.271 29.630 0.00 0.00 0.00 1.94
1358 6926 5.047847 CACTACATATTACAGGACCAACCG 58.952 45.833 0.00 0.00 44.74 4.44
1359 6927 4.814771 GCACTACATATTACAGGACCAACC 59.185 45.833 0.00 0.00 39.35 3.77
1382 6950 4.684703 ACACCGTACGAAATTCAGAAAGAG 59.315 41.667 18.76 0.00 0.00 2.85
1419 6987 7.694545 AAGGAACTCGACACATATCCTATAGGA 60.695 40.741 23.76 23.76 44.94 2.94
1427 6995 4.657436 AGGAAGGAACTCGACACATATC 57.343 45.455 0.00 0.00 38.49 1.63
1429 6997 4.884668 AAAGGAAGGAACTCGACACATA 57.115 40.909 0.00 0.00 38.49 2.29
1448 7017 9.862149 GGTAGATCCCCTTTCTATTATCAAAAA 57.138 33.333 0.00 0.00 0.00 1.94
1521 7090 0.109179 CCATCACAATGCACGGGTTG 60.109 55.000 0.00 0.00 0.00 3.77
1558 7130 4.876107 TCATGATTTTTCGGTTAGGAGAGC 59.124 41.667 0.00 0.00 0.00 4.09
1562 7134 7.175816 TGTTGAATCATGATTTTTCGGTTAGGA 59.824 33.333 21.57 0.00 0.00 2.94
1570 7142 8.726870 ATTGGGATGTTGAATCATGATTTTTC 57.273 30.769 21.57 11.06 0.00 2.29
1573 7145 9.826574 CTTAATTGGGATGTTGAATCATGATTT 57.173 29.630 21.57 5.84 0.00 2.17
1731 7695 2.637872 TCCGTTGAATCAAAGAGACCCT 59.362 45.455 10.38 0.00 0.00 4.34
1732 7696 3.053831 TCCGTTGAATCAAAGAGACCC 57.946 47.619 10.38 0.00 0.00 4.46
1733 7697 5.629079 AAATCCGTTGAATCAAAGAGACC 57.371 39.130 10.38 0.00 0.00 3.85
1734 7698 6.668323 TGAAAATCCGTTGAATCAAAGAGAC 58.332 36.000 10.38 0.00 0.00 3.36
1735 7699 6.875948 TGAAAATCCGTTGAATCAAAGAGA 57.124 33.333 10.38 6.54 0.00 3.10
1736 7700 7.912250 CCTATGAAAATCCGTTGAATCAAAGAG 59.088 37.037 10.38 1.52 0.00 2.85
1737 7701 7.609918 TCCTATGAAAATCCGTTGAATCAAAGA 59.390 33.333 10.38 5.09 0.00 2.52
1738 7702 7.761409 TCCTATGAAAATCCGTTGAATCAAAG 58.239 34.615 0.00 0.00 0.00 2.77
1739 7703 7.695480 TCCTATGAAAATCCGTTGAATCAAA 57.305 32.000 0.00 0.00 0.00 2.69
1740 7704 7.775093 AGATCCTATGAAAATCCGTTGAATCAA 59.225 33.333 0.00 0.00 0.00 2.57
1741 7705 7.282585 AGATCCTATGAAAATCCGTTGAATCA 58.717 34.615 0.00 0.00 0.00 2.57
1742 7706 7.736447 AGATCCTATGAAAATCCGTTGAATC 57.264 36.000 0.00 0.00 0.00 2.52
1743 7707 8.408601 CAAAGATCCTATGAAAATCCGTTGAAT 58.591 33.333 0.00 0.00 0.00 2.57
1744 7708 7.609918 TCAAAGATCCTATGAAAATCCGTTGAA 59.390 33.333 0.00 0.00 0.00 2.69
1745 7709 7.109501 TCAAAGATCCTATGAAAATCCGTTGA 58.890 34.615 0.00 0.00 0.00 3.18
1746 7710 7.320443 TCAAAGATCCTATGAAAATCCGTTG 57.680 36.000 0.00 0.00 0.00 4.10
1747 7711 7.067494 CCTTCAAAGATCCTATGAAAATCCGTT 59.933 37.037 6.81 0.00 33.08 4.44
1748 7712 6.543831 CCTTCAAAGATCCTATGAAAATCCGT 59.456 38.462 6.81 0.00 33.08 4.69
1749 7713 6.767902 TCCTTCAAAGATCCTATGAAAATCCG 59.232 38.462 6.81 0.00 33.08 4.18
1750 7714 8.703378 ATCCTTCAAAGATCCTATGAAAATCC 57.297 34.615 6.81 0.00 33.08 3.01
1753 7717 9.973661 TGTAATCCTTCAAAGATCCTATGAAAA 57.026 29.630 6.81 0.82 33.08 2.29
1754 7718 9.973661 TTGTAATCCTTCAAAGATCCTATGAAA 57.026 29.630 6.81 0.00 33.08 2.69
1756 7720 9.565090 CATTGTAATCCTTCAAAGATCCTATGA 57.435 33.333 0.00 0.00 0.00 2.15
1757 7721 8.295288 GCATTGTAATCCTTCAAAGATCCTATG 58.705 37.037 0.00 0.00 0.00 2.23
1758 7722 8.223330 AGCATTGTAATCCTTCAAAGATCCTAT 58.777 33.333 0.00 0.00 0.00 2.57
1759 7723 7.577303 AGCATTGTAATCCTTCAAAGATCCTA 58.423 34.615 0.00 0.00 0.00 2.94
1760 7724 6.430007 AGCATTGTAATCCTTCAAAGATCCT 58.570 36.000 0.00 0.00 0.00 3.24
1761 7725 6.705863 AGCATTGTAATCCTTCAAAGATCC 57.294 37.500 0.00 0.00 0.00 3.36
1762 7726 8.348507 CCTAAGCATTGTAATCCTTCAAAGATC 58.651 37.037 0.00 0.00 0.00 2.75
1763 7727 8.055181 TCCTAAGCATTGTAATCCTTCAAAGAT 58.945 33.333 0.00 0.00 0.00 2.40
1764 7728 7.402054 TCCTAAGCATTGTAATCCTTCAAAGA 58.598 34.615 0.00 0.00 0.00 2.52
1765 7729 7.630242 TCCTAAGCATTGTAATCCTTCAAAG 57.370 36.000 0.00 0.00 0.00 2.77
1766 7730 8.415950 TTTCCTAAGCATTGTAATCCTTCAAA 57.584 30.769 0.00 0.00 0.00 2.69
1767 7731 8.593945 ATTTCCTAAGCATTGTAATCCTTCAA 57.406 30.769 0.00 0.00 0.00 2.69
1768 7732 8.593945 AATTTCCTAAGCATTGTAATCCTTCA 57.406 30.769 0.00 0.00 0.00 3.02
1769 7733 9.875691 AAAATTTCCTAAGCATTGTAATCCTTC 57.124 29.630 0.00 0.00 0.00 3.46
1770 7734 9.875691 GAAAATTTCCTAAGCATTGTAATCCTT 57.124 29.630 0.00 0.00 0.00 3.36
1771 7735 8.478066 GGAAAATTTCCTAAGCATTGTAATCCT 58.522 33.333 17.01 0.00 46.57 3.24
1772 7736 8.648557 GGAAAATTTCCTAAGCATTGTAATCC 57.351 34.615 17.01 0.00 46.57 3.01
1788 7752 7.142680 TCAAACGACCAATGTAGGAAAATTTC 58.857 34.615 0.00 0.00 0.00 2.17
1789 7753 7.045126 TCAAACGACCAATGTAGGAAAATTT 57.955 32.000 0.00 0.00 0.00 1.82
1790 7754 6.642707 TCAAACGACCAATGTAGGAAAATT 57.357 33.333 0.00 0.00 0.00 1.82
1791 7755 6.834168 ATCAAACGACCAATGTAGGAAAAT 57.166 33.333 0.00 0.00 0.00 1.82
1792 7756 6.566942 CGAATCAAACGACCAATGTAGGAAAA 60.567 38.462 0.00 0.00 0.00 2.29
1793 7757 5.106869 CGAATCAAACGACCAATGTAGGAAA 60.107 40.000 0.00 0.00 0.00 3.13
1794 7758 4.390603 CGAATCAAACGACCAATGTAGGAA 59.609 41.667 0.00 0.00 0.00 3.36
1795 7759 3.930229 CGAATCAAACGACCAATGTAGGA 59.070 43.478 0.00 0.00 0.00 2.94
1796 7760 3.682858 ACGAATCAAACGACCAATGTAGG 59.317 43.478 0.00 0.00 34.70 3.18
1797 7761 4.921470 ACGAATCAAACGACCAATGTAG 57.079 40.909 0.00 0.00 34.70 2.74
1798 7762 4.865925 CCTACGAATCAAACGACCAATGTA 59.134 41.667 0.00 0.00 34.70 2.29
1799 7763 3.682858 CCTACGAATCAAACGACCAATGT 59.317 43.478 0.00 0.00 34.70 2.71
1800 7764 3.930229 TCCTACGAATCAAACGACCAATG 59.070 43.478 0.00 0.00 34.70 2.82
1801 7765 4.196626 TCCTACGAATCAAACGACCAAT 57.803 40.909 0.00 0.00 34.70 3.16
1802 7766 3.663995 TCCTACGAATCAAACGACCAA 57.336 42.857 0.00 0.00 34.70 3.67
1803 7767 3.880047 ATCCTACGAATCAAACGACCA 57.120 42.857 0.00 0.00 34.70 4.02
1804 7768 4.178540 TCAATCCTACGAATCAAACGACC 58.821 43.478 0.00 0.00 34.70 4.79
1805 7769 5.773239 TTCAATCCTACGAATCAAACGAC 57.227 39.130 0.00 0.00 34.70 4.34
1806 7770 5.522460 GGATTCAATCCTACGAATCAAACGA 59.478 40.000 9.43 0.00 46.12 3.85
1807 7771 5.738370 GGATTCAATCCTACGAATCAAACG 58.262 41.667 9.43 0.00 46.12 3.60
1839 7803 9.444600 GTAGTACACATGAATCCTTAGGAAAAA 57.555 33.333 4.56 0.00 34.34 1.94
1840 7804 8.598916 TGTAGTACACATGAATCCTTAGGAAAA 58.401 33.333 4.56 0.00 30.37 2.29
1841 7805 8.141298 TGTAGTACACATGAATCCTTAGGAAA 57.859 34.615 4.56 0.00 30.37 3.13
1842 7806 7.727578 TGTAGTACACATGAATCCTTAGGAA 57.272 36.000 4.56 0.00 30.37 3.36
1843 7807 7.914427 ATGTAGTACACATGAATCCTTAGGA 57.086 36.000 2.37 2.37 46.41 2.94
1856 7820 3.945981 TCCTGCGAAATGTAGTACACA 57.054 42.857 4.80 0.00 42.69 3.72
1857 7821 5.581085 AGAATTCCTGCGAAATGTAGTACAC 59.419 40.000 4.80 0.00 0.00 2.90
1858 7822 5.730550 AGAATTCCTGCGAAATGTAGTACA 58.269 37.500 5.24 5.24 0.00 2.90
1859 7823 7.277098 TGTTAGAATTCCTGCGAAATGTAGTAC 59.723 37.037 0.65 0.00 0.00 2.73
1860 7824 7.324935 TGTTAGAATTCCTGCGAAATGTAGTA 58.675 34.615 0.65 0.00 0.00 1.82
1861 7825 6.170506 TGTTAGAATTCCTGCGAAATGTAGT 58.829 36.000 0.65 0.00 0.00 2.73
1862 7826 6.662414 TGTTAGAATTCCTGCGAAATGTAG 57.338 37.500 0.65 0.00 0.00 2.74
1863 7827 6.260050 GGATGTTAGAATTCCTGCGAAATGTA 59.740 38.462 0.65 0.00 0.00 2.29
1864 7828 5.066505 GGATGTTAGAATTCCTGCGAAATGT 59.933 40.000 0.65 0.00 0.00 2.71
1865 7829 5.066375 TGGATGTTAGAATTCCTGCGAAATG 59.934 40.000 0.65 0.00 0.00 2.32
1866 7830 5.066505 GTGGATGTTAGAATTCCTGCGAAAT 59.933 40.000 0.65 0.00 0.00 2.17
1867 7831 4.394920 GTGGATGTTAGAATTCCTGCGAAA 59.605 41.667 0.65 0.00 0.00 3.46
1868 7832 3.938963 GTGGATGTTAGAATTCCTGCGAA 59.061 43.478 0.65 0.00 0.00 4.70
1869 7833 3.197766 AGTGGATGTTAGAATTCCTGCGA 59.802 43.478 0.65 0.00 0.00 5.10
1870 7834 3.535561 AGTGGATGTTAGAATTCCTGCG 58.464 45.455 0.65 0.00 0.00 5.18
1871 7835 3.879892 GGAGTGGATGTTAGAATTCCTGC 59.120 47.826 0.65 0.00 0.00 4.85
1872 7836 5.102953 TGGAGTGGATGTTAGAATTCCTG 57.897 43.478 0.65 0.00 0.00 3.86
1873 7837 5.501156 GTTGGAGTGGATGTTAGAATTCCT 58.499 41.667 0.65 0.00 0.00 3.36
1874 7838 4.640647 GGTTGGAGTGGATGTTAGAATTCC 59.359 45.833 0.65 0.00 0.00 3.01
1875 7839 5.501156 AGGTTGGAGTGGATGTTAGAATTC 58.499 41.667 0.00 0.00 0.00 2.17
1876 7840 5.251700 AGAGGTTGGAGTGGATGTTAGAATT 59.748 40.000 0.00 0.00 0.00 2.17
1877 7841 4.785376 AGAGGTTGGAGTGGATGTTAGAAT 59.215 41.667 0.00 0.00 0.00 2.40
1878 7842 4.168101 AGAGGTTGGAGTGGATGTTAGAA 58.832 43.478 0.00 0.00 0.00 2.10
1879 7843 3.791320 AGAGGTTGGAGTGGATGTTAGA 58.209 45.455 0.00 0.00 0.00 2.10
1880 7844 4.256920 CAAGAGGTTGGAGTGGATGTTAG 58.743 47.826 0.00 0.00 0.00 2.34
1881 7845 3.559171 GCAAGAGGTTGGAGTGGATGTTA 60.559 47.826 0.00 0.00 33.87 2.41
1882 7846 2.815589 GCAAGAGGTTGGAGTGGATGTT 60.816 50.000 0.00 0.00 33.87 2.71
1883 7847 1.271597 GCAAGAGGTTGGAGTGGATGT 60.272 52.381 0.00 0.00 33.87 3.06
1884 7848 1.271543 TGCAAGAGGTTGGAGTGGATG 60.272 52.381 0.00 0.00 33.87 3.51
1885 7849 1.067295 TGCAAGAGGTTGGAGTGGAT 58.933 50.000 0.00 0.00 33.87 3.41
1886 7850 0.843309 TTGCAAGAGGTTGGAGTGGA 59.157 50.000 0.00 0.00 35.16 4.02
1887 7851 1.202806 TCTTGCAAGAGGTTGGAGTGG 60.203 52.381 25.16 0.00 35.16 4.00
1888 7852 2.260844 TCTTGCAAGAGGTTGGAGTG 57.739 50.000 25.16 0.00 35.16 3.51
1889 7853 3.297134 TTTCTTGCAAGAGGTTGGAGT 57.703 42.857 27.02 0.00 35.16 3.85
1890 7854 3.192212 GGATTTCTTGCAAGAGGTTGGAG 59.808 47.826 27.02 0.00 35.16 3.86
1891 7855 3.157087 GGATTTCTTGCAAGAGGTTGGA 58.843 45.455 27.02 10.54 36.22 3.53
1892 7856 3.160269 AGGATTTCTTGCAAGAGGTTGG 58.840 45.455 27.02 1.05 36.22 3.77
1893 7857 4.861102 AAGGATTTCTTGCAAGAGGTTG 57.139 40.909 27.02 1.82 36.22 3.77
1894 7858 4.502087 GCAAAGGATTTCTTGCAAGAGGTT 60.502 41.667 27.02 16.57 35.03 3.50
1895 7859 3.006217 GCAAAGGATTTCTTGCAAGAGGT 59.994 43.478 27.02 19.84 35.03 3.85
1896 7860 3.257624 AGCAAAGGATTTCTTGCAAGAGG 59.742 43.478 27.02 12.35 35.03 3.69
1897 7861 4.516365 AGCAAAGGATTTCTTGCAAGAG 57.484 40.909 27.02 15.07 35.03 2.85
1898 7862 4.942761 AAGCAAAGGATTTCTTGCAAGA 57.057 36.364 25.16 25.16 35.03 3.02
1899 7863 5.049886 GGAAAAGCAAAGGATTTCTTGCAAG 60.050 40.000 20.81 20.81 35.03 4.01
1900 7864 4.815846 GGAAAAGCAAAGGATTTCTTGCAA 59.184 37.500 9.24 0.00 35.03 4.08
1901 7865 4.379652 GGAAAAGCAAAGGATTTCTTGCA 58.620 39.130 9.24 0.00 35.03 4.08
1902 7866 3.748048 GGGAAAAGCAAAGGATTTCTTGC 59.252 43.478 0.00 0.00 35.03 4.01
1903 7867 3.989817 CGGGAAAAGCAAAGGATTTCTTG 59.010 43.478 0.00 0.00 35.03 3.02
1904 7868 3.641436 ACGGGAAAAGCAAAGGATTTCTT 59.359 39.130 0.00 0.00 35.03 2.52
1905 7869 3.005791 CACGGGAAAAGCAAAGGATTTCT 59.994 43.478 0.00 0.00 35.03 2.52
1906 7870 3.005367 TCACGGGAAAAGCAAAGGATTTC 59.995 43.478 0.00 0.00 35.03 2.17
1907 7871 2.962421 TCACGGGAAAAGCAAAGGATTT 59.038 40.909 0.00 0.00 40.26 2.17
1908 7872 2.296190 GTCACGGGAAAAGCAAAGGATT 59.704 45.455 0.00 0.00 0.00 3.01
1909 7873 1.886542 GTCACGGGAAAAGCAAAGGAT 59.113 47.619 0.00 0.00 0.00 3.24
1910 7874 1.314730 GTCACGGGAAAAGCAAAGGA 58.685 50.000 0.00 0.00 0.00 3.36
1911 7875 1.028905 TGTCACGGGAAAAGCAAAGG 58.971 50.000 0.00 0.00 0.00 3.11
1912 7876 1.403679 TGTGTCACGGGAAAAGCAAAG 59.596 47.619 0.00 0.00 0.00 2.77
1913 7877 1.403679 CTGTGTCACGGGAAAAGCAAA 59.596 47.619 3.65 0.00 0.00 3.68
1914 7878 1.021202 CTGTGTCACGGGAAAAGCAA 58.979 50.000 3.65 0.00 0.00 3.91
1915 7879 0.107410 ACTGTGTCACGGGAAAAGCA 60.107 50.000 16.20 0.00 0.00 3.91
1916 7880 0.586802 GACTGTGTCACGGGAAAAGC 59.413 55.000 16.20 0.00 32.09 3.51
1917 7881 1.948104 TGACTGTGTCACGGGAAAAG 58.052 50.000 16.20 0.69 37.67 2.27
1918 7882 2.404923 TTGACTGTGTCACGGGAAAA 57.595 45.000 16.20 4.64 42.60 2.29
1919 7883 2.011222 GTTTGACTGTGTCACGGGAAA 58.989 47.619 16.20 11.02 42.60 3.13
1920 7884 1.066071 TGTTTGACTGTGTCACGGGAA 60.066 47.619 16.20 5.69 42.60 3.97
1921 7885 0.537653 TGTTTGACTGTGTCACGGGA 59.462 50.000 16.20 0.00 42.60 5.14
1922 7886 1.374560 TTGTTTGACTGTGTCACGGG 58.625 50.000 16.20 5.58 42.60 5.28
1923 7887 2.418628 AGTTTGTTTGACTGTGTCACGG 59.581 45.455 10.40 10.40 42.60 4.94
1924 7888 3.124466 TGAGTTTGTTTGACTGTGTCACG 59.876 43.478 0.00 0.00 42.60 4.35
1925 7889 4.678509 TGAGTTTGTTTGACTGTGTCAC 57.321 40.909 0.00 0.00 42.60 3.67
1926 7890 5.697473 TTTGAGTTTGTTTGACTGTGTCA 57.303 34.783 0.00 0.00 41.09 3.58
1927 7891 5.743872 GGATTTGAGTTTGTTTGACTGTGTC 59.256 40.000 0.00 0.00 0.00 3.67
1928 7892 5.418840 AGGATTTGAGTTTGTTTGACTGTGT 59.581 36.000 0.00 0.00 0.00 3.72
1929 7893 5.894807 AGGATTTGAGTTTGTTTGACTGTG 58.105 37.500 0.00 0.00 0.00 3.66
1930 7894 7.823745 ATAGGATTTGAGTTTGTTTGACTGT 57.176 32.000 0.00 0.00 0.00 3.55
1931 7895 8.454106 CCTATAGGATTTGAGTTTGTTTGACTG 58.546 37.037 14.11 0.00 37.39 3.51
1932 7896 7.611855 CCCTATAGGATTTGAGTTTGTTTGACT 59.388 37.037 21.07 0.00 38.24 3.41
1933 7897 7.610305 TCCCTATAGGATTTGAGTTTGTTTGAC 59.390 37.037 21.07 0.00 40.93 3.18
1934 7898 7.695055 TCCCTATAGGATTTGAGTTTGTTTGA 58.305 34.615 21.07 0.00 40.93 2.69
1935 7899 7.938140 TCCCTATAGGATTTGAGTTTGTTTG 57.062 36.000 21.07 0.00 40.93 2.93
1950 7914 4.627255 GCATGTCCATTGGATCCCTATAGG 60.627 50.000 12.27 12.27 32.73 2.57
1951 7915 4.521146 GCATGTCCATTGGATCCCTATAG 58.479 47.826 9.90 0.00 32.73 1.31
1952 7916 3.266772 GGCATGTCCATTGGATCCCTATA 59.733 47.826 9.90 0.00 32.73 1.31
1953 7917 2.042162 GGCATGTCCATTGGATCCCTAT 59.958 50.000 9.90 0.00 32.73 2.57
1954 7918 1.425066 GGCATGTCCATTGGATCCCTA 59.575 52.381 9.90 0.00 32.73 3.53
1955 7919 0.186873 GGCATGTCCATTGGATCCCT 59.813 55.000 9.90 0.00 32.73 4.20
1956 7920 0.106066 TGGCATGTCCATTGGATCCC 60.106 55.000 9.90 7.65 40.72 3.85
1957 7921 3.518766 TGGCATGTCCATTGGATCC 57.481 52.632 9.01 4.20 40.72 3.36
1966 7930 3.003689 CGTAGGATTGAAATGGCATGTCC 59.996 47.826 14.98 10.67 0.00 4.02
1967 7931 4.214980 CGTAGGATTGAAATGGCATGTC 57.785 45.455 10.86 10.86 0.00 3.06
1989 7953 7.078011 TGCAAAAACACAAAAATAGGGAAAC 57.922 32.000 0.00 0.00 0.00 2.78
1990 7954 6.881602 ACTGCAAAAACACAAAAATAGGGAAA 59.118 30.769 0.00 0.00 0.00 3.13
1991 7955 6.410540 ACTGCAAAAACACAAAAATAGGGAA 58.589 32.000 0.00 0.00 0.00 3.97
1992 7956 5.983540 ACTGCAAAAACACAAAAATAGGGA 58.016 33.333 0.00 0.00 0.00 4.20
1993 7957 5.236263 GGACTGCAAAAACACAAAAATAGGG 59.764 40.000 0.00 0.00 0.00 3.53
1994 7958 6.048509 AGGACTGCAAAAACACAAAAATAGG 58.951 36.000 0.00 0.00 0.00 2.57
1995 7959 8.702438 CATAGGACTGCAAAAACACAAAAATAG 58.298 33.333 0.00 0.00 0.00 1.73
1996 7960 8.417106 TCATAGGACTGCAAAAACACAAAAATA 58.583 29.630 0.00 0.00 0.00 1.40
1997 7961 7.271511 TCATAGGACTGCAAAAACACAAAAAT 58.728 30.769 0.00 0.00 0.00 1.82
1998 7962 6.634805 TCATAGGACTGCAAAAACACAAAAA 58.365 32.000 0.00 0.00 0.00 1.94
1999 7963 6.214191 TCATAGGACTGCAAAAACACAAAA 57.786 33.333 0.00 0.00 0.00 2.44
2000 7964 5.843673 TCATAGGACTGCAAAAACACAAA 57.156 34.783 0.00 0.00 0.00 2.83
2001 7965 5.843673 TTCATAGGACTGCAAAAACACAA 57.156 34.783 0.00 0.00 0.00 3.33
2002 7966 5.534278 TGATTCATAGGACTGCAAAAACACA 59.466 36.000 0.00 0.00 0.00 3.72
2003 7967 6.012658 TGATTCATAGGACTGCAAAAACAC 57.987 37.500 0.00 0.00 0.00 3.32
2004 7968 6.647334 TTGATTCATAGGACTGCAAAAACA 57.353 33.333 0.00 0.00 0.00 2.83
2005 7969 7.370383 TCTTTGATTCATAGGACTGCAAAAAC 58.630 34.615 4.57 0.00 0.00 2.43
2006 7970 7.309377 CCTCTTTGATTCATAGGACTGCAAAAA 60.309 37.037 4.57 0.00 0.00 1.94
2007 7971 6.151648 CCTCTTTGATTCATAGGACTGCAAAA 59.848 38.462 4.57 0.00 0.00 2.44
2008 7972 5.649395 CCTCTTTGATTCATAGGACTGCAAA 59.351 40.000 4.57 0.00 0.00 3.68
2009 7973 5.188434 CCTCTTTGATTCATAGGACTGCAA 58.812 41.667 4.57 0.00 0.00 4.08
2010 7974 4.774124 CCTCTTTGATTCATAGGACTGCA 58.226 43.478 4.57 0.00 0.00 4.41
2011 7975 3.563390 GCCTCTTTGATTCATAGGACTGC 59.437 47.826 12.17 4.39 0.00 4.40
2012 7976 4.133078 GGCCTCTTTGATTCATAGGACTG 58.867 47.826 12.17 0.00 32.21 3.51
2013 7977 3.137360 GGGCCTCTTTGATTCATAGGACT 59.863 47.826 0.84 0.00 35.54 3.85
2014 7978 3.137360 AGGGCCTCTTTGATTCATAGGAC 59.863 47.826 0.00 9.80 34.35 3.85
2015 7979 3.397527 AGGGCCTCTTTGATTCATAGGA 58.602 45.455 0.00 0.85 0.00 2.94
2016 7980 3.872459 AGGGCCTCTTTGATTCATAGG 57.128 47.619 0.00 5.38 0.00 2.57
2017 7981 7.645058 TTTTTAGGGCCTCTTTGATTCATAG 57.355 36.000 10.74 0.00 0.00 2.23
2116 8080 4.651778 TGAAGTTACAACTCCATCCTTGG 58.348 43.478 0.00 0.00 45.15 3.61
2173 8139 7.944729 ACTAGATATGTCCTTTTTGCATGTT 57.055 32.000 0.00 0.00 0.00 2.71
2184 8150 6.951198 CCTGGATACTCAACTAGATATGTCCT 59.049 42.308 0.00 0.00 37.61 3.85
2235 8201 3.070576 GACATGCAACAGGGGCCC 61.071 66.667 17.12 17.12 0.00 5.80


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

AutoCloner maintained by Alex Coulton.