Multiple sequence alignment - TraesCS3B01G235400

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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 TraesCS3B01G235400 chr3B 100.000 2390 0 0 1 2390 368117106 368114717 0.000000e+00 4414.0
1 TraesCS3B01G235400 chr3B 95.706 163 7 0 2020 2182 368107151 368106989 1.820000e-66 263.0
2 TraesCS3B01G235400 chr3B 96.694 121 4 0 1687 1807 187490317 187490197 4.030000e-48 202.0
3 TraesCS3B01G235400 chr3B 97.436 117 3 0 1687 1803 767289836 767289720 1.450000e-47 200.0
4 TraesCS3B01G235400 chr3B 95.868 121 5 0 1687 1807 246163970 246163850 1.870000e-46 196.0
5 TraesCS3B01G235400 chr3A 96.301 1703 42 17 1 1687 368523486 368521789 0.000000e+00 2776.0
6 TraesCS3B01G235400 chr3A 96.711 152 2 2 1808 1956 368521778 368521627 1.420000e-62 250.0
7 TraesCS3B01G235400 chr3D 95.991 1696 45 10 1 1687 281905479 281903798 0.000000e+00 2734.0
8 TraesCS3B01G235400 chr3D 95.930 172 6 1 1808 1978 281903787 281903616 6.510000e-71 278.0
9 TraesCS3B01G235400 chr3D 95.935 123 5 0 1687 1809 589208738 589208616 1.450000e-47 200.0
10 TraesCS3B01G235400 chr3D 85.641 195 17 8 2020 2207 272091167 272090977 6.740000e-46 195.0
11 TraesCS3B01G235400 chr3D 86.188 181 16 6 2020 2193 272086371 272086193 1.130000e-43 187.0
12 TraesCS3B01G235400 chr3D 84.615 130 17 2 59 187 345758100 345758227 2.490000e-25 126.0
13 TraesCS3B01G235400 chr3D 93.333 75 4 1 1960 2034 247889343 247889270 2.510000e-20 110.0
14 TraesCS3B01G235400 chr3D 98.361 61 1 0 1974 2034 152827198 152827258 9.030000e-20 108.0
15 TraesCS3B01G235400 chr3D 98.333 60 1 0 1975 2034 241405854 241405913 3.250000e-19 106.0
16 TraesCS3B01G235400 chr2D 91.901 284 18 2 2109 2390 331757896 331758176 2.230000e-105 392.0
17 TraesCS3B01G235400 chr2D 87.302 126 13 2 59 183 534132803 534132926 8.910000e-30 141.0
18 TraesCS3B01G235400 chr2D 86.154 130 15 2 59 187 609284292 609284419 1.150000e-28 137.0
19 TraesCS3B01G235400 chr7B 98.374 123 2 0 1687 1809 482820018 482819896 1.440000e-52 217.0
20 TraesCS3B01G235400 chr7B 96.694 121 4 0 1687 1807 630546873 630546993 4.030000e-48 202.0
21 TraesCS3B01G235400 chr6A 95.968 124 5 0 1689 1812 201366870 201366993 4.030000e-48 202.0
22 TraesCS3B01G235400 chr7A 95.902 122 5 0 1687 1808 33544235 33544114 5.210000e-47 198.0
23 TraesCS3B01G235400 chr7A 82.547 212 24 12 2020 2221 217767318 217767110 8.780000e-40 174.0
24 TraesCS3B01G235400 chr5B 94.444 126 7 0 1687 1812 563355350 563355475 6.740000e-46 195.0
25 TraesCS3B01G235400 chr5B 84.804 204 18 9 2020 2214 208429412 208429611 2.420000e-45 193.0
26 TraesCS3B01G235400 chr5B 82.547 212 24 12 2020 2221 325080833 325080625 8.780000e-40 174.0
27 TraesCS3B01G235400 chr5B 98.387 62 1 0 1973 2034 208429394 208429455 2.510000e-20 110.0
28 TraesCS3B01G235400 chr5B 79.470 151 28 2 38 187 704167751 704167899 1.170000e-18 104.0
29 TraesCS3B01G235400 chr6B 82.407 216 29 8 2020 2227 458495698 458495912 1.890000e-41 180.0
30 TraesCS3B01G235400 chr6B 82.547 212 24 12 2020 2221 415879357 415879565 8.780000e-40 174.0
31 TraesCS3B01G235400 chr6B 82.812 128 18 3 57 183 46348562 46348686 6.980000e-21 111.0
32 TraesCS3B01G235400 chr6B 98.361 61 1 0 1974 2034 458495681 458495741 9.030000e-20 108.0
33 TraesCS3B01G235400 chr4B 82.547 212 24 12 2020 2221 165291399 165291607 8.780000e-40 174.0
34 TraesCS3B01G235400 chr4B 98.361 61 1 0 1974 2034 439195473 439195533 9.030000e-20 108.0
35 TraesCS3B01G235400 chr4A 84.921 126 16 2 59 183 669391333 669391210 8.970000e-25 124.0
36 TraesCS3B01G235400 chr5D 91.954 87 6 1 2302 2388 541690342 541690257 1.160000e-23 121.0
37 TraesCS3B01G235400 chr2A 100.000 59 0 0 1978 2036 672091162 672091104 2.510000e-20 110.0
38 TraesCS3B01G235400 chr2A 100.000 58 0 0 1977 2034 233461328 233461385 9.030000e-20 108.0
39 TraesCS3B01G235400 chr1A 100.000 58 0 0 1977 2034 551164376 551164433 9.030000e-20 108.0
40 TraesCS3B01G235400 chr1B 79.245 159 24 7 26 181 196371007 196370855 4.200000e-18 102.0
41 TraesCS3B01G235400 chr2B 97.500 40 1 0 328 367 19447818 19447779 4.260000e-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 TraesCS3B01G235400 chr3B 368114717 368117106 2389 True 4414 4414 100.0000 1 2390 1 chr3B.!!$R4 2389
1 TraesCS3B01G235400 chr3A 368521627 368523486 1859 True 1513 2776 96.5060 1 1956 2 chr3A.!!$R1 1955
2 TraesCS3B01G235400 chr3D 281903616 281905479 1863 True 1506 2734 95.9605 1 1978 2 chr3D.!!$R5 1977

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
120 121 1.359848 GCATATGCTATAGCGCGGTT 58.64 50.0 19.09 7.2 45.83 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2094 0.032017 GGGGCTCCTCTTCTAGGTCA 60.032 60.0 0.0 0.0 46.62 4.02 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
104 105 5.692204 GTGTACAATGTCTCGCTAATAGCAT 59.308 40.000 13.15 0.00 42.58 3.79
120 121 1.359848 GCATATGCTATAGCGCGGTT 58.640 50.000 19.09 7.20 45.83 4.44
121 122 2.536365 GCATATGCTATAGCGCGGTTA 58.464 47.619 19.09 8.05 45.83 2.85
135 136 2.800544 CGCGGTTAAGCATGCTAATAGT 59.199 45.455 23.00 7.43 36.85 2.12
246 254 7.111455 CCATGTATACAATGCGTATTTCGTTTG 59.889 37.037 10.14 0.00 41.25 2.93
251 259 6.432802 ACAATGCGTATTTCGTTTGAAAAG 57.567 33.333 0.00 0.00 46.53 2.27
623 632 4.881850 AGAAAATATGTGGTAAAGGAGGCG 59.118 41.667 0.00 0.00 0.00 5.52
811 820 4.911390 AGGCAAGTATTAGTTGAGCTTGT 58.089 39.130 14.17 0.00 38.84 3.16
898 913 1.803334 TTTATGTGCCTGGTCACGAC 58.197 50.000 13.83 0.00 39.73 4.34
1003 1018 5.643348 TCTGCGTTATGATTGAAACTGATGT 59.357 36.000 0.00 0.00 0.00 3.06
1193 1208 1.239296 CCTGCTGCAGTTGCTAAGCA 61.239 55.000 26.41 15.52 44.40 3.91
1255 1270 2.302199 ATCCGAAGATGAGCAGCGCA 62.302 55.000 11.47 0.00 0.00 6.09
1319 1334 1.069924 CGTGACGCTGCTGAGAAGAG 61.070 60.000 0.48 0.00 0.00 2.85
1421 1440 1.751927 CCTGCTGGCCTTGGATGTC 60.752 63.158 3.32 0.00 0.00 3.06
1444 1463 1.755783 CTCCCCCTGCAATTCCAGC 60.756 63.158 0.00 0.00 0.00 4.85
1507 1526 2.942376 CAAATAGTATGGCTTGGCGTGA 59.058 45.455 0.00 0.00 0.00 4.35
1568 1587 2.561419 TCCAGTCTCTAGGAAACGGTTG 59.439 50.000 0.00 0.00 0.00 3.77
1619 1638 6.657117 TGGAGTCTATTCTGGAGATATTCTCG 59.343 42.308 0.00 0.00 44.28 4.04
1626 1645 1.132588 GGAGATATTCTCGCGCACAC 58.867 55.000 8.75 0.00 44.28 3.82
1687 1707 0.908656 AGCCTGTCTGGAGATGTGCT 60.909 55.000 0.00 0.00 38.35 4.40
1689 1709 0.900421 CCTGTCTGGAGATGTGCTGA 59.100 55.000 0.00 0.00 38.35 4.26
1691 1711 0.248565 TGTCTGGAGATGTGCTGAGC 59.751 55.000 0.00 0.00 0.00 4.26
1692 1712 0.536260 GTCTGGAGATGTGCTGAGCT 59.464 55.000 5.83 0.00 0.00 4.09
1694 1714 1.206610 TCTGGAGATGTGCTGAGCTTC 59.793 52.381 5.83 0.03 0.00 3.86
1695 1715 0.978907 TGGAGATGTGCTGAGCTTCA 59.021 50.000 5.83 5.66 0.00 3.02
1696 1716 1.066358 TGGAGATGTGCTGAGCTTCAG 60.066 52.381 5.83 8.34 46.90 3.02
1697 1717 1.066286 GGAGATGTGCTGAGCTTCAGT 60.066 52.381 5.83 0.00 45.94 3.41
1698 1718 2.001159 GAGATGTGCTGAGCTTCAGTG 58.999 52.381 5.83 0.00 45.94 3.66
1699 1719 0.447011 GATGTGCTGAGCTTCAGTGC 59.553 55.000 5.83 7.93 45.94 4.40
1700 1720 0.959372 ATGTGCTGAGCTTCAGTGCC 60.959 55.000 5.83 4.50 45.94 5.01
1701 1721 1.598962 GTGCTGAGCTTCAGTGCCA 60.599 57.895 5.83 2.88 45.94 4.92
1702 1722 0.959372 GTGCTGAGCTTCAGTGCCAT 60.959 55.000 5.83 0.00 45.94 4.40
1703 1723 0.614812 TGCTGAGCTTCAGTGCCATA 59.385 50.000 5.83 0.00 45.94 2.74
1704 1724 1.003464 TGCTGAGCTTCAGTGCCATAA 59.997 47.619 5.83 0.00 45.94 1.90
1705 1725 1.399791 GCTGAGCTTCAGTGCCATAAC 59.600 52.381 0.00 0.00 45.94 1.89
1706 1726 2.938756 GCTGAGCTTCAGTGCCATAACT 60.939 50.000 0.00 0.00 45.94 2.24
1707 1727 5.022100 GCTGAGCTTCAGTGCCATAACTG 62.022 52.174 0.00 0.00 45.94 3.16
1708 1728 1.399791 GAGCTTCAGTGCCATAACTGC 59.600 52.381 0.00 0.00 45.93 4.40
1709 1729 1.167851 GCTTCAGTGCCATAACTGCA 58.832 50.000 0.00 0.00 45.93 4.41
1714 1734 4.001248 TGCCATAACTGCACCTGC 57.999 55.556 0.00 0.00 42.50 4.85
1725 1745 2.987547 CACCTGCAGTTGGGCCAG 60.988 66.667 13.81 0.00 0.00 4.85
1726 1746 3.501911 ACCTGCAGTTGGGCCAGT 61.502 61.111 13.81 0.00 0.00 4.00
1727 1747 2.987547 CCTGCAGTTGGGCCAGTG 60.988 66.667 13.81 10.07 0.00 3.66
1728 1748 2.113774 CTGCAGTTGGGCCAGTGA 59.886 61.111 19.26 0.00 0.00 3.41
1729 1749 2.203337 TGCAGTTGGGCCAGTGAC 60.203 61.111 19.26 10.14 0.00 3.67
1730 1750 2.203337 GCAGTTGGGCCAGTGACA 60.203 61.111 19.26 0.00 0.00 3.58
1731 1751 1.604593 GCAGTTGGGCCAGTGACAT 60.605 57.895 19.26 0.00 0.00 3.06
1732 1752 1.870055 GCAGTTGGGCCAGTGACATG 61.870 60.000 19.26 10.64 0.00 3.21
1733 1753 0.538057 CAGTTGGGCCAGTGACATGT 60.538 55.000 6.23 0.00 0.00 3.21
1734 1754 0.538057 AGTTGGGCCAGTGACATGTG 60.538 55.000 6.23 0.00 0.00 3.21
1735 1755 1.228521 TTGGGCCAGTGACATGTGG 60.229 57.895 6.23 0.00 36.85 4.17
1736 1756 2.361610 GGGCCAGTGACATGTGGG 60.362 66.667 1.15 0.06 34.06 4.61
1738 1758 3.064324 GCCAGTGACATGTGGGCC 61.064 66.667 1.15 0.00 38.70 5.80
1739 1759 2.759114 CCAGTGACATGTGGGCCT 59.241 61.111 1.15 0.00 0.00 5.19
1740 1760 1.990424 CCAGTGACATGTGGGCCTA 59.010 57.895 1.15 0.00 0.00 3.93
1741 1761 0.327924 CCAGTGACATGTGGGCCTAA 59.672 55.000 1.15 0.00 0.00 2.69
1742 1762 1.453155 CAGTGACATGTGGGCCTAAC 58.547 55.000 1.15 1.86 0.00 2.34
1743 1763 1.064003 AGTGACATGTGGGCCTAACA 58.936 50.000 1.15 13.18 0.00 2.41
1744 1764 1.003580 AGTGACATGTGGGCCTAACAG 59.996 52.381 1.15 10.70 0.00 3.16
1745 1765 1.003118 GTGACATGTGGGCCTAACAGA 59.997 52.381 1.15 0.00 0.00 3.41
1746 1766 1.915489 TGACATGTGGGCCTAACAGAT 59.085 47.619 1.15 7.52 0.00 2.90
1747 1767 2.292267 GACATGTGGGCCTAACAGATG 58.708 52.381 1.15 13.76 43.08 2.90
1748 1768 1.064463 ACATGTGGGCCTAACAGATGG 60.064 52.381 17.86 10.17 42.11 3.51
1753 1773 3.833304 GCCTAACAGATGGCTGGC 58.167 61.111 0.00 0.00 46.60 4.85
1754 1774 1.825622 GCCTAACAGATGGCTGGCC 60.826 63.158 4.43 4.43 46.60 5.36
1755 1775 1.152881 CCTAACAGATGGCTGGCCC 60.153 63.158 9.28 0.00 46.60 5.80
1769 1789 2.894919 GCCCACATGCCATTGACC 59.105 61.111 0.00 0.00 0.00 4.02
1770 1790 2.724273 GCCCACATGCCATTGACCC 61.724 63.158 0.00 0.00 0.00 4.46
1771 1791 1.305129 CCCACATGCCATTGACCCA 60.305 57.895 0.00 0.00 0.00 4.51
1772 1792 0.903924 CCCACATGCCATTGACCCAA 60.904 55.000 0.00 0.00 0.00 4.12
1773 1793 0.247185 CCACATGCCATTGACCCAAC 59.753 55.000 0.00 0.00 0.00 3.77
1774 1794 1.259609 CACATGCCATTGACCCAACT 58.740 50.000 0.00 0.00 0.00 3.16
1775 1795 1.067425 CACATGCCATTGACCCAACTG 60.067 52.381 0.00 0.00 0.00 3.16
1776 1796 0.108520 CATGCCATTGACCCAACTGC 60.109 55.000 0.00 0.00 0.00 4.40
1777 1797 0.542467 ATGCCATTGACCCAACTGCA 60.542 50.000 7.20 7.20 37.52 4.41
1778 1798 1.180456 TGCCATTGACCCAACTGCAG 61.180 55.000 13.48 13.48 31.46 4.41
1779 1799 1.880819 GCCATTGACCCAACTGCAGG 61.881 60.000 19.93 2.94 0.00 4.85
1780 1800 0.540365 CCATTGACCCAACTGCAGGT 60.540 55.000 19.93 9.19 39.75 4.00
1781 1801 0.599558 CATTGACCCAACTGCAGGTG 59.400 55.000 25.38 25.38 36.17 4.00
1782 1802 1.181098 ATTGACCCAACTGCAGGTGC 61.181 55.000 26.87 13.45 36.17 5.01
1792 1812 2.668212 GCAGGTGCAGTTACGGCA 60.668 61.111 6.01 6.01 41.59 5.69
1797 1817 2.422165 TGCAGTTACGGCACCGAA 59.578 55.556 17.40 3.00 42.83 4.30
1798 1818 1.666553 TGCAGTTACGGCACCGAAG 60.667 57.895 17.40 1.68 42.83 3.79
1799 1819 3.023591 GCAGTTACGGCACCGAAGC 62.024 63.158 17.40 8.00 42.83 3.86
1800 1820 1.666553 CAGTTACGGCACCGAAGCA 60.667 57.895 17.40 0.00 42.83 3.91
1801 1821 1.374252 AGTTACGGCACCGAAGCAG 60.374 57.895 17.40 0.02 42.83 4.24
1802 1822 2.740826 TTACGGCACCGAAGCAGC 60.741 61.111 17.40 0.00 42.83 5.25
1811 1831 2.604174 CCGAAGCAGCGTCCGTTTT 61.604 57.895 2.43 0.00 0.00 2.43
1842 1862 2.050144 AGACTCACCTTCAGCCTTCAA 58.950 47.619 0.00 0.00 0.00 2.69
1881 1903 9.976255 TGTTGCAATAATCAACGTTTATAGTAC 57.024 29.630 0.59 0.00 44.88 2.73
1994 2016 1.249407 TTTGTTGAACCGGTATGGGC 58.751 50.000 8.00 0.00 44.64 5.36
1995 2017 0.609681 TTGTTGAACCGGTATGGGCC 60.610 55.000 8.00 0.00 44.64 5.80
1996 2018 1.751544 GTTGAACCGGTATGGGCCC 60.752 63.158 17.59 17.59 44.64 5.80
1997 2019 1.926489 TTGAACCGGTATGGGCCCT 60.926 57.895 25.70 11.37 44.64 5.19
1998 2020 0.620990 TTGAACCGGTATGGGCCCTA 60.621 55.000 25.70 10.18 44.64 3.53
1999 2021 1.052124 TGAACCGGTATGGGCCCTAG 61.052 60.000 25.70 9.38 44.64 3.02
2000 2022 2.393144 GAACCGGTATGGGCCCTAGC 62.393 65.000 25.70 19.83 44.64 3.42
2011 2033 3.641017 GCCCTAGCCCATCAAGATC 57.359 57.895 0.00 0.00 0.00 2.75
2012 2034 1.063183 GCCCTAGCCCATCAAGATCT 58.937 55.000 0.00 0.00 0.00 2.75
2013 2035 1.271271 GCCCTAGCCCATCAAGATCTG 60.271 57.143 0.00 0.00 0.00 2.90
2014 2036 2.053244 CCCTAGCCCATCAAGATCTGT 58.947 52.381 0.00 0.00 0.00 3.41
2015 2037 2.038295 CCCTAGCCCATCAAGATCTGTC 59.962 54.545 0.00 0.00 0.00 3.51
2016 2038 2.971330 CCTAGCCCATCAAGATCTGTCT 59.029 50.000 0.00 0.00 35.82 3.41
2017 2039 3.006752 CCTAGCCCATCAAGATCTGTCTC 59.993 52.174 0.00 0.00 32.15 3.36
2018 2040 2.761809 AGCCCATCAAGATCTGTCTCT 58.238 47.619 0.00 0.00 32.15 3.10
2019 2041 3.113824 AGCCCATCAAGATCTGTCTCTT 58.886 45.455 0.00 0.00 35.88 2.85
2024 2046 2.035530 CAAGATCTGTCTCTTGGGCC 57.964 55.000 0.00 0.00 45.46 5.80
2025 2047 0.915364 AAGATCTGTCTCTTGGGCCC 59.085 55.000 17.59 17.59 34.22 5.80
2026 2048 0.252881 AGATCTGTCTCTTGGGCCCA 60.253 55.000 24.45 24.45 0.00 5.36
2027 2049 0.620556 GATCTGTCTCTTGGGCCCAA 59.379 55.000 34.90 34.90 0.00 4.12
2039 2061 4.692930 GCCCAAGCCCATCAAGAT 57.307 55.556 0.00 0.00 0.00 2.40
2040 2062 2.423388 GCCCAAGCCCATCAAGATC 58.577 57.895 0.00 0.00 0.00 2.75
2041 2063 0.106318 GCCCAAGCCCATCAAGATCT 60.106 55.000 0.00 0.00 0.00 2.75
2042 2064 1.688772 CCCAAGCCCATCAAGATCTG 58.311 55.000 0.00 0.00 0.00 2.90
2043 2065 1.064166 CCCAAGCCCATCAAGATCTGT 60.064 52.381 0.00 0.00 0.00 3.41
2044 2066 2.295885 CCAAGCCCATCAAGATCTGTC 58.704 52.381 0.00 0.00 0.00 3.51
2045 2067 2.092538 CCAAGCCCATCAAGATCTGTCT 60.093 50.000 0.00 0.00 35.82 3.41
2046 2068 3.204526 CAAGCCCATCAAGATCTGTCTC 58.795 50.000 0.00 0.00 32.15 3.36
2047 2069 2.761809 AGCCCATCAAGATCTGTCTCT 58.238 47.619 0.00 0.00 32.15 3.10
2048 2070 3.113824 AGCCCATCAAGATCTGTCTCTT 58.886 45.455 0.00 0.00 35.88 2.85
2053 2075 2.035530 CAAGATCTGTCTCTTGGGCC 57.964 55.000 0.00 0.00 45.46 5.80
2054 2076 0.915364 AAGATCTGTCTCTTGGGCCC 59.085 55.000 17.59 17.59 34.22 5.80
2055 2077 0.252881 AGATCTGTCTCTTGGGCCCA 60.253 55.000 24.45 24.45 0.00 5.36
2056 2078 0.620556 GATCTGTCTCTTGGGCCCAA 59.379 55.000 34.90 34.90 0.00 4.12
2068 2090 2.123982 GCCCAAGCCCATGAGAGG 60.124 66.667 0.00 0.00 0.00 3.69
2069 2091 2.988839 GCCCAAGCCCATGAGAGGT 61.989 63.158 0.00 0.00 0.00 3.85
2070 2092 1.077212 CCCAAGCCCATGAGAGGTG 60.077 63.158 0.00 0.00 0.00 4.00
2071 2093 1.751927 CCAAGCCCATGAGAGGTGC 60.752 63.158 0.00 0.00 0.00 5.01
2072 2094 1.302285 CAAGCCCATGAGAGGTGCT 59.698 57.895 0.00 0.00 36.96 4.40
2073 2095 1.030488 CAAGCCCATGAGAGGTGCTG 61.030 60.000 0.00 0.00 36.00 4.41
2074 2096 1.203441 AAGCCCATGAGAGGTGCTGA 61.203 55.000 0.00 0.00 36.00 4.26
2075 2097 1.451028 GCCCATGAGAGGTGCTGAC 60.451 63.158 0.00 0.00 0.00 3.51
2076 2098 1.222936 CCCATGAGAGGTGCTGACC 59.777 63.158 0.00 0.00 43.52 4.02
2100 2122 4.439901 AGGAGCCCCTCTTCCCCC 62.440 72.222 0.00 0.00 38.86 5.40
2101 2123 4.439901 GGAGCCCCTCTTCCCCCT 62.440 72.222 0.00 0.00 0.00 4.79
2102 2124 3.093172 GAGCCCCTCTTCCCCCTG 61.093 72.222 0.00 0.00 0.00 4.45
2103 2125 3.952799 GAGCCCCTCTTCCCCCTGT 62.953 68.421 0.00 0.00 0.00 4.00
2104 2126 3.412408 GCCCCTCTTCCCCCTGTC 61.412 72.222 0.00 0.00 0.00 3.51
2105 2127 2.692741 CCCCTCTTCCCCCTGTCC 60.693 72.222 0.00 0.00 0.00 4.02
2106 2128 2.692741 CCCTCTTCCCCCTGTCCC 60.693 72.222 0.00 0.00 0.00 4.46
2107 2129 3.083997 CCTCTTCCCCCTGTCCCG 61.084 72.222 0.00 0.00 0.00 5.14
2108 2130 2.284699 CTCTTCCCCCTGTCCCGT 60.285 66.667 0.00 0.00 0.00 5.28
2109 2131 2.606519 TCTTCCCCCTGTCCCGTG 60.607 66.667 0.00 0.00 0.00 4.94
2110 2132 4.410400 CTTCCCCCTGTCCCGTGC 62.410 72.222 0.00 0.00 0.00 5.34
2113 2135 4.722700 CCCCCTGTCCCGTGCAAG 62.723 72.222 0.00 0.00 0.00 4.01
2124 2146 4.030452 GTGCAAGCCGCCACAGAC 62.030 66.667 0.00 0.00 41.33 3.51
2125 2147 4.560743 TGCAAGCCGCCACAGACA 62.561 61.111 0.00 0.00 41.33 3.41
2126 2148 4.030452 GCAAGCCGCCACAGACAC 62.030 66.667 0.00 0.00 32.94 3.67
2127 2149 3.357079 CAAGCCGCCACAGACACC 61.357 66.667 0.00 0.00 0.00 4.16
2128 2150 3.872603 AAGCCGCCACAGACACCA 61.873 61.111 0.00 0.00 0.00 4.17
2129 2151 3.414136 AAGCCGCCACAGACACCAA 62.414 57.895 0.00 0.00 0.00 3.67
2130 2152 2.902423 AAGCCGCCACAGACACCAAA 62.902 55.000 0.00 0.00 0.00 3.28
2131 2153 3.030652 CCGCCACAGACACCAAAC 58.969 61.111 0.00 0.00 0.00 2.93
2132 2154 2.551912 CCGCCACAGACACCAAACC 61.552 63.158 0.00 0.00 0.00 3.27
2133 2155 2.551912 CGCCACAGACACCAAACCC 61.552 63.158 0.00 0.00 0.00 4.11
2134 2156 1.454847 GCCACAGACACCAAACCCA 60.455 57.895 0.00 0.00 0.00 4.51
2135 2157 1.734388 GCCACAGACACCAAACCCAC 61.734 60.000 0.00 0.00 0.00 4.61
2136 2158 1.444119 CCACAGACACCAAACCCACG 61.444 60.000 0.00 0.00 0.00 4.94
2137 2159 1.822186 ACAGACACCAAACCCACGC 60.822 57.895 0.00 0.00 0.00 5.34
2138 2160 2.590575 AGACACCAAACCCACGCG 60.591 61.111 3.53 3.53 0.00 6.01
2139 2161 2.589442 GACACCAAACCCACGCGA 60.589 61.111 15.93 0.00 0.00 5.87
2140 2162 2.590575 ACACCAAACCCACGCGAG 60.591 61.111 15.93 4.16 0.00 5.03
2141 2163 4.025401 CACCAAACCCACGCGAGC 62.025 66.667 15.93 0.00 0.00 5.03
2144 2166 4.072088 CAAACCCACGCGAGCGAC 62.072 66.667 24.72 0.00 42.83 5.19
2150 2172 4.700365 CACGCGAGCGACCAGACA 62.700 66.667 24.72 0.00 42.83 3.41
2151 2173 4.702081 ACGCGAGCGACCAGACAC 62.702 66.667 24.72 0.00 42.83 3.67
2153 2175 4.400109 GCGAGCGACCAGACACGA 62.400 66.667 0.00 0.00 0.00 4.35
2154 2176 2.202362 CGAGCGACCAGACACGAG 60.202 66.667 0.00 0.00 0.00 4.18
2155 2177 2.677979 CGAGCGACCAGACACGAGA 61.678 63.158 0.00 0.00 0.00 4.04
2156 2178 1.135731 GAGCGACCAGACACGAGAG 59.864 63.158 0.00 0.00 0.00 3.20
2168 2190 3.441241 ACGAGAGTGAACCCTGTCT 57.559 52.632 0.00 0.00 46.97 3.41
2169 2191 2.581216 ACGAGAGTGAACCCTGTCTA 57.419 50.000 0.00 0.00 46.97 2.59
2170 2192 2.872732 ACGAGAGTGAACCCTGTCTAA 58.127 47.619 0.00 0.00 46.97 2.10
2171 2193 3.228453 ACGAGAGTGAACCCTGTCTAAA 58.772 45.455 0.00 0.00 46.97 1.85
2172 2194 3.256136 ACGAGAGTGAACCCTGTCTAAAG 59.744 47.826 0.00 0.00 46.97 1.85
2173 2195 3.367498 CGAGAGTGAACCCTGTCTAAAGG 60.367 52.174 0.00 0.00 37.05 3.11
2174 2196 3.579151 GAGAGTGAACCCTGTCTAAAGGT 59.421 47.826 0.00 0.00 35.34 3.50
2175 2197 4.748701 AGAGTGAACCCTGTCTAAAGGTA 58.251 43.478 0.00 0.00 35.34 3.08
2176 2198 4.527427 AGAGTGAACCCTGTCTAAAGGTAC 59.473 45.833 0.00 0.00 35.34 3.34
2177 2199 3.581770 AGTGAACCCTGTCTAAAGGTACC 59.418 47.826 2.73 2.73 35.34 3.34
2178 2200 2.908351 TGAACCCTGTCTAAAGGTACCC 59.092 50.000 8.74 0.00 35.34 3.69
2179 2201 1.962558 ACCCTGTCTAAAGGTACCCC 58.037 55.000 8.74 0.00 35.34 4.95
2180 2202 1.210538 CCCTGTCTAAAGGTACCCCC 58.789 60.000 8.74 0.00 35.34 5.40
2205 2227 6.379386 CATGATTCAACATGGTATCAGATGC 58.621 40.000 2.80 0.00 42.45 3.91
2206 2228 4.823442 TGATTCAACATGGTATCAGATGCC 59.177 41.667 10.57 10.57 35.37 4.40
2207 2229 2.837498 TCAACATGGTATCAGATGCCG 58.163 47.619 12.51 2.40 37.93 5.69
2208 2230 1.875514 CAACATGGTATCAGATGCCGG 59.124 52.381 12.51 9.67 37.93 6.13
2209 2231 1.131638 ACATGGTATCAGATGCCGGT 58.868 50.000 12.51 10.26 37.93 5.28
2210 2232 1.202687 ACATGGTATCAGATGCCGGTG 60.203 52.381 12.51 14.76 37.93 4.94
2211 2233 1.070601 CATGGTATCAGATGCCGGTGA 59.929 52.381 12.51 0.00 37.93 4.02
2212 2234 0.464036 TGGTATCAGATGCCGGTGAC 59.536 55.000 12.51 0.00 37.93 3.67
2225 2247 3.775654 GTGACGGAGGGGCCTGAG 61.776 72.222 0.84 0.00 0.00 3.35
2237 2259 3.003173 CCTGAGGGCTGACGGGAA 61.003 66.667 0.00 0.00 34.76 3.97
2238 2260 2.581354 CTGAGGGCTGACGGGAAG 59.419 66.667 0.00 0.00 0.00 3.46
2239 2261 3.003173 TGAGGGCTGACGGGAAGG 61.003 66.667 0.00 0.00 0.00 3.46
2240 2262 3.787001 GAGGGCTGACGGGAAGGG 61.787 72.222 0.00 0.00 0.00 3.95
2245 2267 4.101448 CTGACGGGAAGGGGGCAG 62.101 72.222 0.00 0.00 0.00 4.85
2272 2294 4.074526 GCAGAGGTGCGCTGGAGA 62.075 66.667 9.73 0.00 40.71 3.71
2273 2295 2.183811 CAGAGGTGCGCTGGAGAG 59.816 66.667 9.73 0.00 0.00 3.20
2274 2296 3.073735 AGAGGTGCGCTGGAGAGG 61.074 66.667 9.73 0.00 0.00 3.69
2275 2297 3.071206 GAGGTGCGCTGGAGAGGA 61.071 66.667 9.73 0.00 0.00 3.71
2276 2298 3.363844 GAGGTGCGCTGGAGAGGAC 62.364 68.421 9.73 0.00 35.63 3.85
2278 2300 3.695606 GTGCGCTGGAGAGGACCA 61.696 66.667 9.73 0.00 38.33 4.02
2325 2347 2.742372 GGCGCTGCCTTCTTTCGA 60.742 61.111 7.64 0.00 46.69 3.71
2326 2348 2.744768 GGCGCTGCCTTCTTTCGAG 61.745 63.158 7.64 0.00 46.69 4.04
2327 2349 2.744768 GCGCTGCCTTCTTTCGAGG 61.745 63.158 0.00 0.00 37.35 4.63
2328 2350 1.079819 CGCTGCCTTCTTTCGAGGA 60.080 57.895 0.00 0.00 36.33 3.71
2329 2351 1.080995 CGCTGCCTTCTTTCGAGGAG 61.081 60.000 0.00 0.00 36.33 3.69
2330 2352 0.247736 GCTGCCTTCTTTCGAGGAGA 59.752 55.000 0.00 0.00 36.33 3.71
2331 2353 1.738700 GCTGCCTTCTTTCGAGGAGAG 60.739 57.143 0.00 0.00 36.33 3.20
2332 2354 0.898320 TGCCTTCTTTCGAGGAGAGG 59.102 55.000 3.85 3.85 36.33 3.69
2333 2355 0.461163 GCCTTCTTTCGAGGAGAGGC 60.461 60.000 13.71 13.71 36.33 4.70
2334 2356 0.179124 CCTTCTTTCGAGGAGAGGCG 60.179 60.000 4.97 0.00 36.33 5.52
2335 2357 0.179124 CTTCTTTCGAGGAGAGGCGG 60.179 60.000 1.59 0.00 0.00 6.13
2336 2358 2.202810 CTTTCGAGGAGAGGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
2337 2359 2.680352 TTTCGAGGAGAGGCGGCT 60.680 61.111 13.09 13.09 0.00 5.52
2338 2360 2.897641 CTTTCGAGGAGAGGCGGCTG 62.898 65.000 19.63 0.00 0.00 4.85
2339 2361 4.742649 TCGAGGAGAGGCGGCTGT 62.743 66.667 19.63 14.17 0.00 4.40
2340 2362 4.504916 CGAGGAGAGGCGGCTGTG 62.505 72.222 19.63 0.00 0.00 3.66
2341 2363 4.828925 GAGGAGAGGCGGCTGTGC 62.829 72.222 19.63 19.56 0.00 4.57
2377 2399 2.360350 ACGCAAGGCATGTCAGGG 60.360 61.111 0.00 2.47 46.39 4.45
2378 2400 3.818787 CGCAAGGCATGTCAGGGC 61.819 66.667 2.31 2.31 0.00 5.19
2379 2401 2.362120 GCAAGGCATGTCAGGGCT 60.362 61.111 7.88 7.88 43.79 5.19
2380 2402 2.707849 GCAAGGCATGTCAGGGCTG 61.708 63.158 14.81 9.74 41.44 4.85
2381 2403 2.362120 AAGGCATGTCAGGGCTGC 60.362 61.111 14.81 0.57 41.44 5.25
2382 2404 2.915504 AAGGCATGTCAGGGCTGCT 61.916 57.895 14.81 0.00 41.44 4.24
2383 2405 3.138798 GGCATGTCAGGGCTGCTG 61.139 66.667 3.47 0.00 36.18 4.41
2384 2406 3.823330 GCATGTCAGGGCTGCTGC 61.823 66.667 7.10 7.10 38.76 5.25
2385 2407 2.045242 CATGTCAGGGCTGCTGCT 60.045 61.111 15.64 0.00 39.59 4.24
2386 2408 2.045242 ATGTCAGGGCTGCTGCTG 60.045 61.111 15.64 7.00 39.59 4.41
2387 2409 2.599757 ATGTCAGGGCTGCTGCTGA 61.600 57.895 15.64 9.32 39.59 4.26
2388 2410 2.745492 GTCAGGGCTGCTGCTGAC 60.745 66.667 17.89 17.89 37.27 3.51
2389 2411 4.383861 TCAGGGCTGCTGCTGACG 62.384 66.667 15.64 2.43 39.59 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.416154 TTTTTCAGTGTGTATGCTACAGTAC 57.584 36.000 0.00 0.00 39.77 2.73
40 41 4.202357 CCATTCCTAGCAAGCCATAGTGTA 60.202 45.833 0.00 0.00 0.00 2.90
51 52 1.119684 TAGCGAGCCATTCCTAGCAA 58.880 50.000 0.00 0.00 36.14 3.91
104 105 2.029739 TGCTTAACCGCGCTATAGCATA 60.030 45.455 23.99 6.36 42.21 3.14
120 121 9.066892 CCTTAAAATCCACTATTAGCATGCTTA 57.933 33.333 28.02 18.49 0.00 3.09
121 122 7.470563 GCCTTAAAATCCACTATTAGCATGCTT 60.471 37.037 28.02 11.78 0.00 3.91
135 136 2.411504 GCGCCGGCCTTAAAATCCA 61.412 57.895 23.46 0.00 0.00 3.41
192 193 9.613428 AGGAGTATTTTTCAAATCGTGATCATA 57.387 29.630 0.00 0.00 35.70 2.15
898 913 9.892130 ACTAGGTCCTTGAATTATTAAGTGAAG 57.108 33.333 7.38 0.00 0.00 3.02
932 947 1.730612 GTAAGTTCTTTAGCGCGCCTT 59.269 47.619 30.33 22.92 0.00 4.35
1255 1270 2.026822 CCAGCATCCACTTGTAGACCTT 60.027 50.000 0.00 0.00 0.00 3.50
1319 1334 3.446516 AGCCTTCTCCTCATTGATTTTGC 59.553 43.478 0.00 0.00 0.00 3.68
1421 1440 1.827344 GGAATTGCAGGGGGAGAAAAG 59.173 52.381 0.00 0.00 0.00 2.27
1568 1587 7.712205 ACCATCATAATTTTGCATCTAAAAGGC 59.288 33.333 0.00 0.00 33.49 4.35
1619 1638 2.444351 GAGCAATCATTTAGTGTGCGC 58.556 47.619 0.00 0.00 0.00 6.09
1626 1645 5.870978 CCTTGGTTTTGGAGCAATCATTTAG 59.129 40.000 0.00 0.00 44.11 1.85
1687 1707 2.703416 CAGTTATGGCACTGAAGCTCA 58.297 47.619 0.00 0.00 46.29 4.26
1689 1709 1.271543 TGCAGTTATGGCACTGAAGCT 60.272 47.619 7.69 0.00 46.29 3.74
1697 1717 4.001248 GCAGGTGCAGTTATGGCA 57.999 55.556 0.00 0.00 41.59 4.92
1708 1728 2.987547 CTGGCCCAACTGCAGGTG 60.988 66.667 25.38 25.38 0.00 4.00
1709 1729 3.501911 ACTGGCCCAACTGCAGGT 61.502 61.111 19.93 9.19 0.00 4.00
1710 1730 2.987547 CACTGGCCCAACTGCAGG 60.988 66.667 19.93 1.24 0.00 4.85
1711 1731 2.113774 TCACTGGCCCAACTGCAG 59.886 61.111 13.48 13.48 0.00 4.41
1712 1732 2.203337 GTCACTGGCCCAACTGCA 60.203 61.111 0.00 0.00 0.00 4.41
1713 1733 1.604593 ATGTCACTGGCCCAACTGC 60.605 57.895 0.00 0.00 0.00 4.40
1714 1734 0.538057 ACATGTCACTGGCCCAACTG 60.538 55.000 0.00 0.00 0.00 3.16
1715 1735 0.538057 CACATGTCACTGGCCCAACT 60.538 55.000 0.00 0.00 0.00 3.16
1716 1736 1.526575 CCACATGTCACTGGCCCAAC 61.527 60.000 0.00 0.00 0.00 3.77
1717 1737 1.228521 CCACATGTCACTGGCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
1718 1738 2.435663 CCACATGTCACTGGCCCA 59.564 61.111 0.00 0.00 0.00 5.36
1719 1739 2.361610 CCCACATGTCACTGGCCC 60.362 66.667 0.00 0.00 0.00 5.80
1720 1740 3.064324 GCCCACATGTCACTGGCC 61.064 66.667 12.14 0.00 36.07 5.36
1721 1741 2.196997 TAGGCCCACATGTCACTGGC 62.197 60.000 14.02 14.02 41.42 4.85
1722 1742 0.327924 TTAGGCCCACATGTCACTGG 59.672 55.000 0.00 0.00 0.00 4.00
1723 1743 1.271325 TGTTAGGCCCACATGTCACTG 60.271 52.381 0.00 0.00 0.00 3.66
1724 1744 1.003580 CTGTTAGGCCCACATGTCACT 59.996 52.381 0.00 0.00 0.00 3.41
1725 1745 1.003118 TCTGTTAGGCCCACATGTCAC 59.997 52.381 0.00 0.00 0.00 3.67
1726 1746 1.357137 TCTGTTAGGCCCACATGTCA 58.643 50.000 0.00 0.00 0.00 3.58
1727 1747 2.292267 CATCTGTTAGGCCCACATGTC 58.708 52.381 0.00 0.00 0.00 3.06
1728 1748 1.064463 CCATCTGTTAGGCCCACATGT 60.064 52.381 0.00 0.00 0.00 3.21
1729 1749 1.683943 CCATCTGTTAGGCCCACATG 58.316 55.000 0.00 0.00 0.00 3.21
1730 1750 0.106519 GCCATCTGTTAGGCCCACAT 60.107 55.000 0.00 0.00 45.18 3.21
1731 1751 1.302949 GCCATCTGTTAGGCCCACA 59.697 57.895 0.00 1.28 45.18 4.17
1732 1752 4.242602 GCCATCTGTTAGGCCCAC 57.757 61.111 0.00 0.00 45.18 4.61
1737 1757 1.152881 GGGCCAGCCATCTGTTAGG 60.153 63.158 11.50 0.00 38.66 2.69
1738 1758 0.749454 GTGGGCCAGCCATCTGTTAG 60.749 60.000 6.40 0.00 38.66 2.34
1739 1759 1.302949 GTGGGCCAGCCATCTGTTA 59.697 57.895 6.40 0.00 38.66 2.41
1740 1760 2.036256 GTGGGCCAGCCATCTGTT 59.964 61.111 6.40 0.00 38.66 3.16
1741 1761 2.619446 ATGTGGGCCAGCCATCTGT 61.619 57.895 6.40 0.00 38.66 3.41
1742 1762 2.125326 CATGTGGGCCAGCCATCTG 61.125 63.158 6.40 0.00 40.02 2.90
1743 1763 2.277737 CATGTGGGCCAGCCATCT 59.722 61.111 6.40 0.00 37.98 2.90
1744 1764 3.534056 GCATGTGGGCCAGCCATC 61.534 66.667 6.40 0.00 37.98 3.51
1752 1772 2.724273 GGGTCAATGGCATGTGGGC 61.724 63.158 0.00 0.00 43.73 5.36
1753 1773 0.903924 TTGGGTCAATGGCATGTGGG 60.904 55.000 0.00 0.00 0.00 4.61
1754 1774 0.247185 GTTGGGTCAATGGCATGTGG 59.753 55.000 0.00 0.00 0.00 4.17
1755 1775 1.067425 CAGTTGGGTCAATGGCATGTG 60.067 52.381 0.00 1.95 0.00 3.21
1756 1776 1.259609 CAGTTGGGTCAATGGCATGT 58.740 50.000 0.00 0.00 0.00 3.21
1757 1777 0.108520 GCAGTTGGGTCAATGGCATG 60.109 55.000 0.00 0.00 0.00 4.06
1758 1778 0.542467 TGCAGTTGGGTCAATGGCAT 60.542 50.000 0.00 0.00 33.05 4.40
1759 1779 1.152589 TGCAGTTGGGTCAATGGCA 60.153 52.632 0.00 0.00 34.62 4.92
1760 1780 1.588082 CTGCAGTTGGGTCAATGGC 59.412 57.895 5.25 0.00 0.00 4.40
1761 1781 0.540365 ACCTGCAGTTGGGTCAATGG 60.540 55.000 13.81 0.00 0.00 3.16
1762 1782 0.599558 CACCTGCAGTTGGGTCAATG 59.400 55.000 13.81 0.00 32.95 2.82
1763 1783 1.181098 GCACCTGCAGTTGGGTCAAT 61.181 55.000 13.63 0.00 41.59 2.57
1764 1784 1.827789 GCACCTGCAGTTGGGTCAA 60.828 57.895 13.63 0.00 41.59 3.18
1765 1785 2.203337 GCACCTGCAGTTGGGTCA 60.203 61.111 13.63 0.00 41.59 4.02
1775 1795 2.668212 TGCCGTAACTGCACCTGC 60.668 61.111 0.00 0.00 42.50 4.85
1780 1800 1.666553 CTTCGGTGCCGTAACTGCA 60.667 57.895 10.60 0.00 40.74 4.41
1781 1801 3.023591 GCTTCGGTGCCGTAACTGC 62.024 63.158 10.60 5.63 40.74 4.40
1782 1802 1.626654 CTGCTTCGGTGCCGTAACTG 61.627 60.000 10.60 0.00 40.74 3.16
1783 1803 1.374252 CTGCTTCGGTGCCGTAACT 60.374 57.895 10.60 0.00 40.74 2.24
1784 1804 3.023591 GCTGCTTCGGTGCCGTAAC 62.024 63.158 10.60 0.00 40.74 2.50
1785 1805 2.740826 GCTGCTTCGGTGCCGTAA 60.741 61.111 10.60 3.41 40.74 3.18
1792 1812 3.802418 AAACGGACGCTGCTTCGGT 62.802 57.895 12.48 12.48 0.00 4.69
1793 1813 2.113131 AAAAACGGACGCTGCTTCGG 62.113 55.000 11.28 11.28 0.00 4.30
1794 1814 1.278637 AAAAACGGACGCTGCTTCG 59.721 52.632 0.00 1.36 0.00 3.79
1811 1831 6.574465 GCTGAAGGTGAGTCTTAGATACCAAA 60.574 42.308 13.10 1.68 33.88 3.28
1842 1862 1.999648 TGCAACAAAATCCAGAGGCT 58.000 45.000 0.00 0.00 0.00 4.58
1881 1903 2.009108 CATGCTCAACGGGTCATCG 58.991 57.895 0.00 0.00 0.00 3.84
1978 2000 1.751544 GGGCCCATACCGGTTCAAC 60.752 63.158 19.95 0.00 0.00 3.18
1979 2001 0.620990 TAGGGCCCATACCGGTTCAA 60.621 55.000 27.56 0.00 0.00 2.69
1980 2002 1.003182 TAGGGCCCATACCGGTTCA 59.997 57.895 27.56 0.00 0.00 3.18
1981 2003 1.752833 CTAGGGCCCATACCGGTTC 59.247 63.158 27.56 0.00 0.00 3.62
1982 2004 2.449450 GCTAGGGCCCATACCGGTT 61.449 63.158 27.56 2.06 0.00 4.44
1983 2005 2.847715 GCTAGGGCCCATACCGGT 60.848 66.667 27.56 13.98 0.00 5.28
1993 2015 1.063183 AGATCTTGATGGGCTAGGGC 58.937 55.000 0.00 0.00 37.82 5.19
1994 2016 2.038295 GACAGATCTTGATGGGCTAGGG 59.962 54.545 0.00 0.00 0.00 3.53
1995 2017 2.971330 AGACAGATCTTGATGGGCTAGG 59.029 50.000 0.00 0.00 0.00 3.02
1996 2018 3.896888 AGAGACAGATCTTGATGGGCTAG 59.103 47.826 0.00 0.00 34.34 3.42
1997 2019 3.921104 AGAGACAGATCTTGATGGGCTA 58.079 45.455 0.00 0.00 34.34 3.93
1998 2020 2.761809 AGAGACAGATCTTGATGGGCT 58.238 47.619 0.00 0.00 34.34 5.19
1999 2021 3.557228 AAGAGACAGATCTTGATGGGC 57.443 47.619 0.00 0.00 38.12 5.36
2006 2028 0.915364 GGGCCCAAGAGACAGATCTT 59.085 55.000 19.95 0.00 40.17 2.40
2007 2029 0.252881 TGGGCCCAAGAGACAGATCT 60.253 55.000 26.33 0.00 38.15 2.75
2008 2030 0.620556 TTGGGCCCAAGAGACAGATC 59.379 55.000 34.07 0.00 0.00 2.75
2009 2031 2.791253 TTGGGCCCAAGAGACAGAT 58.209 52.632 34.07 0.00 0.00 2.90
2010 2032 4.330056 TTGGGCCCAAGAGACAGA 57.670 55.556 34.07 9.11 0.00 3.41
2022 2044 0.106318 AGATCTTGATGGGCTTGGGC 60.106 55.000 0.00 0.00 37.82 5.36
2023 2045 1.064166 ACAGATCTTGATGGGCTTGGG 60.064 52.381 0.00 0.00 0.00 4.12
2024 2046 2.092538 AGACAGATCTTGATGGGCTTGG 60.093 50.000 0.00 0.00 0.00 3.61
2025 2047 3.118334 AGAGACAGATCTTGATGGGCTTG 60.118 47.826 0.00 0.00 34.34 4.01
2026 2048 3.113824 AGAGACAGATCTTGATGGGCTT 58.886 45.455 0.00 0.00 34.34 4.35
2027 2049 2.761809 AGAGACAGATCTTGATGGGCT 58.238 47.619 0.00 0.00 34.34 5.19
2028 2050 3.557228 AAGAGACAGATCTTGATGGGC 57.443 47.619 0.00 0.00 38.12 5.36
2035 2057 0.915364 GGGCCCAAGAGACAGATCTT 59.085 55.000 19.95 0.00 40.17 2.40
2036 2058 0.252881 TGGGCCCAAGAGACAGATCT 60.253 55.000 26.33 0.00 38.15 2.75
2037 2059 0.620556 TTGGGCCCAAGAGACAGATC 59.379 55.000 34.07 0.00 0.00 2.75
2038 2060 2.791253 TTGGGCCCAAGAGACAGAT 58.209 52.632 34.07 0.00 0.00 2.90
2039 2061 4.330056 TTGGGCCCAAGAGACAGA 57.670 55.556 34.07 9.11 0.00 3.41
2051 2073 2.123982 CCTCTCATGGGCTTGGGC 60.124 66.667 0.00 0.00 37.82 5.36
2052 2074 1.077212 CACCTCTCATGGGCTTGGG 60.077 63.158 0.00 0.00 0.00 4.12
2053 2075 1.751927 GCACCTCTCATGGGCTTGG 60.752 63.158 0.00 0.00 0.00 3.61
2054 2076 1.030488 CAGCACCTCTCATGGGCTTG 61.030 60.000 0.00 0.00 33.47 4.01
2055 2077 1.203441 TCAGCACCTCTCATGGGCTT 61.203 55.000 0.00 0.00 33.47 4.35
2056 2078 1.614525 TCAGCACCTCTCATGGGCT 60.615 57.895 0.00 0.00 35.18 5.19
2057 2079 1.451028 GTCAGCACCTCTCATGGGC 60.451 63.158 0.00 0.00 0.00 5.36
2058 2080 1.222936 GGTCAGCACCTCTCATGGG 59.777 63.158 0.00 0.00 40.00 4.00
2059 2081 4.950479 GGTCAGCACCTCTCATGG 57.050 61.111 0.00 0.00 40.00 3.66
2067 2089 1.754226 CTCCTCTTCTAGGTCAGCACC 59.246 57.143 0.00 0.00 46.62 5.01
2068 2090 1.136110 GCTCCTCTTCTAGGTCAGCAC 59.864 57.143 0.00 0.00 46.62 4.40
2069 2091 1.479709 GCTCCTCTTCTAGGTCAGCA 58.520 55.000 0.00 0.00 46.62 4.41
2070 2092 0.750249 GGCTCCTCTTCTAGGTCAGC 59.250 60.000 0.00 0.00 46.62 4.26
2071 2093 1.408969 GGGCTCCTCTTCTAGGTCAG 58.591 60.000 0.00 0.00 46.62 3.51
2072 2094 0.032017 GGGGCTCCTCTTCTAGGTCA 60.032 60.000 0.00 0.00 46.62 4.02
2073 2095 0.263468 AGGGGCTCCTCTTCTAGGTC 59.737 60.000 0.00 0.00 46.62 3.85
2074 2096 2.427016 AGGGGCTCCTCTTCTAGGT 58.573 57.895 0.00 0.00 46.62 3.08
2084 2106 4.439901 AGGGGGAAGAGGGGCTCC 62.440 72.222 0.00 0.00 0.00 4.70
2085 2107 3.093172 CAGGGGGAAGAGGGGCTC 61.093 72.222 0.00 0.00 0.00 4.70
2086 2108 3.952799 GACAGGGGGAAGAGGGGCT 62.953 68.421 0.00 0.00 0.00 5.19
2087 2109 3.412408 GACAGGGGGAAGAGGGGC 61.412 72.222 0.00 0.00 0.00 5.80
2088 2110 2.692741 GGACAGGGGGAAGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
2089 2111 2.692741 GGGACAGGGGGAAGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
2090 2112 3.083997 CGGGACAGGGGGAAGAGG 61.084 72.222 0.00 0.00 0.00 3.69
2091 2113 2.284699 ACGGGACAGGGGGAAGAG 60.285 66.667 0.00 0.00 0.00 2.85
2092 2114 2.606519 CACGGGACAGGGGGAAGA 60.607 66.667 0.00 0.00 0.00 2.87
2093 2115 4.410400 GCACGGGACAGGGGGAAG 62.410 72.222 0.00 0.00 0.00 3.46
2096 2118 4.722700 CTTGCACGGGACAGGGGG 62.723 72.222 0.00 0.00 0.00 5.40
2109 2131 4.030452 GTGTCTGTGGCGGCTTGC 62.030 66.667 11.43 0.88 45.38 4.01
2110 2132 3.357079 GGTGTCTGTGGCGGCTTG 61.357 66.667 11.43 0.00 0.00 4.01
2111 2133 2.902423 TTTGGTGTCTGTGGCGGCTT 62.902 55.000 11.43 0.00 0.00 4.35
2112 2134 3.414136 TTTGGTGTCTGTGGCGGCT 62.414 57.895 11.43 0.00 0.00 5.52
2113 2135 2.904866 TTTGGTGTCTGTGGCGGC 60.905 61.111 0.00 0.00 0.00 6.53
2114 2136 2.551912 GGTTTGGTGTCTGTGGCGG 61.552 63.158 0.00 0.00 0.00 6.13
2115 2137 2.551912 GGGTTTGGTGTCTGTGGCG 61.552 63.158 0.00 0.00 0.00 5.69
2116 2138 1.454847 TGGGTTTGGTGTCTGTGGC 60.455 57.895 0.00 0.00 0.00 5.01
2117 2139 1.444119 CGTGGGTTTGGTGTCTGTGG 61.444 60.000 0.00 0.00 0.00 4.17
2118 2140 2.021722 CGTGGGTTTGGTGTCTGTG 58.978 57.895 0.00 0.00 0.00 3.66
2119 2141 1.822186 GCGTGGGTTTGGTGTCTGT 60.822 57.895 0.00 0.00 0.00 3.41
2120 2142 2.892334 CGCGTGGGTTTGGTGTCTG 61.892 63.158 0.00 0.00 0.00 3.51
2121 2143 2.590575 CGCGTGGGTTTGGTGTCT 60.591 61.111 0.00 0.00 0.00 3.41
2122 2144 2.589442 TCGCGTGGGTTTGGTGTC 60.589 61.111 5.77 0.00 0.00 3.67
2123 2145 2.590575 CTCGCGTGGGTTTGGTGT 60.591 61.111 5.77 0.00 0.00 4.16
2124 2146 4.025401 GCTCGCGTGGGTTTGGTG 62.025 66.667 5.77 0.00 0.00 4.17
2127 2149 4.072088 GTCGCTCGCGTGGGTTTG 62.072 66.667 22.00 0.73 40.74 2.93
2133 2155 4.700365 TGTCTGGTCGCTCGCGTG 62.700 66.667 5.77 4.44 40.74 5.34
2134 2156 4.702081 GTGTCTGGTCGCTCGCGT 62.702 66.667 5.77 0.00 40.74 6.01
2136 2158 4.400109 TCGTGTCTGGTCGCTCGC 62.400 66.667 0.00 0.00 0.00 5.03
2137 2159 2.202362 CTCGTGTCTGGTCGCTCG 60.202 66.667 0.00 0.00 0.00 5.03
2138 2160 1.135731 CTCTCGTGTCTGGTCGCTC 59.864 63.158 0.00 0.00 0.00 5.03
2139 2161 1.601197 ACTCTCGTGTCTGGTCGCT 60.601 57.895 0.00 0.00 0.00 4.93
2140 2162 1.442857 CACTCTCGTGTCTGGTCGC 60.443 63.158 0.00 0.00 36.39 5.19
2141 2163 0.591659 TTCACTCTCGTGTCTGGTCG 59.408 55.000 0.00 0.00 41.89 4.79
2142 2164 1.336056 GGTTCACTCTCGTGTCTGGTC 60.336 57.143 0.00 0.00 41.89 4.02
2143 2165 0.674534 GGTTCACTCTCGTGTCTGGT 59.325 55.000 0.00 0.00 41.89 4.00
2144 2166 0.038159 GGGTTCACTCTCGTGTCTGG 60.038 60.000 0.00 0.00 41.89 3.86
2145 2167 0.962489 AGGGTTCACTCTCGTGTCTG 59.038 55.000 0.00 0.00 41.89 3.51
2146 2168 0.962489 CAGGGTTCACTCTCGTGTCT 59.038 55.000 0.00 0.00 41.89 3.41
2147 2169 0.674534 ACAGGGTTCACTCTCGTGTC 59.325 55.000 0.00 0.00 41.89 3.67
2148 2170 0.674534 GACAGGGTTCACTCTCGTGT 59.325 55.000 0.00 0.00 41.89 4.49
2149 2171 0.962489 AGACAGGGTTCACTCTCGTG 59.038 55.000 0.00 0.00 42.59 4.35
2150 2172 2.581216 TAGACAGGGTTCACTCTCGT 57.419 50.000 0.00 0.00 0.00 4.18
2151 2173 3.367498 CCTTTAGACAGGGTTCACTCTCG 60.367 52.174 0.00 0.00 0.00 4.04
2152 2174 3.579151 ACCTTTAGACAGGGTTCACTCTC 59.421 47.826 0.00 0.00 38.42 3.20
2153 2175 3.588569 ACCTTTAGACAGGGTTCACTCT 58.411 45.455 0.00 0.00 38.42 3.24
2154 2176 4.322574 GGTACCTTTAGACAGGGTTCACTC 60.323 50.000 4.06 0.00 38.42 3.51
2155 2177 3.581770 GGTACCTTTAGACAGGGTTCACT 59.418 47.826 4.06 0.00 38.42 3.41
2156 2178 3.935315 GGTACCTTTAGACAGGGTTCAC 58.065 50.000 4.06 0.00 38.42 3.18
2181 2203 6.379386 GCATCTGATACCATGTTGAATCATG 58.621 40.000 0.00 0.00 43.14 3.07
2182 2204 5.475909 GGCATCTGATACCATGTTGAATCAT 59.524 40.000 1.90 0.00 0.00 2.45
2183 2205 4.823442 GGCATCTGATACCATGTTGAATCA 59.177 41.667 1.90 0.00 0.00 2.57
2184 2206 4.083643 CGGCATCTGATACCATGTTGAATC 60.084 45.833 7.65 0.00 0.00 2.52
2185 2207 3.817084 CGGCATCTGATACCATGTTGAAT 59.183 43.478 7.65 0.00 0.00 2.57
2186 2208 3.205338 CGGCATCTGATACCATGTTGAA 58.795 45.455 7.65 0.00 0.00 2.69
2187 2209 2.485302 CCGGCATCTGATACCATGTTGA 60.485 50.000 7.65 0.00 0.00 3.18
2188 2210 1.875514 CCGGCATCTGATACCATGTTG 59.124 52.381 7.65 0.00 0.00 3.33
2189 2211 1.490490 ACCGGCATCTGATACCATGTT 59.510 47.619 0.00 0.00 0.00 2.71
2190 2212 1.131638 ACCGGCATCTGATACCATGT 58.868 50.000 0.00 1.19 0.00 3.21
2191 2213 1.070601 TCACCGGCATCTGATACCATG 59.929 52.381 0.00 5.06 0.00 3.66
2192 2214 1.070758 GTCACCGGCATCTGATACCAT 59.929 52.381 0.00 0.00 0.00 3.55
2193 2215 0.464036 GTCACCGGCATCTGATACCA 59.536 55.000 0.00 0.00 0.00 3.25
2194 2216 0.597637 CGTCACCGGCATCTGATACC 60.598 60.000 0.00 0.00 0.00 2.73
2195 2217 2.886859 CGTCACCGGCATCTGATAC 58.113 57.895 0.00 0.00 0.00 2.24
2208 2230 3.775654 CTCAGGCCCCTCCGTCAC 61.776 72.222 0.00 0.00 40.77 3.67
2220 2242 3.003173 TTCCCGTCAGCCCTCAGG 61.003 66.667 0.00 0.00 0.00 3.86
2221 2243 2.581354 CTTCCCGTCAGCCCTCAG 59.419 66.667 0.00 0.00 0.00 3.35
2222 2244 3.003173 CCTTCCCGTCAGCCCTCA 61.003 66.667 0.00 0.00 0.00 3.86
2223 2245 3.787001 CCCTTCCCGTCAGCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
2228 2250 4.101448 CTGCCCCCTTCCCGTCAG 62.101 72.222 0.00 0.00 0.00 3.51
2255 2277 4.074526 TCTCCAGCGCACCTCTGC 62.075 66.667 11.47 0.00 40.38 4.26
2256 2278 2.183811 CTCTCCAGCGCACCTCTG 59.816 66.667 11.47 0.00 0.00 3.35
2257 2279 3.073735 CCTCTCCAGCGCACCTCT 61.074 66.667 11.47 0.00 0.00 3.69
2258 2280 3.071206 TCCTCTCCAGCGCACCTC 61.071 66.667 11.47 0.00 0.00 3.85
2259 2281 3.386237 GTCCTCTCCAGCGCACCT 61.386 66.667 11.47 0.00 0.00 4.00
2260 2282 4.459089 GGTCCTCTCCAGCGCACC 62.459 72.222 11.47 0.88 0.00 5.01
2261 2283 3.655810 CTGGTCCTCTCCAGCGCAC 62.656 68.421 11.47 0.00 46.53 5.34
2262 2284 3.385384 CTGGTCCTCTCCAGCGCA 61.385 66.667 11.47 0.00 46.53 6.09
2308 2330 2.742372 TCGAAAGAAGGCAGCGCC 60.742 61.111 2.29 11.02 42.38 6.53
2309 2331 2.744768 CCTCGAAAGAAGGCAGCGC 61.745 63.158 0.00 0.00 41.32 5.92
2310 2332 1.079819 TCCTCGAAAGAAGGCAGCG 60.080 57.895 0.00 0.00 41.32 5.18
2311 2333 0.247736 TCTCCTCGAAAGAAGGCAGC 59.752 55.000 0.00 0.00 41.32 5.25
2312 2334 1.134848 CCTCTCCTCGAAAGAAGGCAG 60.135 57.143 0.00 0.00 41.32 4.85
2313 2335 0.898320 CCTCTCCTCGAAAGAAGGCA 59.102 55.000 0.00 0.00 41.32 4.75
2314 2336 0.461163 GCCTCTCCTCGAAAGAAGGC 60.461 60.000 11.41 11.41 41.32 4.35
2315 2337 0.179124 CGCCTCTCCTCGAAAGAAGG 60.179 60.000 0.00 0.00 41.32 3.46
2316 2338 0.179124 CCGCCTCTCCTCGAAAGAAG 60.179 60.000 0.00 0.00 41.32 2.85
2317 2339 1.890894 CCGCCTCTCCTCGAAAGAA 59.109 57.895 0.00 0.00 41.32 2.52
2318 2340 2.711922 GCCGCCTCTCCTCGAAAGA 61.712 63.158 0.00 0.00 39.12 2.52
2319 2341 2.202810 GCCGCCTCTCCTCGAAAG 60.203 66.667 0.00 0.00 0.00 2.62
2320 2342 2.680352 AGCCGCCTCTCCTCGAAA 60.680 61.111 0.00 0.00 0.00 3.46
2321 2343 3.452786 CAGCCGCCTCTCCTCGAA 61.453 66.667 0.00 0.00 0.00 3.71
2322 2344 4.742649 ACAGCCGCCTCTCCTCGA 62.743 66.667 0.00 0.00 0.00 4.04
2323 2345 4.504916 CACAGCCGCCTCTCCTCG 62.505 72.222 0.00 0.00 0.00 4.63
2324 2346 4.828925 GCACAGCCGCCTCTCCTC 62.829 72.222 0.00 0.00 0.00 3.71
2356 2378 4.505217 GACATGCCTTGCGTCGCG 62.505 66.667 13.38 0.00 0.00 5.87
2357 2379 3.372676 CTGACATGCCTTGCGTCGC 62.373 63.158 11.10 11.10 32.17 5.19
2358 2380 2.743752 CCTGACATGCCTTGCGTCG 61.744 63.158 0.00 0.00 32.17 5.12
2359 2381 2.401766 CCCTGACATGCCTTGCGTC 61.402 63.158 0.00 0.00 0.00 5.19
2360 2382 2.360350 CCCTGACATGCCTTGCGT 60.360 61.111 0.00 0.00 0.00 5.24
2361 2383 3.818787 GCCCTGACATGCCTTGCG 61.819 66.667 0.00 0.00 0.00 4.85
2362 2384 2.362120 AGCCCTGACATGCCTTGC 60.362 61.111 0.00 0.00 0.00 4.01
2363 2385 2.707849 GCAGCCCTGACATGCCTTG 61.708 63.158 0.00 0.00 33.81 3.61
2364 2386 2.362120 GCAGCCCTGACATGCCTT 60.362 61.111 0.00 0.00 33.81 4.35
2365 2387 3.336568 AGCAGCCCTGACATGCCT 61.337 61.111 0.00 0.00 40.89 4.75
2366 2388 3.138798 CAGCAGCCCTGACATGCC 61.139 66.667 0.00 0.00 44.64 4.40
2367 2389 3.823330 GCAGCAGCCCTGACATGC 61.823 66.667 6.19 2.60 44.64 4.06
2368 2390 2.045242 AGCAGCAGCCCTGACATG 60.045 61.111 6.19 0.00 44.64 3.21
2369 2391 2.045242 CAGCAGCAGCCCTGACAT 60.045 61.111 6.19 0.00 44.64 3.06
2370 2392 3.243816 TCAGCAGCAGCCCTGACA 61.244 61.111 8.85 0.00 44.64 3.58
2372 2394 4.383861 CGTCAGCAGCAGCCCTGA 62.384 66.667 8.85 8.85 44.64 3.86


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

AutoCloner maintained by Alex Coulton.