Multiple sequence alignment - TraesCS5A01G422100

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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 TraesCS5A01G422100 chr5A 100.000 2843 0 0 1 2843 608440497 608437655 0.000000e+00 5251.0
1 TraesCS5A01G422100 chr5A 78.270 474 47 32 2356 2803 608420746 608420303 1.310000e-63 254.0
2 TraesCS5A01G422100 chr5A 85.714 189 21 6 2471 2656 608475083 608474898 8.040000e-46 195.0
3 TraesCS5A01G422100 chr5A 85.345 116 6 6 2156 2271 608475430 608475326 2.990000e-20 110.0
4 TraesCS5A01G422100 chr6D 91.722 1969 148 11 1 1964 465189015 465190973 0.000000e+00 2719.0
5 TraesCS5A01G422100 chr6D 88.034 1897 207 11 11 1892 426849726 426851617 0.000000e+00 2228.0
6 TraesCS5A01G422100 chr6D 80.083 1918 335 30 4 1896 81645074 81646969 0.000000e+00 1382.0
7 TraesCS5A01G422100 chr1D 88.344 1896 201 11 11 1892 471441075 471439186 0.000000e+00 2259.0
8 TraesCS5A01G422100 chr1D 88.133 1896 204 12 11 1892 9328598 9330486 0.000000e+00 2235.0
9 TraesCS5A01G422100 chr2D 88.186 1896 203 11 11 1892 636123080 636121192 0.000000e+00 2241.0
10 TraesCS5A01G422100 chr2D 88.034 1897 207 11 11 1892 18984089 18985980 0.000000e+00 2228.0
11 TraesCS5A01G422100 chr2D 87.876 1897 210 11 11 1892 18880124 18882015 0.000000e+00 2211.0
12 TraesCS5A01G422100 chr3D 88.080 1896 203 11 11 1892 57390144 57392030 0.000000e+00 2228.0
13 TraesCS5A01G422100 chr5D 87.578 1932 216 12 3 1920 34150936 34149015 0.000000e+00 2217.0
14 TraesCS5A01G422100 chr5D 88.726 683 42 15 2156 2826 487758102 487757443 0.000000e+00 802.0
15 TraesCS5A01G422100 chr5D 80.901 555 55 20 2258 2803 487622955 487622443 9.550000e-105 390.0
16 TraesCS5A01G422100 chr5D 88.073 109 6 4 2149 2257 487865267 487865166 3.850000e-24 122.0
17 TraesCS5A01G422100 chr7D 91.408 1548 120 11 422 1964 8441619 8440080 0.000000e+00 2109.0
18 TraesCS5A01G422100 chr7D 89.919 1230 107 13 742 1964 180787669 180788888 0.000000e+00 1568.0
19 TraesCS5A01G422100 chr6A 79.927 1923 321 41 1 1896 97993551 97995435 0.000000e+00 1352.0
20 TraesCS5A01G422100 chr6A 97.368 266 6 1 1839 2104 577695140 577695404 4.320000e-123 451.0
21 TraesCS5A01G422100 chr6A 97.368 266 6 1 1839 2104 577712714 577712978 4.320000e-123 451.0
22 TraesCS5A01G422100 chr7A 96.701 394 13 0 1711 2104 578060984 578061377 0.000000e+00 656.0
23 TraesCS5A01G422100 chr3B 97.006 334 5 2 1772 2105 590445109 590444781 8.900000e-155 556.0
24 TraesCS5A01G422100 chr5B 87.643 437 21 14 2156 2588 600335372 600334965 7.130000e-131 477.0
25 TraesCS5A01G422100 chr5B 94.915 177 6 2 1928 2104 458623457 458623630 1.000000e-69 274.0
26 TraesCS5A01G422100 chr5B 77.958 431 48 23 2399 2803 600288530 600288121 2.850000e-55 226.0
27 TraesCS5A01G422100 chr5B 83.193 119 7 3 2211 2329 600288658 600288553 2.330000e-16 97.1
28 TraesCS5A01G422100 chr3A 96.403 278 9 1 1828 2104 658046177 658045900 9.280000e-125 457.0
29 TraesCS5A01G422100 chr3A 97.531 243 6 0 1862 2104 655805542 655805784 1.580000e-112 416.0
30 TraesCS5A01G422100 chr4A 93.939 132 7 1 1973 2104 702010603 702010473 6.210000e-47 198.0
31 TraesCS5A01G422100 chr1B 94.958 119 4 2 1989 2105 669234240 669234358 4.840000e-43 185.0


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 TraesCS5A01G422100 chr5A 608437655 608440497 2842 True 5251 5251 100.000 1 2843 1 chr5A.!!$R2 2842
1 TraesCS5A01G422100 chr6D 465189015 465190973 1958 False 2719 2719 91.722 1 1964 1 chr6D.!!$F3 1963
2 TraesCS5A01G422100 chr6D 426849726 426851617 1891 False 2228 2228 88.034 11 1892 1 chr6D.!!$F2 1881
3 TraesCS5A01G422100 chr6D 81645074 81646969 1895 False 1382 1382 80.083 4 1896 1 chr6D.!!$F1 1892
4 TraesCS5A01G422100 chr1D 471439186 471441075 1889 True 2259 2259 88.344 11 1892 1 chr1D.!!$R1 1881
5 TraesCS5A01G422100 chr1D 9328598 9330486 1888 False 2235 2235 88.133 11 1892 1 chr1D.!!$F1 1881
6 TraesCS5A01G422100 chr2D 636121192 636123080 1888 True 2241 2241 88.186 11 1892 1 chr2D.!!$R1 1881
7 TraesCS5A01G422100 chr2D 18984089 18985980 1891 False 2228 2228 88.034 11 1892 1 chr2D.!!$F2 1881
8 TraesCS5A01G422100 chr2D 18880124 18882015 1891 False 2211 2211 87.876 11 1892 1 chr2D.!!$F1 1881
9 TraesCS5A01G422100 chr3D 57390144 57392030 1886 False 2228 2228 88.080 11 1892 1 chr3D.!!$F1 1881
10 TraesCS5A01G422100 chr5D 34149015 34150936 1921 True 2217 2217 87.578 3 1920 1 chr5D.!!$R1 1917
11 TraesCS5A01G422100 chr5D 487757443 487758102 659 True 802 802 88.726 2156 2826 1 chr5D.!!$R3 670
12 TraesCS5A01G422100 chr5D 487622443 487622955 512 True 390 390 80.901 2258 2803 1 chr5D.!!$R2 545
13 TraesCS5A01G422100 chr7D 8440080 8441619 1539 True 2109 2109 91.408 422 1964 1 chr7D.!!$R1 1542
14 TraesCS5A01G422100 chr7D 180787669 180788888 1219 False 1568 1568 89.919 742 1964 1 chr7D.!!$F1 1222
15 TraesCS5A01G422100 chr6A 97993551 97995435 1884 False 1352 1352 79.927 1 1896 1 chr6A.!!$F1 1895

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
36 37 0.883370 TGATGATGAGATGCAGCGGC 60.883 55.000 0.31 0.31 35.09 6.53 F
1202 1220 1.691434 GGGTGTGGAGCCAAAATTTCA 59.309 47.619 0.00 0.00 39.79 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1763 0.892755 CAACAGAGCACATGGCCAAT 59.107 50.0 10.96 0.0 46.5 3.16 R
2074 2112 0.033503 CCTATGTTTTTCGGGGCCCT 60.034 55.0 24.38 0.0 0.0 5.19 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.883370 TGATGATGAGATGCAGCGGC 60.883 55.000 0.31 0.31 35.09 6.53
57 58 4.874970 GCAGATTGCAAAGGAAAAAGAGA 58.125 39.130 1.71 0.00 44.26 3.10
65 66 3.797559 AAGGAAAAAGAGAGGTGGAGG 57.202 47.619 0.00 0.00 0.00 4.30
122 124 3.385577 TCTTGCAAAACGTAATTTGGCC 58.614 40.909 13.16 0.00 45.53 5.36
125 127 3.385577 TGCAAAACGTAATTTGGCCTTC 58.614 40.909 13.16 0.00 45.53 3.46
230 234 5.829391 TGTGATGCAAGAACATATTAGGCAT 59.171 36.000 0.00 0.00 42.59 4.40
303 307 5.227569 TGAGTTGATTTCACTCCTTGCTA 57.772 39.130 0.00 0.00 0.00 3.49
312 316 2.302733 TCACTCCTTGCTAATGCTGTGA 59.697 45.455 0.00 0.00 40.48 3.58
510 514 6.553100 ACACATCAGGATTGGGTCTTTTTAAA 59.447 34.615 0.00 0.00 0.00 1.52
552 556 5.645067 AGATTCTCTTGATTTGAATGTCGCA 59.355 36.000 0.00 0.00 31.49 5.10
558 562 5.181811 TCTTGATTTGAATGTCGCAGATGTT 59.818 36.000 0.00 0.00 40.67 2.71
575 579 3.644966 TGTTAGAGGGCAAGGTTATGG 57.355 47.619 0.00 0.00 0.00 2.74
621 631 2.751166 ATCAAGGTGTTCAGTCTCGG 57.249 50.000 0.00 0.00 0.00 4.63
837 849 6.395629 TCTCAAACCTTTGTCTAATACTCGG 58.604 40.000 0.00 0.00 39.18 4.63
898 910 5.316167 TCCAAACTGCACAAGTAAGATCAT 58.684 37.500 0.00 0.00 38.56 2.45
908 920 6.549952 CACAAGTAAGATCATCTTTGAAGGC 58.450 40.000 4.90 0.00 37.89 4.35
927 939 4.274978 AGGCACTAGAGAAGTCTTCTACC 58.725 47.826 15.20 9.78 37.14 3.18
1035 1053 8.623903 TGGCATGATATTCTATTTTCTGTCAAC 58.376 33.333 0.00 0.00 0.00 3.18
1056 1074 7.651704 GTCAACATGGTTAGCAAAAAGTTACAT 59.348 33.333 0.00 0.00 0.00 2.29
1059 1077 7.370383 ACATGGTTAGCAAAAAGTTACATGAG 58.630 34.615 0.00 0.00 37.29 2.90
1117 1135 8.605065 ACATTGAAGGGGTCATTTCATATTTTT 58.395 29.630 0.00 0.00 35.70 1.94
1178 1196 3.127548 AGTGCCAAAGTTATTGCATCGAG 59.872 43.478 0.00 0.00 35.96 4.04
1185 1203 4.689612 AGTTATTGCATCGAGTATGGGT 57.310 40.909 0.00 0.00 35.99 4.51
1186 1204 4.380531 AGTTATTGCATCGAGTATGGGTG 58.619 43.478 0.00 0.00 35.99 4.61
1188 1206 2.022764 TTGCATCGAGTATGGGTGTG 57.977 50.000 0.00 0.00 35.99 3.82
1202 1220 1.691434 GGGTGTGGAGCCAAAATTTCA 59.309 47.619 0.00 0.00 39.79 2.69
1287 1305 9.920133 GATCTACAACTATCAGCTATTGAATCA 57.080 33.333 0.00 0.00 39.77 2.57
1347 1365 4.728882 GCAATTGCTTCATTGACTAGTCGG 60.729 45.833 23.21 10.08 38.21 4.79
1351 1369 5.142061 TGCTTCATTGACTAGTCGGTTTA 57.858 39.130 17.85 0.00 0.00 2.01
1428 1457 9.606631 AATCTGAAGTCTTTGGATGATAGTAAC 57.393 33.333 0.00 0.00 0.00 2.50
1448 1477 6.812160 AGTAACCTACGAAAATCTTGCACTAG 59.188 38.462 0.00 0.00 0.00 2.57
1631 1663 2.894731 TGCCTATCGGATCCTCTTGAT 58.105 47.619 10.75 7.60 36.01 2.57
1675 1707 6.231211 TCGGCTGAAAGAAGTTTCTCTAAAT 58.769 36.000 0.00 0.00 42.39 1.40
1703 1735 7.881775 AACTACTGAAGAATTGTTTGAGGTT 57.118 32.000 0.00 0.00 0.00 3.50
1704 1736 7.264373 ACTACTGAAGAATTGTTTGAGGTTG 57.736 36.000 0.00 0.00 0.00 3.77
1707 1739 5.067805 ACTGAAGAATTGTTTGAGGTTGACC 59.932 40.000 0.00 0.00 0.00 4.02
1731 1763 6.375174 CCATGTTACAAGACAGATTGAATGGA 59.625 38.462 0.00 0.00 35.23 3.41
1737 1769 3.294214 AGACAGATTGAATGGATTGGCC 58.706 45.455 0.00 0.00 37.10 5.36
1745 1777 4.342427 TGGATTGGCCATGTGCTC 57.658 55.556 6.09 0.00 43.33 4.26
1747 1779 0.681887 TGGATTGGCCATGTGCTCTG 60.682 55.000 6.09 0.00 43.33 3.35
1803 1835 9.529325 CTTGATATTGTCATCAATGATTTTGCT 57.471 29.630 0.00 0.00 42.49 3.91
1855 1888 7.119699 TCGTGAAGAATTGAAGCATTATTGTCT 59.880 33.333 0.00 0.00 0.00 3.41
1899 1937 9.832445 TCTATTTAAGGTAATCAAACTAGCAGG 57.168 33.333 0.00 0.00 0.00 4.85
1905 1943 7.394144 AGGTAATCAAACTAGCAGGGAATAT 57.606 36.000 0.00 0.00 0.00 1.28
1907 1945 7.721399 AGGTAATCAAACTAGCAGGGAATATTG 59.279 37.037 0.00 0.00 0.00 1.90
1911 1949 7.391148 TCAAACTAGCAGGGAATATTGTTTC 57.609 36.000 0.00 0.00 0.00 2.78
1913 1951 7.336931 TCAAACTAGCAGGGAATATTGTTTCTC 59.663 37.037 0.00 0.00 0.00 2.87
1914 1952 6.313519 ACTAGCAGGGAATATTGTTTCTCA 57.686 37.500 0.00 0.00 0.00 3.27
1915 1953 6.904626 ACTAGCAGGGAATATTGTTTCTCAT 58.095 36.000 0.00 0.00 0.00 2.90
1916 1954 8.034313 ACTAGCAGGGAATATTGTTTCTCATA 57.966 34.615 0.00 0.00 0.00 2.15
1917 1955 8.664079 ACTAGCAGGGAATATTGTTTCTCATAT 58.336 33.333 0.00 0.00 0.00 1.78
1918 1956 9.512588 CTAGCAGGGAATATTGTTTCTCATATT 57.487 33.333 0.00 0.00 0.00 1.28
1919 1957 8.773033 AGCAGGGAATATTGTTTCTCATATTT 57.227 30.769 0.00 0.00 0.00 1.40
1920 1958 9.866655 AGCAGGGAATATTGTTTCTCATATTTA 57.133 29.630 0.00 0.00 0.00 1.40
1965 2003 8.932610 AGTCTTCCTTTCATGATATGACATAGT 58.067 33.333 0.00 0.00 39.39 2.12
1966 2004 9.202273 GTCTTCCTTTCATGATATGACATAGTC 57.798 37.037 0.00 0.71 39.39 2.59
1967 2005 9.152327 TCTTCCTTTCATGATATGACATAGTCT 57.848 33.333 0.00 0.00 39.39 3.24
1968 2006 9.205719 CTTCCTTTCATGATATGACATAGTCTG 57.794 37.037 0.00 0.00 39.39 3.51
1969 2007 7.157347 TCCTTTCATGATATGACATAGTCTGC 58.843 38.462 0.00 0.00 39.39 4.26
1970 2008 6.090493 CCTTTCATGATATGACATAGTCTGCG 59.910 42.308 0.00 0.00 39.39 5.18
1971 2009 5.712152 TCATGATATGACATAGTCTGCGT 57.288 39.130 0.98 0.00 33.59 5.24
1972 2010 5.464168 TCATGATATGACATAGTCTGCGTG 58.536 41.667 0.98 1.09 33.59 5.34
1973 2011 5.241506 TCATGATATGACATAGTCTGCGTGA 59.758 40.000 0.98 3.10 33.59 4.35
1974 2012 5.712152 TGATATGACATAGTCTGCGTGAT 57.288 39.130 0.98 0.00 33.15 3.06
1975 2013 6.089249 TGATATGACATAGTCTGCGTGATT 57.911 37.500 0.98 0.00 33.15 2.57
1976 2014 7.214467 TGATATGACATAGTCTGCGTGATTA 57.786 36.000 0.98 0.00 33.15 1.75
1977 2015 7.830739 TGATATGACATAGTCTGCGTGATTAT 58.169 34.615 0.98 0.00 33.15 1.28
1978 2016 7.970614 TGATATGACATAGTCTGCGTGATTATC 59.029 37.037 0.98 0.00 33.15 1.75
1979 2017 5.514274 TGACATAGTCTGCGTGATTATCA 57.486 39.130 0.00 0.00 33.15 2.15
1980 2018 5.901552 TGACATAGTCTGCGTGATTATCAA 58.098 37.500 0.00 0.00 33.15 2.57
1981 2019 6.515832 TGACATAGTCTGCGTGATTATCAAT 58.484 36.000 0.00 0.00 33.15 2.57
1982 2020 6.986231 TGACATAGTCTGCGTGATTATCAATT 59.014 34.615 0.00 0.00 33.15 2.32
1983 2021 7.495606 TGACATAGTCTGCGTGATTATCAATTT 59.504 33.333 0.00 0.00 33.15 1.82
1984 2022 8.213518 ACATAGTCTGCGTGATTATCAATTTT 57.786 30.769 0.00 0.00 0.00 1.82
1985 2023 8.677300 ACATAGTCTGCGTGATTATCAATTTTT 58.323 29.630 0.00 0.00 0.00 1.94
2022 2060 8.755941 ACGTCTCAGAATAACAAAATATGATCG 58.244 33.333 0.00 0.00 0.00 3.69
2023 2061 8.217115 CGTCTCAGAATAACAAAATATGATCGG 58.783 37.037 0.00 0.00 0.00 4.18
2024 2062 9.261180 GTCTCAGAATAACAAAATATGATCGGA 57.739 33.333 0.00 0.00 0.00 4.55
2030 2068 9.425893 GAATAACAAAATATGATCGGATATGCG 57.574 33.333 10.76 10.76 0.00 4.73
2031 2069 6.801539 AACAAAATATGATCGGATATGCGT 57.198 33.333 16.54 4.03 0.00 5.24
2032 2070 7.899178 AACAAAATATGATCGGATATGCGTA 57.101 32.000 16.54 1.87 0.00 4.42
2033 2071 7.290857 ACAAAATATGATCGGATATGCGTAC 57.709 36.000 16.54 11.71 0.00 3.67
2034 2072 6.871492 ACAAAATATGATCGGATATGCGTACA 59.129 34.615 16.54 16.43 0.00 2.90
2035 2073 7.549134 ACAAAATATGATCGGATATGCGTACAT 59.451 33.333 23.65 23.65 40.49 2.29
2036 2074 9.030301 CAAAATATGATCGGATATGCGTACATA 57.970 33.333 25.32 25.32 42.85 2.29
2052 2090 9.929180 ATGCGTACATATATATTGCCTATAAGG 57.071 33.333 0.00 0.00 34.55 2.69
2053 2091 8.364894 TGCGTACATATATATTGCCTATAAGGG 58.635 37.037 0.00 0.00 35.37 3.95
2077 2115 2.998316 TTTTTCAACTTGGCCAAGGG 57.002 45.000 41.04 32.87 42.53 3.95
2087 2125 2.920384 GCCAAGGGCCCCGAAAAA 60.920 61.111 21.43 0.00 44.06 1.94
2088 2126 3.056458 CCAAGGGCCCCGAAAAAC 58.944 61.111 21.43 0.00 0.00 2.43
2089 2127 1.834822 CCAAGGGCCCCGAAAAACA 60.835 57.895 21.43 0.00 0.00 2.83
2090 2128 1.191489 CCAAGGGCCCCGAAAAACAT 61.191 55.000 21.43 0.00 0.00 2.71
2091 2129 1.551452 CAAGGGCCCCGAAAAACATA 58.449 50.000 21.43 0.00 0.00 2.29
2092 2130 1.476488 CAAGGGCCCCGAAAAACATAG 59.524 52.381 21.43 0.00 0.00 2.23
2093 2131 0.033503 AGGGCCCCGAAAAACATAGG 60.034 55.000 21.43 0.00 0.00 2.57
2094 2132 1.040893 GGGCCCCGAAAAACATAGGG 61.041 60.000 12.23 0.00 43.41 3.53
2096 2134 2.500352 CCCCGAAAAACATAGGGCC 58.500 57.895 0.00 0.00 42.47 5.80
2097 2135 1.381165 CCCCGAAAAACATAGGGCCG 61.381 60.000 0.00 0.00 42.47 6.13
2098 2136 1.381165 CCCGAAAAACATAGGGCCGG 61.381 60.000 0.00 0.00 37.07 6.13
2099 2137 1.431845 CGAAAAACATAGGGCCGGC 59.568 57.895 21.18 21.18 0.00 6.13
2100 2138 1.813859 GAAAAACATAGGGCCGGCC 59.186 57.895 38.57 38.57 0.00 6.13
2110 2148 3.878667 GGCCGGCCCTGCTATCTT 61.879 66.667 36.64 0.00 0.00 2.40
2111 2149 2.516888 GGCCGGCCCTGCTATCTTA 61.517 63.158 36.64 0.00 0.00 2.10
2112 2150 1.450211 GCCGGCCCTGCTATCTTAA 59.550 57.895 18.11 0.00 0.00 1.85
2113 2151 0.179029 GCCGGCCCTGCTATCTTAAA 60.179 55.000 18.11 0.00 0.00 1.52
2114 2152 1.884235 CCGGCCCTGCTATCTTAAAG 58.116 55.000 0.00 0.00 0.00 1.85
2115 2153 1.543429 CCGGCCCTGCTATCTTAAAGG 60.543 57.143 0.00 0.00 0.00 3.11
2116 2154 1.141053 CGGCCCTGCTATCTTAAAGGT 59.859 52.381 0.00 0.00 0.00 3.50
2117 2155 2.576615 GGCCCTGCTATCTTAAAGGTG 58.423 52.381 0.00 0.00 0.00 4.00
2118 2156 1.950216 GCCCTGCTATCTTAAAGGTGC 59.050 52.381 0.00 0.00 0.00 5.01
2119 2157 2.683742 GCCCTGCTATCTTAAAGGTGCA 60.684 50.000 0.00 0.00 0.00 4.57
2120 2158 3.209410 CCCTGCTATCTTAAAGGTGCAG 58.791 50.000 0.00 0.00 44.97 4.41
2123 2161 4.142609 TGCTATCTTAAAGGTGCAGAGG 57.857 45.455 0.00 0.00 0.00 3.69
2124 2162 3.774766 TGCTATCTTAAAGGTGCAGAGGA 59.225 43.478 0.00 0.00 0.00 3.71
2125 2163 4.123506 GCTATCTTAAAGGTGCAGAGGAC 58.876 47.826 0.00 0.00 0.00 3.85
2126 2164 2.743636 TCTTAAAGGTGCAGAGGACG 57.256 50.000 0.00 0.00 0.00 4.79
2127 2165 1.968493 TCTTAAAGGTGCAGAGGACGT 59.032 47.619 0.00 0.00 0.00 4.34
2128 2166 3.159472 TCTTAAAGGTGCAGAGGACGTA 58.841 45.455 0.00 0.00 0.00 3.57
2129 2167 3.575256 TCTTAAAGGTGCAGAGGACGTAA 59.425 43.478 0.00 0.00 0.00 3.18
2130 2168 2.165319 AAAGGTGCAGAGGACGTAAC 57.835 50.000 0.00 0.00 0.00 2.50
2131 2169 1.339097 AAGGTGCAGAGGACGTAACT 58.661 50.000 0.00 0.00 0.00 2.24
2132 2170 0.889306 AGGTGCAGAGGACGTAACTC 59.111 55.000 10.83 10.83 35.20 3.01
2133 2171 0.889306 GGTGCAGAGGACGTAACTCT 59.111 55.000 14.59 14.59 45.77 3.24
2134 2172 1.135344 GGTGCAGAGGACGTAACTCTC 60.135 57.143 16.81 12.81 43.15 3.20
2135 2173 0.803117 TGCAGAGGACGTAACTCTCG 59.197 55.000 16.81 13.67 43.15 4.04
2136 2174 1.085091 GCAGAGGACGTAACTCTCGA 58.915 55.000 16.81 0.00 43.15 4.04
2137 2175 1.671845 GCAGAGGACGTAACTCTCGAT 59.328 52.381 16.81 0.00 43.15 3.59
2138 2176 2.286536 GCAGAGGACGTAACTCTCGATC 60.287 54.545 16.81 5.94 43.15 3.69
2139 2177 2.937149 CAGAGGACGTAACTCTCGATCA 59.063 50.000 16.81 0.00 43.15 2.92
2140 2178 2.937799 AGAGGACGTAACTCTCGATCAC 59.062 50.000 14.59 0.00 41.26 3.06
2141 2179 2.676839 GAGGACGTAACTCTCGATCACA 59.323 50.000 11.38 0.00 32.28 3.58
2142 2180 2.678836 AGGACGTAACTCTCGATCACAG 59.321 50.000 0.00 0.00 0.00 3.66
2143 2181 2.676839 GGACGTAACTCTCGATCACAGA 59.323 50.000 0.00 0.00 0.00 3.41
2144 2182 3.242478 GGACGTAACTCTCGATCACAGAG 60.242 52.174 14.53 14.53 42.84 3.35
2145 2183 2.096174 ACGTAACTCTCGATCACAGAGC 59.904 50.000 15.63 2.94 41.13 4.09
2146 2184 2.096013 CGTAACTCTCGATCACAGAGCA 59.904 50.000 15.63 4.68 41.13 4.26
2147 2185 2.645730 AACTCTCGATCACAGAGCAC 57.354 50.000 15.63 0.00 41.13 4.40
2148 2186 1.832883 ACTCTCGATCACAGAGCACT 58.167 50.000 15.63 0.00 41.13 4.40
2158 2196 2.670635 CAGAGCACTGTACGGCATC 58.329 57.895 0.23 0.00 39.11 3.91
2163 2201 1.439353 GCACTGTACGGCATCCATGG 61.439 60.000 4.97 4.97 0.00 3.66
2188 2226 3.675995 ATGAGCACCATGAAGGCAA 57.324 47.368 0.00 0.00 43.14 4.52
2192 2234 0.537143 AGCACCATGAAGGCAACGAA 60.537 50.000 0.00 0.00 43.14 3.85
2194 2236 1.067635 GCACCATGAAGGCAACGAATT 60.068 47.619 0.00 0.00 43.14 2.17
2199 2241 1.974265 TGAAGGCAACGAATTCCACA 58.026 45.000 0.00 0.00 46.39 4.17
2206 2248 2.671070 GCAACGAATTCCACATTCCCAC 60.671 50.000 0.00 0.00 0.00 4.61
2207 2249 2.819608 CAACGAATTCCACATTCCCACT 59.180 45.455 0.00 0.00 0.00 4.00
2208 2250 2.436417 ACGAATTCCACATTCCCACTG 58.564 47.619 0.00 0.00 0.00 3.66
2209 2251 1.745087 CGAATTCCACATTCCCACTGG 59.255 52.381 0.00 0.00 0.00 4.00
2210 2252 1.478105 GAATTCCACATTCCCACTGGC 59.522 52.381 0.00 0.00 0.00 4.85
2211 2253 0.324645 ATTCCACATTCCCACTGGCC 60.325 55.000 0.00 0.00 0.00 5.36
2212 2254 1.724148 TTCCACATTCCCACTGGCCA 61.724 55.000 4.71 4.71 0.00 5.36
2342 2384 1.377725 AAGCCAGGCGGTTGATCAG 60.378 57.895 5.55 0.00 33.28 2.90
2345 2387 1.450312 CCAGGCGGTTGATCAGTCC 60.450 63.158 0.00 2.23 0.00 3.85
2381 2423 1.455408 CTTTCGCCACAAATTTTCCGC 59.545 47.619 0.00 0.00 0.00 5.54
2460 2502 8.745590 GTTTATACATACACAGGGGAACAAATT 58.254 33.333 0.00 0.00 0.00 1.82
2558 2608 5.652452 AGCTAATAACAATCCAAGACAACCC 59.348 40.000 0.00 0.00 0.00 4.11
2567 2617 2.506231 TCCAAGACAACCCACAACAGTA 59.494 45.455 0.00 0.00 0.00 2.74
2599 2651 0.537188 TCGGCTCTGTCCCATCTTTC 59.463 55.000 0.00 0.00 0.00 2.62
2656 2713 1.887242 CGCCACCACCATACCGATG 60.887 63.158 0.00 0.00 0.00 3.84
2722 2786 0.823356 TGAACCTGCACTTTGCCTCC 60.823 55.000 0.00 0.00 44.23 4.30
2723 2787 0.538287 GAACCTGCACTTTGCCTCCT 60.538 55.000 0.00 0.00 44.23 3.69
2725 2789 1.676967 CCTGCACTTTGCCTCCTCC 60.677 63.158 0.00 0.00 44.23 4.30
2727 2791 0.251077 CTGCACTTTGCCTCCTCCTT 60.251 55.000 0.00 0.00 44.23 3.36
2728 2792 0.538057 TGCACTTTGCCTCCTCCTTG 60.538 55.000 0.00 0.00 44.23 3.61
2730 2794 1.302832 ACTTTGCCTCCTCCTTGCG 60.303 57.895 0.00 0.00 0.00 4.85
2731 2795 1.003355 CTTTGCCTCCTCCTTGCGA 60.003 57.895 0.00 0.00 0.00 5.10
2732 2796 0.393537 CTTTGCCTCCTCCTTGCGAT 60.394 55.000 0.00 0.00 0.00 4.58
2733 2797 0.038166 TTTGCCTCCTCCTTGCGATT 59.962 50.000 0.00 0.00 0.00 3.34
2734 2798 0.677731 TTGCCTCCTCCTTGCGATTG 60.678 55.000 0.00 0.00 0.00 2.67
2735 2799 2.476320 GCCTCCTCCTTGCGATTGC 61.476 63.158 0.00 0.00 43.20 3.56
2736 2800 1.222936 CCTCCTCCTTGCGATTGCT 59.777 57.895 6.47 0.00 43.34 3.91
2737 2801 0.813210 CCTCCTCCTTGCGATTGCTC 60.813 60.000 6.47 0.00 43.34 4.26
2740 2804 0.731417 CCTCCTTGCGATTGCTCTTG 59.269 55.000 6.47 0.00 43.34 3.02
2781 2845 5.652014 TCAAACTATTTCGCTCCATGGATTT 59.348 36.000 16.63 6.63 0.00 2.17
2782 2846 5.757850 AACTATTTCGCTCCATGGATTTC 57.242 39.130 16.63 6.81 0.00 2.17
2783 2847 4.137543 ACTATTTCGCTCCATGGATTTCC 58.862 43.478 16.63 3.41 0.00 3.13
2826 2890 6.770286 AGCTTGATCAAATAGATAGGGGAA 57.230 37.500 9.88 0.00 37.00 3.97
2827 2891 6.538263 AGCTTGATCAAATAGATAGGGGAAC 58.462 40.000 9.88 0.00 37.00 3.62
2828 2892 5.409826 GCTTGATCAAATAGATAGGGGAACG 59.590 44.000 9.88 0.00 37.00 3.95
2829 2893 6.494666 TTGATCAAATAGATAGGGGAACGT 57.505 37.500 5.45 0.00 37.00 3.99
2830 2894 5.853936 TGATCAAATAGATAGGGGAACGTG 58.146 41.667 0.00 0.00 37.00 4.49
2831 2895 4.067972 TCAAATAGATAGGGGAACGTGC 57.932 45.455 0.00 0.00 0.00 5.34
2832 2896 2.800544 CAAATAGATAGGGGAACGTGCG 59.199 50.000 0.00 0.00 0.00 5.34
2833 2897 0.317479 ATAGATAGGGGAACGTGCGC 59.683 55.000 0.00 0.00 0.00 6.09
2834 2898 1.741327 TAGATAGGGGAACGTGCGCC 61.741 60.000 21.98 21.98 40.90 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.010415 ACCTCTCTTTTTCCTTTGCAATCTG 59.990 40.000 0.00 0.00 0.00 2.90
57 58 1.531602 GCAAAACCTGCCTCCACCT 60.532 57.895 0.00 0.00 46.13 4.00
65 66 7.201470 GCAGAAATTATTCTTAGCAAAACCTGC 60.201 37.037 0.00 0.00 46.71 4.85
122 124 4.319177 ACTTCTCATTTGTTCCTCGGAAG 58.681 43.478 0.00 0.00 34.49 3.46
125 127 3.815401 ACAACTTCTCATTTGTTCCTCGG 59.185 43.478 0.00 0.00 31.78 4.63
173 177 1.067635 GCAATCATTTCAACCGTGCCT 60.068 47.619 0.00 0.00 0.00 4.75
468 472 7.121759 CCTGATGTGTCATCAACCTTTAAGAAT 59.878 37.037 12.44 0.00 32.98 2.40
552 556 4.141390 CCATAACCTTGCCCTCTAACATCT 60.141 45.833 0.00 0.00 0.00 2.90
558 562 1.590591 TGCCATAACCTTGCCCTCTA 58.409 50.000 0.00 0.00 0.00 2.43
575 579 1.134907 CCTTCATGTTGGAGCCATTGC 60.135 52.381 0.00 0.00 37.95 3.56
616 626 3.135994 GGTTAACTTCAAGCAACCGAGA 58.864 45.455 5.42 0.00 31.80 4.04
621 631 4.368315 CTTTGGGGTTAACTTCAAGCAAC 58.632 43.478 5.42 0.00 0.00 4.17
837 849 4.082136 ACACTCTTTATTCGACTCTCCCAC 60.082 45.833 0.00 0.00 0.00 4.61
883 895 6.549952 CCTTCAAAGATGATCTTACTTGTGC 58.450 40.000 8.30 0.00 35.27 4.57
885 897 6.150140 GTGCCTTCAAAGATGATCTTACTTGT 59.850 38.462 8.30 0.00 35.27 3.16
898 910 4.835615 AGACTTCTCTAGTGCCTTCAAAGA 59.164 41.667 0.00 0.00 37.17 2.52
908 920 5.818336 TCATCGGTAGAAGACTTCTCTAGTG 59.182 44.000 20.95 13.93 41.14 2.74
927 939 2.133553 CTTACTGCAGCTGGATCATCG 58.866 52.381 17.12 2.52 0.00 3.84
1035 1053 7.592938 TCTCATGTAACTTTTTGCTAACCATG 58.407 34.615 0.00 0.00 0.00 3.66
1056 1074 4.725359 CATCGATGCACACAATTTTCTCA 58.275 39.130 13.37 0.00 0.00 3.27
1117 1135 6.191315 AGAAGCCTTCATCTCTGTACTTCTA 58.809 40.000 7.29 0.00 40.46 2.10
1178 1196 1.917872 TTTTGGCTCCACACCCATAC 58.082 50.000 0.00 0.00 0.00 2.39
1185 1203 4.478206 TGTTTGAAATTTTGGCTCCACA 57.522 36.364 0.00 0.00 0.00 4.17
1186 1204 5.809719 TTTGTTTGAAATTTTGGCTCCAC 57.190 34.783 0.00 0.00 0.00 4.02
1188 1206 5.163804 ACGTTTTGTTTGAAATTTTGGCTCC 60.164 36.000 0.00 0.00 0.00 4.70
1202 1220 8.083462 TCTTCCTTTTACTTTGACGTTTTGTTT 58.917 29.630 0.00 0.00 0.00 2.83
1260 1278 9.920133 GATTCAATAGCTGATAGTTGTAGATCA 57.080 33.333 0.00 0.00 32.78 2.92
1347 1365 5.772521 TCAAATTCCTTCAGCTGCTTAAAC 58.227 37.500 9.47 0.00 0.00 2.01
1351 1369 4.942761 TTTCAAATTCCTTCAGCTGCTT 57.057 36.364 9.47 0.00 0.00 3.91
1428 1457 6.481954 AAACTAGTGCAAGATTTTCGTAGG 57.518 37.500 0.00 0.00 0.00 3.18
1475 1505 4.604843 TCAAGATCAACATCATGCGAAC 57.395 40.909 0.00 0.00 29.31 3.95
1631 1663 2.561419 GAGGCTACAGTCACAGGTACAA 59.439 50.000 0.00 0.00 0.00 2.41
1675 1707 8.405531 CCTCAAACAATTCTTCAGTAGTTTCAA 58.594 33.333 0.00 0.00 0.00 2.69
1703 1735 5.863965 TCAATCTGTCTTGTAACATGGTCA 58.136 37.500 0.00 0.00 0.00 4.02
1704 1736 6.801539 TTCAATCTGTCTTGTAACATGGTC 57.198 37.500 0.00 0.00 0.00 4.02
1707 1739 7.381766 TCCATTCAATCTGTCTTGTAACATG 57.618 36.000 0.00 0.00 0.00 3.21
1731 1763 0.892755 CAACAGAGCACATGGCCAAT 59.107 50.000 10.96 0.00 46.50 3.16
1737 1769 3.049708 TCCTTCTCAACAGAGCACATG 57.950 47.619 0.00 0.00 0.00 3.21
1745 1777 5.982356 TGTCCAAGATATCCTTCTCAACAG 58.018 41.667 0.00 0.00 31.42 3.16
1747 1779 6.173339 TGTTGTCCAAGATATCCTTCTCAAC 58.827 40.000 16.59 16.59 37.32 3.18
1803 1835 4.553330 ACTTCTTCGGGCATTTCTAGAA 57.447 40.909 0.00 0.00 0.00 2.10
1830 1863 7.246311 AGACAATAATGCTTCAATTCTTCACG 58.754 34.615 0.00 0.00 0.00 4.35
1874 1907 9.057089 CCCTGCTAGTTTGATTACCTTAAATAG 57.943 37.037 0.00 0.00 0.00 1.73
1940 1978 9.202273 GACTATGTCATATCATGAAAGGAAGAC 57.798 37.037 0.00 3.56 41.69 3.01
1943 1981 7.658982 GCAGACTATGTCATATCATGAAAGGAA 59.341 37.037 0.00 0.00 41.69 3.36
1945 1983 6.090493 CGCAGACTATGTCATATCATGAAAGG 59.910 42.308 0.00 0.00 41.69 3.11
1948 1986 5.922544 CACGCAGACTATGTCATATCATGAA 59.077 40.000 0.00 0.00 41.69 2.57
1949 1987 5.241506 TCACGCAGACTATGTCATATCATGA 59.758 40.000 0.00 0.00 34.60 3.07
1996 2034 8.755941 CGATCATATTTTGTTATTCTGAGACGT 58.244 33.333 0.00 0.00 0.00 4.34
1997 2035 8.217115 CCGATCATATTTTGTTATTCTGAGACG 58.783 37.037 0.00 0.00 0.00 4.18
1998 2036 9.261180 TCCGATCATATTTTGTTATTCTGAGAC 57.739 33.333 0.00 0.00 0.00 3.36
2004 2042 9.425893 CGCATATCCGATCATATTTTGTTATTC 57.574 33.333 0.00 0.00 0.00 1.75
2005 2043 8.946085 ACGCATATCCGATCATATTTTGTTATT 58.054 29.630 0.00 0.00 0.00 1.40
2006 2044 8.492673 ACGCATATCCGATCATATTTTGTTAT 57.507 30.769 0.00 0.00 0.00 1.89
2007 2045 7.899178 ACGCATATCCGATCATATTTTGTTA 57.101 32.000 0.00 0.00 0.00 2.41
2008 2046 6.801539 ACGCATATCCGATCATATTTTGTT 57.198 33.333 0.00 0.00 0.00 2.83
2009 2047 6.871492 TGTACGCATATCCGATCATATTTTGT 59.129 34.615 0.00 0.00 0.00 2.83
2010 2048 7.289587 TGTACGCATATCCGATCATATTTTG 57.710 36.000 0.00 0.00 0.00 2.44
2011 2049 9.764363 ATATGTACGCATATCCGATCATATTTT 57.236 29.630 11.69 0.00 42.83 1.82
2017 2055 9.840427 CAATATATATGTACGCATATCCGATCA 57.160 33.333 0.00 0.00 44.59 2.92
2018 2056 8.799091 GCAATATATATGTACGCATATCCGATC 58.201 37.037 0.00 0.00 44.59 3.69
2019 2057 7.759886 GGCAATATATATGTACGCATATCCGAT 59.240 37.037 0.00 0.00 44.59 4.18
2020 2058 7.039993 AGGCAATATATATGTACGCATATCCGA 60.040 37.037 0.00 0.00 44.59 4.55
2021 2059 7.090808 AGGCAATATATATGTACGCATATCCG 58.909 38.462 0.00 0.00 44.59 4.18
2026 2064 9.929180 CCTTATAGGCAATATATATGTACGCAT 57.071 33.333 0.00 0.00 39.03 4.73
2027 2065 8.364894 CCCTTATAGGCAATATATATGTACGCA 58.635 37.037 0.00 0.00 32.73 5.24
2028 2066 8.758633 CCCTTATAGGCAATATATATGTACGC 57.241 38.462 0.00 0.00 32.73 4.42
2058 2096 1.134250 GCCCTTGGCCAAGTTGAAAAA 60.134 47.619 37.09 6.26 44.06 1.94
2059 2097 0.467804 GCCCTTGGCCAAGTTGAAAA 59.532 50.000 37.09 7.04 44.06 2.29
2060 2098 2.132300 GCCCTTGGCCAAGTTGAAA 58.868 52.632 37.09 7.83 44.06 2.69
2061 2099 3.869481 GCCCTTGGCCAAGTTGAA 58.131 55.556 37.09 8.62 44.06 2.69
2071 2109 1.191489 ATGTTTTTCGGGGCCCTTGG 61.191 55.000 24.38 11.89 0.00 3.61
2072 2110 1.476488 CTATGTTTTTCGGGGCCCTTG 59.524 52.381 24.38 15.37 0.00 3.61
2073 2111 1.618616 CCTATGTTTTTCGGGGCCCTT 60.619 52.381 24.38 0.00 0.00 3.95
2074 2112 0.033503 CCTATGTTTTTCGGGGCCCT 60.034 55.000 24.38 0.00 0.00 5.19
2075 2113 1.040893 CCCTATGTTTTTCGGGGCCC 61.041 60.000 15.76 15.76 32.91 5.80
2076 2114 2.500352 CCCTATGTTTTTCGGGGCC 58.500 57.895 0.00 0.00 32.91 5.80
2078 2116 1.381165 CGGCCCTATGTTTTTCGGGG 61.381 60.000 0.00 0.00 37.17 5.73
2079 2117 1.381165 CCGGCCCTATGTTTTTCGGG 61.381 60.000 0.00 0.00 39.76 5.14
2080 2118 2.000215 GCCGGCCCTATGTTTTTCGG 62.000 60.000 18.11 0.00 39.07 4.30
2081 2119 1.431845 GCCGGCCCTATGTTTTTCG 59.568 57.895 18.11 0.00 0.00 3.46
2082 2120 1.813859 GGCCGGCCCTATGTTTTTC 59.186 57.895 36.64 4.38 0.00 2.29
2083 2121 4.027884 GGCCGGCCCTATGTTTTT 57.972 55.556 36.64 0.00 0.00 1.94
2093 2131 2.052047 TTAAGATAGCAGGGCCGGCC 62.052 60.000 38.57 38.57 0.00 6.13
2094 2132 0.179029 TTTAAGATAGCAGGGCCGGC 60.179 55.000 21.18 21.18 0.00 6.13
2095 2133 1.543429 CCTTTAAGATAGCAGGGCCGG 60.543 57.143 0.00 0.00 0.00 6.13
2096 2134 1.141053 ACCTTTAAGATAGCAGGGCCG 59.859 52.381 0.00 0.00 0.00 6.13
2097 2135 2.576615 CACCTTTAAGATAGCAGGGCC 58.423 52.381 0.00 0.00 0.00 5.80
2098 2136 1.950216 GCACCTTTAAGATAGCAGGGC 59.050 52.381 0.00 0.00 0.00 5.19
2099 2137 3.118261 TCTGCACCTTTAAGATAGCAGGG 60.118 47.826 22.55 8.65 46.84 4.45
2100 2138 4.125703 CTCTGCACCTTTAAGATAGCAGG 58.874 47.826 22.55 14.57 46.84 4.85
2102 2140 3.774766 TCCTCTGCACCTTTAAGATAGCA 59.225 43.478 0.00 0.00 0.00 3.49
2103 2141 4.123506 GTCCTCTGCACCTTTAAGATAGC 58.876 47.826 0.00 0.00 0.00 2.97
2104 2142 4.142138 ACGTCCTCTGCACCTTTAAGATAG 60.142 45.833 0.00 0.00 0.00 2.08
2105 2143 3.767673 ACGTCCTCTGCACCTTTAAGATA 59.232 43.478 0.00 0.00 0.00 1.98
2106 2144 2.567615 ACGTCCTCTGCACCTTTAAGAT 59.432 45.455 0.00 0.00 0.00 2.40
2107 2145 1.968493 ACGTCCTCTGCACCTTTAAGA 59.032 47.619 0.00 0.00 0.00 2.10
2108 2146 2.457366 ACGTCCTCTGCACCTTTAAG 57.543 50.000 0.00 0.00 0.00 1.85
2109 2147 3.322828 AGTTACGTCCTCTGCACCTTTAA 59.677 43.478 0.00 0.00 0.00 1.52
2110 2148 2.895404 AGTTACGTCCTCTGCACCTTTA 59.105 45.455 0.00 0.00 0.00 1.85
2111 2149 1.692519 AGTTACGTCCTCTGCACCTTT 59.307 47.619 0.00 0.00 0.00 3.11
2112 2150 1.272769 GAGTTACGTCCTCTGCACCTT 59.727 52.381 0.00 0.00 0.00 3.50
2113 2151 0.889306 GAGTTACGTCCTCTGCACCT 59.111 55.000 0.00 0.00 0.00 4.00
2114 2152 0.889306 AGAGTTACGTCCTCTGCACC 59.111 55.000 14.86 0.00 37.88 5.01
2115 2153 1.466024 CGAGAGTTACGTCCTCTGCAC 60.466 57.143 19.17 7.16 39.36 4.57
2116 2154 0.803117 CGAGAGTTACGTCCTCTGCA 59.197 55.000 19.17 0.00 39.36 4.41
2117 2155 1.085091 TCGAGAGTTACGTCCTCTGC 58.915 55.000 19.17 11.29 39.36 4.26
2118 2156 2.937149 TGATCGAGAGTTACGTCCTCTG 59.063 50.000 19.17 12.57 39.36 3.35
2119 2157 2.937799 GTGATCGAGAGTTACGTCCTCT 59.062 50.000 15.39 15.39 41.91 3.69
2120 2158 2.676839 TGTGATCGAGAGTTACGTCCTC 59.323 50.000 0.00 0.00 0.00 3.71
2121 2159 2.678836 CTGTGATCGAGAGTTACGTCCT 59.321 50.000 0.00 0.00 0.00 3.85
2122 2160 2.676839 TCTGTGATCGAGAGTTACGTCC 59.323 50.000 0.00 0.00 0.00 4.79
2123 2161 3.786161 GCTCTGTGATCGAGAGTTACGTC 60.786 52.174 18.20 2.67 39.42 4.34
2124 2162 2.096174 GCTCTGTGATCGAGAGTTACGT 59.904 50.000 18.20 0.00 39.42 3.57
2125 2163 2.096013 TGCTCTGTGATCGAGAGTTACG 59.904 50.000 18.20 0.00 39.42 3.18
2126 2164 3.127895 AGTGCTCTGTGATCGAGAGTTAC 59.872 47.826 18.20 16.74 39.42 2.50
2127 2165 3.127721 CAGTGCTCTGTGATCGAGAGTTA 59.872 47.826 18.20 8.92 39.42 2.24
2128 2166 2.094803 CAGTGCTCTGTGATCGAGAGTT 60.095 50.000 18.20 6.53 39.42 3.01
2129 2167 1.472082 CAGTGCTCTGTGATCGAGAGT 59.528 52.381 18.20 1.91 39.42 3.24
2130 2168 2.191815 CAGTGCTCTGTGATCGAGAG 57.808 55.000 14.52 14.52 40.10 3.20
2140 2178 0.807667 GGATGCCGTACAGTGCTCTG 60.808 60.000 14.08 14.08 46.18 3.35
2141 2179 1.257750 TGGATGCCGTACAGTGCTCT 61.258 55.000 0.00 0.00 0.00 4.09
2142 2180 0.179073 ATGGATGCCGTACAGTGCTC 60.179 55.000 0.00 0.00 0.00 4.26
2143 2181 0.462581 CATGGATGCCGTACAGTGCT 60.463 55.000 0.00 0.00 0.00 4.40
2144 2182 1.439353 CCATGGATGCCGTACAGTGC 61.439 60.000 5.56 0.00 0.00 4.40
2145 2183 0.177836 TCCATGGATGCCGTACAGTG 59.822 55.000 11.44 0.00 0.00 3.66
2146 2184 1.070758 GATCCATGGATGCCGTACAGT 59.929 52.381 32.05 4.16 34.60 3.55
2147 2185 1.345741 AGATCCATGGATGCCGTACAG 59.654 52.381 32.05 0.00 34.60 2.74
2148 2186 1.423584 AGATCCATGGATGCCGTACA 58.576 50.000 32.05 0.00 34.60 2.90
2149 2187 2.299013 TGTAGATCCATGGATGCCGTAC 59.701 50.000 32.05 23.34 34.60 3.67
2150 2188 2.604139 TGTAGATCCATGGATGCCGTA 58.396 47.619 32.05 14.11 34.60 4.02
2151 2189 1.423584 TGTAGATCCATGGATGCCGT 58.576 50.000 32.05 15.08 34.60 5.68
2152 2190 2.027837 TCATGTAGATCCATGGATGCCG 60.028 50.000 32.05 13.28 42.02 5.69
2153 2191 3.607741 CTCATGTAGATCCATGGATGCC 58.392 50.000 32.05 17.97 42.02 4.40
2154 2192 3.008330 GCTCATGTAGATCCATGGATGC 58.992 50.000 32.05 20.86 42.02 3.91
2158 2196 2.105306 TGGTGCTCATGTAGATCCATGG 59.895 50.000 4.97 4.97 42.02 3.66
2182 2220 2.231235 GGAATGTGGAATTCGTTGCCTT 59.769 45.455 0.00 0.00 0.00 4.35
2188 2226 2.436417 CAGTGGGAATGTGGAATTCGT 58.564 47.619 0.00 0.00 0.00 3.85
2192 2234 0.324645 GGCCAGTGGGAATGTGGAAT 60.325 55.000 12.15 0.00 35.59 3.01
2194 2236 2.159490 TGGCCAGTGGGAATGTGGA 61.159 57.895 12.15 0.00 35.59 4.02
2199 2241 2.036256 GCAGTGGCCAGTGGGAAT 59.964 61.111 35.86 0.00 35.59 3.01
2209 2251 0.250727 TCCAAACTAGTGGCAGTGGC 60.251 55.000 10.30 10.30 38.68 5.01
2210 2252 1.523758 GTCCAAACTAGTGGCAGTGG 58.476 55.000 4.76 4.31 38.68 4.00
2211 2253 1.148310 CGTCCAAACTAGTGGCAGTG 58.852 55.000 4.76 0.00 38.68 3.66
2212 2254 0.034896 CCGTCCAAACTAGTGGCAGT 59.965 55.000 0.00 0.00 38.68 4.40
2221 2263 2.594592 GCCAGCACCGTCCAAACT 60.595 61.111 0.00 0.00 0.00 2.66
2253 2295 1.490693 GCCGGTCTCGATCGTACGTA 61.491 60.000 15.94 2.34 39.00 3.57
2254 2296 2.817423 GCCGGTCTCGATCGTACGT 61.817 63.158 15.94 2.33 39.00 3.57
2255 2297 2.052414 GCCGGTCTCGATCGTACG 60.052 66.667 15.94 9.53 39.00 3.67
2256 2298 1.793134 ATGGCCGGTCTCGATCGTAC 61.793 60.000 15.94 14.09 39.00 3.67
2342 2384 1.578206 GCGCACAAGAAGGAAGGGAC 61.578 60.000 0.30 0.00 0.00 4.46
2345 2387 0.954452 AAAGCGCACAAGAAGGAAGG 59.046 50.000 11.47 0.00 0.00 3.46
2370 2412 4.470462 CTGACTTCTCAGCGGAAAATTTG 58.530 43.478 0.00 0.00 37.72 2.32
2411 2453 2.520979 CTCGGTGATGAAACTCGAGAC 58.479 52.381 21.68 10.48 46.89 3.36
2460 2502 1.393603 CTCCGGTCACATCAGAGCTA 58.606 55.000 0.00 0.00 34.00 3.32
2558 2608 3.262420 GGTGCTAGACCATACTGTTGTG 58.738 50.000 0.00 0.00 45.34 3.33
2599 2651 0.439985 CAGAGACGTGGCGAAACATG 59.560 55.000 0.00 0.00 0.00 3.21
2649 2706 2.203001 CGCATGCACCCATCGGTA 60.203 61.111 19.57 0.00 42.04 4.02
2656 2713 3.188786 GTCGAGACGCATGCACCC 61.189 66.667 19.57 5.66 0.00 4.61
2677 2734 1.008309 GGATCGTCTGCTCTACGCC 60.008 63.158 0.00 0.00 40.12 5.68
2679 2736 2.605823 GGATTGGATCGTCTGCTCTACG 60.606 54.545 0.00 0.00 41.64 3.51
2680 2737 2.362397 TGGATTGGATCGTCTGCTCTAC 59.638 50.000 0.00 0.00 0.00 2.59
2722 2786 0.098376 GCAAGAGCAATCGCAAGGAG 59.902 55.000 0.00 0.00 42.27 3.69
2723 2787 2.174334 GCAAGAGCAATCGCAAGGA 58.826 52.632 0.00 0.00 42.27 3.36
2734 2798 2.603892 CCGATTACATGCATGCAAGAGC 60.604 50.000 28.20 14.11 42.57 4.09
2735 2799 2.031420 CCCGATTACATGCATGCAAGAG 60.031 50.000 28.20 20.62 0.00 2.85
2736 2800 1.948834 CCCGATTACATGCATGCAAGA 59.051 47.619 28.20 12.32 0.00 3.02
2737 2801 1.677576 ACCCGATTACATGCATGCAAG 59.322 47.619 26.68 23.45 0.00 4.01
2740 2804 1.308047 TGACCCGATTACATGCATGC 58.692 50.000 26.53 11.82 0.00 4.06
2743 2807 3.066291 AGTTTGACCCGATTACATGCA 57.934 42.857 0.00 0.00 0.00 3.96
2744 2808 5.751243 AATAGTTTGACCCGATTACATGC 57.249 39.130 0.00 0.00 0.00 4.06
2781 2845 2.680352 GAGCCAGGAGACCACGGA 60.680 66.667 0.00 0.00 0.00 4.69
2782 2846 2.362369 ATGAGCCAGGAGACCACGG 61.362 63.158 0.00 0.00 0.00 4.94
2783 2847 1.153489 CATGAGCCAGGAGACCACG 60.153 63.158 0.00 0.00 0.00 4.94
2813 2877 1.270147 GCGCACGTTCCCCTATCTATT 60.270 52.381 0.30 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.