Multiple sequence alignment - TraesCS5A01G351300

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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 TraesCS5A01G351300 chr5A 100.000 2740 0 0 1 2740 554083460 554080721 0.000000e+00 5060.0
1 TraesCS5A01G351300 chr5A 79.385 1756 303 40 201 1927 554060534 554058809 0.000000e+00 1182.0
2 TraesCS5A01G351300 chr5A 80.342 1577 257 44 212 1750 554201380 554199819 0.000000e+00 1146.0
3 TraesCS5A01G351300 chr5A 80.165 1215 200 35 279 1469 554218689 554217492 0.000000e+00 870.0
4 TraesCS5A01G351300 chr5D 92.391 1945 114 16 59 1991 438521762 438519840 0.000000e+00 2741.0
5 TraesCS5A01G351300 chr5D 83.923 1723 238 28 225 1927 438559120 438557417 0.000000e+00 1611.0
6 TraesCS5A01G351300 chr5D 81.590 1836 287 41 122 1927 438605351 438603537 0.000000e+00 1471.0
7 TraesCS5A01G351300 chr5D 81.434 1702 259 44 201 1874 438545242 438543570 0.000000e+00 1339.0
8 TraesCS5A01G351300 chr5D 82.251 1555 237 26 201 1739 438455282 438453751 0.000000e+00 1306.0
9 TraesCS5A01G351300 chr5D 80.624 1507 250 36 279 1760 438722367 438720878 0.000000e+00 1127.0
10 TraesCS5A01G351300 chr5D 87.321 560 59 7 2189 2740 438519745 438519190 4.980000e-177 630.0
11 TraesCS5A01G351300 chr5D 95.122 41 2 0 2066 2106 438555628 438555588 6.330000e-07 65.8
12 TraesCS5A01G351300 chr5D 87.500 56 3 2 1 56 438521850 438521799 8.190000e-06 62.1
13 TraesCS5A01G351300 chr5B 90.693 1891 141 22 50 1924 533389878 533388007 0.000000e+00 2484.0
14 TraesCS5A01G351300 chr5B 81.308 1835 292 42 122 1927 533509431 533507619 0.000000e+00 1441.0
15 TraesCS5A01G351300 chr5B 82.788 1650 228 31 119 1750 533383964 533382353 0.000000e+00 1423.0
16 TraesCS5A01G351300 chr5B 80.023 1762 283 47 74 1806 533089349 533087628 0.000000e+00 1240.0
17 TraesCS5A01G351300 chrUn 81.228 1678 259 35 119 1775 63292121 63290479 0.000000e+00 1303.0
18 TraesCS5A01G351300 chrUn 87.097 62 5 3 2105 2163 263048883 263048822 1.760000e-07 67.6
19 TraesCS5A01G351300 chrUn 87.097 62 5 3 2105 2163 386641765 386641826 1.760000e-07 67.6
20 TraesCS5A01G351300 chr2A 83.499 503 75 2 2191 2685 723828340 723827838 1.920000e-126 462.0
21 TraesCS5A01G351300 chr2B 82.772 505 79 2 2189 2685 713694945 713694441 6.960000e-121 444.0
22 TraesCS5A01G351300 chr4A 81.980 505 83 2 2189 2685 684977284 684977788 3.260000e-114 422.0
23 TraesCS5A01G351300 chr7D 91.228 57 4 1 2104 2159 369456996 369456940 2.930000e-10 76.8
24 TraesCS5A01G351300 chr7D 85.484 62 6 2 2105 2163 18296076 18296137 8.190000e-06 62.1
25 TraesCS5A01G351300 chr7A 93.617 47 3 0 2122 2168 102521310 102521356 1.360000e-08 71.3
26 TraesCS5A01G351300 chr6B 91.667 48 2 2 2125 2171 196074715 196074761 6.330000e-07 65.8
27 TraesCS5A01G351300 chr1B 91.667 48 2 2 2125 2171 550221778 550221732 6.330000e-07 65.8
28 TraesCS5A01G351300 chr1B 91.667 48 2 2 2125 2171 643257230 643257184 6.330000e-07 65.8
29 TraesCS5A01G351300 chr1B 84.615 65 6 1 2098 2158 142035881 142035817 8.190000e-06 62.1


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 TraesCS5A01G351300 chr5A 554080721 554083460 2739 True 5060.000000 5060 100.000000 1 2740 1 chr5A.!!$R2 2739
1 TraesCS5A01G351300 chr5A 554058809 554060534 1725 True 1182.000000 1182 79.385000 201 1927 1 chr5A.!!$R1 1726
2 TraesCS5A01G351300 chr5A 554199819 554201380 1561 True 1146.000000 1146 80.342000 212 1750 1 chr5A.!!$R3 1538
3 TraesCS5A01G351300 chr5A 554217492 554218689 1197 True 870.000000 870 80.165000 279 1469 1 chr5A.!!$R4 1190
4 TraesCS5A01G351300 chr5D 438603537 438605351 1814 True 1471.000000 1471 81.590000 122 1927 1 chr5D.!!$R3 1805
5 TraesCS5A01G351300 chr5D 438543570 438545242 1672 True 1339.000000 1339 81.434000 201 1874 1 chr5D.!!$R2 1673
6 TraesCS5A01G351300 chr5D 438453751 438455282 1531 True 1306.000000 1306 82.251000 201 1739 1 chr5D.!!$R1 1538
7 TraesCS5A01G351300 chr5D 438519190 438521850 2660 True 1144.366667 2741 89.070667 1 2740 3 chr5D.!!$R5 2739
8 TraesCS5A01G351300 chr5D 438720878 438722367 1489 True 1127.000000 1127 80.624000 279 1760 1 chr5D.!!$R4 1481
9 TraesCS5A01G351300 chr5D 438555588 438559120 3532 True 838.400000 1611 89.522500 225 2106 2 chr5D.!!$R6 1881
10 TraesCS5A01G351300 chr5B 533388007 533389878 1871 True 2484.000000 2484 90.693000 50 1924 1 chr5B.!!$R3 1874
11 TraesCS5A01G351300 chr5B 533507619 533509431 1812 True 1441.000000 1441 81.308000 122 1927 1 chr5B.!!$R4 1805
12 TraesCS5A01G351300 chr5B 533382353 533383964 1611 True 1423.000000 1423 82.788000 119 1750 1 chr5B.!!$R2 1631
13 TraesCS5A01G351300 chr5B 533087628 533089349 1721 True 1240.000000 1240 80.023000 74 1806 1 chr5B.!!$R1 1732
14 TraesCS5A01G351300 chrUn 63290479 63292121 1642 True 1303.000000 1303 81.228000 119 1775 1 chrUn.!!$R1 1656
15 TraesCS5A01G351300 chr2A 723827838 723828340 502 True 462.000000 462 83.499000 2191 2685 1 chr2A.!!$R1 494
16 TraesCS5A01G351300 chr2B 713694441 713694945 504 True 444.000000 444 82.772000 2189 2685 1 chr2B.!!$R1 496
17 TraesCS5A01G351300 chr4A 684977284 684977788 504 False 422.000000 422 81.980000 2189 2685 1 chr4A.!!$F1 496

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
277 327 1.400494 GGGAACATGACATTACCGTGC 59.6 52.381 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 3938 0.247185 CCGACCATGCTGCCATTTTT 59.753 50.0 0.0 0.0 0.0 1.94 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
31 32 4.264253 CATGGACTCAAGGAAAGCATGTA 58.736 43.478 0.00 0.00 0.00 2.29
36 37 3.441572 ACTCAAGGAAAGCATGTATGTGC 59.558 43.478 0.00 0.00 45.38 4.57
42 43 4.222589 GCATGTATGTGCGCGCGT 62.223 61.111 32.35 20.87 35.10 6.01
84 115 4.260139 TGCGGTCTGTGTTTTCTATGTA 57.740 40.909 0.00 0.00 0.00 2.29
92 123 8.443937 GGTCTGTGTTTTCTATGTAAACTGATC 58.556 37.037 0.00 0.00 36.64 2.92
93 124 8.162880 GTCTGTGTTTTCTATGTAAACTGATCG 58.837 37.037 0.00 0.00 36.64 3.69
94 125 8.085909 TCTGTGTTTTCTATGTAAACTGATCGA 58.914 33.333 0.00 0.00 36.64 3.59
95 126 8.771920 TGTGTTTTCTATGTAAACTGATCGAT 57.228 30.769 0.00 0.00 36.64 3.59
277 327 1.400494 GGGAACATGACATTACCGTGC 59.600 52.381 0.00 0.00 0.00 5.34
327 377 8.515414 GGAGAAAGCACAAGATTATAAGTTTGT 58.485 33.333 10.13 10.13 34.31 2.83
777 844 6.821160 ACAAGAGCTTAGATTCTAGCCTTTTC 59.179 38.462 9.91 4.16 38.14 2.29
912 997 6.098266 GGTTTAATATCATCAAAGGGGTTGCT 59.902 38.462 0.00 0.00 37.13 3.91
996 1081 7.161773 AGTTGGAAATATCTTGTTGGATGTG 57.838 36.000 0.00 0.00 0.00 3.21
1015 1100 7.177878 GGATGTGGATATGAAACCCAAGATAT 58.822 38.462 0.00 0.00 0.00 1.63
1075 1160 3.062763 CAAAATGCAAATACCCAACGCA 58.937 40.909 0.00 0.00 36.95 5.24
1104 1189 5.072193 TGGCACATAGTGAGTATCCATTGAT 59.928 40.000 0.58 0.00 35.23 2.57
1488 1620 1.557443 GACCAACGAACTGCCAGACG 61.557 60.000 0.00 6.62 0.00 4.18
1653 1785 1.134220 CCAATCGCCCTGCCTACTTTA 60.134 52.381 0.00 0.00 0.00 1.85
1655 1787 1.497161 ATCGCCCTGCCTACTTTACT 58.503 50.000 0.00 0.00 0.00 2.24
1707 1845 8.814038 AAGAAATATTCAGCCTACAGTCAATT 57.186 30.769 0.00 0.00 0.00 2.32
1711 1849 5.886960 ATTCAGCCTACAGTCAATTGTTC 57.113 39.130 5.13 0.51 32.56 3.18
1808 1967 5.069318 TGGCTCACAAAATAGTGATGTCAA 58.931 37.500 0.00 0.00 46.51 3.18
1876 2040 3.811722 TGTCACGATCTTTGAATGTGC 57.188 42.857 0.00 0.00 0.00 4.57
1901 2067 5.607939 TCTATTCCGTTTCTGCCTCAATA 57.392 39.130 0.00 0.00 0.00 1.90
1902 2068 6.174720 TCTATTCCGTTTCTGCCTCAATAT 57.825 37.500 0.00 0.00 0.00 1.28
1903 2069 7.297936 TCTATTCCGTTTCTGCCTCAATATA 57.702 36.000 0.00 0.00 0.00 0.86
1904 2070 7.732025 TCTATTCCGTTTCTGCCTCAATATAA 58.268 34.615 0.00 0.00 0.00 0.98
1905 2071 6.619801 ATTCCGTTTCTGCCTCAATATAAC 57.380 37.500 0.00 0.00 0.00 1.89
1906 2072 5.092554 TCCGTTTCTGCCTCAATATAACA 57.907 39.130 0.00 0.00 0.00 2.41
1907 2073 5.116180 TCCGTTTCTGCCTCAATATAACAG 58.884 41.667 0.00 0.00 0.00 3.16
1908 2074 4.876107 CCGTTTCTGCCTCAATATAACAGT 59.124 41.667 0.00 0.00 0.00 3.55
1909 2075 5.006746 CCGTTTCTGCCTCAATATAACAGTC 59.993 44.000 0.00 0.00 0.00 3.51
1910 2076 5.812642 CGTTTCTGCCTCAATATAACAGTCT 59.187 40.000 0.00 0.00 0.00 3.24
1911 2077 6.313905 CGTTTCTGCCTCAATATAACAGTCTT 59.686 38.462 0.00 0.00 0.00 3.01
1912 2078 7.491372 CGTTTCTGCCTCAATATAACAGTCTTA 59.509 37.037 0.00 0.00 0.00 2.10
1913 2079 8.821894 GTTTCTGCCTCAATATAACAGTCTTAG 58.178 37.037 0.00 0.00 0.00 2.18
1914 2080 7.661536 TCTGCCTCAATATAACAGTCTTAGT 57.338 36.000 0.00 0.00 0.00 2.24
1915 2081 8.079211 TCTGCCTCAATATAACAGTCTTAGTT 57.921 34.615 0.00 0.00 0.00 2.24
1916 2082 8.540388 TCTGCCTCAATATAACAGTCTTAGTTT 58.460 33.333 0.00 0.00 0.00 2.66
1917 2083 9.817809 CTGCCTCAATATAACAGTCTTAGTTTA 57.182 33.333 0.00 0.00 0.00 2.01
1978 3209 3.743396 GCAGTCTCACGATCTTTGAAGTT 59.257 43.478 0.00 0.00 0.00 2.66
1987 3901 3.665323 CGATCTTTGAAGTTGCGTTCTGG 60.665 47.826 0.00 0.00 0.00 3.86
1988 3902 2.639065 TCTTTGAAGTTGCGTTCTGGT 58.361 42.857 0.00 0.00 0.00 4.00
1989 3903 2.354510 TCTTTGAAGTTGCGTTCTGGTG 59.645 45.455 0.00 0.00 0.00 4.17
1990 3904 1.745232 TTGAAGTTGCGTTCTGGTGT 58.255 45.000 0.00 0.00 0.00 4.16
1991 3905 1.013596 TGAAGTTGCGTTCTGGTGTG 58.986 50.000 0.00 0.00 0.00 3.82
1992 3906 0.317020 GAAGTTGCGTTCTGGTGTGC 60.317 55.000 0.00 0.00 0.00 4.57
1993 3907 1.724582 AAGTTGCGTTCTGGTGTGCC 61.725 55.000 0.00 0.00 0.00 5.01
1994 3908 2.124529 TTGCGTTCTGGTGTGCCA 60.125 55.556 0.00 0.00 43.73 4.92
1995 3909 1.528076 TTGCGTTCTGGTGTGCCAT 60.528 52.632 0.00 0.00 45.05 4.40
1996 3910 1.514678 TTGCGTTCTGGTGTGCCATC 61.515 55.000 0.00 0.00 45.05 3.51
1997 3911 2.690778 GCGTTCTGGTGTGCCATCC 61.691 63.158 0.00 0.00 45.05 3.51
1998 3912 1.003355 CGTTCTGGTGTGCCATCCT 60.003 57.895 0.00 0.00 45.05 3.24
1999 3913 0.606401 CGTTCTGGTGTGCCATCCTT 60.606 55.000 0.00 0.00 45.05 3.36
2000 3914 1.168714 GTTCTGGTGTGCCATCCTTC 58.831 55.000 0.00 0.00 45.05 3.46
2001 3915 1.067295 TTCTGGTGTGCCATCCTTCT 58.933 50.000 0.00 0.00 45.05 2.85
2002 3916 1.951209 TCTGGTGTGCCATCCTTCTA 58.049 50.000 0.00 0.00 45.05 2.10
2003 3917 2.481441 TCTGGTGTGCCATCCTTCTAT 58.519 47.619 0.00 0.00 45.05 1.98
2004 3918 3.653164 TCTGGTGTGCCATCCTTCTATA 58.347 45.455 0.00 0.00 45.05 1.31
2005 3919 4.037222 TCTGGTGTGCCATCCTTCTATAA 58.963 43.478 0.00 0.00 45.05 0.98
2006 3920 4.473196 TCTGGTGTGCCATCCTTCTATAAA 59.527 41.667 0.00 0.00 45.05 1.40
2007 3921 5.132648 TCTGGTGTGCCATCCTTCTATAAAT 59.867 40.000 0.00 0.00 45.05 1.40
2008 3922 5.765510 TGGTGTGCCATCCTTCTATAAATT 58.234 37.500 0.00 0.00 40.46 1.82
2009 3923 5.827797 TGGTGTGCCATCCTTCTATAAATTC 59.172 40.000 0.00 0.00 40.46 2.17
2010 3924 6.064717 GGTGTGCCATCCTTCTATAAATTCT 58.935 40.000 0.00 0.00 34.09 2.40
2011 3925 6.016777 GGTGTGCCATCCTTCTATAAATTCTG 60.017 42.308 0.00 0.00 34.09 3.02
2012 3926 6.543831 GTGTGCCATCCTTCTATAAATTCTGT 59.456 38.462 0.00 0.00 0.00 3.41
2013 3927 6.543465 TGTGCCATCCTTCTATAAATTCTGTG 59.457 38.462 0.00 0.00 0.00 3.66
2014 3928 6.543831 GTGCCATCCTTCTATAAATTCTGTGT 59.456 38.462 0.00 0.00 0.00 3.72
2015 3929 7.067494 GTGCCATCCTTCTATAAATTCTGTGTT 59.933 37.037 0.00 0.00 0.00 3.32
2016 3930 7.615365 TGCCATCCTTCTATAAATTCTGTGTTT 59.385 33.333 0.00 0.00 0.00 2.83
2017 3931 9.120538 GCCATCCTTCTATAAATTCTGTGTTTA 57.879 33.333 0.00 0.00 0.00 2.01
2042 3956 3.818586 AAAAATGGCAGCATGGTCG 57.181 47.368 0.00 0.00 35.86 4.79
2043 3957 0.247185 AAAAATGGCAGCATGGTCGG 59.753 50.000 0.00 0.00 35.86 4.79
2044 3958 0.611618 AAAATGGCAGCATGGTCGGA 60.612 50.000 0.00 0.00 35.86 4.55
2045 3959 1.315257 AAATGGCAGCATGGTCGGAC 61.315 55.000 0.00 0.00 35.86 4.79
2046 3960 2.482796 AATGGCAGCATGGTCGGACA 62.483 55.000 10.76 0.00 35.86 4.02
2047 3961 2.359850 GGCAGCATGGTCGGACAA 60.360 61.111 10.76 0.00 35.86 3.18
2048 3962 1.971167 GGCAGCATGGTCGGACAAA 60.971 57.895 10.76 0.00 35.86 2.83
2049 3963 1.523154 GGCAGCATGGTCGGACAAAA 61.523 55.000 10.76 0.00 35.86 2.44
2050 3964 0.527565 GCAGCATGGTCGGACAAAAT 59.472 50.000 10.76 0.00 35.86 1.82
2051 3965 1.067635 GCAGCATGGTCGGACAAAATT 60.068 47.619 10.76 0.00 35.86 1.82
2052 3966 2.163412 GCAGCATGGTCGGACAAAATTA 59.837 45.455 10.76 0.00 35.86 1.40
2053 3967 3.731867 GCAGCATGGTCGGACAAAATTAG 60.732 47.826 10.76 0.00 35.86 1.73
2054 3968 3.016736 AGCATGGTCGGACAAAATTAGG 58.983 45.455 10.76 0.00 0.00 2.69
2055 3969 2.099098 GCATGGTCGGACAAAATTAGGG 59.901 50.000 10.76 0.00 0.00 3.53
2056 3970 3.352648 CATGGTCGGACAAAATTAGGGT 58.647 45.455 10.76 0.00 0.00 4.34
2057 3971 2.785562 TGGTCGGACAAAATTAGGGTG 58.214 47.619 10.76 0.00 0.00 4.61
2058 3972 1.471287 GGTCGGACAAAATTAGGGTGC 59.529 52.381 10.76 0.00 0.00 5.01
2059 3973 2.156098 GTCGGACAAAATTAGGGTGCA 58.844 47.619 2.62 0.00 0.00 4.57
2060 3974 2.095415 GTCGGACAAAATTAGGGTGCAC 60.095 50.000 8.80 8.80 0.00 4.57
2061 3975 1.883275 CGGACAAAATTAGGGTGCACA 59.117 47.619 20.43 0.00 0.00 4.57
2062 3976 2.095263 CGGACAAAATTAGGGTGCACAG 60.095 50.000 20.43 0.00 0.00 3.66
2063 3977 2.231235 GGACAAAATTAGGGTGCACAGG 59.769 50.000 20.43 0.00 0.00 4.00
2064 3978 3.153919 GACAAAATTAGGGTGCACAGGA 58.846 45.455 20.43 1.26 0.00 3.86
2071 3985 5.552870 ATTAGGGTGCACAGGATAAGTAG 57.447 43.478 20.43 0.00 0.00 2.57
2108 4030 6.043411 GGTCATAATCCACACTTCAGTACTC 58.957 44.000 0.00 0.00 0.00 2.59
2109 4031 6.043411 GTCATAATCCACACTTCAGTACTCC 58.957 44.000 0.00 0.00 0.00 3.85
2110 4032 3.983044 AATCCACACTTCAGTACTCCC 57.017 47.619 0.00 0.00 0.00 4.30
2112 4034 2.526432 TCCACACTTCAGTACTCCCTC 58.474 52.381 0.00 0.00 0.00 4.30
2113 4035 2.110188 TCCACACTTCAGTACTCCCTCT 59.890 50.000 0.00 0.00 0.00 3.69
2114 4036 2.232452 CCACACTTCAGTACTCCCTCTG 59.768 54.545 0.00 0.00 0.00 3.35
2115 4037 2.894126 CACACTTCAGTACTCCCTCTGT 59.106 50.000 0.00 0.00 33.89 3.41
2116 4038 4.079970 CACACTTCAGTACTCCCTCTGTA 58.920 47.826 0.00 0.00 33.89 2.74
2117 4039 4.523173 CACACTTCAGTACTCCCTCTGTAA 59.477 45.833 0.00 0.00 33.89 2.41
2118 4040 5.010719 CACACTTCAGTACTCCCTCTGTAAA 59.989 44.000 0.00 0.00 33.89 2.01
2119 4041 5.010820 ACACTTCAGTACTCCCTCTGTAAAC 59.989 44.000 0.00 0.00 33.89 2.01
2120 4042 5.244178 CACTTCAGTACTCCCTCTGTAAACT 59.756 44.000 0.00 0.00 33.89 2.66
2121 4043 6.433404 CACTTCAGTACTCCCTCTGTAAACTA 59.567 42.308 0.00 0.00 33.89 2.24
2122 4044 7.122948 CACTTCAGTACTCCCTCTGTAAACTAT 59.877 40.741 0.00 0.00 33.89 2.12
2123 4045 7.339976 ACTTCAGTACTCCCTCTGTAAACTATC 59.660 40.741 0.00 0.00 33.89 2.08
2124 4046 6.971340 TCAGTACTCCCTCTGTAAACTATCT 58.029 40.000 0.00 0.00 33.89 1.98
2125 4047 8.098963 TCAGTACTCCCTCTGTAAACTATCTA 57.901 38.462 0.00 0.00 33.89 1.98
2126 4048 8.554870 TCAGTACTCCCTCTGTAAACTATCTAA 58.445 37.037 0.00 0.00 33.89 2.10
2127 4049 9.186837 CAGTACTCCCTCTGTAAACTATCTAAA 57.813 37.037 0.00 0.00 0.00 1.85
2128 4050 9.765295 AGTACTCCCTCTGTAAACTATCTAAAA 57.235 33.333 0.00 0.00 0.00 1.52
2130 4052 8.080363 ACTCCCTCTGTAAACTATCTAAAAGG 57.920 38.462 0.00 0.00 0.00 3.11
2131 4053 7.679025 ACTCCCTCTGTAAACTATCTAAAAGGT 59.321 37.037 0.00 0.00 0.00 3.50
2132 4054 8.075761 TCCCTCTGTAAACTATCTAAAAGGTC 57.924 38.462 0.00 0.00 0.00 3.85
2133 4055 7.899709 TCCCTCTGTAAACTATCTAAAAGGTCT 59.100 37.037 0.00 0.00 0.00 3.85
2134 4056 8.541234 CCCTCTGTAAACTATCTAAAAGGTCTT 58.459 37.037 0.00 0.00 0.00 3.01
2177 4099 9.209175 GGAGTACTAAATATTGATGTGTCATCC 57.791 37.037 0.00 0.00 33.56 3.51
2178 4100 9.988815 GAGTACTAAATATTGATGTGTCATCCT 57.011 33.333 0.00 0.00 33.56 3.24
2179 4101 9.770097 AGTACTAAATATTGATGTGTCATCCTG 57.230 33.333 0.00 0.00 33.56 3.86
2180 4102 7.502120 ACTAAATATTGATGTGTCATCCTGC 57.498 36.000 7.18 0.00 33.56 4.85
2181 4103 7.285566 ACTAAATATTGATGTGTCATCCTGCT 58.714 34.615 7.18 0.00 33.56 4.24
2182 4104 6.387041 AAATATTGATGTGTCATCCTGCTG 57.613 37.500 7.18 0.00 33.56 4.41
2183 4105 1.456296 TTGATGTGTCATCCTGCTGC 58.544 50.000 7.18 0.00 33.56 5.25
2185 4107 1.077212 ATGTGTCATCCTGCTGCCC 60.077 57.895 0.00 0.00 0.00 5.36
2186 4108 2.439156 GTGTCATCCTGCTGCCCC 60.439 66.667 0.00 0.00 0.00 5.80
2187 4109 2.611800 TGTCATCCTGCTGCCCCT 60.612 61.111 0.00 0.00 0.00 4.79
2202 4131 2.116238 GCCCCTTACACCATCTGAGTA 58.884 52.381 0.00 0.00 0.00 2.59
2219 4148 0.321671 GTAAGCTGAGCTGGTCACCA 59.678 55.000 8.16 0.00 39.62 4.17
2222 4151 2.737180 CTGAGCTGGTCACCACGT 59.263 61.111 5.28 0.00 0.00 4.49
2267 4196 1.512926 CTTCTTCCAGGTGGTGAACG 58.487 55.000 0.00 0.00 36.34 3.95
2275 4204 0.529378 AGGTGGTGAACGACGGTATC 59.471 55.000 0.00 0.00 0.00 2.24
2285 4214 2.364579 ACGGTATCCCCAAGGCGA 60.365 61.111 0.00 0.00 0.00 5.54
2303 4232 2.545322 GCGATCATGTCAGAGATGCTCA 60.545 50.000 10.95 0.00 32.06 4.26
2304 4233 3.861508 GCGATCATGTCAGAGATGCTCAT 60.862 47.826 10.95 0.00 32.06 2.90
2323 4252 4.404654 GCGTTGCGGGGCTTTCAG 62.405 66.667 0.00 0.00 0.00 3.02
2339 4268 4.067512 AGGAGGAGCCAGCGGAGA 62.068 66.667 0.00 0.00 40.02 3.71
2386 4315 3.399105 TTGCCGGCGCATGAGGTAT 62.399 57.895 23.90 0.00 46.67 2.73
2389 4318 1.956170 CCGGCGCATGAGGTATCAC 60.956 63.158 10.83 0.00 38.57 3.06
2402 4338 4.072131 GAGGTATCACAGCAACTTTTCCA 58.928 43.478 0.00 0.00 0.00 3.53
2411 4347 0.596082 CAACTTTTCCAATCGCCGGT 59.404 50.000 1.90 0.00 0.00 5.28
2482 4419 2.123077 CTGAGGAGATCCCGCCCT 60.123 66.667 0.00 0.00 40.87 5.19
2484 4421 2.123251 GAGGAGATCCCGCCCTCA 60.123 66.667 13.17 0.00 44.42 3.86
2489 4426 2.192979 GATCCCGCCCTCATGCAA 59.807 61.111 0.00 0.00 0.00 4.08
2490 4427 2.124151 ATCCCGCCCTCATGCAAC 60.124 61.111 0.00 0.00 0.00 4.17
2523 4461 0.692476 AGTACATGAGGCTGGTGCAA 59.308 50.000 0.00 0.00 41.91 4.08
2528 4466 0.329261 ATGAGGCTGGTGCAAAGCTA 59.671 50.000 19.06 9.05 40.64 3.32
2562 4500 1.217183 TCAAGCTACTATCGGAGGGGT 59.783 52.381 0.00 0.00 0.00 4.95
2597 4535 2.914289 CACCTGGAGGAGGATGCC 59.086 66.667 0.00 0.00 46.33 4.40
2629 4567 3.221222 GCTCTCCGGCCACTACAT 58.779 61.111 2.24 0.00 0.00 2.29
2648 4586 2.759973 CCGTCCTGCCTAGAGCCA 60.760 66.667 0.00 0.00 42.71 4.75
2681 4619 2.043248 ACCACCGCCTACTCCGAT 60.043 61.111 0.00 0.00 0.00 4.18
2708 4646 3.555324 TGGTGGCCAAGAGCGTCA 61.555 61.111 7.24 0.00 45.17 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.027455 CGCATGTTTGACACACACGT 59.973 50.000 0.00 0.00 38.61 4.49
48 49 0.657077 CCGCATGTTTGACACACACG 60.657 55.000 0.00 0.00 38.61 4.49
53 84 0.944386 ACAGACCGCATGTTTGACAC 59.056 50.000 0.00 0.00 33.42 3.67
55 86 0.944386 ACACAGACCGCATGTTTGAC 59.056 50.000 0.00 0.00 33.42 3.18
98 129 6.916360 AAATTCCCACACAAGACAATATGT 57.084 33.333 0.00 0.00 0.00 2.29
109 140 1.678627 CCACGTCAAAATTCCCACACA 59.321 47.619 0.00 0.00 0.00 3.72
174 207 4.952335 AGGTGCTCATTTCCATTCCTTTAG 59.048 41.667 0.00 0.00 0.00 1.85
573 640 3.412386 GACTTGCTGACCACCTAACAAT 58.588 45.455 0.00 0.00 0.00 2.71
665 732 4.690280 CCAAGTTTCTGTGTTGCAGTTTTT 59.310 37.500 0.00 0.00 45.23 1.94
777 844 9.811655 CATGCTTTATTATTAGAATGTGTACCG 57.188 33.333 0.00 0.00 0.00 4.02
912 997 4.087182 CGTGAAGATATAGAAGCCCCCTA 58.913 47.826 0.00 0.00 0.00 3.53
942 1027 3.502211 CCCTATGAATTATGGTGAACCGC 59.498 47.826 0.00 0.00 39.43 5.68
996 1081 6.049955 TCCGATATCTTGGGTTTCATATCC 57.950 41.667 0.34 0.00 0.00 2.59
1015 1100 1.483004 TCTCGCCATACCAAAATCCGA 59.517 47.619 0.00 0.00 0.00 4.55
1075 1160 5.602561 TGGATACTCACTATGTGCCAACTAT 59.397 40.000 0.00 0.00 32.98 2.12
1488 1620 7.547370 GTCTGGTGAAGTATCTATAATGGATGC 59.453 40.741 0.00 0.00 0.00 3.91
1653 1785 3.136763 TCAGTTCAGTACTTCGTCGAGT 58.863 45.455 0.00 0.00 33.85 4.18
1655 1787 4.214758 TGATTCAGTTCAGTACTTCGTCGA 59.785 41.667 0.00 0.00 33.85 4.20
1698 1836 6.987992 TCGGTAAAAGTAGAACAATTGACTGT 59.012 34.615 13.59 0.00 0.00 3.55
1700 1838 7.439381 TCTCGGTAAAAGTAGAACAATTGACT 58.561 34.615 13.59 12.94 0.00 3.41
1707 1845 6.320672 CCCTCTATCTCGGTAAAAGTAGAACA 59.679 42.308 0.00 0.00 0.00 3.18
1711 1849 4.022155 GCCCCTCTATCTCGGTAAAAGTAG 60.022 50.000 0.00 0.00 0.00 2.57
1768 1919 4.275689 TGAGCCAGACAATTTACAGTGTTG 59.724 41.667 0.00 0.00 29.18 3.33
1835 1994 6.709846 TGACATCTGAACAACACATGATACAA 59.290 34.615 0.00 0.00 31.12 2.41
1876 2040 4.253685 TGAGGCAGAAACGGAATAGAAAG 58.746 43.478 0.00 0.00 0.00 2.62
1946 2112 7.929941 AGATCGTGAGACTGCTATATTCATA 57.070 36.000 0.00 0.00 46.97 2.15
1989 3903 6.543831 ACACAGAATTTATAGAAGGATGGCAC 59.456 38.462 0.00 0.00 0.00 5.01
1990 3904 6.662755 ACACAGAATTTATAGAAGGATGGCA 58.337 36.000 0.00 0.00 0.00 4.92
1991 3905 7.573968 AACACAGAATTTATAGAAGGATGGC 57.426 36.000 0.00 0.00 0.00 4.40
2024 3938 0.247185 CCGACCATGCTGCCATTTTT 59.753 50.000 0.00 0.00 0.00 1.94
2025 3939 0.611618 TCCGACCATGCTGCCATTTT 60.612 50.000 0.00 0.00 0.00 1.82
2026 3940 1.001020 TCCGACCATGCTGCCATTT 60.001 52.632 0.00 0.00 0.00 2.32
2027 3941 1.750399 GTCCGACCATGCTGCCATT 60.750 57.895 0.00 0.00 0.00 3.16
2028 3942 2.124570 GTCCGACCATGCTGCCAT 60.125 61.111 0.00 0.00 0.00 4.40
2029 3943 2.689035 TTTGTCCGACCATGCTGCCA 62.689 55.000 0.00 0.00 0.00 4.92
2030 3944 1.523154 TTTTGTCCGACCATGCTGCC 61.523 55.000 0.00 0.00 0.00 4.85
2031 3945 0.527565 ATTTTGTCCGACCATGCTGC 59.472 50.000 0.00 0.00 0.00 5.25
2032 3946 3.181497 CCTAATTTTGTCCGACCATGCTG 60.181 47.826 0.00 0.00 0.00 4.41
2033 3947 3.016736 CCTAATTTTGTCCGACCATGCT 58.983 45.455 0.00 0.00 0.00 3.79
2034 3948 2.099098 CCCTAATTTTGTCCGACCATGC 59.901 50.000 0.00 0.00 0.00 4.06
2035 3949 3.128589 CACCCTAATTTTGTCCGACCATG 59.871 47.826 0.00 0.00 0.00 3.66
2036 3950 3.352648 CACCCTAATTTTGTCCGACCAT 58.647 45.455 0.00 0.00 0.00 3.55
2037 3951 2.785562 CACCCTAATTTTGTCCGACCA 58.214 47.619 0.00 0.00 0.00 4.02
2038 3952 1.471287 GCACCCTAATTTTGTCCGACC 59.529 52.381 0.00 0.00 0.00 4.79
2039 3953 2.095415 GTGCACCCTAATTTTGTCCGAC 60.095 50.000 5.22 0.00 0.00 4.79
2040 3954 2.156098 GTGCACCCTAATTTTGTCCGA 58.844 47.619 5.22 0.00 0.00 4.55
2041 3955 1.883275 TGTGCACCCTAATTTTGTCCG 59.117 47.619 15.69 0.00 0.00 4.79
2042 3956 2.231235 CCTGTGCACCCTAATTTTGTCC 59.769 50.000 15.69 0.00 0.00 4.02
2043 3957 3.153919 TCCTGTGCACCCTAATTTTGTC 58.846 45.455 15.69 0.00 0.00 3.18
2044 3958 3.237268 TCCTGTGCACCCTAATTTTGT 57.763 42.857 15.69 0.00 0.00 2.83
2045 3959 5.418840 ACTTATCCTGTGCACCCTAATTTTG 59.581 40.000 15.69 0.00 0.00 2.44
2046 3960 5.580022 ACTTATCCTGTGCACCCTAATTTT 58.420 37.500 15.69 0.00 0.00 1.82
2047 3961 5.193099 ACTTATCCTGTGCACCCTAATTT 57.807 39.130 15.69 0.00 0.00 1.82
2048 3962 4.862641 ACTTATCCTGTGCACCCTAATT 57.137 40.909 15.69 0.00 0.00 1.40
2049 3963 4.969359 ACTACTTATCCTGTGCACCCTAAT 59.031 41.667 15.69 5.42 0.00 1.73
2050 3964 4.161565 CACTACTTATCCTGTGCACCCTAA 59.838 45.833 15.69 5.94 0.00 2.69
2051 3965 3.704566 CACTACTTATCCTGTGCACCCTA 59.295 47.826 15.69 0.00 0.00 3.53
2052 3966 2.501723 CACTACTTATCCTGTGCACCCT 59.498 50.000 15.69 0.00 0.00 4.34
2053 3967 2.420129 CCACTACTTATCCTGTGCACCC 60.420 54.545 15.69 0.00 0.00 4.61
2054 3968 2.500098 TCCACTACTTATCCTGTGCACC 59.500 50.000 15.69 0.00 0.00 5.01
2055 3969 3.887621 TCCACTACTTATCCTGTGCAC 57.112 47.619 10.75 10.75 0.00 4.57
2056 3970 6.747414 AATATCCACTACTTATCCTGTGCA 57.253 37.500 0.00 0.00 0.00 4.57
2057 3971 8.585881 TCTAAATATCCACTACTTATCCTGTGC 58.414 37.037 0.00 0.00 0.00 4.57
2059 3973 9.315363 CCTCTAAATATCCACTACTTATCCTGT 57.685 37.037 0.00 0.00 0.00 4.00
2060 3974 9.315363 ACCTCTAAATATCCACTACTTATCCTG 57.685 37.037 0.00 0.00 0.00 3.86
2061 3975 9.536510 GACCTCTAAATATCCACTACTTATCCT 57.463 37.037 0.00 0.00 0.00 3.24
2062 3976 9.310449 TGACCTCTAAATATCCACTACTTATCC 57.690 37.037 0.00 0.00 0.00 2.59
2071 3985 8.779354 GTGGATTATGACCTCTAAATATCCAC 57.221 38.462 13.28 13.28 44.68 4.02
2108 4030 8.080363 AGACCTTTTAGATAGTTTACAGAGGG 57.920 38.462 0.00 0.00 0.00 4.30
2146 4068 9.656323 ACACATCAATATTTAGTACTCCCTCTA 57.344 33.333 0.00 0.00 0.00 2.43
2147 4069 8.554490 ACACATCAATATTTAGTACTCCCTCT 57.446 34.615 0.00 0.00 0.00 3.69
2148 4070 8.421784 TGACACATCAATATTTAGTACTCCCTC 58.578 37.037 0.00 0.00 0.00 4.30
2149 4071 8.319057 TGACACATCAATATTTAGTACTCCCT 57.681 34.615 0.00 0.00 0.00 4.20
2150 4072 9.209175 GATGACACATCAATATTTAGTACTCCC 57.791 37.037 0.00 0.00 38.69 4.30
2151 4073 9.209175 GGATGACACATCAATATTTAGTACTCC 57.791 37.037 0.00 0.00 38.69 3.85
2152 4074 9.988815 AGGATGACACATCAATATTTAGTACTC 57.011 33.333 0.00 0.00 38.69 2.59
2153 4075 9.770097 CAGGATGACACATCAATATTTAGTACT 57.230 33.333 12.66 0.00 39.69 2.73
2154 4076 8.499162 GCAGGATGACACATCAATATTTAGTAC 58.501 37.037 12.66 0.00 39.69 2.73
2155 4077 8.432013 AGCAGGATGACACATCAATATTTAGTA 58.568 33.333 12.66 0.00 39.69 1.82
2156 4078 7.228108 CAGCAGGATGACACATCAATATTTAGT 59.772 37.037 12.66 0.00 39.69 2.24
2157 4079 7.582352 CAGCAGGATGACACATCAATATTTAG 58.418 38.462 12.66 0.00 39.69 1.85
2158 4080 6.016860 GCAGCAGGATGACACATCAATATTTA 60.017 38.462 12.66 0.00 39.69 1.40
2161 4083 3.819337 GCAGCAGGATGACACATCAATAT 59.181 43.478 12.66 0.00 39.69 1.28
2164 4086 1.456296 GCAGCAGGATGACACATCAA 58.544 50.000 12.66 0.00 39.69 2.57
2171 4093 0.464554 GTAAGGGGCAGCAGGATGAC 60.465 60.000 0.00 0.00 39.69 3.06
2177 4099 0.749454 GATGGTGTAAGGGGCAGCAG 60.749 60.000 0.00 0.00 45.59 4.24
2178 4100 1.207488 AGATGGTGTAAGGGGCAGCA 61.207 55.000 0.00 0.00 46.28 4.41
2179 4101 0.749454 CAGATGGTGTAAGGGGCAGC 60.749 60.000 0.00 0.00 35.19 5.25
2180 4102 0.911769 TCAGATGGTGTAAGGGGCAG 59.088 55.000 0.00 0.00 0.00 4.85
2181 4103 0.911769 CTCAGATGGTGTAAGGGGCA 59.088 55.000 0.00 0.00 0.00 5.36
2182 4104 0.912486 ACTCAGATGGTGTAAGGGGC 59.088 55.000 0.00 0.00 0.00 5.80
2183 4105 3.432326 GCTTACTCAGATGGTGTAAGGGG 60.432 52.174 18.74 5.32 46.35 4.79
2185 4107 4.160439 TCAGCTTACTCAGATGGTGTAAGG 59.840 45.833 18.74 9.97 46.35 2.69
2187 4109 4.382040 GCTCAGCTTACTCAGATGGTGTAA 60.382 45.833 0.00 0.00 39.61 2.41
2202 4131 1.072159 GTGGTGACCAGCTCAGCTT 59.928 57.895 3.58 0.00 46.09 3.74
2242 4171 1.763770 CACCTGGAAGAAGCCCACT 59.236 57.895 0.00 0.00 34.07 4.00
2275 4204 0.816825 CTGACATGATCGCCTTGGGG 60.817 60.000 0.00 0.00 0.00 4.96
2285 4214 4.618693 CGCTATGAGCATCTCTGACATGAT 60.619 45.833 0.00 0.00 42.58 2.45
2303 4232 2.045340 AAAGCCCCGCAACGCTAT 60.045 55.556 0.00 0.00 34.11 2.97
2304 4233 2.744709 GAAAGCCCCGCAACGCTA 60.745 61.111 0.00 0.00 34.11 4.26
2323 4252 3.844090 GTCTCCGCTGGCTCCTCC 61.844 72.222 0.00 0.00 0.00 4.30
2339 4268 1.611261 TGTAGTAGGGCGCCTTGGT 60.611 57.895 28.56 13.15 34.61 3.67
2378 4307 4.702131 GGAAAAGTTGCTGTGATACCTCAT 59.298 41.667 0.00 0.00 32.98 2.90
2386 4315 2.287547 GCGATTGGAAAAGTTGCTGTGA 60.288 45.455 0.00 0.00 0.00 3.58
2389 4318 1.701704 GGCGATTGGAAAAGTTGCTG 58.298 50.000 0.00 0.00 0.00 4.41
2459 4395 3.157252 GGATCTCCTCAGGCGGCA 61.157 66.667 13.08 0.00 0.00 5.69
2466 4403 2.123251 GAGGGCGGGATCTCCTCA 60.123 66.667 15.11 0.00 44.72 3.86
2482 4419 1.634757 GACGCGATGGTGTTGCATGA 61.635 55.000 15.93 0.00 36.92 3.07
2484 4421 2.739704 CGACGCGATGGTGTTGCAT 61.740 57.895 15.93 0.00 36.92 3.96
2489 4426 2.042259 TACTCCGACGCGATGGTGT 61.042 57.895 24.13 24.13 40.22 4.16
2490 4427 1.585521 GTACTCCGACGCGATGGTG 60.586 63.158 15.93 16.90 0.00 4.17
2544 4482 2.040178 CAACCCCTCCGATAGTAGCTT 58.960 52.381 0.00 0.00 0.00 3.74
2616 4554 3.151710 CGGGATGTAGTGGCCGGA 61.152 66.667 5.05 0.00 0.00 5.14
2629 4567 2.442272 GCTCTAGGCAGGACGGGA 60.442 66.667 0.00 0.00 41.35 5.14
2648 4586 1.298667 GGTGCCCATCGTTAGGTGT 59.701 57.895 0.00 0.00 0.00 4.16
2673 4611 3.214123 CGCGGTGGGATCGGAGTA 61.214 66.667 0.00 0.00 0.00 2.59
2708 4646 2.651361 CACGGAGACACGAGGCTT 59.349 61.111 0.00 0.00 37.61 4.35
2715 4653 3.537206 AAGCAGGCCACGGAGACAC 62.537 63.158 5.01 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.