Multiple sequence alignment - TraesCS6A01G315100

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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 TraesCS6A01G315100 chr6A 100.000 2863 0 0 1 2863 551657170 551654308 0.000000e+00 5288.0
1 TraesCS6A01G315100 chr6A 92.045 88 7 0 1924 2011 255182239 255182326 1.080000e-24 124.0
2 TraesCS6A01G315100 chr6D 92.463 1937 128 12 4 1931 405121769 405119842 0.000000e+00 2752.0
3 TraesCS6A01G315100 chr6D 93.812 808 37 8 2066 2863 405119804 405119000 0.000000e+00 1203.0
4 TraesCS6A01G315100 chr6D 83.400 753 116 8 120 868 321234318 321235065 0.000000e+00 689.0
5 TraesCS6A01G315100 chr6D 100.000 77 0 0 2787 2863 405118576 405118500 2.970000e-30 143.0
6 TraesCS6A01G315100 chr6D 92.045 88 7 0 1924 2011 199210415 199210328 1.080000e-24 124.0
7 TraesCS6A01G315100 chr6D 90.588 85 8 0 1927 2011 114156790 114156706 2.330000e-21 113.0
8 TraesCS6A01G315100 chr6D 90.588 85 8 0 1927 2011 163830942 163831026 2.330000e-21 113.0
9 TraesCS6A01G315100 chr6D 89.130 92 9 1 1921 2011 427344848 427344939 2.330000e-21 113.0
10 TraesCS6A01G315100 chr6D 88.764 89 10 0 1924 2012 234424572 234424660 3.020000e-20 110.0
11 TraesCS6A01G315100 chr6D 89.535 86 9 0 1926 2011 245267663 245267748 3.020000e-20 110.0
12 TraesCS6A01G315100 chr6D 89.535 86 9 0 1926 2011 380137065 380136980 3.020000e-20 110.0
13 TraesCS6A01G315100 chr6B 93.591 983 44 11 953 1931 609076805 609075838 0.000000e+00 1448.0
14 TraesCS6A01G315100 chr6B 93.445 595 28 6 2270 2863 609073999 609073415 0.000000e+00 872.0
15 TraesCS6A01G315100 chr6B 94.536 183 10 0 2 184 609077592 609077410 1.680000e-72 283.0
16 TraesCS6A01G315100 chr6B 89.268 205 16 5 2011 2209 609075840 609075636 4.740000e-63 252.0
17 TraesCS6A01G315100 chr6B 93.333 90 6 0 1922 2011 512256530 512256619 1.790000e-27 134.0
18 TraesCS6A01G315100 chr6B 94.118 85 5 0 1927 2011 472612145 472612061 2.310000e-26 130.0
19 TraesCS6A01G315100 chr6B 91.489 94 7 1 1920 2012 359864727 359864634 8.330000e-26 128.0
20 TraesCS6A01G315100 chr4B 85.067 750 100 10 123 868 460406245 460406986 0.000000e+00 754.0
21 TraesCS6A01G315100 chr4B 91.304 92 8 0 1924 2015 565213464 565213373 2.990000e-25 126.0
22 TraesCS6A01G315100 chr1D 84.267 750 110 7 131 876 57063700 57062955 0.000000e+00 725.0
23 TraesCS6A01G315100 chr1D 83.644 752 115 7 123 870 100798590 100799337 0.000000e+00 701.0
24 TraesCS6A01G315100 chr1D 90.385 104 9 1 19 122 273628597 273628699 4.980000e-28 135.0
25 TraesCS6A01G315100 chr1D 92.308 91 7 0 1921 2011 447516561 447516651 2.310000e-26 130.0
26 TraesCS6A01G315100 chr1D 83.898 118 18 1 19 135 191729925 191729808 8.390000e-21 111.0
27 TraesCS6A01G315100 chr1B 83.777 752 114 6 122 870 395940344 395939598 0.000000e+00 706.0
28 TraesCS6A01G315100 chr1B 83.531 759 112 11 123 876 269555886 269555136 0.000000e+00 697.0
29 TraesCS6A01G315100 chr4D 83.508 764 111 13 123 876 499260163 499259405 0.000000e+00 699.0
30 TraesCS6A01G315100 chr4D 93.023 86 6 0 1927 2012 493742438 493742353 2.990000e-25 126.0
31 TraesCS6A01G315100 chr4D 90.426 94 8 1 1918 2011 113929784 113929692 3.870000e-24 122.0
32 TraesCS6A01G315100 chr4D 90.217 92 8 1 1921 2011 22573411 22573320 5.010000e-23 119.0
33 TraesCS6A01G315100 chr4D 88.172 93 10 1 1920 2012 47343819 47343910 3.020000e-20 110.0
34 TraesCS6A01G315100 chr7B 83.267 759 116 9 122 876 387636250 387637001 0.000000e+00 688.0
35 TraesCS6A01G315100 chr7B 92.135 89 7 0 1924 2012 660360587 660360499 2.990000e-25 126.0
36 TraesCS6A01G315100 chr3B 93.548 93 6 0 1919 2011 70273685 70273593 3.850000e-29 139.0
37 TraesCS6A01G315100 chr3B 95.294 85 4 0 1927 2011 10622597 10622513 4.980000e-28 135.0
38 TraesCS6A01G315100 chr5B 94.318 88 5 0 1924 2011 62940320 62940407 4.980000e-28 135.0
39 TraesCS6A01G315100 chr5B 94.118 85 5 0 1927 2011 17545701 17545617 2.310000e-26 130.0
40 TraesCS6A01G315100 chr2D 95.294 85 4 0 1927 2011 619480792 619480876 4.980000e-28 135.0
41 TraesCS6A01G315100 chr3A 93.333 90 6 0 1924 2013 22230722 22230633 1.790000e-27 134.0
42 TraesCS6A01G315100 chr3A 94.444 36 2 0 2229 2264 656958225 656958190 3.980000e-04 56.5
43 TraesCS6A01G315100 chr5A 94.186 86 5 0 1926 2011 98042971 98042886 6.440000e-27 132.0
44 TraesCS6A01G315100 chr3D 94.118 85 5 0 1927 2011 596060112 596060196 2.310000e-26 130.0
45 TraesCS6A01G315100 chr3D 92.135 89 7 0 1923 2011 450878874 450878786 2.990000e-25 126.0
46 TraesCS6A01G315100 chr2B 92.391 92 5 2 1927 2017 166044568 166044478 2.310000e-26 130.0
47 TraesCS6A01G315100 chr5D 93.976 83 5 0 1927 2009 40912870 40912952 2.990000e-25 126.0
48 TraesCS6A01G315100 chr5D 92.135 89 7 0 1926 2014 350331950 350331862 2.990000e-25 126.0
49 TraesCS6A01G315100 chrUn 92.941 85 6 0 1926 2010 111025299 111025383 1.080000e-24 124.0
50 TraesCS6A01G315100 chrUn 91.860 86 7 0 1927 2012 16901709 16901624 1.390000e-23 121.0
51 TraesCS6A01G315100 chrUn 91.765 85 7 0 1927 2011 83591755 83591839 5.010000e-23 119.0
52 TraesCS6A01G315100 chrUn 91.358 81 6 1 1927 2007 36436975 36436896 3.020000e-20 110.0
53 TraesCS6A01G315100 chrUn 90.789 76 7 0 1924 1999 299168581 299168506 5.050000e-18 102.0
54 TraesCS6A01G315100 chrUn 92.754 69 4 1 1927 1995 151501906 151501973 6.530000e-17 99.0
55 TraesCS6A01G315100 chrUn 92.754 69 4 1 1927 1995 342028620 342028553 6.530000e-17 99.0
56 TraesCS6A01G315100 chrUn 89.231 65 7 0 1947 2011 468291699 468291635 6.570000e-12 82.4
57 TraesCS6A01G315100 chrUn 97.368 38 1 0 1971 2008 28684671 28684708 6.620000e-07 65.8
58 TraesCS6A01G315100 chr4A 83.636 110 16 2 14 122 415853562 415853454 5.050000e-18 102.0
59 TraesCS6A01G315100 chr2A 82.105 95 17 0 2622 2716 11484037 11483943 6.570000e-12 82.4


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 TraesCS6A01G315100 chr6A 551654308 551657170 2862 True 5288.00 5288 100.000 1 2863 1 chr6A.!!$R1 2862
1 TraesCS6A01G315100 chr6D 405118500 405121769 3269 True 1366.00 2752 95.425 4 2863 3 chr6D.!!$R4 2859
2 TraesCS6A01G315100 chr6D 321234318 321235065 747 False 689.00 689 83.400 120 868 1 chr6D.!!$F4 748
3 TraesCS6A01G315100 chr6B 609073415 609077592 4177 True 713.75 1448 92.710 2 2863 4 chr6B.!!$R3 2861
4 TraesCS6A01G315100 chr4B 460406245 460406986 741 False 754.00 754 85.067 123 868 1 chr4B.!!$F1 745
5 TraesCS6A01G315100 chr1D 57062955 57063700 745 True 725.00 725 84.267 131 876 1 chr1D.!!$R1 745
6 TraesCS6A01G315100 chr1D 100798590 100799337 747 False 701.00 701 83.644 123 870 1 chr1D.!!$F1 747
7 TraesCS6A01G315100 chr1B 395939598 395940344 746 True 706.00 706 83.777 122 870 1 chr1B.!!$R2 748
8 TraesCS6A01G315100 chr1B 269555136 269555886 750 True 697.00 697 83.531 123 876 1 chr1B.!!$R1 753
9 TraesCS6A01G315100 chr4D 499259405 499260163 758 True 699.00 699 83.508 123 876 1 chr4D.!!$R4 753
10 TraesCS6A01G315100 chr7B 387636250 387637001 751 False 688.00 688 83.267 122 876 1 chr7B.!!$F1 754

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
590 667 0.039180 TTCCGGTACTCTGCCAGAGA 59.961 55.0 27.84 9.06 45.07 3.10 F
1029 1112 0.243636 GCCTCCACAAAACCCAATCG 59.756 55.0 0.00 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1562 0.311165 CCTCCGTAGCCGATGTACTG 59.689 60.0 0.0 0.0 35.63 2.74 R
2004 2102 0.747255 GAAGCCGAGCAGATACTCCA 59.253 55.0 0.0 0.0 32.79 3.86 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
86 87 2.873170 TGTTTAATCTCGCTTGCACG 57.127 45.000 0.00 0.00 0.00 5.34
252 320 9.774071 AGACTAACTTATTAACCTAGTACCCAA 57.226 33.333 0.00 0.00 0.00 4.12
261 331 3.798515 ACCTAGTACCCAATGTCTTCCA 58.201 45.455 0.00 0.00 0.00 3.53
315 386 8.617290 AAATCAGTACCAAACGAAGTCTAAAT 57.383 30.769 0.00 0.00 45.00 1.40
338 410 9.916397 AAATACGATGAAACTTTACGATGATTC 57.084 29.630 0.00 0.00 0.00 2.52
342 414 8.504005 ACGATGAAACTTTACGATGATTCTTTT 58.496 29.630 0.00 0.00 0.00 2.27
355 427 5.060427 TGATTCTTTTTGGACCAGAAGGA 57.940 39.130 15.69 11.39 38.69 3.36
499 572 7.650834 ATTCACAAATATTTCCAAACCAACG 57.349 32.000 0.00 0.00 0.00 4.10
544 618 4.282496 TCCACCACCACAAGTTTATGTTT 58.718 39.130 0.00 0.00 0.00 2.83
548 622 6.337356 CACCACCACAAGTTTATGTTTTTCT 58.663 36.000 0.00 0.00 0.00 2.52
590 667 0.039180 TTCCGGTACTCTGCCAGAGA 59.961 55.000 27.84 9.06 45.07 3.10
604 681 2.948315 GCCAGAGAGGAAATCAATCACC 59.052 50.000 0.00 0.00 41.22 4.02
623 700 1.025812 CGAGGGCTTCTACATCGTCT 58.974 55.000 0.00 0.00 0.00 4.18
628 705 1.666189 GGCTTCTACATCGTCTTTGCC 59.334 52.381 0.00 0.00 0.00 4.52
742 820 4.956700 ACCATGTTCTCCTCGATCTTCTTA 59.043 41.667 0.00 0.00 0.00 2.10
937 1015 7.965107 GGCATGAAAACTATCTAAACAGTCTTG 59.035 37.037 0.00 0.00 0.00 3.02
938 1016 8.507249 GCATGAAAACTATCTAAACAGTCTTGT 58.493 33.333 0.00 0.00 39.87 3.16
944 1022 6.456501 ACTATCTAAACAGTCTTGTGTGTCC 58.543 40.000 0.00 0.00 37.67 4.02
1029 1112 0.243636 GCCTCCACAAAACCCAATCG 59.756 55.000 0.00 0.00 0.00 3.34
1040 1123 0.251121 ACCCAATCGCAATCACACCA 60.251 50.000 0.00 0.00 0.00 4.17
1061 1144 1.226888 GACCGGACATGGACGCTAC 60.227 63.158 9.46 0.00 0.00 3.58
1247 1330 1.376942 CCTGAAGCAGAGGCCACAG 60.377 63.158 5.01 0.00 42.56 3.66
1252 1335 3.054503 GCAGAGGCCACAGTGCAG 61.055 66.667 5.01 0.00 35.91 4.41
1261 1344 4.569180 ACAGTGCAGGCGCCACTT 62.569 61.111 31.54 4.59 37.32 3.16
1262 1345 4.034258 CAGTGCAGGCGCCACTTG 62.034 66.667 31.54 19.92 37.32 3.16
1263 1346 4.254709 AGTGCAGGCGCCACTTGA 62.255 61.111 31.54 4.13 37.32 3.02
1264 1347 3.286751 GTGCAGGCGCCACTTGAA 61.287 61.111 31.54 10.55 37.32 2.69
1273 1366 1.228245 GCCACTTGAAGCAGGGACA 60.228 57.895 6.44 0.00 0.00 4.02
1304 1397 3.535962 CGCAGCTCCTCCTCCTCC 61.536 72.222 0.00 0.00 0.00 4.30
1469 1562 2.035626 TGCTTGCTTACAGCCCCC 59.964 61.111 0.00 0.00 41.51 5.40
1470 1563 2.035626 GCTTGCTTACAGCCCCCA 59.964 61.111 0.00 0.00 41.51 4.96
1471 1564 2.048603 GCTTGCTTACAGCCCCCAG 61.049 63.158 0.00 0.00 41.51 4.45
1473 1566 0.618458 CTTGCTTACAGCCCCCAGTA 59.382 55.000 0.00 0.00 41.51 2.74
1613 1706 8.366401 GTTGATTATCTCATCTCATCTGGAAGA 58.634 37.037 0.00 0.00 40.07 2.87
1633 1726 2.284754 TACTGCCATTCCTGTTTGCA 57.715 45.000 0.00 0.00 0.00 4.08
1643 1736 1.179152 CCTGTTTGCATCATGGCAGA 58.821 50.000 0.00 0.00 45.88 4.26
1646 1739 3.250744 CTGTTTGCATCATGGCAGAAAG 58.749 45.455 0.00 0.00 45.88 2.62
1649 1742 4.202233 TGTTTGCATCATGGCAGAAAGAAA 60.202 37.500 0.00 0.00 45.88 2.52
1650 1743 4.603989 TTGCATCATGGCAGAAAGAAAA 57.396 36.364 0.00 0.00 45.88 2.29
1682 1776 1.131638 ACTGACCCAGAAAGCTGTGA 58.868 50.000 0.45 0.00 40.63 3.58
1683 1777 1.490490 ACTGACCCAGAAAGCTGTGAA 59.510 47.619 0.45 0.00 40.63 3.18
1729 1825 7.224167 ACTGTGTAAGCTCAAGTAGTTTTACAC 59.776 37.037 19.72 19.72 45.87 2.90
1807 1903 5.119588 GTGTGTTTGGATGAATTCAAGCATG 59.880 40.000 13.09 0.00 36.71 4.06
1836 1932 5.610124 CGATTCAGAAAAATGGTTTGCGTTG 60.610 40.000 0.00 0.00 0.00 4.10
1928 2026 5.471257 AGTCAAAGGAGACGAAAGATGTAC 58.529 41.667 0.00 0.00 43.24 2.90
1929 2027 5.244178 AGTCAAAGGAGACGAAAGATGTACT 59.756 40.000 0.00 0.00 43.24 2.73
1930 2028 5.573669 GTCAAAGGAGACGAAAGATGTACTC 59.426 44.000 0.00 0.00 0.00 2.59
1931 2029 4.722361 AAGGAGACGAAAGATGTACTCC 57.278 45.455 0.00 0.00 42.64 3.85
1932 2030 3.025262 AGGAGACGAAAGATGTACTCCC 58.975 50.000 0.00 0.00 43.12 4.30
1933 2031 3.025262 GGAGACGAAAGATGTACTCCCT 58.975 50.000 0.00 0.00 38.23 4.20
1934 2032 3.067040 GGAGACGAAAGATGTACTCCCTC 59.933 52.174 0.00 0.00 38.23 4.30
1935 2033 3.025262 AGACGAAAGATGTACTCCCTCC 58.975 50.000 0.00 0.00 0.00 4.30
1936 2034 1.749634 ACGAAAGATGTACTCCCTCCG 59.250 52.381 0.00 0.00 0.00 4.63
1937 2035 1.749634 CGAAAGATGTACTCCCTCCGT 59.250 52.381 0.00 0.00 0.00 4.69
1938 2036 2.947652 CGAAAGATGTACTCCCTCCGTA 59.052 50.000 0.00 0.00 0.00 4.02
1939 2037 3.379372 CGAAAGATGTACTCCCTCCGTAA 59.621 47.826 0.00 0.00 0.00 3.18
1940 2038 4.142315 CGAAAGATGTACTCCCTCCGTAAA 60.142 45.833 0.00 0.00 0.00 2.01
1941 2039 5.340439 AAAGATGTACTCCCTCCGTAAAG 57.660 43.478 0.00 0.00 0.00 1.85
1942 2040 4.246712 AGATGTACTCCCTCCGTAAAGA 57.753 45.455 0.00 0.00 0.00 2.52
1943 2041 4.607239 AGATGTACTCCCTCCGTAAAGAA 58.393 43.478 0.00 0.00 0.00 2.52
1944 2042 5.021458 AGATGTACTCCCTCCGTAAAGAAA 58.979 41.667 0.00 0.00 0.00 2.52
1945 2043 4.525912 TGTACTCCCTCCGTAAAGAAAC 57.474 45.455 0.00 0.00 0.00 2.78
1946 2044 3.896888 TGTACTCCCTCCGTAAAGAAACA 59.103 43.478 0.00 0.00 0.00 2.83
1947 2045 4.529377 TGTACTCCCTCCGTAAAGAAACAT 59.471 41.667 0.00 0.00 0.00 2.71
1948 2046 5.716228 TGTACTCCCTCCGTAAAGAAACATA 59.284 40.000 0.00 0.00 0.00 2.29
1949 2047 5.750352 ACTCCCTCCGTAAAGAAACATAA 57.250 39.130 0.00 0.00 0.00 1.90
1950 2048 5.731591 ACTCCCTCCGTAAAGAAACATAAG 58.268 41.667 0.00 0.00 0.00 1.73
1951 2049 5.482878 ACTCCCTCCGTAAAGAAACATAAGA 59.517 40.000 0.00 0.00 0.00 2.10
1952 2050 5.974108 TCCCTCCGTAAAGAAACATAAGAG 58.026 41.667 0.00 0.00 0.00 2.85
1953 2051 4.571176 CCCTCCGTAAAGAAACATAAGAGC 59.429 45.833 0.00 0.00 0.00 4.09
1954 2052 5.175859 CCTCCGTAAAGAAACATAAGAGCA 58.824 41.667 0.00 0.00 0.00 4.26
1955 2053 5.817816 CCTCCGTAAAGAAACATAAGAGCAT 59.182 40.000 0.00 0.00 0.00 3.79
1956 2054 6.984474 CCTCCGTAAAGAAACATAAGAGCATA 59.016 38.462 0.00 0.00 0.00 3.14
1957 2055 7.657761 CCTCCGTAAAGAAACATAAGAGCATAT 59.342 37.037 0.00 0.00 0.00 1.78
1958 2056 9.692749 CTCCGTAAAGAAACATAAGAGCATATA 57.307 33.333 0.00 0.00 0.00 0.86
1959 2057 9.692749 TCCGTAAAGAAACATAAGAGCATATAG 57.307 33.333 0.00 0.00 0.00 1.31
1960 2058 9.692749 CCGTAAAGAAACATAAGAGCATATAGA 57.307 33.333 0.00 0.00 0.00 1.98
2030 2128 2.094762 TCTGCTCGGCTTCTAAAACC 57.905 50.000 0.00 0.00 0.00 3.27
2046 2144 0.902531 AACCGACCCATCCTGTACTG 59.097 55.000 0.00 0.00 0.00 2.74
2076 2174 4.142469 GCCAATGGCTAGTTATTCAAACGT 60.142 41.667 18.47 0.00 46.69 3.99
2084 2182 5.390461 GCTAGTTATTCAAACGTCATGTGCA 60.390 40.000 0.00 0.00 0.00 4.57
2167 2268 6.338146 ACACTTCATAAACATAGCGCTAGAA 58.662 36.000 23.37 16.32 0.00 2.10
2250 2361 8.788325 AATGTACTCCCTCTGTAAACAAATAC 57.212 34.615 0.00 0.00 0.00 1.89
2301 3982 7.397192 AGGCAGTAATTCAAGTATCAAAATGGT 59.603 33.333 0.00 0.00 0.00 3.55
2359 4040 4.405680 TGCATAAAAGCTAGCTAGGAGTGA 59.594 41.667 19.70 0.00 34.99 3.41
2367 4048 3.386402 GCTAGCTAGGAGTGAAGATTGGT 59.614 47.826 22.10 0.00 0.00 3.67
2378 4059 1.936547 GAAGATTGGTCTGGTGCGATC 59.063 52.381 0.00 0.00 34.13 3.69
2404 4085 9.846248 CTTGTCTCAACATATAAAAAGAAAGGG 57.154 33.333 0.00 0.00 34.73 3.95
2471 4152 6.709397 GCATGAAGACATCTAAATCATCAGGA 59.291 38.462 0.00 0.00 34.15 3.86
2485 4166 7.747155 AATCATCAGGATAAGAAGCAGAATG 57.253 36.000 0.00 0.00 34.28 2.67
2557 4238 1.626686 TGGGCATACACACAAAAGGG 58.373 50.000 0.00 0.00 0.00 3.95
2632 4314 0.846693 ACCTTTGTGGAGTGCTTCCT 59.153 50.000 8.90 0.00 46.92 3.36
2635 4317 2.294512 CCTTTGTGGAGTGCTTCCTTTC 59.705 50.000 8.90 2.04 46.92 2.62
2636 4318 1.593196 TTGTGGAGTGCTTCCTTTCG 58.407 50.000 8.90 0.00 46.92 3.46
2677 4359 0.690762 TCCAGTAAACTCACCAGCCC 59.309 55.000 0.00 0.00 0.00 5.19
2692 4374 1.111277 AGCCCTTTGTTTGCTTCGTT 58.889 45.000 0.00 0.00 29.17 3.85
2710 4392 3.253677 TCGTTGAGAGTTCTGTTCTCCTC 59.746 47.826 0.29 0.00 40.26 3.71
2716 4398 5.124138 TGAGAGTTCTGTTCTCCTCGAATAC 59.876 44.000 0.29 0.00 40.26 1.89
2765 4447 1.774110 TGCAAGAAACTTCAGGCCAA 58.226 45.000 5.01 0.00 0.00 4.52
2769 4451 2.951642 CAAGAAACTTCAGGCCAACAGA 59.048 45.455 5.01 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.482436 ACTGAAATAACCGCAAGTGGAA 58.518 40.909 6.67 0.00 0.00 3.53
77 78 0.303493 ACAAGTAACACGTGCAAGCG 59.697 50.000 17.22 2.55 30.59 4.68
234 302 8.488668 GGAAGACATTGGGTACTAGGTTAATAA 58.511 37.037 0.00 0.00 0.00 1.40
315 386 8.697846 AAGAATCATCGTAAAGTTTCATCGTA 57.302 30.769 0.00 0.00 0.00 3.43
337 409 3.562182 GGTTCCTTCTGGTCCAAAAAGA 58.438 45.455 13.07 0.00 34.23 2.52
338 410 2.628178 GGGTTCCTTCTGGTCCAAAAAG 59.372 50.000 6.67 6.67 33.03 2.27
342 414 2.158066 TCTAGGGTTCCTTCTGGTCCAA 60.158 50.000 0.00 0.00 34.61 3.53
355 427 1.123928 CTCCCGAAGCATCTAGGGTT 58.876 55.000 2.40 0.00 44.13 4.11
499 572 0.178990 AGTGTTTTGGGTGGCTCTCC 60.179 55.000 0.00 0.00 0.00 3.71
590 667 1.408822 GCCCTCGGTGATTGATTTCCT 60.409 52.381 0.00 0.00 0.00 3.36
604 681 1.025812 AGACGATGTAGAAGCCCTCG 58.974 55.000 0.00 0.00 35.56 4.63
623 700 0.531657 CATCATTGGAAGGCGGCAAA 59.468 50.000 13.08 0.00 0.00 3.68
765 843 5.016051 TCCTAACAAATGCACTGCAAAAA 57.984 34.783 8.03 0.00 43.62 1.94
776 854 6.914215 CACAATTCATCGGATCCTAACAAATG 59.086 38.462 10.75 4.42 0.00 2.32
777 855 6.039717 CCACAATTCATCGGATCCTAACAAAT 59.960 38.462 10.75 0.62 0.00 2.32
870 948 4.192317 CTGAGCCAAGTTATCCCAGTTAC 58.808 47.826 0.00 0.00 0.00 2.50
901 979 8.409358 AGATAGTTTTCATGCCTTGTTAGTTT 57.591 30.769 0.00 0.00 0.00 2.66
904 982 9.774742 GTTTAGATAGTTTTCATGCCTTGTTAG 57.225 33.333 0.00 0.00 0.00 2.34
937 1015 1.217882 CAGAAGGTTGACGGACACAC 58.782 55.000 0.00 0.00 0.00 3.82
938 1016 0.531974 GCAGAAGGTTGACGGACACA 60.532 55.000 0.00 0.00 0.00 3.72
944 1022 3.904136 AATTTCAGCAGAAGGTTGACG 57.096 42.857 0.00 0.00 36.38 4.35
1029 1112 1.021390 CCGGTCTCTGGTGTGATTGC 61.021 60.000 0.00 0.00 0.00 3.56
1040 1123 2.711922 GCGTCCATGTCCGGTCTCT 61.712 63.158 0.00 0.00 0.00 3.10
1061 1144 1.878522 GTGATGCTAGGCGACACCG 60.879 63.158 0.00 0.00 46.52 4.94
1247 1330 3.259425 CTTCAAGTGGCGCCTGCAC 62.259 63.158 29.70 18.10 45.35 4.57
1252 1335 3.741476 CCTGCTTCAAGTGGCGCC 61.741 66.667 22.73 22.73 0.00 6.53
1255 1338 0.823356 TTGTCCCTGCTTCAAGTGGC 60.823 55.000 0.00 0.00 0.00 5.01
1256 1339 1.542915 CATTGTCCCTGCTTCAAGTGG 59.457 52.381 0.00 0.00 0.00 4.00
1257 1340 2.507484 TCATTGTCCCTGCTTCAAGTG 58.493 47.619 0.00 0.00 0.00 3.16
1258 1341 2.957402 TCATTGTCCCTGCTTCAAGT 57.043 45.000 0.00 0.00 0.00 3.16
1259 1342 2.094854 GCTTCATTGTCCCTGCTTCAAG 60.095 50.000 0.00 0.00 0.00 3.02
1260 1343 1.888512 GCTTCATTGTCCCTGCTTCAA 59.111 47.619 0.00 0.00 0.00 2.69
1261 1344 1.538047 GCTTCATTGTCCCTGCTTCA 58.462 50.000 0.00 0.00 0.00 3.02
1262 1345 0.813821 GGCTTCATTGTCCCTGCTTC 59.186 55.000 0.00 0.00 0.00 3.86
1263 1346 0.962356 CGGCTTCATTGTCCCTGCTT 60.962 55.000 0.00 0.00 0.00 3.91
1264 1347 1.377725 CGGCTTCATTGTCCCTGCT 60.378 57.895 0.00 0.00 0.00 4.24
1469 1562 0.311165 CCTCCGTAGCCGATGTACTG 59.689 60.000 0.00 0.00 35.63 2.74
1470 1563 0.822532 CCCTCCGTAGCCGATGTACT 60.823 60.000 0.00 0.00 35.63 2.73
1471 1564 1.658673 CCCTCCGTAGCCGATGTAC 59.341 63.158 0.00 0.00 35.63 2.90
1473 1566 3.537874 GCCCTCCGTAGCCGATGT 61.538 66.667 0.00 0.00 35.63 3.06
1613 1706 2.806434 TGCAAACAGGAATGGCAGTAT 58.194 42.857 0.00 0.00 0.00 2.12
1633 1726 2.498885 GGCCTTTTCTTTCTGCCATGAT 59.501 45.455 0.00 0.00 41.76 2.45
1643 1736 2.965831 GTGGAAGAAGGGCCTTTTCTTT 59.034 45.455 25.99 12.51 43.07 2.52
1646 1739 1.889170 CAGTGGAAGAAGGGCCTTTTC 59.111 52.381 21.92 22.24 0.00 2.29
1649 1742 0.402121 GTCAGTGGAAGAAGGGCCTT 59.598 55.000 21.09 21.09 0.00 4.35
1650 1743 1.492993 GGTCAGTGGAAGAAGGGCCT 61.493 60.000 0.00 0.00 0.00 5.19
1729 1825 6.314018 ACATACAAGAACACAAATACATGCG 58.686 36.000 0.00 0.00 0.00 4.73
1807 1903 6.454186 GCAAACCATTTTTCTGAATCGTATGC 60.454 38.462 0.00 0.00 0.00 3.14
1836 1932 4.086706 TCCTTTCTTCCTGGAAACTGAC 57.913 45.455 10.86 0.00 32.63 3.51
1897 1994 7.878127 TCTTTCGTCTCCTTTGACTAATCAATT 59.122 33.333 0.00 0.00 44.36 2.32
1928 2026 5.974108 TCTTATGTTTCTTTACGGAGGGAG 58.026 41.667 0.00 0.00 0.00 4.30
1929 2027 5.626116 GCTCTTATGTTTCTTTACGGAGGGA 60.626 44.000 0.00 0.00 0.00 4.20
1930 2028 4.571176 GCTCTTATGTTTCTTTACGGAGGG 59.429 45.833 0.00 0.00 0.00 4.30
1931 2029 5.175859 TGCTCTTATGTTTCTTTACGGAGG 58.824 41.667 0.00 0.00 0.00 4.30
1932 2030 6.910536 ATGCTCTTATGTTTCTTTACGGAG 57.089 37.500 0.00 0.00 0.00 4.63
1933 2031 9.692749 CTATATGCTCTTATGTTTCTTTACGGA 57.307 33.333 0.00 0.00 0.00 4.69
1934 2032 9.692749 TCTATATGCTCTTATGTTTCTTTACGG 57.307 33.333 0.00 0.00 0.00 4.02
2001 2099 0.965439 GCCGAGCAGATACTCCATCT 59.035 55.000 0.00 0.00 45.35 2.90
2002 2100 0.965439 AGCCGAGCAGATACTCCATC 59.035 55.000 0.00 0.00 32.79 3.51
2003 2101 1.342819 GAAGCCGAGCAGATACTCCAT 59.657 52.381 0.00 0.00 32.79 3.41
2004 2102 0.747255 GAAGCCGAGCAGATACTCCA 59.253 55.000 0.00 0.00 32.79 3.86
2005 2103 1.036707 AGAAGCCGAGCAGATACTCC 58.963 55.000 0.00 0.00 32.79 3.85
2006 2104 3.992260 TTAGAAGCCGAGCAGATACTC 57.008 47.619 0.00 0.00 0.00 2.59
2007 2105 4.434520 GTTTTAGAAGCCGAGCAGATACT 58.565 43.478 0.00 0.00 0.00 2.12
2008 2106 3.556365 GGTTTTAGAAGCCGAGCAGATAC 59.444 47.826 0.00 0.00 0.00 2.24
2009 2107 3.793559 GGTTTTAGAAGCCGAGCAGATA 58.206 45.455 0.00 0.00 0.00 1.98
2030 2128 4.873746 AATATCAGTACAGGATGGGTCG 57.126 45.455 9.56 0.00 43.62 4.79
2034 2132 5.745312 TGGCTAATATCAGTACAGGATGG 57.255 43.478 9.56 1.16 43.62 3.51
2096 2194 8.945481 TGAACTCACACAATTTCATGAAAAAT 57.055 26.923 23.91 13.52 33.56 1.82
2159 2260 4.789784 TGTTTGGTGTTAAATTCTAGCGC 58.210 39.130 0.00 0.00 0.00 5.92
2160 2261 6.693545 TGTTTGTTTGGTGTTAAATTCTAGCG 59.306 34.615 0.00 0.00 0.00 4.26
2167 2268 7.091443 TCGAGTTTGTTTGTTTGGTGTTAAAT 58.909 30.769 0.00 0.00 0.00 1.40
2218 2329 8.475639 GTTTACAGAGGGAGTACATTCTAATCA 58.524 37.037 0.00 0.00 0.00 2.57
2359 4040 1.556911 AGATCGCACCAGACCAATCTT 59.443 47.619 0.00 0.00 30.42 2.40
2367 4048 1.256812 TGAGACAAGATCGCACCAGA 58.743 50.000 0.00 0.00 31.35 3.86
2378 4059 9.846248 CCCTTTCTTTTTATATGTTGAGACAAG 57.154 33.333 0.00 0.00 39.66 3.16
2404 4085 7.272037 TCCTCAAAATACCAAGTGTTCTTTC 57.728 36.000 0.00 0.00 0.00 2.62
2471 4152 6.244552 TCCTGTGATCATTCTGCTTCTTAT 57.755 37.500 0.00 0.00 0.00 1.73
2485 4166 2.987149 CCGCAATACGTATCCTGTGATC 59.013 50.000 18.12 0.00 41.42 2.92
2557 4238 4.893424 TCTACTGTTCCTGCAAAAACAC 57.107 40.909 8.97 0.00 32.28 3.32
2632 4314 1.950909 AGCAAAAACATCGGTCCGAAA 59.049 42.857 19.76 0.00 39.99 3.46
2635 4317 1.156736 AGAGCAAAAACATCGGTCCG 58.843 50.000 4.39 4.39 0.00 4.79
2636 4318 3.253432 AGAAAGAGCAAAAACATCGGTCC 59.747 43.478 0.00 0.00 0.00 4.46
2677 4359 4.278678 ACTCTCAACGAAGCAAACAAAG 57.721 40.909 0.00 0.00 0.00 2.77
2692 4374 3.141767 TCGAGGAGAACAGAACTCTCA 57.858 47.619 2.54 0.00 41.01 3.27
2710 4392 5.684626 AGGTTTAAGTCGCTATTCGTATTCG 59.315 40.000 0.00 0.00 39.67 3.34
2716 4398 5.773239 TTCAAGGTTTAAGTCGCTATTCG 57.227 39.130 0.00 0.00 40.15 3.34
2765 4447 3.254903 TGCACTGATGTACGTAGTTCTGT 59.745 43.478 0.00 3.60 37.78 3.41
2769 4451 2.029380 TGCTGCACTGATGTACGTAGTT 60.029 45.455 0.00 0.00 37.78 2.24


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

AutoCloner maintained by Alex Coulton.