Multiple sequence alignment - TraesCS6B01G156900

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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 TraesCS6B01G156900 chr6B 100.000 2687 0 0 1 2687 159397625 159394939 0.000000e+00 4963.0
1 TraesCS6B01G156900 chr6B 84.019 1702 263 9 1 1697 159379639 159377942 0.000000e+00 1628.0
2 TraesCS6B01G156900 chr6B 84.522 1654 238 18 1 1645 159403716 159402072 0.000000e+00 1620.0
3 TraesCS6B01G156900 chr6B 84.517 1647 239 14 2 1642 158161371 158163007 0.000000e+00 1615.0
4 TraesCS6B01G156900 chr6B 100.000 139 0 0 1786 1924 159395700 159395562 9.540000e-65 257.0
5 TraesCS6B01G156900 chr6B 100.000 139 0 0 1926 2064 159395840 159395702 9.540000e-65 257.0
6 TraesCS6B01G156900 chr6A 93.870 1925 116 2 2 1925 100799190 100797267 0.000000e+00 2900.0
7 TraesCS6B01G156900 chr6A 92.731 1926 138 2 1 1925 100757083 100755159 0.000000e+00 2780.0
8 TraesCS6B01G156900 chr6A 84.611 1657 246 9 1 1652 100739906 100738254 0.000000e+00 1639.0
9 TraesCS6B01G156900 chr6A 84.415 1649 245 12 2 1644 100227227 100228869 0.000000e+00 1611.0
10 TraesCS6B01G156900 chr6A 92.848 769 31 6 1926 2687 100755298 100754547 0.000000e+00 1094.0
11 TraesCS6B01G156900 chr6A 92.198 769 36 6 1926 2687 100797406 100796655 0.000000e+00 1066.0
12 TraesCS6B01G156900 chr6A 87.342 79 7 3 2066 2142 100363472 100363549 1.330000e-13 87.9
13 TraesCS6B01G156900 chr6D 92.523 1926 139 3 1 1925 83526940 83525019 0.000000e+00 2754.0
14 TraesCS6B01G156900 chr6D 85.082 1649 234 12 2 1644 83158757 83160399 0.000000e+00 1672.0
15 TraesCS6B01G156900 chr6D 95.969 769 23 3 1926 2687 83525158 83524391 0.000000e+00 1242.0
16 TraesCS6B01G156900 chrUn 97.802 182 3 1 2358 2539 273236129 273235949 2.010000e-81 313.0
17 TraesCS6B01G156900 chrUn 97.802 182 3 1 2358 2539 432306218 432306038 2.010000e-81 313.0
18 TraesCS6B01G156900 chr7D 97.802 182 3 1 2358 2539 382015338 382015518 2.010000e-81 313.0
19 TraesCS6B01G156900 chr4D 97.802 182 3 1 2358 2539 123575919 123575739 2.010000e-81 313.0
20 TraesCS6B01G156900 chr2D 97.802 182 3 1 2358 2539 635034592 635034412 2.010000e-81 313.0
21 TraesCS6B01G156900 chr1B 97.802 182 3 1 2358 2539 53342339 53342519 2.010000e-81 313.0


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 TraesCS6B01G156900 chr6B 159394939 159397625 2686 True 1825.666667 4963 100.0000 1 2687 3 chr6B.!!$R3 2686
1 TraesCS6B01G156900 chr6B 159377942 159379639 1697 True 1628.000000 1628 84.0190 1 1697 1 chr6B.!!$R1 1696
2 TraesCS6B01G156900 chr6B 159402072 159403716 1644 True 1620.000000 1620 84.5220 1 1645 1 chr6B.!!$R2 1644
3 TraesCS6B01G156900 chr6B 158161371 158163007 1636 False 1615.000000 1615 84.5170 2 1642 1 chr6B.!!$F1 1640
4 TraesCS6B01G156900 chr6A 100796655 100799190 2535 True 1983.000000 2900 93.0340 2 2687 2 chr6A.!!$R3 2685
5 TraesCS6B01G156900 chr6A 100754547 100757083 2536 True 1937.000000 2780 92.7895 1 2687 2 chr6A.!!$R2 2686
6 TraesCS6B01G156900 chr6A 100738254 100739906 1652 True 1639.000000 1639 84.6110 1 1652 1 chr6A.!!$R1 1651
7 TraesCS6B01G156900 chr6A 100227227 100228869 1642 False 1611.000000 1611 84.4150 2 1644 1 chr6A.!!$F1 1642
8 TraesCS6B01G156900 chr6D 83524391 83526940 2549 True 1998.000000 2754 94.2460 1 2687 2 chr6D.!!$R1 2686
9 TraesCS6B01G156900 chr6D 83158757 83160399 1642 False 1672.000000 1672 85.0820 2 1644 1 chr6D.!!$F1 1642

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
847 850 0.322456 TCGTTGCCCCCAAGATCAAG 60.322 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 2636 0.322816 GGTGCCAGATGCCAAGAAGA 60.323 55.0 0.0 0.0 40.16 2.87 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
123 125 4.154918 GGTGCAGTCTTGTCTGATTTTAGG 59.845 45.833 0.00 0.00 37.61 2.69
138 140 5.771666 TGATTTTAGGATTGGCATCTCCATC 59.228 40.000 16.33 11.35 46.04 3.51
204 206 6.434340 TGTCTAGATACAAGAGCAAGTTCAGA 59.566 38.462 0.00 0.00 0.00 3.27
273 275 6.347644 GCAAAAATAGCACCCTCAAATTTGTC 60.348 38.462 17.47 2.57 0.00 3.18
476 478 6.264970 GTGATATTCGTAAGGGAGAGGTTAGT 59.735 42.308 0.00 0.00 38.47 2.24
512 514 4.097135 CGAGAGAGACTTCAGATTGCCTAA 59.903 45.833 0.00 0.00 0.00 2.69
540 542 1.205417 GACAGTTGGCCATGGAAATGG 59.795 52.381 18.40 7.76 44.44 3.16
543 545 2.038820 CAGTTGGCCATGGAAATGGTTT 59.961 45.455 18.40 0.00 43.53 3.27
692 695 1.202879 TCTCCGTGAAATTGGTTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
757 760 1.204146 GGAAGCTCCCCTGACATGTA 58.796 55.000 0.00 0.00 0.00 2.29
824 827 2.887152 GGAATCTGGAATATTGCCGCTT 59.113 45.455 4.35 0.00 0.00 4.68
847 850 0.322456 TCGTTGCCCCCAAGATCAAG 60.322 55.000 0.00 0.00 0.00 3.02
1071 1074 4.889832 ACTGAGTTCAAGCACAGAAAAG 57.110 40.909 0.00 0.00 34.88 2.27
1137 1140 2.291153 ACTATTGGTGCTGGCATTGAGT 60.291 45.455 0.00 0.00 0.00 3.41
1159 1162 0.329596 AACCAGGCTCTTCATCACCC 59.670 55.000 0.00 0.00 0.00 4.61
1182 1185 3.855689 CATGTTGTGGATGGAAACCTC 57.144 47.619 0.00 0.00 0.00 3.85
1255 1258 2.202851 AAGATGGCAGCTCGCTCG 60.203 61.111 5.40 0.00 41.91 5.03
1297 1300 1.512926 ACTGACGTCAAGGACAATGC 58.487 50.000 20.49 0.00 32.09 3.56
1363 1366 0.814010 GTTGCACGACAGGTTGAGGT 60.814 55.000 0.00 0.00 0.00 3.85
1401 1404 1.187974 TTCCAAGGAACGGCGAGATA 58.812 50.000 16.62 0.00 0.00 1.98
1417 1420 1.062810 AGATAGACCCCTCGAAGCCTT 60.063 52.381 0.00 0.00 0.00 4.35
1419 1422 0.976073 TAGACCCCTCGAAGCCTTGG 60.976 60.000 0.00 0.00 0.00 3.61
1485 1488 1.531365 CCCTTCCCAAGTGCAGCAA 60.531 57.895 0.00 0.00 0.00 3.91
1487 1490 0.971386 CCTTCCCAAGTGCAGCAATT 59.029 50.000 1.22 1.22 0.00 2.32
1499 1502 0.947244 CAGCAATTGGTATCGCTCCC 59.053 55.000 10.31 0.00 30.72 4.30
1536 1539 3.382832 CCGTCCTGCGAGAACCCT 61.383 66.667 0.00 0.00 44.77 4.34
1537 1540 2.657237 CGTCCTGCGAGAACCCTT 59.343 61.111 0.00 0.00 44.77 3.95
1588 1591 4.007644 CCGTGCAGGAGCTGGTCA 62.008 66.667 8.24 0.00 45.00 4.02
1630 1633 1.363744 CACGAGAGCCAATCCAAGAC 58.636 55.000 0.00 0.00 0.00 3.01
1649 1652 0.533951 CAAGGCAAGGGAAATCTGCC 59.466 55.000 4.11 4.11 45.30 4.85
1699 1702 3.503748 GGCTTTCTGAAGAAGCTAGCAAA 59.496 43.478 18.83 5.00 37.23 3.68
1701 1704 4.721142 CTTTCTGAAGAAGCTAGCAAAGC 58.279 43.478 18.83 3.00 42.53 3.51
1790 1793 2.483876 CTCTTTCAGGTCGCACTCAAA 58.516 47.619 0.00 0.00 0.00 2.69
1909 1912 2.789893 CGTGAGCGACTAGAAATTAGCC 59.210 50.000 0.00 0.00 41.33 3.93
1910 1913 3.489398 CGTGAGCGACTAGAAATTAGCCT 60.489 47.826 0.00 0.00 41.33 4.58
1911 1914 3.799420 GTGAGCGACTAGAAATTAGCCTG 59.201 47.826 0.00 0.00 0.00 4.85
1912 1915 3.447586 TGAGCGACTAGAAATTAGCCTGT 59.552 43.478 0.00 0.00 0.00 4.00
1913 1916 4.643334 TGAGCGACTAGAAATTAGCCTGTA 59.357 41.667 0.00 0.00 0.00 2.74
1914 1917 5.126545 TGAGCGACTAGAAATTAGCCTGTAA 59.873 40.000 0.00 0.00 0.00 2.41
1915 1918 5.974108 AGCGACTAGAAATTAGCCTGTAAA 58.026 37.500 0.00 0.00 0.00 2.01
1916 1919 5.811100 AGCGACTAGAAATTAGCCTGTAAAC 59.189 40.000 0.00 0.00 0.00 2.01
1917 1920 5.006455 GCGACTAGAAATTAGCCTGTAAACC 59.994 44.000 0.00 0.00 0.00 3.27
1918 1921 6.103997 CGACTAGAAATTAGCCTGTAAACCA 58.896 40.000 0.00 0.00 0.00 3.67
1919 1922 6.035758 CGACTAGAAATTAGCCTGTAAACCAC 59.964 42.308 0.00 0.00 0.00 4.16
1920 1923 6.775708 ACTAGAAATTAGCCTGTAAACCACA 58.224 36.000 0.00 0.00 35.30 4.17
1921 1924 7.228590 ACTAGAAATTAGCCTGTAAACCACAA 58.771 34.615 0.00 0.00 36.48 3.33
1922 1925 6.575162 AGAAATTAGCCTGTAAACCACAAG 57.425 37.500 0.00 0.00 36.48 3.16
1923 1926 4.783764 AATTAGCCTGTAAACCACAAGC 57.216 40.909 0.00 0.00 43.75 4.01
1925 1928 1.081442 GCCTGTAAACCACAAGCGC 60.081 57.895 0.00 0.00 34.99 5.92
1926 1929 1.515521 GCCTGTAAACCACAAGCGCT 61.516 55.000 2.64 2.64 34.99 5.92
1927 1930 0.517316 CCTGTAAACCACAAGCGCTC 59.483 55.000 12.06 0.00 36.48 5.03
1928 1931 1.225855 CTGTAAACCACAAGCGCTCA 58.774 50.000 12.06 0.00 36.48 4.26
1929 1932 1.601903 CTGTAAACCACAAGCGCTCAA 59.398 47.619 12.06 0.00 36.48 3.02
1930 1933 2.017782 TGTAAACCACAAGCGCTCAAA 58.982 42.857 12.06 0.00 32.95 2.69
1931 1934 2.423892 TGTAAACCACAAGCGCTCAAAA 59.576 40.909 12.06 0.00 32.95 2.44
1932 1935 2.663826 AAACCACAAGCGCTCAAAAA 57.336 40.000 12.06 0.00 0.00 1.94
1954 1957 5.551305 AAAGGAAAAGAAATGGGTCAAGG 57.449 39.130 0.00 0.00 0.00 3.61
1955 1958 4.469469 AGGAAAAGAAATGGGTCAAGGA 57.531 40.909 0.00 0.00 0.00 3.36
1956 1959 5.015813 AGGAAAAGAAATGGGTCAAGGAT 57.984 39.130 0.00 0.00 0.00 3.24
1957 1960 5.406163 AGGAAAAGAAATGGGTCAAGGATT 58.594 37.500 0.00 0.00 0.00 3.01
1971 1974 3.370840 AAGGATTGACTGCTATTGCCA 57.629 42.857 0.00 0.00 38.71 4.92
1972 1975 3.370840 AGGATTGACTGCTATTGCCAA 57.629 42.857 0.00 0.00 38.71 4.52
1973 1976 3.285484 AGGATTGACTGCTATTGCCAAG 58.715 45.455 0.00 0.00 38.71 3.61
1974 1977 2.360165 GGATTGACTGCTATTGCCAAGG 59.640 50.000 0.00 0.00 38.71 3.61
1975 1978 2.877097 TTGACTGCTATTGCCAAGGA 57.123 45.000 0.00 0.00 38.71 3.36
1976 1979 2.408271 TGACTGCTATTGCCAAGGAG 57.592 50.000 0.00 0.00 38.30 3.69
1977 1980 1.908619 TGACTGCTATTGCCAAGGAGA 59.091 47.619 5.74 0.00 36.07 3.71
1978 1981 2.284190 GACTGCTATTGCCAAGGAGAC 58.716 52.381 5.74 0.00 36.07 3.36
1979 1982 1.912043 ACTGCTATTGCCAAGGAGACT 59.088 47.619 5.74 0.00 40.16 3.24
1980 1983 3.107601 ACTGCTATTGCCAAGGAGACTA 58.892 45.455 5.74 0.00 38.01 2.59
1981 1984 3.133721 ACTGCTATTGCCAAGGAGACTAG 59.866 47.826 5.74 0.00 38.01 2.57
1982 1985 3.107601 TGCTATTGCCAAGGAGACTAGT 58.892 45.455 0.00 0.00 38.01 2.57
1983 1986 4.286707 TGCTATTGCCAAGGAGACTAGTA 58.713 43.478 0.00 0.00 38.01 1.82
1984 1987 4.342378 TGCTATTGCCAAGGAGACTAGTAG 59.658 45.833 0.00 0.00 38.01 2.57
1985 1988 3.828875 ATTGCCAAGGAGACTAGTAGC 57.171 47.619 0.00 0.00 42.68 3.58
1986 1989 2.231716 TGCCAAGGAGACTAGTAGCA 57.768 50.000 0.00 0.00 42.68 3.49
1987 1990 1.825474 TGCCAAGGAGACTAGTAGCAC 59.175 52.381 0.00 0.00 42.68 4.40
1988 1991 1.825474 GCCAAGGAGACTAGTAGCACA 59.175 52.381 0.00 0.00 42.68 4.57
1989 1992 2.233922 GCCAAGGAGACTAGTAGCACAA 59.766 50.000 0.00 0.00 42.68 3.33
1990 1993 3.118592 GCCAAGGAGACTAGTAGCACAAT 60.119 47.826 0.00 0.00 42.68 2.71
1991 1994 4.099573 GCCAAGGAGACTAGTAGCACAATA 59.900 45.833 0.00 0.00 42.68 1.90
1992 1995 5.737635 GCCAAGGAGACTAGTAGCACAATAG 60.738 48.000 0.00 0.00 42.68 1.73
1993 1996 5.361285 CCAAGGAGACTAGTAGCACAATAGT 59.639 44.000 0.00 0.00 42.68 2.12
1994 1997 6.460399 CCAAGGAGACTAGTAGCACAATAGTC 60.460 46.154 14.56 14.56 43.71 2.59
1995 1998 5.756918 AGGAGACTAGTAGCACAATAGTCA 58.243 41.667 20.85 0.00 45.09 3.41
1996 1999 5.825679 AGGAGACTAGTAGCACAATAGTCAG 59.174 44.000 20.85 0.00 45.09 3.51
1997 2000 5.506649 GGAGACTAGTAGCACAATAGTCAGC 60.507 48.000 20.85 14.52 45.09 4.26
1998 2001 4.339814 AGACTAGTAGCACAATAGTCAGCC 59.660 45.833 20.85 2.97 45.09 4.85
1999 2002 2.990066 AGTAGCACAATAGTCAGCCC 57.010 50.000 0.00 0.00 0.00 5.19
2000 2003 2.187958 AGTAGCACAATAGTCAGCCCA 58.812 47.619 0.00 0.00 0.00 5.36
2001 2004 2.571653 AGTAGCACAATAGTCAGCCCAA 59.428 45.455 0.00 0.00 0.00 4.12
2002 2005 2.584835 AGCACAATAGTCAGCCCAAA 57.415 45.000 0.00 0.00 0.00 3.28
2003 2006 2.440409 AGCACAATAGTCAGCCCAAAG 58.560 47.619 0.00 0.00 0.00 2.77
2004 2007 2.040278 AGCACAATAGTCAGCCCAAAGA 59.960 45.455 0.00 0.00 0.00 2.52
2005 2008 2.819608 GCACAATAGTCAGCCCAAAGAA 59.180 45.455 0.00 0.00 0.00 2.52
2006 2009 3.255642 GCACAATAGTCAGCCCAAAGAAA 59.744 43.478 0.00 0.00 0.00 2.52
2007 2010 4.616835 GCACAATAGTCAGCCCAAAGAAAG 60.617 45.833 0.00 0.00 0.00 2.62
2008 2011 4.082125 ACAATAGTCAGCCCAAAGAAAGG 58.918 43.478 0.00 0.00 0.00 3.11
2009 2012 4.082125 CAATAGTCAGCCCAAAGAAAGGT 58.918 43.478 0.00 0.00 0.00 3.50
2010 2013 5.222048 ACAATAGTCAGCCCAAAGAAAGGTA 60.222 40.000 0.00 0.00 0.00 3.08
2011 2014 5.717119 ATAGTCAGCCCAAAGAAAGGTAT 57.283 39.130 0.00 0.00 0.00 2.73
2012 2015 3.690460 AGTCAGCCCAAAGAAAGGTATG 58.310 45.455 0.00 0.00 0.00 2.39
2013 2016 3.074538 AGTCAGCCCAAAGAAAGGTATGT 59.925 43.478 0.00 0.00 0.00 2.29
2014 2017 3.191371 GTCAGCCCAAAGAAAGGTATGTG 59.809 47.826 0.00 0.00 0.00 3.21
2015 2018 3.073798 TCAGCCCAAAGAAAGGTATGTGA 59.926 43.478 0.00 0.00 0.00 3.58
2016 2019 3.826157 CAGCCCAAAGAAAGGTATGTGAA 59.174 43.478 0.00 0.00 0.00 3.18
2017 2020 4.280677 CAGCCCAAAGAAAGGTATGTGAAA 59.719 41.667 0.00 0.00 0.00 2.69
2018 2021 5.047092 CAGCCCAAAGAAAGGTATGTGAAAT 60.047 40.000 0.00 0.00 0.00 2.17
2019 2022 5.185828 AGCCCAAAGAAAGGTATGTGAAATC 59.814 40.000 0.00 0.00 0.00 2.17
2020 2023 5.047377 GCCCAAAGAAAGGTATGTGAAATCA 60.047 40.000 0.00 0.00 0.00 2.57
2021 2024 6.389906 CCCAAAGAAAGGTATGTGAAATCAC 58.610 40.000 6.60 6.60 46.59 3.06
2022 2025 6.209391 CCCAAAGAAAGGTATGTGAAATCACT 59.791 38.462 14.15 3.56 46.55 3.41
2023 2026 7.393234 CCCAAAGAAAGGTATGTGAAATCACTA 59.607 37.037 14.15 2.32 46.55 2.74
2024 2027 8.237267 CCAAAGAAAGGTATGTGAAATCACTAC 58.763 37.037 14.15 12.56 46.55 2.73
2025 2028 7.923414 AAGAAAGGTATGTGAAATCACTACC 57.077 36.000 21.75 21.75 46.55 3.18
2029 2032 6.145338 AGGTATGTGAAATCACTACCTACG 57.855 41.667 26.11 0.00 46.59 3.51
2030 2033 5.655532 AGGTATGTGAAATCACTACCTACGT 59.344 40.000 26.11 16.35 46.59 3.57
2031 2034 5.747197 GGTATGTGAAATCACTACCTACGTG 59.253 44.000 21.86 0.00 46.55 4.49
2032 2035 5.654603 ATGTGAAATCACTACCTACGTGA 57.345 39.130 14.15 0.00 46.55 4.35
2033 2036 5.055642 TGTGAAATCACTACCTACGTGAG 57.944 43.478 14.15 0.00 46.55 3.51
2034 2037 3.858238 GTGAAATCACTACCTACGTGAGC 59.142 47.826 6.30 0.00 43.82 4.26
2035 2038 2.846039 AATCACTACCTACGTGAGCG 57.154 50.000 0.00 0.00 43.82 5.03
2036 2039 2.034104 ATCACTACCTACGTGAGCGA 57.966 50.000 0.00 0.00 43.82 4.93
2037 2040 1.081892 TCACTACCTACGTGAGCGAC 58.918 55.000 0.00 0.00 42.00 5.19
2038 2041 1.085091 CACTACCTACGTGAGCGACT 58.915 55.000 0.00 0.00 42.00 4.18
2039 2042 2.094026 TCACTACCTACGTGAGCGACTA 60.094 50.000 0.00 0.00 42.00 2.59
2040 2043 2.284684 CACTACCTACGTGAGCGACTAG 59.715 54.545 0.00 0.00 42.00 2.57
2041 2044 2.167281 ACTACCTACGTGAGCGACTAGA 59.833 50.000 0.00 0.00 42.00 2.43
2042 2045 2.105006 ACCTACGTGAGCGACTAGAA 57.895 50.000 0.00 0.00 42.00 2.10
2043 2046 2.430465 ACCTACGTGAGCGACTAGAAA 58.570 47.619 0.00 0.00 42.00 2.52
2044 2047 3.015327 ACCTACGTGAGCGACTAGAAAT 58.985 45.455 0.00 0.00 42.00 2.17
2045 2048 3.442977 ACCTACGTGAGCGACTAGAAATT 59.557 43.478 0.00 0.00 42.00 1.82
2046 2049 4.637534 ACCTACGTGAGCGACTAGAAATTA 59.362 41.667 0.00 0.00 42.00 1.40
2047 2050 5.206299 CCTACGTGAGCGACTAGAAATTAG 58.794 45.833 0.00 0.00 42.00 1.73
2048 2051 3.436496 ACGTGAGCGACTAGAAATTAGC 58.564 45.455 0.00 0.00 42.00 3.09
2064 2067 2.940994 TAGCCTGTAAACCACAAGCA 57.059 45.000 1.28 0.00 45.50 3.91
2129 2132 4.349342 AGAAAGAGCAAGAGAGGAAAGGAA 59.651 41.667 0.00 0.00 0.00 3.36
2145 2148 0.606673 GGAACAACCTGCTCTGGTCC 60.607 60.000 0.00 0.00 42.05 4.46
2247 2256 1.620819 ACGAGTCTGACTTCCAAGCAT 59.379 47.619 12.27 0.00 0.00 3.79
2312 2321 6.592607 CAGCTTTGCAATTAAACTCCATCATT 59.407 34.615 0.00 0.00 0.00 2.57
2464 2473 8.786898 CAGGAGATTGAAACTTTTCTACATGAA 58.213 33.333 0.00 0.00 38.02 2.57
2471 2480 6.318648 TGAAACTTTTCTACATGAAGTGTGCT 59.681 34.615 0.00 0.00 37.60 4.40
2555 2564 6.741992 TTACCTAAGTGCTGTTGATTGATG 57.258 37.500 0.00 0.00 0.00 3.07
2622 2634 5.048782 TGTTAATGCTGCTCAAACCTAGTTG 60.049 40.000 0.00 0.00 0.00 3.16
2623 2635 2.638480 TGCTGCTCAAACCTAGTTGT 57.362 45.000 0.00 0.00 0.00 3.32
2624 2636 2.930950 TGCTGCTCAAACCTAGTTGTT 58.069 42.857 0.00 0.00 0.00 2.83
2628 2640 4.319839 GCTGCTCAAACCTAGTTGTTCTTC 60.320 45.833 0.00 0.00 0.00 2.87
2630 2642 5.437060 TGCTCAAACCTAGTTGTTCTTCTT 58.563 37.500 0.00 0.00 0.00 2.52
2647 2660 2.036098 TGGCATCTGGCACCCTTG 59.964 61.111 1.83 0.00 46.12 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
476 478 7.606839 TGAAGTCTCTCTCGTTTCTATCACTTA 59.393 37.037 0.00 0.00 0.00 2.24
512 514 3.007182 CCATGGCCAACTGTCAGAAAAAT 59.993 43.478 10.96 0.00 0.00 1.82
540 542 1.997669 CACTACGGCTCTCCAGAAAC 58.002 55.000 0.00 0.00 0.00 2.78
543 545 1.304134 TGCACTACGGCTCTCCAGA 60.304 57.895 0.00 0.00 34.04 3.86
641 643 3.877508 AGGTCAACTTCTCAAACTTTCCG 59.122 43.478 0.00 0.00 0.00 4.30
824 827 1.416401 GATCTTGGGGGCAACGAGATA 59.584 52.381 9.56 0.00 38.80 1.98
847 850 1.826385 CTCACAAATCTGGTCACCCC 58.174 55.000 0.00 0.00 0.00 4.95
1071 1074 1.812922 CTGTCTCAGCGCACCATCC 60.813 63.158 11.47 0.00 0.00 3.51
1137 1140 2.027192 GGTGATGAAGAGCCTGGTTGTA 60.027 50.000 0.00 0.00 0.00 2.41
1182 1185 3.882888 TCTCAAGCAACTTGTTTACAGGG 59.117 43.478 7.18 0.00 41.66 4.45
1297 1300 1.002990 TGGTGTCATCCAGCAGCAG 60.003 57.895 0.00 0.00 46.19 4.24
1335 1338 0.174617 TGTCGTGCAACTCACTGTCA 59.825 50.000 0.00 0.00 43.46 3.58
1363 1366 1.985473 AATCTCACAGGCTTGTTGCA 58.015 45.000 0.00 0.00 45.15 4.08
1401 1404 2.294078 CCAAGGCTTCGAGGGGTCT 61.294 63.158 0.00 0.00 0.00 3.85
1417 1420 0.960364 GATGTTTCGCTGGCTTCCCA 60.960 55.000 0.00 0.00 39.32 4.37
1419 1422 0.449388 CTGATGTTTCGCTGGCTTCC 59.551 55.000 0.00 0.00 0.00 3.46
1485 1488 1.837090 GTGGGGGAGCGATACCAAT 59.163 57.895 3.30 0.00 34.26 3.16
1487 1490 2.939760 ATCGTGGGGGAGCGATACCA 62.940 60.000 3.30 0.00 44.65 3.25
1536 1539 0.987294 CCCTTCTCCAGCTCCTTGAA 59.013 55.000 0.00 0.00 0.00 2.69
1537 1540 0.117140 TCCCTTCTCCAGCTCCTTGA 59.883 55.000 0.00 0.00 0.00 3.02
1588 1591 1.739750 CTGATATCCTTGGCCCCTCT 58.260 55.000 0.00 0.00 0.00 3.69
1630 1633 0.533951 GGCAGATTTCCCTTGCCTTG 59.466 55.000 7.44 0.00 41.99 3.61
1649 1652 0.673437 ACACGATTGCCCAAACAAGG 59.327 50.000 0.00 0.00 31.96 3.61
1651 1654 1.066303 GTCACACGATTGCCCAAACAA 59.934 47.619 0.00 0.00 0.00 2.83
1742 1745 1.466167 CAAAACGGAGACATGAGCTGG 59.534 52.381 0.00 0.00 0.00 4.85
1790 1793 6.157820 TCCTTGACCCATTTCTTTTCCTTTTT 59.842 34.615 0.00 0.00 0.00 1.94
1811 1814 3.370840 TGGCAATAGCAGTCAATCCTT 57.629 42.857 0.00 0.00 44.61 3.36
1825 1828 3.107601 TGCTACTAGTCTCCTTGGCAAT 58.892 45.455 0.00 0.00 0.00 3.56
1909 1912 1.225855 TGAGCGCTTGTGGTTTACAG 58.774 50.000 13.26 0.00 41.10 2.74
1910 1913 1.669604 TTGAGCGCTTGTGGTTTACA 58.330 45.000 13.26 0.00 37.56 2.41
1911 1914 2.766970 TTTGAGCGCTTGTGGTTTAC 57.233 45.000 13.26 0.00 0.00 2.01
1912 1915 3.784701 TTTTTGAGCGCTTGTGGTTTA 57.215 38.095 13.26 0.00 0.00 2.01
1913 1916 2.663826 TTTTTGAGCGCTTGTGGTTT 57.336 40.000 13.26 0.00 0.00 3.27
1930 1933 6.157820 TCCTTGACCCATTTCTTTTCCTTTTT 59.842 34.615 0.00 0.00 0.00 1.94
1931 1934 5.665360 TCCTTGACCCATTTCTTTTCCTTTT 59.335 36.000 0.00 0.00 0.00 2.27
1932 1935 5.215845 TCCTTGACCCATTTCTTTTCCTTT 58.784 37.500 0.00 0.00 0.00 3.11
1933 1936 4.814967 TCCTTGACCCATTTCTTTTCCTT 58.185 39.130 0.00 0.00 0.00 3.36
1934 1937 4.469469 TCCTTGACCCATTTCTTTTCCT 57.531 40.909 0.00 0.00 0.00 3.36
1935 1938 5.245977 TCAATCCTTGACCCATTTCTTTTCC 59.754 40.000 0.00 0.00 34.08 3.13
1936 1939 6.345096 TCAATCCTTGACCCATTTCTTTTC 57.655 37.500 0.00 0.00 34.08 2.29
1949 1952 3.282021 GGCAATAGCAGTCAATCCTTGA 58.718 45.455 0.00 0.00 44.61 3.02
1950 1953 3.018856 TGGCAATAGCAGTCAATCCTTG 58.981 45.455 0.00 0.00 44.61 3.61
1951 1954 3.370840 TGGCAATAGCAGTCAATCCTT 57.629 42.857 0.00 0.00 44.61 3.36
1952 1955 3.285484 CTTGGCAATAGCAGTCAATCCT 58.715 45.455 0.00 0.00 44.61 3.24
1953 1956 2.360165 CCTTGGCAATAGCAGTCAATCC 59.640 50.000 0.00 0.00 44.61 3.01
1954 1957 3.282021 TCCTTGGCAATAGCAGTCAATC 58.718 45.455 0.00 0.00 44.61 2.67
1955 1958 3.054139 TCTCCTTGGCAATAGCAGTCAAT 60.054 43.478 0.00 0.00 44.61 2.57
1956 1959 2.305635 TCTCCTTGGCAATAGCAGTCAA 59.694 45.455 0.00 0.00 44.61 3.18
1957 1960 1.908619 TCTCCTTGGCAATAGCAGTCA 59.091 47.619 0.00 0.00 44.61 3.41
1958 1961 2.093235 AGTCTCCTTGGCAATAGCAGTC 60.093 50.000 0.00 0.00 44.61 3.51
1959 1962 1.912043 AGTCTCCTTGGCAATAGCAGT 59.088 47.619 0.00 0.00 44.61 4.40
1960 1963 2.706339 AGTCTCCTTGGCAATAGCAG 57.294 50.000 0.00 0.00 44.61 4.24
1961 1964 3.107601 ACTAGTCTCCTTGGCAATAGCA 58.892 45.455 0.00 0.00 44.61 3.49
1962 1965 3.828875 ACTAGTCTCCTTGGCAATAGC 57.171 47.619 0.00 0.00 41.10 2.97
1963 1966 4.342378 TGCTACTAGTCTCCTTGGCAATAG 59.658 45.833 0.00 1.62 0.00 1.73
1964 1967 4.099573 GTGCTACTAGTCTCCTTGGCAATA 59.900 45.833 0.00 0.00 0.00 1.90
1965 1968 3.107601 TGCTACTAGTCTCCTTGGCAAT 58.892 45.455 0.00 0.00 0.00 3.56
1966 1969 2.233922 GTGCTACTAGTCTCCTTGGCAA 59.766 50.000 0.00 0.00 0.00 4.52
1967 1970 1.825474 GTGCTACTAGTCTCCTTGGCA 59.175 52.381 0.00 0.00 0.00 4.92
1968 1971 1.825474 TGTGCTACTAGTCTCCTTGGC 59.175 52.381 0.00 0.00 0.00 4.52
1969 1972 4.744795 ATTGTGCTACTAGTCTCCTTGG 57.255 45.455 0.00 0.00 0.00 3.61
1970 1973 6.095580 TGACTATTGTGCTACTAGTCTCCTTG 59.904 42.308 0.00 0.00 41.16 3.61
1971 1974 6.188407 TGACTATTGTGCTACTAGTCTCCTT 58.812 40.000 0.00 0.00 41.16 3.36
1972 1975 5.756918 TGACTATTGTGCTACTAGTCTCCT 58.243 41.667 0.00 0.00 41.16 3.69
1973 1976 5.506649 GCTGACTATTGTGCTACTAGTCTCC 60.507 48.000 0.00 0.00 41.16 3.71
1974 1977 5.506649 GGCTGACTATTGTGCTACTAGTCTC 60.507 48.000 0.00 0.00 41.16 3.36
1975 1978 4.339814 GGCTGACTATTGTGCTACTAGTCT 59.660 45.833 0.00 0.00 41.16 3.24
1976 1979 4.500035 GGGCTGACTATTGTGCTACTAGTC 60.500 50.000 0.00 10.17 41.03 2.59
1977 1980 3.385111 GGGCTGACTATTGTGCTACTAGT 59.615 47.826 0.00 0.00 0.00 2.57
1978 1981 3.384789 TGGGCTGACTATTGTGCTACTAG 59.615 47.826 0.00 0.00 0.00 2.57
1979 1982 3.371034 TGGGCTGACTATTGTGCTACTA 58.629 45.455 0.00 0.00 0.00 1.82
1980 1983 2.187958 TGGGCTGACTATTGTGCTACT 58.812 47.619 0.00 0.00 0.00 2.57
1981 1984 2.691409 TGGGCTGACTATTGTGCTAC 57.309 50.000 0.00 0.00 0.00 3.58
1982 1985 3.263170 TCTTTGGGCTGACTATTGTGCTA 59.737 43.478 0.00 0.00 0.00 3.49
1983 1986 2.040278 TCTTTGGGCTGACTATTGTGCT 59.960 45.455 0.00 0.00 0.00 4.40
1984 1987 2.436417 TCTTTGGGCTGACTATTGTGC 58.564 47.619 0.00 0.00 0.00 4.57
1985 1988 4.082571 CCTTTCTTTGGGCTGACTATTGTG 60.083 45.833 0.00 0.00 0.00 3.33
1986 1989 4.082125 CCTTTCTTTGGGCTGACTATTGT 58.918 43.478 0.00 0.00 0.00 2.71
1987 1990 4.082125 ACCTTTCTTTGGGCTGACTATTG 58.918 43.478 0.00 0.00 0.00 1.90
1988 1991 4.388577 ACCTTTCTTTGGGCTGACTATT 57.611 40.909 0.00 0.00 0.00 1.73
1989 1992 5.044846 ACATACCTTTCTTTGGGCTGACTAT 60.045 40.000 0.00 0.00 0.00 2.12
1990 1993 4.288626 ACATACCTTTCTTTGGGCTGACTA 59.711 41.667 0.00 0.00 0.00 2.59
1991 1994 3.074538 ACATACCTTTCTTTGGGCTGACT 59.925 43.478 0.00 0.00 0.00 3.41
1992 1995 3.191371 CACATACCTTTCTTTGGGCTGAC 59.809 47.826 0.00 0.00 0.00 3.51
1993 1996 3.073798 TCACATACCTTTCTTTGGGCTGA 59.926 43.478 0.00 0.00 0.00 4.26
1994 1997 3.420893 TCACATACCTTTCTTTGGGCTG 58.579 45.455 0.00 0.00 0.00 4.85
1995 1998 3.806949 TCACATACCTTTCTTTGGGCT 57.193 42.857 0.00 0.00 0.00 5.19
1996 1999 4.864704 TTTCACATACCTTTCTTTGGGC 57.135 40.909 0.00 0.00 0.00 5.36
1997 2000 6.389906 GTGATTTCACATACCTTTCTTTGGG 58.610 40.000 5.84 0.00 45.75 4.12
2000 2003 8.164070 AGGTAGTGATTTCACATACCTTTCTTT 58.836 33.333 22.56 10.42 46.48 2.52
2001 2004 7.690256 AGGTAGTGATTTCACATACCTTTCTT 58.310 34.615 22.56 10.86 46.48 2.52
2002 2005 7.259088 AGGTAGTGATTTCACATACCTTTCT 57.741 36.000 22.56 11.08 46.48 2.52
2003 2006 7.222224 CGTAGGTAGTGATTTCACATACCTTTC 59.778 40.741 27.67 22.50 46.48 2.62
2004 2007 7.039882 CGTAGGTAGTGATTTCACATACCTTT 58.960 38.462 27.67 17.26 46.48 3.11
2005 2008 6.154021 ACGTAGGTAGTGATTTCACATACCTT 59.846 38.462 27.67 17.34 46.48 3.50
2009 2012 9.731643 CGCTCACGTAGGTAGTGATTTCACATA 62.732 44.444 12.87 0.76 46.07 2.29
2011 2014 7.822303 CGCTCACGTAGGTAGTGATTTCACA 62.822 48.000 12.87 0.00 46.07 3.58
2012 2015 3.858238 GCTCACGTAGGTAGTGATTTCAC 59.142 47.826 2.41 2.41 46.07 3.18
2013 2016 3.427098 CGCTCACGTAGGTAGTGATTTCA 60.427 47.826 0.00 0.00 46.07 2.69
2014 2017 3.106672 CGCTCACGTAGGTAGTGATTTC 58.893 50.000 0.00 0.00 46.07 2.17
2015 2018 2.751259 TCGCTCACGTAGGTAGTGATTT 59.249 45.455 0.00 0.00 46.07 2.17
2016 2019 2.097142 GTCGCTCACGTAGGTAGTGATT 59.903 50.000 0.00 0.00 46.07 2.57
2017 2020 1.669779 GTCGCTCACGTAGGTAGTGAT 59.330 52.381 0.00 0.00 46.07 3.06
2018 2021 1.081892 GTCGCTCACGTAGGTAGTGA 58.918 55.000 0.00 0.00 45.23 3.41
2019 2022 1.085091 AGTCGCTCACGTAGGTAGTG 58.915 55.000 0.00 0.00 41.18 2.74
2020 2023 2.167281 TCTAGTCGCTCACGTAGGTAGT 59.833 50.000 0.00 0.00 41.18 2.73
2021 2024 2.819115 TCTAGTCGCTCACGTAGGTAG 58.181 52.381 0.00 0.00 41.18 3.18
2022 2025 2.967599 TCTAGTCGCTCACGTAGGTA 57.032 50.000 0.00 0.00 41.18 3.08
2023 2026 2.105006 TTCTAGTCGCTCACGTAGGT 57.895 50.000 0.00 0.00 41.18 3.08
2024 2027 3.694535 ATTTCTAGTCGCTCACGTAGG 57.305 47.619 0.00 0.00 41.18 3.18
2025 2028 4.671516 GCTAATTTCTAGTCGCTCACGTAG 59.328 45.833 0.00 0.00 41.18 3.51
2026 2029 4.497006 GGCTAATTTCTAGTCGCTCACGTA 60.497 45.833 0.00 0.00 41.18 3.57
2027 2030 3.436496 GCTAATTTCTAGTCGCTCACGT 58.564 45.455 0.00 0.00 41.18 4.49
2028 2031 2.789893 GGCTAATTTCTAGTCGCTCACG 59.210 50.000 0.00 0.00 42.01 4.35
2029 2032 3.799420 CAGGCTAATTTCTAGTCGCTCAC 59.201 47.826 0.00 0.00 0.00 3.51
2030 2033 3.447586 ACAGGCTAATTTCTAGTCGCTCA 59.552 43.478 0.00 0.00 0.00 4.26
2031 2034 4.048241 ACAGGCTAATTTCTAGTCGCTC 57.952 45.455 0.00 0.00 0.00 5.03
2032 2035 5.593679 TTACAGGCTAATTTCTAGTCGCT 57.406 39.130 0.00 0.00 0.00 4.93
2033 2036 5.006455 GGTTTACAGGCTAATTTCTAGTCGC 59.994 44.000 0.00 0.00 0.00 5.19
2034 2037 6.035758 GTGGTTTACAGGCTAATTTCTAGTCG 59.964 42.308 0.00 0.00 0.00 4.18
2035 2038 6.877322 TGTGGTTTACAGGCTAATTTCTAGTC 59.123 38.462 0.00 0.00 33.42 2.59
2036 2039 6.775708 TGTGGTTTACAGGCTAATTTCTAGT 58.224 36.000 0.00 0.00 33.42 2.57
2037 2040 7.681939 TTGTGGTTTACAGGCTAATTTCTAG 57.318 36.000 0.00 0.00 41.10 2.43
2038 2041 7.681939 CTTGTGGTTTACAGGCTAATTTCTA 57.318 36.000 0.00 0.00 41.10 2.10
2039 2042 6.575162 CTTGTGGTTTACAGGCTAATTTCT 57.425 37.500 0.00 0.00 41.10 2.52
2048 2051 4.096732 GCTTATGCTTGTGGTTTACAGG 57.903 45.455 0.00 0.00 41.10 4.00
2129 2132 1.462238 AGGGACCAGAGCAGGTTGT 60.462 57.895 0.00 0.00 43.38 3.32
2145 2148 4.197750 CAGAAGGGATGAAATGAGACAGG 58.802 47.826 0.00 0.00 0.00 4.00
2328 2337 7.489435 CACATCTTCTCTAAATCATGTACGTGT 59.511 37.037 14.63 0.00 0.00 4.49
2471 2480 2.031120 CCCTTGACTCTTTGGCAAACA 58.969 47.619 8.93 2.56 44.14 2.83
2555 2564 3.555956 CGATAGCTACAACACACCATTCC 59.444 47.826 0.00 0.00 0.00 3.01
2596 2605 4.243007 AGGTTTGAGCAGCATTAACAAC 57.757 40.909 0.00 0.00 0.00 3.32
2622 2634 1.200948 GTGCCAGATGCCAAGAAGAAC 59.799 52.381 0.00 0.00 40.16 3.01
2623 2635 1.538047 GTGCCAGATGCCAAGAAGAA 58.462 50.000 0.00 0.00 40.16 2.52
2624 2636 0.322816 GGTGCCAGATGCCAAGAAGA 60.323 55.000 0.00 0.00 40.16 2.87
2628 2640 1.304713 AAGGGTGCCAGATGCCAAG 60.305 57.895 0.00 0.00 40.16 3.61
2630 2642 2.036098 CAAGGGTGCCAGATGCCA 59.964 61.111 0.00 0.00 40.16 4.92
2647 2660 1.510480 GCATCCTGCCAATACGAGCC 61.510 60.000 0.00 0.00 37.42 4.70


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

AutoCloner maintained by Alex Coulton.