Multiple sequence alignment - TraesCS2B01G285900

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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 TraesCS2B01G285900 chr2B 100.000 4519 0 0 1 4519 393855255 393859773 0.000000e+00 8346.0
1 TraesCS2B01G285900 chr2B 84.111 579 59 23 1 551 377793031 377792458 3.100000e-146 529.0
2 TraesCS2B01G285900 chr2B 82.509 566 74 17 1 545 588831411 588831972 1.470000e-129 473.0
3 TraesCS2B01G285900 chr2B 94.444 54 2 1 1919 1972 546887123 546887071 1.040000e-11 82.4
4 TraesCS2B01G285900 chr2D 96.256 2564 80 9 1961 4519 324859359 324861911 0.000000e+00 4189.0
5 TraesCS2B01G285900 chr2D 95.113 1371 46 11 551 1904 324857994 324859360 0.000000e+00 2141.0
6 TraesCS2B01G285900 chr2D 83.681 576 64 19 1 551 500650112 500649542 2.410000e-142 516.0
7 TraesCS2B01G285900 chr2A 94.530 2066 79 13 1961 4022 393343228 393341193 0.000000e+00 3158.0
8 TraesCS2B01G285900 chr2A 95.339 1373 40 14 551 1904 393344594 393343227 0.000000e+00 2159.0
9 TraesCS2B01G285900 chr2A 96.033 479 19 0 4041 4519 393341116 393340638 0.000000e+00 780.0
10 TraesCS2B01G285900 chr2A 91.549 71 5 1 1903 1972 778925490 778925420 3.720000e-16 97.1
11 TraesCS2B01G285900 chr6A 93.860 456 26 2 3686 4140 4814533 4814987 0.000000e+00 686.0
12 TraesCS2B01G285900 chr3D 90.000 480 46 2 4041 4519 481515290 481515768 1.790000e-173 619.0
13 TraesCS2B01G285900 chr3D 83.821 581 55 22 1 545 151442024 151442601 2.410000e-142 516.0
14 TraesCS2B01G285900 chr3B 86.847 555 60 10 3974 4519 642485279 642485829 3.870000e-170 608.0
15 TraesCS2B01G285900 chr3B 81.212 165 17 11 1 153 38346714 38346552 2.210000e-23 121.0
16 TraesCS2B01G285900 chr3B 80.723 166 17 12 1 153 38249909 38249746 1.030000e-21 115.0
17 TraesCS2B01G285900 chr3B 95.238 63 2 1 1903 1964 51954461 51954523 1.030000e-16 99.0
18 TraesCS2B01G285900 chr3B 92.000 50 4 0 1913 1962 674477230 674477279 2.260000e-08 71.3
19 TraesCS2B01G285900 chr3A 86.413 552 67 6 3973 4519 624528430 624528978 8.370000e-167 597.0
20 TraesCS2B01G285900 chr6D 84.694 588 49 21 1 551 92569 91986 2.380000e-152 549.0
21 TraesCS2B01G285900 chr6D 84.444 585 55 16 1 551 248011081 248010499 1.110000e-150 544.0
22 TraesCS2B01G285900 chr6D 81.967 183 18 13 1 168 463496997 463496815 1.690000e-29 141.0
23 TraesCS2B01G285900 chr6D 83.453 139 12 8 41 168 194062873 194062735 7.940000e-23 119.0
24 TraesCS2B01G285900 chr7D 84.300 586 53 22 1 551 520799680 520799099 1.850000e-148 536.0
25 TraesCS2B01G285900 chr5A 84.348 575 56 26 1 545 619464634 619465204 2.390000e-147 532.0
26 TraesCS2B01G285900 chr7A 84.107 560 72 13 1 545 14736504 14737061 4.000000e-145 525.0
27 TraesCS2B01G285900 chr7A 83.448 580 70 20 1 557 457693344 457692768 2.410000e-142 516.0
28 TraesCS2B01G285900 chr4B 80.462 563 77 18 4 551 449340677 449340133 2.530000e-107 399.0
29 TraesCS2B01G285900 chr4B 83.333 162 13 11 1 149 486688907 486689067 2.190000e-28 137.0
30 TraesCS2B01G285900 chr4B 80.982 163 15 14 1 150 541099742 541099901 1.030000e-21 115.0
31 TraesCS2B01G285900 chr4B 90.789 76 3 4 1889 1962 358188516 358188443 1.030000e-16 99.0
32 TraesCS2B01G285900 chr4B 95.000 60 3 0 1903 1962 583334510 583334451 1.340000e-15 95.3
33 TraesCS2B01G285900 chr1A 82.514 183 17 11 1 168 291268836 291269018 3.640000e-31 147.0
34 TraesCS2B01G285900 chrUn 85.321 109 5 8 1 99 476316823 476316930 8.000000e-18 102.0
35 TraesCS2B01G285900 chr5D 95.238 63 2 1 1902 1963 416804000 416804062 1.030000e-16 99.0
36 TraesCS2B01G285900 chr4A 93.220 59 3 1 1898 1956 717628745 717628688 8.050000e-13 86.1
37 TraesCS2B01G285900 chr5B 91.667 60 3 1 1903 1962 479729494 479729437 1.040000e-11 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 TraesCS2B01G285900 chr2B 393855255 393859773 4518 False 8346.000000 8346 100.000000 1 4519 1 chr2B.!!$F1 4518
1 TraesCS2B01G285900 chr2B 377792458 377793031 573 True 529.000000 529 84.111000 1 551 1 chr2B.!!$R1 550
2 TraesCS2B01G285900 chr2B 588831411 588831972 561 False 473.000000 473 82.509000 1 545 1 chr2B.!!$F2 544
3 TraesCS2B01G285900 chr2D 324857994 324861911 3917 False 3165.000000 4189 95.684500 551 4519 2 chr2D.!!$F1 3968
4 TraesCS2B01G285900 chr2D 500649542 500650112 570 True 516.000000 516 83.681000 1 551 1 chr2D.!!$R1 550
5 TraesCS2B01G285900 chr2A 393340638 393344594 3956 True 2032.333333 3158 95.300667 551 4519 3 chr2A.!!$R2 3968
6 TraesCS2B01G285900 chr3D 151442024 151442601 577 False 516.000000 516 83.821000 1 545 1 chr3D.!!$F1 544
7 TraesCS2B01G285900 chr3B 642485279 642485829 550 False 608.000000 608 86.847000 3974 4519 1 chr3B.!!$F2 545
8 TraesCS2B01G285900 chr3A 624528430 624528978 548 False 597.000000 597 86.413000 3973 4519 1 chr3A.!!$F1 546
9 TraesCS2B01G285900 chr6D 91986 92569 583 True 549.000000 549 84.694000 1 551 1 chr6D.!!$R1 550
10 TraesCS2B01G285900 chr6D 248010499 248011081 582 True 544.000000 544 84.444000 1 551 1 chr6D.!!$R3 550
11 TraesCS2B01G285900 chr7D 520799099 520799680 581 True 536.000000 536 84.300000 1 551 1 chr7D.!!$R1 550
12 TraesCS2B01G285900 chr5A 619464634 619465204 570 False 532.000000 532 84.348000 1 545 1 chr5A.!!$F1 544
13 TraesCS2B01G285900 chr7A 14736504 14737061 557 False 525.000000 525 84.107000 1 545 1 chr7A.!!$F1 544
14 TraesCS2B01G285900 chr7A 457692768 457693344 576 True 516.000000 516 83.448000 1 557 1 chr7A.!!$R1 556
15 TraesCS2B01G285900 chr4B 449340133 449340677 544 True 399.000000 399 80.462000 4 551 1 chr4B.!!$R2 547

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
661 717 0.387929 TGTCCGTTCCACTGACAGTC 59.612 55.0 4.74 0.0 37.41 3.51 F
1922 1991 0.249398 ACTCCCTCCGTTCCGATTTG 59.751 55.0 0.00 0.0 0.00 2.32 F
1923 1992 0.535335 CTCCCTCCGTTCCGATTTGA 59.465 55.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2065 2.485814 CCTAGCCTGCAAAACTCAGAAC 59.514 50.000 0.00 0.00 33.54 3.01 R
3151 3221 1.956170 GGTCGTGTGCACTGTCCTG 60.956 63.158 19.41 1.51 0.00 3.86 R
3592 3665 2.037136 GCATTCAGCTCGCACCAGT 61.037 57.895 0.00 0.00 41.15 4.00 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
26 27 5.123979 GTGATGAAACAGGAACCAATACCTC 59.876 44.000 0.00 0.00 33.91 3.85
29 30 3.721087 AACAGGAACCAATACCTCTGG 57.279 47.619 0.00 0.00 40.05 3.86
62 63 6.442112 GCAAGAAATAGTGATGAAATAGGGC 58.558 40.000 0.00 0.00 0.00 5.19
63 64 6.662616 CAAGAAATAGTGATGAAATAGGGCG 58.337 40.000 0.00 0.00 0.00 6.13
64 65 4.757149 AGAAATAGTGATGAAATAGGGCGC 59.243 41.667 0.00 0.00 0.00 6.53
178 210 7.975058 TCATGTATTTAAGAAACATGCATGTGG 59.025 33.333 31.98 7.06 46.43 4.17
230 265 4.865365 TGGCGTTTTTAAACTGAAAACTGG 59.135 37.500 9.80 0.00 42.13 4.00
249 286 3.245443 CATTGATGCACGCATGTCC 57.755 52.632 9.70 0.00 36.70 4.02
277 314 5.234752 AGTGTGCTAATGTGTCATCGTTTA 58.765 37.500 0.00 0.00 0.00 2.01
454 497 3.576550 GGTTAAGGCCATCTTTGTTTGGA 59.423 43.478 5.01 0.00 36.93 3.53
470 515 4.251268 GTTTGGACCGTAGCTACAATCTT 58.749 43.478 23.21 2.29 0.00 2.40
472 517 5.664294 TTGGACCGTAGCTACAATCTTAA 57.336 39.130 23.21 14.46 0.00 1.85
547 598 2.860971 GCAAAGCACGGACCTTTTTACC 60.861 50.000 0.00 0.00 30.52 2.85
562 615 6.183360 ACCTTTTTACCAGTTCACAACTCATG 60.183 38.462 0.00 0.00 40.46 3.07
594 647 1.168407 CCGCGCAATTCCTCATCCAT 61.168 55.000 8.75 0.00 0.00 3.41
658 714 3.973206 ATAATGTCCGTTCCACTGACA 57.027 42.857 3.96 3.96 44.32 3.58
661 717 0.387929 TGTCCGTTCCACTGACAGTC 59.612 55.000 4.74 0.00 37.41 3.51
669 725 4.954118 ACTGACAGTCGGGCCCCA 62.954 66.667 18.66 0.00 0.00 4.96
767 823 4.796231 CGGCGAAGACTCCCGTGG 62.796 72.222 0.00 0.00 37.36 4.94
800 856 2.041301 CCCACCTCACCCCCGATA 60.041 66.667 0.00 0.00 0.00 2.92
1024 1080 1.309688 GAGCTGGTCTCCTCCTCCT 59.690 63.158 0.00 0.00 35.77 3.69
1098 1160 2.649034 GAGGTCAACGAGTCGCCA 59.351 61.111 13.59 0.00 0.00 5.69
1484 1546 9.877178 AATGTAAAATAAATGTTGGCGGAAATA 57.123 25.926 0.00 0.00 0.00 1.40
1588 1654 0.669318 CTAACCCGCATGTGTCACGT 60.669 55.000 5.38 0.00 0.00 4.49
1651 1717 2.755650 GTCGTATTCGGATTCCATGCT 58.244 47.619 3.09 0.00 37.69 3.79
1688 1754 4.707448 TCCAAACAAAAGTAAGAGCCACAA 59.293 37.500 0.00 0.00 0.00 3.33
1727 1793 1.071605 CTTTAGCACTGGTGTCGAGC 58.928 55.000 2.64 0.00 0.00 5.03
1729 1795 1.185618 TTAGCACTGGTGTCGAGCCT 61.186 55.000 7.38 0.00 0.00 4.58
1730 1796 1.185618 TAGCACTGGTGTCGAGCCTT 61.186 55.000 7.38 0.00 0.00 4.35
1733 1799 1.308998 CACTGGTGTCGAGCCTTTTT 58.691 50.000 7.38 0.00 0.00 1.94
1859 1927 8.890893 TCTGGGCAGAAATATACCATCAGGTAG 61.891 44.444 0.58 0.00 43.11 3.18
1907 1976 8.637986 ACTCTTCATGTTCTTATCATCTACTCC 58.362 37.037 0.00 0.00 0.00 3.85
1908 1977 7.957002 TCTTCATGTTCTTATCATCTACTCCC 58.043 38.462 0.00 0.00 0.00 4.30
1909 1978 7.786943 TCTTCATGTTCTTATCATCTACTCCCT 59.213 37.037 0.00 0.00 0.00 4.20
1910 1979 7.531857 TCATGTTCTTATCATCTACTCCCTC 57.468 40.000 0.00 0.00 0.00 4.30
1911 1980 6.495181 TCATGTTCTTATCATCTACTCCCTCC 59.505 42.308 0.00 0.00 0.00 4.30
1912 1981 4.827835 TGTTCTTATCATCTACTCCCTCCG 59.172 45.833 0.00 0.00 0.00 4.63
1913 1982 4.726035 TCTTATCATCTACTCCCTCCGT 57.274 45.455 0.00 0.00 0.00 4.69
1914 1983 5.063017 TCTTATCATCTACTCCCTCCGTT 57.937 43.478 0.00 0.00 0.00 4.44
1915 1984 5.071370 TCTTATCATCTACTCCCTCCGTTC 58.929 45.833 0.00 0.00 0.00 3.95
1916 1985 2.068834 TCATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
1917 1986 0.669077 CATCTACTCCCTCCGTTCCG 59.331 60.000 0.00 0.00 0.00 4.30
1918 1987 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
1919 1988 0.549950 TCTACTCCCTCCGTTCCGAT 59.450 55.000 0.00 0.00 0.00 4.18
1920 1989 1.064166 TCTACTCCCTCCGTTCCGATT 60.064 52.381 0.00 0.00 0.00 3.34
1921 1990 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
1922 1991 0.249398 ACTCCCTCCGTTCCGATTTG 59.751 55.000 0.00 0.00 0.00 2.32
1923 1992 0.535335 CTCCCTCCGTTCCGATTTGA 59.465 55.000 0.00 0.00 0.00 2.69
1924 1993 0.978151 TCCCTCCGTTCCGATTTGAA 59.022 50.000 0.00 0.00 0.00 2.69
1925 1994 1.084289 CCCTCCGTTCCGATTTGAAC 58.916 55.000 0.00 0.00 40.96 3.18
1926 1995 1.338769 CCCTCCGTTCCGATTTGAACT 60.339 52.381 0.00 0.00 41.95 3.01
1927 1996 2.093869 CCCTCCGTTCCGATTTGAACTA 60.094 50.000 0.00 0.00 41.95 2.24
1928 1997 3.592059 CCTCCGTTCCGATTTGAACTAA 58.408 45.455 0.00 0.00 41.95 2.24
1929 1998 3.998341 CCTCCGTTCCGATTTGAACTAAA 59.002 43.478 0.00 0.00 41.95 1.85
1930 1999 4.453136 CCTCCGTTCCGATTTGAACTAAAA 59.547 41.667 0.00 0.00 41.95 1.52
1931 2000 5.347012 TCCGTTCCGATTTGAACTAAAAC 57.653 39.130 0.00 0.00 41.95 2.43
1932 2001 4.213906 TCCGTTCCGATTTGAACTAAAACC 59.786 41.667 0.00 0.00 41.95 3.27
1933 2002 4.023878 CCGTTCCGATTTGAACTAAAACCA 60.024 41.667 0.00 0.00 41.95 3.67
1934 2003 4.907582 CGTTCCGATTTGAACTAAAACCAC 59.092 41.667 0.00 0.00 41.95 4.16
1935 2004 4.735662 TCCGATTTGAACTAAAACCACG 57.264 40.909 0.00 0.00 0.00 4.94
1936 2005 4.378774 TCCGATTTGAACTAAAACCACGA 58.621 39.130 0.00 0.00 0.00 4.35
1937 2006 4.211794 TCCGATTTGAACTAAAACCACGAC 59.788 41.667 0.00 0.00 0.00 4.34
1938 2007 4.138817 CGATTTGAACTAAAACCACGACG 58.861 43.478 0.00 0.00 0.00 5.12
1939 2008 4.084952 CGATTTGAACTAAAACCACGACGA 60.085 41.667 0.00 0.00 0.00 4.20
1940 2009 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1941 2010 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1942 2011 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1943 2012 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1944 2013 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
1945 2014 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
1946 2015 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
1947 2016 5.531634 ACTAAAACCACGACGAGTAAATCA 58.468 37.500 0.00 0.00 0.00 2.57
1948 2017 4.985044 AAAACCACGACGAGTAAATCAG 57.015 40.909 0.00 0.00 0.00 2.90
1949 2018 3.928727 AACCACGACGAGTAAATCAGA 57.071 42.857 0.00 0.00 0.00 3.27
1950 2019 3.928727 ACCACGACGAGTAAATCAGAA 57.071 42.857 0.00 0.00 0.00 3.02
1951 2020 3.572584 ACCACGACGAGTAAATCAGAAC 58.427 45.455 0.00 0.00 0.00 3.01
1952 2021 2.592897 CCACGACGAGTAAATCAGAACG 59.407 50.000 0.00 0.00 0.00 3.95
1953 2022 3.485633 CACGACGAGTAAATCAGAACGA 58.514 45.455 0.00 0.00 0.00 3.85
1954 2023 3.910170 CACGACGAGTAAATCAGAACGAA 59.090 43.478 0.00 0.00 0.00 3.85
1955 2024 4.029198 CACGACGAGTAAATCAGAACGAAG 59.971 45.833 0.00 0.00 0.00 3.79
1956 2025 3.542704 CGACGAGTAAATCAGAACGAAGG 59.457 47.826 0.00 0.00 0.00 3.46
1957 2026 3.846360 ACGAGTAAATCAGAACGAAGGG 58.154 45.455 0.00 0.00 0.00 3.95
1958 2027 3.508793 ACGAGTAAATCAGAACGAAGGGA 59.491 43.478 0.00 0.00 0.00 4.20
1959 2028 4.106197 CGAGTAAATCAGAACGAAGGGAG 58.894 47.826 0.00 0.00 0.00 4.30
1996 2065 8.638685 ATTCAAGGAATTATGCGAGATTTTTG 57.361 30.769 0.00 0.00 0.00 2.44
2038 2107 1.831736 AGTCTCCCCACCGATAAGTTG 59.168 52.381 0.00 0.00 0.00 3.16
2041 2110 2.108168 CTCCCCACCGATAAGTTGAGA 58.892 52.381 0.00 0.00 0.00 3.27
2417 2486 2.351726 GAGACGTTTCCCCATTGAATCG 59.648 50.000 0.00 0.00 41.10 3.34
2623 2692 6.070897 TGGTAATTGTCACACATTGAACAG 57.929 37.500 0.00 0.00 35.39 3.16
2627 2696 4.898829 TTGTCACACATTGAACAGGAAG 57.101 40.909 0.00 0.00 35.39 3.46
2666 2735 6.170506 TGTAACTCAGTGCTCGGAATTTATT 58.829 36.000 0.00 0.00 0.00 1.40
2671 2740 5.972935 TCAGTGCTCGGAATTTATTGACTA 58.027 37.500 0.00 0.00 0.00 2.59
2846 2915 6.597280 TGGCCTCCAAAATTTTATTGTAATGC 59.403 34.615 3.32 0.00 0.00 3.56
2975 3044 4.499188 CGTGACTCACTGTTAGGAGTTCAA 60.499 45.833 7.58 0.00 44.03 2.69
3073 3143 2.577700 TGTGAAGCCACCAAACGTATT 58.422 42.857 0.00 0.00 42.53 1.89
3151 3221 3.259625 GGTCTATGGGCTACAGATCTTCC 59.740 52.174 0.00 0.00 0.00 3.46
3152 3222 3.898123 GTCTATGGGCTACAGATCTTCCA 59.102 47.826 0.00 0.00 0.00 3.53
3153 3223 4.021544 GTCTATGGGCTACAGATCTTCCAG 60.022 50.000 0.00 0.00 0.00 3.86
3154 3224 1.500474 TGGGCTACAGATCTTCCAGG 58.500 55.000 0.00 0.00 0.00 4.45
3156 3226 1.414550 GGGCTACAGATCTTCCAGGAC 59.585 57.143 0.00 0.00 0.00 3.85
3158 3228 2.102252 GGCTACAGATCTTCCAGGACAG 59.898 54.545 0.00 0.00 0.00 3.51
3159 3229 2.763448 GCTACAGATCTTCCAGGACAGT 59.237 50.000 0.00 0.00 0.00 3.55
3160 3230 3.430098 GCTACAGATCTTCCAGGACAGTG 60.430 52.174 0.00 0.00 0.00 3.66
3161 3231 1.277557 ACAGATCTTCCAGGACAGTGC 59.722 52.381 0.00 0.00 0.00 4.40
3162 3232 1.277273 CAGATCTTCCAGGACAGTGCA 59.723 52.381 0.00 0.00 0.00 4.57
3163 3233 1.277557 AGATCTTCCAGGACAGTGCAC 59.722 52.381 9.40 9.40 0.00 4.57
3164 3234 1.002430 GATCTTCCAGGACAGTGCACA 59.998 52.381 21.04 0.00 0.00 4.57
3165 3235 0.106708 TCTTCCAGGACAGTGCACAC 59.893 55.000 21.04 9.77 0.00 3.82
3166 3236 1.224069 CTTCCAGGACAGTGCACACG 61.224 60.000 21.04 12.28 36.20 4.49
3195 3265 5.100259 GTGCACGTGTATATACTTGTGTCT 58.900 41.667 25.36 2.02 35.74 3.41
3196 3266 5.575606 GTGCACGTGTATATACTTGTGTCTT 59.424 40.000 25.36 1.76 35.74 3.01
3197 3267 6.090358 GTGCACGTGTATATACTTGTGTCTTT 59.910 38.462 25.36 1.24 35.74 2.52
3231 3304 9.734984 TTTATTTACTTCTAAGTTCCTCCCTTG 57.265 33.333 0.00 0.00 40.37 3.61
3250 3323 3.526931 TGCTCCCTTCTTACTTGATCG 57.473 47.619 0.00 0.00 0.00 3.69
3592 3665 5.070981 TGGAAGTGCCCAAAATTTTACATGA 59.929 36.000 2.44 0.00 34.97 3.07
3704 3777 3.826729 GGCCCTGTAACTGTGAATTTTCT 59.173 43.478 0.00 0.00 0.00 2.52
3719 3792 6.197842 GTGAATTTTCTGTCTTCTGCTTGTTG 59.802 38.462 0.00 0.00 0.00 3.33
3752 3825 2.712057 ATTTGGTTGAGAGCTTTGCG 57.288 45.000 0.00 0.00 0.00 4.85
3871 3944 4.127171 TGCCGACTGGAGCTTAATATTTC 58.873 43.478 0.00 0.00 37.49 2.17
3903 3976 7.936847 TGTTACCAGTCTCTTGAATTATGTGTT 59.063 33.333 0.00 0.00 0.00 3.32
4010 4085 7.452880 TTCAAGAATGTGAGAAATACTTGGG 57.547 36.000 0.00 0.00 35.49 4.12
4081 4220 1.754803 CAGCTGAATGGTGGATGCATT 59.245 47.619 8.42 0.00 40.23 3.56
4179 4320 2.105806 GATGTCGATGAGGAGCCCCC 62.106 65.000 0.00 0.00 0.00 5.40
4243 4384 0.456995 CCTTCGTCGAGCTTCCACTC 60.457 60.000 0.00 0.00 0.00 3.51
4382 4523 3.718210 GAACCTCGCCGGCTCGAAT 62.718 63.158 26.68 7.84 38.08 3.34
4394 4535 0.742281 GCTCGAATCTGCTTGGCTCA 60.742 55.000 0.00 0.00 0.00 4.26
4469 4610 2.534011 TTGGGGATGAGGTGGCCA 60.534 61.111 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.464008 CATACATGCCAGAGGTATTGGTT 58.536 43.478 0.00 0.00 38.02 3.67
26 27 4.581824 ACTATTTCTTGCCATACATGCCAG 59.418 41.667 0.00 0.00 0.00 4.85
29 30 5.756195 TCACTATTTCTTGCCATACATGC 57.244 39.130 0.00 0.00 0.00 4.06
62 63 1.892819 ATGGTCTCTGGTGGACTGCG 61.893 60.000 0.00 0.00 34.47 5.18
63 64 1.195115 TATGGTCTCTGGTGGACTGC 58.805 55.000 0.00 0.00 34.47 4.40
64 65 5.614324 TTTATATGGTCTCTGGTGGACTG 57.386 43.478 0.00 0.00 34.47 3.51
199 233 5.589452 TCAGTTTAAAAACGCCAACTTAGGA 59.411 36.000 0.18 0.00 43.51 2.94
242 277 2.106683 GCACACTACGGGGACATGC 61.107 63.158 0.00 0.00 0.00 4.06
249 286 2.268298 GACACATTAGCACACTACGGG 58.732 52.381 0.00 0.00 0.00 5.28
277 314 7.170828 GGGCGAGTAAAGAAAAATGACAAAAAT 59.829 33.333 0.00 0.00 0.00 1.82
378 420 2.352503 ATTTCAACACGGCTTGCATC 57.647 45.000 0.00 0.00 0.00 3.91
429 472 5.245075 CCAAACAAAGATGGCCTTAACCTAA 59.755 40.000 3.32 0.00 34.00 2.69
439 482 0.958822 ACGGTCCAAACAAAGATGGC 59.041 50.000 0.00 0.00 36.62 4.40
525 576 0.104120 AAAAAGGTCCGTGCTTTGCC 59.896 50.000 0.00 0.00 0.00 4.52
530 581 1.142262 ACTGGTAAAAAGGTCCGTGCT 59.858 47.619 0.00 0.00 0.00 4.40
537 588 5.258051 TGAGTTGTGAACTGGTAAAAAGGT 58.742 37.500 0.00 0.00 43.03 3.50
547 598 2.154462 GGGGACATGAGTTGTGAACTG 58.846 52.381 0.00 0.00 43.03 3.16
562 615 3.131478 CGCGGTTGGATTGGGGAC 61.131 66.667 0.00 0.00 0.00 4.46
658 714 3.846405 TTCTCAGTGGGGCCCGACT 62.846 63.158 32.16 32.16 0.00 4.18
661 717 2.124570 CATTCTCAGTGGGGCCCG 60.125 66.667 19.83 3.38 0.00 6.13
669 725 1.482593 CCGGCTACTTCCATTCTCAGT 59.517 52.381 0.00 0.00 0.00 3.41
748 804 3.300765 ACGGGAGTCTTCGCCGTT 61.301 61.111 5.48 0.00 43.33 4.44
767 823 2.985847 GGGCCCAGTGAACAGTGC 60.986 66.667 19.95 0.00 0.00 4.40
797 853 0.238817 TTGGGCGTGTGCGTTTTATC 59.761 50.000 0.00 0.00 44.10 1.75
798 854 0.669077 TTTGGGCGTGTGCGTTTTAT 59.331 45.000 0.00 0.00 44.10 1.40
799 855 0.454600 TTTTGGGCGTGTGCGTTTTA 59.545 45.000 0.00 0.00 44.10 1.52
800 856 0.179097 ATTTTGGGCGTGTGCGTTTT 60.179 45.000 0.00 0.00 44.10 2.43
1230 1292 2.760634 TCAGTAATGAGCCGAAGCAA 57.239 45.000 0.00 0.00 43.56 3.91
1484 1546 7.436320 AATTAACATTGATTACATTGCCCCT 57.564 32.000 0.00 0.00 32.65 4.79
1519 1581 4.570926 AGGAATCAGTATTGGGAGATCCA 58.429 43.478 0.47 0.00 45.43 3.41
1532 1594 6.015095 GGGTGAAATCAAAAGAAGGAATCAGT 60.015 38.462 0.00 0.00 0.00 3.41
1588 1654 4.131596 GTTTGTTGGTAGGTTAGCACAGA 58.868 43.478 0.00 0.00 35.67 3.41
1633 1699 4.690748 ACATAAGCATGGAATCCGAATACG 59.309 41.667 0.00 0.00 36.39 3.06
1651 1717 5.576563 TTGTTTGGAGGAGGAAGACATAA 57.423 39.130 0.00 0.00 0.00 1.90
1733 1799 8.672815 GCCAAGCCAATTATTAATTAGCAAAAA 58.327 29.630 17.81 0.00 37.86 1.94
1912 1981 4.907582 CGTGGTTTTAGTTCAAATCGGAAC 59.092 41.667 0.00 0.00 45.87 3.62
1913 1982 4.815308 TCGTGGTTTTAGTTCAAATCGGAA 59.185 37.500 0.00 0.00 0.00 4.30
1914 1983 4.211794 GTCGTGGTTTTAGTTCAAATCGGA 59.788 41.667 0.00 0.00 0.00 4.55
1915 1984 4.460505 GTCGTGGTTTTAGTTCAAATCGG 58.539 43.478 0.00 0.00 0.00 4.18
1916 1985 4.084952 TCGTCGTGGTTTTAGTTCAAATCG 60.085 41.667 0.00 0.00 0.00 3.34
1917 1986 5.050567 ACTCGTCGTGGTTTTAGTTCAAATC 60.051 40.000 0.00 0.00 0.00 2.17
1918 1987 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1919 1988 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1920 1989 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1921 1990 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1922 1991 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
1923 1992 5.984926 TGATTTACTCGTCGTGGTTTTAGTT 59.015 36.000 0.00 0.00 0.00 2.24
1924 1993 5.531634 TGATTTACTCGTCGTGGTTTTAGT 58.468 37.500 0.00 0.00 0.00 2.24
1925 1994 5.860182 TCTGATTTACTCGTCGTGGTTTTAG 59.140 40.000 0.00 0.00 0.00 1.85
1926 1995 5.771469 TCTGATTTACTCGTCGTGGTTTTA 58.229 37.500 0.00 0.00 0.00 1.52
1927 1996 4.624015 TCTGATTTACTCGTCGTGGTTTT 58.376 39.130 0.00 0.00 0.00 2.43
1928 1997 4.247267 TCTGATTTACTCGTCGTGGTTT 57.753 40.909 0.00 0.00 0.00 3.27
1929 1998 3.928727 TCTGATTTACTCGTCGTGGTT 57.071 42.857 0.00 0.00 0.00 3.67
1930 1999 3.572584 GTTCTGATTTACTCGTCGTGGT 58.427 45.455 0.00 0.00 0.00 4.16
1931 2000 2.592897 CGTTCTGATTTACTCGTCGTGG 59.407 50.000 0.00 0.00 0.00 4.94
1932 2001 3.485633 TCGTTCTGATTTACTCGTCGTG 58.514 45.455 0.00 0.00 0.00 4.35
1933 2002 3.818961 TCGTTCTGATTTACTCGTCGT 57.181 42.857 0.00 0.00 0.00 4.34
1934 2003 3.542704 CCTTCGTTCTGATTTACTCGTCG 59.457 47.826 0.00 0.00 0.00 5.12
1935 2004 3.858238 CCCTTCGTTCTGATTTACTCGTC 59.142 47.826 0.00 0.00 0.00 4.20
1936 2005 3.508793 TCCCTTCGTTCTGATTTACTCGT 59.491 43.478 0.00 0.00 0.00 4.18
1937 2006 4.106029 TCCCTTCGTTCTGATTTACTCG 57.894 45.455 0.00 0.00 0.00 4.18
1938 2007 5.074584 ACTCCCTTCGTTCTGATTTACTC 57.925 43.478 0.00 0.00 0.00 2.59
1939 2008 5.715753 ACTACTCCCTTCGTTCTGATTTACT 59.284 40.000 0.00 0.00 0.00 2.24
1940 2009 5.963594 ACTACTCCCTTCGTTCTGATTTAC 58.036 41.667 0.00 0.00 0.00 2.01
1941 2010 6.014840 ACAACTACTCCCTTCGTTCTGATTTA 60.015 38.462 0.00 0.00 0.00 1.40
1942 2011 5.221661 ACAACTACTCCCTTCGTTCTGATTT 60.222 40.000 0.00 0.00 0.00 2.17
1943 2012 4.283722 ACAACTACTCCCTTCGTTCTGATT 59.716 41.667 0.00 0.00 0.00 2.57
1944 2013 3.833070 ACAACTACTCCCTTCGTTCTGAT 59.167 43.478 0.00 0.00 0.00 2.90
1945 2014 3.228453 ACAACTACTCCCTTCGTTCTGA 58.772 45.455 0.00 0.00 0.00 3.27
1946 2015 3.662247 ACAACTACTCCCTTCGTTCTG 57.338 47.619 0.00 0.00 0.00 3.02
1947 2016 5.997384 AATACAACTACTCCCTTCGTTCT 57.003 39.130 0.00 0.00 0.00 3.01
1948 2017 8.713737 AATAAATACAACTACTCCCTTCGTTC 57.286 34.615 0.00 0.00 0.00 3.95
1949 2018 8.316214 TGAATAAATACAACTACTCCCTTCGTT 58.684 33.333 0.00 0.00 0.00 3.85
1950 2019 7.844009 TGAATAAATACAACTACTCCCTTCGT 58.156 34.615 0.00 0.00 0.00 3.85
1951 2020 8.712285 TTGAATAAATACAACTACTCCCTTCG 57.288 34.615 0.00 0.00 0.00 3.79
1952 2021 9.110502 CCTTGAATAAATACAACTACTCCCTTC 57.889 37.037 0.00 0.00 0.00 3.46
1953 2022 8.832735 TCCTTGAATAAATACAACTACTCCCTT 58.167 33.333 0.00 0.00 0.00 3.95
1954 2023 8.388656 TCCTTGAATAAATACAACTACTCCCT 57.611 34.615 0.00 0.00 0.00 4.20
1955 2024 9.628500 ATTCCTTGAATAAATACAACTACTCCC 57.372 33.333 0.00 0.00 29.72 4.30
1996 2065 2.485814 CCTAGCCTGCAAAACTCAGAAC 59.514 50.000 0.00 0.00 33.54 3.01
2483 2552 8.593134 ATGCTATACATGTCCACCTGAACAGG 62.593 46.154 17.94 17.94 45.57 4.00
2595 2664 7.994425 TCAATGTGTGACAATTACCAGTATT 57.006 32.000 0.00 0.00 0.00 1.89
2666 2735 4.334203 ACGACACAACATTTTTGCTAGTCA 59.666 37.500 0.00 0.00 0.00 3.41
2671 2740 4.096382 AGAAGACGACACAACATTTTTGCT 59.904 37.500 0.00 0.00 0.00 3.91
2811 2880 2.978156 TTGGAGGCCAAGACAGAAAT 57.022 45.000 5.01 0.00 38.75 2.17
2846 2915 3.891366 AGTCCCAACCTGACAATTTTCAG 59.109 43.478 13.64 13.64 42.46 3.02
2949 3018 3.635373 ACTCCTAACAGTGAGTCACGAAA 59.365 43.478 17.40 4.33 37.24 3.46
2950 3019 3.220110 ACTCCTAACAGTGAGTCACGAA 58.780 45.455 17.40 4.00 37.24 3.85
2975 3044 7.910584 ACCAAAAAGGAATTAAGCATGATTCT 58.089 30.769 0.00 0.00 41.22 2.40
3073 3143 6.116711 TCAGGTGCAGTAAACATTAGGTTA 57.883 37.500 0.00 0.00 39.29 2.85
3138 3208 2.763448 ACTGTCCTGGAAGATCTGTAGC 59.237 50.000 0.00 0.00 34.07 3.58
3151 3221 1.956170 GGTCGTGTGCACTGTCCTG 60.956 63.158 19.41 1.51 0.00 3.86
3152 3222 2.421739 GGTCGTGTGCACTGTCCT 59.578 61.111 19.41 0.00 0.00 3.85
3153 3223 3.036084 CGGTCGTGTGCACTGTCC 61.036 66.667 19.41 15.60 0.00 4.02
3154 3224 2.279252 ACGGTCGTGTGCACTGTC 60.279 61.111 19.41 8.25 0.00 3.51
3231 3304 3.528597 ACGATCAAGTAAGAAGGGAGC 57.471 47.619 0.00 0.00 0.00 4.70
3390 3463 3.522553 GGGAGTGTGTGTATAAGACAGC 58.477 50.000 0.00 0.00 39.29 4.40
3592 3665 2.037136 GCATTCAGCTCGCACCAGT 61.037 57.895 0.00 0.00 41.15 4.00
3618 3691 2.842208 TTTGGAAAACACACAGCTCG 57.158 45.000 0.00 0.00 0.00 5.03
3688 3761 6.853362 GCAGAAGACAGAAAATTCACAGTTAC 59.147 38.462 0.00 0.00 0.00 2.50
3693 3766 5.357878 ACAAGCAGAAGACAGAAAATTCACA 59.642 36.000 0.00 0.00 0.00 3.58
3704 3777 4.009675 AGAAACACAACAAGCAGAAGACA 58.990 39.130 0.00 0.00 0.00 3.41
3719 3792 4.119136 CAACCAAATTCCACCAGAAACAC 58.881 43.478 0.00 0.00 38.21 3.32
3903 3976 5.013704 TGACTTTTGAGGCCCTCTACAATAA 59.986 40.000 12.94 0.00 0.00 1.40
4081 4220 7.540474 AGAATTTAGTAGCCTGATCCGAATA 57.460 36.000 0.00 0.00 0.00 1.75
4179 4320 4.899239 GATGCCGTCCCCTGCTCG 62.899 72.222 0.00 0.00 0.00 5.03
4243 4384 1.201647 ACTACATCGTCACCAGGTTCG 59.798 52.381 7.43 7.43 0.00 3.95
4249 4390 1.405391 CCATGCACTACATCGTCACCA 60.405 52.381 0.00 0.00 36.64 4.17
4382 4523 0.837691 TCTTCCCTGAGCCAAGCAGA 60.838 55.000 0.00 0.00 35.39 4.26
4394 4535 3.090532 GACCCGGCCATCTTCCCT 61.091 66.667 2.24 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.