Multiple sequence alignment - TraesCS1B01G212300

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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 TraesCS1B01G212300 chr1B 100.000 2741 0 0 1 2741 385653915 385656655 0.000000e+00 5062.0
1 TraesCS1B01G212300 chr1B 95.000 960 40 7 24 979 260710315 260711270 0.000000e+00 1500.0
2 TraesCS1B01G212300 chr1A 94.486 943 43 6 975 1908 355627083 355628025 0.000000e+00 1445.0
3 TraesCS1B01G212300 chr1A 84.193 601 59 26 2164 2741 355628194 355628781 3.990000e-153 551.0
4 TraesCS1B01G212300 chr6B 93.717 955 51 9 24 975 427657943 427656995 0.000000e+00 1423.0
5 TraesCS1B01G212300 chr6B 90.586 956 84 6 24 977 351405565 351404614 0.000000e+00 1262.0
6 TraesCS1B01G212300 chr6B 88.462 52 4 2 1913 1962 702660199 702660148 8.200000e-06 62.1
7 TraesCS1B01G212300 chr5B 93.139 962 45 17 24 976 106179720 106178771 0.000000e+00 1391.0
8 TraesCS1B01G212300 chr5B 91.718 978 74 6 1 975 195874541 195875514 0.000000e+00 1351.0
9 TraesCS1B01G212300 chr5B 91.088 965 64 20 24 975 201311650 201310695 0.000000e+00 1286.0
10 TraesCS1B01G212300 chr5B 90.387 957 85 6 24 976 127645264 127644311 0.000000e+00 1251.0
11 TraesCS1B01G212300 chr1D 93.562 932 41 3 975 1904 284043340 284044254 0.000000e+00 1371.0
12 TraesCS1B01G212300 chr1D 86.700 594 41 19 2164 2741 284045492 284046063 2.320000e-175 625.0
13 TraesCS1B01G212300 chr3B 90.756 952 78 10 30 976 441952760 441951814 0.000000e+00 1262.0
14 TraesCS1B01G212300 chrUn 90.481 956 84 7 24 975 78360959 78360007 0.000000e+00 1254.0
15 TraesCS1B01G212300 chr2A 96.552 58 1 1 1900 1956 652869335 652869392 8.080000e-16 95.3
16 TraesCS1B01G212300 chr2A 93.333 45 2 1 1914 1957 655284554 655284510 6.340000e-07 65.8
17 TraesCS1B01G212300 chr2B 91.071 56 3 1 1900 1955 225254363 225254310 1.050000e-09 75.0
18 TraesCS1B01G212300 chr2B 95.455 44 1 1 1916 1958 735930848 735930891 4.900000e-08 69.4
19 TraesCS1B01G212300 chr7A 93.478 46 2 1 1911 1955 218248640 218248685 1.760000e-07 67.6
20 TraesCS1B01G212300 chr7A 95.238 42 1 1 1916 1956 594413632 594413673 6.340000e-07 65.8
21 TraesCS1B01G212300 chr5D 95.238 42 1 1 1915 1955 475838321 475838362 6.340000e-07 65.8
22 TraesCS1B01G212300 chr3D 90.000 50 3 2 1919 1967 39423066 39423018 2.280000e-06 63.9


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 TraesCS1B01G212300 chr1B 385653915 385656655 2740 False 5062 5062 100.0000 1 2741 1 chr1B.!!$F2 2740
1 TraesCS1B01G212300 chr1B 260710315 260711270 955 False 1500 1500 95.0000 24 979 1 chr1B.!!$F1 955
2 TraesCS1B01G212300 chr1A 355627083 355628781 1698 False 998 1445 89.3395 975 2741 2 chr1A.!!$F1 1766
3 TraesCS1B01G212300 chr6B 427656995 427657943 948 True 1423 1423 93.7170 24 975 1 chr6B.!!$R2 951
4 TraesCS1B01G212300 chr6B 351404614 351405565 951 True 1262 1262 90.5860 24 977 1 chr6B.!!$R1 953
5 TraesCS1B01G212300 chr5B 106178771 106179720 949 True 1391 1391 93.1390 24 976 1 chr5B.!!$R1 952
6 TraesCS1B01G212300 chr5B 195874541 195875514 973 False 1351 1351 91.7180 1 975 1 chr5B.!!$F1 974
7 TraesCS1B01G212300 chr5B 201310695 201311650 955 True 1286 1286 91.0880 24 975 1 chr5B.!!$R3 951
8 TraesCS1B01G212300 chr5B 127644311 127645264 953 True 1251 1251 90.3870 24 976 1 chr5B.!!$R2 952
9 TraesCS1B01G212300 chr1D 284043340 284046063 2723 False 998 1371 90.1310 975 2741 2 chr1D.!!$F1 1766
10 TraesCS1B01G212300 chr3B 441951814 441952760 946 True 1262 1262 90.7560 30 976 1 chr3B.!!$R1 946
11 TraesCS1B01G212300 chrUn 78360007 78360959 952 True 1254 1254 90.4810 24 975 1 chrUn.!!$R1 951

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
701 714 0.042731 TCCGGAGAAGATCCCCAAGT 59.957 55.0 0.0 0.0 46.5 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 1965 0.032017 AGCTACTCCCTCCGTTCCAT 60.032 55.0 0.0 0.0 0.0 3.41 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
19 20 0.540365 CAGCAACACATCCAACCCCT 60.540 55.000 0.00 0.00 0.00 4.79
245 246 1.788229 AAAAACACCAAGGACCAGGG 58.212 50.000 7.79 4.13 0.00 4.45
451 456 2.720659 CGAGTCTCCGGATCATCCA 58.279 57.895 3.57 0.00 35.91 3.41
701 714 0.042731 TCCGGAGAAGATCCCCAAGT 59.957 55.000 0.00 0.00 46.50 3.16
804 817 8.977267 TTGTTGATTGTGGATCATATGTATCA 57.023 30.769 1.90 0.00 44.01 2.15
914 933 1.210545 TTCCGCGTGTTCTTCGTGTC 61.211 55.000 4.92 0.00 37.14 3.67
1085 1104 1.539496 GGTTCACCAGCGTGTTCTACA 60.539 52.381 0.00 0.00 41.09 2.74
1186 1205 1.649664 CTCCTGCTTCCATGAACTCG 58.350 55.000 0.00 0.00 0.00 4.18
1196 1215 1.982395 ATGAACTCGGCCTCGGTGA 60.982 57.895 0.00 0.00 36.95 4.02
1267 1286 1.472728 GCCAGACGATACACCGGAAAT 60.473 52.381 9.46 0.00 0.00 2.17
1270 1289 2.603110 CAGACGATACACCGGAAATGTG 59.397 50.000 9.46 0.00 39.63 3.21
1273 1292 1.745232 GATACACCGGAAATGTGGCA 58.255 50.000 9.46 0.00 38.05 4.92
1482 1502 2.371306 GAGTTCTTCTACTCGGAGGCT 58.629 52.381 10.23 0.00 35.62 4.58
1539 1559 1.444895 CCTTGCAATGTCGCTTGGC 60.445 57.895 0.00 0.00 0.00 4.52
1559 1579 4.202121 TGGCTATTACCTGAACTCGATGAC 60.202 45.833 0.00 0.00 0.00 3.06
1733 1753 0.387929 ACGGTGAAGAAAGTCGAGCA 59.612 50.000 0.00 0.00 0.00 4.26
1743 1763 3.103911 GTCGAGCACCGGTGAACG 61.104 66.667 38.30 34.77 43.80 3.95
1799 1819 9.787435 TTTTATCCTCTTTGTTGTGTATGTACT 57.213 29.630 0.00 0.00 0.00 2.73
1804 1824 6.146184 CCTCTTTGTTGTGTATGTACTGTCTG 59.854 42.308 0.00 0.00 0.00 3.51
1839 1860 6.533819 TGATGTAATTAAATACCGCCGAAG 57.466 37.500 0.00 0.00 0.00 3.79
1848 1869 0.527565 TACCGCCGAAGTTCCTGTAC 59.472 55.000 0.00 0.00 0.00 2.90
1857 1878 3.181774 CGAAGTTCCTGTACTTGTGTTCG 59.818 47.826 0.00 0.00 38.43 3.95
1869 1896 9.279904 CTGTACTTGTGTTCGTTTGAATAAAAA 57.720 29.630 0.00 0.00 36.29 1.94
1901 1928 6.039616 TGGAACACAAATGAAACAAAGCTAC 58.960 36.000 0.00 0.00 0.00 3.58
1902 1929 6.127479 TGGAACACAAATGAAACAAAGCTACT 60.127 34.615 0.00 0.00 0.00 2.57
1903 1930 6.417930 GGAACACAAATGAAACAAAGCTACTC 59.582 38.462 0.00 0.00 0.00 2.59
1906 1933 5.010012 CACAAATGAAACAAAGCTACTCCCT 59.990 40.000 0.00 0.00 0.00 4.20
1907 1934 5.241728 ACAAATGAAACAAAGCTACTCCCTC 59.758 40.000 0.00 0.00 0.00 4.30
1908 1935 4.640771 ATGAAACAAAGCTACTCCCTCA 57.359 40.909 0.00 0.00 0.00 3.86
1909 1936 4.008074 TGAAACAAAGCTACTCCCTCAG 57.992 45.455 0.00 0.00 0.00 3.35
1910 1937 3.391296 TGAAACAAAGCTACTCCCTCAGT 59.609 43.478 0.00 0.00 39.41 3.41
1911 1938 3.686916 AACAAAGCTACTCCCTCAGTC 57.313 47.619 0.00 0.00 36.43 3.51
1912 1939 1.903183 ACAAAGCTACTCCCTCAGTCC 59.097 52.381 0.00 0.00 36.43 3.85
1913 1940 1.208293 CAAAGCTACTCCCTCAGTCCC 59.792 57.143 0.00 0.00 36.43 4.46
1914 1941 0.413832 AAGCTACTCCCTCAGTCCCA 59.586 55.000 0.00 0.00 36.43 4.37
1915 1942 0.639392 AGCTACTCCCTCAGTCCCAT 59.361 55.000 0.00 0.00 36.43 4.00
1916 1943 1.860240 AGCTACTCCCTCAGTCCCATA 59.140 52.381 0.00 0.00 36.43 2.74
1917 1944 2.247635 AGCTACTCCCTCAGTCCCATAA 59.752 50.000 0.00 0.00 36.43 1.90
1918 1945 3.116551 AGCTACTCCCTCAGTCCCATAAT 60.117 47.826 0.00 0.00 36.43 1.28
1919 1946 3.007398 GCTACTCCCTCAGTCCCATAATG 59.993 52.174 0.00 0.00 36.43 1.90
1920 1947 3.136641 ACTCCCTCAGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
1921 1948 4.280789 ACTCCCTCAGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
1922 1949 4.631234 ACTCCCTCAGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
1923 1950 4.656112 ACTCCCTCAGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
1924 1951 4.890988 TCCCTCAGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
1925 1952 5.285401 TCCCTCAGTCCCATAATGTAAGAA 58.715 41.667 0.00 0.00 0.00 2.52
1926 1953 5.729229 TCCCTCAGTCCCATAATGTAAGAAA 59.271 40.000 0.00 0.00 0.00 2.52
1927 1954 5.823045 CCCTCAGTCCCATAATGTAAGAAAC 59.177 44.000 0.00 0.00 0.00 2.78
1928 1955 5.523916 CCTCAGTCCCATAATGTAAGAAACG 59.476 44.000 0.00 0.00 0.00 3.60
1929 1956 6.045072 TCAGTCCCATAATGTAAGAAACGT 57.955 37.500 0.00 0.00 0.00 3.99
1930 1957 6.103997 TCAGTCCCATAATGTAAGAAACGTC 58.896 40.000 0.00 0.00 0.00 4.34
1931 1958 6.070995 TCAGTCCCATAATGTAAGAAACGTCT 60.071 38.462 0.00 0.00 34.72 4.18
1932 1959 6.594159 CAGTCCCATAATGTAAGAAACGTCTT 59.406 38.462 0.00 0.00 46.18 3.01
1933 1960 7.762615 CAGTCCCATAATGTAAGAAACGTCTTA 59.237 37.037 0.00 0.00 42.53 2.10
1945 1972 6.642683 AGAAACGTCTTACATTATGGAACG 57.357 37.500 0.62 0.62 0.00 3.95
1946 1973 5.579511 AGAAACGTCTTACATTATGGAACGG 59.420 40.000 6.60 0.00 0.00 4.44
1947 1974 4.724074 ACGTCTTACATTATGGAACGGA 57.276 40.909 6.60 0.00 0.00 4.69
1948 1975 4.679662 ACGTCTTACATTATGGAACGGAG 58.320 43.478 6.60 0.00 0.00 4.63
1949 1976 4.049186 CGTCTTACATTATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
1950 1977 4.377897 GTCTTACATTATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
1951 1978 4.100498 GTCTTACATTATGGAACGGAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
1952 1979 4.344102 TCTTACATTATGGAACGGAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
1953 1980 2.478292 ACATTATGGAACGGAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
1954 1981 3.649843 ACATTATGGAACGGAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
1955 1982 3.641906 ACATTATGGAACGGAGGGAGTAG 59.358 47.826 0.00 0.00 0.00 2.57
1983 2010 2.332063 GCAGCTGCATACCCTCTTTA 57.668 50.000 33.36 0.00 41.59 1.85
1986 2013 3.745480 GCAGCTGCATACCCTCTTTATCA 60.745 47.826 33.36 0.00 41.59 2.15
2000 2027 8.539544 ACCCTCTTTATCATTTTTATTTGGGTG 58.460 33.333 0.00 0.00 39.85 4.61
2008 2035 7.841282 TCATTTTTATTTGGGTGAGGTGTAA 57.159 32.000 0.00 0.00 0.00 2.41
2009 2036 7.891561 TCATTTTTATTTGGGTGAGGTGTAAG 58.108 34.615 0.00 0.00 0.00 2.34
2015 2042 4.447138 TTGGGTGAGGTGTAAGAAATGT 57.553 40.909 0.00 0.00 0.00 2.71
2016 2043 3.750371 TGGGTGAGGTGTAAGAAATGTG 58.250 45.455 0.00 0.00 0.00 3.21
2018 2045 4.003648 GGGTGAGGTGTAAGAAATGTGAG 58.996 47.826 0.00 0.00 0.00 3.51
2019 2046 4.262894 GGGTGAGGTGTAAGAAATGTGAGA 60.263 45.833 0.00 0.00 0.00 3.27
2020 2047 5.305585 GGTGAGGTGTAAGAAATGTGAGAA 58.694 41.667 0.00 0.00 0.00 2.87
2027 2808 6.355638 GTGTAAGAAATGTGAGAACTGAACG 58.644 40.000 0.00 0.00 0.00 3.95
2031 2812 4.273480 AGAAATGTGAGAACTGAACGTTGG 59.727 41.667 5.00 0.23 35.56 3.77
2034 2815 1.940613 GTGAGAACTGAACGTTGGCTT 59.059 47.619 5.00 0.00 35.56 4.35
2036 2817 3.184581 GTGAGAACTGAACGTTGGCTTAG 59.815 47.826 5.00 0.00 35.56 2.18
2049 2830 1.340991 TGGCTTAGTGGCAGGAATTCC 60.341 52.381 17.31 17.31 46.76 3.01
2096 2877 0.736325 CCGCCTTCGAATTCTCACGT 60.736 55.000 0.00 0.00 38.10 4.49
2098 2879 1.201812 CGCCTTCGAATTCTCACGTTG 60.202 52.381 0.00 0.00 38.10 4.10
2099 2880 1.128692 GCCTTCGAATTCTCACGTTGG 59.871 52.381 0.00 0.00 0.00 3.77
2106 3153 0.396435 ATTCTCACGTTGGTGCTGGA 59.604 50.000 0.00 0.00 44.03 3.86
2118 3165 2.717639 GTGCTGGAACTGGACCATAT 57.282 50.000 0.00 0.00 42.24 1.78
2154 3202 5.725110 GTGTAACCAGCAATACATCTCTG 57.275 43.478 0.00 0.00 34.77 3.35
2324 3394 2.965831 AGCTGGATCGGCAATAGACTAA 59.034 45.455 11.02 0.00 38.37 2.24
2325 3395 3.006323 AGCTGGATCGGCAATAGACTAAG 59.994 47.826 11.02 0.00 38.37 2.18
2326 3396 3.243907 GCTGGATCGGCAATAGACTAAGT 60.244 47.826 4.71 0.00 35.55 2.24
2327 3397 4.022242 GCTGGATCGGCAATAGACTAAGTA 60.022 45.833 4.71 0.00 35.55 2.24
2328 3398 5.704888 CTGGATCGGCAATAGACTAAGTAG 58.295 45.833 0.00 0.00 0.00 2.57
2329 3399 5.138276 TGGATCGGCAATAGACTAAGTAGT 58.862 41.667 0.00 0.00 39.71 2.73
2330 3400 5.009710 TGGATCGGCAATAGACTAAGTAGTG 59.990 44.000 0.00 0.00 36.50 2.74
2331 3401 4.913335 TCGGCAATAGACTAAGTAGTGG 57.087 45.455 0.00 0.00 36.50 4.00
2385 3475 1.608590 TGGCTGCTTGTTTTAGCTCAC 59.391 47.619 0.00 0.00 41.76 3.51
2386 3476 1.068264 GGCTGCTTGTTTTAGCTCACC 60.068 52.381 0.00 0.00 41.76 4.02
2412 3502 0.234884 GCTAATCGCGCGGCTTAATT 59.765 50.000 31.69 22.84 0.00 1.40
2413 3503 1.458064 GCTAATCGCGCGGCTTAATTA 59.542 47.619 31.69 22.73 0.00 1.40
2481 3571 1.276421 TGACCAGAAGTAGAGCCAAGC 59.724 52.381 0.00 0.00 0.00 4.01
2482 3572 0.247736 ACCAGAAGTAGAGCCAAGCG 59.752 55.000 0.00 0.00 0.00 4.68
2499 3589 2.629051 AGCGCCCAAGTCATAAACTAC 58.371 47.619 2.29 0.00 37.17 2.73
2500 3590 2.236395 AGCGCCCAAGTCATAAACTACT 59.764 45.455 2.29 0.00 37.17 2.57
2501 3591 2.351726 GCGCCCAAGTCATAAACTACTG 59.648 50.000 0.00 0.00 37.17 2.74
2502 3592 2.936498 CGCCCAAGTCATAAACTACTGG 59.064 50.000 0.00 0.00 37.17 4.00
2503 3593 2.683362 GCCCAAGTCATAAACTACTGGC 59.317 50.000 0.00 0.00 37.17 4.85
2504 3594 3.872240 GCCCAAGTCATAAACTACTGGCA 60.872 47.826 0.00 0.00 41.87 4.92
2505 3595 4.331968 CCCAAGTCATAAACTACTGGCAA 58.668 43.478 0.00 0.00 37.17 4.52
2506 3596 4.396166 CCCAAGTCATAAACTACTGGCAAG 59.604 45.833 0.00 0.00 37.17 4.01
2513 3603 0.178992 AACTACTGGCAAGGCAAGCA 60.179 50.000 0.00 0.00 31.74 3.91
2515 3605 1.930908 CTACTGGCAAGGCAAGCAGC 61.931 60.000 0.00 0.00 44.65 5.25
2547 3645 2.514824 GGATGCCTTCCGCTCACC 60.515 66.667 0.00 0.00 38.78 4.02
2548 3646 2.514824 GATGCCTTCCGCTCACCC 60.515 66.667 0.00 0.00 38.78 4.61
2549 3647 3.329542 GATGCCTTCCGCTCACCCA 62.330 63.158 0.00 0.00 38.78 4.51
2550 3648 3.628646 ATGCCTTCCGCTCACCCAC 62.629 63.158 0.00 0.00 38.78 4.61
2556 3654 4.003788 CCGCTCACCCACGGTCTT 62.004 66.667 0.00 0.00 44.46 3.01
2557 3655 2.432628 CGCTCACCCACGGTCTTC 60.433 66.667 0.00 0.00 31.02 2.87
2558 3656 2.932234 CGCTCACCCACGGTCTTCT 61.932 63.158 0.00 0.00 31.02 2.85
2559 3657 1.371558 GCTCACCCACGGTCTTCTT 59.628 57.895 0.00 0.00 31.02 2.52
2574 3672 4.170256 GTCTTCTTTCTCCTCGCTGTTAG 58.830 47.826 0.00 0.00 0.00 2.34
2577 3675 3.353557 TCTTTCTCCTCGCTGTTAGCTA 58.646 45.455 0.00 0.00 39.60 3.32
2578 3676 3.128938 TCTTTCTCCTCGCTGTTAGCTAC 59.871 47.826 0.00 0.00 39.60 3.58
2579 3677 1.015109 TCTCCTCGCTGTTAGCTACG 58.985 55.000 0.00 0.00 39.60 3.51
2589 3707 4.669728 CGCTGTTAGCTACGAGTATGTTAC 59.330 45.833 0.00 0.00 39.60 2.50
2591 3709 5.908499 GCTGTTAGCTACGAGTATGTTACTC 59.092 44.000 0.00 4.88 43.66 2.59
2651 3769 3.577649 TCTGAGCTTAACTCTGAACCG 57.422 47.619 10.17 0.00 46.73 4.44
2657 3775 4.561105 AGCTTAACTCTGAACCGAAAGAG 58.439 43.478 0.00 0.00 44.57 2.85
2659 3777 4.623595 GCTTAACTCTGAACCGAAAGAGAG 59.376 45.833 6.69 0.00 42.15 3.20
2660 3778 5.565045 GCTTAACTCTGAACCGAAAGAGAGA 60.565 44.000 6.69 0.00 42.15 3.10
2661 3779 4.513198 AACTCTGAACCGAAAGAGAGAG 57.487 45.455 6.69 0.00 42.15 3.20
2667 3785 3.445450 TGAACCGAAAGAGAGAGATGAGG 59.555 47.826 0.00 0.00 0.00 3.86
2675 3793 2.442878 AGAGAGAGATGAGGAGCAGCTA 59.557 50.000 0.00 0.00 44.71 3.32
2676 3794 3.117550 AGAGAGAGATGAGGAGCAGCTAA 60.118 47.826 0.00 0.00 44.71 3.09
2678 3796 3.828451 AGAGAGATGAGGAGCAGCTAATC 59.172 47.826 0.00 0.00 44.71 1.75
2679 3797 3.573538 GAGAGATGAGGAGCAGCTAATCA 59.426 47.826 10.67 10.67 44.71 2.57
2680 3798 3.575256 AGAGATGAGGAGCAGCTAATCAG 59.425 47.826 13.13 0.00 44.71 2.90
2681 3799 3.307506 AGATGAGGAGCAGCTAATCAGT 58.692 45.455 13.13 2.84 42.46 3.41
2682 3800 4.478203 AGATGAGGAGCAGCTAATCAGTA 58.522 43.478 13.13 0.00 42.46 2.74
2683 3801 4.523943 AGATGAGGAGCAGCTAATCAGTAG 59.476 45.833 13.13 0.00 42.46 2.57
2684 3802 3.903467 TGAGGAGCAGCTAATCAGTAGA 58.097 45.455 0.00 0.00 30.50 2.59
2724 3842 4.476752 GCCGCCCACGTCCCATAA 62.477 66.667 0.00 0.00 37.70 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.539438 TGAGGGGTTGGATGTGTTGC 60.539 55.000 0.00 0.00 0.00 4.17
19 20 2.025155 GCTCGAGTCATAGGTCCTTGA 58.975 52.381 15.13 0.00 0.00 3.02
191 192 1.741770 GCATGTCTTCCGCTTCCGT 60.742 57.895 0.00 0.00 0.00 4.69
230 231 2.460853 CCACCCTGGTCCTTGGTGT 61.461 63.158 21.70 8.73 46.49 4.16
701 714 3.523564 CCTAAAGAGGGGTCTTGAATCCA 59.476 47.826 0.00 0.00 39.48 3.41
758 771 6.263754 ACAAAGGGAAAGGATACAATGGAAT 58.736 36.000 0.00 0.00 41.41 3.01
804 817 4.222810 TGCTAGATCACCACACACATAAGT 59.777 41.667 0.00 0.00 0.00 2.24
991 1010 2.454832 ATAGCATCCATGGACGCCCG 62.455 60.000 28.25 10.43 33.38 6.13
1085 1104 0.593128 GTTTGGCACATCGAAGCTGT 59.407 50.000 7.62 0.00 39.30 4.40
1186 1205 0.465705 TCATGAAGATCACCGAGGCC 59.534 55.000 0.00 0.00 0.00 5.19
1196 1215 6.343703 TCACGACAAAGATCATCATGAAGAT 58.656 36.000 13.06 13.06 37.48 2.40
1374 1394 4.641645 CTCAGGTTGTGGCCGGCA 62.642 66.667 30.85 12.04 0.00 5.69
1482 1502 2.814604 CTCCGCATCGACATGGGA 59.185 61.111 4.77 1.03 44.08 4.37
1509 1529 1.603456 TTGCAAGGAACGAGAATGCA 58.397 45.000 0.00 0.00 44.54 3.96
1539 1559 5.515797 TGGTCATCGAGTTCAGGTAATAG 57.484 43.478 0.00 0.00 0.00 1.73
1559 1579 2.664185 CAGCGATGGCCGAGATGG 60.664 66.667 0.00 0.00 41.76 3.51
1743 1763 2.970324 TGACCGACAGCAAACCGC 60.970 61.111 0.00 0.00 42.91 5.68
1799 1819 3.446873 ACATCAAAGTGGTTTTGCAGACA 59.553 39.130 4.91 0.00 44.69 3.41
1831 1851 0.037605 AAGTACAGGAACTTCGGCGG 60.038 55.000 7.21 0.00 34.60 6.13
1839 1860 4.330620 TCAAACGAACACAAGTACAGGAAC 59.669 41.667 0.00 0.00 0.00 3.62
1848 1869 7.110511 GCACTTTTTATTCAAACGAACACAAG 58.889 34.615 0.00 0.00 0.00 3.16
1869 1896 3.030291 TCATTTGTGTTCCAAAGGCACT 58.970 40.909 0.00 0.00 45.79 4.40
1901 1928 4.901849 TCTTACATTATGGGACTGAGGGAG 59.098 45.833 0.00 0.00 0.00 4.30
1902 1929 4.890988 TCTTACATTATGGGACTGAGGGA 58.109 43.478 0.00 0.00 0.00 4.20
1903 1930 5.630415 TTCTTACATTATGGGACTGAGGG 57.370 43.478 0.00 0.00 0.00 4.30
1906 1933 6.045072 ACGTTTCTTACATTATGGGACTGA 57.955 37.500 0.00 0.00 0.00 3.41
1907 1934 6.106673 AGACGTTTCTTACATTATGGGACTG 58.893 40.000 0.00 0.00 0.00 3.51
1908 1935 6.295719 AGACGTTTCTTACATTATGGGACT 57.704 37.500 0.00 0.00 0.00 3.85
1909 1936 6.980051 AAGACGTTTCTTACATTATGGGAC 57.020 37.500 0.00 0.00 40.54 4.46
1920 1947 7.276218 CCGTTCCATAATGTAAGACGTTTCTTA 59.724 37.037 0.00 0.00 42.44 2.10
1921 1948 6.091713 CCGTTCCATAATGTAAGACGTTTCTT 59.908 38.462 0.00 0.00 44.70 2.52
1922 1949 5.579511 CCGTTCCATAATGTAAGACGTTTCT 59.420 40.000 0.00 0.00 0.00 2.52
1923 1950 5.577945 TCCGTTCCATAATGTAAGACGTTTC 59.422 40.000 0.00 0.00 0.00 2.78
1924 1951 5.481105 TCCGTTCCATAATGTAAGACGTTT 58.519 37.500 0.00 0.00 0.00 3.60
1925 1952 5.075858 TCCGTTCCATAATGTAAGACGTT 57.924 39.130 0.00 0.00 0.00 3.99
1926 1953 4.441079 CCTCCGTTCCATAATGTAAGACGT 60.441 45.833 0.00 0.00 0.00 4.34
1927 1954 4.049186 CCTCCGTTCCATAATGTAAGACG 58.951 47.826 0.00 0.00 0.00 4.18
1928 1955 4.100498 TCCCTCCGTTCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
1929 1956 4.291792 TCCCTCCGTTCCATAATGTAAGA 58.708 43.478 0.00 0.00 0.00 2.10
1930 1957 4.101119 ACTCCCTCCGTTCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
1931 1958 4.035112 ACTCCCTCCGTTCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
1932 1959 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
1933 1960 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
1934 1961 3.555168 GCTACTCCCTCCGTTCCATAATG 60.555 52.174 0.00 0.00 0.00 1.90
1935 1962 2.633481 GCTACTCCCTCCGTTCCATAAT 59.367 50.000 0.00 0.00 0.00 1.28
1936 1963 2.037144 GCTACTCCCTCCGTTCCATAA 58.963 52.381 0.00 0.00 0.00 1.90
1937 1964 1.217183 AGCTACTCCCTCCGTTCCATA 59.783 52.381 0.00 0.00 0.00 2.74
1938 1965 0.032017 AGCTACTCCCTCCGTTCCAT 60.032 55.000 0.00 0.00 0.00 3.41
1939 1966 0.683504 GAGCTACTCCCTCCGTTCCA 60.684 60.000 0.00 0.00 0.00 3.53
1940 1967 0.396001 AGAGCTACTCCCTCCGTTCC 60.396 60.000 0.00 0.00 0.00 3.62
1941 1968 0.741915 CAGAGCTACTCCCTCCGTTC 59.258 60.000 0.00 0.00 0.00 3.95
1942 1969 0.039911 ACAGAGCTACTCCCTCCGTT 59.960 55.000 0.00 0.00 0.00 4.44
1943 1970 0.039911 AACAGAGCTACTCCCTCCGT 59.960 55.000 0.00 0.00 0.00 4.69
1944 1971 1.134965 CAAACAGAGCTACTCCCTCCG 60.135 57.143 0.00 0.00 0.00 4.63
1945 1972 1.406205 GCAAACAGAGCTACTCCCTCC 60.406 57.143 0.00 0.00 0.00 4.30
1946 1973 1.276421 TGCAAACAGAGCTACTCCCTC 59.724 52.381 0.00 0.00 0.00 4.30
1947 1974 1.352083 TGCAAACAGAGCTACTCCCT 58.648 50.000 0.00 0.00 0.00 4.20
1948 1975 3.935993 TGCAAACAGAGCTACTCCC 57.064 52.632 0.00 0.00 0.00 4.30
1983 2010 6.933514 ACACCTCACCCAAATAAAAATGAT 57.066 33.333 0.00 0.00 0.00 2.45
1986 2013 8.485578 TTCTTACACCTCACCCAAATAAAAAT 57.514 30.769 0.00 0.00 0.00 1.82
1994 2021 4.141287 CACATTTCTTACACCTCACCCAA 58.859 43.478 0.00 0.00 0.00 4.12
1997 2024 4.894784 TCTCACATTTCTTACACCTCACC 58.105 43.478 0.00 0.00 0.00 4.02
2000 2027 6.223852 TCAGTTCTCACATTTCTTACACCTC 58.776 40.000 0.00 0.00 0.00 3.85
2008 2035 4.273480 CCAACGTTCAGTTCTCACATTTCT 59.727 41.667 0.00 0.00 42.02 2.52
2009 2036 4.527564 CCAACGTTCAGTTCTCACATTTC 58.472 43.478 0.00 0.00 42.02 2.17
2015 2042 2.325583 AAGCCAACGTTCAGTTCTCA 57.674 45.000 0.00 0.00 42.02 3.27
2016 2043 3.184581 CACTAAGCCAACGTTCAGTTCTC 59.815 47.826 0.00 0.00 42.02 2.87
2018 2045 2.223377 CCACTAAGCCAACGTTCAGTTC 59.777 50.000 0.00 0.00 42.02 3.01
2019 2046 2.218603 CCACTAAGCCAACGTTCAGTT 58.781 47.619 0.00 0.00 45.45 3.16
2020 2047 1.878953 CCACTAAGCCAACGTTCAGT 58.121 50.000 0.00 0.00 0.00 3.41
2027 2808 1.839424 ATTCCTGCCACTAAGCCAAC 58.161 50.000 0.00 0.00 0.00 3.77
2031 2812 1.017387 CGGAATTCCTGCCACTAAGC 58.983 55.000 22.05 0.00 0.00 3.09
2034 2815 1.223487 GCCGGAATTCCTGCCACTA 59.777 57.895 25.81 0.00 39.91 2.74
2045 2826 4.462280 GGGTTCGACGGCCGGAAT 62.462 66.667 31.76 8.67 39.14 3.01
2084 2865 1.136252 CAGCACCAACGTGAGAATTCG 60.136 52.381 0.00 0.00 43.14 3.34
2096 2877 1.150536 GGTCCAGTTCCAGCACCAA 59.849 57.895 0.00 0.00 0.00 3.67
2098 2879 0.618458 TATGGTCCAGTTCCAGCACC 59.382 55.000 0.00 0.00 38.42 5.01
2099 2880 2.717639 ATATGGTCCAGTTCCAGCAC 57.282 50.000 0.00 0.00 38.42 4.40
2106 3153 4.307032 AGTGCAGAAATATGGTCCAGTT 57.693 40.909 0.00 0.00 0.00 3.16
2154 3202 0.109597 CTGCAAATGTGAACCGCTCC 60.110 55.000 0.00 0.00 0.00 4.70
2324 3394 4.065281 GCGTCCACGGCCACTACT 62.065 66.667 2.24 0.00 40.23 2.57
2400 3490 2.546789 ACCACTTATAATTAAGCCGCGC 59.453 45.455 0.00 0.00 38.74 6.86
2412 3502 1.917273 GCGACTTGCGACCACTTATA 58.083 50.000 0.00 0.00 44.57 0.98
2413 3503 2.750815 GCGACTTGCGACCACTTAT 58.249 52.632 0.00 0.00 44.57 1.73
2481 3571 2.936498 CCAGTAGTTTATGACTTGGGCG 59.064 50.000 0.00 0.00 39.86 6.13
2482 3572 2.683362 GCCAGTAGTTTATGACTTGGGC 59.317 50.000 0.00 0.00 36.94 5.36
2499 3589 4.415332 CGCTGCTTGCCTTGCCAG 62.415 66.667 0.00 0.00 38.78 4.85
2502 3592 4.773117 GAGCGCTGCTTGCCTTGC 62.773 66.667 18.48 0.00 39.88 4.01
2503 3593 4.456253 CGAGCGCTGCTTGCCTTG 62.456 66.667 18.48 0.00 39.88 3.61
2504 3594 4.996434 ACGAGCGCTGCTTGCCTT 62.996 61.111 18.48 0.00 43.36 4.35
2513 3603 1.140589 CCAGATTCAGACGAGCGCT 59.859 57.895 11.27 11.27 0.00 5.92
2515 3605 1.485397 CATCCAGATTCAGACGAGCG 58.515 55.000 0.00 0.00 0.00 5.03
2541 3639 0.250338 AAAGAAGACCGTGGGTGAGC 60.250 55.000 0.00 0.00 35.25 4.26
2542 3640 1.344763 AGAAAGAAGACCGTGGGTGAG 59.655 52.381 0.00 0.00 35.25 3.51
2545 3643 0.685660 GGAGAAAGAAGACCGTGGGT 59.314 55.000 0.00 0.00 39.44 4.51
2546 3644 0.977395 AGGAGAAAGAAGACCGTGGG 59.023 55.000 0.00 0.00 0.00 4.61
2547 3645 1.402984 CGAGGAGAAAGAAGACCGTGG 60.403 57.143 0.00 0.00 0.00 4.94
2548 3646 1.983972 CGAGGAGAAAGAAGACCGTG 58.016 55.000 0.00 0.00 0.00 4.94
2549 3647 0.244178 GCGAGGAGAAAGAAGACCGT 59.756 55.000 0.00 0.00 0.00 4.83
2550 3648 0.528470 AGCGAGGAGAAAGAAGACCG 59.472 55.000 0.00 0.00 0.00 4.79
2551 3649 1.273886 ACAGCGAGGAGAAAGAAGACC 59.726 52.381 0.00 0.00 0.00 3.85
2552 3650 2.734276 ACAGCGAGGAGAAAGAAGAC 57.266 50.000 0.00 0.00 0.00 3.01
2553 3651 3.367498 GCTAACAGCGAGGAGAAAGAAGA 60.367 47.826 0.00 0.00 0.00 2.87
2554 3652 2.926838 GCTAACAGCGAGGAGAAAGAAG 59.073 50.000 0.00 0.00 0.00 2.85
2555 3653 2.960819 GCTAACAGCGAGGAGAAAGAA 58.039 47.619 0.00 0.00 0.00 2.52
2556 3654 2.656560 GCTAACAGCGAGGAGAAAGA 57.343 50.000 0.00 0.00 0.00 2.52
2589 3707 5.823209 TTGATAATGCATCCAGTTGTGAG 57.177 39.130 0.00 0.00 32.09 3.51
2591 3709 6.822073 CATTTGATAATGCATCCAGTTGTG 57.178 37.500 0.00 0.00 35.15 3.33
2649 3767 2.034558 GCTCCTCATCTCTCTCTTTCGG 59.965 54.545 0.00 0.00 0.00 4.30
2651 3769 3.491447 GCTGCTCCTCATCTCTCTCTTTC 60.491 52.174 0.00 0.00 0.00 2.62
2657 3775 3.573538 TGATTAGCTGCTCCTCATCTCTC 59.426 47.826 4.91 0.00 0.00 3.20
2659 3777 3.321682 ACTGATTAGCTGCTCCTCATCTC 59.678 47.826 4.91 0.00 0.00 2.75
2660 3778 3.307506 ACTGATTAGCTGCTCCTCATCT 58.692 45.455 4.91 0.00 0.00 2.90
2661 3779 3.749665 ACTGATTAGCTGCTCCTCATC 57.250 47.619 4.91 4.85 0.00 2.92
2667 3785 5.964958 AGATCTCTACTGATTAGCTGCTC 57.035 43.478 4.91 0.00 0.00 4.26
2674 3792 7.881775 TGTAGCACAAGATCTCTACTGATTA 57.118 36.000 16.20 0.00 34.19 1.75
2675 3793 6.782082 TGTAGCACAAGATCTCTACTGATT 57.218 37.500 16.20 0.00 34.19 2.57
2676 3794 6.548993 TGATGTAGCACAAGATCTCTACTGAT 59.451 38.462 16.20 6.44 34.19 2.90
2678 3796 5.976534 GTGATGTAGCACAAGATCTCTACTG 59.023 44.000 16.20 5.89 38.63 2.74
2679 3797 5.890985 AGTGATGTAGCACAAGATCTCTACT 59.109 40.000 16.20 6.76 41.19 2.57
2680 3798 6.142818 AGTGATGTAGCACAAGATCTCTAC 57.857 41.667 10.84 10.84 41.19 2.59
2681 3799 6.782082 AAGTGATGTAGCACAAGATCTCTA 57.218 37.500 0.00 0.00 41.19 2.43
2682 3800 5.674052 AAGTGATGTAGCACAAGATCTCT 57.326 39.130 0.00 0.00 41.19 3.10
2683 3801 5.005203 CGAAAGTGATGTAGCACAAGATCTC 59.995 44.000 0.00 0.00 41.19 2.75
2684 3802 4.867047 CGAAAGTGATGTAGCACAAGATCT 59.133 41.667 2.93 0.00 41.19 2.75


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

AutoCloner maintained by Alex Coulton.