Multiple sequence alignment - TraesCS4A01G153900

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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 TraesCS4A01G153900 chr4A 100.000 2141 0 0 1 2141 309515371 309517511 0.000000e+00 3954
1 TraesCS4A01G153900 chr5D 97.124 1947 54 2 1 1945 503218458 503220404 0.000000e+00 3284
2 TraesCS4A01G153900 chr5D 96.918 1947 58 2 1 1945 503277986 503276040 0.000000e+00 3262
3 TraesCS4A01G153900 chr5D 96.456 1947 67 2 1 1945 6189180 6191126 0.000000e+00 3212
4 TraesCS4A01G153900 chr5D 91.262 206 15 3 1936 2141 82880138 82879936 5.820000e-71 278
5 TraesCS4A01G153900 chr1A 97.021 1947 56 2 1 1945 554512488 554514434 0.000000e+00 3273
6 TraesCS4A01G153900 chr1A 95.897 195 8 0 1947 2141 340353442 340353636 1.230000e-82 316
7 TraesCS4A01G153900 chr3B 96.867 1947 59 2 1 1945 201527264 201529210 0.000000e+00 3256
8 TraesCS4A01G153900 chr3D 96.713 1947 59 4 1 1945 589279302 589277359 0.000000e+00 3236
9 TraesCS4A01G153900 chr6D 96.662 1947 63 2 1 1945 168255166 168257112 0.000000e+00 3234
10 TraesCS4A01G153900 chr3A 96.559 1947 63 4 1 1945 672909767 672907823 0.000000e+00 3221
11 TraesCS4A01G153900 chrUn 96.456 1947 66 3 1 1945 216518362 216516417 0.000000e+00 3210
12 TraesCS4A01G153900 chr5A 96.410 195 7 0 1947 2141 381955076 381955270 2.650000e-84 322
13 TraesCS4A01G153900 chr5A 95.385 195 9 0 1947 2141 381922597 381922791 5.740000e-81 311
14 TraesCS4A01G153900 chr2A 95.385 195 8 1 1947 2141 348666457 348666264 2.060000e-80 309
15 TraesCS4A01G153900 chr2A 94.359 195 10 1 1947 2141 348674827 348674634 4.470000e-77 298
16 TraesCS4A01G153900 chr7A 93.846 195 11 1 1947 2141 324049558 324049751 2.080000e-75 292
17 TraesCS4A01G153900 chr7B 92.347 196 14 1 1947 2141 317705626 317705431 5.820000e-71 278
18 TraesCS4A01G153900 chr5B 91.542 201 15 2 1942 2141 215571649 215571450 2.090000e-70 276


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 TraesCS4A01G153900 chr4A 309515371 309517511 2140 False 3954 3954 100.000 1 2141 1 chr4A.!!$F1 2140
1 TraesCS4A01G153900 chr5D 503218458 503220404 1946 False 3284 3284 97.124 1 1945 1 chr5D.!!$F2 1944
2 TraesCS4A01G153900 chr5D 503276040 503277986 1946 True 3262 3262 96.918 1 1945 1 chr5D.!!$R2 1944
3 TraesCS4A01G153900 chr5D 6189180 6191126 1946 False 3212 3212 96.456 1 1945 1 chr5D.!!$F1 1944
4 TraesCS4A01G153900 chr1A 554512488 554514434 1946 False 3273 3273 97.021 1 1945 1 chr1A.!!$F2 1944
5 TraesCS4A01G153900 chr3B 201527264 201529210 1946 False 3256 3256 96.867 1 1945 1 chr3B.!!$F1 1944
6 TraesCS4A01G153900 chr3D 589277359 589279302 1943 True 3236 3236 96.713 1 1945 1 chr3D.!!$R1 1944
7 TraesCS4A01G153900 chr6D 168255166 168257112 1946 False 3234 3234 96.662 1 1945 1 chr6D.!!$F1 1944
8 TraesCS4A01G153900 chr3A 672907823 672909767 1944 True 3221 3221 96.559 1 1945 1 chr3A.!!$R1 1944
9 TraesCS4A01G153900 chrUn 216516417 216518362 1945 True 3210 3210 96.456 1 1945 1 chrUn.!!$R1 1944

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
230 232 0.466739 TAGGCGCTTATGACCTCCGA 60.467 55.0 7.64 0.0 34.92 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 1978 1.619827 CATTGCACATTTGGGTGAGGT 59.38 47.619 0.0 0.0 41.32 3.85 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
91 93 8.986991 AGCCCTCTAGGATGTAAAATATATCTG 58.013 37.037 0.00 0.00 38.24 2.90
159 161 9.096823 TCAATTAGGGTCGTATTCTATGGTTAT 57.903 33.333 0.00 0.00 0.00 1.89
229 231 0.603569 ATAGGCGCTTATGACCTCCG 59.396 55.000 11.70 0.00 34.92 4.63
230 232 0.466739 TAGGCGCTTATGACCTCCGA 60.467 55.000 7.64 0.00 34.92 4.55
267 269 7.152645 GCGGTAATGATTCCTCTAGAATTACA 58.847 38.462 18.02 6.82 45.52 2.41
375 377 5.071250 TGCTCGGGATAGGTGTTTTGTATAT 59.929 40.000 0.00 0.00 0.00 0.86
470 472 5.820947 GGTTGAAGGGTAATGATCATACGTT 59.179 40.000 9.04 10.09 0.00 3.99
647 649 4.963276 TGATTCTTGCCCAATAAACGAG 57.037 40.909 0.00 0.00 0.00 4.18
708 710 6.329197 TCCATAAATCGACTTTCCCTCCTATT 59.671 38.462 0.00 0.00 0.00 1.73
711 713 5.959583 AATCGACTTTCCCTCCTATTCTT 57.040 39.130 0.00 0.00 0.00 2.52
719 721 6.273495 ACTTTCCCTCCTATTCTTTGAGTTCT 59.727 38.462 0.00 0.00 0.00 3.01
962 964 4.023107 ACAGGGATCATCGTACATCGTAAG 60.023 45.833 0.00 0.00 40.80 2.34
1067 1069 2.305927 TGAAAACACCTCTCTGGATCCC 59.694 50.000 9.90 0.00 39.71 3.85
1088 1090 4.943705 CCCCGAATTGAAAGAGAGATTGAA 59.056 41.667 0.00 0.00 0.00 2.69
1219 1221 2.442413 TGAACAACCGGGATCCATTTC 58.558 47.619 15.23 6.67 0.00 2.17
1244 1246 6.428159 CCTTATGATACCTAGTTGGCATTGAC 59.572 42.308 0.00 0.00 40.22 3.18
1317 1319 9.561069 AAAGACGTATATTCCTTGCTCATTATT 57.439 29.630 0.00 0.00 0.00 1.40
1370 1372 6.373495 GTGGGACTAATCGTTTTCATTTACCT 59.627 38.462 0.00 0.00 0.00 3.08
1429 1432 8.373220 CCTATCGGGTATTTTAGTGATAGGTTT 58.627 37.037 14.88 0.00 45.27 3.27
1593 1597 9.010029 GGAAAAGACAATGTTCCATACTAAAGA 57.990 33.333 0.00 0.00 40.53 2.52
1600 1604 7.610305 ACAATGTTCCATACTAAAGAATTCGGT 59.390 33.333 0.00 1.30 0.00 4.69
1756 1760 0.901827 TGCGAGCCAAGGTAAGATCA 59.098 50.000 0.00 0.00 0.00 2.92
1878 1882 1.556911 AGAGGCAATCGTGTCAGGAAT 59.443 47.619 0.00 0.00 0.00 3.01
1880 1884 1.278985 AGGCAATCGTGTCAGGAATCA 59.721 47.619 0.00 0.00 0.00 2.57
1881 1885 2.083774 GGCAATCGTGTCAGGAATCAA 58.916 47.619 0.00 0.00 0.00 2.57
1936 1940 5.674525 TGGAACGAGCATGAAGAGATTAAT 58.325 37.500 0.00 0.00 0.00 1.40
1945 1949 6.991531 AGCATGAAGAGATTAATGAGACTTCC 59.008 38.462 0.00 0.00 34.70 3.46
1946 1950 6.073873 GCATGAAGAGATTAATGAGACTTCCG 60.074 42.308 0.00 0.00 34.70 4.30
1947 1951 6.531503 TGAAGAGATTAATGAGACTTCCGT 57.468 37.500 0.00 0.00 34.70 4.69
1948 1952 7.640597 TGAAGAGATTAATGAGACTTCCGTA 57.359 36.000 0.00 0.00 34.70 4.02
1949 1953 8.063200 TGAAGAGATTAATGAGACTTCCGTAA 57.937 34.615 0.00 0.00 34.70 3.18
1950 1954 7.974501 TGAAGAGATTAATGAGACTTCCGTAAC 59.025 37.037 0.00 0.00 34.70 2.50
1951 1955 7.406031 AGAGATTAATGAGACTTCCGTAACA 57.594 36.000 0.00 0.00 0.00 2.41
1952 1956 7.259161 AGAGATTAATGAGACTTCCGTAACAC 58.741 38.462 0.00 0.00 0.00 3.32
1953 1957 6.338937 AGATTAATGAGACTTCCGTAACACC 58.661 40.000 0.00 0.00 0.00 4.16
1954 1958 3.329929 AATGAGACTTCCGTAACACCC 57.670 47.619 0.00 0.00 0.00 4.61
1955 1959 0.971386 TGAGACTTCCGTAACACCCC 59.029 55.000 0.00 0.00 0.00 4.95
1956 1960 0.971386 GAGACTTCCGTAACACCCCA 59.029 55.000 0.00 0.00 0.00 4.96
1957 1961 1.345415 GAGACTTCCGTAACACCCCAA 59.655 52.381 0.00 0.00 0.00 4.12
1958 1962 1.982958 AGACTTCCGTAACACCCCAAT 59.017 47.619 0.00 0.00 0.00 3.16
1959 1963 3.175594 AGACTTCCGTAACACCCCAATA 58.824 45.455 0.00 0.00 0.00 1.90
1960 1964 3.583966 AGACTTCCGTAACACCCCAATAA 59.416 43.478 0.00 0.00 0.00 1.40
1961 1965 4.226620 AGACTTCCGTAACACCCCAATAAT 59.773 41.667 0.00 0.00 0.00 1.28
1962 1966 4.520179 ACTTCCGTAACACCCCAATAATC 58.480 43.478 0.00 0.00 0.00 1.75
1963 1967 4.019141 ACTTCCGTAACACCCCAATAATCA 60.019 41.667 0.00 0.00 0.00 2.57
1964 1968 4.571369 TCCGTAACACCCCAATAATCAA 57.429 40.909 0.00 0.00 0.00 2.57
1965 1969 4.519213 TCCGTAACACCCCAATAATCAAG 58.481 43.478 0.00 0.00 0.00 3.02
1966 1970 3.630312 CCGTAACACCCCAATAATCAAGG 59.370 47.826 0.00 0.00 0.00 3.61
1967 1971 4.266714 CGTAACACCCCAATAATCAAGGT 58.733 43.478 0.00 0.00 0.00 3.50
1968 1972 5.430007 CGTAACACCCCAATAATCAAGGTA 58.570 41.667 0.00 0.00 0.00 3.08
1969 1973 5.295045 CGTAACACCCCAATAATCAAGGTAC 59.705 44.000 0.00 0.00 0.00 3.34
1970 1974 4.938575 ACACCCCAATAATCAAGGTACA 57.061 40.909 0.00 0.00 0.00 2.90
1971 1975 4.855340 ACACCCCAATAATCAAGGTACAG 58.145 43.478 0.00 0.00 0.00 2.74
1972 1976 4.291249 ACACCCCAATAATCAAGGTACAGT 59.709 41.667 0.00 0.00 0.00 3.55
1973 1977 5.489637 ACACCCCAATAATCAAGGTACAGTA 59.510 40.000 0.00 0.00 0.00 2.74
1974 1978 6.012333 ACACCCCAATAATCAAGGTACAGTAA 60.012 38.462 0.00 0.00 0.00 2.24
1975 1979 6.317893 CACCCCAATAATCAAGGTACAGTAAC 59.682 42.308 0.00 0.00 0.00 2.50
1976 1980 5.826208 CCCCAATAATCAAGGTACAGTAACC 59.174 44.000 0.00 0.00 40.06 2.85
1985 1989 3.775261 GGTACAGTAACCTCACCCAAA 57.225 47.619 0.00 0.00 36.53 3.28
1986 1990 4.296621 GGTACAGTAACCTCACCCAAAT 57.703 45.455 0.00 0.00 36.53 2.32
1987 1991 4.007659 GGTACAGTAACCTCACCCAAATG 58.992 47.826 0.00 0.00 36.53 2.32
1988 1992 3.876309 ACAGTAACCTCACCCAAATGT 57.124 42.857 0.00 0.00 0.00 2.71
1989 1993 3.486383 ACAGTAACCTCACCCAAATGTG 58.514 45.455 0.00 0.00 37.59 3.21
1990 1994 2.228822 CAGTAACCTCACCCAAATGTGC 59.771 50.000 0.00 0.00 36.17 4.57
1991 1995 2.158534 AGTAACCTCACCCAAATGTGCA 60.159 45.455 0.00 0.00 36.17 4.57
1992 1996 1.786937 AACCTCACCCAAATGTGCAA 58.213 45.000 0.00 0.00 36.17 4.08
1993 1997 2.014010 ACCTCACCCAAATGTGCAAT 57.986 45.000 0.00 0.00 36.17 3.56
1994 1998 1.619827 ACCTCACCCAAATGTGCAATG 59.380 47.619 0.00 0.00 36.17 2.82
1995 1999 1.619827 CCTCACCCAAATGTGCAATGT 59.380 47.619 0.00 0.00 36.17 2.71
1996 2000 2.353011 CCTCACCCAAATGTGCAATGTC 60.353 50.000 0.00 0.00 36.17 3.06
1997 2001 2.296752 CTCACCCAAATGTGCAATGTCA 59.703 45.455 0.00 0.00 36.17 3.58
1998 2002 2.898612 TCACCCAAATGTGCAATGTCAT 59.101 40.909 0.00 0.00 36.17 3.06
1999 2003 3.056678 TCACCCAAATGTGCAATGTCATC 60.057 43.478 0.00 0.00 36.17 2.92
2000 2004 2.898612 ACCCAAATGTGCAATGTCATCA 59.101 40.909 0.00 0.00 0.00 3.07
2001 2005 3.056393 ACCCAAATGTGCAATGTCATCAG 60.056 43.478 0.00 0.00 0.00 2.90
2002 2006 3.517602 CCAAATGTGCAATGTCATCAGG 58.482 45.455 0.00 0.00 0.00 3.86
2003 2007 3.056393 CCAAATGTGCAATGTCATCAGGT 60.056 43.478 0.00 0.00 0.00 4.00
2004 2008 4.561938 CCAAATGTGCAATGTCATCAGGTT 60.562 41.667 0.00 0.00 0.00 3.50
2005 2009 4.877378 AATGTGCAATGTCATCAGGTTT 57.123 36.364 0.00 0.00 0.00 3.27
2006 2010 4.877378 ATGTGCAATGTCATCAGGTTTT 57.123 36.364 0.00 0.00 0.00 2.43
2007 2011 5.981088 ATGTGCAATGTCATCAGGTTTTA 57.019 34.783 0.00 0.00 0.00 1.52
2008 2012 5.981088 TGTGCAATGTCATCAGGTTTTAT 57.019 34.783 0.00 0.00 0.00 1.40
2009 2013 6.343716 TGTGCAATGTCATCAGGTTTTATT 57.656 33.333 0.00 0.00 0.00 1.40
2010 2014 7.459795 TGTGCAATGTCATCAGGTTTTATTA 57.540 32.000 0.00 0.00 0.00 0.98
2011 2015 7.890515 TGTGCAATGTCATCAGGTTTTATTAA 58.109 30.769 0.00 0.00 0.00 1.40
2012 2016 8.028354 TGTGCAATGTCATCAGGTTTTATTAAG 58.972 33.333 0.00 0.00 0.00 1.85
2013 2017 7.009540 GTGCAATGTCATCAGGTTTTATTAAGC 59.990 37.037 0.00 0.00 0.00 3.09
2014 2018 6.476706 GCAATGTCATCAGGTTTTATTAAGCC 59.523 38.462 0.00 0.00 35.04 4.35
2015 2019 7.546358 CAATGTCATCAGGTTTTATTAAGCCA 58.454 34.615 0.06 0.00 37.12 4.75
2016 2020 7.716799 ATGTCATCAGGTTTTATTAAGCCAA 57.283 32.000 0.06 0.00 37.12 4.52
2017 2021 7.716799 TGTCATCAGGTTTTATTAAGCCAAT 57.283 32.000 0.06 0.00 37.12 3.16
2018 2022 8.133024 TGTCATCAGGTTTTATTAAGCCAATT 57.867 30.769 0.06 0.00 37.12 2.32
2019 2023 8.592809 TGTCATCAGGTTTTATTAAGCCAATTT 58.407 29.630 0.06 0.00 37.12 1.82
2020 2024 8.872845 GTCATCAGGTTTTATTAAGCCAATTTG 58.127 33.333 0.06 0.00 37.12 2.32
2021 2025 7.548780 TCATCAGGTTTTATTAAGCCAATTTGC 59.451 33.333 0.06 0.00 37.12 3.68
2022 2026 6.169800 TCAGGTTTTATTAAGCCAATTTGCC 58.830 36.000 0.00 0.00 37.12 4.52
2023 2027 5.936956 CAGGTTTTATTAAGCCAATTTGCCA 59.063 36.000 0.00 0.00 37.12 4.92
2024 2028 5.937540 AGGTTTTATTAAGCCAATTTGCCAC 59.062 36.000 0.00 0.00 37.12 5.01
2025 2029 5.937540 GGTTTTATTAAGCCAATTTGCCACT 59.062 36.000 0.00 0.00 34.95 4.00
2026 2030 6.429692 GGTTTTATTAAGCCAATTTGCCACTT 59.570 34.615 0.00 0.00 34.95 3.16
2027 2031 7.297391 GTTTTATTAAGCCAATTTGCCACTTG 58.703 34.615 0.00 0.00 0.00 3.16
2028 2032 4.888326 ATTAAGCCAATTTGCCACTTGA 57.112 36.364 0.00 1.87 0.00 3.02
2029 2033 4.888326 TTAAGCCAATTTGCCACTTGAT 57.112 36.364 0.00 0.00 0.00 2.57
2030 2034 2.754946 AGCCAATTTGCCACTTGATG 57.245 45.000 0.00 0.00 0.00 3.07
2031 2035 2.250031 AGCCAATTTGCCACTTGATGA 58.750 42.857 0.00 0.00 0.00 2.92
2032 2036 2.633967 AGCCAATTTGCCACTTGATGAA 59.366 40.909 0.00 0.00 0.00 2.57
2033 2037 3.071312 AGCCAATTTGCCACTTGATGAAA 59.929 39.130 0.00 0.00 0.00 2.69
2034 2038 3.814283 GCCAATTTGCCACTTGATGAAAA 59.186 39.130 0.00 0.00 0.00 2.29
2035 2039 4.456566 GCCAATTTGCCACTTGATGAAAAT 59.543 37.500 0.00 0.00 0.00 1.82
2036 2040 5.391203 GCCAATTTGCCACTTGATGAAAATC 60.391 40.000 0.00 0.00 0.00 2.17
2037 2041 5.122711 CCAATTTGCCACTTGATGAAAATCC 59.877 40.000 0.00 0.00 0.00 3.01
2038 2042 3.574284 TTGCCACTTGATGAAAATCCG 57.426 42.857 0.00 0.00 0.00 4.18
2039 2043 2.789213 TGCCACTTGATGAAAATCCGA 58.211 42.857 0.00 0.00 0.00 4.55
2040 2044 2.749076 TGCCACTTGATGAAAATCCGAG 59.251 45.455 0.00 0.00 0.00 4.63
2041 2045 2.749621 GCCACTTGATGAAAATCCGAGT 59.250 45.455 0.00 0.00 0.00 4.18
2042 2046 3.181506 GCCACTTGATGAAAATCCGAGTC 60.182 47.826 0.00 0.00 0.00 3.36
2043 2047 4.002982 CCACTTGATGAAAATCCGAGTCA 58.997 43.478 0.00 0.00 0.00 3.41
2044 2048 4.455533 CCACTTGATGAAAATCCGAGTCAA 59.544 41.667 0.00 0.00 0.00 3.18
2045 2049 5.048782 CCACTTGATGAAAATCCGAGTCAAA 60.049 40.000 0.00 0.00 0.00 2.69
2046 2050 6.349611 CCACTTGATGAAAATCCGAGTCAAAT 60.350 38.462 0.00 0.00 0.00 2.32
2047 2051 7.086376 CACTTGATGAAAATCCGAGTCAAATT 58.914 34.615 0.00 0.00 0.00 1.82
2048 2052 7.272084 CACTTGATGAAAATCCGAGTCAAATTC 59.728 37.037 0.00 0.00 0.00 2.17
2049 2053 6.816134 TGATGAAAATCCGAGTCAAATTCA 57.184 33.333 0.00 0.00 0.00 2.57
2050 2054 7.213216 TGATGAAAATCCGAGTCAAATTCAA 57.787 32.000 0.00 0.00 0.00 2.69
2051 2055 7.656412 TGATGAAAATCCGAGTCAAATTCAAA 58.344 30.769 0.00 0.00 0.00 2.69
2052 2056 8.306038 TGATGAAAATCCGAGTCAAATTCAAAT 58.694 29.630 0.00 0.00 0.00 2.32
2053 2057 9.143631 GATGAAAATCCGAGTCAAATTCAAATT 57.856 29.630 0.00 0.00 0.00 1.82
2054 2058 8.885494 TGAAAATCCGAGTCAAATTCAAATTT 57.115 26.923 0.00 0.00 39.07 1.82
2055 2059 8.977505 TGAAAATCCGAGTCAAATTCAAATTTC 58.022 29.630 0.00 0.00 36.52 2.17
2056 2060 8.885494 AAAATCCGAGTCAAATTCAAATTTCA 57.115 26.923 0.00 0.00 36.52 2.69
2057 2061 8.885494 AAATCCGAGTCAAATTCAAATTTCAA 57.115 26.923 0.00 0.00 36.52 2.69
2058 2062 8.885494 AATCCGAGTCAAATTCAAATTTCAAA 57.115 26.923 0.00 0.00 36.52 2.69
2059 2063 9.492973 AATCCGAGTCAAATTCAAATTTCAAAT 57.507 25.926 0.00 0.00 36.52 2.32
2061 2065 9.973450 TCCGAGTCAAATTCAAATTTCAAATAA 57.027 25.926 0.00 0.00 36.52 1.40
2109 2113 9.919348 CAAACTGTCAAATAAAAATGTTCAAGG 57.081 29.630 0.00 0.00 0.00 3.61
2110 2114 9.883142 AAACTGTCAAATAAAAATGTTCAAGGA 57.117 25.926 0.00 0.00 0.00 3.36
2115 2119 9.597999 GTCAAATAAAAATGTTCAAGGATTTGC 57.402 29.630 0.00 0.00 34.54 3.68
2116 2120 9.334947 TCAAATAAAAATGTTCAAGGATTTGCA 57.665 25.926 0.00 0.00 34.54 4.08
2117 2121 9.947669 CAAATAAAAATGTTCAAGGATTTGCAA 57.052 25.926 0.00 0.00 34.21 4.08
2124 2128 9.504708 AAATGTTCAAGGATTTGCAAATATTCA 57.495 25.926 24.15 15.27 34.21 2.57
2125 2129 7.887996 TGTTCAAGGATTTGCAAATATTCAC 57.112 32.000 24.15 17.98 34.21 3.18
2126 2130 6.873076 TGTTCAAGGATTTGCAAATATTCACC 59.127 34.615 24.15 19.32 34.21 4.02
2127 2131 6.602410 TCAAGGATTTGCAAATATTCACCA 57.398 33.333 24.15 3.38 34.21 4.17
2128 2132 7.002250 TCAAGGATTTGCAAATATTCACCAA 57.998 32.000 24.15 8.18 34.21 3.67
2129 2133 7.098477 TCAAGGATTTGCAAATATTCACCAAG 58.902 34.615 24.15 15.48 34.21 3.61
2130 2134 6.610075 AGGATTTGCAAATATTCACCAAGT 57.390 33.333 24.15 3.38 0.00 3.16
2131 2135 7.716799 AGGATTTGCAAATATTCACCAAGTA 57.283 32.000 24.15 0.00 0.00 2.24
2132 2136 8.310122 AGGATTTGCAAATATTCACCAAGTAT 57.690 30.769 24.15 2.71 0.00 2.12
2133 2137 8.761689 AGGATTTGCAAATATTCACCAAGTATT 58.238 29.630 24.15 2.05 0.00 1.89
2134 2138 9.382275 GGATTTGCAAATATTCACCAAGTATTT 57.618 29.630 24.15 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 93 2.505819 ACACTATGGGGATGGTGAGAAC 59.494 50.000 5.65 0.00 36.65 3.01
135 137 9.096823 TCATAACCATAGAATACGACCCTAATT 57.903 33.333 0.00 0.00 0.00 1.40
288 290 6.777091 TCCACGAAATAATTTGATCCATGGAT 59.223 34.615 27.66 27.66 37.59 3.41
470 472 3.369175 TGGGCCATACAATGCATTACAA 58.631 40.909 12.53 0.60 0.00 2.41
634 636 4.514781 AAAAAGTCCTCGTTTATTGGGC 57.485 40.909 0.00 0.00 0.00 5.36
711 713 9.880064 CGAATTCTTATCGATACTAGAACTCAA 57.120 33.333 20.09 4.45 42.76 3.02
771 773 6.708502 TCCATACATAACGAATTGGTATGGTG 59.291 38.462 21.76 7.96 45.91 4.17
884 886 7.102346 CCCAACTCATAATTGGTAAATTTGCA 58.898 34.615 8.59 0.00 44.46 4.08
1067 1069 6.404074 CCCTTTCAATCTCTCTTTCAATTCGG 60.404 42.308 0.00 0.00 0.00 4.30
1219 1221 6.428159 GTCAATGCCAACTAGGTATCATAAGG 59.572 42.308 0.00 0.00 42.47 2.69
1317 1319 7.335924 CGAGGTTTGGGAATAAGTGATTTTCTA 59.664 37.037 0.00 0.00 0.00 2.10
1321 1323 5.183140 CACGAGGTTTGGGAATAAGTGATTT 59.817 40.000 0.00 0.00 0.00 2.17
1370 1372 4.211920 ACGAAAAGGGTTTTCCATGAGAA 58.788 39.130 0.00 0.00 44.73 2.87
1429 1432 2.816411 AGGATCGTCCAGTTCCTACAA 58.184 47.619 6.78 0.00 44.94 2.41
1529 1533 9.342308 CCTAGCATATGAAAGAATGAAAAGGTA 57.658 33.333 6.97 0.00 0.00 3.08
1600 1604 2.635915 ACTGGAACTCGTGGTTATGGAA 59.364 45.455 0.00 0.00 38.41 3.53
1650 1654 5.248477 TGTGGAATACTAATGGATAGGGCTC 59.752 44.000 0.00 0.00 35.81 4.70
1714 1718 4.034285 ACCCCAAGTTTGTCTATGAAGG 57.966 45.455 0.00 0.00 0.00 3.46
1756 1760 2.143419 GGTCCCATGATCCCGAGCT 61.143 63.158 0.00 0.00 0.00 4.09
1878 1882 4.940654 CCTTTTGGCCAAAGAAAAACTTGA 59.059 37.500 28.79 10.94 44.40 3.02
1880 1884 4.917385 ACCTTTTGGCCAAAGAAAAACTT 58.083 34.783 28.79 7.93 44.40 2.66
1881 1885 4.568072 ACCTTTTGGCCAAAGAAAAACT 57.432 36.364 28.79 7.71 44.40 2.66
1907 1911 1.808411 TCATGCTCGTTCCAAGTTCC 58.192 50.000 0.00 0.00 0.00 3.62
1945 1949 4.266714 ACCTTGATTATTGGGGTGTTACG 58.733 43.478 0.00 0.00 0.00 3.18
1946 1950 6.181908 TGTACCTTGATTATTGGGGTGTTAC 58.818 40.000 0.00 0.00 0.00 2.50
1947 1951 6.012333 ACTGTACCTTGATTATTGGGGTGTTA 60.012 38.462 0.00 0.00 0.00 2.41
1948 1952 5.222254 ACTGTACCTTGATTATTGGGGTGTT 60.222 40.000 0.00 0.00 0.00 3.32
1949 1953 4.291249 ACTGTACCTTGATTATTGGGGTGT 59.709 41.667 0.00 0.00 0.00 4.16
1950 1954 4.855340 ACTGTACCTTGATTATTGGGGTG 58.145 43.478 0.00 0.00 0.00 4.61
1951 1955 6.420638 GTTACTGTACCTTGATTATTGGGGT 58.579 40.000 0.00 0.00 0.00 4.95
1952 1956 5.826208 GGTTACTGTACCTTGATTATTGGGG 59.174 44.000 0.00 0.00 35.23 4.96
1953 1957 6.659824 AGGTTACTGTACCTTGATTATTGGG 58.340 40.000 0.00 0.00 46.39 4.12
1965 1969 3.775261 TTTGGGTGAGGTTACTGTACC 57.225 47.619 0.00 0.00 38.53 3.34
1966 1970 4.454504 CACATTTGGGTGAGGTTACTGTAC 59.545 45.833 0.00 0.00 41.32 2.90
1967 1971 4.647611 CACATTTGGGTGAGGTTACTGTA 58.352 43.478 0.00 0.00 41.32 2.74
1968 1972 3.486383 CACATTTGGGTGAGGTTACTGT 58.514 45.455 0.00 0.00 41.32 3.55
1969 1973 2.228822 GCACATTTGGGTGAGGTTACTG 59.771 50.000 0.00 0.00 41.32 2.74
1970 1974 2.158534 TGCACATTTGGGTGAGGTTACT 60.159 45.455 0.00 0.00 41.32 2.24
1971 1975 2.235016 TGCACATTTGGGTGAGGTTAC 58.765 47.619 0.00 0.00 41.32 2.50
1972 1976 2.666272 TGCACATTTGGGTGAGGTTA 57.334 45.000 0.00 0.00 41.32 2.85
1973 1977 1.786937 TTGCACATTTGGGTGAGGTT 58.213 45.000 0.00 0.00 41.32 3.50
1974 1978 1.619827 CATTGCACATTTGGGTGAGGT 59.380 47.619 0.00 0.00 41.32 3.85
1975 1979 1.619827 ACATTGCACATTTGGGTGAGG 59.380 47.619 0.00 0.00 41.32 3.86
1976 1980 2.296752 TGACATTGCACATTTGGGTGAG 59.703 45.455 0.00 0.00 41.32 3.51
1977 1981 2.314246 TGACATTGCACATTTGGGTGA 58.686 42.857 0.00 0.00 41.32 4.02
1978 1982 2.816204 TGACATTGCACATTTGGGTG 57.184 45.000 0.00 0.00 41.72 4.61
1979 1983 2.898612 TGATGACATTGCACATTTGGGT 59.101 40.909 0.00 0.00 0.00 4.51
1980 1984 3.517602 CTGATGACATTGCACATTTGGG 58.482 45.455 0.00 0.00 0.00 4.12
1981 1985 3.056393 ACCTGATGACATTGCACATTTGG 60.056 43.478 0.00 0.00 0.00 3.28
1982 1986 4.182693 ACCTGATGACATTGCACATTTG 57.817 40.909 0.00 0.00 0.00 2.32
1983 1987 4.877378 AACCTGATGACATTGCACATTT 57.123 36.364 0.00 0.00 0.00 2.32
1984 1988 4.877378 AAACCTGATGACATTGCACATT 57.123 36.364 0.00 0.00 0.00 2.71
1985 1989 4.877378 AAAACCTGATGACATTGCACAT 57.123 36.364 0.00 0.00 0.00 3.21
1986 1990 5.981088 ATAAAACCTGATGACATTGCACA 57.019 34.783 0.00 0.00 0.00 4.57
1987 1991 7.009540 GCTTAATAAAACCTGATGACATTGCAC 59.990 37.037 0.00 0.00 0.00 4.57
1988 1992 7.035004 GCTTAATAAAACCTGATGACATTGCA 58.965 34.615 0.00 0.00 0.00 4.08
1989 1993 6.476706 GGCTTAATAAAACCTGATGACATTGC 59.523 38.462 0.00 0.00 0.00 3.56
1990 1994 7.546358 TGGCTTAATAAAACCTGATGACATTG 58.454 34.615 0.00 0.00 0.00 2.82
1991 1995 7.716799 TGGCTTAATAAAACCTGATGACATT 57.283 32.000 0.00 0.00 0.00 2.71
1992 1996 7.716799 TTGGCTTAATAAAACCTGATGACAT 57.283 32.000 0.00 0.00 0.00 3.06
1993 1997 7.716799 ATTGGCTTAATAAAACCTGATGACA 57.283 32.000 0.00 0.00 0.00 3.58
1994 1998 8.872845 CAAATTGGCTTAATAAAACCTGATGAC 58.127 33.333 0.00 0.00 0.00 3.06
1995 1999 7.548780 GCAAATTGGCTTAATAAAACCTGATGA 59.451 33.333 0.00 0.00 0.00 2.92
1996 2000 7.201635 GGCAAATTGGCTTAATAAAACCTGATG 60.202 37.037 12.54 0.00 40.14 3.07
1997 2001 6.823182 GGCAAATTGGCTTAATAAAACCTGAT 59.177 34.615 12.54 0.00 40.14 2.90
1998 2002 6.169800 GGCAAATTGGCTTAATAAAACCTGA 58.830 36.000 12.54 0.00 40.14 3.86
1999 2003 5.936956 TGGCAAATTGGCTTAATAAAACCTG 59.063 36.000 20.08 0.00 44.10 4.00
2000 2004 5.937540 GTGGCAAATTGGCTTAATAAAACCT 59.062 36.000 20.08 0.00 44.10 3.50
2001 2005 5.937540 AGTGGCAAATTGGCTTAATAAAACC 59.062 36.000 20.08 0.00 44.10 3.27
2002 2006 7.172361 TCAAGTGGCAAATTGGCTTAATAAAAC 59.828 33.333 20.08 7.57 44.10 2.43
2003 2007 7.220030 TCAAGTGGCAAATTGGCTTAATAAAA 58.780 30.769 20.08 0.00 44.10 1.52
2004 2008 6.763355 TCAAGTGGCAAATTGGCTTAATAAA 58.237 32.000 20.08 0.00 44.10 1.40
2005 2009 6.352016 TCAAGTGGCAAATTGGCTTAATAA 57.648 33.333 20.08 0.00 44.10 1.40
2006 2010 5.991933 TCAAGTGGCAAATTGGCTTAATA 57.008 34.783 20.08 0.00 44.10 0.98
2007 2011 4.888326 TCAAGTGGCAAATTGGCTTAAT 57.112 36.364 20.08 0.00 44.10 1.40
2008 2012 4.282957 TCATCAAGTGGCAAATTGGCTTAA 59.717 37.500 20.08 0.00 44.10 1.85
2009 2013 3.831333 TCATCAAGTGGCAAATTGGCTTA 59.169 39.130 20.08 0.00 44.10 3.09
2010 2014 2.633967 TCATCAAGTGGCAAATTGGCTT 59.366 40.909 20.08 4.72 44.10 4.35
2011 2015 2.250031 TCATCAAGTGGCAAATTGGCT 58.750 42.857 20.08 0.00 44.10 4.75
2012 2016 2.747396 TCATCAAGTGGCAAATTGGC 57.253 45.000 12.92 12.92 44.03 4.52
2013 2017 5.122711 GGATTTTCATCAAGTGGCAAATTGG 59.877 40.000 0.66 0.00 0.00 3.16
2014 2018 5.163933 CGGATTTTCATCAAGTGGCAAATTG 60.164 40.000 0.00 0.00 0.00 2.32
2015 2019 4.931002 CGGATTTTCATCAAGTGGCAAATT 59.069 37.500 0.00 0.00 0.00 1.82
2016 2020 4.220382 TCGGATTTTCATCAAGTGGCAAAT 59.780 37.500 0.00 0.00 0.00 2.32
2017 2021 3.571828 TCGGATTTTCATCAAGTGGCAAA 59.428 39.130 0.00 0.00 0.00 3.68
2018 2022 3.153130 TCGGATTTTCATCAAGTGGCAA 58.847 40.909 0.00 0.00 0.00 4.52
2019 2023 2.749076 CTCGGATTTTCATCAAGTGGCA 59.251 45.455 0.00 0.00 0.00 4.92
2020 2024 2.749621 ACTCGGATTTTCATCAAGTGGC 59.250 45.455 0.00 0.00 29.89 5.01
2021 2025 4.002982 TGACTCGGATTTTCATCAAGTGG 58.997 43.478 0.00 0.00 30.74 4.00
2022 2026 5.611796 TTGACTCGGATTTTCATCAAGTG 57.388 39.130 0.00 0.00 30.74 3.16
2023 2027 6.824305 ATTTGACTCGGATTTTCATCAAGT 57.176 33.333 0.00 0.00 32.38 3.16
2024 2028 7.307694 TGAATTTGACTCGGATTTTCATCAAG 58.692 34.615 0.00 0.00 0.00 3.02
2025 2029 7.213216 TGAATTTGACTCGGATTTTCATCAA 57.787 32.000 0.00 0.00 0.00 2.57
2026 2030 6.816134 TGAATTTGACTCGGATTTTCATCA 57.184 33.333 0.00 0.00 0.00 3.07
2027 2031 8.693542 ATTTGAATTTGACTCGGATTTTCATC 57.306 30.769 0.00 0.00 0.00 2.92
2028 2032 9.492973 AAATTTGAATTTGACTCGGATTTTCAT 57.507 25.926 1.14 0.00 37.24 2.57
2029 2033 8.885494 AAATTTGAATTTGACTCGGATTTTCA 57.115 26.923 1.14 0.00 37.24 2.69
2030 2034 8.977505 TGAAATTTGAATTTGACTCGGATTTTC 58.022 29.630 6.44 0.00 38.64 2.29
2031 2035 8.885494 TGAAATTTGAATTTGACTCGGATTTT 57.115 26.923 6.44 0.00 38.64 1.82
2032 2036 8.885494 TTGAAATTTGAATTTGACTCGGATTT 57.115 26.923 6.44 0.00 38.64 2.17
2033 2037 8.885494 TTTGAAATTTGAATTTGACTCGGATT 57.115 26.923 6.44 0.00 38.64 3.01
2035 2039 9.973450 TTATTTGAAATTTGAATTTGACTCGGA 57.027 25.926 6.44 0.00 38.64 4.55
2083 2087 9.919348 CCTTGAACATTTTTATTTGACAGTTTG 57.081 29.630 0.00 0.00 0.00 2.93
2084 2088 9.883142 TCCTTGAACATTTTTATTTGACAGTTT 57.117 25.926 0.00 0.00 0.00 2.66
2089 2093 9.597999 GCAAATCCTTGAACATTTTTATTTGAC 57.402 29.630 0.00 0.00 35.92 3.18
2090 2094 9.334947 TGCAAATCCTTGAACATTTTTATTTGA 57.665 25.926 0.00 0.00 35.92 2.69
2091 2095 9.947669 TTGCAAATCCTTGAACATTTTTATTTG 57.052 25.926 0.00 0.00 36.58 2.32
2098 2102 9.504708 TGAATATTTGCAAATCCTTGAACATTT 57.495 25.926 27.28 3.17 34.14 2.32
2099 2103 8.938906 GTGAATATTTGCAAATCCTTGAACATT 58.061 29.630 27.28 17.83 34.14 2.71
2100 2104 7.550196 GGTGAATATTTGCAAATCCTTGAACAT 59.450 33.333 27.28 10.57 34.14 2.71
2101 2105 6.873076 GGTGAATATTTGCAAATCCTTGAACA 59.127 34.615 27.28 15.23 34.14 3.18
2102 2106 6.873076 TGGTGAATATTTGCAAATCCTTGAAC 59.127 34.615 27.28 18.29 34.14 3.18
2103 2107 7.002250 TGGTGAATATTTGCAAATCCTTGAA 57.998 32.000 27.28 10.11 34.14 2.69
2104 2108 6.602410 TGGTGAATATTTGCAAATCCTTGA 57.398 33.333 27.28 13.87 34.14 3.02
2105 2109 6.875195 ACTTGGTGAATATTTGCAAATCCTTG 59.125 34.615 27.28 18.23 35.49 3.61
2106 2110 7.008021 ACTTGGTGAATATTTGCAAATCCTT 57.992 32.000 27.28 20.70 0.00 3.36
2107 2111 6.610075 ACTTGGTGAATATTTGCAAATCCT 57.390 33.333 27.28 15.75 0.00 3.24
2108 2112 8.947055 AATACTTGGTGAATATTTGCAAATCC 57.053 30.769 27.28 20.98 0.00 3.01


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

AutoCloner maintained by Alex Coulton.