Multiple sequence alignment - TraesCS5A01G421400

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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 TraesCS5A01G421400 chr5A 100.000 2162 0 0 1 2162 607273889 607276050 0.000000e+00 3993
1 TraesCS5A01G421400 chr5D 97.652 2002 46 1 1 2001 503217707 503219708 0.000000e+00 3435
2 TraesCS5A01G421400 chr5D 97.449 1999 50 1 4 2001 503278734 503276736 0.000000e+00 3408
3 TraesCS5A01G421400 chr5D 97.203 2002 55 1 1 2001 6188429 6190430 0.000000e+00 3386
4 TraesCS5A01G421400 chr3B 97.652 2002 46 1 1 2001 201526513 201528514 0.000000e+00 3435
5 TraesCS5A01G421400 chr1A 97.602 2002 47 1 1 2001 554511737 554513738 0.000000e+00 3430
6 TraesCS5A01G421400 chr6D 97.552 2002 48 1 1 2001 168254415 168256416 0.000000e+00 3424
7 TraesCS5A01G421400 chrUn 97.549 1999 47 2 4 2001 93410139 93408142 0.000000e+00 3419
8 TraesCS5A01G421400 chrUn 97.349 1999 51 2 4 2001 216519110 216517113 0.000000e+00 3397
9 TraesCS5A01G421400 chr3D 97.399 1999 48 3 4 2001 589280050 589278055 0.000000e+00 3400
10 TraesCS5A01G421400 chr3D 98.540 137 2 0 2004 2140 450237123 450237259 2.140000e-60 243
11 TraesCS5A01G421400 chr6A 99.270 137 1 0 2004 2140 437962162 437962026 4.610000e-62 248
12 TraesCS5A01G421400 chr7D 98.540 137 2 0 2004 2140 177571390 177571526 2.140000e-60 243
13 TraesCS5A01G421400 chr7A 98.540 137 2 0 2004 2140 220843855 220843719 2.140000e-60 243
14 TraesCS5A01G421400 chr7A 98.540 137 2 0 2004 2140 462018684 462018820 2.140000e-60 243
15 TraesCS5A01G421400 chr4B 98.540 137 2 0 2004 2140 355502995 355503131 2.140000e-60 243
16 TraesCS5A01G421400 chr4A 98.540 137 2 0 2004 2140 182790397 182790533 2.140000e-60 243
17 TraesCS5A01G421400 chr3A 98.540 137 2 0 2004 2140 674131602 674131466 2.140000e-60 243
18 TraesCS5A01G421400 chr2D 98.540 137 2 0 2004 2140 80625429 80625565 2.140000e-60 243


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 TraesCS5A01G421400 chr5A 607273889 607276050 2161 False 3993 3993 100.000 1 2162 1 chr5A.!!$F1 2161
1 TraesCS5A01G421400 chr5D 503217707 503219708 2001 False 3435 3435 97.652 1 2001 1 chr5D.!!$F2 2000
2 TraesCS5A01G421400 chr5D 503276736 503278734 1998 True 3408 3408 97.449 4 2001 1 chr5D.!!$R1 1997
3 TraesCS5A01G421400 chr5D 6188429 6190430 2001 False 3386 3386 97.203 1 2001 1 chr5D.!!$F1 2000
4 TraesCS5A01G421400 chr3B 201526513 201528514 2001 False 3435 3435 97.652 1 2001 1 chr3B.!!$F1 2000
5 TraesCS5A01G421400 chr1A 554511737 554513738 2001 False 3430 3430 97.602 1 2001 1 chr1A.!!$F1 2000
6 TraesCS5A01G421400 chr6D 168254415 168256416 2001 False 3424 3424 97.552 1 2001 1 chr6D.!!$F1 2000
7 TraesCS5A01G421400 chrUn 93408142 93410139 1997 True 3419 3419 97.549 4 2001 1 chrUn.!!$R1 1997
8 TraesCS5A01G421400 chrUn 216517113 216519110 1997 True 3397 3397 97.349 4 2001 1 chrUn.!!$R2 1997
9 TraesCS5A01G421400 chr3D 589278055 589280050 1995 True 3400 3400 97.399 4 2001 1 chr3D.!!$R1 1997

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
994 995 0.949582 ACCTCCCCCTCTATGCCTTA 59.05 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2126 0.105658 CCCGGGTGAGAAGGAGGATA 60.106 60.0 14.18 0.0 0.0 2.59 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
301 302 3.953542 TCTACATCCTAGGTCTCTGCA 57.046 47.619 9.08 0.00 0.00 4.41
311 312 1.556911 AGGTCTCTGCATTCCGTCATT 59.443 47.619 0.00 0.00 0.00 2.57
451 452 5.535753 ACCACTGCTTAGCTTTCAATTTT 57.464 34.783 5.60 0.00 0.00 1.82
943 944 6.659242 ACCAGATATGTCTTTTTGATTCCGTT 59.341 34.615 0.00 0.00 30.42 4.44
994 995 0.949582 ACCTCCCCCTCTATGCCTTA 59.050 55.000 0.00 0.00 0.00 2.69
1098 1099 0.108281 GCCTGTCTACGGTTCCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
1108 1109 1.070786 GTTCCCTTCCGTGTGCTCA 59.929 57.895 0.00 0.00 0.00 4.26
1109 1110 0.534203 GTTCCCTTCCGTGTGCTCAA 60.534 55.000 0.00 0.00 0.00 3.02
1291 1294 4.473196 TCCAGGTAGTCAATGGCTATTCAA 59.527 41.667 0.00 0.00 33.92 2.69
1338 1341 4.396166 AGAGTTCGACCCAATGCTTTATTG 59.604 41.667 0.00 0.00 44.67 1.90
1480 1483 3.701542 TGCTCTGAGTTCCAGTATCGATT 59.298 43.478 1.71 0.00 43.38 3.34
1848 1851 5.128499 TGAAAGAGAGATTGAGAGGGATCAC 59.872 44.000 0.00 0.00 0.00 3.06
2001 2004 7.998383 TGATACCTAGTTGGCATTGATAACAAT 59.002 33.333 0.00 0.00 42.07 2.71
2002 2005 9.502091 GATACCTAGTTGGCATTGATAACAATA 57.498 33.333 0.00 0.00 41.07 1.90
2003 2006 7.568199 ACCTAGTTGGCATTGATAACAATAC 57.432 36.000 0.00 0.00 41.07 1.89
2004 2007 6.546034 ACCTAGTTGGCATTGATAACAATACC 59.454 38.462 7.81 7.81 45.34 2.73
2005 2008 5.852282 AGTTGGCATTGATAACAATACCC 57.148 39.130 11.38 9.19 44.83 3.69
2006 2009 4.338118 AGTTGGCATTGATAACAATACCCG 59.662 41.667 11.38 0.00 44.83 5.28
2007 2010 3.892284 TGGCATTGATAACAATACCCGT 58.108 40.909 11.38 0.00 44.83 5.28
2008 2011 3.629855 TGGCATTGATAACAATACCCGTG 59.370 43.478 11.38 0.00 44.83 4.94
2009 2012 3.550030 GGCATTGATAACAATACCCGTGC 60.550 47.826 4.02 1.78 43.76 5.34
2010 2013 3.848191 GCATTGATAACAATACCCGTGCG 60.848 47.826 0.00 0.00 43.76 5.34
2011 2014 2.676632 TGATAACAATACCCGTGCGT 57.323 45.000 0.00 0.00 0.00 5.24
2012 2015 2.975266 TGATAACAATACCCGTGCGTT 58.025 42.857 0.00 0.00 0.00 4.84
2013 2016 2.673862 TGATAACAATACCCGTGCGTTG 59.326 45.455 0.00 0.00 0.00 4.10
2014 2017 0.797542 TAACAATACCCGTGCGTTGC 59.202 50.000 0.00 0.00 0.00 4.17
2015 2018 1.167155 AACAATACCCGTGCGTTGCA 61.167 50.000 0.00 0.00 35.60 4.08
2016 2019 1.167155 ACAATACCCGTGCGTTGCAA 61.167 50.000 0.00 0.00 41.47 4.08
2017 2020 0.727793 CAATACCCGTGCGTTGCAAC 60.728 55.000 19.89 19.89 41.47 4.17
2029 2032 2.401017 GTTGCAACGGGAGAGAAAAC 57.599 50.000 14.90 0.00 0.00 2.43
2030 2033 1.673920 GTTGCAACGGGAGAGAAAACA 59.326 47.619 14.90 0.00 0.00 2.83
2031 2034 2.270352 TGCAACGGGAGAGAAAACAT 57.730 45.000 0.00 0.00 0.00 2.71
2032 2035 3.410631 TGCAACGGGAGAGAAAACATA 57.589 42.857 0.00 0.00 0.00 2.29
2033 2036 3.745799 TGCAACGGGAGAGAAAACATAA 58.254 40.909 0.00 0.00 0.00 1.90
2034 2037 3.500680 TGCAACGGGAGAGAAAACATAAC 59.499 43.478 0.00 0.00 0.00 1.89
2035 2038 3.500680 GCAACGGGAGAGAAAACATAACA 59.499 43.478 0.00 0.00 0.00 2.41
2036 2039 4.612939 GCAACGGGAGAGAAAACATAACAC 60.613 45.833 0.00 0.00 0.00 3.32
2037 2040 4.345859 ACGGGAGAGAAAACATAACACA 57.654 40.909 0.00 0.00 0.00 3.72
2038 2041 4.062991 ACGGGAGAGAAAACATAACACAC 58.937 43.478 0.00 0.00 0.00 3.82
2039 2042 3.122948 CGGGAGAGAAAACATAACACACG 59.877 47.826 0.00 0.00 0.00 4.49
2040 2043 3.120304 GGGAGAGAAAACATAACACACGC 60.120 47.826 0.00 0.00 0.00 5.34
2041 2044 3.746492 GGAGAGAAAACATAACACACGCT 59.254 43.478 0.00 0.00 0.00 5.07
2042 2045 4.143094 GGAGAGAAAACATAACACACGCTC 60.143 45.833 0.00 0.00 0.00 5.03
2043 2046 4.632153 AGAGAAAACATAACACACGCTCT 58.368 39.130 0.00 0.00 0.00 4.09
2044 2047 5.057149 AGAGAAAACATAACACACGCTCTT 58.943 37.500 0.00 0.00 0.00 2.85
2045 2048 6.220930 AGAGAAAACATAACACACGCTCTTA 58.779 36.000 0.00 0.00 0.00 2.10
2046 2049 6.704493 AGAGAAAACATAACACACGCTCTTAA 59.296 34.615 0.00 0.00 0.00 1.85
2047 2050 6.656003 AGAAAACATAACACACGCTCTTAAC 58.344 36.000 0.00 0.00 0.00 2.01
2048 2051 6.482308 AGAAAACATAACACACGCTCTTAACT 59.518 34.615 0.00 0.00 0.00 2.24
2049 2052 5.840940 AACATAACACACGCTCTTAACTC 57.159 39.130 0.00 0.00 0.00 3.01
2050 2053 4.878439 ACATAACACACGCTCTTAACTCA 58.122 39.130 0.00 0.00 0.00 3.41
2051 2054 5.294356 ACATAACACACGCTCTTAACTCAA 58.706 37.500 0.00 0.00 0.00 3.02
2052 2055 5.176958 ACATAACACACGCTCTTAACTCAAC 59.823 40.000 0.00 0.00 0.00 3.18
2053 2056 3.173668 ACACACGCTCTTAACTCAACA 57.826 42.857 0.00 0.00 0.00 3.33
2054 2057 3.527533 ACACACGCTCTTAACTCAACAA 58.472 40.909 0.00 0.00 0.00 2.83
2055 2058 3.308866 ACACACGCTCTTAACTCAACAAC 59.691 43.478 0.00 0.00 0.00 3.32
2056 2059 2.870411 ACACGCTCTTAACTCAACAACC 59.130 45.455 0.00 0.00 0.00 3.77
2057 2060 2.869801 CACGCTCTTAACTCAACAACCA 59.130 45.455 0.00 0.00 0.00 3.67
2058 2061 3.498397 CACGCTCTTAACTCAACAACCAT 59.502 43.478 0.00 0.00 0.00 3.55
2059 2062 3.746492 ACGCTCTTAACTCAACAACCATC 59.254 43.478 0.00 0.00 0.00 3.51
2060 2063 3.745975 CGCTCTTAACTCAACAACCATCA 59.254 43.478 0.00 0.00 0.00 3.07
2061 2064 4.377431 CGCTCTTAACTCAACAACCATCAC 60.377 45.833 0.00 0.00 0.00 3.06
2062 2065 4.757149 GCTCTTAACTCAACAACCATCACT 59.243 41.667 0.00 0.00 0.00 3.41
2063 2066 5.106908 GCTCTTAACTCAACAACCATCACTC 60.107 44.000 0.00 0.00 0.00 3.51
2064 2067 5.924356 TCTTAACTCAACAACCATCACTCA 58.076 37.500 0.00 0.00 0.00 3.41
2065 2068 6.353323 TCTTAACTCAACAACCATCACTCAA 58.647 36.000 0.00 0.00 0.00 3.02
2066 2069 6.483307 TCTTAACTCAACAACCATCACTCAAG 59.517 38.462 0.00 0.00 0.00 3.02
2067 2070 4.422073 ACTCAACAACCATCACTCAAGA 57.578 40.909 0.00 0.00 0.00 3.02
2068 2071 4.130118 ACTCAACAACCATCACTCAAGAC 58.870 43.478 0.00 0.00 0.00 3.01
2069 2072 3.476552 TCAACAACCATCACTCAAGACC 58.523 45.455 0.00 0.00 0.00 3.85
2070 2073 3.118075 TCAACAACCATCACTCAAGACCA 60.118 43.478 0.00 0.00 0.00 4.02
2071 2074 2.851195 ACAACCATCACTCAAGACCAC 58.149 47.619 0.00 0.00 0.00 4.16
2072 2075 2.172505 ACAACCATCACTCAAGACCACA 59.827 45.455 0.00 0.00 0.00 4.17
2073 2076 3.213506 CAACCATCACTCAAGACCACAA 58.786 45.455 0.00 0.00 0.00 3.33
2074 2077 3.795688 ACCATCACTCAAGACCACAAT 57.204 42.857 0.00 0.00 0.00 2.71
2075 2078 4.908601 ACCATCACTCAAGACCACAATA 57.091 40.909 0.00 0.00 0.00 1.90
2076 2079 4.836825 ACCATCACTCAAGACCACAATAG 58.163 43.478 0.00 0.00 0.00 1.73
2077 2080 4.194640 CCATCACTCAAGACCACAATAGG 58.805 47.826 0.00 0.00 0.00 2.57
2078 2081 4.323792 CCATCACTCAAGACCACAATAGGT 60.324 45.833 0.00 0.00 46.82 3.08
2089 2092 5.520748 ACCACAATAGGTCCATCTTCTTT 57.479 39.130 0.00 0.00 37.28 2.52
2090 2093 5.256474 ACCACAATAGGTCCATCTTCTTTG 58.744 41.667 0.00 0.00 37.28 2.77
2091 2094 5.222130 ACCACAATAGGTCCATCTTCTTTGT 60.222 40.000 0.00 0.00 37.28 2.83
2092 2095 5.711976 CCACAATAGGTCCATCTTCTTTGTT 59.288 40.000 0.00 0.00 0.00 2.83
2093 2096 6.209391 CCACAATAGGTCCATCTTCTTTGTTT 59.791 38.462 0.00 0.00 0.00 2.83
2094 2097 7.255942 CCACAATAGGTCCATCTTCTTTGTTTT 60.256 37.037 0.00 0.00 0.00 2.43
2095 2098 8.143835 CACAATAGGTCCATCTTCTTTGTTTTT 58.856 33.333 0.00 0.00 0.00 1.94
2096 2099 8.143835 ACAATAGGTCCATCTTCTTTGTTTTTG 58.856 33.333 0.00 0.00 0.00 2.44
2097 2100 4.948847 AGGTCCATCTTCTTTGTTTTTGC 58.051 39.130 0.00 0.00 0.00 3.68
2098 2101 3.735746 GGTCCATCTTCTTTGTTTTTGCG 59.264 43.478 0.00 0.00 0.00 4.85
2099 2102 4.499019 GGTCCATCTTCTTTGTTTTTGCGA 60.499 41.667 0.00 0.00 0.00 5.10
2100 2103 4.676924 GTCCATCTTCTTTGTTTTTGCGAG 59.323 41.667 0.00 0.00 0.00 5.03
2101 2104 3.983344 CCATCTTCTTTGTTTTTGCGAGG 59.017 43.478 0.00 0.00 0.00 4.63
2102 2105 3.078594 TCTTCTTTGTTTTTGCGAGGC 57.921 42.857 0.00 0.00 0.00 4.70
2103 2106 2.425312 TCTTCTTTGTTTTTGCGAGGCA 59.575 40.909 0.00 0.00 36.47 4.75
2104 2107 3.068024 TCTTCTTTGTTTTTGCGAGGCAT 59.932 39.130 0.00 0.00 38.76 4.40
2105 2108 3.011949 TCTTTGTTTTTGCGAGGCATC 57.988 42.857 0.00 0.00 38.76 3.91
2106 2109 2.360483 TCTTTGTTTTTGCGAGGCATCA 59.640 40.909 0.00 0.00 38.76 3.07
2107 2110 3.005684 TCTTTGTTTTTGCGAGGCATCAT 59.994 39.130 0.00 0.00 38.76 2.45
2108 2111 4.217334 TCTTTGTTTTTGCGAGGCATCATA 59.783 37.500 0.00 0.00 38.76 2.15
2109 2112 4.717233 TTGTTTTTGCGAGGCATCATAT 57.283 36.364 0.00 0.00 38.76 1.78
2110 2113 4.717233 TGTTTTTGCGAGGCATCATATT 57.283 36.364 0.00 0.00 38.76 1.28
2111 2114 5.070770 TGTTTTTGCGAGGCATCATATTT 57.929 34.783 0.00 0.00 38.76 1.40
2112 2115 4.863689 TGTTTTTGCGAGGCATCATATTTG 59.136 37.500 0.00 0.00 38.76 2.32
2113 2116 4.717233 TTTTGCGAGGCATCATATTTGT 57.283 36.364 0.00 0.00 38.76 2.83
2114 2117 3.696281 TTGCGAGGCATCATATTTGTG 57.304 42.857 0.00 0.00 38.76 3.33
2115 2118 2.642427 TGCGAGGCATCATATTTGTGT 58.358 42.857 0.00 0.00 31.71 3.72
2116 2119 3.016031 TGCGAGGCATCATATTTGTGTT 58.984 40.909 0.00 0.00 31.71 3.32
2117 2120 3.181498 TGCGAGGCATCATATTTGTGTTG 60.181 43.478 0.00 0.00 31.71 3.33
2118 2121 3.365832 CGAGGCATCATATTTGTGTTGC 58.634 45.455 0.00 2.75 41.70 4.17
2121 2124 1.854126 GCATCATATTTGTGTTGCCGC 59.146 47.619 0.42 0.00 38.34 6.53
2122 2125 2.480073 GCATCATATTTGTGTTGCCGCT 60.480 45.455 0.00 0.00 38.34 5.52
2123 2126 3.772932 CATCATATTTGTGTTGCCGCTT 58.227 40.909 0.00 0.00 0.00 4.68
2124 2127 4.733230 GCATCATATTTGTGTTGCCGCTTA 60.733 41.667 0.00 0.00 38.34 3.09
2125 2128 5.522456 CATCATATTTGTGTTGCCGCTTAT 58.478 37.500 0.00 0.00 0.00 1.73
2126 2129 5.168526 TCATATTTGTGTTGCCGCTTATC 57.831 39.130 0.00 0.00 0.00 1.75
2127 2130 2.939460 ATTTGTGTTGCCGCTTATCC 57.061 45.000 0.00 0.00 0.00 2.59
2128 2131 1.904287 TTTGTGTTGCCGCTTATCCT 58.096 45.000 0.00 0.00 0.00 3.24
2129 2132 1.448985 TTGTGTTGCCGCTTATCCTC 58.551 50.000 0.00 0.00 0.00 3.71
2130 2133 0.392461 TGTGTTGCCGCTTATCCTCC 60.392 55.000 0.00 0.00 0.00 4.30
2131 2134 0.107654 GTGTTGCCGCTTATCCTCCT 60.108 55.000 0.00 0.00 0.00 3.69
2132 2135 0.618458 TGTTGCCGCTTATCCTCCTT 59.382 50.000 0.00 0.00 0.00 3.36
2133 2136 1.300481 GTTGCCGCTTATCCTCCTTC 58.700 55.000 0.00 0.00 0.00 3.46
2134 2137 1.134371 GTTGCCGCTTATCCTCCTTCT 60.134 52.381 0.00 0.00 0.00 2.85
2135 2138 0.753262 TGCCGCTTATCCTCCTTCTC 59.247 55.000 0.00 0.00 0.00 2.87
2136 2139 0.753262 GCCGCTTATCCTCCTTCTCA 59.247 55.000 0.00 0.00 0.00 3.27
2137 2140 1.539280 GCCGCTTATCCTCCTTCTCAC 60.539 57.143 0.00 0.00 0.00 3.51
2138 2141 1.069358 CCGCTTATCCTCCTTCTCACC 59.931 57.143 0.00 0.00 0.00 4.02
2139 2142 1.069358 CGCTTATCCTCCTTCTCACCC 59.931 57.143 0.00 0.00 0.00 4.61
2140 2143 1.069358 GCTTATCCTCCTTCTCACCCG 59.931 57.143 0.00 0.00 0.00 5.28
2141 2144 1.689273 CTTATCCTCCTTCTCACCCGG 59.311 57.143 0.00 0.00 0.00 5.73
2142 2145 0.105658 TATCCTCCTTCTCACCCGGG 60.106 60.000 22.25 22.25 0.00 5.73
2143 2146 1.886730 ATCCTCCTTCTCACCCGGGA 61.887 60.000 32.02 4.01 0.00 5.14
2144 2147 1.612442 CCTCCTTCTCACCCGGGAA 60.612 63.158 32.02 14.33 0.00 3.97
2145 2148 0.983378 CCTCCTTCTCACCCGGGAAT 60.983 60.000 32.02 1.07 0.00 3.01
2146 2149 0.179000 CTCCTTCTCACCCGGGAATG 59.821 60.000 32.02 17.29 0.00 2.67
2147 2150 0.546747 TCCTTCTCACCCGGGAATGT 60.547 55.000 32.02 0.00 0.00 2.71
2148 2151 1.200519 CCTTCTCACCCGGGAATGTA 58.799 55.000 32.02 8.41 0.00 2.29
2149 2152 1.768870 CCTTCTCACCCGGGAATGTAT 59.231 52.381 32.02 0.00 0.00 2.29
2150 2153 2.224305 CCTTCTCACCCGGGAATGTATC 60.224 54.545 32.02 0.00 0.00 2.24
2160 2163 1.680338 GGAATGTATCCTGTGCACCC 58.320 55.000 15.69 0.00 45.56 4.61
2161 2164 1.299541 GAATGTATCCTGTGCACCCG 58.700 55.000 15.69 5.26 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 5.630121 AGATCCATCTGTCTAGAGATCGTT 58.370 41.667 10.21 0.00 38.60 3.85
301 302 4.949856 AGAACATAAGCCAAATGACGGAAT 59.050 37.500 0.00 0.00 0.00 3.01
311 312 5.252547 TGCTACATGAAGAACATAAGCCAA 58.747 37.500 0.00 0.00 41.98 4.52
451 452 7.174413 TCACATTTAATTTGATGGTCAGAGGA 58.826 34.615 5.92 0.00 0.00 3.71
482 483 4.982241 TGTTTCAAAGAGAGGAGGACAT 57.018 40.909 0.00 0.00 0.00 3.06
483 484 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.00 0.00 4.02
649 650 5.655090 TGATCCAATTTGACTACCTCTACGA 59.345 40.000 0.00 0.00 0.00 3.43
725 726 9.739276 TGAGTGAGGTTTGAACTATTGATTTAT 57.261 29.630 0.00 0.00 0.00 1.40
745 746 3.561313 GGAAATGCCCTACCTTTGAGTGA 60.561 47.826 0.00 0.00 0.00 3.41
819 820 7.856415 AGAGATATATTTTACATCCCAGAGGC 58.144 38.462 0.00 0.00 0.00 4.70
943 944 8.770828 GCGCCTATACTGTAAAATAGATTTTCA 58.229 33.333 0.00 2.75 40.24 2.69
959 960 2.826725 GGAGGTCATAAGCGCCTATACT 59.173 50.000 2.29 0.00 39.49 2.12
1098 1099 1.066858 ACACCTATCTTGAGCACACGG 60.067 52.381 0.00 0.00 0.00 4.94
1166 1167 8.927675 TTCTATTCCACTTCTAGATAGAGGAC 57.072 38.462 15.45 0.00 34.00 3.85
1195 1196 2.574369 TGATCATTACCCTTCAACCGGT 59.426 45.455 0.00 0.00 36.08 5.28
1279 1282 3.954258 GGTGGTAGCTTTGAATAGCCATT 59.046 43.478 0.00 0.00 42.20 3.16
1291 1294 3.868619 TTGGTGTTAAGGTGGTAGCTT 57.131 42.857 0.00 0.00 39.52 3.74
1338 1341 2.961526 TCGGGATTCACTAAGACAGC 57.038 50.000 0.00 0.00 0.00 4.40
1525 1528 9.739276 ATCATCCATACATAACGAATTGGTATT 57.261 29.630 0.00 0.00 0.00 1.89
1605 1608 3.654201 GCTGGATGCACACGAACA 58.346 55.556 0.00 0.00 42.31 3.18
1751 1754 7.534239 GCCATCTCGGAATATTTTCGATTTAAC 59.466 37.037 12.88 3.62 36.56 2.01
1753 1756 6.708502 TGCCATCTCGGAATATTTTCGATTTA 59.291 34.615 12.88 5.46 36.56 1.40
1848 1851 5.926542 TCCAAATAGCGAGAATTAGGATTCG 59.073 40.000 0.00 0.00 45.10 3.34
1901 1904 9.155975 TCTTTGCTAAAGAGAAATGATCACTAC 57.844 33.333 0.00 0.00 42.31 2.73
2001 2004 3.339464 CGTTGCAACGCACGGGTA 61.339 61.111 35.89 0.00 46.06 3.69
2010 2013 1.673920 TGTTTTCTCTCCCGTTGCAAC 59.326 47.619 19.89 19.89 0.00 4.17
2011 2014 2.045561 TGTTTTCTCTCCCGTTGCAA 57.954 45.000 0.00 0.00 0.00 4.08
2012 2015 2.270352 ATGTTTTCTCTCCCGTTGCA 57.730 45.000 0.00 0.00 0.00 4.08
2013 2016 3.500680 TGTTATGTTTTCTCTCCCGTTGC 59.499 43.478 0.00 0.00 0.00 4.17
2014 2017 4.513692 TGTGTTATGTTTTCTCTCCCGTTG 59.486 41.667 0.00 0.00 0.00 4.10
2015 2018 4.514066 GTGTGTTATGTTTTCTCTCCCGTT 59.486 41.667 0.00 0.00 0.00 4.44
2016 2019 4.062991 GTGTGTTATGTTTTCTCTCCCGT 58.937 43.478 0.00 0.00 0.00 5.28
2017 2020 3.122948 CGTGTGTTATGTTTTCTCTCCCG 59.877 47.826 0.00 0.00 0.00 5.14
2018 2021 3.120304 GCGTGTGTTATGTTTTCTCTCCC 60.120 47.826 0.00 0.00 0.00 4.30
2019 2022 3.746492 AGCGTGTGTTATGTTTTCTCTCC 59.254 43.478 0.00 0.00 0.00 3.71
2020 2023 4.686554 AGAGCGTGTGTTATGTTTTCTCTC 59.313 41.667 0.00 0.00 0.00 3.20
2021 2024 4.632153 AGAGCGTGTGTTATGTTTTCTCT 58.368 39.130 0.00 0.00 0.00 3.10
2022 2025 4.992381 AGAGCGTGTGTTATGTTTTCTC 57.008 40.909 0.00 0.00 0.00 2.87
2023 2026 6.482308 AGTTAAGAGCGTGTGTTATGTTTTCT 59.518 34.615 0.00 0.00 0.00 2.52
2024 2027 6.656003 AGTTAAGAGCGTGTGTTATGTTTTC 58.344 36.000 0.00 0.00 0.00 2.29
2025 2028 6.259167 TGAGTTAAGAGCGTGTGTTATGTTTT 59.741 34.615 0.00 0.00 0.00 2.43
2026 2029 5.756347 TGAGTTAAGAGCGTGTGTTATGTTT 59.244 36.000 0.00 0.00 0.00 2.83
2027 2030 5.294356 TGAGTTAAGAGCGTGTGTTATGTT 58.706 37.500 0.00 0.00 0.00 2.71
2028 2031 4.878439 TGAGTTAAGAGCGTGTGTTATGT 58.122 39.130 0.00 0.00 0.00 2.29
2029 2032 5.176774 TGTTGAGTTAAGAGCGTGTGTTATG 59.823 40.000 0.00 0.00 0.00 1.90
2030 2033 5.294356 TGTTGAGTTAAGAGCGTGTGTTAT 58.706 37.500 0.00 0.00 0.00 1.89
2031 2034 4.684877 TGTTGAGTTAAGAGCGTGTGTTA 58.315 39.130 0.00 0.00 0.00 2.41
2032 2035 3.527533 TGTTGAGTTAAGAGCGTGTGTT 58.472 40.909 0.00 0.00 0.00 3.32
2033 2036 3.173668 TGTTGAGTTAAGAGCGTGTGT 57.826 42.857 0.00 0.00 0.00 3.72
2034 2037 3.303132 GGTTGTTGAGTTAAGAGCGTGTG 60.303 47.826 0.00 0.00 0.00 3.82
2035 2038 2.870411 GGTTGTTGAGTTAAGAGCGTGT 59.130 45.455 0.00 0.00 0.00 4.49
2036 2039 2.869801 TGGTTGTTGAGTTAAGAGCGTG 59.130 45.455 0.00 0.00 0.00 5.34
2037 2040 3.188159 TGGTTGTTGAGTTAAGAGCGT 57.812 42.857 0.00 0.00 0.00 5.07
2038 2041 3.745975 TGATGGTTGTTGAGTTAAGAGCG 59.254 43.478 0.00 0.00 0.00 5.03
2039 2042 4.757149 AGTGATGGTTGTTGAGTTAAGAGC 59.243 41.667 0.00 0.00 0.00 4.09
2040 2043 5.991606 TGAGTGATGGTTGTTGAGTTAAGAG 59.008 40.000 0.00 0.00 0.00 2.85
2041 2044 5.924356 TGAGTGATGGTTGTTGAGTTAAGA 58.076 37.500 0.00 0.00 0.00 2.10
2042 2045 6.483307 TCTTGAGTGATGGTTGTTGAGTTAAG 59.517 38.462 0.00 0.00 0.00 1.85
2043 2046 6.260050 GTCTTGAGTGATGGTTGTTGAGTTAA 59.740 38.462 0.00 0.00 0.00 2.01
2044 2047 5.758296 GTCTTGAGTGATGGTTGTTGAGTTA 59.242 40.000 0.00 0.00 0.00 2.24
2045 2048 4.576463 GTCTTGAGTGATGGTTGTTGAGTT 59.424 41.667 0.00 0.00 0.00 3.01
2046 2049 4.130118 GTCTTGAGTGATGGTTGTTGAGT 58.870 43.478 0.00 0.00 0.00 3.41
2047 2050 3.499918 GGTCTTGAGTGATGGTTGTTGAG 59.500 47.826 0.00 0.00 0.00 3.02
2048 2051 3.118075 TGGTCTTGAGTGATGGTTGTTGA 60.118 43.478 0.00 0.00 0.00 3.18
2049 2052 3.003689 GTGGTCTTGAGTGATGGTTGTTG 59.996 47.826 0.00 0.00 0.00 3.33
2050 2053 3.214328 GTGGTCTTGAGTGATGGTTGTT 58.786 45.455 0.00 0.00 0.00 2.83
2051 2054 2.172505 TGTGGTCTTGAGTGATGGTTGT 59.827 45.455 0.00 0.00 0.00 3.32
2052 2055 2.849942 TGTGGTCTTGAGTGATGGTTG 58.150 47.619 0.00 0.00 0.00 3.77
2053 2056 3.576078 TTGTGGTCTTGAGTGATGGTT 57.424 42.857 0.00 0.00 0.00 3.67
2054 2057 3.795688 ATTGTGGTCTTGAGTGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
2055 2058 4.194640 CCTATTGTGGTCTTGAGTGATGG 58.805 47.826 0.00 0.00 0.00 3.51
2056 2059 4.836825 ACCTATTGTGGTCTTGAGTGATG 58.163 43.478 0.00 0.00 34.86 3.07
2067 2070 5.222130 ACAAAGAAGATGGACCTATTGTGGT 60.222 40.000 0.00 0.00 44.10 4.16
2068 2071 5.256474 ACAAAGAAGATGGACCTATTGTGG 58.744 41.667 0.00 0.00 0.00 4.17
2069 2072 6.824305 AACAAAGAAGATGGACCTATTGTG 57.176 37.500 0.00 0.00 0.00 3.33
2070 2073 7.839680 AAAACAAAGAAGATGGACCTATTGT 57.160 32.000 0.00 0.00 0.00 2.71
2071 2074 7.116805 GCAAAAACAAAGAAGATGGACCTATTG 59.883 37.037 0.00 0.00 0.00 1.90
2072 2075 7.154656 GCAAAAACAAAGAAGATGGACCTATT 58.845 34.615 0.00 0.00 0.00 1.73
2073 2076 6.570378 CGCAAAAACAAAGAAGATGGACCTAT 60.570 38.462 0.00 0.00 0.00 2.57
2074 2077 5.278266 CGCAAAAACAAAGAAGATGGACCTA 60.278 40.000 0.00 0.00 0.00 3.08
2075 2078 4.499696 CGCAAAAACAAAGAAGATGGACCT 60.500 41.667 0.00 0.00 0.00 3.85
2076 2079 3.735746 CGCAAAAACAAAGAAGATGGACC 59.264 43.478 0.00 0.00 0.00 4.46
2077 2080 4.606961 TCGCAAAAACAAAGAAGATGGAC 58.393 39.130 0.00 0.00 0.00 4.02
2078 2081 4.261572 CCTCGCAAAAACAAAGAAGATGGA 60.262 41.667 0.00 0.00 0.00 3.41
2079 2082 3.983344 CCTCGCAAAAACAAAGAAGATGG 59.017 43.478 0.00 0.00 0.00 3.51
2080 2083 3.426525 GCCTCGCAAAAACAAAGAAGATG 59.573 43.478 0.00 0.00 0.00 2.90
2081 2084 3.068024 TGCCTCGCAAAAACAAAGAAGAT 59.932 39.130 0.00 0.00 34.76 2.40
2082 2085 2.425312 TGCCTCGCAAAAACAAAGAAGA 59.575 40.909 0.00 0.00 34.76 2.87
2083 2086 2.808244 TGCCTCGCAAAAACAAAGAAG 58.192 42.857 0.00 0.00 34.76 2.85
2084 2087 2.949451 TGCCTCGCAAAAACAAAGAA 57.051 40.000 0.00 0.00 34.76 2.52
2085 2088 2.360483 TGATGCCTCGCAAAAACAAAGA 59.640 40.909 0.00 0.00 43.62 2.52
2086 2089 2.741612 TGATGCCTCGCAAAAACAAAG 58.258 42.857 0.00 0.00 43.62 2.77
2087 2090 2.879002 TGATGCCTCGCAAAAACAAA 57.121 40.000 0.00 0.00 43.62 2.83
2088 2091 4.717233 ATATGATGCCTCGCAAAAACAA 57.283 36.364 0.00 0.00 43.62 2.83
2089 2092 4.717233 AATATGATGCCTCGCAAAAACA 57.283 36.364 0.00 0.00 43.62 2.83
2090 2093 4.864247 ACAAATATGATGCCTCGCAAAAAC 59.136 37.500 0.00 0.00 43.62 2.43
2091 2094 4.863689 CACAAATATGATGCCTCGCAAAAA 59.136 37.500 0.00 0.00 43.62 1.94
2092 2095 4.082300 ACACAAATATGATGCCTCGCAAAA 60.082 37.500 0.00 0.00 43.62 2.44
2093 2096 3.443329 ACACAAATATGATGCCTCGCAAA 59.557 39.130 0.00 0.00 43.62 3.68
2094 2097 3.016031 ACACAAATATGATGCCTCGCAA 58.984 40.909 0.00 0.00 43.62 4.85
2095 2098 2.642427 ACACAAATATGATGCCTCGCA 58.358 42.857 0.00 0.00 44.86 5.10
2096 2099 3.365832 CAACACAAATATGATGCCTCGC 58.634 45.455 0.00 0.00 0.00 5.03
2097 2100 3.365832 GCAACACAAATATGATGCCTCG 58.634 45.455 0.00 0.00 32.22 4.63
2098 2101 3.709987 GGCAACACAAATATGATGCCTC 58.290 45.455 17.01 0.00 43.92 4.70
2099 2102 2.099592 CGGCAACACAAATATGATGCCT 59.900 45.455 20.40 0.00 44.49 4.75
2100 2103 2.462889 CGGCAACACAAATATGATGCC 58.537 47.619 14.96 14.96 43.88 4.40
2101 2104 1.854126 GCGGCAACACAAATATGATGC 59.146 47.619 0.00 0.00 35.20 3.91
2102 2105 3.425577 AGCGGCAACACAAATATGATG 57.574 42.857 1.45 0.00 0.00 3.07
2103 2106 5.278463 GGATAAGCGGCAACACAAATATGAT 60.278 40.000 1.45 0.00 0.00 2.45
2104 2107 4.036262 GGATAAGCGGCAACACAAATATGA 59.964 41.667 1.45 0.00 0.00 2.15
2105 2108 4.036734 AGGATAAGCGGCAACACAAATATG 59.963 41.667 1.45 0.00 0.00 1.78
2106 2109 4.207165 AGGATAAGCGGCAACACAAATAT 58.793 39.130 1.45 0.00 0.00 1.28
2107 2110 3.616219 AGGATAAGCGGCAACACAAATA 58.384 40.909 1.45 0.00 0.00 1.40
2108 2111 2.423538 GAGGATAAGCGGCAACACAAAT 59.576 45.455 1.45 0.00 0.00 2.32
2109 2112 1.810151 GAGGATAAGCGGCAACACAAA 59.190 47.619 1.45 0.00 0.00 2.83
2110 2113 1.448985 GAGGATAAGCGGCAACACAA 58.551 50.000 1.45 0.00 0.00 3.33
2111 2114 0.392461 GGAGGATAAGCGGCAACACA 60.392 55.000 1.45 0.00 0.00 3.72
2112 2115 0.107654 AGGAGGATAAGCGGCAACAC 60.108 55.000 1.45 0.00 0.00 3.32
2113 2116 0.618458 AAGGAGGATAAGCGGCAACA 59.382 50.000 1.45 0.00 0.00 3.33
2114 2117 1.134371 AGAAGGAGGATAAGCGGCAAC 60.134 52.381 1.45 0.00 0.00 4.17
2115 2118 1.139058 GAGAAGGAGGATAAGCGGCAA 59.861 52.381 1.45 0.00 0.00 4.52
2116 2119 0.753262 GAGAAGGAGGATAAGCGGCA 59.247 55.000 1.45 0.00 0.00 5.69
2117 2120 0.753262 TGAGAAGGAGGATAAGCGGC 59.247 55.000 0.00 0.00 0.00 6.53
2118 2121 1.069358 GGTGAGAAGGAGGATAAGCGG 59.931 57.143 0.00 0.00 0.00 5.52
2119 2122 1.069358 GGGTGAGAAGGAGGATAAGCG 59.931 57.143 0.00 0.00 0.00 4.68
2120 2123 1.069358 CGGGTGAGAAGGAGGATAAGC 59.931 57.143 0.00 0.00 0.00 3.09
2121 2124 1.689273 CCGGGTGAGAAGGAGGATAAG 59.311 57.143 0.00 0.00 0.00 1.73
2122 2125 1.691482 CCCGGGTGAGAAGGAGGATAA 60.691 57.143 14.18 0.00 0.00 1.75
2123 2126 0.105658 CCCGGGTGAGAAGGAGGATA 60.106 60.000 14.18 0.00 0.00 2.59
2124 2127 1.383248 CCCGGGTGAGAAGGAGGAT 60.383 63.158 14.18 0.00 0.00 3.24
2125 2128 2.038975 CCCGGGTGAGAAGGAGGA 59.961 66.667 14.18 0.00 0.00 3.71
2126 2129 0.983378 ATTCCCGGGTGAGAAGGAGG 60.983 60.000 22.86 0.00 0.00 4.30
2127 2130 0.179000 CATTCCCGGGTGAGAAGGAG 59.821 60.000 22.86 0.00 0.00 3.69
2128 2131 0.546747 ACATTCCCGGGTGAGAAGGA 60.547 55.000 22.86 0.00 0.00 3.36
2129 2132 1.200519 TACATTCCCGGGTGAGAAGG 58.799 55.000 22.86 11.81 0.00 3.46
2130 2133 2.224305 GGATACATTCCCGGGTGAGAAG 60.224 54.545 22.86 8.42 38.75 2.85
2131 2134 1.766496 GGATACATTCCCGGGTGAGAA 59.234 52.381 22.86 7.75 38.75 2.87
2132 2135 1.062428 AGGATACATTCCCGGGTGAGA 60.062 52.381 22.86 6.65 46.81 3.27
2133 2136 1.070758 CAGGATACATTCCCGGGTGAG 59.929 57.143 22.86 13.71 46.81 3.51
2134 2137 1.128200 CAGGATACATTCCCGGGTGA 58.872 55.000 22.86 11.42 46.81 4.02
2135 2138 0.837272 ACAGGATACATTCCCGGGTG 59.163 55.000 22.86 15.59 46.81 4.61
2136 2139 0.837272 CACAGGATACATTCCCGGGT 59.163 55.000 22.86 2.78 46.81 5.28
2137 2140 0.535102 GCACAGGATACATTCCCGGG 60.535 60.000 16.85 16.85 46.81 5.73
2138 2141 0.180171 TGCACAGGATACATTCCCGG 59.820 55.000 0.00 0.00 46.81 5.73
2139 2142 1.299541 GTGCACAGGATACATTCCCG 58.700 55.000 13.17 0.00 46.81 5.14
2140 2143 1.680338 GGTGCACAGGATACATTCCC 58.320 55.000 20.43 0.00 46.81 3.97
2141 2144 1.680338 GGGTGCACAGGATACATTCC 58.320 55.000 20.43 2.18 45.85 3.01
2142 2145 1.299541 CGGGTGCACAGGATACATTC 58.700 55.000 20.43 0.00 41.41 2.67
2143 2146 3.476740 CGGGTGCACAGGATACATT 57.523 52.632 20.43 0.00 41.41 2.71


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

AutoCloner maintained by Alex Coulton.