Multiple sequence alignment - TraesCS5D01G407700

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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 TraesCS5D01G407700 chr5D 100.000 6287 0 0 1 6287 472640924 472634638 0.000000e+00 11611
1 TraesCS5D01G407700 chr5B 95.928 4985 138 23 527 5464 580087444 580082478 0.000000e+00 8021
2 TraesCS5D01G407700 chr5B 85.360 403 34 17 5888 6274 580082167 580081774 1.640000e-105 394
3 TraesCS5D01G407700 chr5B 85.285 333 13 9 5499 5825 580082477 580082175 1.700000e-80 311
4 TraesCS5D01G407700 chr5B 97.692 130 3 0 358 487 580087570 580087441 2.280000e-54 224
5 TraesCS5D01G407700 chr5B 82.938 211 20 7 163 362 580087823 580087618 6.480000e-40 176
6 TraesCS5D01G407700 chr5A 94.866 2084 85 11 817 2897 592280787 592278723 0.000000e+00 3236
7 TraesCS5D01G407700 chr5A 90.977 1197 65 20 4647 5825 592277187 592276016 0.000000e+00 1572
8 TraesCS5D01G407700 chr5A 92.375 1036 64 10 3595 4624 592278206 592277180 0.000000e+00 1461
9 TraesCS5D01G407700 chr5A 89.730 779 40 17 44 816 592281561 592280817 0.000000e+00 959
10 TraesCS5D01G407700 chr5A 95.110 409 18 2 3167 3573 592278668 592278260 1.480000e-180 643
11 TraesCS5D01G407700 chr5A 83.988 331 17 11 5888 6190 592276008 592275686 1.030000e-72 285
12 TraesCS5D01G407700 chr6D 83.333 84 11 3 5573 5655 439799912 439799993 2.430000e-09 75


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 TraesCS5D01G407700 chr5D 472634638 472640924 6286 True 11611.000000 11611 100.000000 1 6287 1 chr5D.!!$R1 6286
1 TraesCS5D01G407700 chr5B 580081774 580087823 6049 True 1825.200000 8021 89.440600 163 6274 5 chr5B.!!$R1 6111
2 TraesCS5D01G407700 chr5A 592275686 592281561 5875 True 1359.333333 3236 91.174333 44 6190 6 chr5A.!!$R1 6146

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
649 722 0.034574 TCAAACACCACTGGCACTGT 60.035 50.000 0.00 0.00 42.57 3.55 F
1161 1270 0.034337 ACTTCGGCGGCACTTTCTTA 59.966 50.000 10.53 0.00 0.00 2.10 F
2054 2163 0.105039 GAATCCACTAGTCCTGGCGG 59.895 60.000 0.00 0.00 0.00 6.13 F
2995 3106 2.100749 CACGCCTCCACATGATGTAGTA 59.899 50.000 0.00 0.00 0.00 1.82 F
4022 4169 0.461548 GACATGCTCATCGGGAGTGA 59.538 55.000 0.00 0.00 45.88 3.41 F
4666 4815 3.648067 TCTCTGAACTTCCATGGTTCTGT 59.352 43.478 12.58 3.86 42.27 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2205 0.242825 CTGGATGCTGTTGGTTGCAG 59.757 55.000 0.00 0.00 42.74 4.41 R
2995 3106 0.612732 TGGATCCGTACGTGGTCCTT 60.613 55.000 26.16 2.63 33.17 3.36 R
3853 3998 2.742053 TCTTCGCAATTTGTAGCACCTC 59.258 45.455 0.00 0.00 0.00 3.85 R
4990 5154 0.965866 GCCCAGGTCCCTAAACTTGC 60.966 60.000 0.00 0.00 0.00 4.01 R
5018 5182 1.143073 ACTGGGTTCCCTGAACTTGAC 59.857 52.381 19.15 0.00 41.70 3.18 R
5952 6133 1.202973 CGCATACGAGCAGGAGAACG 61.203 60.000 0.00 0.00 43.93 3.95 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
37 38 9.942850 AAAAATATTTACATTTGGGAACAGAGG 57.057 29.630 0.01 0.00 44.54 3.69
38 39 8.893563 AAATATTTACATTTGGGAACAGAGGA 57.106 30.769 0.00 0.00 44.54 3.71
39 40 8.525290 AATATTTACATTTGGGAACAGAGGAG 57.475 34.615 0.00 0.00 44.54 3.69
40 41 4.993705 TTACATTTGGGAACAGAGGAGT 57.006 40.909 0.00 0.00 44.54 3.85
41 42 6.442541 TTTACATTTGGGAACAGAGGAGTA 57.557 37.500 0.00 0.00 44.54 2.59
42 43 4.559862 ACATTTGGGAACAGAGGAGTAG 57.440 45.455 0.00 0.00 44.54 2.57
49 50 5.450453 TGGGAACAGAGGAGTAGAAGATAG 58.550 45.833 0.00 0.00 35.01 2.08
55 56 5.717178 ACAGAGGAGTAGAAGATAGCACAAA 59.283 40.000 0.00 0.00 0.00 2.83
77 78 7.228706 ACAAACGATACAAAAGTGAAAGGAGAT 59.771 33.333 0.00 0.00 0.00 2.75
78 79 7.745620 AACGATACAAAAGTGAAAGGAGATT 57.254 32.000 0.00 0.00 0.00 2.40
82 83 9.543018 CGATACAAAAGTGAAAGGAGATTAAAC 57.457 33.333 0.00 0.00 0.00 2.01
86 87 8.895737 ACAAAAGTGAAAGGAGATTAAACGTTA 58.104 29.630 0.00 0.00 0.00 3.18
92 93 8.771766 GTGAAAGGAGATTAAACGTTAAGACTT 58.228 33.333 0.00 0.00 0.00 3.01
122 124 5.505181 AAAGTCATAGGTCAACCAGTCAT 57.495 39.130 1.33 0.00 38.89 3.06
124 126 5.599999 AGTCATAGGTCAACCAGTCATAC 57.400 43.478 1.33 0.00 38.89 2.39
125 127 4.098044 AGTCATAGGTCAACCAGTCATACG 59.902 45.833 1.33 0.00 38.89 3.06
126 128 4.021229 TCATAGGTCAACCAGTCATACGT 58.979 43.478 1.33 0.00 38.89 3.57
127 129 5.066893 GTCATAGGTCAACCAGTCATACGTA 59.933 44.000 0.00 0.00 38.89 3.57
128 130 5.653330 TCATAGGTCAACCAGTCATACGTAA 59.347 40.000 0.00 0.00 38.89 3.18
129 131 4.451629 AGGTCAACCAGTCATACGTAAG 57.548 45.455 0.00 0.00 40.92 2.34
130 132 2.928116 GGTCAACCAGTCATACGTAAGC 59.072 50.000 0.00 0.00 36.98 3.09
131 133 3.368116 GGTCAACCAGTCATACGTAAGCT 60.368 47.826 0.00 0.00 36.98 3.74
132 134 4.243270 GTCAACCAGTCATACGTAAGCTT 58.757 43.478 3.48 3.48 45.62 3.74
133 135 4.689345 GTCAACCAGTCATACGTAAGCTTT 59.311 41.667 3.20 0.00 45.62 3.51
134 136 5.865552 GTCAACCAGTCATACGTAAGCTTTA 59.134 40.000 3.20 0.00 45.62 1.85
135 137 6.534079 GTCAACCAGTCATACGTAAGCTTTAT 59.466 38.462 3.20 0.00 45.62 1.40
136 138 6.755141 TCAACCAGTCATACGTAAGCTTTATC 59.245 38.462 3.20 0.00 45.62 1.75
161 163 3.562182 ACCTGGGAAAGAAACGTTCAAT 58.438 40.909 0.00 0.00 0.00 2.57
187 189 6.554334 TTCTGCAGTAGTACCATTTTCAAC 57.446 37.500 14.67 0.00 0.00 3.18
188 190 5.001232 TCTGCAGTAGTACCATTTTCAACC 58.999 41.667 14.67 0.00 0.00 3.77
190 192 5.381757 TGCAGTAGTACCATTTTCAACCTT 58.618 37.500 0.00 0.00 0.00 3.50
191 193 6.535540 TGCAGTAGTACCATTTTCAACCTTA 58.464 36.000 0.00 0.00 0.00 2.69
192 194 6.653320 TGCAGTAGTACCATTTTCAACCTTAG 59.347 38.462 0.00 0.00 0.00 2.18
193 195 6.877322 GCAGTAGTACCATTTTCAACCTTAGA 59.123 38.462 0.00 0.00 0.00 2.10
194 196 7.553044 GCAGTAGTACCATTTTCAACCTTAGAT 59.447 37.037 0.00 0.00 0.00 1.98
221 223 0.172578 CCAATGCATGACAGCCACTG 59.827 55.000 0.00 0.00 37.52 3.66
299 314 1.498865 AAGTTTCAGCAGTGACGGCG 61.499 55.000 4.80 4.80 36.08 6.46
316 331 2.477863 CGGCGCCCATTTTAAAGAAGAG 60.478 50.000 23.46 0.00 0.00 2.85
317 332 2.752903 GGCGCCCATTTTAAAGAAGAGA 59.247 45.455 18.11 0.00 0.00 3.10
649 722 0.034574 TCAAACACCACTGGCACTGT 60.035 50.000 0.00 0.00 42.57 3.55
765 839 6.369629 TCAATTGTGGGTTCCTTTTCTCTTA 58.630 36.000 5.13 0.00 0.00 2.10
771 845 5.048643 GTGGGTTCCTTTTCTCTTAAGCTTC 60.049 44.000 0.00 0.00 0.00 3.86
776 850 7.608376 GGTTCCTTTTCTCTTAAGCTTCTGTAT 59.392 37.037 0.00 0.00 0.00 2.29
777 851 9.654663 GTTCCTTTTCTCTTAAGCTTCTGTATA 57.345 33.333 0.00 0.00 0.00 1.47
804 878 9.726438 ATCTTTGTATGTCTTAGTTTTAGCTGT 57.274 29.630 0.00 0.00 0.00 4.40
813 887 8.150945 TGTCTTAGTTTTAGCTGTCTCAGATTT 58.849 33.333 0.00 0.00 32.44 2.17
848 951 7.451732 TGACAGACTGTATATCCTAGGTCTAC 58.548 42.308 8.41 9.48 33.50 2.59
857 960 9.352191 TGTATATCCTAGGTCTACAAAGTTCTC 57.648 37.037 9.08 0.00 0.00 2.87
867 970 8.537858 AGGTCTACAAAGTTCTCGGTAAAATAT 58.462 33.333 0.00 0.00 0.00 1.28
906 1009 3.194062 GAGCTAGTTCTGACAGATTGGC 58.806 50.000 5.87 11.19 0.00 4.52
1111 1220 3.502979 GCTCCCTCGAGATTACTACGATT 59.497 47.826 15.71 0.00 38.52 3.34
1161 1270 0.034337 ACTTCGGCGGCACTTTCTTA 59.966 50.000 10.53 0.00 0.00 2.10
1219 1328 2.681848 GGTGACAGGCATCTGATGAAAG 59.318 50.000 21.30 11.12 43.49 2.62
1305 1414 1.753073 ACGATAAAGTACCACCTCCCG 59.247 52.381 0.00 0.00 0.00 5.14
1470 1579 1.262417 TCGTGGTACAAGGCTCATCA 58.738 50.000 0.00 0.00 44.16 3.07
1649 1758 1.055040 ACAGAGGAAGCTTCAGTGCT 58.945 50.000 27.02 15.00 46.40 4.40
1754 1863 2.167281 AGAGACGGATGATCAACCAGTG 59.833 50.000 20.74 8.11 0.00 3.66
1781 1890 2.567615 AGGCACAAGGTAACGAAGAGAT 59.432 45.455 0.00 0.00 46.39 2.75
1968 2077 3.545481 GTGACGACGCAGCCATCG 61.545 66.667 11.32 11.32 43.97 3.84
1982 2091 3.806521 CAGCCATCGAATTCACTAAGGAG 59.193 47.826 6.22 0.00 0.00 3.69
2011 2120 1.388065 TTTCCAACCGCACAACAGGG 61.388 55.000 0.00 0.00 0.00 4.45
2052 2161 2.435805 TCATGAATCCACTAGTCCTGGC 59.564 50.000 0.00 0.00 0.00 4.85
2053 2162 0.824109 TGAATCCACTAGTCCTGGCG 59.176 55.000 0.00 0.00 0.00 5.69
2054 2163 0.105039 GAATCCACTAGTCCTGGCGG 59.895 60.000 0.00 0.00 0.00 6.13
2146 2255 3.181367 CAGGTCCTGCAACATCGC 58.819 61.111 5.79 0.00 0.00 4.58
2591 2701 7.287927 ACATGTACTAGTCTGTAACATAGGCAT 59.712 37.037 0.00 0.00 0.00 4.40
2688 2799 8.754991 TCCTAACTTTTTCATTAACAAGGACA 57.245 30.769 0.00 0.00 0.00 4.02
2886 2997 5.182001 GCAGATAAACTGGTAAGCCCATATG 59.818 44.000 0.00 0.00 44.15 1.78
2905 3016 6.638063 CCATATGAATTCACCTGCGTTATTTG 59.362 38.462 11.07 0.00 0.00 2.32
2995 3106 2.100749 CACGCCTCCACATGATGTAGTA 59.899 50.000 0.00 0.00 0.00 1.82
3146 3257 8.451908 AGAAACATAAGAAGCTTGTGTTTAGT 57.548 30.769 24.77 16.72 41.54 2.24
3170 3281 8.889717 AGTGGAACAATACCGTTATTCTAAATG 58.110 33.333 0.00 0.00 44.16 2.32
3653 3798 8.455903 ACAAAATACATATGATGGACTTCTGG 57.544 34.615 10.38 0.00 33.60 3.86
3667 3812 6.299141 TGGACTTCTGGATATAAATGAAGGC 58.701 40.000 0.00 0.00 40.83 4.35
3853 3998 5.534654 TCTTTTTAATGACCTGGAAGTGTGG 59.465 40.000 0.00 0.00 0.00 4.17
4022 4169 0.461548 GACATGCTCATCGGGAGTGA 59.538 55.000 0.00 0.00 45.88 3.41
4092 4241 9.388506 ACATGGTCTTTGAGATATAACTTTGAG 57.611 33.333 0.00 0.00 0.00 3.02
4251 4400 6.463995 TTAAAAGTTTGACTGGAAGCATGT 57.536 33.333 0.00 0.00 37.60 3.21
4319 4468 8.955061 ATGAGAATTCACTTTAAACATGAACG 57.045 30.769 8.44 0.00 35.28 3.95
4380 4529 6.804534 TTTTCTTGCAGAATTTAACACACG 57.195 33.333 0.00 0.00 33.67 4.49
4460 4609 7.120579 TCTGTTTTGTATTCTCAAATACGCCAT 59.879 33.333 4.40 0.00 46.87 4.40
4666 4815 3.648067 TCTCTGAACTTCCATGGTTCTGT 59.352 43.478 12.58 3.86 42.27 3.41
5018 5182 1.063717 AGGGACCTGGGCATGTAATTG 60.064 52.381 0.00 0.00 0.00 2.32
5210 5376 1.272313 ACTCATGGAGCAATGCTGGTT 60.272 47.619 14.48 0.00 39.88 3.67
5264 5430 1.593006 AGTCGCAACTTGTCTTCGTTG 59.407 47.619 0.00 0.00 42.47 4.10
5337 5503 3.055167 ACACCACTCTATGCATGCTTGTA 60.055 43.478 20.33 8.39 0.00 2.41
5445 5619 3.935818 TGTTGGTCCCTCAAGTTTACA 57.064 42.857 0.00 0.00 0.00 2.41
5446 5620 4.237976 TGTTGGTCCCTCAAGTTTACAA 57.762 40.909 0.00 0.00 0.00 2.41
5447 5621 4.204012 TGTTGGTCCCTCAAGTTTACAAG 58.796 43.478 0.00 0.00 0.00 3.16
5507 5681 5.628797 ATTTGGTCCCTTGTGTTTCAAAT 57.371 34.783 0.00 0.00 35.48 2.32
5565 5739 3.383505 GGTATTGGGCTGGTATTGAAACC 59.616 47.826 0.00 0.00 40.19 3.27
5741 5922 2.432972 CGCTTTGGGCCATTGCAC 60.433 61.111 24.28 7.14 43.03 4.57
5744 5925 0.174162 GCTTTGGGCCATTGCACTAG 59.826 55.000 21.36 7.10 43.18 2.57
5745 5926 0.174162 CTTTGGGCCATTGCACTAGC 59.826 55.000 7.26 0.00 43.18 3.42
5746 5927 0.251742 TTTGGGCCATTGCACTAGCT 60.252 50.000 7.26 0.00 43.18 3.32
5747 5928 0.680921 TTGGGCCATTGCACTAGCTC 60.681 55.000 7.26 0.00 43.18 4.09
5748 5929 1.825622 GGGCCATTGCACTAGCTCC 60.826 63.158 4.39 0.00 42.74 4.70
5749 5930 1.077501 GGCCATTGCACTAGCTCCA 60.078 57.895 0.00 0.00 42.74 3.86
5750 5931 0.680921 GGCCATTGCACTAGCTCCAA 60.681 55.000 0.00 0.00 42.74 3.53
5751 5932 0.453390 GCCATTGCACTAGCTCCAAC 59.547 55.000 0.00 0.00 42.74 3.77
5752 5933 1.825090 CCATTGCACTAGCTCCAACA 58.175 50.000 0.00 0.00 42.74 3.33
5753 5934 2.372264 CCATTGCACTAGCTCCAACAT 58.628 47.619 0.00 0.00 42.74 2.71
5754 5935 2.098607 CCATTGCACTAGCTCCAACATG 59.901 50.000 0.00 0.00 42.74 3.21
5755 5936 1.825090 TTGCACTAGCTCCAACATGG 58.175 50.000 0.00 0.00 42.74 3.66
5756 5937 0.677731 TGCACTAGCTCCAACATGGC 60.678 55.000 0.00 0.00 42.74 4.40
5830 6011 4.933064 CTGCTCCCGACGCGATCC 62.933 72.222 15.93 0.00 0.00 3.36
5840 6021 4.794439 CGCGATCCGTCACAGGCA 62.794 66.667 0.00 0.00 0.00 4.75
5841 6022 2.202932 GCGATCCGTCACAGGCAT 60.203 61.111 0.00 0.00 0.00 4.40
5842 6023 2.528743 GCGATCCGTCACAGGCATG 61.529 63.158 0.00 0.00 0.00 4.06
5843 6024 1.884464 CGATCCGTCACAGGCATGG 60.884 63.158 2.31 0.00 0.00 3.66
5844 6025 1.522092 GATCCGTCACAGGCATGGA 59.478 57.895 2.31 0.00 0.00 3.41
5845 6026 0.811616 GATCCGTCACAGGCATGGAC 60.812 60.000 2.31 6.61 0.00 4.02
5846 6027 2.257409 ATCCGTCACAGGCATGGACC 62.257 60.000 2.31 0.00 0.00 4.46
5847 6028 2.665000 CGTCACAGGCATGGACCT 59.335 61.111 2.31 0.00 42.30 3.85
5848 6029 1.448540 CGTCACAGGCATGGACCTC 60.449 63.158 2.31 0.00 38.26 3.85
5849 6030 1.448540 GTCACAGGCATGGACCTCG 60.449 63.158 2.31 0.00 38.26 4.63
5850 6031 1.609210 TCACAGGCATGGACCTCGA 60.609 57.895 2.31 0.00 38.26 4.04
5851 6032 1.448540 CACAGGCATGGACCTCGAC 60.449 63.158 2.31 0.00 38.26 4.20
5852 6033 2.202797 CAGGCATGGACCTCGACG 60.203 66.667 0.00 0.00 38.26 5.12
5853 6034 4.148825 AGGCATGGACCTCGACGC 62.149 66.667 0.00 0.00 33.62 5.19
5989 6170 1.663379 CGCCGTCTACCACCTCATCA 61.663 60.000 0.00 0.00 0.00 3.07
6040 6243 2.262915 GCGAGCTGGTGTAGTGCT 59.737 61.111 0.00 0.00 40.02 4.40
6041 6244 1.374758 GCGAGCTGGTGTAGTGCTT 60.375 57.895 0.00 0.00 37.16 3.91
6042 6245 1.355066 GCGAGCTGGTGTAGTGCTTC 61.355 60.000 0.00 0.00 37.16 3.86
6043 6246 0.737715 CGAGCTGGTGTAGTGCTTCC 60.738 60.000 0.00 0.00 37.16 3.46
6044 6247 0.610687 GAGCTGGTGTAGTGCTTCCT 59.389 55.000 0.00 0.00 37.16 3.36
6045 6248 1.002544 GAGCTGGTGTAGTGCTTCCTT 59.997 52.381 0.00 0.00 37.16 3.36
6119 6322 1.565156 GCCGAACGCACACAAGATGA 61.565 55.000 0.00 0.00 37.47 2.92
6135 6338 2.357009 AGATGATCGACAAAATGCTGCC 59.643 45.455 0.00 0.00 0.00 4.85
6157 6365 2.091444 TCTGCATCCCAGAGAGATGAGA 60.091 50.000 4.98 2.86 45.44 3.27
6211 6419 0.109532 TCAAAACCGAGGACATGCCA 59.890 50.000 8.58 0.00 40.02 4.92
6226 6434 0.966875 TGCCAGCCCAATACAGCTTG 60.967 55.000 0.00 0.00 37.18 4.01
6236 6444 2.109425 ATACAGCTTGGTTTCCGGTC 57.891 50.000 0.00 0.00 0.00 4.79
6241 6449 0.822121 GCTTGGTTTCCGGTCTTGGT 60.822 55.000 0.00 0.00 0.00 3.67
6248 6456 3.548616 GGTTTCCGGTCTTGGTTTAAACG 60.549 47.826 12.07 0.00 28.84 3.60
6253 6461 2.032636 CGGTCTTGGTTTAAACGTGTCC 60.033 50.000 12.07 10.03 0.00 4.02
6264 6472 7.328005 TGGTTTAAACGTGTCCAGTTTTAAAAC 59.672 33.333 21.06 21.06 41.44 2.43
6270 6478 5.587043 ACGTGTCCAGTTTTAAAACATGAGA 59.413 36.000 28.03 19.68 41.30 3.27
6272 6480 6.438763 GTGTCCAGTTTTAAAACATGAGAGG 58.561 40.000 28.03 19.19 41.30 3.69
6273 6481 6.262273 GTGTCCAGTTTTAAAACATGAGAGGA 59.738 38.462 28.03 20.67 41.30 3.71
6274 6482 6.831353 TGTCCAGTTTTAAAACATGAGAGGAA 59.169 34.615 28.03 13.95 41.30 3.36
6275 6483 7.340743 TGTCCAGTTTTAAAACATGAGAGGAAA 59.659 33.333 28.03 17.51 41.30 3.13
6276 6484 8.360390 GTCCAGTTTTAAAACATGAGAGGAAAT 58.640 33.333 28.03 4.83 41.30 2.17
6277 6485 8.359642 TCCAGTTTTAAAACATGAGAGGAAATG 58.640 33.333 28.03 14.85 41.30 2.32
6278 6486 8.143835 CCAGTTTTAAAACATGAGAGGAAATGT 58.856 33.333 28.03 4.26 41.30 2.71
6279 6487 9.185192 CAGTTTTAAAACATGAGAGGAAATGTC 57.815 33.333 28.03 0.39 41.30 3.06
6280 6488 8.912988 AGTTTTAAAACATGAGAGGAAATGTCA 58.087 29.630 28.03 0.00 41.30 3.58
6281 6489 9.528018 GTTTTAAAACATGAGAGGAAATGTCAA 57.472 29.630 23.12 0.00 35.99 3.18
6283 6491 9.528018 TTTAAAACATGAGAGGAAATGTCAAAC 57.472 29.630 0.00 0.00 35.99 2.93
6284 6492 6.713762 AAACATGAGAGGAAATGTCAAACA 57.286 33.333 0.00 0.00 35.99 2.83
6285 6493 6.713762 AACATGAGAGGAAATGTCAAACAA 57.286 33.333 0.00 0.00 35.99 2.83
6286 6494 6.713762 ACATGAGAGGAAATGTCAAACAAA 57.286 33.333 0.00 0.00 34.38 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.942850 CCTCTGTTCCCAAATGTAAATATTTTT 57.057 29.630 5.91 0.00 0.00 1.94
12 13 9.320295 TCCTCTGTTCCCAAATGTAAATATTTT 57.680 29.630 5.91 0.00 0.00 1.82
13 14 8.893563 TCCTCTGTTCCCAAATGTAAATATTT 57.106 30.769 5.89 5.89 0.00 1.40
14 15 8.116026 ACTCCTCTGTTCCCAAATGTAAATATT 58.884 33.333 0.00 0.00 0.00 1.28
15 16 7.643123 ACTCCTCTGTTCCCAAATGTAAATAT 58.357 34.615 0.00 0.00 0.00 1.28
16 17 7.027874 ACTCCTCTGTTCCCAAATGTAAATA 57.972 36.000 0.00 0.00 0.00 1.40
17 18 5.892348 ACTCCTCTGTTCCCAAATGTAAAT 58.108 37.500 0.00 0.00 0.00 1.40
18 19 5.319043 ACTCCTCTGTTCCCAAATGTAAA 57.681 39.130 0.00 0.00 0.00 2.01
19 20 4.993705 ACTCCTCTGTTCCCAAATGTAA 57.006 40.909 0.00 0.00 0.00 2.41
20 21 5.338632 TCTACTCCTCTGTTCCCAAATGTA 58.661 41.667 0.00 0.00 0.00 2.29
21 22 4.168101 TCTACTCCTCTGTTCCCAAATGT 58.832 43.478 0.00 0.00 0.00 2.71
22 23 4.826274 TCTACTCCTCTGTTCCCAAATG 57.174 45.455 0.00 0.00 0.00 2.32
23 24 5.094387 TCTTCTACTCCTCTGTTCCCAAAT 58.906 41.667 0.00 0.00 0.00 2.32
24 25 4.489737 TCTTCTACTCCTCTGTTCCCAAA 58.510 43.478 0.00 0.00 0.00 3.28
25 26 4.127918 TCTTCTACTCCTCTGTTCCCAA 57.872 45.455 0.00 0.00 0.00 4.12
26 27 3.827817 TCTTCTACTCCTCTGTTCCCA 57.172 47.619 0.00 0.00 0.00 4.37
27 28 4.279922 GCTATCTTCTACTCCTCTGTTCCC 59.720 50.000 0.00 0.00 0.00 3.97
28 29 4.890581 TGCTATCTTCTACTCCTCTGTTCC 59.109 45.833 0.00 0.00 0.00 3.62
29 30 5.358442 TGTGCTATCTTCTACTCCTCTGTTC 59.642 44.000 0.00 0.00 0.00 3.18
30 31 5.265191 TGTGCTATCTTCTACTCCTCTGTT 58.735 41.667 0.00 0.00 0.00 3.16
31 32 4.861196 TGTGCTATCTTCTACTCCTCTGT 58.139 43.478 0.00 0.00 0.00 3.41
32 33 5.843673 TTGTGCTATCTTCTACTCCTCTG 57.156 43.478 0.00 0.00 0.00 3.35
33 34 5.163602 CGTTTGTGCTATCTTCTACTCCTCT 60.164 44.000 0.00 0.00 0.00 3.69
34 35 5.038033 CGTTTGTGCTATCTTCTACTCCTC 58.962 45.833 0.00 0.00 0.00 3.71
35 36 4.705507 TCGTTTGTGCTATCTTCTACTCCT 59.294 41.667 0.00 0.00 0.00 3.69
36 37 4.995124 TCGTTTGTGCTATCTTCTACTCC 58.005 43.478 0.00 0.00 0.00 3.85
37 38 7.194278 TGTATCGTTTGTGCTATCTTCTACTC 58.806 38.462 0.00 0.00 0.00 2.59
38 39 7.096884 TGTATCGTTTGTGCTATCTTCTACT 57.903 36.000 0.00 0.00 0.00 2.57
39 40 7.751047 TTGTATCGTTTGTGCTATCTTCTAC 57.249 36.000 0.00 0.00 0.00 2.59
40 41 8.766000 TTTTGTATCGTTTGTGCTATCTTCTA 57.234 30.769 0.00 0.00 0.00 2.10
41 42 7.387948 ACTTTTGTATCGTTTGTGCTATCTTCT 59.612 33.333 0.00 0.00 0.00 2.85
42 43 7.478667 CACTTTTGTATCGTTTGTGCTATCTTC 59.521 37.037 0.00 0.00 0.00 2.87
49 50 5.173131 CCTTTCACTTTTGTATCGTTTGTGC 59.827 40.000 0.00 0.00 0.00 4.57
55 56 8.842358 TTAATCTCCTTTCACTTTTGTATCGT 57.158 30.769 0.00 0.00 0.00 3.73
119 121 7.924412 CCAGGTAAAGATAAAGCTTACGTATGA 59.076 37.037 12.31 0.00 0.00 2.15
120 122 7.170998 CCCAGGTAAAGATAAAGCTTACGTATG 59.829 40.741 0.00 0.00 0.00 2.39
122 124 6.380846 TCCCAGGTAAAGATAAAGCTTACGTA 59.619 38.462 0.00 0.00 0.00 3.57
124 126 5.667466 TCCCAGGTAAAGATAAAGCTTACG 58.333 41.667 0.00 0.00 0.00 3.18
125 127 7.827729 TCTTTCCCAGGTAAAGATAAAGCTTAC 59.172 37.037 3.05 0.00 37.89 2.34
126 128 7.924541 TCTTTCCCAGGTAAAGATAAAGCTTA 58.075 34.615 3.05 0.00 37.89 3.09
127 129 6.790319 TCTTTCCCAGGTAAAGATAAAGCTT 58.210 36.000 3.05 0.00 37.89 3.74
128 130 6.388619 TCTTTCCCAGGTAAAGATAAAGCT 57.611 37.500 3.05 0.00 37.89 3.74
129 131 7.313646 GTTTCTTTCCCAGGTAAAGATAAAGC 58.686 38.462 7.99 0.00 41.34 3.51
130 132 7.174426 ACGTTTCTTTCCCAGGTAAAGATAAAG 59.826 37.037 7.99 9.64 41.34 1.85
131 133 6.999871 ACGTTTCTTTCCCAGGTAAAGATAAA 59.000 34.615 7.99 0.00 41.34 1.40
132 134 6.536447 ACGTTTCTTTCCCAGGTAAAGATAA 58.464 36.000 7.99 3.77 41.34 1.75
133 135 6.117975 ACGTTTCTTTCCCAGGTAAAGATA 57.882 37.500 7.99 1.15 41.34 1.98
134 136 4.981812 ACGTTTCTTTCCCAGGTAAAGAT 58.018 39.130 7.99 0.00 41.34 2.40
135 137 4.426736 ACGTTTCTTTCCCAGGTAAAGA 57.573 40.909 3.05 3.05 40.33 2.52
136 138 4.577283 TGAACGTTTCTTTCCCAGGTAAAG 59.423 41.667 0.46 0.00 35.66 1.85
161 163 6.530120 TGAAAATGGTACTACTGCAGAAAGA 58.470 36.000 23.35 0.00 0.00 2.52
168 170 5.959618 AAGGTTGAAAATGGTACTACTGC 57.040 39.130 0.00 0.00 0.00 4.40
187 189 8.725148 GTCATGCATTGGTATTCTAATCTAAGG 58.275 37.037 0.00 0.00 0.00 2.69
188 190 9.276590 TGTCATGCATTGGTATTCTAATCTAAG 57.723 33.333 0.00 0.00 0.00 2.18
190 192 7.388776 GCTGTCATGCATTGGTATTCTAATCTA 59.611 37.037 0.00 0.00 0.00 1.98
191 193 6.206243 GCTGTCATGCATTGGTATTCTAATCT 59.794 38.462 0.00 0.00 0.00 2.40
192 194 6.376978 GCTGTCATGCATTGGTATTCTAATC 58.623 40.000 0.00 0.00 0.00 1.75
193 195 5.242393 GGCTGTCATGCATTGGTATTCTAAT 59.758 40.000 0.00 0.00 34.04 1.73
194 196 4.580167 GGCTGTCATGCATTGGTATTCTAA 59.420 41.667 0.00 0.00 34.04 2.10
221 223 1.135286 GCATGTTGCAGGAAGGTAAGC 60.135 52.381 0.00 0.00 44.26 3.09
299 314 8.432110 TTTGTTTTCTCTTCTTTAAAATGGGC 57.568 30.769 0.00 0.00 0.00 5.36
316 331 6.687958 CCAGTTGCATTTGTCATTTTGTTTTC 59.312 34.615 0.00 0.00 0.00 2.29
317 332 6.404513 CCCAGTTGCATTTGTCATTTTGTTTT 60.405 34.615 0.00 0.00 0.00 2.43
519 589 2.029649 CACCTTTGAAGCAATGAGTGGG 60.030 50.000 0.00 0.00 0.00 4.61
649 722 2.449464 ACAGCTTCATATTGCTTGCCA 58.551 42.857 0.00 0.00 37.44 4.92
739 812 5.660864 AGAGAAAAGGAACCCACAATTGAAA 59.339 36.000 13.59 0.00 0.00 2.69
788 862 8.541133 AAATCTGAGACAGCTAAAACTAAGAC 57.459 34.615 0.00 0.00 0.00 3.01
819 922 7.355101 ACCTAGGATATACAGTCTGTCAGAAA 58.645 38.462 17.98 0.00 0.00 2.52
848 951 7.372451 TGGTCATATTTTACCGAGAACTTTG 57.628 36.000 0.00 0.00 38.70 2.77
857 960 2.678836 TGGCGTTGGTCATATTTTACCG 59.321 45.455 0.00 0.00 38.70 4.02
867 970 0.682292 TCAGTACATGGCGTTGGTCA 59.318 50.000 0.00 0.00 0.00 4.02
906 1009 8.900511 TGCATAAATTCAGAAGAAATTTCTCG 57.099 30.769 20.71 12.41 37.29 4.04
1126 1235 4.035675 GCCGAAGTTGCAGATAAGCTTTAT 59.964 41.667 3.20 0.00 34.99 1.40
1219 1328 1.743394 CCAAGAAATGTCCCGGCTAAC 59.257 52.381 0.00 0.00 0.00 2.34
1305 1414 1.751927 CATGCTCAGTTGCTCCCCC 60.752 63.158 0.00 0.00 0.00 5.40
1470 1579 1.142748 CGCCTCTTTCTCGGCATCT 59.857 57.895 0.00 0.00 46.62 2.90
1695 1804 1.673665 CTCCAGCTGACCACTTGCC 60.674 63.158 17.39 0.00 0.00 4.52
1754 1863 5.870978 TCTTCGTTACCTTGTGCCTTATAAC 59.129 40.000 0.00 0.00 0.00 1.89
1781 1890 1.492764 TCTGGCTGCAGAGATCATGA 58.507 50.000 20.43 0.00 0.00 3.07
1968 2077 8.794335 AATTAGTGTTCCTCCTTAGTGAATTC 57.206 34.615 0.00 0.00 0.00 2.17
1982 2091 2.554893 TGCGGTTGGAAATTAGTGTTCC 59.445 45.455 0.00 0.00 44.19 3.62
2011 2120 6.491745 TCATGACTAGGTTCAGATATCTCCAC 59.508 42.308 1.03 2.30 0.00 4.02
2052 2161 4.465512 GCACTGATGTTGCCGCCG 62.466 66.667 0.00 0.00 0.00 6.46
2053 2162 2.419057 TTTGCACTGATGTTGCCGCC 62.419 55.000 0.00 0.00 0.00 6.13
2054 2163 1.007502 TTTGCACTGATGTTGCCGC 60.008 52.632 0.00 0.00 0.00 6.53
2085 2194 2.811317 GTTGCAGCCGACCTCTCG 60.811 66.667 0.00 0.00 39.83 4.04
2096 2205 0.242825 CTGGATGCTGTTGGTTGCAG 59.757 55.000 0.00 0.00 42.74 4.41
2098 2207 0.961019 TTCTGGATGCTGTTGGTTGC 59.039 50.000 0.00 0.00 0.00 4.17
2146 2255 3.057946 GGTGTAGAAGCAAAAGGAAGCAG 60.058 47.826 0.00 0.00 0.00 4.24
2187 2296 3.612479 GCACAAGAGTATTTGGTTGCAGG 60.612 47.826 0.00 0.00 33.03 4.85
2591 2701 5.592282 TGACAAAAACAATCCTAGCTTGACA 59.408 36.000 9.50 0.00 0.00 3.58
2668 2778 8.360390 GGAAGATGTCCTTGTTAATGAAAAAGT 58.640 33.333 0.00 0.00 43.98 2.66
2688 2799 9.739276 TTTGTATGACATCAACTTTAGGAAGAT 57.261 29.630 0.00 0.00 36.69 2.40
2886 2997 5.699839 ACTTCAAATAACGCAGGTGAATTC 58.300 37.500 0.00 0.00 0.00 2.17
2905 3016 1.546029 GGTCCCCTTGATTGCAACTTC 59.454 52.381 0.00 0.00 0.00 3.01
2959 3070 4.098196 GGAGGCGTGAATACTCTAGTTTCT 59.902 45.833 0.00 0.00 0.00 2.52
2995 3106 0.612732 TGGATCCGTACGTGGTCCTT 60.613 55.000 26.16 2.63 33.17 3.36
3085 3196 3.364460 TGTTGGCCTATACAGCATTGT 57.636 42.857 3.32 0.00 41.39 2.71
3126 3237 6.801539 TCCACTAAACACAAGCTTCTTATG 57.198 37.500 0.00 0.00 0.00 1.90
3146 3257 7.337184 TGCATTTAGAATAACGGTATTGTTCCA 59.663 33.333 11.19 0.00 33.32 3.53
3170 3281 6.454795 TGTATTTCTCAATTTCAACCCTTGC 58.545 36.000 0.00 0.00 0.00 4.01
3629 3774 8.681486 TCCAGAAGTCCATCATATGTATTTTG 57.319 34.615 1.90 0.00 0.00 2.44
3667 3812 7.255035 CCTGCAGTCATTGTTTCTCTATTATGG 60.255 40.741 13.81 0.00 0.00 2.74
3853 3998 2.742053 TCTTCGCAATTTGTAGCACCTC 59.258 45.455 0.00 0.00 0.00 3.85
4243 4392 3.326747 AGTAACGTCTTGGACATGCTTC 58.673 45.455 0.00 0.00 32.09 3.86
4280 4429 8.043710 AGTGAATTCTCATTAATCGTTTCTCCT 58.956 33.333 7.05 0.00 33.05 3.69
4319 4468 3.864789 TCAAATAGGAGGAATGCTCCC 57.135 47.619 17.47 0.00 43.64 4.30
4460 4609 5.046878 ACATCGACCTGTGTTACCATAAAGA 60.047 40.000 0.00 0.00 0.00 2.52
4730 4890 7.179338 AGCTTATCCCTACTCACAAGTATATGG 59.821 40.741 0.00 0.00 37.36 2.74
4990 5154 0.965866 GCCCAGGTCCCTAAACTTGC 60.966 60.000 0.00 0.00 0.00 4.01
5018 5182 1.143073 ACTGGGTTCCCTGAACTTGAC 59.857 52.381 19.15 0.00 41.70 3.18
5112 5278 3.579302 CCCCCTGCACACTCCCAA 61.579 66.667 0.00 0.00 0.00 4.12
5210 5376 1.202582 GTCTTCGCTCAGGCTCAGTTA 59.797 52.381 0.00 0.00 36.09 2.24
5235 5401 2.351726 ACAAGTTGCGACTTCAGTGAAC 59.648 45.455 16.79 0.00 44.14 3.18
5445 5619 5.032846 TGAGGGATCCAATGTCTACTTCTT 58.967 41.667 15.23 0.00 0.00 2.52
5446 5620 4.624913 TGAGGGATCCAATGTCTACTTCT 58.375 43.478 15.23 0.00 0.00 2.85
5447 5621 5.306678 AGATGAGGGATCCAATGTCTACTTC 59.693 44.000 15.23 3.93 0.00 3.01
5484 5658 5.428184 TTTGAAACACAAGGGACCAAATT 57.572 34.783 0.00 0.00 39.77 1.82
5507 5681 3.744238 TCTGGACGAAACATGTCTGAA 57.256 42.857 0.00 0.00 36.58 3.02
5565 5739 9.046296 ACTGTTCGATAAAATGCCTAGAATAAG 57.954 33.333 0.00 0.00 0.00 1.73
5666 5847 2.936032 AGGAGGGCCACCAAGGTC 60.936 66.667 22.59 0.00 43.09 3.85
5745 5926 3.499737 GTCGGCGCCATGTTGGAG 61.500 66.667 28.98 7.38 40.96 3.86
5787 5968 2.097160 CGTTGCTGAGCATGACGC 59.903 61.111 17.20 1.87 36.32 5.19
5825 6006 1.884464 CCATGCCTGTGACGGATCG 60.884 63.158 0.00 0.00 0.00 3.69
5827 6008 1.221840 GTCCATGCCTGTGACGGAT 59.778 57.895 0.00 0.00 0.00 4.18
5828 6009 2.662596 GTCCATGCCTGTGACGGA 59.337 61.111 0.00 0.00 0.00 4.69
5829 6010 2.436646 GGTCCATGCCTGTGACGG 60.437 66.667 0.00 0.00 0.00 4.79
5830 6011 1.448540 GAGGTCCATGCCTGTGACG 60.449 63.158 0.00 0.00 39.34 4.35
5832 6013 1.609210 TCGAGGTCCATGCCTGTGA 60.609 57.895 0.00 0.00 39.34 3.58
5833 6014 1.448540 GTCGAGGTCCATGCCTGTG 60.449 63.158 0.00 0.00 39.34 3.66
5834 6015 2.982130 GTCGAGGTCCATGCCTGT 59.018 61.111 0.00 0.00 39.34 4.00
5835 6016 2.202797 CGTCGAGGTCCATGCCTG 60.203 66.667 0.00 0.00 39.34 4.85
5836 6017 4.148825 GCGTCGAGGTCCATGCCT 62.149 66.667 7.01 0.00 42.53 4.75
5846 6027 4.531912 TAGCTTCCGCGCGTCGAG 62.532 66.667 29.95 22.30 42.32 4.04
5847 6028 4.824166 GTAGCTTCCGCGCGTCGA 62.824 66.667 29.95 17.25 42.32 4.20
5952 6133 1.202973 CGCATACGAGCAGGAGAACG 61.203 60.000 0.00 0.00 43.93 3.95
6027 6230 1.443802 GAAGGAAGCACTACACCAGC 58.556 55.000 0.00 0.00 0.00 4.85
6040 6243 1.600636 CTTGCGCTGGTGGAAGGAA 60.601 57.895 9.73 0.00 34.08 3.36
6041 6244 2.032528 CTTGCGCTGGTGGAAGGA 59.967 61.111 9.73 0.00 34.08 3.36
6043 6246 2.281761 ACCTTGCGCTGGTGGAAG 60.282 61.111 21.36 9.94 36.30 3.46
6119 6322 1.741706 CAGAGGCAGCATTTTGTCGAT 59.258 47.619 0.00 0.00 0.00 3.59
6135 6338 2.297880 CTCATCTCTCTGGGATGCAGAG 59.702 54.545 0.00 0.00 45.50 3.35
6157 6365 1.212935 GTTACTGCCACCCCATCTCAT 59.787 52.381 0.00 0.00 0.00 2.90
6226 6434 3.548616 CGTTTAAACCAAGACCGGAAACC 60.549 47.826 9.46 0.00 0.00 3.27
6236 6444 4.625972 AACTGGACACGTTTAAACCAAG 57.374 40.909 12.66 4.26 0.00 3.61
6241 6449 8.861101 CATGTTTTAAAACTGGACACGTTTAAA 58.139 29.630 26.76 6.55 39.59 1.52
6248 6456 6.262273 TCCTCTCATGTTTTAAAACTGGACAC 59.738 38.462 26.76 5.01 39.59 3.67
6253 6461 9.185192 GACATTTCCTCTCATGTTTTAAAACTG 57.815 33.333 26.76 21.54 39.59 3.16


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

AutoCloner maintained by Alex Coulton.