Multiple sequence alignment - TraesCS1B01G262000

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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 TraesCS1B01G262000 chr1B 100.000 9069 0 0 1 9069 460281920 460272852 0 16748
1 TraesCS1B01G262000 chr1D 94.338 5281 192 53 3853 9068 343182644 343177406 0 7997
2 TraesCS1B01G262000 chr1D 91.440 3937 170 49 1 3863 343186856 343183013 0 5249
3 TraesCS1B01G262000 chr1A 94.241 5122 180 42 3995 9069 442805014 442799961 0 7718
4 TraesCS1B01G262000 chr1A 90.367 4090 215 65 1 3981 442809016 442804997 0 5204
5 TraesCS1B01G262000 chr7A 92.817 529 29 5 8142 8662 280227047 280226520 0 758


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 TraesCS1B01G262000 chr1B 460272852 460281920 9068 True 16748 16748 100.000 1 9069 1 chr1B.!!$R1 9068
1 TraesCS1B01G262000 chr1D 343177406 343186856 9450 True 6623 7997 92.889 1 9068 2 chr1D.!!$R1 9067
2 TraesCS1B01G262000 chr1A 442799961 442809016 9055 True 6461 7718 92.304 1 9069 2 chr1A.!!$R1 9068
3 TraesCS1B01G262000 chr7A 280226520 280227047 527 True 758 758 92.817 8142 8662 1 chr7A.!!$R1 520

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
412 422 0.625849 AAGATGCGGGGTCCTGAAAT 59.374 50.0 0.00 0.00 0.00 2.17 F
1684 1713 0.173255 CTTTCCGGCCGCATTTGAAT 59.827 50.0 22.85 0.00 0.00 2.57 F
2698 2767 0.237498 CGTCCTTCGCCCTTTTGAAC 59.763 55.0 0.00 0.00 0.00 3.18 F
2783 2853 0.249447 GGGCTGTGTTTTCAAGTGCC 60.249 55.0 0.00 0.00 39.32 5.01 F
3971 4480 0.039165 GGCTGTGCTAAGTTTGCCAC 60.039 55.0 6.84 6.02 40.04 5.01 F
3987 4496 0.102120 CCACCAGCGCTTGTTCAAAA 59.898 50.0 12.08 0.00 0.00 2.44 F
4955 5480 0.168788 TGCTGCATTTGCTAACGCTC 59.831 50.0 0.00 0.00 42.66 5.03 F
6668 7212 0.323302 TGCGGACAAAGTAGATGCCA 59.677 50.0 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1791 0.658897 GAACCACAGGCGAAACGAAA 59.341 50.0 0.00 0.00 0.00 3.46 R
3540 3663 0.036732 AAAGAAGGAGGCGTGCATGA 59.963 50.0 10.93 0.00 0.00 3.07 R
3968 4477 0.102120 TTTTGAACAAGCGCTGGTGG 59.898 50.0 20.41 7.68 0.00 4.61 R
3993 4502 0.179113 CAACGCTGGTGGCAAACTTT 60.179 50.0 0.00 0.00 41.91 2.66 R
4793 5318 0.887387 GCTTGTTAGGCCACCAACGA 60.887 55.0 5.01 5.08 0.00 3.85 R
4961 5486 1.620822 AAACAATCCTGTGCTCCACC 58.379 50.0 0.00 0.00 35.37 4.61 R
6706 7252 0.399833 TATGACCTGCACACAAGGCA 59.600 50.0 0.00 0.00 39.32 4.75 R
8244 8799 0.736053 GAAACACCAGCACCAACGAA 59.264 50.0 0.00 0.00 0.00 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
27 28 9.562583 GTACAATGGAGAATATCGATCTCTTAC 57.437 37.037 12.89 9.17 42.38 2.34
95 96 7.090173 CCAAACCCTACAAAAATCATACACAG 58.910 38.462 0.00 0.00 0.00 3.66
115 116 6.876257 ACACAGAAATCTAAGAGATGGTCAAC 59.124 38.462 0.00 0.00 34.65 3.18
116 117 6.314896 CACAGAAATCTAAGAGATGGTCAACC 59.685 42.308 0.00 0.00 34.65 3.77
117 118 5.521735 CAGAAATCTAAGAGATGGTCAACCG 59.478 44.000 0.00 0.00 34.65 4.44
119 120 1.480954 TCTAAGAGATGGTCAACCGCC 59.519 52.381 0.00 0.00 39.43 6.13
126 129 3.124921 GGTCAACCGCCGTGGATG 61.125 66.667 4.58 3.08 41.73 3.51
142 145 2.293955 TGGATGTCCAATGCATTATGCG 59.706 45.455 12.53 0.00 44.85 4.73
145 148 4.156556 GGATGTCCAATGCATTATGCGTAT 59.843 41.667 12.53 1.87 42.67 3.06
177 181 5.746245 TCAAATCTCAAAACGCGTGATTTTT 59.254 32.000 23.79 14.40 35.84 1.94
201 205 5.663456 ACAAATGGGTAAGCATGCAAATAG 58.337 37.500 21.98 1.41 0.00 1.73
204 208 2.689471 TGGGTAAGCATGCAAATAGCTG 59.311 45.455 21.98 0.00 45.94 4.24
205 209 2.035066 GGGTAAGCATGCAAATAGCTGG 59.965 50.000 21.98 0.00 45.94 4.85
206 210 2.951642 GGTAAGCATGCAAATAGCTGGA 59.048 45.455 21.98 0.00 45.94 3.86
208 212 4.761739 GGTAAGCATGCAAATAGCTGGATA 59.238 41.667 21.98 0.00 45.94 2.59
209 213 5.241506 GGTAAGCATGCAAATAGCTGGATAA 59.758 40.000 21.98 0.00 45.94 1.75
211 215 6.415206 AAGCATGCAAATAGCTGGATAATT 57.585 33.333 21.98 0.00 45.94 1.40
214 218 7.277396 AGCATGCAAATAGCTGGATAATTTTT 58.723 30.769 21.98 0.00 45.94 1.94
289 299 1.068250 GGCTCTACCCTCGCACATC 59.932 63.158 0.00 0.00 0.00 3.06
305 315 3.432186 GCACATCACAGCCTATCCTTACA 60.432 47.826 0.00 0.00 0.00 2.41
339 349 7.241628 ACACCCAATAGAGAAAAATTCTTCCT 58.758 34.615 0.00 0.00 40.87 3.36
340 350 8.390921 ACACCCAATAGAGAAAAATTCTTCCTA 58.609 33.333 0.00 0.00 40.87 2.94
359 369 2.052782 AATTCGCCTGTACCCAATCC 57.947 50.000 0.00 0.00 0.00 3.01
404 414 1.674322 CCGAACAAAGATGCGGGGT 60.674 57.895 0.00 0.00 40.08 4.95
412 422 0.625849 AAGATGCGGGGTCCTGAAAT 59.374 50.000 0.00 0.00 0.00 2.17
476 486 4.467084 CACCCGGTCCGGTCCATG 62.467 72.222 28.39 16.53 46.80 3.66
723 739 2.799452 GCCCGTACCCGCTAATCCA 61.799 63.158 0.00 0.00 0.00 3.41
726 742 1.068585 CGTACCCGCTAATCCACCC 59.931 63.158 0.00 0.00 0.00 4.61
728 744 2.135581 TACCCGCTAATCCACCCCG 61.136 63.158 0.00 0.00 0.00 5.73
913 929 2.190488 AAAGCTTGGGCGGAGAGAGG 62.190 60.000 0.00 0.00 44.37 3.69
914 930 4.847444 GCTTGGGCGGAGAGAGGC 62.847 72.222 0.00 0.00 0.00 4.70
927 947 4.157120 GAGGCCACGCATACGGGT 62.157 66.667 5.01 0.00 42.77 5.28
935 955 1.125633 ACGCATACGGGTAGGGAATT 58.874 50.000 0.00 0.00 46.04 2.17
953 974 5.341169 GGAATTGAGAGGGAGGAGAGATAT 58.659 45.833 0.00 0.00 0.00 1.63
956 977 3.340403 TGAGAGGGAGGAGAGATATCCA 58.660 50.000 0.00 0.00 42.26 3.41
1640 1667 1.130186 TCGTGTGCGCGTAGTGTTATA 59.870 47.619 8.43 0.00 41.96 0.98
1641 1668 1.251002 CGTGTGCGCGTAGTGTTATAC 59.749 52.381 8.43 0.00 41.96 1.47
1684 1713 0.173255 CTTTCCGGCCGCATTTGAAT 59.827 50.000 22.85 0.00 0.00 2.57
1761 1791 0.898320 CAGACGGTTGGATCTGGTCT 59.102 55.000 0.00 0.00 38.97 3.85
1780 1810 0.658897 TTTCGTTTCGCCTGTGGTTC 59.341 50.000 0.00 0.00 0.00 3.62
1822 1852 8.408601 CCCACTTGAATATCTCCTGTTTTATTG 58.591 37.037 0.00 0.00 0.00 1.90
1845 1875 3.566997 GGGGCCTAATAACCAAAAAGGGA 60.567 47.826 0.84 0.00 43.89 4.20
1846 1876 3.449737 GGGCCTAATAACCAAAAAGGGAC 59.550 47.826 0.84 0.00 43.89 4.46
1847 1877 3.129813 GGCCTAATAACCAAAAAGGGACG 59.870 47.826 0.00 0.00 43.89 4.79
1880 1911 6.640907 GCTTCCAAATGACGTTTTCTTTATGT 59.359 34.615 0.00 0.00 0.00 2.29
1881 1912 7.169140 GCTTCCAAATGACGTTTTCTTTATGTT 59.831 33.333 0.00 0.00 0.00 2.71
1882 1913 9.672086 CTTCCAAATGACGTTTTCTTTATGTTA 57.328 29.630 0.00 0.00 0.00 2.41
1883 1914 9.453325 TTCCAAATGACGTTTTCTTTATGTTAC 57.547 29.630 0.00 0.00 0.00 2.50
1884 1915 8.842280 TCCAAATGACGTTTTCTTTATGTTACT 58.158 29.630 0.00 0.00 0.00 2.24
1885 1916 9.113876 CCAAATGACGTTTTCTTTATGTTACTC 57.886 33.333 0.00 0.00 0.00 2.59
1886 1917 9.113876 CAAATGACGTTTTCTTTATGTTACTCC 57.886 33.333 0.00 0.00 0.00 3.85
1887 1918 8.617290 AATGACGTTTTCTTTATGTTACTCCT 57.383 30.769 0.00 0.00 0.00 3.69
1888 1919 9.715121 AATGACGTTTTCTTTATGTTACTCCTA 57.285 29.630 0.00 0.00 0.00 2.94
1889 1920 8.524870 TGACGTTTTCTTTATGTTACTCCTAC 57.475 34.615 0.00 0.00 0.00 3.18
1890 1921 8.362639 TGACGTTTTCTTTATGTTACTCCTACT 58.637 33.333 0.00 0.00 0.00 2.57
1891 1922 9.846248 GACGTTTTCTTTATGTTACTCCTACTA 57.154 33.333 0.00 0.00 0.00 1.82
1922 1980 7.290857 AGCGGCATCGTTAATAATAGTATTG 57.709 36.000 5.70 0.00 38.89 1.90
1947 2005 1.083847 GTTCGACGAACCAACACGC 60.084 57.895 26.57 2.32 36.65 5.34
2013 2071 4.025647 CGAGAGAGCCAATAATTTTCCGTC 60.026 45.833 0.00 0.00 0.00 4.79
2039 2097 1.065418 CCACCAGAGGCGGAGTTATTT 60.065 52.381 0.00 0.00 0.00 1.40
2493 2562 4.144418 GGGCACCGTTGTGTGTTA 57.856 55.556 0.00 0.00 44.65 2.41
2507 2576 0.963962 GTGTTACGGTCTGGTGAGGA 59.036 55.000 0.00 0.00 0.00 3.71
2638 2707 3.012119 TTAGCATGTGCCCCGGGA 61.012 61.111 26.32 0.42 43.38 5.14
2680 2749 1.333791 GGTCTCGACAAAACCTTTGCG 60.334 52.381 0.00 4.79 0.00 4.85
2696 2765 4.371975 CGTCCTTCGCCCTTTTGA 57.628 55.556 0.00 0.00 0.00 2.69
2698 2767 0.237498 CGTCCTTCGCCCTTTTGAAC 59.763 55.000 0.00 0.00 0.00 3.18
2783 2853 0.249447 GGGCTGTGTTTTCAAGTGCC 60.249 55.000 0.00 0.00 39.32 5.01
2805 2875 1.298859 GCGGCTCGAAATGTGGTCTT 61.299 55.000 0.00 0.00 0.00 3.01
2812 2882 3.599343 TCGAAATGTGGTCTTCCATCTG 58.401 45.455 0.00 0.00 46.20 2.90
2839 2909 1.450312 GGCTGGGGTGACGAATGAG 60.450 63.158 0.00 0.00 0.00 2.90
2858 2928 1.369692 CACGCTTGGTCACCAGGTA 59.630 57.895 7.94 0.00 33.81 3.08
2915 2996 9.528018 TTCTTACGCAAGAAAAGAAAATCAATT 57.472 25.926 8.39 0.00 45.61 2.32
2956 3037 4.963276 CAGAATGGGCGAACTTTATGAA 57.037 40.909 0.00 0.00 0.00 2.57
2957 3038 5.309323 CAGAATGGGCGAACTTTATGAAA 57.691 39.130 0.00 0.00 0.00 2.69
3008 3099 2.571611 GCATTTGTCGCGTCGCTG 60.572 61.111 16.36 9.11 0.00 5.18
3069 3160 8.166726 AGAGGGAATAATTTTCTCTTGTCTTGT 58.833 33.333 4.82 0.00 31.52 3.16
3106 3197 9.101655 CTGAATTGTCATGATACAACATGTAGA 57.898 33.333 0.00 0.00 45.21 2.59
3203 3297 2.287788 GCATAGGAACCAAATCATGCGG 60.288 50.000 0.00 0.00 30.62 5.69
3205 3299 1.141665 GGAACCAAATCATGCGGCC 59.858 57.895 0.00 0.00 0.00 6.13
3206 3300 1.226660 GAACCAAATCATGCGGCCG 60.227 57.895 24.05 24.05 0.00 6.13
3207 3301 1.933115 GAACCAAATCATGCGGCCGT 61.933 55.000 28.70 4.23 0.00 5.68
3209 3303 0.678366 ACCAAATCATGCGGCCGTAA 60.678 50.000 28.70 16.51 0.00 3.18
3210 3304 0.667993 CCAAATCATGCGGCCGTAAT 59.332 50.000 28.70 18.19 0.00 1.89
3211 3305 1.334960 CCAAATCATGCGGCCGTAATC 60.335 52.381 28.70 10.62 0.00 1.75
3214 3308 1.967319 ATCATGCGGCCGTAATCTTT 58.033 45.000 28.70 3.15 0.00 2.52
3215 3309 1.745232 TCATGCGGCCGTAATCTTTT 58.255 45.000 28.70 2.25 0.00 2.27
3216 3310 2.088423 TCATGCGGCCGTAATCTTTTT 58.912 42.857 28.70 1.36 0.00 1.94
3217 3311 2.096819 TCATGCGGCCGTAATCTTTTTC 59.903 45.455 28.70 6.03 0.00 2.29
3287 3382 2.282462 CCTTGGGGGACACACAGC 60.282 66.667 0.00 0.00 37.23 4.40
3288 3383 2.833913 CCTTGGGGGACACACAGCT 61.834 63.158 0.00 0.00 37.23 4.24
3365 3469 2.673523 GGAGACATGCCCTGCAGT 59.326 61.111 13.81 0.00 43.65 4.40
3391 3495 1.226603 GTGGCCTACGCGAGTACAG 60.227 63.158 15.93 1.02 46.88 2.74
3447 3554 1.676014 CGTCACCCCAGTCAGAATTCC 60.676 57.143 0.65 0.00 0.00 3.01
3448 3555 1.351017 GTCACCCCAGTCAGAATTCCA 59.649 52.381 0.65 0.00 0.00 3.53
3449 3556 2.025887 GTCACCCCAGTCAGAATTCCAT 60.026 50.000 0.65 0.00 0.00 3.41
3450 3557 2.239654 TCACCCCAGTCAGAATTCCATC 59.760 50.000 0.65 0.00 0.00 3.51
3486 3609 1.533625 CAATCAAACGGAAGGAGCCA 58.466 50.000 0.00 0.00 0.00 4.75
3487 3610 1.470098 CAATCAAACGGAAGGAGCCAG 59.530 52.381 0.00 0.00 0.00 4.85
3488 3611 0.984230 ATCAAACGGAAGGAGCCAGA 59.016 50.000 0.00 0.00 0.00 3.86
3489 3612 0.321671 TCAAACGGAAGGAGCCAGAG 59.678 55.000 0.00 0.00 0.00 3.35
3490 3613 0.674895 CAAACGGAAGGAGCCAGAGG 60.675 60.000 0.00 0.00 0.00 3.69
3491 3614 1.128188 AAACGGAAGGAGCCAGAGGT 61.128 55.000 0.00 0.00 0.00 3.85
3492 3615 1.545706 AACGGAAGGAGCCAGAGGTC 61.546 60.000 0.00 0.00 39.90 3.85
3540 3663 3.580731 CGCCACCGTGGAAAATTAAATT 58.419 40.909 22.37 0.00 40.96 1.82
3542 3665 4.561105 GCCACCGTGGAAAATTAAATTCA 58.439 39.130 22.37 0.00 40.96 2.57
3572 3695 0.955919 CTTCTTTCCACCACGGCCTC 60.956 60.000 0.00 0.00 33.14 4.70
3623 3746 4.027884 TCGGATTCGAGAAGCCCA 57.972 55.556 13.70 0.00 43.59 5.36
3635 3758 0.464554 GAAGCCCAAAGATCTCCGGG 60.465 60.000 20.53 20.53 42.03 5.73
3637 3760 2.193248 CCCAAAGATCTCCGGGCC 59.807 66.667 14.79 0.00 0.00 5.80
3638 3761 2.203070 CCAAAGATCTCCGGGCCG 60.203 66.667 21.46 21.46 0.00 6.13
3639 3762 2.731571 CCAAAGATCTCCGGGCCGA 61.732 63.158 30.79 12.88 0.00 5.54
3640 3763 1.227380 CAAAGATCTCCGGGCCGAG 60.227 63.158 30.79 21.99 0.00 4.63
3819 3950 2.235402 TCCTGAGAAAATCGGTACACCC 59.765 50.000 0.00 0.00 31.71 4.61
3845 3976 2.506217 CGGCTGCTCTCGCGTTTA 60.506 61.111 5.77 0.00 39.65 2.01
3846 3977 2.508891 CGGCTGCTCTCGCGTTTAG 61.509 63.158 5.77 3.21 39.65 1.85
3847 3978 1.446272 GGCTGCTCTCGCGTTTAGT 60.446 57.895 5.77 0.00 39.65 2.24
3848 3979 1.414527 GGCTGCTCTCGCGTTTAGTC 61.415 60.000 5.77 0.00 39.65 2.59
3850 3981 1.983972 CTGCTCTCGCGTTTAGTCTT 58.016 50.000 5.77 0.00 39.65 3.01
3851 3982 1.914700 CTGCTCTCGCGTTTAGTCTTC 59.085 52.381 5.77 0.00 39.65 2.87
3954 4463 8.031277 AGATTTTGAATTGACAACTCATTAGGC 58.969 33.333 0.00 0.00 0.00 3.93
3967 4476 4.697352 ACTCATTAGGCTGTGCTAAGTTTG 59.303 41.667 0.00 0.00 0.00 2.93
3968 4477 3.440173 TCATTAGGCTGTGCTAAGTTTGC 59.560 43.478 0.00 2.06 0.00 3.68
3969 4478 1.821216 TAGGCTGTGCTAAGTTTGCC 58.179 50.000 6.84 0.00 40.54 4.52
3970 4479 0.178992 AGGCTGTGCTAAGTTTGCCA 60.179 50.000 6.84 4.02 42.46 4.92
3971 4480 0.039165 GGCTGTGCTAAGTTTGCCAC 60.039 55.000 6.84 6.02 40.04 5.01
3972 4481 0.039165 GCTGTGCTAAGTTTGCCACC 60.039 55.000 6.84 0.00 0.00 4.61
3973 4482 1.317613 CTGTGCTAAGTTTGCCACCA 58.682 50.000 6.84 0.95 0.00 4.17
3984 4493 3.286751 GCCACCAGCGCTTGTTCA 61.287 61.111 12.08 0.00 0.00 3.18
3985 4494 2.844451 GCCACCAGCGCTTGTTCAA 61.844 57.895 12.08 0.00 0.00 2.69
3986 4495 1.732917 CCACCAGCGCTTGTTCAAA 59.267 52.632 12.08 0.00 0.00 2.69
3987 4496 0.102120 CCACCAGCGCTTGTTCAAAA 59.898 50.000 12.08 0.00 0.00 2.44
3988 4497 1.470632 CCACCAGCGCTTGTTCAAAAA 60.471 47.619 12.08 0.00 0.00 1.94
4111 4621 0.883833 CTGCTAAGCCACCAACCTTG 59.116 55.000 0.00 0.00 0.00 3.61
4232 4748 4.726825 TGTGCCTAGGAAAAGGAAGGATAT 59.273 41.667 14.75 0.00 39.15 1.63
4237 4753 7.073725 TGCCTAGGAAAAGGAAGGATATACAAT 59.926 37.037 14.75 0.00 39.15 2.71
4267 4783 2.411069 CAGAGAGATGTTCTGCAACACG 59.589 50.000 0.00 0.00 45.47 4.49
4281 4799 1.271379 CAACACGTAGAGGGTGCTGTA 59.729 52.381 0.00 0.00 36.01 2.74
4300 4819 8.094548 GTGCTGTAATATCACCATCCAATACTA 58.905 37.037 0.00 0.00 0.00 1.82
4312 4831 7.010552 CACCATCCAATACTACTTTTCTTCTCG 59.989 40.741 0.00 0.00 0.00 4.04
4313 4832 7.042335 CCATCCAATACTACTTTTCTTCTCGT 58.958 38.462 0.00 0.00 0.00 4.18
4314 4833 7.549488 CCATCCAATACTACTTTTCTTCTCGTT 59.451 37.037 0.00 0.00 0.00 3.85
4367 4886 2.358619 GCCCCCACACTTATGCCA 59.641 61.111 0.00 0.00 0.00 4.92
4472 4991 1.642037 TTCTCTCCACGCCGTACTCG 61.642 60.000 0.00 3.34 0.00 4.18
4530 5055 2.079170 TCCACACAAGGCCATTTCAA 57.921 45.000 5.01 0.00 0.00 2.69
4590 5115 5.643664 GAATGAAACTGCATCATGCTAACA 58.356 37.500 11.84 4.78 45.31 2.41
4685 5210 0.667487 CTGCGTGACTGTACCCACTG 60.667 60.000 8.02 4.29 0.00 3.66
4695 5220 2.559668 CTGTACCCACTGACGAACCTTA 59.440 50.000 0.00 0.00 0.00 2.69
4792 5317 3.846588 AGAGGATTCCTGTCCAAAAGCTA 59.153 43.478 10.74 0.00 40.90 3.32
4793 5318 4.476479 AGAGGATTCCTGTCCAAAAGCTAT 59.524 41.667 10.74 0.00 40.90 2.97
4807 5332 1.200519 AGCTATCGTTGGTGGCCTAA 58.799 50.000 3.32 0.00 0.00 2.69
4955 5480 0.168788 TGCTGCATTTGCTAACGCTC 59.831 50.000 0.00 0.00 42.66 5.03
4959 5484 1.468520 TGCATTTGCTAACGCTCTTCC 59.531 47.619 3.94 0.00 42.66 3.46
4961 5486 1.062587 CATTTGCTAACGCTCTTCCCG 59.937 52.381 0.00 0.00 36.97 5.14
5011 5538 8.311650 TCTTTTGAAACTAGATAGCACACTTC 57.688 34.615 0.00 0.00 0.00 3.01
5596 6126 2.485038 GGAGCATTTGGGCATTGTTTTG 59.515 45.455 0.00 0.00 35.83 2.44
5618 6148 4.218200 TGTGTGGTGCAATTTATCTTCCTG 59.782 41.667 0.00 0.00 0.00 3.86
5754 6285 2.260434 GTGGTCCTAGTTCGCGCA 59.740 61.111 8.75 0.00 0.00 6.09
5755 6286 2.092882 GTGGTCCTAGTTCGCGCAC 61.093 63.158 8.75 0.00 0.00 5.34
5756 6287 2.273179 TGGTCCTAGTTCGCGCACT 61.273 57.895 17.02 17.02 0.00 4.40
5844 6378 4.886496 ACAGGTTCTAGGTCCTAACAAC 57.114 45.455 0.00 6.04 32.26 3.32
5990 6524 5.955959 TGACACACTGACTATAATACCTGGT 59.044 40.000 4.05 4.05 0.00 4.00
6031 6565 9.794719 AGTTTTCTTCACCTAGCTAACTTTAAT 57.205 29.630 0.00 0.00 0.00 1.40
6043 6577 5.645497 AGCTAACTTTAATGTTGCCTCTCAG 59.355 40.000 15.08 5.58 0.00 3.35
6061 6596 6.986817 CCTCTCAGTGACAAAGAAAAGTTAGA 59.013 38.462 0.00 0.00 0.00 2.10
6105 6640 9.614792 ATTTTAGTAACATGTTAGATCACCTCC 57.385 33.333 18.56 3.99 0.00 4.30
6114 6649 5.437060 TGTTAGATCACCTCCCTTTATTGC 58.563 41.667 0.00 0.00 0.00 3.56
6185 6720 5.036117 TCCAAGTATAATCTCAACCTGCC 57.964 43.478 0.00 0.00 0.00 4.85
6213 6748 9.899226 GCCTTGCTTAATTTCTAATAAGTATGG 57.101 33.333 9.59 9.59 39.68 2.74
6284 6819 4.104579 AGGGTTTTGGCCAAAATCTTCATT 59.895 37.500 39.54 23.55 41.64 2.57
6285 6820 4.216042 GGGTTTTGGCCAAAATCTTCATTG 59.784 41.667 39.54 0.00 41.64 2.82
6286 6821 4.320421 GGTTTTGGCCAAAATCTTCATTGC 60.320 41.667 38.65 24.58 41.64 3.56
6339 6874 6.443934 TTCTTGTTAGCTTTGTAAAGTGCA 57.556 33.333 0.00 0.00 38.28 4.57
6349 6884 1.616865 TGTAAAGTGCACTCGGCTACT 59.383 47.619 21.95 0.00 45.15 2.57
6361 6896 3.321111 ACTCGGCTACTCTGTCTTTCAAA 59.679 43.478 0.00 0.00 0.00 2.69
6377 6912 2.929641 TCAAATGTGGCACTCTGTTGA 58.070 42.857 19.83 17.66 0.00 3.18
6386 6921 2.618241 GGCACTCTGTTGACATGTTTGA 59.382 45.455 0.00 0.00 0.00 2.69
6394 6929 3.761218 TGTTGACATGTTTGACCTTGTGT 59.239 39.130 0.00 0.00 0.00 3.72
6411 6946 6.268387 ACCTTGTGTCATTTCCTTGATCATTT 59.732 34.615 0.00 0.00 0.00 2.32
6588 7132 6.322712 AGCTCATACTACTACTTTTCCTCCAG 59.677 42.308 0.00 0.00 0.00 3.86
6596 7140 1.959282 ACTTTTCCTCCAGCTTGCTTG 59.041 47.619 0.00 0.00 0.00 4.01
6668 7212 0.323302 TGCGGACAAAGTAGATGCCA 59.677 50.000 0.00 0.00 0.00 4.92
6706 7252 7.873505 GTCATAACTAACACCTGTCTTCTCTTT 59.126 37.037 0.00 0.00 0.00 2.52
6815 7361 1.268539 GCAGGAAACCAAACAGTGTCG 60.269 52.381 0.00 0.00 0.00 4.35
6880 7426 6.539173 TGCCGGTTGGTGATTAATTATAGAT 58.461 36.000 1.90 0.00 37.67 1.98
6926 7473 4.178545 ACCAAATGAGATTTTGCTTCCG 57.821 40.909 0.00 0.00 35.67 4.30
7334 7883 0.531657 CCACTCTCCTGCTGTCTGAG 59.468 60.000 0.00 0.00 0.00 3.35
7376 7925 2.874701 GTCACTTGTCACTGACAGCAAT 59.125 45.455 11.67 0.00 43.69 3.56
7438 7987 4.406649 AGGGTATGTACGCTTAAGGCTTTA 59.593 41.667 4.45 0.00 45.71 1.85
7458 8009 3.127425 AGCTTACCAGAACCTTGTCAC 57.873 47.619 0.00 0.00 0.00 3.67
7459 8010 2.706190 AGCTTACCAGAACCTTGTCACT 59.294 45.455 0.00 0.00 0.00 3.41
7460 8011 3.136626 AGCTTACCAGAACCTTGTCACTT 59.863 43.478 0.00 0.00 0.00 3.16
7461 8012 3.251004 GCTTACCAGAACCTTGTCACTTG 59.749 47.826 0.00 0.00 0.00 3.16
7462 8013 4.451900 CTTACCAGAACCTTGTCACTTGT 58.548 43.478 0.00 0.00 0.00 3.16
7463 8014 2.919228 ACCAGAACCTTGTCACTTGTC 58.081 47.619 0.00 0.00 0.00 3.18
7464 8015 2.505819 ACCAGAACCTTGTCACTTGTCT 59.494 45.455 0.00 0.00 0.00 3.41
7554 8105 8.737168 TTGCAGTAGTAGAATTTGCATCTTAT 57.263 30.769 0.00 0.00 43.46 1.73
7603 8154 2.742372 GTGATGCGCGGGAACAGT 60.742 61.111 8.83 0.00 0.00 3.55
7678 8229 3.691342 TTCGTGAGGGTGAGGCCG 61.691 66.667 0.00 0.00 38.44 6.13
8166 8717 1.947456 GGTTCGTGGAGCAGTTTTTCT 59.053 47.619 0.00 0.00 0.00 2.52
8181 8732 3.485463 TTTTCTTCTTCTTCCGAGGCA 57.515 42.857 0.00 0.00 0.00 4.75
8244 8799 4.821805 CCTGTGTATTCTGTTTGGTGACTT 59.178 41.667 0.00 0.00 0.00 3.01
8555 9139 6.258727 TGATCACTTGTGTTGTTCTTCTCTTC 59.741 38.462 0.00 0.00 0.00 2.87
8561 9145 7.174946 ACTTGTGTTGTTCTTCTCTTCTTTGAA 59.825 33.333 0.00 0.00 0.00 2.69
8812 9402 5.821204 GCTTGTATGTAGCCCACAAATTAG 58.179 41.667 0.00 0.00 41.55 1.73
8818 9408 4.780815 TGTAGCCCACAAATTAGAGATGG 58.219 43.478 0.00 0.00 32.95 3.51
8821 9411 2.689983 GCCCACAAATTAGAGATGGTGG 59.310 50.000 0.00 0.00 44.09 4.61
8880 9471 4.082625 TGCCAAAACTCAGCATAATGTGAG 60.083 41.667 6.98 6.98 44.92 3.51
8890 9481 7.507277 ACTCAGCATAATGTGAGACTATCCTTA 59.493 37.037 13.16 0.00 42.49 2.69
8922 9513 5.751680 CACACTACTTCAAAACATCACCTG 58.248 41.667 0.00 0.00 0.00 4.00
9018 9609 5.814188 TCAAGGACATGAAATCAGAGATTCG 59.186 40.000 0.00 0.00 0.00 3.34
9030 9621 3.897505 TCAGAGATTCGGAGCATTATCCA 59.102 43.478 0.00 0.00 39.53 3.41
9057 9648 4.164294 GTGTTCAATCTTCAATGCTGAGC 58.836 43.478 0.00 0.00 31.69 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.429478 TGACCACGTGTAAGAGATCGA 58.571 47.619 15.65 0.00 0.00 3.59
27 28 4.386951 TCCCGCCATGACCACGTG 62.387 66.667 9.08 9.08 0.00 4.49
95 96 4.271291 GCGGTTGACCATCTCTTAGATTTC 59.729 45.833 0.51 0.00 31.32 2.17
119 120 3.854414 GCATAATGCATTGGACATCCACG 60.854 47.826 22.27 0.00 44.29 4.94
126 129 3.119849 GGGATACGCATAATGCATTGGAC 60.120 47.826 22.27 9.44 45.36 4.02
138 141 4.978099 AGATTTGAAGATGGGATACGCAT 58.022 39.130 0.00 0.00 39.69 4.73
142 145 7.189512 CGTTTTGAGATTTGAAGATGGGATAC 58.810 38.462 0.00 0.00 0.00 2.24
145 148 4.082787 GCGTTTTGAGATTTGAAGATGGGA 60.083 41.667 0.00 0.00 0.00 4.37
177 181 5.674052 ATTTGCATGCTTACCCATTTGTA 57.326 34.783 20.33 0.00 0.00 2.41
217 221 9.787435 AATGAATTATCCAGCTATTTACGGTTA 57.213 29.630 0.00 0.00 0.00 2.85
219 223 7.936847 TCAATGAATTATCCAGCTATTTACGGT 59.063 33.333 0.00 0.00 0.00 4.83
220 224 8.322906 TCAATGAATTATCCAGCTATTTACGG 57.677 34.615 0.00 0.00 0.00 4.02
247 257 6.209788 CCCTGTTTTGGCAAGTAGGTAATTTA 59.790 38.462 18.82 0.00 0.00 1.40
289 299 1.480954 ACCGTGTAAGGATAGGCTGTG 59.519 52.381 0.00 0.00 34.73 3.66
305 315 6.549433 TTCTCTATTGGGTGTAATAACCGT 57.451 37.500 0.00 0.00 41.52 4.83
333 343 2.433239 GGGTACAGGCGAATTAGGAAGA 59.567 50.000 0.00 0.00 0.00 2.87
339 349 2.775384 AGGATTGGGTACAGGCGAATTA 59.225 45.455 0.00 0.00 0.00 1.40
340 350 1.564348 AGGATTGGGTACAGGCGAATT 59.436 47.619 0.00 0.00 0.00 2.17
394 404 0.107017 CATTTCAGGACCCCGCATCT 60.107 55.000 0.00 0.00 0.00 2.90
404 414 1.299648 CCAGCCGTCCATTTCAGGA 59.700 57.895 0.00 0.00 34.64 3.86
412 422 3.716195 CACCATCCCAGCCGTCCA 61.716 66.667 0.00 0.00 0.00 4.02
470 480 3.995506 CTTGGCCCCGTCCATGGAC 62.996 68.421 31.59 31.59 41.40 4.02
471 481 3.727258 CTTGGCCCCGTCCATGGA 61.727 66.667 11.44 11.44 35.77 3.41
472 482 4.820744 CCTTGGCCCCGTCCATGG 62.821 72.222 4.97 4.97 42.63 3.66
473 483 3.727258 TCCTTGGCCCCGTCCATG 61.727 66.667 0.00 0.00 35.77 3.66
474 484 3.728373 GTCCTTGGCCCCGTCCAT 61.728 66.667 0.00 0.00 35.77 3.41
477 487 4.410400 CTGGTCCTTGGCCCCGTC 62.410 72.222 0.00 0.00 0.00 4.79
571 584 3.200593 CAGAGATGGGCTGCACGC 61.201 66.667 0.50 0.00 38.13 5.34
913 929 2.279918 CCTACCCGTATGCGTGGC 60.280 66.667 1.69 0.00 36.15 5.01
914 930 1.678598 TTCCCTACCCGTATGCGTGG 61.679 60.000 1.69 5.84 36.15 4.94
916 932 1.125633 AATTCCCTACCCGTATGCGT 58.874 50.000 1.69 0.00 36.15 5.24
917 933 1.069513 TCAATTCCCTACCCGTATGCG 59.930 52.381 0.00 0.00 37.95 4.73
918 934 2.367567 TCTCAATTCCCTACCCGTATGC 59.632 50.000 0.00 0.00 0.00 3.14
927 947 2.865809 TCTCCTCCCTCTCAATTCCCTA 59.134 50.000 0.00 0.00 0.00 3.53
935 955 3.333381 CTGGATATCTCTCCTCCCTCTCA 59.667 52.174 2.05 0.00 36.20 3.27
953 974 2.589157 CCCCGCACTAACCACTGGA 61.589 63.158 0.71 0.00 0.00 3.86
956 977 2.203877 TCCCCCGCACTAACCACT 60.204 61.111 0.00 0.00 0.00 4.00
1397 1419 1.783031 CGGTATAGGCTCGTGCTCGT 61.783 60.000 9.61 0.00 39.59 4.18
1410 1432 3.612681 GGCTGCGCCTCCGGTATA 61.613 66.667 4.18 0.00 46.69 1.47
1600 1627 9.066939 CACACGAGGATTAATTAATAGAGATCG 57.933 37.037 10.68 15.73 0.00 3.69
1640 1667 5.542635 GGAAATCTTAAGGGAAAAAGGGTGT 59.457 40.000 1.85 0.00 0.00 4.16
1641 1668 5.046591 GGGAAATCTTAAGGGAAAAAGGGTG 60.047 44.000 1.85 0.00 0.00 4.61
1684 1713 7.066525 ACAGACAGATTGAAACTAACGGAAAAA 59.933 33.333 0.00 0.00 0.00 1.94
1761 1791 0.658897 GAACCACAGGCGAAACGAAA 59.341 50.000 0.00 0.00 0.00 3.46
1780 1810 1.178534 TGGGAAAAGCTTGCGGAAGG 61.179 55.000 18.86 0.29 0.00 3.46
1822 1852 2.769663 CCTTTTTGGTTATTAGGCCCCC 59.230 50.000 0.00 0.00 0.00 5.40
1880 1911 4.261909 GCCGCTTTAGCATAGTAGGAGTAA 60.262 45.833 2.29 0.00 42.21 2.24
1881 1912 3.255149 GCCGCTTTAGCATAGTAGGAGTA 59.745 47.826 2.29 0.00 42.21 2.59
1882 1913 2.036089 GCCGCTTTAGCATAGTAGGAGT 59.964 50.000 2.29 0.00 42.21 3.85
1883 1914 2.035961 TGCCGCTTTAGCATAGTAGGAG 59.964 50.000 2.29 0.00 42.21 3.69
1884 1915 2.036387 TGCCGCTTTAGCATAGTAGGA 58.964 47.619 2.29 0.00 42.21 2.94
1885 1916 2.526304 TGCCGCTTTAGCATAGTAGG 57.474 50.000 2.29 0.00 42.21 3.18
1892 1923 1.728068 TTAACGATGCCGCTTTAGCA 58.272 45.000 2.29 0.00 45.94 3.49
1922 1980 2.370393 GGTTCGTCGAACTGGCGTC 61.370 63.158 31.00 14.29 41.70 5.19
1947 2005 2.512974 GACGTAATGGGCCCGGTG 60.513 66.667 19.37 7.57 0.00 4.94
1979 2037 1.021920 GCTCTCTCGCCCCAGTTTTC 61.022 60.000 0.00 0.00 0.00 2.29
2080 2138 2.668632 GTGGCCAGGATTGACCGA 59.331 61.111 5.11 0.00 44.74 4.69
2493 2562 3.374402 CGCTCCTCACCAGACCGT 61.374 66.667 0.00 0.00 0.00 4.83
2539 2608 0.829182 GGAGCATATGCCCCCAAAGG 60.829 60.000 23.96 0.00 43.38 3.11
2540 2609 0.106066 TGGAGCATATGCCCCCAAAG 60.106 55.000 27.52 0.00 38.26 2.77
2541 2610 0.106066 CTGGAGCATATGCCCCCAAA 60.106 55.000 28.56 12.16 41.50 3.28
2542 2611 1.538167 CTGGAGCATATGCCCCCAA 59.462 57.895 28.56 17.89 41.50 4.12
2543 2612 3.137385 GCTGGAGCATATGCCCCCA 62.137 63.158 27.64 27.64 38.26 4.96
2544 2613 2.282745 GCTGGAGCATATGCCCCC 60.283 66.667 23.99 23.40 38.26 5.40
2638 2707 1.238439 CGTTGCCAAATCTGGTGACT 58.762 50.000 0.00 0.00 45.53 3.41
2680 2749 0.237498 CGTTCAAAAGGGCGAAGGAC 59.763 55.000 0.00 0.00 0.00 3.85
2691 2760 5.575606 CGCTAGTTAATCTCCTCGTTCAAAA 59.424 40.000 0.00 0.00 0.00 2.44
2695 2764 4.548991 TCGCTAGTTAATCTCCTCGTTC 57.451 45.455 0.00 0.00 0.00 3.95
2696 2765 4.579340 TCATCGCTAGTTAATCTCCTCGTT 59.421 41.667 0.00 0.00 0.00 3.85
2698 2767 4.023963 TGTCATCGCTAGTTAATCTCCTCG 60.024 45.833 0.00 0.00 0.00 4.63
2783 2853 3.864686 CACATTTCGAGCCGCGGG 61.865 66.667 29.38 10.87 41.33 6.13
2805 2875 1.146930 GCCCGAAGATGCAGATGGA 59.853 57.895 0.00 0.00 0.00 3.41
2812 2882 4.115199 ACCCCAGCCCGAAGATGC 62.115 66.667 0.00 0.00 0.00 3.91
2839 2909 2.725203 TACCTGGTGACCAAGCGTGC 62.725 60.000 10.23 0.00 30.80 5.34
2931 3012 2.514458 AAGTTCGCCCATTCTGGAAT 57.486 45.000 0.00 0.00 40.96 3.01
2956 3037 8.352201 TCGAAAACAGAGATGACAAATCAAATT 58.648 29.630 0.00 0.00 38.69 1.82
2957 3038 7.874940 TCGAAAACAGAGATGACAAATCAAAT 58.125 30.769 0.00 0.00 38.69 2.32
3008 3099 2.870411 ACTCTTACGTGTCCAACTTTGC 59.130 45.455 0.00 0.00 0.00 3.68
3041 3132 9.674068 AAGACAAGAGAAAATTATTCCCTCTAC 57.326 33.333 8.66 5.53 34.18 2.59
3042 3133 9.672673 CAAGACAAGAGAAAATTATTCCCTCTA 57.327 33.333 8.66 0.00 34.18 2.43
3137 3231 6.568869 GCTCTCATAGTGACAGTGAAGTAAT 58.431 40.000 0.00 0.00 0.00 1.89
3141 3235 3.127721 TCGCTCTCATAGTGACAGTGAAG 59.872 47.826 0.00 0.00 39.84 3.02
3203 3297 9.326339 CTACAACTTAAAGAAAAAGATTACGGC 57.674 33.333 0.00 0.00 0.00 5.68
3205 3299 9.872757 TGCTACAACTTAAAGAAAAAGATTACG 57.127 29.630 0.00 0.00 0.00 3.18
3210 3304 9.445786 CGAATTGCTACAACTTAAAGAAAAAGA 57.554 29.630 0.00 0.00 0.00 2.52
3211 3305 9.445786 TCGAATTGCTACAACTTAAAGAAAAAG 57.554 29.630 0.00 0.00 0.00 2.27
3214 3308 9.959749 ATTTCGAATTGCTACAACTTAAAGAAA 57.040 25.926 0.00 0.00 0.00 2.52
3215 3309 9.393249 CATTTCGAATTGCTACAACTTAAAGAA 57.607 29.630 7.08 0.00 0.00 2.52
3216 3310 7.537306 GCATTTCGAATTGCTACAACTTAAAGA 59.463 33.333 28.73 0.00 35.95 2.52
3217 3311 7.201350 GGCATTTCGAATTGCTACAACTTAAAG 60.201 37.037 32.17 0.78 38.88 1.85
3279 3374 6.070767 ACTGAAACTATACCATAGCTGTGTGT 60.071 38.462 9.80 9.33 0.00 3.72
3280 3375 6.256539 CACTGAAACTATACCATAGCTGTGTG 59.743 42.308 9.80 3.78 0.00 3.82
3281 3376 6.341316 CACTGAAACTATACCATAGCTGTGT 58.659 40.000 9.80 0.00 0.00 3.72
3282 3377 5.755375 CCACTGAAACTATACCATAGCTGTG 59.245 44.000 2.99 2.99 0.00 3.66
3283 3378 5.661312 TCCACTGAAACTATACCATAGCTGT 59.339 40.000 0.00 0.00 0.00 4.40
3284 3379 6.161855 TCCACTGAAACTATACCATAGCTG 57.838 41.667 0.00 0.00 0.00 4.24
3285 3380 6.808321 TTCCACTGAAACTATACCATAGCT 57.192 37.500 0.00 0.00 0.00 3.32
3391 3495 1.201414 CCACGCCAATACCAAAGGAAC 59.799 52.381 0.00 0.00 0.00 3.62
3436 3543 2.093447 GGGTCGTGATGGAATTCTGACT 60.093 50.000 5.23 0.00 0.00 3.41
3447 3554 0.592500 CGATCAGACGGGTCGTGATG 60.593 60.000 14.29 0.00 41.37 3.07
3448 3555 1.728069 CGATCAGACGGGTCGTGAT 59.272 57.895 0.00 11.13 41.37 3.06
3449 3556 3.047718 GCGATCAGACGGGTCGTGA 62.048 63.158 9.96 0.00 41.37 4.35
3450 3557 2.579787 GCGATCAGACGGGTCGTG 60.580 66.667 9.96 0.00 41.37 4.35
3486 3609 1.405821 CATTAACTCGCTCGGACCTCT 59.594 52.381 0.00 0.00 0.00 3.69
3487 3610 1.536284 CCATTAACTCGCTCGGACCTC 60.536 57.143 0.00 0.00 0.00 3.85
3488 3611 0.460311 CCATTAACTCGCTCGGACCT 59.540 55.000 0.00 0.00 0.00 3.85
3489 3612 0.458669 TCCATTAACTCGCTCGGACC 59.541 55.000 0.00 0.00 0.00 4.46
3490 3613 1.557651 GTCCATTAACTCGCTCGGAC 58.442 55.000 0.00 0.00 36.46 4.79
3491 3614 0.458669 GGTCCATTAACTCGCTCGGA 59.541 55.000 0.00 0.00 0.00 4.55
3492 3615 0.529992 GGGTCCATTAACTCGCTCGG 60.530 60.000 0.00 0.00 0.00 4.63
3493 3616 0.174845 TGGGTCCATTAACTCGCTCG 59.825 55.000 0.00 0.00 0.00 5.03
3540 3663 0.036732 AAAGAAGGAGGCGTGCATGA 59.963 50.000 10.93 0.00 0.00 3.07
3542 3665 0.678048 GGAAAGAAGGAGGCGTGCAT 60.678 55.000 0.00 0.00 0.00 3.96
3572 3695 2.254350 TCGCTCTTCGACACGTGG 59.746 61.111 21.57 2.57 43.16 4.94
3623 3746 2.435693 CCTCGGCCCGGAGATCTTT 61.436 63.158 0.73 0.00 36.08 2.52
3637 3760 3.160047 ATCCAGCCAGCCTCCTCG 61.160 66.667 0.00 0.00 0.00 4.63
3638 3761 1.765657 AGATCCAGCCAGCCTCCTC 60.766 63.158 0.00 0.00 0.00 3.71
3639 3762 2.071262 CAGATCCAGCCAGCCTCCT 61.071 63.158 0.00 0.00 0.00 3.69
3640 3763 2.509916 CAGATCCAGCCAGCCTCC 59.490 66.667 0.00 0.00 0.00 4.30
3748 3871 2.438434 CCCACGGAATGCCTGGTC 60.438 66.667 7.28 0.00 33.27 4.02
3777 3901 1.719780 CGGTCTTTCGAGAAGAAACGG 59.280 52.381 17.60 8.54 43.35 4.44
3844 3975 3.727387 GCCCCTGCCTGAAGACTA 58.273 61.111 0.00 0.00 0.00 2.59
3942 4451 4.256920 ACTTAGCACAGCCTAATGAGTTG 58.743 43.478 0.00 0.00 0.00 3.16
3954 4463 1.267806 CTGGTGGCAAACTTAGCACAG 59.732 52.381 0.00 0.00 0.00 3.66
3967 4476 2.348605 TTTGAACAAGCGCTGGTGGC 62.349 55.000 20.41 14.46 37.64 5.01
3968 4477 0.102120 TTTTGAACAAGCGCTGGTGG 59.898 50.000 20.41 7.68 0.00 4.61
3969 4478 1.919918 TTTTTGAACAAGCGCTGGTG 58.080 45.000 20.41 13.41 0.00 4.17
3993 4502 0.179113 CAACGCTGGTGGCAAACTTT 60.179 50.000 0.00 0.00 41.91 2.66
3994 4503 1.437160 CAACGCTGGTGGCAAACTT 59.563 52.632 0.00 0.00 41.91 2.66
3995 4504 3.119193 CAACGCTGGTGGCAAACT 58.881 55.556 0.00 0.00 41.91 2.66
3996 4505 2.658268 GCAACGCTGGTGGCAAAC 60.658 61.111 0.00 0.00 42.99 2.93
3997 4506 3.910490 GGCAACGCTGGTGGCAAA 61.910 61.111 13.61 0.00 45.44 3.68
4077 4586 1.600916 GCAGGAAACCGACAAGGCT 60.601 57.895 0.00 0.00 46.52 4.58
4111 4621 5.063438 GCGGGAAATCTTTAAAAATGCTTCC 59.937 40.000 0.00 0.00 0.00 3.46
4237 4753 5.618862 CAGAACATCTCTCTGCTTTCGCAA 61.619 45.833 0.00 0.00 37.83 4.85
4246 4762 2.411069 CGTGTTGCAGAACATCTCTCTG 59.589 50.000 0.00 0.00 43.95 3.35
4249 4765 2.533266 ACGTGTTGCAGAACATCTCT 57.467 45.000 0.00 0.00 43.95 3.10
4262 4778 1.624336 TACAGCACCCTCTACGTGTT 58.376 50.000 0.00 0.00 33.61 3.32
4264 4780 2.961526 ATTACAGCACCCTCTACGTG 57.038 50.000 0.00 0.00 0.00 4.49
4313 4832 8.024285 GGACCAATACGTTGTTCAATTATTGAA 58.976 33.333 15.46 15.46 38.58 2.69
4314 4833 7.362229 GGGACCAATACGTTGTTCAATTATTGA 60.362 37.037 19.73 3.20 33.70 2.57
4472 4991 4.935808 AGTCCATTCGTGTCATTTTCTACC 59.064 41.667 0.00 0.00 0.00 3.18
4530 5055 4.635765 CACCATCATAACACAGGACGAAAT 59.364 41.667 0.00 0.00 0.00 2.17
4590 5115 2.356793 GCTCTGTCGTGCAGCACT 60.357 61.111 23.15 0.00 44.66 4.40
4695 5220 4.200874 CGTAGTCAGATCTTCACCTACCT 58.799 47.826 0.00 0.00 0.00 3.08
4792 5317 1.821216 CTTGTTAGGCCACCAACGAT 58.179 50.000 5.01 0.00 0.00 3.73
4793 5318 0.887387 GCTTGTTAGGCCACCAACGA 60.887 55.000 5.01 5.08 0.00 3.85
4807 5332 2.386661 AACGTAGCTAGCATGCTTGT 57.613 45.000 28.02 16.03 43.74 3.16
4955 5480 2.046892 CTGTGCTCCACCGGGAAG 60.047 66.667 6.32 0.26 44.38 3.46
4959 5484 1.746615 CAATCCTGTGCTCCACCGG 60.747 63.158 0.00 0.00 39.55 5.28
4961 5486 1.620822 AAACAATCCTGTGCTCCACC 58.379 50.000 0.00 0.00 35.37 4.61
5011 5538 4.383052 TGCAAAACGTACACAGTGTTTTTG 59.617 37.500 25.16 25.16 42.20 2.44
5187 5717 4.501229 CCTTTCTGGATCTTGATCCTCTCG 60.501 50.000 24.74 13.59 41.29 4.04
5398 5928 2.614983 GCCTTTCACAACGTTAACCTGA 59.385 45.455 0.00 0.00 0.00 3.86
5596 6126 4.737054 CAGGAAGATAAATTGCACCACAC 58.263 43.478 0.00 0.00 0.00 3.82
5754 6285 6.040842 TCACCACCGTTAGAAAAAGTAGTAGT 59.959 38.462 0.00 0.00 0.00 2.73
5755 6286 6.449698 TCACCACCGTTAGAAAAAGTAGTAG 58.550 40.000 0.00 0.00 0.00 2.57
5756 6287 6.403866 TCACCACCGTTAGAAAAAGTAGTA 57.596 37.500 0.00 0.00 0.00 1.82
5844 6378 9.620259 ACTAATTTAGCCTAAAAATGGAGAGAG 57.380 33.333 0.21 0.00 0.00 3.20
5990 6524 8.999431 GTGAAGAAAACTACACATCCAAATAGA 58.001 33.333 0.00 0.00 34.05 1.98
6031 6565 2.170397 TCTTTGTCACTGAGAGGCAACA 59.830 45.455 0.00 0.00 41.41 3.33
6043 6577 9.173939 CATTCATGTCTAACTTTTCTTTGTCAC 57.826 33.333 0.00 0.00 0.00 3.67
6080 6615 8.044908 GGGAGGTGATCTAACATGTTACTAAAA 58.955 37.037 14.35 0.00 0.00 1.52
6082 6617 6.901300 AGGGAGGTGATCTAACATGTTACTAA 59.099 38.462 14.35 3.91 0.00 2.24
6102 6637 8.787852 GTTAGAATTCCTATGCAATAAAGGGAG 58.212 37.037 0.65 0.00 0.00 4.30
6114 6649 6.830912 TGGAGGTGATGTTAGAATTCCTATG 58.169 40.000 0.65 0.00 0.00 2.23
6213 6748 6.128254 GGCTCTATGTCAAACCTTAACTGAAC 60.128 42.308 0.00 0.00 0.00 3.18
6284 6819 2.159382 GTTAAGGCAGCTTACTTGGCA 58.841 47.619 9.37 0.00 42.98 4.92
6285 6820 2.437413 AGTTAAGGCAGCTTACTTGGC 58.563 47.619 9.37 0.00 41.05 4.52
6286 6821 4.072131 TCAAGTTAAGGCAGCTTACTTGG 58.928 43.478 16.28 3.24 33.71 3.61
6339 6874 2.515854 TGAAAGACAGAGTAGCCGAGT 58.484 47.619 0.00 0.00 0.00 4.18
6349 6884 3.554934 AGTGCCACATTTGAAAGACAGA 58.445 40.909 0.00 0.00 0.00 3.41
6361 6896 2.156917 CATGTCAACAGAGTGCCACAT 58.843 47.619 0.00 0.00 0.00 3.21
6386 6921 4.728772 TGATCAAGGAAATGACACAAGGT 58.271 39.130 0.00 0.00 30.82 3.50
6596 7140 5.349543 CCCAAAAGAATATTCTTGCAACTGC 59.650 40.000 27.25 0.00 46.22 4.40
6668 7212 7.442364 GGTGTTAGTTATGACATCATGCACTAT 59.558 37.037 12.87 0.00 35.35 2.12
6706 7252 0.399833 TATGACCTGCACACAAGGCA 59.600 50.000 0.00 0.00 39.32 4.75
6926 7473 4.345257 ACCCACATATCTCATGACAGTACC 59.655 45.833 0.00 0.00 0.00 3.34
7040 7587 7.069877 ACAAGAACCCACTAACTGTAATGTA 57.930 36.000 0.00 0.00 0.00 2.29
7216 7765 5.001232 TCAGATACCAACACCTTAACAAGC 58.999 41.667 0.00 0.00 0.00 4.01
7334 7883 2.167075 CCTTCCAAATGCCATTGAGGTC 59.833 50.000 8.50 0.00 40.61 3.85
7376 7925 1.765074 GGGTCCCTTGTAGTTGCCA 59.235 57.895 0.00 0.00 0.00 4.92
7438 7987 2.706190 AGTGACAAGGTTCTGGTAAGCT 59.294 45.455 0.00 0.00 0.00 3.74
7554 8105 3.689161 CCTGCAAAGATGATCCGTAAACA 59.311 43.478 0.00 0.00 0.00 2.83
7624 8175 3.851128 TTGGACGACGGGCACACA 61.851 61.111 0.00 0.00 0.00 3.72
8244 8799 0.736053 GAAACACCAGCACCAACGAA 59.264 50.000 0.00 0.00 0.00 3.85
8436 8995 3.074412 GCATCCAGTTCTTTCTCCGAAA 58.926 45.455 0.00 0.00 0.00 3.46
8555 9139 1.318576 AGTTTGCCTCCCGTTCAAAG 58.681 50.000 0.00 0.00 31.30 2.77
8561 9145 1.286248 AAGGATAGTTTGCCTCCCGT 58.714 50.000 0.00 0.00 32.07 5.28
8621 9205 2.098117 GGAACATGCACAGTCTAATGGC 59.902 50.000 0.00 0.00 0.00 4.40
8812 9402 1.747355 CACTTCATTGGCCACCATCTC 59.253 52.381 3.88 0.00 31.53 2.75
8818 9408 4.702131 AGAGTTTATCACTTCATTGGCCAC 59.298 41.667 3.88 0.00 35.01 5.01
8821 9411 4.156556 TGCAGAGTTTATCACTTCATTGGC 59.843 41.667 0.00 0.00 35.01 4.52
8880 9471 4.326548 GTGTGCTGTTTCGTAAGGATAGTC 59.673 45.833 0.00 0.00 38.47 2.59
8890 9481 3.173668 TGAAGTAGTGTGCTGTTTCGT 57.826 42.857 0.00 0.00 0.00 3.85
8922 9513 3.444388 AGTAGACGGTGTCCTGAAGAATC 59.556 47.826 0.00 0.00 32.18 2.52
9018 9609 4.458989 TGAACACAAAGTGGATAATGCTCC 59.541 41.667 1.93 0.00 37.94 4.70
9030 9621 5.981315 CAGCATTGAAGATTGAACACAAAGT 59.019 36.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.