Multiple sequence alignment - TraesCS1A01G251400

Loading Multiple Alignment...

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 TraesCS1A01G251400 chr1A 100.000 9033 0 0 1 9033 442809006 442799974 0.000000e+00 16681
1 TraesCS1A01G251400 chr1D 94.199 5137 173 44 3983 9033 343182515 343177418 0.000000e+00 7720
2 TraesCS1A01G251400 chr1D 92.839 2011 97 26 1902 3892 343184996 343183013 0.000000e+00 2872
3 TraesCS1A01G251400 chr1D 93.869 1892 84 13 1 1888 343186846 343184983 0.000000e+00 2822
4 TraesCS1A01G251400 chr1D 92.241 116 7 1 3882 3997 343182644 343182531 7.260000e-36 163
5 TraesCS1A01G251400 chr1B 94.265 5109 178 42 3993 9033 460277926 460272865 0.000000e+00 7705
6 TraesCS1A01G251400 chr1B 90.341 4079 217 63 1 4010 460281910 460277940 0.000000e+00 5186
7 TraesCS1A01G251400 chr7A 88.065 553 27 14 8106 8644 280227047 280226520 3.580000e-173 619


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 TraesCS1A01G251400 chr1A 442799974 442809006 9032 True 16681.00 16681 100.000 1 9033 1 chr1A.!!$R1 9032
1 TraesCS1A01G251400 chr1D 343177418 343186846 9428 True 3394.25 7720 93.287 1 9033 4 chr1D.!!$R1 9032
2 TraesCS1A01G251400 chr1B 460272865 460281910 9045 True 6445.50 7705 92.303 1 9033 2 chr1B.!!$R1 9032
3 TraesCS1A01G251400 chr7A 280226520 280227047 527 True 619.00 619 88.065 8106 8644 1 chr7A.!!$R1 538

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
308 311 0.388294 AGCCTATCCTTACGCGGTTC 59.612 55.0 12.47 0.00 0.00 3.62 F
317 320 0.388391 TTACGCGGTTCTTACACCCG 60.388 55.0 12.47 0.00 44.46 5.28 F
1691 1704 0.389391 TTTCCGGCCGCATTTGAAAA 59.611 45.0 22.85 7.79 0.00 2.29 F
2016 2045 0.250770 GGAAAAACTGGGGCGAGAGT 60.251 55.0 0.00 0.00 0.00 3.24 F
3784 3873 0.179129 CAATCAACCAGGCATTCCGC 60.179 55.0 0.00 0.00 41.28 5.54 F
4445 4975 0.319555 TCTTTTCTCTCCACGCCGTG 60.320 55.0 10.95 10.95 0.00 4.94 F
4585 5115 0.320683 TGCTAACTGTGCTGCACGAT 60.321 50.0 25.88 16.97 37.14 3.73 F
5643 6193 0.323816 TTGTGCCCACAAGACCACAA 60.324 50.0 9.61 0.00 45.42 3.33 F
6311 6864 0.591170 TTAGCTTTGTGAAGTGCGCC 59.409 50.0 4.18 0.00 35.25 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1937 0.167908 CGATGCCGCTTTAGCACAAA 59.832 50.000 2.29 0.00 44.40 2.83 R
2016 2045 0.528017 TGCGCGGAAAATTATTGGCA 59.472 45.000 8.83 0.00 0.00 4.92 R
3238 3312 0.109365 TGCGTGGCAATTCGAATTGG 60.109 50.000 38.24 27.17 44.54 3.16 R
3793 3882 0.667487 CGAGAAGAAACGCAGCCAGA 60.667 55.000 0.00 0.00 0.00 3.86 R
5539 6089 0.247185 AATGCCCAAATGCTCCAACG 59.753 50.000 0.00 0.00 0.00 4.10 R
6311 6864 0.323629 TTGAAAGACAGGGTAGCCGG 59.676 55.000 9.72 9.72 0.00 6.13 R
6542 7104 4.137543 AGCAAGTTGGAGGAAAAGTAGTG 58.862 43.478 4.75 0.00 0.00 2.74 R
6620 7182 0.035056 AGGGCATCTTCTTTGTCCGG 60.035 55.000 0.00 0.00 43.78 5.14 R
8084 8659 0.243095 GGATGTACGACGGCCTATCC 59.757 60.000 0.00 3.54 0.00 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
23 24 5.366460 AGAATACCGATCTCTTAGACGTGA 58.634 41.667 0.00 0.00 0.00 4.35
29 30 3.911365 CGATCTCTTAGACGTGATCATGC 59.089 47.826 15.01 7.90 34.98 4.06
34 35 1.040893 TAGACGTGATCATGCCGGGT 61.041 55.000 15.01 0.00 0.00 5.28
134 135 3.159472 TGGATATCCAATGCATTCTGCC 58.841 45.455 22.52 6.19 42.63 4.85
141 142 0.466189 AATGCATTCTGCCTACCCCG 60.466 55.000 5.99 0.00 44.23 5.73
199 201 5.719173 TGGTAAGCATGCAAATACCTTTTC 58.281 37.500 30.73 15.77 38.85 2.29
308 311 0.388294 AGCCTATCCTTACGCGGTTC 59.612 55.000 12.47 0.00 0.00 3.62
317 320 0.388391 TTACGCGGTTCTTACACCCG 60.388 55.000 12.47 0.00 44.46 5.28
330 333 7.011202 GGTTCTTACACCCGATAGAGAAAAATC 59.989 40.741 0.00 0.00 39.76 2.17
447 450 4.048470 GGTCCAACCAGGCTCCCC 62.048 72.222 0.00 0.00 38.42 4.81
676 687 4.182339 GGCTGACCTTAACTAACTACTGC 58.818 47.826 0.00 0.00 0.00 4.40
677 688 4.182339 GCTGACCTTAACTAACTACTGCC 58.818 47.826 0.00 0.00 0.00 4.85
678 689 4.322499 GCTGACCTTAACTAACTACTGCCA 60.322 45.833 0.00 0.00 0.00 4.92
684 695 0.606604 ACTAACTACTGCCACCACCG 59.393 55.000 0.00 0.00 0.00 4.94
718 729 2.739132 CCCGTACCCGCTAATCCC 59.261 66.667 0.00 0.00 0.00 3.85
874 886 2.804090 GCGTCCGTCGAACACCTC 60.804 66.667 0.00 0.00 42.86 3.85
930 942 2.281761 GCATCATACGGGCAGGGG 60.282 66.667 0.00 0.00 0.00 4.79
931 943 2.431683 CATCATACGGGCAGGGGG 59.568 66.667 0.00 0.00 0.00 5.40
936 948 3.768833 ATACGGGCAGGGGGTCGAT 62.769 63.158 0.00 0.00 0.00 3.59
947 959 1.228925 GGGTCGATAGGGAGGGAGG 60.229 68.421 0.00 0.00 0.00 4.30
962 974 1.146263 GAGGGATAGCCGGTGGTTG 59.854 63.158 1.90 0.00 33.83 3.77
980 992 3.782443 GTGCGGGGGAGTGGGTAG 61.782 72.222 0.00 0.00 0.00 3.18
1065 1077 3.785859 GATCAGGTGGCGGCCAGA 61.786 66.667 24.58 17.04 32.34 3.86
1216 1228 1.752198 CTCAACTGGTTCCCCGTCA 59.248 57.895 0.00 0.00 0.00 4.35
1368 1380 2.254651 GAGCTCGTCGTCACCGTT 59.745 61.111 0.00 0.00 35.01 4.44
1656 1668 6.017325 CGCGTAGTGTTATTTACCCTTTTTC 58.983 40.000 0.00 0.00 0.00 2.29
1691 1704 0.389391 TTTCCGGCCGCATTTGAAAA 59.611 45.000 22.85 7.79 0.00 2.29
1742 1756 3.296842 ATCTCCCGTTTTGGCCCCC 62.297 63.158 0.00 0.00 35.87 5.40
1820 1834 4.339530 GCTTTTCCCACTTGAATATCTCCC 59.660 45.833 0.00 0.00 0.00 4.30
1888 1917 5.010112 TCCAAATGACGTTTTCTTTATGGCA 59.990 36.000 0.00 0.00 0.00 4.92
1889 1918 5.118510 CCAAATGACGTTTTCTTTATGGCAC 59.881 40.000 0.00 0.00 0.00 5.01
1890 1919 5.705609 AATGACGTTTTCTTTATGGCACT 57.294 34.783 0.00 0.00 0.00 4.40
1891 1920 4.742438 TGACGTTTTCTTTATGGCACTC 57.258 40.909 0.00 0.00 0.00 3.51
1892 1921 3.500680 TGACGTTTTCTTTATGGCACTCC 59.499 43.478 0.00 0.00 0.00 3.85
1893 1922 3.751518 ACGTTTTCTTTATGGCACTCCT 58.248 40.909 0.00 0.00 0.00 3.69
1894 1923 3.751698 ACGTTTTCTTTATGGCACTCCTC 59.248 43.478 0.00 0.00 0.00 3.71
1895 1924 3.127030 CGTTTTCTTTATGGCACTCCTCC 59.873 47.826 0.00 0.00 0.00 4.30
1896 1925 4.336280 GTTTTCTTTATGGCACTCCTCCT 58.664 43.478 0.00 0.00 0.00 3.69
1897 1926 3.914426 TTCTTTATGGCACTCCTCCTC 57.086 47.619 0.00 0.00 0.00 3.71
1898 1927 2.119495 TCTTTATGGCACTCCTCCTCC 58.881 52.381 0.00 0.00 0.00 4.30
1899 1928 2.122768 CTTTATGGCACTCCTCCTCCT 58.877 52.381 0.00 0.00 0.00 3.69
1900 1929 3.052109 TCTTTATGGCACTCCTCCTCCTA 60.052 47.826 0.00 0.00 0.00 2.94
1901 1930 2.685106 TATGGCACTCCTCCTCCTAG 57.315 55.000 0.00 0.00 0.00 3.02
1902 1931 0.639392 ATGGCACTCCTCCTCCTAGT 59.361 55.000 0.00 0.00 0.00 2.57
1903 1932 0.413832 TGGCACTCCTCCTCCTAGTT 59.586 55.000 0.00 0.00 0.00 2.24
1904 1933 1.203313 TGGCACTCCTCCTCCTAGTTT 60.203 52.381 0.00 0.00 0.00 2.66
1905 1934 1.909986 GGCACTCCTCCTCCTAGTTTT 59.090 52.381 0.00 0.00 0.00 2.43
1906 1935 2.306219 GGCACTCCTCCTCCTAGTTTTT 59.694 50.000 0.00 0.00 0.00 1.94
1934 1963 3.493129 TGCTAAAGCGGCATCGTTAATAG 59.507 43.478 1.45 0.00 45.83 1.73
1961 1990 3.110178 CGCCAGTTCGACGAACCC 61.110 66.667 31.41 20.62 42.85 4.11
1978 2007 4.752879 CACACGTACCGGGCCCAG 62.753 72.222 24.92 14.49 31.12 4.45
2016 2045 0.250770 GGAAAAACTGGGGCGAGAGT 60.251 55.000 0.00 0.00 0.00 3.24
2032 2061 3.695816 GAGAGTGCCAATAATTTTCCGC 58.304 45.455 0.00 0.00 0.00 5.54
2062 2091 1.482593 CCAGAGGCGGAGTTATTCAGT 59.517 52.381 0.00 0.00 0.00 3.41
2067 2096 1.202545 GGCGGAGTTATTCAGTCCTCC 60.203 57.143 0.00 0.00 41.81 4.30
2113 2142 1.599047 CTCAGCCGGTCAATCCTGT 59.401 57.895 1.90 0.00 0.00 4.00
2166 2195 1.226802 CATCACGAGGTCGCTGGAG 60.227 63.158 0.00 0.00 44.43 3.86
2187 2216 0.955905 TGCAAAACCCTACGGCTTTC 59.044 50.000 0.00 0.00 0.00 2.62
2235 2264 2.034812 TCCGTGCGCCAACTTTATTTTT 59.965 40.909 4.18 0.00 0.00 1.94
2236 2265 2.407026 CCGTGCGCCAACTTTATTTTTC 59.593 45.455 4.18 0.00 0.00 2.29
2365 2402 5.913137 TTGCCAAATTAATGTACTCCTGG 57.087 39.130 0.00 0.00 0.00 4.45
2366 2403 4.929479 TGCCAAATTAATGTACTCCTGGT 58.071 39.130 0.00 0.00 0.00 4.00
2367 2404 6.068461 TGCCAAATTAATGTACTCCTGGTA 57.932 37.500 0.00 0.00 0.00 3.25
2438 2475 1.216710 CTCTGACGCCCTTGTCCTC 59.783 63.158 0.00 0.00 38.11 3.71
2479 2525 4.373116 GGTTCCACTCGAGCGGCA 62.373 66.667 14.87 0.27 0.00 5.69
2607 2672 5.215160 GCGGCATAAAATATTTCAGGTGAG 58.785 41.667 0.10 0.00 0.00 3.51
2613 2678 5.904362 AAAATATTTCAGGTGAGTCTGGC 57.096 39.130 0.10 0.00 35.58 4.85
2703 2768 5.600069 GCCCCTTTTGAATGAGGAGATTAAT 59.400 40.000 0.00 0.00 34.91 1.40
2757 2822 7.382898 TGCTTTGGAGTTGTTTTTAACTTTCT 58.617 30.769 0.00 0.00 40.78 2.52
2773 2838 2.869233 TTCTGGCTGTGTTTTCAAGC 57.131 45.000 0.00 0.00 35.13 4.01
2812 2877 3.265221 TGAGGTCTGCCATCTTCATCTTT 59.735 43.478 0.00 0.00 37.19 2.52
2829 2894 2.969300 TTTGGGCTGGGGTGACGAAC 62.969 60.000 0.00 0.00 0.00 3.95
2840 2905 0.782384 GTGACGAACGATCACGCTTT 59.218 50.000 0.14 0.00 43.96 3.51
2892 2962 5.278022 GGAGATTCGGGAATGCATTTCTTAC 60.278 44.000 17.29 2.14 34.56 2.34
2917 2987 5.916883 ACGCAAGAAAAGAACATCAATGAAG 59.083 36.000 0.00 0.00 43.62 3.02
2919 2989 6.805271 CGCAAGAAAAGAACATCAATGAAGAT 59.195 34.615 0.00 0.00 43.02 2.40
2921 2991 9.070149 GCAAGAAAAGAACATCAATGAAGATAC 57.930 33.333 0.00 0.00 0.00 2.24
2939 3009 9.052759 TGAAGATACTTGAAAGTTTACCAGAAC 57.947 33.333 0.21 0.00 40.37 3.01
2994 3064 2.151202 GTTTTCGAGATTGACTGCCCA 58.849 47.619 0.00 0.00 0.00 5.36
3112 3182 6.788243 TCTGAATTGTCATGATACAACATGC 58.212 36.000 0.00 0.00 44.79 4.06
3114 3184 7.067737 TCTGAATTGTCATGATACAACATGCAT 59.932 33.333 0.00 0.00 44.79 3.96
3116 3186 5.900865 TTGTCATGATACAACATGCATGT 57.099 34.783 26.61 26.61 44.79 3.21
3271 3345 2.794631 GCCACGCATAATAACTTGTGCC 60.795 50.000 2.18 0.00 44.12 5.01
3414 3488 1.849097 CCTACGCGAGTACAATTCCC 58.151 55.000 15.93 0.00 46.88 3.97
3511 3585 0.933097 CCCGTCTGATCGCAATCAAG 59.067 55.000 0.00 0.00 41.33 3.02
3582 3666 2.543067 AAATCCCTGCACGCCTCCTC 62.543 60.000 0.00 0.00 0.00 3.71
3600 3684 2.429930 CTTTCCACCACGGCCTGA 59.570 61.111 0.00 0.00 33.14 3.86
3630 3714 4.477975 GCGACTCGACTGGACCCG 62.478 72.222 1.63 0.00 0.00 5.28
3718 3807 4.803426 CCGCTCCTCCGACTGTGC 62.803 72.222 0.00 0.00 0.00 4.57
3784 3873 0.179129 CAATCAACCAGGCATTCCGC 60.179 55.000 0.00 0.00 41.28 5.54
3793 3882 4.796495 GCATTCCGCGGGTCCCTT 62.796 66.667 27.83 0.57 0.00 3.95
3908 4376 2.434884 CAGCGGTAGGTGGTGCAG 60.435 66.667 0.00 0.00 41.81 4.41
3976 4444 9.219603 TCTCACGAGATTTTGAATTGATAACTT 57.780 29.630 0.00 0.00 31.41 2.66
4038 4541 0.524414 CATATGCATGTGGGCCGATG 59.476 55.000 15.17 10.31 0.00 3.84
4094 4597 1.464997 CTTGTCGGTTTCCTGCTAAGC 59.535 52.381 0.00 0.00 0.00 3.09
4160 4665 2.229784 CCAAATTGACAACTGAGAGGCC 59.770 50.000 0.00 0.00 0.00 5.19
4161 4666 2.206576 AATTGACAACTGAGAGGCCC 57.793 50.000 0.00 0.00 0.00 5.80
4222 4730 2.305927 TCCTGTGCCTAGGAAAAAGGAG 59.694 50.000 14.75 0.00 43.71 3.69
4223 4731 2.040412 CCTGTGCCTAGGAAAAAGGAGT 59.960 50.000 14.75 0.00 40.42 3.85
4250 4780 3.004839 TGTTCTGCGATACATAGAGAGGC 59.995 47.826 0.00 0.00 0.00 4.70
4305 4835 5.111989 TCTCCTCTCGCAATAATTGAACAG 58.888 41.667 0.00 0.00 0.00 3.16
4324 4854 1.227263 CGTATTGGTCCCTGCTCGG 60.227 63.158 0.00 0.00 0.00 4.63
4369 4899 4.570369 TGTGCTAATGTCCATGTACATTCG 59.430 41.667 18.71 14.16 44.79 3.34
4405 4935 6.189859 TCTCTCGGTTATACCCACTTTTCTA 58.810 40.000 0.00 0.00 33.75 2.10
4445 4975 0.319555 TCTTTTCTCTCCACGCCGTG 60.320 55.000 10.95 10.95 0.00 4.94
4463 4993 2.930040 CGTGCTCCGTAGAAAATGACAT 59.070 45.455 0.00 0.00 0.00 3.06
4469 4999 5.504665 GCTCCGTAGAAAATGACATGAATGG 60.505 44.000 0.00 0.00 0.00 3.16
4470 5000 5.739959 TCCGTAGAAAATGACATGAATGGA 58.260 37.500 0.00 0.00 0.00 3.41
4471 5001 5.584649 TCCGTAGAAAATGACATGAATGGAC 59.415 40.000 0.00 0.00 0.00 4.02
4472 5002 5.586243 CCGTAGAAAATGACATGAATGGACT 59.414 40.000 0.00 0.00 0.00 3.85
4473 5003 6.761242 CCGTAGAAAATGACATGAATGGACTA 59.239 38.462 0.00 0.00 0.00 2.59
4474 5004 7.254455 CCGTAGAAAATGACATGAATGGACTAC 60.254 40.741 0.00 4.47 0.00 2.73
4585 5115 0.320683 TGCTAACTGTGCTGCACGAT 60.321 50.000 25.88 16.97 37.14 3.73
4630 5160 4.340950 AGTTCAAAACATCAAACGGGTGAT 59.659 37.500 0.00 0.00 38.84 3.06
4728 5272 9.221933 TGAGGCTAAAAACATTTCGTATTCTAA 57.778 29.630 0.00 0.00 0.00 2.10
4885 5432 5.283060 ACAGAATTTTACTGATGACGCAC 57.717 39.130 0.00 0.00 38.55 5.34
4917 5464 7.169645 CCGTATTTATTTGCTGCATTTGCTAAT 59.830 33.333 1.84 10.08 42.66 1.73
5023 5573 3.000041 TCGCTAATCGAAATGCACAGTT 59.000 40.909 0.00 0.00 45.36 3.16
5405 5955 7.882271 GTGAAAGGCCTGAAGATATATGAAGAT 59.118 37.037 5.69 0.00 0.00 2.40
5643 6193 0.323816 TTGTGCCCACAAGACCACAA 60.324 50.000 9.61 0.00 45.42 3.33
5729 6282 1.667724 GTCCTAGTTCGCGCACTACTA 59.332 52.381 14.68 11.25 0.00 1.82
5730 6283 1.667724 TCCTAGTTCGCGCACTACTAC 59.332 52.381 14.68 0.00 0.00 2.73
5731 6284 1.669779 CCTAGTTCGCGCACTACTACT 59.330 52.381 14.68 5.15 0.00 2.57
5789 6342 5.753921 ACTTTTGTGCTAACTGACTCAGTAC 59.246 40.000 12.22 7.40 44.62 2.73
5813 6366 5.482878 CCTACAGGTTCTAGGTCCTAACAAA 59.517 44.000 0.00 0.00 32.26 2.83
5875 6428 0.804364 TGTTGCATAGAAAGCTGCCG 59.196 50.000 0.00 0.00 37.59 5.69
5890 6443 4.386711 AGCTGCCGGTTATCCTAATTTAC 58.613 43.478 1.90 0.00 0.00 2.01
5939 6492 3.040147 ACAACCATCAACCTAGTGACG 57.960 47.619 0.00 0.00 0.00 4.35
5987 6540 4.062293 TGGATGTGTAGTTTTCTTCACCG 58.938 43.478 0.00 0.00 44.12 4.94
6111 6664 6.314917 AGGAATTCTAACAACACCTCCAAAT 58.685 36.000 5.23 0.00 0.00 2.32
6169 6722 2.924421 ACCTGCTAGCCTTGCTTAATC 58.076 47.619 13.29 0.00 40.44 1.75
6173 6726 3.801698 TGCTAGCCTTGCTTAATCTCTG 58.198 45.455 13.29 0.00 40.44 3.35
6228 6781 3.666274 CCCACAACGTTGGTATAGTTCA 58.334 45.455 30.34 0.00 34.44 3.18
6229 6782 4.258543 CCCACAACGTTGGTATAGTTCAT 58.741 43.478 30.34 4.08 34.44 2.57
6233 6786 6.592607 CCACAACGTTGGTATAGTTCATTAGT 59.407 38.462 30.34 2.21 0.00 2.24
6302 6855 7.701924 TGACAGAATTTTCTTGTTAGCTTTGTG 59.298 33.333 0.00 0.00 34.74 3.33
6311 6864 0.591170 TTAGCTTTGTGAAGTGCGCC 59.409 50.000 4.18 0.00 35.25 6.53
6371 6924 1.126488 TTTGCCCTTGTGCCATTTCA 58.874 45.000 0.00 0.00 0.00 2.69
6378 6931 3.441163 CCTTGTGCCATTTCATTGATCG 58.559 45.455 0.00 0.00 0.00 3.69
6415 6968 9.883142 AATTCTCTAGTTTCAAATCTAGGTGAG 57.117 33.333 7.62 0.00 35.65 3.51
6451 7004 4.410099 TCAACAAGCAGATCAAAGGGAAT 58.590 39.130 0.00 0.00 0.00 3.01
6530 7090 7.360113 ACCAATTGTATGTTCAGGAAAACTT 57.640 32.000 4.43 0.00 0.00 2.66
6542 7104 5.003804 TCAGGAAAACTTTCAGCTCATACC 58.996 41.667 4.67 0.00 38.92 2.73
6616 7178 0.767375 ATCCTTGCATGGGTATCGCT 59.233 50.000 17.95 0.00 0.00 4.93
6620 7182 1.869767 CTTGCATGGGTATCGCTTCTC 59.130 52.381 0.00 0.00 0.00 2.87
6630 7192 0.895530 ATCGCTTCTCCGGACAAAGA 59.104 50.000 20.91 11.47 0.00 2.52
6668 7232 6.094048 GCATGATGTCATAACTAACACCTGTT 59.906 38.462 0.00 0.00 37.13 3.16
6853 7417 9.005777 GCCGGTTGGTGATTAATTATAGAATAA 57.994 33.333 1.90 0.00 37.67 1.40
6913 7477 4.118410 GCTTCCTGTACTGTCATGAGATG 58.882 47.826 0.00 0.00 0.00 2.90
6931 7495 3.328931 AGATGTGTGGGTCAAATCTGAGT 59.671 43.478 0.43 0.00 46.13 3.41
6936 7501 5.013079 TGTGTGGGTCAAATCTGAGTAGAAT 59.987 40.000 0.00 0.00 36.32 2.40
6960 7525 5.289595 TGCTAGTCTGTACACACTTTTCTG 58.710 41.667 9.18 0.00 0.00 3.02
6963 7528 2.548480 GTCTGTACACACTTTTCTGCCC 59.452 50.000 0.00 0.00 0.00 5.36
7065 7630 9.613428 TCAACTGTCCATATTAAGTATCTTTGG 57.387 33.333 0.00 0.00 0.00 3.28
7132 7697 8.920174 ACCAATGCTACTACACTATATAACACA 58.080 33.333 0.00 0.00 0.00 3.72
7139 7704 7.406031 ACTACACTATATAACACACAGTGCT 57.594 36.000 0.00 0.00 40.17 4.40
7166 7731 7.797121 TCTTCAGGGCATGAACATATATAGA 57.203 36.000 10.99 1.01 43.09 1.98
7229 7795 9.696917 GGTATCTGAAAGTGATGAAATTGTTTT 57.303 29.630 0.00 0.00 33.76 2.43
7409 7975 3.558829 GGGTATGTACGCTTAAGGCTTTC 59.441 47.826 4.45 0.00 39.13 2.62
7457 8032 7.422399 CCATTTCCACTTTCTTTTCGACTTTA 58.578 34.615 0.00 0.00 0.00 1.85
7460 8035 6.839820 TCCACTTTCTTTTCGACTTTACTC 57.160 37.500 0.00 0.00 0.00 2.59
7472 8047 5.683859 TCGACTTTACTCTTACTGTTCGTC 58.316 41.667 0.00 0.00 0.00 4.20
7487 8062 3.243636 TGTTCGTCTAACCGAAGAAAGCT 60.244 43.478 0.00 0.00 46.45 3.74
7496 8071 2.288395 ACCGAAGAAAGCTTTGCATTGG 60.288 45.455 18.30 16.46 34.70 3.16
7741 8316 4.481112 GCCGGCATGCAGAAACCG 62.481 66.667 24.80 12.32 45.21 4.44
7744 8319 3.064324 GGCATGCAGAAACCGCCT 61.064 61.111 21.36 0.00 39.73 5.52
7747 8322 1.503542 CATGCAGAAACCGCCTCAC 59.496 57.895 0.00 0.00 0.00 3.51
8084 8659 1.802960 GCATAGCCGTTGGATCTGATG 59.197 52.381 0.00 0.00 0.00 3.07
8402 8989 0.336737 ATCTCCTCCTCTGGTTCGGT 59.663 55.000 0.00 0.00 0.00 4.69
8419 9006 1.197721 CGGTGAAAGAACTGGATGCAC 59.802 52.381 0.00 0.00 0.00 4.57
8435 9022 6.121590 TGGATGCACACATACATAGATGTTT 58.878 36.000 0.00 0.00 42.46 2.83
8470 9057 0.030638 CGAGTTTGGGTTTGCAGGTG 59.969 55.000 0.00 0.00 0.00 4.00
8471 9058 0.389025 GAGTTTGGGTTTGCAGGTGG 59.611 55.000 0.00 0.00 0.00 4.61
8472 9059 1.048160 AGTTTGGGTTTGCAGGTGGG 61.048 55.000 0.00 0.00 0.00 4.61
8473 9060 1.002274 TTTGGGTTTGCAGGTGGGT 59.998 52.632 0.00 0.00 0.00 4.51
8474 9061 1.045911 TTTGGGTTTGCAGGTGGGTC 61.046 55.000 0.00 0.00 0.00 4.46
8475 9062 2.600470 GGGTTTGCAGGTGGGTCC 60.600 66.667 0.00 0.00 0.00 4.46
8516 9103 8.755977 AGATTATGCATTGAATTTCCTCTGTTT 58.244 29.630 3.54 0.00 0.00 2.83
8655 9251 1.021202 CAGTTTGACAAGCAACCGGA 58.979 50.000 9.46 0.00 35.91 5.14
8715 9311 4.083802 CCGAAACAGACTGATTTCTTGGAC 60.084 45.833 10.08 0.00 33.49 4.02
8803 9403 5.224888 CCACAAATTGAAGATGTTGACCAG 58.775 41.667 0.00 0.00 0.00 4.00
8836 9437 6.899393 AACTCTGCATTTCTTATGGTTTGA 57.101 33.333 0.00 0.00 0.00 2.69
8857 9459 6.631971 TGACAAAACTCAGCATAATGTGAA 57.368 33.333 0.00 0.00 0.00 3.18
8914 9516 5.249393 ACATCACCTAATTCTTCAGGACACT 59.751 40.000 0.00 0.00 35.76 3.55
8995 9597 6.714278 TCAAGGACATGAAATCAGAGATTCA 58.286 36.000 0.00 4.38 39.66 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.202359 CGAAAATAAATGGCCACCCGG 60.202 52.381 8.16 0.00 0.00 5.73
34 35 3.667497 TGTTGCGAAAATAAATGGCCA 57.333 38.095 8.56 8.56 0.00 5.36
134 135 3.887621 TGAGATTTGAAGACGGGGTAG 57.112 47.619 0.00 0.00 0.00 3.18
141 142 3.659444 CACGCGTTTTGAGATTTGAAGAC 59.341 43.478 10.22 0.00 0.00 3.01
176 178 5.480073 AGAAAAGGTATTTGCATGCTTACCA 59.520 36.000 29.82 8.74 37.22 3.25
199 201 4.114073 TGCATGCTTTTCTCAACAACAAG 58.886 39.130 20.33 0.00 0.00 3.16
279 282 3.931907 AAGGATAGGCTGTAATGTGCA 57.068 42.857 0.00 0.00 0.00 4.57
308 311 6.583562 AGGATTTTTCTCTATCGGGTGTAAG 58.416 40.000 0.00 0.00 0.00 2.34
317 320 7.359347 GCGAATACGGAAGGATTTTTCTCTATC 60.359 40.741 0.00 0.00 46.90 2.08
330 333 1.537562 GGTACAGGCGAATACGGAAGG 60.538 57.143 0.00 0.00 40.15 3.46
475 478 0.918983 CTGGTCCTTGGGCCTTATCA 59.081 55.000 11.92 0.00 0.00 2.15
672 683 4.954970 CAAGGCGGTGGTGGCAGT 62.955 66.667 0.00 0.00 36.77 4.40
684 695 3.567797 GCGCAGATCCGACAAGGC 61.568 66.667 0.30 0.00 40.77 4.35
874 886 2.611974 AGCTTTTTGTAATGGCGTCG 57.388 45.000 0.00 0.00 0.00 5.12
930 942 1.228925 CCCTCCCTCCCTATCGACC 60.229 68.421 0.00 0.00 0.00 4.79
931 943 0.410270 ATCCCTCCCTCCCTATCGAC 59.590 60.000 0.00 0.00 0.00 4.20
936 948 1.801302 CGGCTATCCCTCCCTCCCTA 61.801 65.000 0.00 0.00 0.00 3.53
947 959 1.451387 CACCAACCACCGGCTATCC 60.451 63.158 0.00 0.00 0.00 2.59
975 987 4.971125 GCGATCGCCAGGCTACCC 62.971 72.222 29.48 0.00 34.56 3.69
1216 1228 4.383552 GGAGTAGAACTTCTGCATGTGGAT 60.384 45.833 9.28 0.00 31.12 3.41
1533 1545 2.282958 TCGTCTTCCGTGGAGGCT 60.283 61.111 0.00 0.00 40.77 4.58
1656 1668 3.288092 CGGAAAGGGAAATCTTAAGGGG 58.712 50.000 1.85 0.00 0.00 4.79
1691 1704 6.710744 ACAGACAGATTGAAACTAACGGAAAT 59.289 34.615 0.00 0.00 0.00 2.17
1742 1756 0.324943 ATCCAACCGTCTGTGGAAGG 59.675 55.000 0.00 0.00 44.74 3.46
1744 1758 1.001974 CAGATCCAACCGTCTGTGGAA 59.998 52.381 0.00 0.00 37.62 3.53
1748 1762 0.608640 GACCAGATCCAACCGTCTGT 59.391 55.000 0.00 0.00 40.12 3.41
1820 1834 7.393841 TTGGTTATTAGGTCCCAATAAAACG 57.606 36.000 4.29 0.00 32.20 3.60
1832 1847 3.446968 GGCCCCTTTTTGGTTATTAGGT 58.553 45.455 0.00 0.00 0.00 3.08
1906 1935 2.671596 GATGCCGCTTTAGCACAAAAA 58.328 42.857 2.29 0.00 44.40 1.94
1907 1936 1.400888 CGATGCCGCTTTAGCACAAAA 60.401 47.619 2.29 0.00 44.40 2.44
1908 1937 0.167908 CGATGCCGCTTTAGCACAAA 59.832 50.000 2.29 0.00 44.40 2.83
1909 1938 0.953471 ACGATGCCGCTTTAGCACAA 60.953 50.000 2.29 0.00 44.40 3.33
1910 1939 0.953471 AACGATGCCGCTTTAGCACA 60.953 50.000 2.29 0.00 44.40 4.57
1911 1940 1.003851 TAACGATGCCGCTTTAGCAC 58.996 50.000 2.29 0.00 44.40 4.40
1912 1941 1.728068 TTAACGATGCCGCTTTAGCA 58.272 45.000 2.29 0.00 45.94 3.49
1913 1942 3.493503 ACTATTAACGATGCCGCTTTAGC 59.506 43.478 0.00 0.00 39.95 3.09
1914 1943 5.919141 ACTACTATTAACGATGCCGCTTTAG 59.081 40.000 0.00 0.00 39.95 1.85
1934 1963 2.850647 GTCGAACTGGCGTGAATACTAC 59.149 50.000 0.00 0.00 0.00 2.73
1978 2007 0.533951 CCCCTAACCACCAGACGTAC 59.466 60.000 0.00 0.00 0.00 3.67
2016 2045 0.528017 TGCGCGGAAAATTATTGGCA 59.472 45.000 8.83 0.00 0.00 4.92
2067 2096 2.815308 CCGTCCGATCCTCCCAAG 59.185 66.667 0.00 0.00 0.00 3.61
2098 2127 1.918293 TGGACAGGATTGACCGGCT 60.918 57.895 0.00 0.00 41.31 5.52
2140 2169 1.683790 GACCTCGTGATGCCGTTTCG 61.684 60.000 0.00 0.00 0.00 3.46
2254 2291 3.819016 TTCCCAAAAGGGTGGCCGG 62.819 63.158 0.00 0.00 37.34 6.13
2365 2402 1.672881 ACAGGCGATGGTAGTACGTAC 59.327 52.381 18.10 18.10 0.00 3.67
2366 2403 1.942657 GACAGGCGATGGTAGTACGTA 59.057 52.381 0.00 0.00 0.00 3.57
2367 2404 0.737219 GACAGGCGATGGTAGTACGT 59.263 55.000 0.00 0.00 0.00 3.57
2368 2405 0.316772 CGACAGGCGATGGTAGTACG 60.317 60.000 0.00 0.00 44.57 3.67
2380 2417 4.966787 TTTGCACCCCCGACAGGC 62.967 66.667 0.00 0.00 35.76 4.85
2479 2525 3.319198 AACGGTGGTGCCCTCGAT 61.319 61.111 11.79 1.73 0.00 3.59
2613 2678 4.569180 CCCGGGGGCACATGCTAG 62.569 72.222 14.71 0.00 41.70 3.42
2627 2692 2.046285 GCCAAATCTGGTGACCCCG 61.046 63.158 0.00 0.00 45.53 5.73
2647 2712 2.356553 TTTTGTCGAGACCGGCGG 60.357 61.111 27.06 27.06 44.62 6.13
2703 2768 2.029739 TCAAACTCGGTGTCATCGCTAA 60.030 45.455 0.00 0.00 0.00 3.09
2757 2822 1.065600 GCGCTTGAAAACACAGCCA 59.934 52.632 0.00 0.00 0.00 4.75
2787 2852 1.487976 TGAAGATGGCAGACCTCATCC 59.512 52.381 0.00 0.00 40.27 3.51
2812 2877 3.948719 GTTCGTCACCCCAGCCCA 61.949 66.667 0.00 0.00 0.00 5.36
2829 2894 0.439985 CTGGTGACAAAGCGTGATCG 59.560 55.000 0.00 0.00 42.06 3.69
2861 2926 3.305744 GCATTCCCGAATCTCCTACTCTC 60.306 52.174 0.00 0.00 0.00 3.20
2862 2927 2.630580 GCATTCCCGAATCTCCTACTCT 59.369 50.000 0.00 0.00 0.00 3.24
2863 2928 2.365617 TGCATTCCCGAATCTCCTACTC 59.634 50.000 0.00 0.00 0.00 2.59
2864 2929 2.398588 TGCATTCCCGAATCTCCTACT 58.601 47.619 0.00 0.00 0.00 2.57
2865 2930 2.910688 TGCATTCCCGAATCTCCTAC 57.089 50.000 0.00 0.00 0.00 3.18
2866 2931 4.103153 AGAAATGCATTCCCGAATCTCCTA 59.897 41.667 13.38 0.00 38.94 2.94
2873 2938 3.126171 CGTGTAAGAAATGCATTCCCGAA 59.874 43.478 13.38 0.00 38.94 4.30
2892 2962 5.214417 TCATTGATGTTCTTTTCTTGCGTG 58.786 37.500 0.00 0.00 0.00 5.34
2917 2987 6.128363 CCCGTTCTGGTAAACTTTCAAGTATC 60.128 42.308 0.00 0.00 35.16 2.24
2919 2989 5.058490 CCCGTTCTGGTAAACTTTCAAGTA 58.942 41.667 0.00 0.00 35.16 2.24
2921 2991 3.304458 GCCCGTTCTGGTAAACTTTCAAG 60.304 47.826 0.00 0.00 35.15 3.02
2932 3002 0.393820 TAAAGTTCGCCCGTTCTGGT 59.606 50.000 0.00 0.00 35.15 4.00
2968 3038 4.143221 GCAGTCAATCTCGAAAACAGAGAC 60.143 45.833 0.00 0.00 46.12 3.36
2994 3064 0.109781 GACGCGACAAATGCAACCAT 60.110 50.000 15.93 0.00 0.00 3.55
3050 3120 8.071177 AGACAAGAGAAAATTATTCCCAATGG 57.929 34.615 0.00 0.00 0.00 3.16
3051 3121 9.362539 CAAGACAAGAGAAAATTATTCCCAATG 57.637 33.333 0.00 0.00 0.00 2.82
3053 3123 8.704849 TCAAGACAAGAGAAAATTATTCCCAA 57.295 30.769 0.00 0.00 0.00 4.12
3054 3124 8.704849 TTCAAGACAAGAGAAAATTATTCCCA 57.295 30.769 0.00 0.00 0.00 4.37
3127 3197 9.912634 CTAACCTGATGAGCAATTTCTTTAAAA 57.087 29.630 0.00 0.00 0.00 1.52
3128 3198 9.077885 ACTAACCTGATGAGCAATTTCTTTAAA 57.922 29.630 0.00 0.00 0.00 1.52
3129 3199 8.635765 ACTAACCTGATGAGCAATTTCTTTAA 57.364 30.769 0.00 0.00 0.00 1.52
3130 3200 8.635765 AACTAACCTGATGAGCAATTTCTTTA 57.364 30.769 0.00 0.00 0.00 1.85
3132 3202 6.716628 TGAACTAACCTGATGAGCAATTTCTT 59.283 34.615 0.00 0.00 0.00 2.52
3133 3203 6.150140 GTGAACTAACCTGATGAGCAATTTCT 59.850 38.462 0.00 0.00 0.00 2.52
3134 3204 6.150140 AGTGAACTAACCTGATGAGCAATTTC 59.850 38.462 0.00 0.00 0.00 2.17
3137 3207 4.940046 CAGTGAACTAACCTGATGAGCAAT 59.060 41.667 0.00 0.00 0.00 3.56
3238 3312 0.109365 TGCGTGGCAATTCGAATTGG 60.109 50.000 38.24 27.17 44.54 3.16
3248 3322 3.671971 GCACAAGTTATTATGCGTGGCAA 60.672 43.478 0.00 0.00 43.62 4.52
3367 3441 2.362120 GGCTGCAGGGCATGTCTT 60.362 61.111 17.12 0.00 38.13 3.01
3414 3488 1.065709 ACCCACGCCAATACTACCAAG 60.066 52.381 0.00 0.00 0.00 3.61
3557 3641 2.427095 AGGCGTGCAGGGATTTAATTTC 59.573 45.455 8.72 0.00 0.00 2.17
3582 3666 2.672996 CAGGCCGTGGTGGAAAGG 60.673 66.667 0.00 0.00 42.00 3.11
3630 3714 1.227292 GGCTTCTCGAACCCGATCC 60.227 63.158 0.00 0.00 44.62 3.36
3637 3721 2.545731 GAGATCTTGGGCTTCTCGAAC 58.454 52.381 0.00 0.00 0.00 3.95
3715 3804 4.072088 GCCACGTGTACAGCGCAC 62.072 66.667 15.65 0.00 0.00 5.34
3784 3873 4.785453 GCAGCCAGAAGGGACCCG 62.785 72.222 4.40 0.00 40.01 5.28
3793 3882 0.667487 CGAGAAGAAACGCAGCCAGA 60.667 55.000 0.00 0.00 0.00 3.86
3799 3888 2.132762 GGTCTTTCGAGAAGAAACGCA 58.867 47.619 10.34 0.00 43.35 5.24
4038 4541 4.566987 TGATCACATCAGCTGAGCATATC 58.433 43.478 22.96 19.99 33.59 1.63
4094 4597 0.609131 ATGCTTCGAAGGTTGGTGGG 60.609 55.000 25.77 0.00 0.00 4.61
4222 4730 5.763088 TCTATGTATCGCAGAACATCTCAC 58.237 41.667 0.00 0.00 43.58 3.51
4223 4731 5.765182 TCTCTATGTATCGCAGAACATCTCA 59.235 40.000 0.00 0.00 43.58 3.27
4305 4835 1.883084 CGAGCAGGGACCAATACGC 60.883 63.158 0.00 0.00 0.00 4.42
4324 4854 2.112815 GCATAAGTGTGGGGGCGAC 61.113 63.158 0.00 0.00 0.00 5.19
4388 4918 6.257193 CGTGGATGTAGAAAAGTGGGTATAAC 59.743 42.308 0.00 0.00 0.00 1.89
4405 4935 1.675641 GGCTGCCTTTCGTGGATGT 60.676 57.895 12.43 0.00 0.00 3.06
4445 4975 5.504665 CCATTCATGTCATTTTCTACGGAGC 60.505 44.000 0.00 0.00 0.00 4.70
4463 4993 3.693807 AGGTGTAGTCGTAGTCCATTCA 58.306 45.455 0.00 0.00 0.00 2.57
4469 4999 4.510038 TTTCCAAGGTGTAGTCGTAGTC 57.490 45.455 0.00 0.00 0.00 2.59
4470 5000 4.343239 AGTTTTCCAAGGTGTAGTCGTAGT 59.657 41.667 0.00 0.00 0.00 2.73
4471 5001 4.879598 AGTTTTCCAAGGTGTAGTCGTAG 58.120 43.478 0.00 0.00 0.00 3.51
4472 5002 4.942761 AGTTTTCCAAGGTGTAGTCGTA 57.057 40.909 0.00 0.00 0.00 3.43
4473 5003 3.832615 AGTTTTCCAAGGTGTAGTCGT 57.167 42.857 0.00 0.00 0.00 4.34
4474 5004 4.727235 GAAGTTTTCCAAGGTGTAGTCG 57.273 45.455 0.00 0.00 0.00 4.18
4505 5035 3.804036 ACACAGGACGAAACTGAAATGA 58.196 40.909 11.48 0.00 39.24 2.57
4585 5115 7.139287 ACTTACACTAGACTAGATGGCTCTA 57.861 40.000 16.55 0.00 34.56 2.43
4591 5121 9.692749 TGTTTTGAACTTACACTAGACTAGATG 57.307 33.333 16.55 12.23 0.00 2.90
4630 5160 3.315191 GCAGCAACAAAAGGTCTAGTTGA 59.685 43.478 8.19 0.00 42.87 3.18
4728 5272 6.139679 TGGACAGGAATCCTCTAACAATTT 57.860 37.500 0.00 0.00 39.75 1.82
4731 5275 5.576563 TTTGGACAGGAATCCTCTAACAA 57.423 39.130 0.00 0.00 39.75 2.83
4732 5276 5.560724 CTTTTGGACAGGAATCCTCTAACA 58.439 41.667 0.00 0.00 39.75 2.41
4733 5277 4.396478 GCTTTTGGACAGGAATCCTCTAAC 59.604 45.833 0.00 0.00 39.75 2.34
4885 5432 5.879237 TGCAGCAAATAAATACGGAAGAAG 58.121 37.500 0.00 0.00 0.00 2.85
4917 5464 1.134128 TGTGCTCCACTGAGAAAAGCA 60.134 47.619 3.96 3.96 41.42 3.91
5405 5955 2.618241 GAGCTCCATTGTTGTGAACACA 59.382 45.455 0.87 3.39 41.97 3.72
5539 6089 0.247185 AATGCCCAAATGCTCCAACG 59.753 50.000 0.00 0.00 0.00 4.10
5612 6162 1.004277 TGGGCACAACAGAAGTATCCC 59.996 52.381 0.00 0.00 33.81 3.85
5643 6193 8.811017 CATCAATTGGATAGTATCAGAGGTAGT 58.189 37.037 12.19 0.00 33.95 2.73
5729 6282 3.818773 CCATCACCACCGTTAGAAAAAGT 59.181 43.478 0.00 0.00 0.00 2.66
5730 6283 3.818773 ACCATCACCACCGTTAGAAAAAG 59.181 43.478 0.00 0.00 0.00 2.27
5731 6284 3.822940 ACCATCACCACCGTTAGAAAAA 58.177 40.909 0.00 0.00 0.00 1.94
5789 6342 4.607239 TGTTAGGACCTAGAACCTGTAGG 58.393 47.826 14.91 0.00 42.62 3.18
5890 6443 4.707563 TCACATGCGAGTTTTACATTTCG 58.292 39.130 0.00 0.00 36.23 3.46
5939 6492 3.325135 AGGCCAGGTATTATAGTCAGTGC 59.675 47.826 5.01 0.00 0.00 4.40
5987 6540 3.995048 AGAGGCAACGTTAAAGTTAGCTC 59.005 43.478 19.36 15.92 46.39 4.09
6228 6781 6.825610 TGAAGATTTTGGCCAAAACACTAAT 58.174 32.000 38.97 26.22 42.32 1.73
6229 6782 6.227298 TGAAGATTTTGGCCAAAACACTAA 57.773 33.333 38.97 27.18 42.32 2.24
6233 6786 5.642919 GCATATGAAGATTTTGGCCAAAACA 59.357 36.000 38.97 31.56 42.32 2.83
6311 6864 0.323629 TTGAAAGACAGGGTAGCCGG 59.676 55.000 9.72 9.72 0.00 6.13
6371 6924 8.498054 AGAGAATTAACATCACAACGATCAAT 57.502 30.769 0.00 0.00 29.21 2.57
6415 6968 6.372659 TCTGCTTGTTGAAGAATATGAAGGTC 59.627 38.462 0.00 0.00 0.00 3.85
6451 7004 4.518590 CCGAGCTGAATGATCTCTCTCTTA 59.481 45.833 0.00 0.00 0.00 2.10
6530 7090 5.248477 AGGAAAAGTAGTGGTATGAGCTGAA 59.752 40.000 0.00 0.00 0.00 3.02
6542 7104 4.137543 AGCAAGTTGGAGGAAAAGTAGTG 58.862 43.478 4.75 0.00 0.00 2.74
6616 7178 2.615493 GGCATCTTCTTTGTCCGGAGAA 60.615 50.000 10.51 10.51 0.00 2.87
6620 7182 0.035056 AGGGCATCTTCTTTGTCCGG 60.035 55.000 0.00 0.00 43.78 5.14
6668 7232 1.032014 GCACACAAGGCCAAGAGAAA 58.968 50.000 5.01 0.00 0.00 2.52
6853 7417 9.295825 TGGTTTCATCAAGTTTAGTTGTATGAT 57.704 29.630 10.45 0.00 30.74 2.45
6859 7423 8.870160 TCATTTGGTTTCATCAAGTTTAGTTG 57.130 30.769 0.00 0.00 0.00 3.16
6913 7477 4.537135 TCTACTCAGATTTGACCCACAC 57.463 45.455 0.00 0.00 0.00 3.82
6931 7495 6.835819 AGTGTGTACAGACTAGCAATTCTA 57.164 37.500 23.11 0.00 32.73 2.10
6936 7501 5.753438 CAGAAAAGTGTGTACAGACTAGCAA 59.247 40.000 24.43 0.00 33.43 3.91
6960 7525 0.251608 TGGCTGGTTCTTTAAGGGGC 60.252 55.000 0.00 0.00 0.00 5.80
6963 7528 3.004734 CACAAGTGGCTGGTTCTTTAAGG 59.995 47.826 0.00 0.00 0.00 2.69
7131 7696 1.000938 GCCCTGAAGAAAAGCACTGTG 60.001 52.381 2.76 2.76 0.00 3.66
7132 7697 1.322442 GCCCTGAAGAAAAGCACTGT 58.678 50.000 0.00 0.00 0.00 3.55
7139 7704 9.288576 CTATATATGTTCATGCCCTGAAGAAAA 57.711 33.333 0.00 0.00 44.44 2.29
7166 7731 9.090692 CAAGTTTCAAACATTTGAGTTCTCAAT 57.909 29.630 14.67 4.49 46.68 2.57
7409 7975 2.069273 CTGACAAGGTTCTGGTAAGCG 58.931 52.381 0.00 0.00 0.00 4.68
7457 8032 4.067896 TCGGTTAGACGAACAGTAAGAGT 58.932 43.478 0.75 0.00 40.34 3.24
7460 8035 5.039480 TCTTCGGTTAGACGAACAGTAAG 57.961 43.478 0.75 3.61 46.68 2.34
7472 8047 3.896648 TGCAAAGCTTTCTTCGGTTAG 57.103 42.857 9.23 0.00 0.00 2.34
7487 8062 6.208402 TGCAAATTCTACTACTCCAATGCAAA 59.792 34.615 0.00 0.00 37.16 3.68
7496 8071 7.988904 ACGTAAGATGCAAATTCTACTACTC 57.011 36.000 0.00 0.00 43.62 2.59
7524 8099 2.306805 AGTGACCTGCAAAGATGATCCA 59.693 45.455 0.00 0.00 0.00 3.41
7645 8220 2.584391 GCTGAGGTCCACCGGAGTT 61.584 63.158 9.46 0.00 42.08 3.01
7831 8406 2.186903 GCGACCATCATGACGGGT 59.813 61.111 18.28 18.28 37.70 5.28
7834 8409 3.630148 GCGGCGACCATCATGACG 61.630 66.667 12.98 0.00 0.00 4.35
7942 8517 1.001269 GTTGTACCTCTTGGGCCCC 60.001 63.158 22.27 0.37 39.10 5.80
8084 8659 0.243095 GGATGTACGACGGCCTATCC 59.757 60.000 0.00 3.54 0.00 2.59
8233 8820 1.599797 GACCAGACCAAACCCCACG 60.600 63.158 0.00 0.00 0.00 4.94
8402 8989 2.929641 TGTGTGCATCCAGTTCTTTCA 58.070 42.857 0.00 0.00 0.00 2.69
8419 9006 6.902224 TGAACGGAAACATCTATGTATGTG 57.098 37.500 0.00 0.00 40.80 3.21
8435 9022 0.389817 CTCGGCAGAACATGAACGGA 60.390 55.000 0.00 0.00 33.33 4.69
8470 9057 6.936968 ATCTTTCTACCTGTATATGGACCC 57.063 41.667 2.30 0.00 0.00 4.46
8471 9058 9.877178 CATAATCTTTCTACCTGTATATGGACC 57.123 37.037 2.30 0.00 0.00 4.46
8472 9059 9.372369 GCATAATCTTTCTACCTGTATATGGAC 57.628 37.037 2.30 0.00 0.00 4.02
8473 9060 9.100197 TGCATAATCTTTCTACCTGTATATGGA 57.900 33.333 2.30 0.00 0.00 3.41
8474 9061 9.896645 ATGCATAATCTTTCTACCTGTATATGG 57.103 33.333 0.00 0.00 0.00 2.74
8516 9103 8.506168 AAAAGAGAAGAACAACACAAGTGATA 57.494 30.769 7.28 0.00 0.00 2.15
8655 9251 5.743636 AACCTGGTCATTTGCACAATATT 57.256 34.783 0.00 0.00 0.00 1.28
8789 9389 8.443937 GTTTATCACTTACTGGTCAACATCTTC 58.556 37.037 0.00 0.00 0.00 2.87
8836 9437 7.042797 AGTTTCACATTATGCTGAGTTTTGT 57.957 32.000 0.00 0.00 0.00 2.83
8857 9459 2.484264 GTGCTGTTTCGCAAGGATAGTT 59.516 45.455 0.00 0.00 42.32 2.24
8914 9516 1.186200 AGCATGCTTCGGAGTAGACA 58.814 50.000 16.30 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.