Multiple sequence alignment - TraesCS2A01G396200

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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 TraesCS2A01G396200 chr2A 100.000 3541 0 0 1 3541 649622322 649618782 0.000000e+00 6540.0
1 TraesCS2A01G396200 chr2A 91.463 82 6 1 1 81 338603418 338603337 1.040000e-20 111.0
2 TraesCS2A01G396200 chr2B 91.706 3412 162 54 144 3541 592531499 592528195 0.000000e+00 4621.0
3 TraesCS2A01G396200 chr2D 93.419 2188 100 20 875 3054 503584800 503582649 0.000000e+00 3203.0
4 TraesCS2A01G396200 chr2D 89.790 666 49 10 144 795 503585484 503584824 0.000000e+00 835.0
5 TraesCS2A01G396200 chr2D 93.548 62 4 0 3191 3252 503582601 503582540 3.760000e-15 93.5
6 TraesCS2A01G396200 chr4D 89.732 224 22 1 1656 1879 480815045 480814823 5.790000e-73 285.0
7 TraesCS2A01G396200 chr4D 89.916 119 12 0 1273 1391 480815446 480815328 1.700000e-33 154.0
8 TraesCS2A01G396200 chr4B 90.278 216 21 0 1664 1879 608624696 608624481 2.080000e-72 283.0
9 TraesCS2A01G396200 chr4B 90.000 140 12 1 497 636 335599575 335599438 2.810000e-41 180.0
10 TraesCS2A01G396200 chr5A 89.524 210 22 0 1664 1873 662752327 662752536 2.100000e-67 267.0
11 TraesCS2A01G396200 chr5A 100.000 33 0 0 68 100 511870796 511870764 1.060000e-05 62.1
12 TraesCS2A01G396200 chr1A 93.750 80 2 3 1 77 139917155 139917076 2.230000e-22 117.0
13 TraesCS2A01G396200 chr1A 97.059 68 2 0 1 68 507823456 507823389 8.030000e-22 115.0
14 TraesCS2A01G396200 chr1A 93.333 75 5 0 1 75 360013061 360013135 1.040000e-20 111.0
15 TraesCS2A01G396200 chr1A 91.358 81 3 3 1 81 6871898 6871822 1.340000e-19 108.0
16 TraesCS2A01G396200 chr6A 94.667 75 3 1 2 75 577232541 577232615 8.030000e-22 115.0
17 TraesCS2A01G396200 chr5D 91.463 82 6 1 1 81 217335719 217335800 1.040000e-20 111.0
18 TraesCS2A01G396200 chr1D 91.463 82 6 1 1 81 96912610 96912691 1.040000e-20 111.0
19 TraesCS2A01G396200 chr1D 92.500 80 3 3 1 77 247865386 247865307 1.040000e-20 111.0


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 TraesCS2A01G396200 chr2A 649618782 649622322 3540 True 6540.000000 6540 100.000000 1 3541 1 chr2A.!!$R2 3540
1 TraesCS2A01G396200 chr2B 592528195 592531499 3304 True 4621.000000 4621 91.706000 144 3541 1 chr2B.!!$R1 3397
2 TraesCS2A01G396200 chr2D 503582540 503585484 2944 True 1377.166667 3203 92.252333 144 3252 3 chr2D.!!$R1 3108
3 TraesCS2A01G396200 chr4D 480814823 480815446 623 True 219.500000 285 89.824000 1273 1879 2 chr4D.!!$R1 606

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
173 174 0.178978 TGGGCCACTGCATTTACACA 60.179 50.0 0.0 0.0 40.13 3.72 F
1892 1985 0.248289 GGTAAGCCACTCAGCCGTAA 59.752 55.0 0.0 0.0 34.09 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1996 0.034059 AAGAGAGTGTGTGGCTTCGG 59.966 55.0 0.0 0.0 0.00 4.30 R
3276 3376 0.034896 GACCTCCACCGTTGATGTGT 59.965 55.0 0.0 0.0 31.71 3.72 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
21 22 4.870221 GGTTGTTGAGTTAAGAACGTGT 57.130 40.909 0.00 0.00 41.94 4.49
22 23 4.584394 GGTTGTTGAGTTAAGAACGTGTG 58.416 43.478 0.00 0.00 41.94 3.82
23 24 4.093850 GGTTGTTGAGTTAAGAACGTGTGT 59.906 41.667 0.00 0.00 41.94 3.72
24 25 5.391203 GGTTGTTGAGTTAAGAACGTGTGTT 60.391 40.000 0.00 0.00 41.94 3.32
25 26 6.183360 GGTTGTTGAGTTAAGAACGTGTGTTA 60.183 38.462 0.00 0.00 41.94 2.41
26 27 7.404203 GTTGTTGAGTTAAGAACGTGTGTTAT 58.596 34.615 0.00 0.00 38.78 1.89
27 28 6.939627 TGTTGAGTTAAGAACGTGTGTTATG 58.060 36.000 0.00 0.00 38.78 1.90
28 29 6.535865 TGTTGAGTTAAGAACGTGTGTTATGT 59.464 34.615 0.00 0.00 38.78 2.29
29 30 7.064847 TGTTGAGTTAAGAACGTGTGTTATGTT 59.935 33.333 0.00 0.00 41.14 2.71
30 31 7.542534 TGAGTTAAGAACGTGTGTTATGTTT 57.457 32.000 0.00 0.00 38.60 2.83
31 32 7.976826 TGAGTTAAGAACGTGTGTTATGTTTT 58.023 30.769 0.00 0.00 38.60 2.43
32 33 8.117988 TGAGTTAAGAACGTGTGTTATGTTTTC 58.882 33.333 0.00 0.00 38.60 2.29
33 34 8.205131 AGTTAAGAACGTGTGTTATGTTTTCT 57.795 30.769 0.00 0.00 38.60 2.52
34 35 8.333186 AGTTAAGAACGTGTGTTATGTTTTCTC 58.667 33.333 0.00 0.00 38.60 2.87
35 36 6.920569 AAGAACGTGTGTTATGTTTTCTCT 57.079 33.333 0.00 0.00 38.60 3.10
36 37 6.920569 AGAACGTGTGTTATGTTTTCTCTT 57.079 33.333 0.00 0.00 38.60 2.85
37 38 6.945072 AGAACGTGTGTTATGTTTTCTCTTC 58.055 36.000 0.00 0.00 38.60 2.87
38 39 5.668558 ACGTGTGTTATGTTTTCTCTTCC 57.331 39.130 0.00 0.00 0.00 3.46
39 40 4.210537 ACGTGTGTTATGTTTTCTCTTCCG 59.789 41.667 0.00 0.00 0.00 4.30
40 41 4.210537 CGTGTGTTATGTTTTCTCTTCCGT 59.789 41.667 0.00 0.00 0.00 4.69
41 42 5.277154 CGTGTGTTATGTTTTCTCTTCCGTT 60.277 40.000 0.00 0.00 0.00 4.44
42 43 6.074195 CGTGTGTTATGTTTTCTCTTCCGTTA 60.074 38.462 0.00 0.00 0.00 3.18
43 44 7.067728 GTGTGTTATGTTTTCTCTTCCGTTAC 58.932 38.462 0.00 0.00 0.00 2.50
44 45 6.762187 TGTGTTATGTTTTCTCTTCCGTTACA 59.238 34.615 0.00 0.00 0.00 2.41
45 46 7.280428 TGTGTTATGTTTTCTCTTCCGTTACAA 59.720 33.333 0.00 0.00 0.00 2.41
46 47 7.585210 GTGTTATGTTTTCTCTTCCGTTACAAC 59.415 37.037 0.00 0.00 0.00 3.32
55 56 3.637714 CGTTACAACGCACAGGCT 58.362 55.556 1.04 0.00 46.06 4.58
56 57 1.491563 CGTTACAACGCACAGGCTC 59.508 57.895 1.04 0.00 46.06 4.70
57 58 0.944311 CGTTACAACGCACAGGCTCT 60.944 55.000 1.04 0.00 46.06 4.09
58 59 1.226746 GTTACAACGCACAGGCTCTT 58.773 50.000 0.00 0.00 38.10 2.85
59 60 1.602377 GTTACAACGCACAGGCTCTTT 59.398 47.619 0.00 0.00 38.10 2.52
60 61 1.961793 TACAACGCACAGGCTCTTTT 58.038 45.000 0.00 0.00 38.10 2.27
61 62 0.381801 ACAACGCACAGGCTCTTTTG 59.618 50.000 0.00 0.00 38.10 2.44
62 63 0.936297 CAACGCACAGGCTCTTTTGC 60.936 55.000 0.00 0.00 38.10 3.68
63 64 1.103398 AACGCACAGGCTCTTTTGCT 61.103 50.000 5.64 0.00 38.10 3.91
64 65 0.250295 ACGCACAGGCTCTTTTGCTA 60.250 50.000 5.64 0.00 38.10 3.49
65 66 0.445436 CGCACAGGCTCTTTTGCTAG 59.555 55.000 5.64 0.00 38.10 3.42
66 67 1.528129 GCACAGGCTCTTTTGCTAGT 58.472 50.000 0.00 0.00 36.96 2.57
67 68 2.699954 GCACAGGCTCTTTTGCTAGTA 58.300 47.619 0.00 0.00 36.96 1.82
68 69 3.074412 GCACAGGCTCTTTTGCTAGTAA 58.926 45.455 0.00 0.00 36.96 2.24
69 70 3.691609 GCACAGGCTCTTTTGCTAGTAAT 59.308 43.478 0.00 0.00 36.96 1.89
70 71 4.156739 GCACAGGCTCTTTTGCTAGTAATT 59.843 41.667 0.00 0.00 36.96 1.40
71 72 5.354234 GCACAGGCTCTTTTGCTAGTAATTA 59.646 40.000 0.00 0.00 36.96 1.40
72 73 6.038714 GCACAGGCTCTTTTGCTAGTAATTAT 59.961 38.462 0.00 0.00 36.96 1.28
73 74 7.226720 GCACAGGCTCTTTTGCTAGTAATTATA 59.773 37.037 0.00 0.00 36.96 0.98
74 75 9.109393 CACAGGCTCTTTTGCTAGTAATTATAA 57.891 33.333 0.00 0.00 0.00 0.98
75 76 9.853177 ACAGGCTCTTTTGCTAGTAATTATAAT 57.147 29.630 0.00 0.00 0.00 1.28
102 103 7.745620 AATCTCTCGAAAACACCTTATTTGT 57.254 32.000 0.00 0.00 0.00 2.83
103 104 6.539649 TCTCTCGAAAACACCTTATTTGTG 57.460 37.500 0.00 0.00 39.63 3.33
104 105 5.468746 TCTCTCGAAAACACCTTATTTGTGG 59.531 40.000 0.00 0.00 38.05 4.17
105 106 5.127491 TCTCGAAAACACCTTATTTGTGGT 58.873 37.500 0.00 0.00 38.05 4.16
106 107 6.289834 TCTCGAAAACACCTTATTTGTGGTA 58.710 36.000 0.00 0.00 38.05 3.25
107 108 6.938030 TCTCGAAAACACCTTATTTGTGGTAT 59.062 34.615 0.00 0.00 38.05 2.73
108 109 7.446013 TCTCGAAAACACCTTATTTGTGGTATT 59.554 33.333 0.00 0.00 38.05 1.89
109 110 8.618702 TCGAAAACACCTTATTTGTGGTATTA 57.381 30.769 0.00 0.00 38.05 0.98
110 111 9.064706 TCGAAAACACCTTATTTGTGGTATTAA 57.935 29.630 0.00 0.00 38.05 1.40
111 112 9.849166 CGAAAACACCTTATTTGTGGTATTAAT 57.151 29.630 0.00 0.00 38.05 1.40
115 116 9.975218 AACACCTTATTTGTGGTATTAATCTCT 57.025 29.630 0.00 0.00 38.05 3.10
116 117 9.396022 ACACCTTATTTGTGGTATTAATCTCTG 57.604 33.333 0.00 0.00 38.05 3.35
117 118 8.345565 CACCTTATTTGTGGTATTAATCTCTGC 58.654 37.037 0.00 0.00 34.79 4.26
118 119 8.275040 ACCTTATTTGTGGTATTAATCTCTGCT 58.725 33.333 0.00 0.00 34.36 4.24
119 120 8.562892 CCTTATTTGTGGTATTAATCTCTGCTG 58.437 37.037 0.00 0.00 0.00 4.41
120 121 9.330063 CTTATTTGTGGTATTAATCTCTGCTGA 57.670 33.333 0.00 0.00 0.00 4.26
121 122 9.679661 TTATTTGTGGTATTAATCTCTGCTGAA 57.320 29.630 0.00 0.00 0.00 3.02
122 123 7.994425 TTTGTGGTATTAATCTCTGCTGAAA 57.006 32.000 0.00 0.00 0.00 2.69
123 124 7.615582 TTGTGGTATTAATCTCTGCTGAAAG 57.384 36.000 0.00 0.00 0.00 2.62
124 125 6.946340 TGTGGTATTAATCTCTGCTGAAAGA 58.054 36.000 0.00 0.00 34.07 2.52
125 126 7.394016 TGTGGTATTAATCTCTGCTGAAAGAA 58.606 34.615 0.00 0.00 34.07 2.52
126 127 7.882791 TGTGGTATTAATCTCTGCTGAAAGAAA 59.117 33.333 0.00 0.00 34.07 2.52
127 128 8.730680 GTGGTATTAATCTCTGCTGAAAGAAAA 58.269 33.333 0.00 0.00 34.07 2.29
128 129 8.950210 TGGTATTAATCTCTGCTGAAAGAAAAG 58.050 33.333 0.00 0.00 34.07 2.27
129 130 9.167311 GGTATTAATCTCTGCTGAAAGAAAAGA 57.833 33.333 0.00 0.00 34.07 2.52
132 133 8.545229 TTAATCTCTGCTGAAAGAAAAGAGAG 57.455 34.615 6.80 0.00 34.07 3.20
133 134 5.798125 TCTCTGCTGAAAGAAAAGAGAGA 57.202 39.130 0.00 0.00 34.07 3.10
134 135 6.166984 TCTCTGCTGAAAGAAAAGAGAGAA 57.833 37.500 0.00 0.00 34.07 2.87
135 136 6.586344 TCTCTGCTGAAAGAAAAGAGAGAAA 58.414 36.000 0.00 0.00 34.07 2.52
136 137 6.481644 TCTCTGCTGAAAGAAAAGAGAGAAAC 59.518 38.462 0.00 0.00 34.07 2.78
137 138 6.115446 TCTGCTGAAAGAAAAGAGAGAAACA 58.885 36.000 0.00 0.00 34.07 2.83
138 139 6.769822 TCTGCTGAAAGAAAAGAGAGAAACAT 59.230 34.615 0.00 0.00 34.07 2.71
139 140 6.732154 TGCTGAAAGAAAAGAGAGAAACATG 58.268 36.000 0.00 0.00 34.07 3.21
140 141 6.543465 TGCTGAAAGAAAAGAGAGAAACATGA 59.457 34.615 0.00 0.00 34.07 3.07
141 142 7.076983 GCTGAAAGAAAAGAGAGAAACATGAG 58.923 38.462 0.00 0.00 34.07 2.90
142 143 7.255070 GCTGAAAGAAAAGAGAGAAACATGAGT 60.255 37.037 0.00 0.00 34.07 3.41
149 150 2.999355 GAGAGAAACATGAGTGGAGTGC 59.001 50.000 0.00 0.00 0.00 4.40
173 174 0.178978 TGGGCCACTGCATTTACACA 60.179 50.000 0.00 0.00 40.13 3.72
391 408 2.223377 CAGGCAAAAGAGTTACGTGGAC 59.777 50.000 0.00 0.00 0.00 4.02
456 473 3.869272 CCGCGCTGTCAATCTGCC 61.869 66.667 5.56 0.00 37.66 4.85
463 480 1.674962 GCTGTCAATCTGCCATTCTCC 59.325 52.381 0.00 0.00 35.43 3.71
469 486 0.543277 ATCTGCCATTCTCCGCTTCA 59.457 50.000 0.00 0.00 0.00 3.02
472 489 1.747355 CTGCCATTCTCCGCTTCATTT 59.253 47.619 0.00 0.00 0.00 2.32
495 512 9.678941 ATTTTTCTCATACTTTTCTTCGGTTTC 57.321 29.630 0.00 0.00 0.00 2.78
542 560 4.812476 CGTTCCATGGCGGCGAGA 62.812 66.667 12.98 0.00 33.14 4.04
645 663 3.782244 GCAGGAGCGTGTTCTGCG 61.782 66.667 4.65 0.00 43.28 5.18
658 676 4.034258 CTGCGCTTGGCCACACAG 62.034 66.667 3.88 7.05 42.61 3.66
696 714 0.739561 AAGCGGCCTAGTAGTTCGAG 59.260 55.000 0.00 0.00 0.00 4.04
704 722 2.224549 CCTAGTAGTTCGAGCGATCTGG 59.775 54.545 12.32 3.16 0.00 3.86
706 724 0.930742 GTAGTTCGAGCGATCTGGCG 60.931 60.000 12.32 0.00 38.18 5.69
801 819 2.308866 TCCTCCAGATTTCCAGTTTCCC 59.691 50.000 0.00 0.00 0.00 3.97
802 820 2.310052 CCTCCAGATTTCCAGTTTCCCT 59.690 50.000 0.00 0.00 0.00 4.20
803 821 3.350833 CTCCAGATTTCCAGTTTCCCTG 58.649 50.000 0.00 0.00 41.15 4.45
812 830 2.979678 TCCAGTTTCCCTGCTACTTCTT 59.020 45.455 0.00 0.00 40.06 2.52
820 838 1.484240 CCTGCTACTTCTTCCTCCAGG 59.516 57.143 0.00 0.00 33.27 4.45
844 862 0.509499 CACACGCGTACGAAACCAAT 59.491 50.000 21.65 0.00 43.93 3.16
878 896 1.230324 GACGTCTTTGCCTTGCTTCT 58.770 50.000 8.70 0.00 0.00 2.85
879 897 1.604278 GACGTCTTTGCCTTGCTTCTT 59.396 47.619 8.70 0.00 0.00 2.52
880 898 1.334869 ACGTCTTTGCCTTGCTTCTTG 59.665 47.619 0.00 0.00 0.00 3.02
881 899 1.603802 CGTCTTTGCCTTGCTTCTTGA 59.396 47.619 0.00 0.00 0.00 3.02
882 900 2.227388 CGTCTTTGCCTTGCTTCTTGAT 59.773 45.455 0.00 0.00 0.00 2.57
883 901 3.304928 CGTCTTTGCCTTGCTTCTTGATT 60.305 43.478 0.00 0.00 0.00 2.57
915 933 1.836802 CCTCTCTCCTCTTCCCCTTTG 59.163 57.143 0.00 0.00 0.00 2.77
1393 1411 1.086696 CTGGCAAATGGAGGTACGTG 58.913 55.000 0.00 0.00 0.00 4.49
1427 1476 3.861276 TTCGCTATCTTTCCTCGTTGA 57.139 42.857 0.00 0.00 0.00 3.18
1490 1539 1.373435 CGGTTGGGCTTGACTGGTA 59.627 57.895 0.00 0.00 0.00 3.25
1653 1706 4.437524 GCGAAGAACTCCAGGCTAAAATTC 60.438 45.833 0.00 0.00 0.00 2.17
1867 1960 3.017581 ATCCCCGGCCTCTGCTTT 61.018 61.111 0.00 0.00 37.74 3.51
1886 1979 3.188786 GCGCGGTAAGCCACTCAG 61.189 66.667 8.83 0.00 44.76 3.35
1887 1980 3.188786 CGCGGTAAGCCACTCAGC 61.189 66.667 0.00 0.00 44.76 4.26
1889 1982 2.509336 CGGTAAGCCACTCAGCCG 60.509 66.667 0.00 0.00 34.09 5.52
1890 1983 2.663196 GGTAAGCCACTCAGCCGT 59.337 61.111 0.00 0.00 34.09 5.68
1891 1984 1.895238 GGTAAGCCACTCAGCCGTA 59.105 57.895 0.00 0.00 34.09 4.02
1892 1985 0.248289 GGTAAGCCACTCAGCCGTAA 59.752 55.000 0.00 0.00 34.09 3.18
1893 1986 1.338389 GGTAAGCCACTCAGCCGTAAA 60.338 52.381 0.00 0.00 34.09 2.01
1894 1987 1.730612 GTAAGCCACTCAGCCGTAAAC 59.269 52.381 0.00 0.00 0.00 2.01
1899 1992 1.950909 CCACTCAGCCGTAAACCAAAA 59.049 47.619 0.00 0.00 0.00 2.44
1902 1995 0.945813 TCAGCCGTAAACCAAAACCG 59.054 50.000 0.00 0.00 0.00 4.44
1903 1996 0.662077 CAGCCGTAAACCAAAACCGC 60.662 55.000 0.00 0.00 0.00 5.68
1904 1997 1.372004 GCCGTAAACCAAAACCGCC 60.372 57.895 0.00 0.00 0.00 6.13
1905 1998 1.081972 CCGTAAACCAAAACCGCCG 60.082 57.895 0.00 0.00 0.00 6.46
1906 1999 1.505477 CCGTAAACCAAAACCGCCGA 61.505 55.000 0.00 0.00 0.00 5.54
1907 2000 0.307146 CGTAAACCAAAACCGCCGAA 59.693 50.000 0.00 0.00 0.00 4.30
1908 2001 1.660896 CGTAAACCAAAACCGCCGAAG 60.661 52.381 0.00 0.00 0.00 3.79
1909 2002 0.311477 TAAACCAAAACCGCCGAAGC 59.689 50.000 0.00 0.00 0.00 3.86
1911 2004 3.291383 CCAAAACCGCCGAAGCCA 61.291 61.111 0.00 0.00 34.57 4.75
1914 2007 2.841160 AAAACCGCCGAAGCCACAC 61.841 57.895 0.00 0.00 34.57 3.82
1917 2010 4.988598 CCGCCGAAGCCACACACT 62.989 66.667 0.00 0.00 34.57 3.55
1918 2011 3.414700 CGCCGAAGCCACACACTC 61.415 66.667 0.00 0.00 34.57 3.51
1919 2012 2.031163 GCCGAAGCCACACACTCT 59.969 61.111 0.00 0.00 0.00 3.24
1920 2013 2.029844 GCCGAAGCCACACACTCTC 61.030 63.158 0.00 0.00 0.00 3.20
1921 2014 1.668294 CCGAAGCCACACACTCTCT 59.332 57.895 0.00 0.00 0.00 3.10
1922 2015 0.034059 CCGAAGCCACACACTCTCTT 59.966 55.000 0.00 0.00 0.00 2.85
1923 2016 1.541233 CCGAAGCCACACACTCTCTTT 60.541 52.381 0.00 0.00 0.00 2.52
1924 2017 1.795286 CGAAGCCACACACTCTCTTTC 59.205 52.381 0.00 0.00 0.00 2.62
1933 2026 4.278170 CACACACTCTCTTTCTGTCTCTCT 59.722 45.833 0.00 0.00 0.00 3.10
1936 2029 3.826157 CACTCTCTTTCTGTCTCTCTGGT 59.174 47.826 0.00 0.00 0.00 4.00
1938 2031 4.522789 ACTCTCTTTCTGTCTCTCTGGTTC 59.477 45.833 0.00 0.00 0.00 3.62
1945 2038 4.821589 CTCTCTGGTTCGCCGGGC 62.822 72.222 9.54 9.54 43.91 6.13
1993 2086 2.335369 GACTCGCCACGTGTCTGT 59.665 61.111 15.65 7.57 43.80 3.41
1994 2087 1.729838 GACTCGCCACGTGTCTGTC 60.730 63.158 15.65 12.63 43.80 3.51
2143 2236 1.226491 CAAGGTACGTACGGCGAGG 60.226 63.158 21.06 5.67 44.77 4.63
2145 2238 3.512516 GGTACGTACGGCGAGGCT 61.513 66.667 21.06 0.00 44.77 4.58
2161 2254 0.802607 GGCTAACGACCTCTTGCTCG 60.803 60.000 0.00 0.00 35.96 5.03
2163 2256 1.618861 CTAACGACCTCTTGCTCGTG 58.381 55.000 0.00 0.00 42.21 4.35
2166 2259 2.932234 CGACCTCTTGCTCGTGGGT 61.932 63.158 0.00 0.00 0.00 4.51
2168 2261 2.743928 CCTCTTGCTCGTGGGTGC 60.744 66.667 0.00 0.00 0.00 5.01
2169 2262 2.031012 CTCTTGCTCGTGGGTGCA 59.969 61.111 0.00 0.00 40.60 4.57
2170 2263 2.031012 TCTTGCTCGTGGGTGCAG 59.969 61.111 0.00 0.00 42.88 4.41
2171 2264 2.281070 CTTGCTCGTGGGTGCAGT 60.281 61.111 0.00 0.00 42.88 4.40
2172 2265 1.005037 CTTGCTCGTGGGTGCAGTA 60.005 57.895 0.00 0.00 42.88 2.74
2173 2266 1.005037 TTGCTCGTGGGTGCAGTAG 60.005 57.895 0.00 0.00 42.88 2.57
2174 2267 2.815647 GCTCGTGGGTGCAGTAGC 60.816 66.667 0.00 0.00 42.57 3.58
2188 2281 2.040544 GTAGCCAGTGCGTGCCAAT 61.041 57.895 0.00 0.00 44.33 3.16
2196 2289 0.249238 GTGCGTGCCAATTTGGTGAA 60.249 50.000 16.62 0.84 40.46 3.18
2199 2292 2.142319 GCGTGCCAATTTGGTGAATTT 58.858 42.857 16.62 0.00 40.46 1.82
2200 2293 2.547634 GCGTGCCAATTTGGTGAATTTT 59.452 40.909 16.62 0.00 40.46 1.82
2201 2294 3.363871 GCGTGCCAATTTGGTGAATTTTC 60.364 43.478 16.62 0.00 40.46 2.29
2202 2295 3.186205 CGTGCCAATTTGGTGAATTTTCC 59.814 43.478 16.62 0.00 40.46 3.13
2203 2296 4.388485 GTGCCAATTTGGTGAATTTTCCT 58.612 39.130 16.62 0.00 40.46 3.36
2206 2299 5.221884 TGCCAATTTGGTGAATTTTCCTGAT 60.222 36.000 16.62 0.00 40.46 2.90
2207 2300 5.706833 GCCAATTTGGTGAATTTTCCTGATT 59.293 36.000 16.62 0.95 40.46 2.57
2208 2301 6.207221 GCCAATTTGGTGAATTTTCCTGATTT 59.793 34.615 16.62 0.00 40.46 2.17
2363 2456 3.588906 TGCTGTGCTGTGCTGTGC 61.589 61.111 0.00 0.00 0.00 4.57
2364 2457 3.285215 GCTGTGCTGTGCTGTGCT 61.285 61.111 0.00 0.00 0.00 4.40
2365 2458 2.637589 CTGTGCTGTGCTGTGCTG 59.362 61.111 0.00 0.00 0.00 4.41
2366 2459 2.124612 TGTGCTGTGCTGTGCTGT 60.125 55.556 0.00 0.00 0.00 4.40
2367 2460 2.330393 GTGCTGTGCTGTGCTGTG 59.670 61.111 0.00 0.00 0.00 3.66
2368 2461 3.588906 TGCTGTGCTGTGCTGTGC 61.589 61.111 0.00 0.00 0.00 4.57
2369 2462 3.285215 GCTGTGCTGTGCTGTGCT 61.285 61.111 0.00 0.00 0.00 4.40
2371 2464 2.124612 TGTGCTGTGCTGTGCTGT 60.125 55.556 0.00 0.00 0.00 4.40
2372 2465 2.330393 GTGCTGTGCTGTGCTGTG 59.670 61.111 0.00 0.00 0.00 3.66
2373 2466 2.182181 GTGCTGTGCTGTGCTGTGA 61.182 57.895 0.00 0.00 0.00 3.58
2374 2467 2.182181 TGCTGTGCTGTGCTGTGAC 61.182 57.895 0.00 0.00 0.00 3.67
2375 2468 2.901292 GCTGTGCTGTGCTGTGACC 61.901 63.158 0.00 0.00 0.00 4.02
2376 2469 1.524393 CTGTGCTGTGCTGTGACCA 60.524 57.895 0.00 0.00 0.00 4.02
2377 2470 1.779025 CTGTGCTGTGCTGTGACCAC 61.779 60.000 0.00 0.00 0.00 4.16
2378 2471 1.524621 GTGCTGTGCTGTGACCACT 60.525 57.895 1.62 0.00 34.38 4.00
2379 2472 1.524393 TGCTGTGCTGTGACCACTG 60.524 57.895 1.62 2.43 35.88 3.66
2380 2473 1.227645 GCTGTGCTGTGACCACTGA 60.228 57.895 10.57 0.00 35.08 3.41
2381 2474 1.502163 GCTGTGCTGTGACCACTGAC 61.502 60.000 10.57 6.85 35.08 3.51
2557 2650 0.615331 TGAAGGACTCTGGACATGGC 59.385 55.000 0.00 0.00 0.00 4.40
2582 2675 1.219124 CGCAGCCAGAAGAGCCTTA 59.781 57.895 0.00 0.00 0.00 2.69
2691 2785 2.530151 AGTCCAGGGCCAGAAGCA 60.530 61.111 6.18 0.00 46.50 3.91
2728 2822 1.125711 GTGGTGGTGGTGTACTCCCT 61.126 60.000 11.36 0.00 31.60 4.20
2729 2823 1.125093 TGGTGGTGGTGTACTCCCTG 61.125 60.000 11.36 0.00 31.60 4.45
2730 2824 1.125711 GGTGGTGGTGTACTCCCTGT 61.126 60.000 11.36 0.00 31.60 4.00
2731 2825 0.763035 GTGGTGGTGTACTCCCTGTT 59.237 55.000 11.36 0.00 31.60 3.16
2801 2895 0.737219 GCACAGATGGTTCATGAGGC 59.263 55.000 0.00 0.00 0.00 4.70
2806 2900 1.911357 AGATGGTTCATGAGGCTGTGA 59.089 47.619 0.00 0.00 0.00 3.58
2814 2908 3.959293 TCATGAGGCTGTGACATGATTT 58.041 40.909 11.36 0.00 43.17 2.17
2815 2909 4.338012 TCATGAGGCTGTGACATGATTTT 58.662 39.130 11.36 0.00 43.17 1.82
2816 2910 5.499313 TCATGAGGCTGTGACATGATTTTA 58.501 37.500 11.36 0.00 43.17 1.52
2852 2950 2.680352 AGGTCTCACCGCGTCCAT 60.680 61.111 4.92 0.00 44.90 3.41
2871 2969 6.920758 CGTCCATATTTTTGTTTTGTGGAGAA 59.079 34.615 0.00 0.00 35.17 2.87
3122 3222 2.167487 CTCTTCCAACTCTAGCCACTCC 59.833 54.545 0.00 0.00 0.00 3.85
3129 3229 4.187694 CAACTCTAGCCACTCCTGATTTC 58.812 47.826 0.00 0.00 0.00 2.17
3147 3247 6.103997 TGATTTCCTAAACACGGAGATGTAC 58.896 40.000 0.00 0.00 30.75 2.90
3270 3370 2.360585 GCCCTTCCCCTCCCAAAG 59.639 66.667 0.00 0.00 0.00 2.77
3272 3372 1.800229 GCCCTTCCCCTCCCAAAGAA 61.800 60.000 0.00 0.00 0.00 2.52
3275 3375 2.427150 CCCTTCCCCTCCCAAAGAAAAA 60.427 50.000 0.00 0.00 0.00 1.94
3293 3393 1.604604 AAACACATCAACGGTGGAGG 58.395 50.000 0.00 0.00 40.54 4.30
3375 3475 3.972227 CAGGACTGTTTCTGCCCG 58.028 61.111 0.00 0.00 0.00 6.13
3379 3479 2.027625 GACTGTTTCTGCCCGTCCG 61.028 63.158 0.00 0.00 0.00 4.79
3392 3492 2.862776 CGTCCGTCGCGTGTTTTGT 61.863 57.895 5.77 0.00 0.00 2.83
3428 3528 4.097286 GCCTTCTTTGATAATTAACCCGCA 59.903 41.667 0.00 0.00 0.00 5.69
3431 3531 6.127730 CCTTCTTTGATAATTAACCCGCAGTT 60.128 38.462 0.00 0.00 42.83 3.16
3447 3547 5.354234 CCCGCAGTTTATCTTTAAGTGACAT 59.646 40.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.093850 ACACACGTTCTTAACTCAACAACC 59.906 41.667 0.00 0.00 0.00 3.77
1 2 5.212589 ACACACGTTCTTAACTCAACAAC 57.787 39.130 0.00 0.00 0.00 3.32
2 3 5.866335 AACACACGTTCTTAACTCAACAA 57.134 34.783 0.00 0.00 0.00 2.83
3 4 6.535865 ACATAACACACGTTCTTAACTCAACA 59.464 34.615 0.00 0.00 36.52 3.33
4 5 6.940714 ACATAACACACGTTCTTAACTCAAC 58.059 36.000 0.00 0.00 36.52 3.18
5 6 7.542534 AACATAACACACGTTCTTAACTCAA 57.457 32.000 0.00 0.00 36.52 3.02
6 7 7.542534 AAACATAACACACGTTCTTAACTCA 57.457 32.000 0.00 0.00 36.52 3.41
7 8 8.333186 AGAAAACATAACACACGTTCTTAACTC 58.667 33.333 0.00 0.00 36.52 3.01
8 9 8.205131 AGAAAACATAACACACGTTCTTAACT 57.795 30.769 0.00 0.00 36.52 2.24
9 10 8.333186 AGAGAAAACATAACACACGTTCTTAAC 58.667 33.333 0.00 0.00 36.52 2.01
10 11 8.428186 AGAGAAAACATAACACACGTTCTTAA 57.572 30.769 0.00 0.00 36.52 1.85
11 12 8.428186 AAGAGAAAACATAACACACGTTCTTA 57.572 30.769 0.00 0.00 36.52 2.10
12 13 6.920569 AGAGAAAACATAACACACGTTCTT 57.079 33.333 0.00 0.00 36.52 2.52
13 14 6.018180 GGAAGAGAAAACATAACACACGTTCT 60.018 38.462 0.00 0.00 36.52 3.01
14 15 6.134061 GGAAGAGAAAACATAACACACGTTC 58.866 40.000 0.00 0.00 36.52 3.95
15 16 5.277154 CGGAAGAGAAAACATAACACACGTT 60.277 40.000 0.00 0.00 39.24 3.99
16 17 4.210537 CGGAAGAGAAAACATAACACACGT 59.789 41.667 0.00 0.00 0.00 4.49
17 18 4.210537 ACGGAAGAGAAAACATAACACACG 59.789 41.667 0.00 0.00 0.00 4.49
18 19 5.668558 ACGGAAGAGAAAACATAACACAC 57.331 39.130 0.00 0.00 0.00 3.82
19 20 6.762187 TGTAACGGAAGAGAAAACATAACACA 59.238 34.615 0.00 0.00 0.00 3.72
20 21 7.181143 TGTAACGGAAGAGAAAACATAACAC 57.819 36.000 0.00 0.00 0.00 3.32
21 22 7.632721 GTTGTAACGGAAGAGAAAACATAACA 58.367 34.615 0.00 0.00 0.00 2.41
39 40 1.226746 AAGAGCCTGTGCGTTGTAAC 58.773 50.000 0.00 0.00 44.33 2.50
40 41 1.961793 AAAGAGCCTGTGCGTTGTAA 58.038 45.000 0.00 0.00 44.33 2.41
41 42 1.601903 CAAAAGAGCCTGTGCGTTGTA 59.398 47.619 0.00 0.00 44.33 2.41
42 43 0.381801 CAAAAGAGCCTGTGCGTTGT 59.618 50.000 0.00 0.00 44.33 3.32
43 44 0.936297 GCAAAAGAGCCTGTGCGTTG 60.936 55.000 0.00 0.00 44.33 4.10
44 45 1.103398 AGCAAAAGAGCCTGTGCGTT 61.103 50.000 0.00 0.00 44.33 4.84
45 46 0.250295 TAGCAAAAGAGCCTGTGCGT 60.250 50.000 0.00 0.00 44.33 5.24
46 47 0.445436 CTAGCAAAAGAGCCTGTGCG 59.555 55.000 0.00 0.00 44.33 5.34
47 48 1.528129 ACTAGCAAAAGAGCCTGTGC 58.472 50.000 0.00 0.00 37.26 4.57
48 49 5.886960 AATTACTAGCAAAAGAGCCTGTG 57.113 39.130 0.00 0.00 34.23 3.66
49 50 9.853177 ATTATAATTACTAGCAAAAGAGCCTGT 57.147 29.630 0.00 0.00 34.23 4.00
76 77 8.630037 ACAAATAAGGTGTTTTCGAGAGATTTT 58.370 29.630 0.00 0.00 41.60 1.82
77 78 8.076178 CACAAATAAGGTGTTTTCGAGAGATTT 58.924 33.333 0.00 0.00 41.60 2.17
78 79 7.308589 CCACAAATAAGGTGTTTTCGAGAGATT 60.309 37.037 0.00 0.00 35.61 2.40
79 80 6.149474 CCACAAATAAGGTGTTTTCGAGAGAT 59.851 38.462 0.00 0.00 35.61 2.75
80 81 5.468746 CCACAAATAAGGTGTTTTCGAGAGA 59.531 40.000 0.00 0.00 34.46 3.10
81 82 5.238650 ACCACAAATAAGGTGTTTTCGAGAG 59.761 40.000 0.00 0.00 36.60 3.20
82 83 5.127491 ACCACAAATAAGGTGTTTTCGAGA 58.873 37.500 0.00 0.00 36.60 4.04
83 84 5.432885 ACCACAAATAAGGTGTTTTCGAG 57.567 39.130 0.00 0.00 36.60 4.04
84 85 7.513371 AATACCACAAATAAGGTGTTTTCGA 57.487 32.000 0.00 0.00 36.01 3.71
85 86 9.849166 ATTAATACCACAAATAAGGTGTTTTCG 57.151 29.630 0.00 0.00 39.51 3.46
89 90 9.975218 AGAGATTAATACCACAAATAAGGTGTT 57.025 29.630 0.00 0.00 41.33 3.32
90 91 9.396022 CAGAGATTAATACCACAAATAAGGTGT 57.604 33.333 0.00 0.00 38.87 4.16
91 92 8.345565 GCAGAGATTAATACCACAAATAAGGTG 58.654 37.037 0.00 0.00 38.87 4.00
92 93 8.275040 AGCAGAGATTAATACCACAAATAAGGT 58.725 33.333 0.00 0.00 41.89 3.50
93 94 8.562892 CAGCAGAGATTAATACCACAAATAAGG 58.437 37.037 0.00 0.00 0.00 2.69
94 95 9.330063 TCAGCAGAGATTAATACCACAAATAAG 57.670 33.333 0.00 0.00 0.00 1.73
95 96 9.679661 TTCAGCAGAGATTAATACCACAAATAA 57.320 29.630 0.00 0.00 0.00 1.40
96 97 9.679661 TTTCAGCAGAGATTAATACCACAAATA 57.320 29.630 0.00 0.00 0.00 1.40
97 98 8.579850 TTTCAGCAGAGATTAATACCACAAAT 57.420 30.769 0.00 0.00 0.00 2.32
98 99 7.882791 TCTTTCAGCAGAGATTAATACCACAAA 59.117 33.333 0.00 0.00 0.00 2.83
99 100 7.394016 TCTTTCAGCAGAGATTAATACCACAA 58.606 34.615 0.00 0.00 0.00 3.33
100 101 6.946340 TCTTTCAGCAGAGATTAATACCACA 58.054 36.000 0.00 0.00 0.00 4.17
101 102 7.849804 TTCTTTCAGCAGAGATTAATACCAC 57.150 36.000 0.00 0.00 0.00 4.16
102 103 8.862325 TTTTCTTTCAGCAGAGATTAATACCA 57.138 30.769 0.00 0.00 0.00 3.25
103 104 9.167311 TCTTTTCTTTCAGCAGAGATTAATACC 57.833 33.333 0.00 0.00 0.00 2.73
106 107 9.165035 CTCTCTTTTCTTTCAGCAGAGATTAAT 57.835 33.333 0.00 0.00 39.37 1.40
107 108 8.370940 TCTCTCTTTTCTTTCAGCAGAGATTAA 58.629 33.333 0.00 0.00 39.37 1.40
108 109 7.901029 TCTCTCTTTTCTTTCAGCAGAGATTA 58.099 34.615 0.00 0.00 39.37 1.75
109 110 6.767456 TCTCTCTTTTCTTTCAGCAGAGATT 58.233 36.000 0.00 0.00 39.37 2.40
110 111 6.357579 TCTCTCTTTTCTTTCAGCAGAGAT 57.642 37.500 0.00 0.00 39.37 2.75
111 112 5.798125 TCTCTCTTTTCTTTCAGCAGAGA 57.202 39.130 0.00 0.00 38.12 3.10
112 113 6.259608 TGTTTCTCTCTTTTCTTTCAGCAGAG 59.740 38.462 0.00 0.00 33.56 3.35
113 114 6.115446 TGTTTCTCTCTTTTCTTTCAGCAGA 58.885 36.000 0.00 0.00 0.00 4.26
114 115 6.369059 TGTTTCTCTCTTTTCTTTCAGCAG 57.631 37.500 0.00 0.00 0.00 4.24
115 116 6.543465 TCATGTTTCTCTCTTTTCTTTCAGCA 59.457 34.615 0.00 0.00 0.00 4.41
116 117 6.963796 TCATGTTTCTCTCTTTTCTTTCAGC 58.036 36.000 0.00 0.00 0.00 4.26
117 118 8.068977 CACTCATGTTTCTCTCTTTTCTTTCAG 58.931 37.037 0.00 0.00 0.00 3.02
118 119 7.012704 CCACTCATGTTTCTCTCTTTTCTTTCA 59.987 37.037 0.00 0.00 0.00 2.69
119 120 7.227512 TCCACTCATGTTTCTCTCTTTTCTTTC 59.772 37.037 0.00 0.00 0.00 2.62
120 121 7.056635 TCCACTCATGTTTCTCTCTTTTCTTT 58.943 34.615 0.00 0.00 0.00 2.52
121 122 6.595682 TCCACTCATGTTTCTCTCTTTTCTT 58.404 36.000 0.00 0.00 0.00 2.52
122 123 6.179906 TCCACTCATGTTTCTCTCTTTTCT 57.820 37.500 0.00 0.00 0.00 2.52
123 124 5.994668 ACTCCACTCATGTTTCTCTCTTTTC 59.005 40.000 0.00 0.00 0.00 2.29
124 125 5.762218 CACTCCACTCATGTTTCTCTCTTTT 59.238 40.000 0.00 0.00 0.00 2.27
125 126 5.303971 CACTCCACTCATGTTTCTCTCTTT 58.696 41.667 0.00 0.00 0.00 2.52
126 127 4.802248 GCACTCCACTCATGTTTCTCTCTT 60.802 45.833 0.00 0.00 0.00 2.85
127 128 3.306641 GCACTCCACTCATGTTTCTCTCT 60.307 47.826 0.00 0.00 0.00 3.10
128 129 2.999355 GCACTCCACTCATGTTTCTCTC 59.001 50.000 0.00 0.00 0.00 3.20
129 130 2.289945 GGCACTCCACTCATGTTTCTCT 60.290 50.000 0.00 0.00 0.00 3.10
130 131 2.079925 GGCACTCCACTCATGTTTCTC 58.920 52.381 0.00 0.00 0.00 2.87
131 132 1.421268 TGGCACTCCACTCATGTTTCT 59.579 47.619 0.00 0.00 37.47 2.52
132 133 1.896220 TGGCACTCCACTCATGTTTC 58.104 50.000 0.00 0.00 37.47 2.78
133 134 2.363306 TTGGCACTCCACTCATGTTT 57.637 45.000 0.00 0.00 43.33 2.83
134 135 2.363306 TTTGGCACTCCACTCATGTT 57.637 45.000 0.00 0.00 43.33 2.71
135 136 2.165167 CATTTGGCACTCCACTCATGT 58.835 47.619 0.00 0.00 43.33 3.21
136 137 1.475280 CCATTTGGCACTCCACTCATG 59.525 52.381 0.00 0.00 43.33 3.07
137 138 1.617804 CCCATTTGGCACTCCACTCAT 60.618 52.381 0.00 0.00 43.33 2.90
138 139 0.251297 CCCATTTGGCACTCCACTCA 60.251 55.000 0.00 0.00 43.33 3.41
139 140 2.571548 CCCATTTGGCACTCCACTC 58.428 57.895 0.00 0.00 43.33 3.51
140 141 4.850193 CCCATTTGGCACTCCACT 57.150 55.556 0.00 0.00 43.33 4.00
149 150 0.325602 AAATGCAGTGGCCCATTTGG 59.674 50.000 14.60 0.00 39.45 3.28
162 163 0.595588 CGTTGGGCTGTGTAAATGCA 59.404 50.000 0.00 0.00 0.00 3.96
272 281 3.454447 TGATGTATCCCCATCGTGAGTTT 59.546 43.478 0.00 0.00 43.39 2.66
273 282 3.038280 TGATGTATCCCCATCGTGAGTT 58.962 45.455 0.00 0.00 43.39 3.01
274 283 2.365617 GTGATGTATCCCCATCGTGAGT 59.634 50.000 0.00 0.00 43.39 3.41
403 420 0.603975 AGAACGAAGGGCTGCTGTTC 60.604 55.000 0.00 6.84 39.28 3.18
456 473 5.300969 TGAGAAAAATGAAGCGGAGAATG 57.699 39.130 0.00 0.00 0.00 2.67
463 480 8.733857 AAGAAAAGTATGAGAAAAATGAAGCG 57.266 30.769 0.00 0.00 0.00 4.68
469 486 9.678941 GAAACCGAAGAAAAGTATGAGAAAAAT 57.321 29.630 0.00 0.00 0.00 1.82
472 489 6.206048 GGGAAACCGAAGAAAAGTATGAGAAA 59.794 38.462 0.00 0.00 43.64 2.52
526 544 3.195698 GTCTCGCCGCCATGGAAC 61.196 66.667 18.40 2.03 42.00 3.62
547 565 2.180159 TACTTTGGTCTGAGCCCCGC 62.180 60.000 4.17 0.00 0.00 6.13
556 574 2.662866 TCCGATCGGATACTTTGGTCT 58.337 47.619 32.59 0.00 39.76 3.85
598 616 1.748493 CCTTCTCTTCTCTGGACCGAG 59.252 57.143 6.93 6.93 0.00 4.63
801 819 2.183679 ACCTGGAGGAAGAAGTAGCAG 58.816 52.381 0.00 0.00 38.94 4.24
802 820 2.327325 ACCTGGAGGAAGAAGTAGCA 57.673 50.000 0.00 0.00 38.94 3.49
803 821 3.339141 CAAACCTGGAGGAAGAAGTAGC 58.661 50.000 0.00 0.00 38.94 3.58
812 830 1.227823 CGTGTGCAAACCTGGAGGA 60.228 57.895 0.17 0.00 38.94 3.71
820 838 0.315220 TTTCGTACGCGTGTGCAAAC 60.315 50.000 24.59 10.01 42.97 2.93
878 896 3.242867 AGAGGTGACTGGACTCAATCAA 58.757 45.455 0.00 0.00 44.43 2.57
879 897 2.828520 GAGAGGTGACTGGACTCAATCA 59.171 50.000 0.00 0.00 44.43 2.57
880 898 3.096092 AGAGAGGTGACTGGACTCAATC 58.904 50.000 0.00 0.00 44.43 2.67
881 899 3.096092 GAGAGAGGTGACTGGACTCAAT 58.904 50.000 0.00 0.00 44.43 2.57
882 900 2.520069 GAGAGAGGTGACTGGACTCAA 58.480 52.381 0.00 0.00 44.43 3.02
883 901 1.272203 GGAGAGAGGTGACTGGACTCA 60.272 57.143 0.00 0.00 44.43 3.41
1393 1411 1.801512 GCGAAAACGAATGGCTGGC 60.802 57.895 0.00 0.00 0.00 4.85
1427 1476 2.126580 GTCGCCACTCGCTAACGT 60.127 61.111 0.00 0.00 41.18 3.99
1595 1644 1.003839 TTCTACCAAGGTGCCGCTG 60.004 57.895 1.07 0.00 0.00 5.18
1639 1692 0.746563 CGCCCGAATTTTAGCCTGGA 60.747 55.000 0.00 0.00 0.00 3.86
1882 1975 1.069500 CGGTTTTGGTTTACGGCTGAG 60.069 52.381 0.00 0.00 0.00 3.35
1883 1976 0.945813 CGGTTTTGGTTTACGGCTGA 59.054 50.000 0.00 0.00 0.00 4.26
1886 1979 1.372004 GGCGGTTTTGGTTTACGGC 60.372 57.895 0.00 0.00 42.56 5.68
1887 1980 1.081972 CGGCGGTTTTGGTTTACGG 60.082 57.895 0.00 0.00 0.00 4.02
1889 1982 1.927268 GCTTCGGCGGTTTTGGTTTAC 60.927 52.381 7.21 0.00 0.00 2.01
1890 1983 0.311477 GCTTCGGCGGTTTTGGTTTA 59.689 50.000 7.21 0.00 0.00 2.01
1891 1984 1.066752 GCTTCGGCGGTTTTGGTTT 59.933 52.632 7.21 0.00 0.00 3.27
1892 1985 2.725641 GCTTCGGCGGTTTTGGTT 59.274 55.556 7.21 0.00 0.00 3.67
1893 1986 3.292159 GGCTTCGGCGGTTTTGGT 61.292 61.111 7.21 0.00 42.91 3.67
1894 1987 3.291383 TGGCTTCGGCGGTTTTGG 61.291 61.111 7.21 0.00 42.91 3.28
1902 1995 2.029844 GAGAGTGTGTGGCTTCGGC 61.030 63.158 0.00 0.00 40.88 5.54
1903 1996 0.034059 AAGAGAGTGTGTGGCTTCGG 59.966 55.000 0.00 0.00 0.00 4.30
1904 1997 1.795286 GAAAGAGAGTGTGTGGCTTCG 59.205 52.381 0.00 0.00 0.00 3.79
1905 1998 2.805099 CAGAAAGAGAGTGTGTGGCTTC 59.195 50.000 0.00 0.00 0.00 3.86
1906 1999 2.171448 ACAGAAAGAGAGTGTGTGGCTT 59.829 45.455 0.00 0.00 0.00 4.35
1907 2000 1.765314 ACAGAAAGAGAGTGTGTGGCT 59.235 47.619 0.00 0.00 0.00 4.75
1908 2001 2.139118 GACAGAAAGAGAGTGTGTGGC 58.861 52.381 0.00 0.00 0.00 5.01
1909 2002 3.320541 AGAGACAGAAAGAGAGTGTGTGG 59.679 47.826 0.00 0.00 0.00 4.17
1911 2004 4.278170 CAGAGAGACAGAAAGAGAGTGTGT 59.722 45.833 0.00 0.00 0.00 3.72
1914 2007 3.826157 ACCAGAGAGACAGAAAGAGAGTG 59.174 47.826 0.00 0.00 0.00 3.51
1917 2010 3.504134 CGAACCAGAGAGACAGAAAGAGA 59.496 47.826 0.00 0.00 0.00 3.10
1918 2011 3.832276 CGAACCAGAGAGACAGAAAGAG 58.168 50.000 0.00 0.00 0.00 2.85
1919 2012 2.029828 GCGAACCAGAGAGACAGAAAGA 60.030 50.000 0.00 0.00 0.00 2.52
1920 2013 2.333014 GCGAACCAGAGAGACAGAAAG 58.667 52.381 0.00 0.00 0.00 2.62
1921 2014 1.000955 GGCGAACCAGAGAGACAGAAA 59.999 52.381 0.00 0.00 35.26 2.52
1922 2015 0.603569 GGCGAACCAGAGAGACAGAA 59.396 55.000 0.00 0.00 35.26 3.02
1923 2016 1.587043 CGGCGAACCAGAGAGACAGA 61.587 60.000 0.00 0.00 34.57 3.41
1924 2017 1.153939 CGGCGAACCAGAGAGACAG 60.154 63.158 0.00 0.00 34.57 3.51
1945 2038 0.179045 GGATGGTTCCGACAGATGGG 60.179 60.000 0.00 0.00 30.72 4.00
1955 2048 2.047830 AGACCCTAATCGGATGGTTCC 58.952 52.381 0.59 0.00 38.81 3.62
1972 2065 1.729838 GACACGTGGCGAGTCAGAC 60.730 63.158 21.57 0.00 44.29 3.51
1993 2086 1.306997 CCCAAGGCCCTGTAGGAGA 60.307 63.158 0.00 0.00 38.24 3.71
1994 2087 0.695803 ATCCCAAGGCCCTGTAGGAG 60.696 60.000 0.00 0.00 38.24 3.69
2156 2249 2.656646 CTACTGCACCCACGAGCA 59.343 61.111 0.00 0.00 39.25 4.26
2157 2250 2.815647 GCTACTGCACCCACGAGC 60.816 66.667 0.00 0.00 39.41 5.03
2161 2254 1.672356 CACTGGCTACTGCACCCAC 60.672 63.158 0.00 0.00 41.91 4.61
2163 2256 2.747855 GCACTGGCTACTGCACCC 60.748 66.667 0.00 0.00 41.91 4.61
2166 2259 2.357396 CACGCACTGGCTACTGCA 60.357 61.111 2.89 0.00 41.91 4.41
2168 2261 3.121030 GGCACGCACTGGCTACTG 61.121 66.667 0.00 0.00 42.36 2.74
2169 2262 2.469465 ATTGGCACGCACTGGCTACT 62.469 55.000 6.51 0.00 45.96 2.57
2170 2263 1.586154 AATTGGCACGCACTGGCTAC 61.586 55.000 6.51 0.00 45.96 3.58
2171 2264 0.893270 AAATTGGCACGCACTGGCTA 60.893 50.000 6.51 0.00 45.96 3.93
2172 2265 2.202395 AAATTGGCACGCACTGGCT 61.202 52.632 6.51 0.00 45.96 4.75
2173 2266 2.023223 CAAATTGGCACGCACTGGC 61.023 57.895 0.00 0.00 45.98 4.85
2174 2267 1.373246 CCAAATTGGCACGCACTGG 60.373 57.895 0.00 0.00 0.00 4.00
2179 2272 1.794512 AATTCACCAAATTGGCACGC 58.205 45.000 12.67 0.00 42.67 5.34
2214 2307 2.445427 CCACCACCACATAATCAGCAA 58.555 47.619 0.00 0.00 0.00 3.91
2365 2458 1.598130 GGGTCAGTGGTCACAGCAC 60.598 63.158 3.82 0.00 46.20 4.40
2366 2459 1.631071 TTGGGTCAGTGGTCACAGCA 61.631 55.000 3.82 0.00 0.00 4.41
2367 2460 0.886490 CTTGGGTCAGTGGTCACAGC 60.886 60.000 3.82 0.00 0.00 4.40
2368 2461 0.469917 ACTTGGGTCAGTGGTCACAG 59.530 55.000 3.82 0.00 0.00 3.66
2369 2462 0.180171 CACTTGGGTCAGTGGTCACA 59.820 55.000 3.82 0.00 40.60 3.58
2371 2464 0.468226 GTCACTTGGGTCAGTGGTCA 59.532 55.000 1.14 0.00 43.92 4.02
2372 2465 0.468226 TGTCACTTGGGTCAGTGGTC 59.532 55.000 1.14 0.00 43.92 4.02
2373 2466 0.180406 GTGTCACTTGGGTCAGTGGT 59.820 55.000 0.00 0.00 43.92 4.16
2374 2467 0.180171 TGTGTCACTTGGGTCAGTGG 59.820 55.000 4.27 0.00 43.92 4.00
2375 2468 1.134401 ACTGTGTCACTTGGGTCAGTG 60.134 52.381 4.27 0.00 44.96 3.66
2376 2469 1.204146 ACTGTGTCACTTGGGTCAGT 58.796 50.000 4.27 0.00 0.00 3.41
2377 2470 2.755650 GTACTGTGTCACTTGGGTCAG 58.244 52.381 4.27 0.00 0.00 3.51
2378 2471 1.067974 CGTACTGTGTCACTTGGGTCA 59.932 52.381 4.27 0.00 0.00 4.02
2379 2472 1.604693 CCGTACTGTGTCACTTGGGTC 60.605 57.143 4.27 0.00 0.00 4.46
2380 2473 0.391597 CCGTACTGTGTCACTTGGGT 59.608 55.000 4.27 1.35 0.00 4.51
2381 2474 0.320421 CCCGTACTGTGTCACTTGGG 60.320 60.000 4.27 4.61 0.00 4.12
2447 2540 1.168407 CCTGCACTCACCACAACCAG 61.168 60.000 0.00 0.00 0.00 4.00
2570 2663 6.349243 AGATGAGATCATAAGGCTCTTCTG 57.651 41.667 0.00 0.00 39.92 3.02
2623 2717 6.508777 TCAATAGCAACCACCAAAAAGTAAC 58.491 36.000 0.00 0.00 0.00 2.50
2625 2719 6.909550 ATCAATAGCAACCACCAAAAAGTA 57.090 33.333 0.00 0.00 0.00 2.24
2681 2775 2.094675 TCATTAGCTTTGCTTCTGGCC 58.905 47.619 0.00 0.00 40.44 5.36
2685 2779 3.631227 GCCTGATCATTAGCTTTGCTTCT 59.369 43.478 0.00 0.00 40.44 2.85
2691 2785 3.285484 CCACTGCCTGATCATTAGCTTT 58.715 45.455 12.18 0.00 0.00 3.51
2728 2822 0.602638 CCTGCAGCCGAGTAACAACA 60.603 55.000 8.66 0.00 0.00 3.33
2729 2823 1.298859 CCCTGCAGCCGAGTAACAAC 61.299 60.000 8.66 0.00 0.00 3.32
2730 2824 1.003839 CCCTGCAGCCGAGTAACAA 60.004 57.895 8.66 0.00 0.00 2.83
2731 2825 2.662596 CCCTGCAGCCGAGTAACA 59.337 61.111 8.66 0.00 0.00 2.41
2852 2950 7.616313 AGTTGGTTCTCCACAAAACAAAAATA 58.384 30.769 0.00 0.00 44.22 1.40
2984 3082 3.619038 GGAAAAGTACTGAATCTCCAGCG 59.381 47.826 0.00 0.00 37.68 5.18
3059 3159 6.239217 ACAATAGTGTGGCATTCTATCTCA 57.761 37.500 12.41 0.00 36.31 3.27
3061 3161 6.418101 ACAACAATAGTGTGGCATTCTATCT 58.582 36.000 0.00 4.16 38.27 1.98
3071 3171 4.754618 TGAGTAGCAACAACAATAGTGTGG 59.245 41.667 0.00 0.00 38.27 4.17
3122 3222 5.178797 ACATCTCCGTGTTTAGGAAATCAG 58.821 41.667 0.00 0.00 37.32 2.90
3129 3229 4.992319 TGTTTGTACATCTCCGTGTTTAGG 59.008 41.667 0.00 0.00 33.62 2.69
3147 3247 7.916977 TCTCTTCAAAATCAACAGTGATGTTTG 59.083 33.333 0.00 3.74 44.02 2.93
3192 3292 7.978975 GCTGGCCAATGTTAGTTTTGATTATTA 59.021 33.333 7.01 0.00 0.00 0.98
3193 3293 6.818142 GCTGGCCAATGTTAGTTTTGATTATT 59.182 34.615 7.01 0.00 0.00 1.40
3200 3300 1.623311 GGGCTGGCCAATGTTAGTTTT 59.377 47.619 16.34 0.00 37.98 2.43
3272 3372 2.360801 CCTCCACCGTTGATGTGTTTTT 59.639 45.455 0.00 0.00 31.71 1.94
3275 3375 0.472471 ACCTCCACCGTTGATGTGTT 59.528 50.000 0.00 0.00 31.71 3.32
3276 3376 0.034896 GACCTCCACCGTTGATGTGT 59.965 55.000 0.00 0.00 31.71 3.72
3277 3377 0.673644 GGACCTCCACCGTTGATGTG 60.674 60.000 0.00 0.00 35.64 3.21
3278 3378 1.125093 TGGACCTCCACCGTTGATGT 61.125 55.000 0.00 0.00 42.01 3.06
3279 3379 1.676968 TGGACCTCCACCGTTGATG 59.323 57.895 0.00 0.00 42.01 3.07
3280 3380 4.225860 TGGACCTCCACCGTTGAT 57.774 55.556 0.00 0.00 42.01 2.57
3363 3463 2.027625 GACGGACGGGCAGAAACAG 61.028 63.158 0.00 0.00 0.00 3.16
3375 3475 0.160182 CTACAAAACACGCGACGGAC 59.840 55.000 15.93 0.00 0.00 4.79
3392 3492 3.782656 AAGAAGGCGGGAAGTTTTCTA 57.217 42.857 0.00 0.00 0.00 2.10
3401 3501 4.885325 GGTTAATTATCAAAGAAGGCGGGA 59.115 41.667 0.00 0.00 0.00 5.14
3404 3504 4.788521 GCGGGTTAATTATCAAAGAAGGCG 60.789 45.833 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.